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330 <span class="md-nav__icon md-icon"></span> 331 </label> 332 333 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false"> 334 <label class="md-nav__title" for="__nav_2"> 335 <span class="md-nav__icon md-icon"></span> 336 337 338 Basic info 339 340 341 </label> 342 <ul class="md-nav__list" data-md-scrollfix> 343 344 345 346 347 348 349 350 <li class="md-nav__item"> 351 <a href="../what-is-easybuild/" class="md-nav__link"> 352 353 354 355 <span class="md-ellipsis"> 356 357 358 What is EasyBuild? 359 360 361 362 </span> 363 364 365 366 </a> 367 </li> 368 369 370 371 372 373 374 375 376 377 378 <li class="md-nav__item"> 379 <a href="../terminology/" class="md-nav__link"> 380 381 382 383 <span class="md-ellipsis"> 384 385 386 Terminology 387 388 389 390 </span> 391 392 393 394 </a> 395 </li> 396 397 398 399 400 </ul> 401 </nav> 402 403 </li> 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 <li class="md-nav__item md-nav__item--nested"> 419 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class="md-nav__link"> 490 491 492 493 <span class="md-ellipsis"> 494 495 496 Configuration 497 498 499 500 </span> 501 502 503 504 </a> 505 </li> 506 507 508 509 510 511 512 513 514 515 516 <li class="md-nav__item"> 517 <a href="../using-easybuild/" class="md-nav__link"> 518 519 520 521 <span class="md-ellipsis"> 522 523 524 Basic usage 525 526 527 528 </span> 529 530 531 532 </a> 533 </li> 534 535 536 537 538 539 540 541 542 543 544 <li class="md-nav__item"> 545 <a href="../typical-workflow-example/" class="md-nav__link"> 546 547 548 549 <span class="md-ellipsis"> 550 551 552 Typical workflow example 553 554 555 556 </span> 557 558 559 560 </a> 561 </li> 562 563 564 565 566 </ul> 567 </nav> 568 569 </li> 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 <li class="md-nav__item md-nav__item--nested"> 585 586 587 588 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" > 589 590 591 <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0"> 592 593 594 595 <span class="md-ellipsis"> 596 597 598 Using EasyBuild 599 600 601 602 </span> 603 604 605 606 <span class="md-nav__icon md-icon"></span> 607 </label> 608 609 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false"> 610 <label class="md-nav__title" for="__nav_4"> 611 <span class="md-nav__icon md-icon"></span> 612 613 614 Using EasyBuild 615 616 617 </label> 618 <ul class="md-nav__list" data-md-scrollfix> 619 620 621 622 623 624 625 626 <li class="md-nav__item"> 627 <a href="../backup-modules/" class="md-nav__link"> 628 629 630 631 <span class="md-ellipsis"> 632 633 634 Backing up existing modules 635 636 637 638 </span> 639 640 641 642 </a> 643 </li> 644 645 646 647 648 649 650 651 652 653 654 <li class="md-nav__item"> 655 <a href="../common-toolchains/" class="md-nav__link"> 656 657 658 659 <span class="md-ellipsis"> 660 661 662 Common toolchains 663 664 665 666 </span> 667 668 669 670 </a> 671 </li> 672 673 674 675 676 677 678 679 680 681 682 <li class="md-nav__item"> 683 <a href="../controlling-compiler-optimization-flags/" class="md-nav__link"> 684 685 686 687 <span class="md-ellipsis"> 688 689 690 Controlling optimization flags 691 692 693 694 </span> 695 696 697 698 </a> 699 </li> 700 701 702 703 704 705 706 707 708 709 710 <li class="md-nav__item"> 711 <a href="../datasets/" class="md-nav__link"> 712 713 714 715 <span class="md-ellipsis"> 716 717 718 Datasets 719 720 721 722 </span> 723 724 725 726 </a> 727 </li> 728 729 730 731 732 733 734 735 736 737 738 <li class="md-nav__item"> 739 <a href="../detecting-loaded-modules/" class="md-nav__link"> 740 741 742 743 <span class="md-ellipsis"> 744 745 746 Detecting loaded modules 747 748 749 750 </span> 751 752 753 754 </a> 755 </li> 756 757 758 759 760 761 762 763 764 765 766 <li class="md-nav__item"> 767 <a href="../log-files/" class="md-nav__link"> 768 769 770 771 <span class="md-ellipsis"> 772 773 774 EasyBuild log files 775 776 777 778 </span> 779 780 781 782 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914 Partial installations 915 916 917 918 </span> 919 920 921 922 </a> 923 </li> 924 925 926 927 928 929 930 931 932 933 934 <li class="md-nav__item"> 935 <a href="../python-2-3-compatibility/" class="md-nav__link"> 936 937 938 939 <span class="md-ellipsis"> 940 941 942 Compatibility with Python 3 943 944 945 946 </span> 947 948 949 950 </a> 951 </li> 952 953 954 955 956 957 958 959 960 961 962 <li class="md-nav__item"> 963 <a href="../progress-bars/" class="md-nav__link"> 964 965 966 967 <span class="md-ellipsis"> 968 969 970 Progress bars 971 972 973 974 </span> 975 976 977 978 </a> 979 </li> 980 981 982 983 984 985 986 987 988 989 990 <li class="md-nav__item"> 991 <a href="../easyconfigs-search-index/" class="md-nav__link"> 992 993 994 995 <span class="md-ellipsis"> 996 997 998 Search index for easyconfigs 999 1000 1001 1002 </span> 1003 1004 1005 1006 </a> 1007 </li> 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 <li class="md-nav__item"> 1019 <a href="../system-toolchain/" class="md-nav__link"> 1020 1021 1022 1023 <span class="md-ellipsis"> 1024 1025 1026 System toolchain 1027 1028 1029 1030 </span> 1031 1032 1033 1034 </a> 1035 </li> 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 <li class="md-nav__item"> 1047 <a href="../submitting-jobs/" class="md-nav__link"> 1048 1049 1050 1051 <span class="md-ellipsis"> 1052 1053 1054 Submitting installations as jobs 1055 1056 1057 1058 </span> 1059 1060 1061 1062 </a> 1063 </li> 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 <li class="md-nav__item"> 1075 <a href="../tracing-progress/" class="md-nav__link"> 1076 1077 1078 1079 <span class="md-ellipsis"> 1080 1081 1082 Tracing installation progress 1083 1084 1085 1086 </span> 1087 1088 1089 1090 </a> 1091 </li> 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 <li class="md-nav__item"> 1103 <a href="../writing-easyconfig-files/" class="md-nav__link"> 1104 1105 1106 1107 <span class="md-ellipsis"> 1108 1109 1110 Writing easyconfig files 1111 1112 1113 1114 </span> 1115 1116 1117 1118 </a> 1119 </li> 1120 1121 1122 1123 1124 </ul> 1125 </nav> 1126 1127 </li> 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 <li class="md-nav__item md-nav__item--nested"> 1143 1144 1145 1146 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" > 1147 1148 1149 <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0"> 1150 1151 1152 1153 <span class="md-ellipsis"> 1154 1155 1156 Advanced topics 1157 1158 1159 1160 </span> 1161 1162 1163 1164 <span class="md-nav__icon md-icon"></span> 1165 </label> 1166 1167 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false"> 1168 <label class="md-nav__title" for="__nav_5"> 1169 <span class="md-nav__icon md-icon"></span> 1170 1171 1172 Advanced topics 1173 1174 1175 </label> 1176 <ul class="md-nav__list" data-md-scrollfix> 1177 1178 1179 1180 1181 1182 1183 1184 <li class="md-nav__item"> 1185 <a href="../cray-support/" class="md-nav__link"> 1186 1187 1188 1189 <span class="md-ellipsis"> 1190 1191 1192 Cray support 1193 1194 1195 1196 </span> 1197 1198 1199 1200 </a> 1201 </li> 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 <li class="md-nav__item"> 1213 <a href="../hooks/" class="md-nav__link"> 1214 1215 1216 1217 <span class="md-ellipsis"> 1218 1219 1220 Customizing EasyBuild via hooks 1221 1222 1223 1224 </span> 1225 1226 1227 1228 </a> 1229 </li> 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 <li class="md-nav__item"> 1241 <a href="../including-additional-python-modules/" class="md-nav__link"> 1242 1243 1244 1245 <span class="md-ellipsis"> 1246 1247 1248 Including Python modules 1249 1250 1251 1252 </span> 1253 1254 1255 1256 </a> 1257 </li> 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 <li class="md-nav__item"> 1269 <a href="../python-search-path/" class="md-nav__link"> 1270 1271 1272 1273 <span class="md-ellipsis"> 1274 1275 1276 Customizing Python search path 1277 1278 1279 1280 </span> 1281 1282 1283 1284 </a> 1285 </li> 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 <li class="md-nav__item"> 1297 <a href="../packaging-support/" class="md-nav__link"> 1298 1299 1300 1301 <span class="md-ellipsis"> 1302 1303 1304 Packaging support 1305 1306 1307 1308 </span> 1309 1310 1311 1312 </a> 1313 </li> 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 <li class="md-nav__item"> 1325 <a href="../rpath-support/" class="md-nav__link"> 1326 1327 1328 1329 <span class="md-ellipsis"> 1330 1331 1332 RPATH support 1333 1334 1335 1336 </span> 1337 1338 1339 1340 </a> 1341 </li> 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 <li class="md-nav__item"> 1353 <a href="../using-external-modules/" class="md-nav__link"> 1354 1355 1356 1357 <span class="md-ellipsis"> 1358 1359 1360 Using external modules 1361 1362 1363 1364 </span> 1365 1366 1367 1368 </a> 1369 </li> 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 <li class="md-nav__item"> 1381 <a href="../wrapping-dependencies/" class="md-nav__link"> 1382 1383 1384 1385 <span class="md-ellipsis"> 1386 1387 1388 Wrapping dependencies 1389 1390 1391 1392 </span> 1393 1394 1395 1396 </a> 1397 </li> 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 <li class="md-nav__item"> 1409 <a href="../easystack-files/" class="md-nav__link"> 1410 1411 1412 1413 <span class="md-ellipsis"> 1414 1415 1416 Easystack files 1417 1418 1419 1420 </span> 1421 1422 1423 1424 </a> 1425 </li> 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 <li class="md-nav__item"> 1437 <a href="../entrypoints/" class="md-nav__link"> 1438 1439 1440 1441 <span class="md-ellipsis"> 1442 1443 1444 Using entrypoints 1445 1446 1447 1448 </span> 1449 1450 1451 1452 </a> 1453 </li> 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 <li class="md-nav__item"> 1465 <a href="../installing-extensions-in-parallel/" class="md-nav__link"> 1466 1467 1468 1469 <span class="md-ellipsis"> 1470 1471 1472 Installing extensions in parallel 1473 1474 1475 1476 </span> 1477 1478 1479 1480 </a> 1481 </li> 1482 1483 1484 1485 1486 </ul> 1487 </nav> 1488 1489 </li> 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 <li class="md-nav__item md-nav__item--nested"> 1505 1506 1507 1508 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" > 1509 1510 1511 <label class="md-nav__link" for="__nav_6" id="__nav_6_label" tabindex="0"> 1512 1513 1514 1515 <span class="md-ellipsis"> 1516 1517 1518 For developers/contributors 1519 1520 1521 1522 </span> 1523 1524 1525
1526 <span class="md-nav__icon md-icon"></span> 1527 </label> 1528 1529 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false"> 1530 <label class="md-nav__title" for="__nav_6"> 1531 <span class="md-nav__icon md-icon"></span> 1532 1533 1534 For developers/contributors 1535 1536 1537 </label> 1538 <ul class="md-nav__list" data-md-scrollfix> 1539 1540 1541 1542 1543 1544 1545 1546 <li class="md-nav__item"> 1547 <a href="../archived-easyconfigs/" class="md-nav__link"> 1548 1549 1550 1551 <span class="md-ellipsis"> 1552 1553 1554 Archived easyconfigs 1555 1556 1557 1558 </span> 1559 1560 1561 1562 </a> 1563 </li> 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 <li class="md-nav__item"> 1575 <a href="../code-style/" class="md-nav__link"> 1576 1577 1578 1579 <span class="md-ellipsis"> 1580 1581 1582 Code style 1583 1584 1585 1586 </span> 1587 1588 1589 1590 </a> 1591 </li> 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 <li class="md-nav__item"> 1603 <a href="../contributing/" class="md-nav__link"> 1604 1605 1606 1607 <span class="md-ellipsis"> 1608 1609 1610 Contributing to EasyBuild 1611 1612 1613 1614 </span> 1615 1616 1617 1618 </a> 1619 </li> 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 <li class="md-nav__item"> 1631 <a href="../integration-with-github/" class="md-nav__link"> 1632 1633 1634 1635 <span class="md-ellipsis"> 1636 1637 1638 GitHub integration 1639 1640 1641 1642 </span> 1643 1644 1645 1646 </a> 1647 </li> 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 <li class="md-nav__item"> 1659 <a href="../implementing-easyblocks/" class="md-nav__link"> 1660 1661 1662 1663 <span class="md-ellipsis"> 1664 1665 1666 Implementing easyblocks 1667 1668 1669 1670 </span> 1671 1672 1673 1674 </a> 1675 </li> 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 <li class="md-nav__item"> 1687 <a href="../easyconfig-files-local-variables/" class="md-nav__link"> 1688 1689 1690 1691 <span class="md-ellipsis"> 1692 1693 1694 Local variables in easyconfigs 1695 1696 1697 1698 </span> 1699 1700 1701 1702 </a> 1703 </li> 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 <li class="md-nav__item"> 1715 <a href="../patch-files/" class="md-nav__link"> 1716 1717 1718 1719 <span class="md-ellipsis"> 1720 1721 1722 Patch files 1723 1724 1725 1726 </span> 1727 1728 1729 1730 </a> 1731 </li> 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 <li class="md-nav__item"> 1743 <a href="../unit-tests/" class="md-nav__link"> 1744 1745 1746 1747 <span class="md-ellipsis"> 1748 1749 1750 Unit tests 1751 1752 1753 1754 </span> 1755 1756 1757 1758 </a> 1759 </li> 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 <li class="md-nav__item"> 1771 <a href="../framework-overview/" class="md-nav__link"> 1772 1773 1774 1775 <span class="md-ellipsis"> 1776 1777 1778 Framework overview 1779 1780 1781 1782 </span> 1783 1784 1785 1786 </a> 1787 </li> 1788 1789 1790 1791 1792 </ul> 1793 </nav> 1794 1795 </li> 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 <li class="md-nav__item md-nav__item--nested"> 1811 1812 1813 1814 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_7" > 1815 1816 1817 <label class="md-nav__link" for="__nav_7" id="__nav_7_label" tabindex="0"> 1818 1819 1820 1821 <span class="md-ellipsis"> 1822 1823 1824 Experimental features 1825 1826 1827 1828 </span> 1829 1830 1831 1832 <span class="md-nav__icon md-icon"></span> 1833 </label> 1834 1835 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false"> 1836 <label class="md-nav__title" for="__nav_7"> 1837 <span class="md-nav__icon md-icon"></span> 1838 1839 1840 Experimental features 1841 1842 1843 </label> 1844 <ul class="md-nav__list" data-md-scrollfix> 1845 1846 1847 1848 1849 1850 1851 1852 <li class="md-nav__item"> 1853 <a href="../experimental-features/" class="md-nav__link"> 1854 1855 1856 1857 <span class="md-ellipsis"> 1858 1859 1860 (overview) 1861 1862 1863 1864 </span> 1865 1866 1867 1868 </a> 1869 </li> 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 <li class="md-nav__item"> 1881 <a href="../containers/" class="md-nav__link"> 1882 1883 1884 1885 <span class="md-ellipsis"> 1886 1887 1888 Creating container images/recipes 1889 1890 1891 1892 </span> 1893 1894 1895 1896 </a> 1897 </li> 1898 1899 1900 1901 1902 </ul> 1903 </nav> 1904 1905 </li> 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 <li class="md-nav__item md-nav__item--nested"> 1921 1922 1923 1924 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8" > 1925 1926 1927 <label class="md-nav__link" for="__nav_8" id="__nav_8_label" tabindex="0"> 1928 1929 1930 1931 <span class="md-ellipsis"> 1932 1933 1934 Version-specific info 1935 1936 1937 1938 </span> 1939 1940 1941
1942 <span class="md-nav__icon md-icon"></span> 1943 </label> 1944 1945 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false"> 1946 <label class="md-nav__title" for="__nav_8"> 1947 <span class="md-nav__icon md-icon"></span> 1948 1949 1950 Version-specific info 1951 1952 1953 </label> 1954 <ul class="md-nav__list" data-md-scrollfix> 1955 1956 1957 1958 1959 1960 1961 1962 <li class="md-nav__item"> 1963 <a href="../version-specific/" class="md-nav__link"> 1964 1965 1966 1967 <span class="md-ellipsis"> 1968 1969 1970 (overview) 1971 1972 1973 1974 </span> 1975 1976 1977 1978 </a> 1979 </li> 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 <li class="md-nav__item"> 1991 <a href="../version-specific/config-file-constants/" class="md-nav__link"> 1992 1993 1994 1995 <span class="md-ellipsis"> 1996 1997 1998 Constants for config files 1999 2000 2001 2002 </span> 2003 2004 2005 2006 </a> 2007 </li> 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 <li class="md-nav__item"> 2019 <a href="../version-specific/easyconfig-constants/" class="md-nav__link"> 2020 2021 2022 2023 <span class="md-ellipsis"> 2024 2025 2026 Constants for easyconfigs 2027 2028 2029 2030 </span> 2031 2032 2033 2034 </a> 2035 </li> 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 <li class="md-nav__item"> 2047 <a href="../version-specific/easyblocks/" class="md-nav__link"> 2048 2049 2050 2051 <span class="md-ellipsis"> 2052 2053 2054 Easyblocks 2055 2056 2057 2058 </span> 2059 2060 2061 2062 </a> 2063 </li> 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 <li class="md-nav__item"> 2075 <a href="../version-specific/eb-help/" class="md-nav__link"> 2076 2077 2078 2079 <span class="md-ellipsis"> 2080 2081 2082 EasyBuild configuration options 2083 2084 2085 2086 </span> 2087 2088 2089 2090 </a> 2091 </li> 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 <li class="md-nav__item"> 2103 <a href="../version-specific/easyconfig-parameters/" class="md-nav__link"> 2104 2105 2106 2107 <span class="md-ellipsis"> 2108 2109 2110 Easyconfig parameters 2111 2112 2113 2114 </span> 2115 2116 2117 2118 </a> 2119 </li> 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 <li class="md-nav__item"> 2131 <a href="../version-specific/generic-easyblocks/" class="md-nav__link"> 2132 2133 2134 2135 <span class="md-ellipsis"> 2136 2137 2138 Generic easyblocks 2139 2140 2141 2142 </span> 2143 2144 2145 2146 </a> 2147 </li> 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 <li class="md-nav__item"> 2159 <a href="../version-specific/easyconfig-license-constants/" class="md-nav__link"> 2160 2161 2162 2163 <span class="md-ellipsis"> 2164 2165 2166 License constants for easyconfigs 2167 2168 2169 2170 </span> 2171 2172 2173 2174 </a> 2175 </li> 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 <li class="md-nav__item"> 2187 <a href="../version-specific/easyconfig-templates/" class="md-nav__link"> 2188 2189 2190 2191 <span class="md-ellipsis"> 2192 2193 2194 Templates for easyconfigs 2195 2196 2197 2198 </span> 2199 2200 2201 2202 </a> 2203 </li> 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 <li class="md-nav__item"> 2215 <a href="../version-specific/toolchain-opts/" class="md-nav__link"> 2216 2217 2218 2219 <span class="md-ellipsis"> 2220 2221 2222 Toolchain options 2223 2224 2225 2226 </span> 2227 2228 2229 2230 </a> 2231 </li> 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 <li class="md-nav__item"> 2243 <a href="../version-specific/toolchains/" class="md-nav__link"> 2244 2245 2246 2247 <span class="md-ellipsis"> 2248 2249 2250 Toolchains 2251 2252 2253 2254 </span> 2255 2256 2257 2258 </a> 2259 </li> 2260 2261 2262 2263 2264 </ul> 2265 </nav> 2266 2267 </li> 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 <li class="md-nav__item md-nav__item--active"> 2280 2281 <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc"> 2282 2283 2284 2285 2286 2287 <label class="md-nav__link md-nav__link--active" for="__toc"> 2288 2289 2290 2291 <span class="md-ellipsis"> 2292 2293 2294 EasyBuild release notes 2295 2296 2297 2298 </span> 2299 2300 2301
2302 <span class="md-nav__icon md-icon"></span> 2303 </label> 2304 2305 <a href="./" class="md-nav__link md-nav__link--active"> 2306 2307 2308 2309 <span class="md-ellipsis"> 2310 2311 2312 EasyBuild release notes 2313 2314 2315 2316 </span> 2317 2318 2319 2320 </a> 2321 2322 2323 2324<nav class="md-nav md-nav--secondary" aria-label="Table of contents"> 2325 2326 2327 2328 2329 2330 2331 <label class="md-nav__title" for="__toc"> 2332 <span class="md-nav__icon md-icon"></span> 2333 Table of contents 2334 </label> 2335 <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix> 2336 2337 <li class="md-nav__item"> 2338 <a href="#release_notes_eb540" class="md-nav__link"> 2339 <span class="md-ellipsis"> 2340 2341 EasyBuild v5.4.0 (9 Aug 2026) 2342 2343 </span> 2344 </a> 2345 2346</li> 2347 2348 <li class="md-nav__item"> 2349 <a href="#release_notes_eb531" class="md-nav__link"> 2350 <span class="md-ellipsis"> 2351 2352 EasyBuild v5.3.1 (19 Jun 2026) 2353 2354 </span> 2355 </a> 2356 2357</li> 2358 2359 <li class="md-nav__item"> 2360 <a href="#release_notes_eb530" class="md-nav__link"> 2361 <span class="md-ellipsis"> 2362 2363 EasyBuild v5.3.0 (10 Apr 2026) 2364 2365 </span> 2366 </a> 2367 2368</li> 2369 2370 <li class="md-nav__item"> 2371 <a href="#release_notes_eb521" class="md-nav__link"> 2372 <span class="md-ellipsis"> 2373 2374 EasyBuild v5.2.1 (20 Feb 2026) 2375 2376 </span> 2377 </a> 2378 2379</li> 2380 2381 <li class="md-nav__item"> 2382 <a href="#release_notes_eb520" class="md-nav__link"> 2383 <span class="md-ellipsis"> 2384 2385 EasyBuild v5.2.0 (23 Dec 2025) 2386 2387 </span> 2388 </a> 2389 2390</li> 2391 2392 <li class="md-nav__item"> 2393 <a href="#release_notes_eb512" class="md-nav__link"> 2394 <span class="md-ellipsis"> 2395 2396 EasyBuild v5.1.2 (26 Sept 2025) 2397 2398 </span> 2399 </a> 2400 2401</li> 2402 2403 <li class="md-nav__item"> 2404 <a href="#release_notes_eb511" class="md-nav__link"> 2405 <span class="md-ellipsis"> 2406 2407 EasyBuild v5.1.1 (6 July 2025) 2408 2409 </span> 2410 </a> 2411 2412</li> 2413 2414 <li class="md-nav__item"> 2415 <a href="#release_notes_eb510" class="md-nav__link"> 2416 <span class="md-ellipsis"> 2417 2418 EasyBuild v5.1.0 (26 May 2025) 2419 2420 </span> 2421 </a> 2422 2423</li> 2424 2425 <li class="md-nav__item"> 2426 <a href="#release_notes_eb500" class="md-nav__link"> 2427 <span class="md-ellipsis"> 2428 2429 EasyBuild v5.0.0 (18 Mar 2025) 2430 2431 </span> 2432 </a> 2433 2434</li> 2435 2436 <li class="md-nav__item"> 2437 <a href="#release_notes_eb494" class="md-nav__link"> 2438 <span class="md-ellipsis"> 2439 2440 EasyBuild v4.9.4 (22 Sept 2024) 2441 2442 </span> 2443 </a> 2444 2445</li> 2446 2447 <li class="md-nav__item"> 2448 <a href="#release_notes_eb493" class="md-nav__link"> 2449 <span class="md-ellipsis"> 2450 2451 EasyBuild v4.9.3 (14 Sept 2024) 2452 2453 </span> 2454 </a> 2455 2456</li> 2457 2458 <li class="md-nav__item"> 2459 <a href="#release_notes_eb492" class="md-nav__link"> 2460 <span class="md-ellipsis"> 2461 2462 EasyBuild v4.9.2 (12 June 2024) 2463 2464 </span> 2465 </a> 2466 2467</li> 2468 2469 <li class="md-nav__item"> 2470 <a href="#release_notes_eb491" class="md-nav__link"> 2471 <span class="md-ellipsis"> 2472 2473 EasyBuild v4.9.1 (5 April 2024) 2474 2475 </span> 2476 </a> 2477 2478</li> 2479 2480 <li class="md-nav__item"> 2481 <a href="#release_notes_eb490" class="md-nav__link"> 2482 <span class="md-ellipsis"> 2483 2484 EasyBuild v4.9.0 (29 Dec 2023) 2485 2486 </span> 2487 </a> 2488 2489</li> 2490 2491 <li class="md-nav__item"> 2492 <a href="#release_notes_eb482" class="md-nav__link"> 2493 <span class="md-ellipsis"> 2494 2495 EasyBuild v4.8.2 (29 Oct 2023) 2496 2497 </span> 2498 </a> 2499 2500</li> 2501 2502 <li class="md-nav__item"> 2503 <a href="#release_notes_eb481" class="md-nav__link"> 2504 <span class="md-ellipsis"> 2505 2506 EasyBuild v4.8.1 (11 Sept 2023) 2507 2508 </span> 2509 </a> 2510 2511</li> 2512 2513 <li class="md-nav__item"> 2514 <a href="#release_notes_eb480" class="md-nav__link"> 2515 <span class="md-ellipsis"> 2516 2517 EasyBuild v4.8.0 (7 July 2023) 2518 2519 </span> 2520 </a> 2521 2522</li> 2523 2524 <li class="md-nav__item"> 2525 <a href="#release_notes_eb472" class="md-nav__link"> 2526 <span class="md-ellipsis"> 2527 2528 EasyBuild v4.7.2 (27 May 2023) 2529 2530 </span> 2531 </a> 2532 2533</li> 2534 2535 <li class="md-nav__item"> 2536 <a href="#release_notes_eb471" class="md-nav__link"> 2537 <span class="md-ellipsis"> 2538 2539 EasyBuild v4.7.1 (20 March 2023) 2540 2541 </span> 2542 </a> 2543 2544</li> 2545 2546 <li class="md-nav__item"> 2547 <a href="#release_notes_eb470" class="md-nav__link"> 2548 <span class="md-ellipsis"> 2549 2550 EasyBuild v4.7.0 (January 9th 2023) 2551 2552 </span> 2553 </a> 2554 2555</li> 2556 2557 <li class="md-nav__item"> 2558 <a href="#release_notes_eb462" class="md-nav__link"> 2559 <span class="md-ellipsis"> 2560 2561 EasyBuild v4.6.2 (October 21st 2022) 2562 2563 </span> 2564 </a> 2565 2566</li> 2567 2568 <li class="md-nav__item"> 2569 <a href="#release_notes_eb461" class="md-nav__link"> 2570 <span class="md-ellipsis"> 2571 2572 EasyBuild v4.6.1 (September 12th 2022) 2573 2574 </span> 2575 </a> 2576 2577</li> 2578 2579 <li class="md-nav__item"> 2580 <a href="#release_notes_eb460" class="md-nav__link"> 2581 <span class="md-ellipsis"> 2582 2583 EasyBuild v4.6.0 (July 8th 2022) 2584 2585 </span> 2586 </a> 2587 2588</li> 2589 2590 <li class="md-nav__item"> 2591 <a href="#release_notes_eb455" class="md-nav__link"> 2592 <span class="md-ellipsis"> 2593 2594 EasyBuild v4.5.5 (June 8th 2022) 2595 2596 </span> 2597 </a> 2598 2599</li> 2600 2601 <li class="md-nav__item"> 2602 <a href="#release_notes_eb454" class="md-nav__link"> 2603 <span class="md-ellipsis"> 2604 2605 EasyBuild v4.5.4 (March 31st 2022) 2606 2607 </span> 2608 </a> 2609 2610</li> 2611 2612 <li class="md-nav__item"> 2613 <a href="#release_notes_eb453" class="md-nav__link"> 2614 <span class="md-ellipsis"> 2615 2616 EasyBuild v4.5.3 (February 11th 2022) 2617 2618 </span> 2619 </a> 2620 2621</li> 2622 2623 <li class="md-nav__item"> 2624 <a href="#release_notes_eb452" class="md-nav__link"> 2625 <span class="md-ellipsis"> 2626 2627 EasyBuild v4.5.2 (January 24th 2022) 2628 2629 </span> 2630 </a> 2631 2632</li> 2633 2634 <li class="md-nav__item"> 2635 <a href="#release_notes_eb451" class="md-nav__link"> 2636 <span class="md-ellipsis"> 2637 2638 EasyBuild v4.5.1 (December 13th 2021) 2639 2640 </span> 2641 </a> 2642 2643</li> 2644 2645 <li class="md-nav__item"> 2646 <a href="#release_notes_eb450" class="md-nav__link"> 2647 <span class="md-ellipsis"> 2648 2649 EasyBuild v4.5.0 (October 29th 2021) 2650 2651 </span> 2652 </a> 2653 2654</li> 2655 2656 <li class="md-nav__item"> 2657 <a href="#release_notes_eb442" class="md-nav__link"> 2658 <span class="md-ellipsis"> 2659 2660 EasyBuild v4.4.2 (September 7th 2021) 2661 2662 </span> 2663 </a> 2664 2665</li> 2666 2667 <li class="md-nav__item"> 2668 <a href="#release_notes_eb441" class="md-nav__link"> 2669 <span class="md-ellipsis"> 2670 2671 EasyBuild v4.4.1 (July 6th 2021) 2672 2673 </span> 2674 </a> 2675 2676</li> 2677 2678 <li class="md-nav__item"> 2679 <a href="#release_notes_eb440" class="md-nav__link"> 2680 <span class="md-ellipsis"> 2681 2682 EasyBuild v4.4.0 (June 2nd 2021) 2683 2684 </span> 2685 </a> 2686 2687</li> 2688 2689 <li class="md-nav__item"> 2690 <a href="#release_notes_eb434" class="md-nav__link"> 2691 <span class="md-ellipsis"> 2692 2693 EasyBuild v4.3.4 (Apr 9th 2021) 2694 2695 </span> 2696 </a> 2697 2698</li> 2699 2700 <li class="md-nav__item"> 2701 <a href="#release_notes_eb433" class="md-nav__link"> 2702 <span class="md-ellipsis"> 2703 2704 EasyBuild v4.3.3 (Feb 23rd 2021) 2705 2706 </span> 2707 </a> 2708 2709</li> 2710 2711 <li class="md-nav__item"> 2712 <a href="#release_notes_eb432" class="md-nav__link"> 2713 <span class="md-ellipsis"> 2714 2715 EasyBuild v4.3.2 (December 10th 2020) 2716 2717 </span> 2718 </a> 2719 2720</li> 2721 2722 <li class="md-nav__item"> 2723 <a href="#release_notes_eb431" class="md-nav__link"> 2724 <span class="md-ellipsis"> 2725 2726 EasyBuild v4.3.1 (October 29th 2020) 2727 2728 </span> 2729 </a> 2730 2731</li> 2732 2733 <li class="md-nav__item"> 2734 <a href="#release_notes_eb430" class="md-nav__link"> 2735 <span class="md-ellipsis"> 2736 2737 EasyBuild v4.3.0 (September 13th 2020) 2738 2739 </span> 2740 </a> 2741 2742</li> 2743 2744 <li class="md-nav__item"> 2745 <a href="#release_notes_eb422" class="md-nav__link"> 2746 <span class="md-ellipsis"> 2747
2748 EasyBuild v4.2.2 (July 8th 2020) 2749 2750 </span> 2751 </a> 2752 2753</li> 2754 2755 <li class="md-nav__item"> 2756 <a href="#release_notes_eb421" class="md-nav__link"> 2757 <span class="md-ellipsis"> 2758 2759 EasyBuild v4.2.1 (May 20th 2020) 2760 2761 </span> 2762 </a> 2763 2764</li> 2765 2766 <li class="md-nav__item"> 2767 <a href="#release_notes_eb420" class="md-nav__link"> 2768 <span class="md-ellipsis"> 2769 2770 EasyBuild v4.2.0 (April 14th 2020) 2771 2772 </span> 2773 </a> 2774 2775</li> 2776 2777 <li class="md-nav__item"> 2778 <a href="#release_notes_eb412" class="md-nav__link"> 2779 <span class="md-ellipsis"> 2780 2781 EasyBuild v4.1.2 (March 16th 2020) 2782 2783 </span> 2784 </a> 2785 2786</li> 2787 2788 <li class="md-nav__item"> 2789 <a href="#release_notes_eb411" class="md-nav__link"> 2790 <span class="md-ellipsis"> 2791 2792 EasyBuild v4.1.1 (January 16th 2020) 2793 2794 </span> 2795 </a> 2796 2797</li> 2798 2799 <li class="md-nav__item"> 2800 <a href="#release_notes_eb410" class="md-nav__link"> 2801 <span class="md-ellipsis"> 2802 2803 EasyBuild v4.1.0 (December 4th 2019) 2804 2805 </span> 2806 </a> 2807 2808</li> 2809 2810 <li class="md-nav__item"> 2811 <a href="#release_notes_eb401" class="md-nav__link"> 2812 <span class="md-ellipsis"> 2813 2814 EasyBuild v4.0.1 (October 15th 2019) 2815 2816 </span> 2817 </a> 2818 2819</li> 2820 2821 <li class="md-nav__item"> 2822 <a href="#release_notes_eb400" class="md-nav__link"> 2823 <span class="md-ellipsis"> 2824 2825 EasyBuild v4.0.0 (September 20th 2019) 2826 2827 </span> 2828 </a> 2829 2830</li> 2831 2832 <li class="md-nav__item"> 2833 <a href="#release_notes_eb394" class="md-nav__link"> 2834 <span class="md-ellipsis"> 2835 2836 EasyBuild v3.9.4 (August 23rd 2019) 2837 2838 </span> 2839 </a> 2840 2841</li> 2842 2843 <li class="md-nav__item"> 2844 <a href="#release_notes_eb393" class="md-nav__link"> 2845 <span class="md-ellipsis"> 2846 2847 EasyBuild v3.9.3 (July 8th 2019) 2848 2849 </span> 2850 </a> 2851 2852</li> 2853 2854 <li class="md-nav__item"> 2855 <a href="#release_notes_eb392" class="md-nav__link"> 2856 <span class="md-ellipsis"> 2857 2858 EasyBuild v3.9.2 (June 9th 2019) 2859 2860 </span> 2861 </a> 2862 2863</li> 2864 2865 <li class="md-nav__item"> 2866 <a href="#release_notes_eb391" class="md-nav__link"> 2867 <span class="md-ellipsis"> 2868 2869 EasyBuild v3.9.1 (May 20th 2019) 2870 2871 </span> 2872 </a> 2873 2874</li> 2875 2876 <li class="md-nav__item"> 2877 <a href="#release_notes_eb390" class="md-nav__link"> 2878 <span class="md-ellipsis"> 2879 2880 EasyBuild v3.9.0 (April 12th 2019) 2881 2882 </span> 2883 </a> 2884 2885</li> 2886 2887 <li class="md-nav__item"> 2888 <a href="#release_notes_eb381" class="md-nav__link"> 2889 <span class="md-ellipsis"> 2890 2891 EasyBuild v3.8.1 (January 29th 2019) 2892 2893 </span> 2894 </a> 2895 2896</li> 2897 2898 <li class="md-nav__item"> 2899 <a href="#release_notes_eb380" class="md-nav__link"> 2900 <span class="md-ellipsis"> 2901 2902 EasyBuild v3.8.0 (December 18th 2018) 2903 2904 </span> 2905 </a> 2906 2907</li> 2908 2909 <li class="md-nav__item"> 2910 <a href="#release_notes_eb371" class="md-nav__link"> 2911 <span class="md-ellipsis"> 2912 2913 EasyBuild v3.7.1 (October 18th 2018) 2914 2915 </span> 2916 </a> 2917 2918</li> 2919 2920 <li class="md-nav__item"> 2921 <a href="#release_notes_eb370" class="md-nav__link"> 2922 <span class="md-ellipsis"> 2923 2924 EasyBuild v3.7.0 (September 25th 2018) 2925 2926 </span> 2927 </a> 2928 2929</li> 2930 2931 <li class="md-nav__item"> 2932 <a href="#release_notes_eb362" class="md-nav__link"> 2933 <span class="md-ellipsis"> 2934 2935 EasyBuild v3.6.2 (July 11th 2018) 2936 2937 </span> 2938 </a> 2939 2940</li> 2941 2942 <li class="md-nav__item"> 2943 <a href="#release_notes_eb361" class="md-nav__link"> 2944 <span class="md-ellipsis"> 2945 2946 EasyBuild v3.6.1 (May 26th 2018) 2947 2948 </span> 2949 </a> 2950 2951</li> 2952 2953 <li class="md-nav__item"> 2954 <a href="#release_notes_eb360" class="md-nav__link"> 2955 <span class="md-ellipsis"> 2956 2957 EasyBuild v3.6.0 (April 26th 2018) 2958 2959 </span> 2960 </a> 2961 2962</li> 2963 2964 <li class="md-nav__item"> 2965 <a href="#release_notes_eb353" class="md-nav__link"> 2966 <span class="md-ellipsis"> 2967 2968 EasyBuild v3.5.3 (March 7th 2018) 2969 2970 </span> 2971 </a> 2972 2973</li> 2974 2975 <li class="md-nav__item"> 2976 <a href="#release_notes_eb352" class="md-nav__link"> 2977 <span class="md-ellipsis"> 2978 2979 EasyBuild v3.5.2 (March 2nd 2018) 2980 2981 </span> 2982 </a> 2983 2984</li> 2985 2986 <li class="md-nav__item"> 2987 <a href="#release_notes_eb351" class="md-nav__link"> 2988 <span class="md-ellipsis"> 2989 2990 EasyBuild v3.5.1 (January 16th 2018) 2991 2992 </span> 2993 </a> 2994 2995</li> 2996 2997 <li class="md-nav__item"> 2998 <a href="#release_notes_eb350" class="md-nav__link"> 2999 <span class="md-ellipsis"> 3000 3001 EasyBuild v3.5.0 (December 15th 2017) 3002 3003 </span> 3004 </a> 3005 3006</li> 3007 3008 <li class="md-nav__item"> 3009 <a href="#release_notes_eb341" class="md-nav__link"> 3010 <span class="md-ellipsis"> 3011 3012 EasyBuild v3.4.1 (October 17th 2017) 3013 3014 </span> 3015 </a> 3016 3017</li> 3018 3019 <li class="md-nav__item"> 3020 <a href="#release_notes_eb340" class="md-nav__link"> 3021 <span class="md-ellipsis"> 3022 3023 EasyBuild v3.4.0 (September 10th 2017) 3024 3025 </span> 3026 </a> 3027 3028</li> 3029 3030 <li class="md-nav__item"> 3031 <a href="#release_notes_eb331" class="md-nav__link"> 3032 <span class="md-ellipsis"> 3033 3034 EasyBuild v3.3.1 (July 12th 2017) 3035 3036 </span> 3037 </a> 3038 3039</li> 3040 3041 <li class="md-nav__item"> 3042 <a href="#release_notes_eb330" class="md-nav__link"> 3043 <span class="md-ellipsis"> 3044 3045 EasyBuild v3.3.0 (June 26th 2017) 3046 3047 </span> 3048 </a> 3049 3050</li> 3051 3052 <li class="md-nav__item"> 3053 <a href="#release_notes_eb321" class="md-nav__link"> 3054 <span class="md-ellipsis"> 3055 3056 EasyBuild v3.2.1 (May 12th 2017) 3057 3058 </span> 3059 </a> 3060 3061</li> 3062 3063 <li class="md-nav__item"> 3064 <a href="#release_notes_eb320" class="md-nav__link"> 3065 <span class="md-ellipsis"> 3066 3067 EasyBuild v3.2.0 (May 5th 2017) 3068 3069 </span> 3070 </a> 3071 3072</li> 3073 3074 <li class="md-nav__item"> 3075 <a href="#release_notes_eb312" class="md-nav__link"> 3076 <span class="md-ellipsis"> 3077 3078 EasyBuild v3.1.2 (March 20th 2017) 3079 3080 </span> 3081 </a> 3082 3083</li> 3084 3085 <li class="md-nav__item"> 3086 <a href="#release_notes_eb311" class="md-nav__link"> 3087 <span class="md-ellipsis"> 3088 3089 EasyBuild v3.1.1 (March 7th 2017) 3090 3091 </span> 3092 </a> 3093 3094</li> 3095 3096 <li class="md-nav__item"> 3097 <a href="#release_notes_eb310" class="md-nav__link"> 3098 <span class="md-ellipsis"> 3099 3100 EasyBuild v3.1.0 (February 3rd 2017) 3101 3102 </span> 3103 </a> 3104 3105</li> 3106 3107 <li class="md-nav__item"> 3108 <a href="#release_notes_eb302" class="md-nav__link"> 3109 <span class="md-ellipsis"> 3110 3111 EasyBuild v3.0.2 (December 22nd 2016) 3112 3113 </span> 3114 </a> 3115 3116</li> 3117 3118 <li class="md-nav__item"> 3119 <a href="#release_notes_eb301" class="md-nav__link"> 3120 <span class="md-ellipsis"> 3121 3122 EasyBuild v3.0.1 (November 30th 2016) 3123 3124 </span> 3125 </a> 3126 3127</li> 3128 3129 <li class="md-nav__item"> 3130 <a href="#release_notes_eb300" class="md-nav__link"> 3131 <span class="md-ellipsis"> 3132 3133 EasyBuild v3.0.0 (November 16th 2016) 3134 3135 </span> 3136 </a> 3137 3138</li> 3139 3140 <li class="md-nav__item"> 3141 <a href="#release_notes_eb290" class="md-nav__link"> 3142 <span class="md-ellipsis"> 3143 3144 EasyBuild v2.9.0 (September 23rd 2016) 3145 3146 </span> 3147 </a> 3148 3149</li> 3150 3151 <li class="md-nav__item"> 3152 <a href="#release_notes_eb282" class="md-nav__link"> 3153 <span class="md-ellipsis"> 3154 3155 EasyBuild v2.8.2 (July 13th 2016) 3156 3157 </span> 3158 </a> 3159 3160</li> 3161 3162 <li class="md-nav__item"> 3163 <a href="#release_notes_eb281" class="md-nav__link"> 3164 <span class="md-ellipsis"> 3165 3166 EasyBuild v2.8.1 (May 30th 2016) 3167 3168 </span> 3169 </a> 3170 3171</li> 3172 3173 <li class="md-nav__item"> 3174 <a href="#release_notes_eb280" class="md-nav__link"> 3175 <span class="md-ellipsis"> 3176 3177 EasyBuild v2.8.0 (May 18th 2016) 3178 3179 </span> 3180 </a> 3181 3182</li> 3183 3184 <li class="md-nav__item"> 3185 <a href="#release_notes_eb270" class="md-nav__link"> 3186 <span class="md-ellipsis"> 3187 3188 EasyBuild v2.7.0 (March 20th 2016) 3189 3190 </span> 3191 </a> 3192 3193</li> 3194 3195 <li class="md-nav__item"> 3196 <a href="#release_notes_eb260" class="md-nav__link"> 3197 <span class="md-ellipsis"> 3198 3199 EasyBuild v2.6.0 (January 26th 2016) 3200 3201 </span> 3202 </a> 3203 3204</li> 3205 3206 <li class="md-nav__item"> 3207 <a href="#release_notes_eb250" class="md-nav__link"> 3208 <span class="md-ellipsis"> 3209 3210 EasyBuild v2.5.0 (December 17th 2015) 3211 3212 </span> 3213 </a> 3214 3215</li> 3216 3217 <li class="md-nav__item"> 3218 <a href="#release_notes_eb240" class="md-nav__link"> 3219 <span class="md-ellipsis"> 3220 3221 EasyBuild v2.4.0 (November 10th 2015) 3222 3223 </span> 3224 </a> 3225 3226</li> 3227 3228 <li class="md-nav__item"> 3229 <a href="#release_notes_eb230" class="md-nav__link"> 3230 <span class="md-ellipsis"> 3231 3232 EasyBuild v2.3.0 (September 2nd 2015) 3233 3234 </span> 3235 </a> 3236 3237</li> 3238 3239 <li class="md-nav__item"> 3240 <a href="#release_notes_eb220" class="md-nav__link"> 3241 <span class="md-ellipsis"> 3242 3243 EasyBuild v2.2.0 (July 15th 2015) 3244 3245 </span> 3246 </a> 3247 3248</li> 3249 3250 <li class="md-nav__item"> 3251 <a href="#release_notes_eb211" class="md-nav__link"> 3252 <span class="md-ellipsis"> 3253 3254 EasyBuild v2.1.1 (May 18th 2015) 3255 3256 </span> 3257 </a> 3258 3259</li> 3260 3261 <li class="md-nav__item"> 3262 <a href="#release_notes_v2.1.0" class="md-nav__link"> 3263 <span class="md-ellipsis"> 3264 3265 EasyBuild v2.1.0 (April 30th 2015) 3266 3267 </span> 3268 </a> 3269 3270</li> 3271 3272 <li class="md-nav__item"> 3273 <a href="#release_notes_v2.0.0" class="md-nav__link"> 3274 <span class="md-ellipsis"> 3275 3276 EasyBuild v2.0.0 (March 6th 2015) 3277 3278 </span> 3279 </a> 3280 3281</li> 3282 3283 <li class="md-nav__item"> 3284 <a href="#easybuild-v1162-march-6th-2015" class="md-nav__link"> 3285 <span class="md-ellipsis"> 3286 3287 EasyBuild v1.16.2 (March 6th 2015) 3288 3289 </span> 3290 </a> 3291 3292</li> 3293 3294 <li class="md-nav__item"> 3295 <a href="#easybuild-v1161-december-19th-2014" class="md-nav__link"> 3296 <span class="md-ellipsis"> 3297 3298 EasyBuild v1.16.1 (December 19th 2014) 3299 3300 </span> 3301 </a> 3302 3303</li> 3304 3305 <li class="md-nav__item"> 3306 <a href="#easybuild-v1160-december-18th-2014" class="md-nav__link"> 3307 <span class="md-ellipsis"> 3308 3309 EasyBuild v1.16.0 (December 18th 2014) 3310 3311 </span> 3312 </a> 3313 3314</li> 3315 3316 <li class="md-nav__item"> 3317 <a href="#easybuild-v1152-october-7th-2014" class="md-nav__link"> 3318 <span class="md-ellipsis"> 3319 3320 EasyBuild v1.15.2 (October 7th 2014) 3321 3322 </span> 3323 </a> 3324 3325</li> 3326 3327 <li class="md-nav__item"> 3328 <a href="#easybuild-v1151-september-23rd-2014" class="md-nav__link"> 3329 <span class="md-ellipsis"> 3330 3331 EasyBuild v1.15.1 (September 23rd 2014) 3332 3333 </span> 3334 </a> 3335 3336</li> 3337 3338 <li class="md-nav__item"> 3339 <a href="#easybuild-v1150-september-12th-2014" class="md-nav__link"> 3340 <span class="md-ellipsis"> 3341 3342 EasyBuild v1.15.0 (September 12th 2014) 3343 3344 </span> 3345 </a> 3346 3347</li> 3348 3349 <li class="md-nav__item"> 3350 <a href="#easybuild-v1140-july-9th-2014" class="md-nav__link"> 3351 <span class="md-ellipsis"> 3352 3353 EasyBuild v1.14.0 (July 9th 2014) 3354 3355 </span> 3356 </a> 3357 3358</li> 3359 3360 <li class="md-nav__item"> 3361 <a href="#easybuild-v1130-may-29th-2014" class="md-nav__link"> 3362 <span class="md-ellipsis"> 3363 3364 EasyBuild v1.13.0 (May 29th 2014) 3365 3366 </span> 3367 </a> 3368 3369</li> 3370 3371 <li class="md-nav__item"> 3372 <a href="#easybuild-v1121-april-25th-2014" class="md-nav__link"> 3373 <span class="md-ellipsis"> 3374 3375 EasyBuild v1.12.1 (April 25th 2014) 3376 3377 </span> 3378 </a> 3379 3380</li> 3381 3382 <li class="md-nav__item"> 3383 <a href="#easybuild-v1120-april-4th-2014" class="md-nav__link"> 3384 <span class="md-ellipsis"> 3385 3386 EasyBuild v1.12.0 (April 4th 2014) 3387 3388 </span> 3389 </a> 3390 3391</li> 3392 3393 <li class="md-nav__item"> 3394 <a href="#easybuild-v1111-february-28th-2014" class="md-nav__link"> 3395 <span class="md-ellipsis"> 3396 3397 EasyBuild v1.11.1 (February 28th 2014) 3398 3399 </span> 3400 </a> 3401 3402</li> 3403 3404 <li class="md-nav__item"> 3405 <a href="#easybuild-v1110-february-16th-2014" class="md-nav__link"> 3406 <span class="md-ellipsis"> 3407 3408 EasyBuild v1.11.0 (February 16th 2014) 3409 3410 </span> 3411 </a> 3412 3413</li> 3414 3415 <li class="md-nav__item"> 3416 <a href="#easybuild-v1100-december-24th-2013" class="md-nav__link"> 3417 <span class="md-ellipsis"> 3418
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5584 5585 llvm_compilers 5586 5587 5588 5589 </span> 5590 5591 5592 5593 </a> 5594 </li> 5595 5596 5597 5598 5599 5600 5601 5602 5603 5604 5605 <li class="md-nav__item"> 5606 <a href="../api/easybuild/toolchains/compiler/nvhpc/" class="md-nav__link"> 5607 5608 5609 5610 <span class="md-ellipsis"> 5611 5612 5613 nvhpc 5614 5615 5616 5617 </span> 5618 5619 5620 5621 </a> 5622 </li> 5623 5624 5625 5626 5627 5628 5629 5630 5631 5632 5633 <li class="md-nav__item"> 5634 <a href="../api/easybuild/toolchains/compiler/nvidia_compilers/" class="md-nav__link"> 5635 5636 5637 5638 <span class="md-ellipsis"> 5639 5640 5641 nvidia_compilers 5642 5643 5644 5645 </span> 5646 5647 5648 5649 </a> 5650 </li> 5651 5652 5653 5654 5655 5656 5657 5658 5659 5660 5661 <li class="md-nav__item"> 5662 <a href="../api/easybuild/toolchains/compiler/pgi/" class="md-nav__link"> 5663 5664 5665 5666 <span class="md-ellipsis"> 5667 5668 5669 pgi 5670 5671 5672 5673 </span> 5674 5675 5676 5677 </a> 5678 </li> 5679 5680 5681 5682 5683 5684 5685 5686 5687 5688 5689 <li class="md-nav__item"> 5690 <a href="../api/easybuild/toolchains/compiler/rocm_compilers/" class="md-nav__link"> 5691 5692 5693 5694 <span class="md-ellipsis"> 5695 5696 5697 rocm_compilers 5698 5699 5700 5701 </span> 5702 5703 5704 5705 </a> 5706 </li> 5707 5708 5709 5710 5711 5712 5713 5714 5715 5716 5717 <li class="md-nav__item"> 5718 <a href="../api/easybuild/toolchains/compiler/systemcompiler/" class="md-nav__link"> 5719 5720 5721 5722 <span class="md-ellipsis"> 5723 5724 5725 systemcompiler 5726 5727 5728 5729 </span> 5730 5731 5732 5733 </a> 5734 </li> 5735 5736 5737 5738 5739 </ul> 5740 </nav> 5741 5742 </li> 5743 5744 5745 5746 5747 5748 5749 5750 5751 5752 5753 <li class="md-nav__item"> 5754 <a href="../api/easybuild/toolchains/craycce/" class="md-nav__link"> 5755 5756 5757 5758 <span class="md-ellipsis"> 5759 5760 5761 craycce 5762 5763 5764 5765 </span> 5766 5767 5768 5769 </a> 5770 </li> 5771 5772 5773 5774 5775 5776 5777 5778 5779 5780 5781 <li class="md-nav__item"> 5782 <a href="../api/easybuild/toolchains/craygnu/" class="md-nav__link"> 5783 5784 5785 5786 <span class="md-ellipsis"> 5787 5788 5789 craygnu 5790 5791 5792 5793 </span> 5794 5795 5796 5797 </a> 5798 </li> 5799 5800 5801 5802 5803 5804 5805 5806 5807 5808 5809 <li class="md-nav__item"> 5810 <a href="../api/easybuild/toolchains/crayintel/" class="md-nav__link"> 5811 5812 5813 5814 <span class="md-ellipsis"> 5815 5816 5817 crayintel 5818 5819 5820 5821 </span> 5822 5823 5824 5825 </a> 5826 </li> 5827 5828 5829 5830 5831 5832 5833 5834 5835 5836 5837 <li class="md-nav__item"> 5838 <a href="../api/easybuild/toolchains/craypgi/" class="md-nav__link"> 5839 5840 5841 5842 <span class="md-ellipsis"> 5843 5844 5845 craypgi 5846 5847 5848 5849 </span> 5850 5851 5852 5853 </a> 5854 </li> 5855 5856 5857 5858 5859 5860 5861 5862 5863 5864 5865 <li class="md-nav__item"> 5866 <a href="../api/easybuild/toolchains/fcc/" class="md-nav__link"> 5867 5868 5869 5870 <span class="md-ellipsis"> 5871 5872 5873 fcc 5874 5875 5876 5877 </span> 5878 5879 5880 5881 </a> 5882 </li> 5883 5884 5885 5886 5887 5888 5889 5890 5891 5892 5893 <li class="md-nav__item"> 5894 <a href="../api/easybuild/toolchains/ffmpi/" class="md-nav__link"> 5895 5896 5897 5898 <span class="md-ellipsis"> 5899 5900 5901 ffmpi 5902 5903 5904 5905 </span> 5906 5907 5908 5909 </a> 5910 </li> 5911 5912 5913 5914 5915 5916 5917 5918 5919 5920 5921 5922 5923 5924 5925 5926 <li class="md-nav__item md-nav__item--nested"> 5927 5928 5929 5930 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_11_1_6_15" > 5931 5932 5933 <div class="md-nav__link md-nav__container"> 5934 <a href="../api/easybuild/toolchains/fft/" class="md-nav__link "> 5935 5936 5937 5938 <span class="md-ellipsis"> 5939 5940 5941 fft 5942 5943 5944 5945 </span> 5946 5947 5948 5949 </a> 5950 5951 5952 <label class="md-nav__link " for="__nav_11_1_6_15" id="__nav_11_1_6_15_label" tabindex="0">
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6029 6030 6031 <li class="md-nav__item"> 6032 <a href="../api/easybuild/toolchains/fft/intelfftw/" class="md-nav__link"> 6033 6034 6035 6036 <span class="md-ellipsis"> 6037 6038 6039 intelfftw 6040 6041 6042 6043 </span> 6044 6045 6046 6047 </a> 6048 </li> 6049 6050 6051 6052 6053 </ul> 6054 </nav> 6055 6056 </li> 6057 6058 6059 6060 6061 6062 6063 6064 6065 6066 6067 <li class="md-nav__item"> 6068 <a href="../api/easybuild/toolchains/foss/" class="md-nav__link"> 6069 6070 6071 6072 <span class="md-ellipsis"> 6073 6074 6075 foss 6076 6077 6078 6079 </span> 6080 6081 6082 6083 </a> 6084 </li> 6085 6086 6087 6088 6089 6090 6091 6092 6093 6094 6095 <li class="md-nav__item"> 6096 <a href="../api/easybuild/toolchains/fosscuda/" class="md-nav__link"> 6097 6098 6099 6100 <span class="md-ellipsis"> 6101 6102 6103 fosscuda 6104 6105 6106 6107 </span> 6108 6109 6110 6111 </a> 6112 </li> 6113 6114 6115 6116 6117 6118 6119 6120 6121 6122 6123 <li class="md-nav__item"> 6124 <a href="../api/easybuild/toolchains/fujitsu/" class="md-nav__link"> 6125 6126 6127 6128 <span class="md-ellipsis"> 6129 6130 6131 fujitsu 6132 6133 6134 6135 </span> 6136 6137 6138 6139 </a> 6140 </li> 6141 6142 6143 6144 6145 6146 6147 6148 6149 6150 6151 <li class="md-nav__item"> 6152 <a href="../api/easybuild/toolchains/gcc/" class="md-nav__link"> 6153 6154 6155 6156 <span class="md-ellipsis"> 6157 6158 6159 gcc 6160 6161 6162 6163 </span> 6164 6165 6166 6167 </a> 6168 </li> 6169 6170 6171 6172 6173 6174 6175 6176 6177 6178 6179 <li class="md-nav__item"> 6180 <a href="../api/easybuild/toolchains/gcccore/" class="md-nav__link"> 6181 6182 6183 6184 <span class="md-ellipsis"> 6185 6186 6187 gcccore 6188 6189 6190 6191 </span> 6192 6193 6194 6195 </a> 6196 </li> 6197 6198 6199 6200 6201 6202 6203 6204 6205 6206 6207 <li class="md-nav__item"> 6208 <a href="../api/easybuild/toolchains/gcccuda/" class="md-nav__link"> 6209 6210 6211 6212 <span class="md-ellipsis"> 6213 6214 6215 gcccuda 6216 6217 6218 6219 </span> 6220 6221 6222 6223 </a> 6224 </li> 6225 6226 6227 6228 6229 6230 6231 6232 6233 6234 6235 <li class="md-nav__item"> 6236 <a href="../api/easybuild/toolchains/gfbf/" class="md-nav__link"> 6237 6238 6239 6240 <span class="md-ellipsis"> 6241 6242 6243 gfbf 6244 6245 6246 6247 </span> 6248 6249 6250 6251 </a> 6252 </li> 6253 6254 6255 6256 6257 6258 6259 6260 6261 6262 6263 <li class="md-nav__item"> 6264 <a href="../api/easybuild/toolchains/gimkl/" class="md-nav__link"> 6265 6266 6267 6268 <span class="md-ellipsis"> 6269 6270 6271 gimkl 6272 6273 6274 6275 </span> 6276 6277 6278 6279 </a> 6280 </li> 6281 6282 6283 6284 6285 6286 6287 6288 6289 6290 6291 <li class="md-nav__item"> 6292 <a href="../api/easybuild/toolchains/gimpi/" class="md-nav__link"> 6293 6294 6295 6296 <span class="md-ellipsis"> 6297 6298 6299 gimpi 6300 6301 6302 6303 </span> 6304 6305 6306 6307 </a> 6308 </li> 6309 6310 6311 6312 6313 6314 6315 6316 6317 6318 6319 <li class="md-nav__item"> 6320 <a href="../api/easybuild/toolchains/gimpic/" class="md-nav__link"> 6321 6322 6323 6324 <span class="md-ellipsis"> 6325 6326 6327 gimpic 6328 6329 6330 6331 </span> 6332 6333 6334 6335 </a> 6336 </li> 6337 6338 6339 6340 6341 6342 6343 6344 6345 6346 6347 <li class="md-nav__item"> 6348 <a href="../api/easybuild/toolchains/giolf/" class="md-nav__link"> 6349 6350 6351 6352 <span class="md-ellipsis"> 6353 6354 6355 giolf 6356 6357 6358 6359 </span> 6360 6361 6362 6363 </a> 6364 </li> 6365 6366 6367 6368 6369 6370 6371 6372 6373 6374 6375 <li class="md-nav__item"> 6376 <a href="../api/easybuild/toolchains/giolfc/" class="md-nav__link"> 6377 6378 6379 6380 <span class="md-ellipsis"> 6381 6382 6383 giolfc 6384 6385 6386 6387 </span> 6388 6389 6390 6391 </a> 6392 </li> 6393 6394 6395 6396 6397 6398 6399 6400 6401 6402 6403 <li class="md-nav__item"> 6404 <a href="../api/easybuild/toolchains/gmacml/" class="md-nav__link"> 6405 6406 6407 6408 <span class="md-ellipsis"> 6409 6410 6411 gmacml 6412 6413 6414 6415 </span> 6416 6417 6418 6419 </a> 6420 </li> 6421 6422 6423 6424 6425 6426 6427 6428 6429 6430 6431 <li class="md-nav__item"> 6432 <a href="../api/easybuild/toolchains/gmkl/" class="md-nav__link"> 6433 6434 6435 6436 <span class="md-ellipsis"> 6437 6438 6439 gmkl 6440 6441 6442 6443 </span> 6444 6445 6446 6447 </a> 6448 </li> 6449 6450 6451 6452 6453 6454 6455 6456 6457 6458 6459 <li class="md-nav__item"> 6460 <a href="../api/easybuild/toolchains/gmklc/" class="md-nav__link"> 6461 6462 6463 6464 <span class="md-ellipsis"> 6465 6466 6467 gmklc 6468 6469 6470 6471 </span> 6472 6473 6474 6475 </a> 6476 </li> 6477 6478 6479 6480 6481 6482 6483 6484 6485 6486 6487 <li class="md-nav__item"> 6488 <a href="../api/easybuild/toolchains/gmpflf/" class="md-nav__link"> 6489 6490 6491 6492 <span class="md-ellipsis"> 6493 6494 6495 gmpflf 6496 6497 6498 6499 </span> 6500 6501 6502 6503 </a> 6504 </li> 6505 6506 6507 6508 6509 6510 6511 6512 6513 6514 6515 <li class="md-nav__item"> 6516 <a href="../api/easybuild/toolchains/gmpich/" class="md-nav__link"> 6517 6518 6519 6520 <span class="md-ellipsis"> 6521 6522 6523 gmpich 6524 6525 6526 6527 </span> 6528 6529 6530 6531 </a> 6532 </li> 6533 6534 6535 6536 6537 6538 6539 6540 6541 6542 6543 <li class="md-nav__item"> 6544 <a href="../api/easybuild/toolchains/gmpich2/" class="md-nav__link"> 6545 6546 6547 6548 <span class="md-ellipsis"> 6549 6550 6551 gmpich2 6552 6553 6554 6555 </span> 6556 6557 6558 6559 </a> 6560 </li> 6561 6562 6563 6564 6565 6566 6567 6568 6569 6570 6571 <li class="md-nav__item"> 6572 <a href="../api/easybuild/toolchains/gmpit/" class="md-nav__link"> 6573 6574 6575 6576 <span class="md-ellipsis"> 6577 6578 6579 gmpit 6580 6581 6582 6583 </span> 6584 6585 6586 6587 </a> 6588 </li> 6589 6590 6591 6592 6593 6594 6595 6596 6597 6598 6599 <li class="md-nav__item"> 6600 <a href="../api/easybuild/toolchains/gmpolf/" class="md-nav__link"> 6601 6602 6603 6604 <span class="md-ellipsis"> 6605 6606 6607 gmpolf 6608 6609 6610 6611 </span> 6612 6613 6614 6615 </a> 6616 </li> 6617 6618 6619 6620 6621 6622 6623 6624 6625 6626 6627 <li class="md-nav__item"> 6628 <a href="../api/easybuild/toolchains/gmvapich2/" class="md-nav__link"> 6629 6630 6631 6632 <span class="md-ellipsis"> 6633 6634 6635 gmvapich2 6636 6637 6638 6639 </span> 6640 6641 6642 6643 </a> 6644 </li> 6645 6646 6647 6648 6649 6650 6651 6652 6653 6654 6655 <li class="md-nav__item"> 6656 <a href="../api/easybuild/toolchains/gmvolf/" class="md-nav__link"> 6657 6658 6659 6660 <span class="md-ellipsis"> 6661 6662 6663 gmvolf 6664 6665 6666 6667 </span> 6668 6669 6670 6671 </a> 6672 </li> 6673 6674 6675 6676 6677 6678 6679 6680 6681 6682 6683 <li class="md-nav__item"> 6684 <a href="../api/easybuild/toolchains/gnu/" class="md-nav__link"> 6685 6686 6687 6688 <span class="md-ellipsis"> 6689 6690 6691 gnu 6692 6693 6694 6695 </span> 6696 6697 6698 6699 </a> 6700 </li> 6701 6702 6703 6704 6705 6706 6707 6708 6709 6710 6711 <li class="md-nav__item"> 6712 <a href="../api/easybuild/toolchains/goalf/" class="md-nav__link"> 6713 6714 6715 6716 <span class="md-ellipsis"> 6717 6718 6719 goalf 6720 6721 6722 6723 </span> 6724 6725 6726 6727 </a> 6728 </li> 6729 6730 6731 6732 6733 6734 6735 6736 6737 6738 6739 <li class="md-nav__item"> 6740 <a href="../api/easybuild/toolchains/gobff/" class="md-nav__link"> 6741 6742 6743 6744 <span class="md-ellipsis"> 6745 6746 6747 gobff 6748 6749 6750 6751 </span> 6752 6753 6754 6755 </a> 6756 </li> 6757 6758 6759 6760 6761 6762 6763 6764 6765 6766 6767 <li class="md-nav__item"> 6768 <a href="../api/easybuild/toolchains/goblf/" class="md-nav__link"> 6769 6770 6771 6772 <span class="md-ellipsis"> 6773 6774 6775 goblf 6776 6777 6778 6779 </span> 6780 6781 6782 6783 </a> 6784 </li> 6785 6786 6787 6788 6789 6790 6791 6792 6793 6794 6795 <li class="md-nav__item"> 6796 <a href="../api/easybuild/toolchains/gofbf/" class="md-nav__link"> 6797 6798 6799 6800 <span class="md-ellipsis"> 6801 6802 6803 gofbf 6804 6805 6806 6807 </span> 6808 6809 6810 6811 </a> 6812 </li> 6813 6814 6815 6816 6817 6818 6819 6820 6821 6822 6823 <li class="md-nav__item"> 6824 <a href="../api/easybuild/toolchains/golf/" class="md-nav__link"> 6825 6826 6827 6828 <span class="md-ellipsis"> 6829 6830 6831 golf 6832 6833 6834 6835 </span> 6836 6837 6838 6839 </a> 6840 </li> 6841 6842 6843 6844 6845 6846 6847 6848 6849 6850 6851 <li class="md-nav__item"> 6852 <a href="../api/easybuild/toolchains/golfc/" class="md-nav__link"> 6853 6854 6855 6856 <span class="md-ellipsis"> 6857 6858 6859 golfc 6860 6861 6862 6863 </span> 6864 6865 6866 6867 </a> 6868 </li> 6869 6870 6871 6872 6873 6874 6875 6876 6877 6878 6879 <li class="md-nav__item"> 6880 <a href="../api/easybuild/toolchains/gomkl/" class="md-nav__link"> 6881 6882 6883 6884 <span class="md-ellipsis"> 6885 6886 6887 gomkl 6888 6889 6890 6891 </span> 6892 6893 6894 6895 </a> 6896 </li> 6897 6898 6899 6900 6901 6902 6903 6904 6905 6906 6907 <li class="md-nav__item"> 6908 <a href="../api/easybuild/toolchains/gomklc/" class="md-nav__link"> 6909 6910 6911 6912 <span class="md-ellipsis"> 6913 6914 6915 gomklc 6916 6917 6918 6919 </span> 6920 6921 6922 6923 </a> 6924 </li> 6925 6926 6927 6928 6929 6930 6931 6932 6933 6934 6935 <li class="md-nav__item"> 6936 <a href="../api/easybuild/toolchains/gompi/" class="md-nav__link"> 6937 6938 6939 6940 <span class="md-ellipsis"> 6941 6942 6943 gompi 6944 6945 6946 6947 </span> 6948 6949 6950 6951 </a> 6952 </li> 6953 6954 6955 6956 6957 6958 6959 6960 6961 6962 6963 <li class="md-nav__item"> 6964 <a href="../api/easybuild/toolchains/gompic/" class="md-nav__link"> 6965 6966 6967 6968 <span class="md-ellipsis"> 6969 6970 6971 gompic 6972 6973 6974 6975 </span> 6976 6977 6978 6979 </a> 6980 </li> 6981 6982 6983 6984 6985 6986 6987 6988 6989 6990 6991 <li class="md-nav__item"> 6992 <a href="../api/easybuild/toolchains/goolf/" class="md-nav__link"> 6993 6994 6995 6996 <span class="md-ellipsis"> 6997 6998 6999 goolf 7000 7001 7002 7003 </span> 7004 7005 7006 7007 </a> 7008 </li> 7009 7010 7011 7012 7013 7014 7015 7016 7017 7018 7019 <li class="md-nav__item"> 7020 <a href="../api/easybuild/toolchains/goolfc/" class="md-nav__link"> 7021 7022 7023 7024 <span class="md-ellipsis"> 7025 7026 7027 goolfc 7028 7029 7030 7031 </span> 7032 7033 7034 7035 </a> 7036 </li> 7037 7038 7039 7040 7041 7042 7043 7044 7045 7046 7047 <li class="md-nav__item"> 7048 <a href="../api/easybuild/toolchains/gpsmpi/" class="md-nav__link"> 7049 7050 7051 7052 <span class="md-ellipsis"> 7053 7054 7055 gpsmpi 7056 7057 7058 7059 </span> 7060 7061 7062 7063 </a> 7064 </li> 7065 7066 7067 7068 7069 7070 7071 7072 7073 7074 7075 <li class="md-nav__item"> 7076 <a href="../api/easybuild/toolchains/gpsolf/" class="md-nav__link"> 7077 7078 7079 7080 <span class="md-ellipsis"> 7081 7082 7083 gpsolf 7084 7085 7086 7087 </span> 7088 7089 7090 7091 </a> 7092 </li> 7093 7094 7095 7096 7097 7098 7099 7100 7101 7102 7103 <li class="md-nav__item"> 7104 <a href="../api/easybuild/toolchains/gqacml/" class="md-nav__link"> 7105 7106 7107 7108 <span class="md-ellipsis"> 7109 7110 7111 gqacml 7112 7113 7114 7115 </span> 7116 7117 7118 7119 </a> 7120 </li> 7121 7122 7123 7124 7125 7126 7127 7128 7129 7130 7131 <li class="md-nav__item"> 7132 <a href="../api/easybuild/toolchains/gsmpi/" class="md-nav__link"> 7133 7134 7135 7136 <span class="md-ellipsis"> 7137 7138 7139 gsmpi 7140 7141 7142 7143 </span> 7144 7145 7146 7147 </a> 7148 </li> 7149 7150 7151 7152 7153 7154 7155 7156 7157 7158 7159 <li class="md-nav__item"> 7160 <a href="../api/easybuild/toolchains/gsolf/" class="md-nav__link"> 7161 7162 7163 7164 <span class="md-ellipsis"> 7165 7166 7167 gsolf 7168 7169 7170 7171 </span> 7172 7173 7174 7175 </a> 7176 </li> 7177 7178 7179 7180 7181 7182 7183 7184 7185 7186 7187 <li class="md-nav__item"> 7188 <a href="../api/easybuild/toolchains/iccifort/" class="md-nav__link"> 7189 7190 7191 7192 <span class="md-ellipsis"> 7193 7194 7195 iccifort 7196 7197 7198 7199 </span> 7200 7201 7202 7203 </a> 7204 </li> 7205 7206 7207 7208 7209 7210 7211 7212 7213 7214 7215 <li class="md-nav__item"> 7216 <a href="../api/easybuild/toolchains/iccifortcuda/" class="md-nav__link"> 7217 7218 7219 7220 <span class="md-ellipsis"> 7221 7222 7223 iccifortcuda 7224 7225 7226 7227 </span> 7228 7229 7230 7231 </a> 7232 </li> 7233 7234 7235 7236 7237 7238 7239 7240 7241 7242 7243 <li class="md-nav__item"> 7244 <a href="../api/easybuild/toolchains/ictce/" class="md-nav__link"> 7245 7246 7247 7248 <span class="md-ellipsis"> 7249 7250 7251 ictce 7252 7253 7254 7255 </span> 7256 7257 7258 7259 </a> 7260 </li> 7261 7262 7263 7264 7265 7266 7267 7268 7269 7270 7271 <li class="md-nav__item"> 7272 <a href="../api/easybuild/toolchains/ifbf/" class="md-nav__link"> 7273 7274 7275 7276 <span class="md-ellipsis"> 7277 7278 7279 ifbf 7280 7281 7282 7283 </span> 7284 7285 7286 7287 </a> 7288 </li> 7289 7290 7291 7292 7293 7294 7295 7296 7297 7298 7299 <li class="md-nav__item"> 7300 <a href="../api/easybuild/toolchains/iibff/" class="md-nav__link"> 7301 7302 7303 7304 <span class="md-ellipsis"> 7305 7306 7307 iibff 7308 7309 7310 7311 </span> 7312 7313 7314 7315 </a> 7316 </li> 7317 7318 7319 7320 7321 7322 7323 7324 7325 7326 7327 <li class="md-nav__item"> 7328 <a href="../api/easybuild/toolchains/iimkl/" class="md-nav__link"> 7329 7330 7331 7332 <span class="md-ellipsis"> 7333 7334 7335 iimkl 7336 7337 7338 7339 </span> 7340 7341 7342 7343 </a> 7344 </li> 7345 7346 7347 7348 7349 7350 7351 7352 7353 7354 7355 <li class="md-nav__item"> 7356 <a href="../api/easybuild/toolchains/iimklc/" class="md-nav__link"> 7357 7358 7359 7360 <span class="md-ellipsis"> 7361 7362 7363 iimklc 7364 7365 7366 7367 </span> 7368 7369 7370 7371 </a> 7372 </li> 7373 7374 7375 7376 7377 7378 7379 7380 7381 7382 7383 <li class="md-nav__item"> 7384 <a href="../api/easybuild/toolchains/iimpi/" class="md-nav__link"> 7385 7386 7387 7388 <span class="md-ellipsis"> 7389 7390 7391 iimpi 7392 7393 7394 7395 </span> 7396 7397 7398 7399 </a> 7400 </li> 7401 7402 7403 7404 7405 7406 7407 7408 7409 7410 7411 <li class="md-nav__item"> 7412 <a href="../api/easybuild/toolchains/iimpic/" class="md-nav__link"> 7413 7414 7415 7416 <span class="md-ellipsis"> 7417 7418 7419 iimpic 7420 7421 7422 7423 </span> 7424 7425 7426 7427 </a> 7428 </li> 7429 7430 7431 7432 7433 7434 7435 7436 7437 7438 7439 <li class="md-nav__item"> 7440 <a href="../api/easybuild/toolchains/iiqmpi/" class="md-nav__link"> 7441 7442 7443 7444 <span class="md-ellipsis"> 7445 7446 7447 iiqmpi 7448 7449 7450 7451 </span> 7452 7453 7454 7455 </a> 7456 </li> 7457 7458 7459 7460 7461 7462 7463 7464 7465 7466 7467 <li class="md-nav__item"> 7468 <a href="../api/easybuild/toolchains/impich/" class="md-nav__link"> 7469 7470 7471 7472 <span class="md-ellipsis"> 7473 7474 7475 impich 7476 7477 7478 7479 </span> 7480 7481 7482 7483 </a> 7484 </li> 7485 7486 7487 7488 7489 7490 7491 7492 7493 7494 7495 <li class="md-nav__item"> 7496 <a href="../api/easybuild/toolchains/impmkl/" class="md-nav__link"> 7497 7498 7499 7500 <span class="md-ellipsis"> 7501
7501 7502 7503 impmkl 7504 7505 7506 7507 </span> 7508 7509 7510 7511 </a> 7512 </li> 7513 7514 7515 7516 7517 7518 7519 7520 7521 7522 7523 <li class="md-nav__item"> 7524 <a href="../api/easybuild/toolchains/intel-para/" class="md-nav__link"> 7525 7526 7527 7528 <span class="md-ellipsis"> 7529 7530 7531 intel-para 7532 7533 7534 7535 </span> 7536 7537 7538 7539 </a> 7540 </li> 7541 7542 7543 7544 7545 7546 7547 7548 7549 7550 7551 <li class="md-nav__item"> 7552 <a href="../api/easybuild/toolchains/intel/" class="md-nav__link"> 7553 7554 7555 7556 <span class="md-ellipsis"> 7557 7558 7559 intel 7560 7561 7562 7563 </span> 7564 7565 7566 7567 </a> 7568 </li> 7569 7570 7571 7572 7573 7574 7575 7576 7577 7578 7579 <li class="md-nav__item"> 7580 <a href="../api/easybuild/toolchains/intel_compilers/" class="md-nav__link"> 7581 7582 7583 7584 <span class="md-ellipsis"> 7585 7586 7587 intel_compilers 7588 7589 7590 7591 </span> 7592 7593 7594 7595 </a> 7596 </li> 7597 7598 7599 7600 7601 7602 7603 7604 7605 7606 7607 <li class="md-nav__item"> 7608 <a href="../api/easybuild/toolchains/intelcuda/" class="md-nav__link"> 7609 7610 7611 7612 <span class="md-ellipsis"> 7613 7614 7615 intelcuda 7616 7617 7618 7619 </span> 7620 7621 7622 7623 </a> 7624 </li> 7625 7626 7627 7628 7629 7630 7631 7632 7633 7634 7635 <li class="md-nav__item"> 7636 <a href="../api/easybuild/toolchains/iofbf/" class="md-nav__link"> 7637 7638 7639 7640 <span class="md-ellipsis"> 7641 7642 7643 iofbf 7644 7645 7646 7647 </span> 7648 7649 7650 7651 </a> 7652 </li> 7653 7654 7655 7656 7657 7658 7659 7660 7661 7662 7663 <li class="md-nav__item"> 7664 <a href="../api/easybuild/toolchains/iomkl/" class="md-nav__link"> 7665 7666 7667 7668 <span class="md-ellipsis"> 7669 7670 7671 iomkl 7672 7673 7674 7675 </span> 7676 7677 7678 7679 </a> 7680 </li> 7681 7682 7683 7684 7685 7686 7687 7688 7689 7690 7691 <li class="md-nav__item"> 7692 <a href="../api/easybuild/toolchains/iomklc/" class="md-nav__link"> 7693 7694 7695 7696 <span class="md-ellipsis"> 7697 7698 7699 iomklc 7700 7701 7702 7703 </span> 7704 7705 7706 7707 </a> 7708 </li> 7709 7710 7711 7712 7713 7714 7715 7716 7717 7718 7719 <li class="md-nav__item"> 7720 <a href="../api/easybuild/toolchains/iompi/" class="md-nav__link"> 7721 7722 7723 7724 <span class="md-ellipsis"> 7725 7726 7727 iompi 7728 7729 7730 7731 </span> 7732 7733 7734 7735 </a> 7736 </li> 7737 7738 7739 7740 7741 7742 7743 7744 7745 7746 7747 <li class="md-nav__item"> 7748 <a href="../api/easybuild/toolchains/iompic/" class="md-nav__link"> 7749 7750 7751 7752 <span class="md-ellipsis"> 7753 7754 7755 iompic 7756 7757 7758 7759 </span> 7760 7761 7762 7763 </a> 7764 </li> 7765 7766 7767 7768 7769 7770 7771 7772 7773 7774 7775 <li class="md-nav__item"> 7776 <a href="../api/easybuild/toolchains/ipsmpi/" class="md-nav__link"> 7777 7778 7779 7780 <span class="md-ellipsis"> 7781 7782 7783 ipsmpi 7784 7785 7786 7787 </span> 7788 7789 7790 7791 </a> 7792 </li> 7793 7794 7795 7796 7797 7798 7799 7800 7801 7802 7803 <li class="md-nav__item"> 7804 <a href="../api/easybuild/toolchains/iqacml/" class="md-nav__link"> 7805 7806 7807 7808 <span class="md-ellipsis"> 7809 7810 7811 iqacml 7812 7813 7814 7815 </span> 7816 7817 7818 7819 </a> 7820 </li> 7821 7822 7823 7824 7825 7826 7827 7828 7829 7830 7831 <li class="md-nav__item"> 7832 <a href="../api/easybuild/toolchains/ismkl/" class="md-nav__link"> 7833 7834 7835 7836 <span class="md-ellipsis"> 7837 7838 7839 ismkl 7840 7841 7842 7843 </span> 7844 7845 7846 7847 </a> 7848 </li> 7849 7850 7851 7852 7853 7854 7855 7856 7857 7858 7859 <li class="md-nav__item"> 7860 <a href="../api/easybuild/toolchains/lfbf/" class="md-nav__link"> 7861 7862 7863 7864 <span class="md-ellipsis"> 7865 7866 7867 lfbf 7868 7869 7870 7871 </span> 7872 7873 7874 7875 </a> 7876 </li> 7877 7878 7879 7880 7881 7882 7883 7884 7885 7886 7887 <li class="md-nav__item"> 7888 <a href="../api/easybuild/toolchains/lfoss/" class="md-nav__link"> 7889 7890 7891 7892 <span class="md-ellipsis"> 7893 7894 7895 lfoss 7896 7897 7898 7899 </span> 7900 7901 7902 7903 </a> 7904 </li> 7905 7906 7907 7908 7909 7910 7911 7912 7913 7914 7915 7916 7917 7918 7919 7920 <li class="md-nav__item md-nav__item--nested"> 7921 7922 7923 7924 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_11_1_6_82" > 7925 7926 7927 <div class="md-nav__link md-nav__container"> 7928 <a href="../api/easybuild/toolchains/linalg/" class="md-nav__link "> 7929 7930 7931 7932 <span class="md-ellipsis"> 7933 7934 7935 linalg 7936 7937 7938 7939 </span> 7940 7941 7942 7943 </a> 7944 7945 7946 <label class="md-nav__link " for="__nav_11_1_6_82" id="__nav_11_1_6_82_label" tabindex="0">
7947 <span class="md-nav__icon md-icon"></span> 7948 </label> 7949 7950 </div> 7951 7952 <nav class="md-nav" data-md-level="4" aria-labelledby="__nav_11_1_6_82_label" aria-expanded="false"> 7953 <label class="md-nav__title" for="__nav_11_1_6_82"> 7954 <span class="md-nav__icon md-icon"></span> 7955 7956 7957 linalg 7958 7959 7960 </label> 7961 <ul class="md-nav__list" data-md-scrollfix> 7962 7963 7964 7965 7966 7967 7968 7969 <li class="md-nav__item"> 7970 <a href="../api/easybuild/toolchains/linalg/acml/" class="md-nav__link"> 7971 7972 7973 7974 <span class="md-ellipsis"> 7975 7976 7977 acml 7978 7979 7980 7981 </span> 7982 7983 7984 7985 </a> 7986 </li> 7987 7988 7989 7990 7991 7992 7993 7994 7995 7996 7997 <li class="md-nav__item"> 7998 <a href="../api/easybuild/toolchains/linalg/atlas/" class="md-nav__link"> 7999 8000 8001 8002 <span class="md-ellipsis"> 8003 8004 8005 atlas 8006 8007 8008 8009 </span> 8010 8011 8012 8013 </a> 8014 </li> 8015 8016 8017 8018 8019 8020 8021 8022 8023 8024 8025 <li class="md-nav__item"> 8026 <a href="../api/easybuild/toolchains/linalg/blacs/" class="md-nav__link"> 8027 8028 8029 8030 <span class="md-ellipsis"> 8031 8032 8033 blacs 8034 8035 8036 8037 </span> 8038 8039 8040 8041 </a> 8042 </li> 8043 8044 8045 8046 8047 8048 8049 8050 8051 8052 8053 <li class="md-nav__item"> 8054 <a href="../api/easybuild/toolchains/linalg/blis/" class="md-nav__link"> 8055 8056 8057 8058 <span class="md-ellipsis"> 8059 8060 8061 blis 8062 8063 8064 8065 </span> 8066 8067 8068 8069 </a> 8070 </li> 8071 8072 8073 8074 8075 8076 8077 8078 8079 8080 8081 <li class="md-nav__item"> 8082 <a href="../api/easybuild/toolchains/linalg/flame/" class="md-nav__link"> 8083 8084 8085 8086 <span class="md-ellipsis"> 8087 8088 8089 flame 8090 8091 8092 8093 </span> 8094 8095 8096 8097 </a> 8098 </li> 8099 8100 8101 8102 8103 8104 8105 8106 8107 8108 8109 <li class="md-nav__item"> 8110 <a href="../api/easybuild/toolchains/linalg/flexiblas/" class="md-nav__link"> 8111 8112 8113 8114 <span class="md-ellipsis"> 8115 8116 8117 flexiblas 8118 8119 8120 8121 </span> 8122 8123 8124 8125 </a> 8126 </li> 8127 8128 8129 8130 8131 8132 8133 8134 8135 8136 8137 <li class="md-nav__item"> 8138 <a href="../api/easybuild/toolchains/linalg/fujitsussl/" class="md-nav__link"> 8139 8140 8141 8142 <span class="md-ellipsis"> 8143 8144 8145 fujitsussl 8146 8147 8148 8149 </span> 8150 8151 8152 8153 </a> 8154 </li> 8155 8156 8157 8158 8159 8160 8161 8162 8163 8164 8165 <li class="md-nav__item"> 8166 <a href="../api/easybuild/toolchains/linalg/gotoblas/" class="md-nav__link"> 8167 8168 8169 8170 <span class="md-ellipsis"> 8171 8172 8173 gotoblas 8174 8175 8176 8177 </span> 8178 8179 8180 8181 </a> 8182 </li> 8183 8184 8185 8186 8187 8188 8189 8190 8191 8192 8193 <li class="md-nav__item"> 8194 <a href="../api/easybuild/toolchains/linalg/intelmkl/" class="md-nav__link"> 8195 8196 8197 8198 <span class="md-ellipsis"> 8199 8200 8201 intelmkl 8202 8203 8204 8205 </span> 8206 8207 8208 8209 </a> 8210 </li> 8211 8212 8213 8214 8215 8216 8217 8218 8219 8220 8221 <li class="md-nav__item"> 8222 <a href="../api/easybuild/toolchains/linalg/lapack/" class="md-nav__link"> 8223 8224 8225 8226 <span class="md-ellipsis"> 8227 8228 8229 lapack 8230 8231 8232 8233 </span> 8234 8235 8236 8237 </a> 8238 </li> 8239 8240 8241 8242 8243 8244 8245 8246 8247 8248 8249 <li class="md-nav__item"> 8250 <a href="../api/easybuild/toolchains/linalg/libsci/" class="md-nav__link"> 8251 8252 8253 8254 <span class="md-ellipsis"> 8255 8256 8257 libsci 8258 8259 8260 8261 </span> 8262 8263 8264 8265 </a> 8266 </li> 8267 8268 8269 8270 8271 8272 8273 8274 8275 8276 8277 <li class="md-nav__item"> 8278 <a href="../api/easybuild/toolchains/linalg/nvblas/" class="md-nav__link"> 8279 8280 8281 8282 <span class="md-ellipsis"> 8283 8284 8285 nvblas 8286 8287 8288 8289 </span> 8290 8291 8292 8293 </a> 8294 </li> 8295 8296 8297 8298 8299 8300 8301 8302 8303 8304 8305 <li class="md-nav__item"> 8306 <a href="../api/easybuild/toolchains/linalg/nvscalapack/" class="md-nav__link"> 8307 8308 8309 8310 <span class="md-ellipsis"> 8311 8312 8313 nvscalapack 8314 8315 8316 8317 </span> 8318 8319 8320 8321 </a> 8322 </li> 8323 8324 8325 8326 8327 8328 8329 8330 8331 8332 8333 <li class="md-nav__item"> 8334 <a href="../api/easybuild/toolchains/linalg/openblas/" class="md-nav__link"> 8335 8336 8337 8338 <span class="md-ellipsis"> 8339 8340 8341 openblas 8342 8343 8344 8345 </span> 8346 8347 8348 8349 </a> 8350 </li> 8351 8352 8353 8354 8355 8356 8357 8358 8359 8360 8361 <li class="md-nav__item"> 8362 <a href="../api/easybuild/toolchains/linalg/scalapack/" class="md-nav__link"> 8363 8364 8365 8366 <span class="md-ellipsis"> 8367 8368 8369 scalapack 8370 8371 8372 8373 </span> 8374 8375 8376 8377 </a> 8378 </li> 8379 8380 8381 8382 8383 </ul> 8384 </nav> 8385 8386 </li> 8387 8388 8389 8390 8391 8392 8393 8394 8395 8396 8397 <li class="md-nav__item"> 8398 <a 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13050 13051 <span class="md-ellipsis"> 13052 13053 13054 Removed functionality 13055 13056 13057 13058 </span> 13059 13060 13061 13062 </a> 13063 </li> 13064 13065 13066 13067 13068 13069 13070 13071 13072 13073 13074 <li class="md-nav__item"> 13075 <a href="../useful-scripts/" class="md-nav__link"> 13076 13077 13078 13079 <span class="md-ellipsis"> 13080 13081 13082 Useful scripts 13083 13084 13085 13086 </span> 13087 13088 13089 13090 </a> 13091 </li> 13092 13093 13094 13095 13096 </ul> 13097 </nav> 13098 13099 </li> 13100 13101 13102 13103 13104 13105 13106 13107 13108 13109 13110 13111 13112 13113 13114 <li class="md-nav__item md-nav__item--nested"> 13115 13116 13117 13118 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_17" > 13119 13120 13121 <label class="md-nav__link" for="__nav_17" id="__nav_17_label" tabindex="0"> 13122 13123 13124 13125 <span class="md-ellipsis"> 13126 13127 13128 EasyBuild v5.0 13129 13130 13131 13132 </span> 13133 13134 13135 13136 <span class="md-nav__icon md-icon"></span> 13137 </label> 13138 13139 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_17_label" aria-expanded="false"> 13140 <label class="md-nav__title" for="__nav_17"> 13141 <span class="md-nav__icon md-icon"></span> 13142 13143 13144 EasyBuild v5.0 13145 13146 13147 </label> 13148 <ul class="md-nav__list" data-md-scrollfix> 13149 13150 13151 13152 13153 13154 13155 13156 <li class="md-nav__item"> 13157 <a href="../easybuild-v5/" class="md-nav__link"> 13158 13159 13160 13161 <span class="md-ellipsis"> 13162 13163 13164 (overview) 13165 13166 13167 13168 </span> 13169 13170 13171 13172 </a> 13173 </li> 13174 13175 13176 13177 13178 13179 13180 13181 13182 13183 13184 <li class="md-nav__item"> 13185 <a href="../easybuild-v5/enhancements/" class="md-nav__link"> 13186 13187 13188 13189 <span class="md-ellipsis"> 13190 13191 13192 Enhancements in EasyBuild v5.0 13193 13194 13195 13196 </span> 13197 13198 13199 13200 </a> 13201 </li> 13202 13203 13204 13205 13206 13207 13208 13209 13210 13211 13212 <li class="md-nav__item"> 13213 <a href="../easybuild-v5/run_shell_cmd/" class="md-nav__link"> 13214 13215 13216 13217 <span class="md-ellipsis"> 13218 13219 13220 Run shell commands function (`run_shell_cmd`) 13221 13222 13223 13224 </span> 13225 13226 13227 13228 </a> 13229 </li> 13230 13231 13232 13233 13234 13235 13236 13237 13238 13239 13240 <li class="md-nav__item"> 13241 <a href="../easybuild-v5/changes/" class="md-nav__link"> 13242 13243 13244 13245 <span class="md-ellipsis"> 13246 13247 13248 Changes in default configuration in EasyBuild v5.0 13249 13250 13251 13252 </span> 13253 13254 13255 13256 </a> 13257 </li> 13258 13259 13260 13261 13262 13263 13264 13265 13266 13267 13268 <li class="md-nav__item"> 13269 <a href="../easybuild-v5/deprecated-functionality/" class="md-nav__link"> 13270 13271 13272 13273 <span class="md-ellipsis"> 13274 13275 13276 Deprecated functionality in EasyBuild v5.0 13277 13278 13279 13280 </span> 13281 13282 13283 13284 </a> 13285 </li> 13286 13287 13288 13289 13290 13291 13292 13293 13294 13295 13296 <li class="md-nav__item"> 13297 <a href="../easybuild-v5/removed-functionality/" class="md-nav__link"> 13298 13299 13300 13301 <span class="md-ellipsis"> 13302 13303 13304 Removed functionality in EasyBuild v5.0 13305 13306 13307 13308 </span> 13309 13310 13311 13312 </a> 13313 </li> 13314 13315 13316 13317 13318 13319 13320 13321 13322 13323 13324 <li class="md-nav__item"> 13325 <a href="../easybuild-v5/known-issues/" class="md-nav__link"> 13326 13327 13328 13329 <span class="md-ellipsis"> 13330 13331 13332 Known issues in EasyBuild v5.0 13333 13334 13335 13336 </span> 13337 13338 13339 13340 </a> 13341 </li> 13342 13343 13344 13345 13346 </ul> 13347 </nav> 13348 13349 </li> 13350 13351 13352 13353 13354 13355 13356 13357 13358 13359 13360 13361 13362 13363 13364 <li class="md-nav__item md-nav__item--nested"> 13365 13366 13367 13368 <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_18" > 13369 13370 13371 <label class="md-nav__link" for="__nav_18" id="__nav_18_label" tabindex="0"> 13372 13373 13374 13375 <span class="md-ellipsis"> 13376 13377 13378 Governance 13379 13380 13381 13382 </span> 13383 13384 13385
13386 <span class="md-nav__icon md-icon"></span> 13387 </label> 13388 13389 <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_18_label" aria-expanded="false"> 13390 <label class="md-nav__title" for="__nav_18"> 13391 <span class="md-nav__icon md-icon"></span> 13392 13393 13394 Governance 13395 13396 13397 </label> 13398 <ul class="md-nav__list" data-md-scrollfix> 13399 13400 13401 13402 13403 13404 13405 13406 <li class="md-nav__item"> 13407 <a href="../governance/charter/" class="md-nav__link"> 13408 13409 13410 13411 <span class="md-ellipsis"> 13412 13413 13414 Charter 13415 13416 13417 13418 </span> 13419 13420 13421 13422 </a> 13423 </li> 13424 13425 13426 13427 13428 13429 13430 13431 13432 13433 13434 <li class="md-nav__item"> 13435 <a href="../governance/code-of-conduct/" class="md-nav__link"> 13436 13437 13438 13439 <span class="md-ellipsis"> 13440 13441 13442 Code of Conduct 13443 13444 13445 13446 </span> 13447 13448 13449 13450 </a> 13451 </li> 13452 13453 13454 13455 13456 13457 13458 13459 13460 13461 13462 <li class="md-nav__item"> 13463 <a href="../governance/governance/" class="md-nav__link"> 13464 13465 13466 13467 <span class="md-ellipsis"> 13468 13469 13470 Governance 13471 13472 13473 13474 </span> 13475 13476 13477 13478 </a> 13479 </li> 13480 13481 13482 13483 13484 13485 13486 13487 13488 13489 13490 <li class="md-nav__item"> 13491 <a href="../governance/policies/" class="md-nav__link"> 13492 13493 13494 13495 <span class="md-ellipsis"> 13496 13497 13498 Policies 13499 13500 13501 13502 </span> 13503 13504 13505 13506 </a> 13507 </li> 13508 13509 13510 13511 13512 13513 13514 13515 13516 13517 13518 <li class="md-nav__item"> 13519 <a href="../governance/steering-committee/" class="md-nav__link"> 13520 13521 13522 13523 <span class="md-ellipsis"> 13524 13525 13526 Steering Committee 13527 13528 13529 13530 </span> 13531 13532 13533 13534 </a> 13535 </li> 13536 13537 13538 13539 13540 </ul> 13541 </nav> 13542 13543 </li> 13544 13545 13546 13547 </ul> 13548</nav> 13549 </div> 13550 </div> 13551 </div> 13552 13553 13554 13555 <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" > 13556 <div class="md-sidebar__scrollwrap"> 13557 <div class="md-sidebar__inner"> 13558 13559 13560<nav class="md-nav md-nav--secondary" aria-label="Table of contents"> 13561 13562 13563 13564 13565 13566 13567 <label class="md-nav__title" for="__toc"> 13568 <span class="md-nav__icon md-icon"></span> 13569 Table of contents 13570 </label> 13571 <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix> 13572 13573 <li class="md-nav__item"> 13574 <a href="#release_notes_eb540" class="md-nav__link"> 13575 <span class="md-ellipsis"> 13576 13577 EasyBuild v5.4.0 (9 Aug 2026) 13578 13579 </span> 13580 </a> 13581 13582</li> 13583 13584 <li class="md-nav__item"> 13585 <a href="#release_notes_eb531" class="md-nav__link"> 13586 <span class="md-ellipsis"> 13587 13588 EasyBuild v5.3.1 (19 Jun 2026) 13589 13590 </span> 13591 </a> 13592 13593</li> 13594 13595 <li class="md-nav__item"> 13596 <a href="#release_notes_eb530" class="md-nav__link"> 13597 <span class="md-ellipsis"> 13598 13599 EasyBuild v5.3.0 (10 Apr 2026) 13600 13601 </span> 13602 </a> 13603 13604</li> 13605 13606 <li class="md-nav__item"> 13607 <a href="#release_notes_eb521" class="md-nav__link"> 13608 <span class="md-ellipsis"> 13609 13610 EasyBuild v5.2.1 (20 Feb 2026) 13611 13612 </span> 13613 </a> 13614 13615</li> 13616 13617 <li class="md-nav__item"> 13618 <a href="#release_notes_eb520" class="md-nav__link"> 13619 <span class="md-ellipsis"> 13620 13621 EasyBuild v5.2.0 (23 Dec 2025) 13622 13623 </span> 13624 </a> 13625 13626</li> 13627 13628 <li class="md-nav__item"> 13629 <a href="#release_notes_eb512" class="md-nav__link"> 13630 <span class="md-ellipsis"> 13631 13632 EasyBuild v5.1.2 (26 Sept 2025) 13633 13634 </span> 13635 </a> 13636 13637</li> 13638 13639 <li class="md-nav__item"> 13640 <a href="#release_notes_eb511" class="md-nav__link"> 13641 <span class="md-ellipsis"> 13642 13643 EasyBuild v5.1.1 (6 July 2025) 13644 13645 </span> 13646 </a> 13647 13648</li> 13649 13650 <li class="md-nav__item"> 13651 <a href="#release_notes_eb510" class="md-nav__link"> 13652 <span class="md-ellipsis"> 13653 13654 EasyBuild v5.1.0 (26 May 2025) 13655 13656 </span> 13657 </a> 13658 13659</li> 13660 13661 <li class="md-nav__item"> 13662 <a href="#release_notes_eb500" class="md-nav__link"> 13663 <span class="md-ellipsis"> 13664 13665 EasyBuild v5.0.0 (18 Mar 2025) 13666 13667 </span> 13668 </a> 13669 13670</li> 13671 13672 <li class="md-nav__item"> 13673 <a href="#release_notes_eb494" class="md-nav__link"> 13674 <span class="md-ellipsis"> 13675 13676 EasyBuild v4.9.4 (22 Sept 2024) 13677 13678 </span> 13679 </a> 13680 13681</li> 13682 13683 <li class="md-nav__item"> 13684 <a href="#release_notes_eb493" class="md-nav__link"> 13685 <span class="md-ellipsis"> 13686 13687 EasyBuild v4.9.3 (14 Sept 2024) 13688 13689 </span> 13690 </a> 13691 13692</li> 13693 13694 <li class="md-nav__item"> 13695 <a href="#release_notes_eb492" class="md-nav__link"> 13696 <span class="md-ellipsis"> 13697 13698 EasyBuild v4.9.2 (12 June 2024) 13699 13700 </span> 13701 </a> 13702 13703</li> 13704 13705 <li class="md-nav__item"> 13706 <a href="#release_notes_eb491" class="md-nav__link"> 13707 <span class="md-ellipsis"> 13708 13709 EasyBuild v4.9.1 (5 April 2024) 13710 13711 </span> 13712 </a> 13713 13714</li> 13715 13716 <li class="md-nav__item"> 13717 <a href="#release_notes_eb490" class="md-nav__link"> 13718 <span class="md-ellipsis"> 13719 13720 EasyBuild v4.9.0 (29 Dec 2023) 13721 13722 </span> 13723 </a> 13724 13725</li> 13726 13727 <li class="md-nav__item"> 13728 <a href="#release_notes_eb482" class="md-nav__link"> 13729 <span class="md-ellipsis"> 13730 13731 EasyBuild v4.8.2 (29 Oct 2023) 13732 13733 </span> 13734 </a> 13735 13736</li> 13737 13738 <li class="md-nav__item"> 13739 <a href="#release_notes_eb481" class="md-nav__link"> 13740 <span class="md-ellipsis"> 13741 13742 EasyBuild v4.8.1 (11 Sept 2023) 13743 13744 </span> 13745 </a> 13746 13747</li> 13748 13749 <li class="md-nav__item"> 13750 <a href="#release_notes_eb480" class="md-nav__link"> 13751 <span class="md-ellipsis"> 13752 13753 EasyBuild v4.8.0 (7 July 2023) 13754 13755 </span> 13756 </a> 13757 13758</li> 13759 13760 <li class="md-nav__item"> 13761 <a href="#release_notes_eb472" class="md-nav__link"> 13762 <span class="md-ellipsis"> 13763 13764 EasyBuild v4.7.2 (27 May 2023) 13765 13766 </span> 13767 </a> 13768 13769</li> 13770 13771 <li class="md-nav__item"> 13772 <a href="#release_notes_eb471" class="md-nav__link"> 13773 <span class="md-ellipsis"> 13774 13775 EasyBuild v4.7.1 (20 March 2023) 13776 13777 </span> 13778 </a> 13779 13780</li> 13781 13782 <li class="md-nav__item"> 13783 <a href="#release_notes_eb470" class="md-nav__link"> 13784 <span class="md-ellipsis"> 13785 13786 EasyBuild v4.7.0 (January 9th 2023) 13787 13788 </span> 13789 </a> 13790 13791</li> 13792 13793 <li class="md-nav__item"> 13794 <a href="#release_notes_eb462" class="md-nav__link"> 13795 <span class="md-ellipsis"> 13796 13797 EasyBuild v4.6.2 (October 21st 2022) 13798 13799 </span> 13800 </a> 13801 13802</li> 13803 13804 <li class="md-nav__item"> 13805 <a href="#release_notes_eb461" class="md-nav__link"> 13806 <span class="md-ellipsis"> 13807 13808 EasyBuild v4.6.1 (September 12th 2022) 13809 13810 </span> 13811 </a> 13812 13813</li> 13814 13815 <li class="md-nav__item"> 13816 <a href="#release_notes_eb460" class="md-nav__link"> 13817 <span class="md-ellipsis"> 13818 13819 EasyBuild v4.6.0 (July 8th 2022) 13820 13821 </span> 13822 </a> 13823 13824</li> 13825 13826 <li class="md-nav__item"> 13827 <a href="#release_notes_eb455" class="md-nav__link"> 13828 <span class="md-ellipsis"> 13829 13830 EasyBuild v4.5.5 (June 8th 2022) 13831 13832 </span> 13833 </a> 13834 13835</li> 13836 13837 <li class="md-nav__item"> 13838 <a href="#release_notes_eb454" class="md-nav__link"> 13839 <span class="md-ellipsis"> 13840 13841 EasyBuild v4.5.4 (March 31st 2022) 13842 13843 </span> 13844 </a> 13845 13846</li> 13847 13848 <li class="md-nav__item"> 13849 <a href="#release_notes_eb453" class="md-nav__link"> 13850 <span class="md-ellipsis"> 13851 13852 EasyBuild v4.5.3 (February 11th 2022) 13853 13854 </span> 13855 </a> 13856 13857</li> 13858 13859 <li class="md-nav__item"> 13860 <a href="#release_notes_eb452" class="md-nav__link"> 13861 <span class="md-ellipsis"> 13862 13863 EasyBuild v4.5.2 (January 24th 2022) 13864 13865 </span> 13866 </a> 13867 13868</li> 13869 13870 <li class="md-nav__item"> 13871 <a href="#release_notes_eb451" class="md-nav__link"> 13872 <span class="md-ellipsis"> 13873 13874 EasyBuild v4.5.1 (December 13th 2021) 13875 13876 </span> 13877 </a> 13878 13879</li> 13880 13881 <li class="md-nav__item"> 13882 <a href="#release_notes_eb450" class="md-nav__link"> 13883 <span class="md-ellipsis"> 13884 13885 EasyBuild v4.5.0 (October 29th 2021) 13886 13887 </span> 13888 </a> 13889 13890</li> 13891 13892 <li class="md-nav__item"> 13893 <a href="#release_notes_eb442" class="md-nav__link"> 13894 <span class="md-ellipsis"> 13895 13896 EasyBuild v4.4.2 (September 7th 2021) 13897 13898 </span> 13899 </a> 13900 13901</li> 13902 13903 <li class="md-nav__item"> 13904 <a href="#release_notes_eb441" class="md-nav__link"> 13905 <span class="md-ellipsis"> 13906 13907 EasyBuild v4.4.1 (July 6th 2021) 13908 13909 </span> 13910 </a> 13911 13912</li> 13913 13914 <li class="md-nav__item"> 13915 <a href="#release_notes_eb440" class="md-nav__link"> 13916 <span class="md-ellipsis"> 13917 13918 EasyBuild v4.4.0 (June 2nd 2021) 13919 13920 </span> 13921 </a> 13922 13923</li> 13924 13925 <li class="md-nav__item"> 13926 <a href="#release_notes_eb434" class="md-nav__link"> 13927 <span class="md-ellipsis"> 13928 13929 EasyBuild v4.3.4 (Apr 9th 2021) 13930 13931 </span> 13932 </a> 13933 13934</li> 13935 13936 <li class="md-nav__item"> 13937 <a href="#release_notes_eb433" class="md-nav__link"> 13938 <span class="md-ellipsis"> 13939 13940 EasyBuild v4.3.3 (Feb 23rd 2021) 13941 13942 </span> 13943 </a> 13944 13945</li> 13946 13947 <li class="md-nav__item"> 13948 <a href="#release_notes_eb432" class="md-nav__link"> 13949 <span class="md-ellipsis"> 13950 13951 EasyBuild v4.3.2 (December 10th 2020) 13952 13953 </span> 13954 </a> 13955 13956</li> 13957 13958 <li class="md-nav__item"> 13959 <a href="#release_notes_eb431" class="md-nav__link"> 13960 <span class="md-ellipsis"> 13961 13962 EasyBuild v4.3.1 (October 29th 2020) 13963 13964 </span> 13965 </a> 13966 13967</li> 13968 13969 <li class="md-nav__item"> 13970 <a href="#release_notes_eb430" class="md-nav__link"> 13971 <span class="md-ellipsis"> 13972 13973 EasyBuild v4.3.0 (September 13th 2020) 13974 13975 </span> 13976 </a> 13977 13978</li> 13979 13980 <li class="md-nav__item"> 13981 <a href="#release_notes_eb422" class="md-nav__link"> 13982 <span class="md-ellipsis"> 13983
13984 EasyBuild v4.2.2 (July 8th 2020) 13985 13986 </span> 13987 </a> 13988 13989</li> 13990 13991 <li class="md-nav__item"> 13992 <a href="#release_notes_eb421" class="md-nav__link"> 13993 <span class="md-ellipsis"> 13994 13995 EasyBuild v4.2.1 (May 20th 2020) 13996 13997 </span> 13998 </a> 13999 14000</li> 14001 14002 <li class="md-nav__item"> 14003 <a href="#release_notes_eb420" class="md-nav__link"> 14004 <span class="md-ellipsis"> 14005 14006 EasyBuild v4.2.0 (April 14th 2020) 14007 14008 </span> 14009 </a> 14010 14011</li> 14012 14013 <li class="md-nav__item"> 14014 <a href="#release_notes_eb412" class="md-nav__link"> 14015 <span class="md-ellipsis"> 14016 14017 EasyBuild v4.1.2 (March 16th 2020) 14018 14019 </span> 14020 </a> 14021 14022</li> 14023 14024 <li class="md-nav__item"> 14025 <a href="#release_notes_eb411" class="md-nav__link"> 14026 <span class="md-ellipsis"> 14027 14028 EasyBuild v4.1.1 (January 16th 2020) 14029 14030 </span> 14031 </a> 14032 14033</li> 14034 14035 <li class="md-nav__item"> 14036 <a href="#release_notes_eb410" class="md-nav__link"> 14037 <span class="md-ellipsis"> 14038 14039 EasyBuild v4.1.0 (December 4th 2019) 14040 14041 </span> 14042 </a> 14043 14044</li> 14045 14046 <li class="md-nav__item"> 14047 <a href="#release_notes_eb401" class="md-nav__link"> 14048 <span class="md-ellipsis"> 14049 14050 EasyBuild v4.0.1 (October 15th 2019) 14051 14052 </span> 14053 </a> 14054 14055</li> 14056 14057 <li class="md-nav__item"> 14058 <a href="#release_notes_eb400" class="md-nav__link"> 14059 <span class="md-ellipsis"> 14060 14061 EasyBuild v4.0.0 (September 20th 2019) 14062 14063 </span> 14064 </a> 14065 14066</li> 14067 14068 <li class="md-nav__item"> 14069 <a href="#release_notes_eb394" class="md-nav__link"> 14070 <span class="md-ellipsis"> 14071 14072 EasyBuild v3.9.4 (August 23rd 2019) 14073 14074 </span> 14075 </a> 14076 14077</li> 14078 14079 <li class="md-nav__item"> 14080 <a href="#release_notes_eb393" class="md-nav__link"> 14081 <span class="md-ellipsis"> 14082 14083 EasyBuild v3.9.3 (July 8th 2019) 14084 14085 </span> 14086 </a> 14087 14088</li> 14089 14090 <li class="md-nav__item"> 14091 <a href="#release_notes_eb392" class="md-nav__link"> 14092 <span class="md-ellipsis"> 14093 14094 EasyBuild v3.9.2 (June 9th 2019) 14095 14096 </span> 14097 </a> 14098 14099</li> 14100 14101 <li class="md-nav__item"> 14102 <a href="#release_notes_eb391" class="md-nav__link"> 14103 <span class="md-ellipsis"> 14104 14105 EasyBuild v3.9.1 (May 20th 2019) 14106 14107 </span> 14108 </a> 14109 14110</li> 14111 14112 <li class="md-nav__item"> 14113 <a href="#release_notes_eb390" class="md-nav__link"> 14114 <span class="md-ellipsis"> 14115 14116 EasyBuild v3.9.0 (April 12th 2019) 14117 14118 </span> 14119 </a> 14120 14121</li> 14122 14123 <li class="md-nav__item"> 14124 <a href="#release_notes_eb381" class="md-nav__link"> 14125 <span class="md-ellipsis"> 14126 14127 EasyBuild v3.8.1 (January 29th 2019) 14128 14129 </span> 14130 </a> 14131 14132</li> 14133 14134 <li class="md-nav__item"> 14135 <a href="#release_notes_eb380" class="md-nav__link"> 14136 <span class="md-ellipsis"> 14137 14138 EasyBuild v3.8.0 (December 18th 2018) 14139 14140 </span> 14141 </a> 14142 14143</li> 14144 14145 <li class="md-nav__item"> 14146 <a href="#release_notes_eb371" class="md-nav__link"> 14147 <span class="md-ellipsis"> 14148 14149 EasyBuild v3.7.1 (October 18th 2018) 14150 14151 </span> 14152 </a> 14153 14154</li> 14155 14156 <li class="md-nav__item"> 14157 <a href="#release_notes_eb370" class="md-nav__link"> 14158 <span class="md-ellipsis"> 14159 14160 EasyBuild v3.7.0 (September 25th 2018) 14161 14162 </span> 14163 </a> 14164 14165</li> 14166 14167 <li class="md-nav__item"> 14168 <a href="#release_notes_eb362" class="md-nav__link"> 14169 <span class="md-ellipsis"> 14170 14171 EasyBuild v3.6.2 (July 11th 2018) 14172 14173 </span> 14174 </a> 14175 14176</li> 14177 14178 <li class="md-nav__item"> 14179 <a href="#release_notes_eb361" class="md-nav__link"> 14180 <span class="md-ellipsis"> 14181 14182 EasyBuild v3.6.1 (May 26th 2018) 14183 14184 </span> 14185 </a> 14186 14187</li> 14188 14189 <li class="md-nav__item"> 14190 <a href="#release_notes_eb360" class="md-nav__link"> 14191 <span class="md-ellipsis"> 14192 14193 EasyBuild v3.6.0 (April 26th 2018) 14194 14195 </span> 14196 </a> 14197 14198</li> 14199 14200 <li class="md-nav__item"> 14201 <a href="#release_notes_eb353" class="md-nav__link"> 14202 <span class="md-ellipsis"> 14203 14204 EasyBuild v3.5.3 (March 7th 2018) 14205 14206 </span> 14207 </a> 14208 14209</li> 14210 14211 <li class="md-nav__item"> 14212 <a href="#release_notes_eb352" class="md-nav__link"> 14213 <span class="md-ellipsis"> 14214 14215 EasyBuild v3.5.2 (March 2nd 2018) 14216 14217 </span> 14218 </a> 14219 14220</li> 14221 14222 <li class="md-nav__item"> 14223 <a href="#release_notes_eb351" class="md-nav__link"> 14224 <span class="md-ellipsis"> 14225 14226 EasyBuild v3.5.1 (January 16th 2018) 14227 14228 </span> 14229 </a> 14230 14231</li> 14232 14233 <li class="md-nav__item"> 14234 <a href="#release_notes_eb350" class="md-nav__link"> 14235 <span class="md-ellipsis"> 14236 14237 EasyBuild v3.5.0 (December 15th 2017) 14238 14239 </span> 14240 </a> 14241 14242</li> 14243 14244 <li class="md-nav__item"> 14245 <a href="#release_notes_eb341" class="md-nav__link"> 14246 <span class="md-ellipsis"> 14247 14248 EasyBuild v3.4.1 (October 17th 2017) 14249 14250 </span> 14251 </a> 14252 14253</li> 14254 14255 <li class="md-nav__item"> 14256 <a href="#release_notes_eb340" class="md-nav__link"> 14257 <span class="md-ellipsis"> 14258 14259 EasyBuild v3.4.0 (September 10th 2017) 14260 14261 </span> 14262 </a> 14263 14264</li> 14265 14266 <li class="md-nav__item"> 14267 <a href="#release_notes_eb331" class="md-nav__link"> 14268 <span class="md-ellipsis"> 14269 14270 EasyBuild v3.3.1 (July 12th 2017) 14271 14272 </span> 14273 </a> 14274 14275</li> 14276 14277 <li class="md-nav__item"> 14278 <a href="#release_notes_eb330" class="md-nav__link"> 14279 <span class="md-ellipsis"> 14280 14281 EasyBuild v3.3.0 (June 26th 2017) 14282 14283 </span> 14284 </a> 14285 14286</li> 14287 14288 <li class="md-nav__item"> 14289 <a href="#release_notes_eb321" class="md-nav__link"> 14290 <span class="md-ellipsis"> 14291 14292 EasyBuild v3.2.1 (May 12th 2017) 14293 14294 </span> 14295 </a> 14296 14297</li> 14298 14299 <li class="md-nav__item"> 14300 <a href="#release_notes_eb320" class="md-nav__link"> 14301 <span class="md-ellipsis"> 14302 14303 EasyBuild v3.2.0 (May 5th 2017) 14304 14305 </span> 14306 </a> 14307 14308</li> 14309 14310 <li class="md-nav__item"> 14311 <a href="#release_notes_eb312" class="md-nav__link"> 14312 <span class="md-ellipsis"> 14313 14314 EasyBuild v3.1.2 (March 20th 2017) 14315 14316 </span> 14317 </a> 14318 14319</li> 14320 14321 <li class="md-nav__item"> 14322 <a href="#release_notes_eb311" class="md-nav__link"> 14323 <span class="md-ellipsis"> 14324 14325 EasyBuild v3.1.1 (March 7th 2017) 14326 14327 </span> 14328 </a> 14329 14330</li> 14331 14332 <li class="md-nav__item"> 14333 <a href="#release_notes_eb310" class="md-nav__link"> 14334 <span class="md-ellipsis"> 14335 14336 EasyBuild v3.1.0 (February 3rd 2017) 14337 14338 </span> 14339 </a> 14340 14341</li> 14342 14343 <li class="md-nav__item"> 14344 <a href="#release_notes_eb302" class="md-nav__link"> 14345 <span class="md-ellipsis"> 14346 14347 EasyBuild v3.0.2 (December 22nd 2016) 14348 14349 </span> 14350 </a> 14351 14352</li> 14353 14354 <li class="md-nav__item"> 14355 <a href="#release_notes_eb301" class="md-nav__link"> 14356 <span class="md-ellipsis"> 14357 14358 EasyBuild v3.0.1 (November 30th 2016) 14359 14360 </span> 14361 </a> 14362 14363</li> 14364 14365 <li class="md-nav__item"> 14366 <a href="#release_notes_eb300" class="md-nav__link"> 14367 <span class="md-ellipsis"> 14368 14369 EasyBuild v3.0.0 (November 16th 2016) 14370 14371 </span> 14372 </a> 14373 14374</li> 14375 14376 <li class="md-nav__item"> 14377 <a href="#release_notes_eb290" class="md-nav__link"> 14378 <span class="md-ellipsis"> 14379 14380 EasyBuild v2.9.0 (September 23rd 2016) 14381 14382 </span> 14383 </a> 14384 14385</li> 14386 14387 <li class="md-nav__item"> 14388 <a href="#release_notes_eb282" class="md-nav__link"> 14389 <span class="md-ellipsis"> 14390 14391 EasyBuild v2.8.2 (July 13th 2016) 14392 14393 </span> 14394 </a> 14395 14396</li> 14397 14398 <li class="md-nav__item"> 14399 <a href="#release_notes_eb281" class="md-nav__link"> 14400 <span class="md-ellipsis"> 14401 14402 EasyBuild v2.8.1 (May 30th 2016) 14403 14404 </span> 14405 </a> 14406 14407</li> 14408 14409 <li class="md-nav__item"> 14410 <a href="#release_notes_eb280" class="md-nav__link"> 14411 <span class="md-ellipsis"> 14412 14413 EasyBuild v2.8.0 (May 18th 2016) 14414 14415 </span> 14416 </a> 14417 14418</li> 14419 14420 <li class="md-nav__item"> 14421 <a href="#release_notes_eb270" class="md-nav__link"> 14422 <span class="md-ellipsis"> 14423 14424 EasyBuild v2.7.0 (March 20th 2016) 14425 14426 </span> 14427 </a> 14428 14429</li> 14430 14431 <li class="md-nav__item"> 14432 <a href="#release_notes_eb260" class="md-nav__link"> 14433 <span class="md-ellipsis"> 14434 14435 EasyBuild v2.6.0 (January 26th 2016) 14436 14437 </span> 14438 </a> 14439 14440</li> 14441 14442 <li class="md-nav__item"> 14443 <a href="#release_notes_eb250" class="md-nav__link"> 14444 <span class="md-ellipsis"> 14445 14446 EasyBuild v2.5.0 (December 17th 2015) 14447 14448 </span> 14449 </a> 14450 14451</li> 14452 14453 <li class="md-nav__item"> 14454 <a href="#release_notes_eb240" class="md-nav__link"> 14455 <span class="md-ellipsis"> 14456 14457 EasyBuild v2.4.0 (November 10th 2015) 14458 14459 </span> 14460 </a> 14461 14462</li> 14463 14464 <li class="md-nav__item"> 14465 <a href="#release_notes_eb230" class="md-nav__link"> 14466 <span class="md-ellipsis"> 14467 14468 EasyBuild v2.3.0 (September 2nd 2015) 14469 14470 </span> 14471 </a> 14472 14473</li> 14474 14475 <li class="md-nav__item"> 14476 <a href="#release_notes_eb220" class="md-nav__link"> 14477 <span class="md-ellipsis"> 14478 14479 EasyBuild v2.2.0 (July 15th 2015) 14480 14481 </span> 14482 </a> 14483 14484</li> 14485 14486 <li class="md-nav__item"> 14487 <a href="#release_notes_eb211" class="md-nav__link"> 14488 <span class="md-ellipsis"> 14489 14490 EasyBuild v2.1.1 (May 18th 2015) 14491 14492 </span> 14493 </a> 14494 14495</li> 14496 14497 <li class="md-nav__item"> 14498 <a href="#release_notes_v2.1.0" class="md-nav__link"> 14499 <span class="md-ellipsis"> 14500 14501 EasyBuild v2.1.0 (April 30th 2015) 14502 14503 </span> 14504 </a> 14505 14506</li> 14507 14508 <li class="md-nav__item"> 14509 <a href="#release_notes_v2.0.0" class="md-nav__link"> 14510 <span class="md-ellipsis"> 14511 14512 EasyBuild v2.0.0 (March 6th 2015) 14513 14514 </span> 14515 </a> 14516 14517</li> 14518 14519 <li class="md-nav__item"> 14520 <a href="#easybuild-v1162-march-6th-2015" class="md-nav__link"> 14521 <span class="md-ellipsis"> 14522 14523 EasyBuild v1.16.2 (March 6th 2015) 14524 14525 </span> 14526 </a> 14527 14528</li> 14529 14530 <li class="md-nav__item"> 14531 <a href="#easybuild-v1161-december-19th-2014" class="md-nav__link"> 14532 <span class="md-ellipsis"> 14533 14534 EasyBuild v1.16.1 (December 19th 2014) 14535 14536 </span> 14537 </a> 14538 14539</li> 14540 14541 <li class="md-nav__item"> 14542 <a href="#easybuild-v1160-december-18th-2014" class="md-nav__link"> 14543 <span class="md-ellipsis"> 14544 14545 EasyBuild v1.16.0 (December 18th 2014) 14546 14547 </span> 14548 </a> 14549 14550</li> 14551 14552 <li class="md-nav__item"> 14553 <a href="#easybuild-v1152-october-7th-2014" class="md-nav__link"> 14554 <span class="md-ellipsis"> 14555 14556 EasyBuild v1.15.2 (October 7th 2014) 14557 14558 </span> 14559 </a> 14560 14561</li> 14562 14563 <li class="md-nav__item"> 14564 <a href="#easybuild-v1151-september-23rd-2014" class="md-nav__link"> 14565 <span class="md-ellipsis"> 14566 14567 EasyBuild v1.15.1 (September 23rd 2014) 14568 14569 </span> 14570 </a> 14571 14572</li> 14573 14574 <li class="md-nav__item"> 14575 <a href="#easybuild-v1150-september-12th-2014" class="md-nav__link"> 14576 <span class="md-ellipsis"> 14577 14578 EasyBuild v1.15.0 (September 12th 2014) 14579 14580 </span> 14581 </a> 14582 14583</li> 14584 14585 <li class="md-nav__item"> 14586 <a href="#easybuild-v1140-july-9th-2014" class="md-nav__link"> 14587 <span class="md-ellipsis"> 14588 14589 EasyBuild v1.14.0 (July 9th 2014) 14590 14591 </span> 14592 </a> 14593 14594</li> 14595 14596 <li class="md-nav__item"> 14597 <a href="#easybuild-v1130-may-29th-2014" class="md-nav__link"> 14598 <span class="md-ellipsis"> 14599 14600 EasyBuild v1.13.0 (May 29th 2014) 14601 14602 </span> 14603 </a> 14604 14605</li> 14606 14607 <li class="md-nav__item"> 14608 <a href="#easybuild-v1121-april-25th-2014" class="md-nav__link"> 14609 <span class="md-ellipsis"> 14610 14611 EasyBuild v1.12.1 (April 25th 2014) 14612 14613 </span> 14614 </a> 14615 14616</li> 14617 14618 <li class="md-nav__item"> 14619 <a href="#easybuild-v1120-april-4th-2014" class="md-nav__link"> 14620 <span class="md-ellipsis"> 14621 14622 EasyBuild v1.12.0 (April 4th 2014) 14623 14624 </span> 14625 </a> 14626 14627</li> 14628 14629 <li class="md-nav__item"> 14630 <a href="#easybuild-v1111-february-28th-2014" class="md-nav__link"> 14631 <span class="md-ellipsis"> 14632 14633 EasyBuild v1.11.1 (February 28th 2014) 14634 14635 </span> 14636 </a> 14637 14638</li> 14639 14640 <li class="md-nav__item"> 14641 <a href="#easybuild-v1110-february-16th-2014" class="md-nav__link"> 14642 <span class="md-ellipsis"> 14643 14644 EasyBuild v1.11.0 (February 16th 2014) 14645 14646 </span> 14647 </a> 14648 14649</li> 14650 14651 <li class="md-nav__item"> 14652 <a href="#easybuild-v1100-december-24th-2013" class="md-nav__link"> 14653 <span class="md-ellipsis"> 14654
14655 EasyBuild v1.10.0 (December 24th 2013) 14656 14657 </span> 14658 </a> 14659 14660</li> 14661 14662 <li class="md-nav__item"> 14663 <a href="#easybuild-v190-november-17th-2013" class="md-nav__link"> 14664 <span class="md-ellipsis"> 14665 14666 EasyBuild v1.9.0 (November 17th 2013) 14667 14668 </span> 14669 </a> 14670 14671</li> 14672 14673 <li class="md-nav__item"> 14674 <a href="#easybuild-v182-october-18th-2013" class="md-nav__link"> 14675 <span class="md-ellipsis"> 14676 14677 EasyBuild v1.8.2 (October 18th 2013) 14678 14679 </span> 14680 </a> 14681 14682</li> 14683 14684 <li class="md-nav__item"> 14685 <a href="#easybuild-v181-october-14th-2013" class="md-nav__link"> 14686 <span class="md-ellipsis"> 14687 14688 EasyBuild v1.8.1 (October 14th 2013) 14689 14690 </span> 14691 </a> 14692 14693</li> 14694 14695 <li class="md-nav__item"> 14696 <a href="#easybuild-v180-october-4th-2013" class="md-nav__link"> 14697 <span class="md-ellipsis"> 14698 14699 EasyBuild v1.8.0 (October 4th 2013) 14700 14701 </span> 14702 </a> 14703 14704</li> 14705 14706 <li class="md-nav__item"> 14707 <a href="#easybuild-v170-september-2nd-2013" class="md-nav__link"> 14708 <span class="md-ellipsis"> 14709 14710 EasyBuild v1.7.0 (September 2nd 2013) 14711 14712 </span> 14713 </a> 14714 14715</li> 14716 14717 <li class="md-nav__item"> 14718 <a href="#easybuild-v160-july-11th-2013" class="md-nav__link"> 14719 <span class="md-ellipsis"> 14720 14721 EasyBuild v1.6.0 (July 11th 2013) 14722 14723 </span> 14724 </a> 14725 14726</li> 14727 14728 <li class="md-nav__item"> 14729 <a href="#easybuild-v150-june-1st-2013" class="md-nav__link"> 14730 <span class="md-ellipsis"> 14731 14732 EasyBuild v1.5.0 (June 1st 2013) 14733 14734 </span> 14735 </a> 14736 14737</li> 14738 14739 <li class="md-nav__item"> 14740 <a href="#easybuild-v140-may-2nd-2013" class="md-nav__link"> 14741 <span class="md-ellipsis"> 14742 14743 EasyBuild v1.4.0 (May 2nd 2013) 14744 14745 </span> 14746 </a> 14747 14748</li> 14749 14750 <li class="md-nav__item"> 14751 <a href="#easybuild-v130-april-1st-2013" class="md-nav__link"> 14752 <span class="md-ellipsis"> 14753 14754 EasyBuild v1.3.0 (April 1st 2013) 14755 14756 </span> 14757 </a> 14758 14759</li> 14760 14761 <li class="md-nav__item"> 14762 <a href="#easybuild-v120-february-28th-2013" class="md-nav__link"> 14763 <span class="md-ellipsis"> 14764 14765 EasyBuild v1.2.0 (February 28th 2013) 14766 14767 </span> 14768 </a> 14769 14770</li> 14771 14772 <li class="md-nav__item"> 14773 <a href="#easybuild-v110-january-27th-2013" class="md-nav__link"> 14774 <span class="md-ellipsis"> 14775 14776 EasyBuild v1.1.0 (January 27th 2013) 14777 14778 </span> 14779 </a> 14780 14781</li> 14782 14783 <li class="md-nav__item"> 14784 <a href="#easybuild-v102-december-8th-2012" class="md-nav__link"> 14785 <span class="md-ellipsis"> 14786 14787 EasyBuild v1.0.2 (December 8th 2012) 14788 14789 </span> 14790 </a> 14791 14792</li> 14793 14794 <li class="md-nav__item"> 14795 <a href="#easybuild-v101-november-24th-2012" class="md-nav__link"> 14796 <span class="md-ellipsis"> 14797 14798 EasyBuild v1.0.1 (November 24th 2012) 14799 14800 </span> 14801 </a> 14802 14803</li> 14804 14805 <li class="md-nav__item"> 14806 <a href="#easybuild-v10-november-13th-2012" class="md-nav__link"> 14807 <span class="md-ellipsis"> 14808 14809 EasyBuild v1.0 (November 13th 2012) 14810 14811 </span> 14812 </a> 14813 14814</li> 14815 14816 <li class="md-nav__item"> 14817 <a href="#easybuild-v08-june-29th-2012" class="md-nav__link"> 14818 <span class="md-ellipsis"> 14819 14820 EasyBuild v0.8 (June 29th 2012) 14821 14822 </span> 14823 </a> 14824 14825</li> 14826 14827 <li class="md-nav__item"> 14828 <a href="#easybuild-v07-june-18th-2012" class="md-nav__link"> 14829 <span class="md-ellipsis"> 14830 14831 EasyBuild v0.7 (June 18th 2012) 14832 14833 </span> 14834 </a> 14835 14836</li> 14837 14838 <li class="md-nav__item"> 14839 <a href="#easybuild-v06-may-11th-2012" class="md-nav__link"> 14840 <span class="md-ellipsis"> 14841 14842 EasyBuild v0.6 (May 11th 2012) 14843 14844 </span> 14845 </a> 14846 14847</li> 14848 14849 <li class="md-nav__item"> 14850 <a href="#easybuild-v05-april-6th-2012" class="md-nav__link"> 14851 <span class="md-ellipsis"> 14852 14853 EasyBuild v0.5 (April 6th 2012) 14854 14855 </span> 14856 </a> 14857 14858</li> 14859 14860 </ul> 14861 14862</nav> 14863 </div> 14864 </div> 14865 </div> 14866 14867 14868 14869 <div class="md-content" data-md-component="content"> 14870 14871 <article class="md-content__inner md-typeset"> 14872 14873 14874 14875 14876 14877
14878 14879 14880<h1 id="release_notes">EasyBuild release notes<a class="headerlink" href="#release_notes" title="Permanent link">¶</a></h1> 14881<p>The latest version of EasyBuild provides support for building and 14882installing <a href="../version-specific/supported-software/"><strong>3,091</strong> different software packages</a>, 14883including 31 different (compiler) toolchains. 14884It contains 210 software-specific easyblocks and 47 generic easyblocks, 14885alongside 10,992 easyconfig files.</p> 14886<h2 id="release_notes_eb540">EasyBuild v5.4.0 (9 Aug 2026)<a class="headerlink" href="#release_notes_eb540" title="Permanent link">¶</a></h2> 14887<p>bugfix/update release</p> 14888<p><strong>framework</strong></p> 14889<ul> 14890<li>enhancements:<ul> 14891<li>improve <code>--bwrap</code> to work with r/o filesystems (overlayfs) and <code>--subdir-{modules,software}</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5173">#5173</a>)</li> 14892<li>format extension names in module files with <code>exts_formatter</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/5186">#5186</a>)</li> 14893<li>use bounded <code>git rev-list</code> for version detection (<a href="https://github.com/easybuilders/easybuild-framework/pull/5201">#5201</a>)</li> 14894<li>reduce number of <code>module load</code> commands used to set up build environment (<a href="https://github.com/easybuilders/easybuild-framework/pull/5211">#5211</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5230">#5230</a>)</li> 14895<li>prefer bsdtar for unpacking ISO files, keep 7z as fallback (<a href="https://github.com/easybuilders/easybuild-framework/pull/5213">#5213</a>)</li> 14896<li>enhance <code>download_file</code> to fallback to <code>https://ftp.gnu.org</code> if downloading from <code>https://ftpmirror.gnu.org</code> fails (<a href="https://github.com/easybuilders/easybuild-framework/pull/5224">#5224</a>)</li> 14897</ul> 14898</li> 14899<li>bug fixes:<ul> 14900<li>do not duplicate sanity checks in each extension (<a href="https://github.com/easybuilders/easybuild-framework/pull/5184">#5184</a>)</li> 14901<li>use correct module in sanity check of extensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/5185">#5185</a>)</li> 14902<li>fix <code>lfbf</code> toolchain description (<a href="https://github.com/easybuilders/easybuild-framework/pull/5217">#5217</a>)</li> 14903<li>don't check for lib and bin paths in sanity check step for each extension (<a href="https://github.com/easybuilders/easybuild-framework/pull/5221">#5221</a>)</li> 14904<li>fix format string in log message in <code>EasyBlock.sanity_check_cuda</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5226">#5226</a>)</li> 14905</ul> 14906</li> 14907<li>other changes<ul> 14908<li>deprecate passing <code>extension</code> option to <code>sanity_check_step</code> & <code>sanity_check_load_module</code> methods in <code>EasyBlock</code> class (<a href="https://github.com/easybuilders/easybuild-framework/pull/5220">#5220</a>)</li> 14909</ul> 14910</li> 14911<li>enhancements and fixes for test suite:<ul> 14912<li>remove CI workflow for Hound style checker (<a href="https://github.com/easybuilders/easybuild-framework/pull/5175">#5175</a>)</li> 14913<li>cater for Python 3.8 deprecation in cryptography package (<a href="https://github.com/easybuilders/easybuild-framework/pull/5204">#5204</a>)</li> 14914<li>split running test suite with Python 3.9 and Lmod 8.x with Lua/Tcl module syntax in two jobs, only use GitHub token with Lua module syntax (<a href="https://github.com/easybuilders/easybuild-framework/pull/5208">#5208</a>)</li> 14915<li>update actions used in CI workflows to latest versions (<a href="https://github.com/easybuilders/easybuild-framework/pull/5209">#5209</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5210">#5210</a>)</li> 14916</ul> 14917</li> 14918</ul> 14919<p><strong>easyblocks</strong></p> 14920<ul> 14921<li>new easyblocks:<ul> 14922<li>custom easyblock for Bandicoot (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3380">#3380</a>)</li> 14923<li>generic <code>CargoMesonNinja</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4171">#4171</a>)</li> 14924</ul> 14925</li> 14926<li>enhancements:<ul> 14927<li>add support for NVHPC to Boost easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3906">#3906</a>)</li> 14928<li>enhance GROMACS easyblock to add support for optarch "<code>X86-64-V?</code>" notation (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3981">#3981</a>)</li> 14929<li>
14929enhance GROMACS easyblock to improve control over PLUMED support (native vs. patching) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3984">#3984</a>)</li> 14930<li>add <code>exts_formatter</code> easyconfig parameter to PythonPackage easyblock to do formatting extension names in module files (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4125">#4125</a>)</li> 14931<li>add extra easyconfig parameter <code>object_storage_ignore_dirs</code> to generic <code>Dataset</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4154">#4154</a>)</li> 14932<li>use bounded "<code>git rev-list</code>" for version detection (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4163">#4163</a>)</li> 14933<li>adapt <code>NvidiaBase</code> generic easyblock for removal of test examples in hpcx v2.50 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4174">#4174</a>)</li> 14934</ul> 14935</li> 14936<li>bug fixes:<ul> 14937<li>fix sanity check step in TensorRT easyblock: <code>sanity_check_paths</code> must have both 'files' and 'dirs' key (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4169">#4169</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4170">#4170</a>)</li> 14938<li>fix <code>test_step</code> not failing in sympy easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4172">#4172</a>)</li> 14939<li>fix OpenMPI and UCX easyblocks w.r.t. ROCm support (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4173">#4173</a>)</li> 14940<li>fix indentation in sanity check of custom easyblock for AEDT (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4181">#4181</a>)</li> 14941<li>fix excessive liberal regex used to pick correct path to ELPA include path in WIEN2k easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4191">#4191</a>)</li> 14942</ul> 14943</li> 14944<li>updates:<ul> 14945<li>refactor Score-P easyblock and update for v10.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4133">#4133</a>)</li> 14946</ul> 14947</li> 14948<li>enhancements and fixes for test suite:<ul> 14949<li>update actions used in CI workflows to latest versions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4168">#4168</a>)</li> 14950<li>remove CI workflow for Hound style checker (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4185">#4185</a>)</li> 14951</ul> 14952</li> 14953<li>other changes:<ul> 14954<li>don't use <code>get_ref</code> to obtain <code>cmds_map</code> value with resolved templated in <code>CmdCp</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3921">#3921</a>)</li> 14955<li>generalize Kokkos mapping in LAMMPS and Kokkos easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4107">#4107</a>)</li> 14956<li>do not pass <code>extension</code> to <code>sanity_check_load_module</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4184">#4184</a>)</li> 14957</ul> 14958</li> 14959</ul> 14960<p><strong>easyconfigs</strong></p> 14961<ul> 14962<li>add easyconfigs for update of (common) toolchains: <code>gmpich/2025b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26490">#26490</a>), <code>gmpich/2026.1</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26447">#26447</a>), <code>gmpflf/2025b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26491">#26491</a>), <code>gmpflf/2026.1</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26492">#26492</a>)</li> 14963<li>added example easyconfig files for 32 new software packages:<ul> 14964<li>2decomp-fft (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26372">#26372</a>), Bandicoot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20962">#20962</a>), cage (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25870">#25870</a>), cfchecker (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25995">#25995</a>), cftime (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25995">#25995</a>), cling-kernel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26428">#26428</a>), 14965coolpuppy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26430">#26430</a>), eQuilibrator (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26507">#26507</a>), freesasa (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26378">#26378</a>
14965), gdc-client (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26300">#26300</a>), gdown (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26345">#26345</a>), IBSimu (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25727">#25727</a>), 14966IMAS-Core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24744">#24744</a>), IMAS-Data-Dictionaries (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24744">#24744</a>), IMAS-MDSplus-models (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24744">#24744</a>), Incompact3d (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26372">#26372</a>), JMAG-Designer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26282">#26282</a>), 14967libcbor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26079">#26079</a>), libfido2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26079">#26079</a>), libseccomp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25914">#25914</a>), myst-nb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26418">#26418</a>), nccmp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25899">#25899</a>), OpenFold3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26370">#26370</a>), 14968Orange3-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25470">#25470</a>), pynco (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25900">#25900</a>), root-kernel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26429">#26429</a>), SLATEC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22171">#22171</a>), soapboxslide (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26472">#26472</a>), stacie (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26473">#26473</a>), 14969tinydft (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26461">#26461</a>), tinyff (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26461">#26461</a>), wayvnc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26381">#26381</a>)</li> 14970</ul> 14971</li> 14972<li>added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 14973<li>absl-py 2.4.0, Advisor 2026.0.0, AmberTools 26.1, archspec 0.2.6, astropy 8.0.1, astropy-testing 8.0.1, awscli 2.35.11, 14974bcrypt 5.0.0, binutils 2.47, Biopython 1.87, Boost.Python-NumPy 1.90.0, boto3 1.43.34, btop 1.4.6, cargo-c 0.10.23, 14975CGAL 6.2, Cling 1.3, code-server 4.125.0, configurable-http-proxy 5.2.0, Coreutils 9.11, cppzmq 4.11.0, cuSPARSELt 0.9.1.1, 14976cuTENSOR 2.7.0.5, ecBuild 3.14.2, DB_File 1.860, FDS 6.11.1, Flask 3.1.3, flatbuffers-python 25.12.19, FLINT 3.5.0, 14977fmt 12.2.0, FUNAERO 1.6.1, gawk 5.4.0, GCC 16.2.0, GDB 17.2, GitPython 3.1.50, GLM 1.0.3, Go 1.26.4, Graphviz 15.1.0, 14978Greenlet 3.5.2, Guile 3.0.11, HiGHS 1.14.0, hiredis 1.4.0, hwloc-CUDA 2.13.0, ICON 2026.04, ImageMagick 7.1.2-26, 14979inih 62, intel-compilers 2026.1.0, iodata 1.0.1, ipp 2026.0.0, ipympl 0.10.0, jax 0.10.1, JupyterHub 5.5.0, 14980JupyterLab 4.5.8, JupyterNotebook 7.5.7, Leptonica 1.87.0, libcerf 3.3, libdwarf 2.3.1, libedit 20260512, libfyaml 0.9.6, 14981libjxl 0.11.2, librsvg 2.62.3, libyuv 20260609, likwid 5.5.1, LMDB 0.9.35, makeinfo 7.3, Markdown 3.10.2, MATLAB 2026a-r2, 14982metakernel 1.0.0, ml_dtypes 0.5.4, modkit 0.6.4, mold 2.41.0, mpi4py 4.1.2, nanobind 2.13.0, netCDF-Fortran 4.6.3, 14983nglview 4.0.1, NiBabel 5.4.2, Nipype 1.11.0, nsync 1.30.0, numba 0.65.1, numdifftools 0.9.42, NVHPC 26.5, 14984nvidia-compilers 26.5, octave-kernel 1.1.0, OPARI2 2.0.10, OpenFAST 5.0.0, OpenForceField-Toolkit 0.18.1, 14985OpenMolcas 26.06, OptiX 9.1.0, OTF2 3.2, PCAngsd 1.36.4, PDM 2.28.0, Pixi 0.70.2, pre-commit 4.6.0, psycopg 3.3.4, 14986PycURL 7.46.0, pydicom 3.0.2, pydantic 2.13.4, pygame 2.6.1, python-irods-client 3.3.0, pyunicore 1.3.7, 14987PyVista 0.48.4, R 4.6.1, R-bundle-CRAN 2026.07, R-bundle-Bioconductor 3.23 w/ R 4.6.1, RDFlib 7.6.0, RDKit 2026.03.4, 14988rkcommon 1.15.2, rpds-py 2026.5.1, ruamel.yaml 0.19.1, ruff 0.15.21, schemdraw 0.23, scikit-build 0.19.0, Score-P 10.1, 14989SDL2_mixer 2.8.1, SNAP-ESA 13.0.0, SOCI 4.1.4, spdlog 1.17.0, spglib 2.7.0, SQLAlchemy 2.0.51, spglib-python 2.7.0, 14990SuiteSparse 7.12.2, sympy 1.14.0, typing-extensions 4.15.0, Vala v0.56.19, Valgrind 3.26.0 w/ Verrou 2.7.0, WRF 4.7.1, 14991xarray 2026.4.0, Xvfb 21.1.23, Yambo 5.3.0 w/ double precision</li> 14992</ul> 14993</li> 14994<li>various bug fixes, including:<ul> 14995<li>add patch for jax 0.8.1 to avoid that "<code>jax version</code>" shows <code>.dev</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25791">#25791</a>)</li> 14996<li>Add missing depencies to jupyter-resource-usage (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25801">#25801</a>)</li> 14997<li>use <code>git_config</code> for all sources for Siesta to guarantee that the versions of externals are correct (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26240">#26240</a>)</li> 14998<li>
14998add "<code>sanity_check_pip_list = False</code>" to PyTorch easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26299">#26299</a>)</li> 14999<li>fix checksum for source tarball of ICON 2024.01 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26324">#26324</a>)</li> 15000<li>add patch to LLVM 21.1.8 to fix MLIR build failure with jax (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26337">#26337</a>)</li> 15001<li>skip unnecessary build step in libxsmm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26339">#26339</a>)</li> 15002<li>add patch for ncurses link issue to hwloc 2.13.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26344">#26344</a>)</li> 15003<li>add patch for glibc >= 2.43 compatibility to libunistring 1.4.1 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26351">#26351</a>)</li> 15004<li>add patch to JsonCpp v1.9.7 to fix ABI breakage for C++11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26354">#26354</a>)</li> 15005<li>apply upstream patch to protobuf-python 6.31.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26377">#26377</a>)</li> 15006<li>add hypothesis build dependency to sympy easyconfigs for sympy 1.13.3 + 1.14.0, required by tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26392">#26392</a>)</li> 15007<li>fix rocm-core version from 6.4.0 => 6.4.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26407">#26407</a>)</li> 15008<li>add patch to fix commit of git clones in Makefile for Scalene 1.5.26 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26431">#26431</a>)</li> 15009<li>fix typos on Triton easyconfigs for path to cuobjdump (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26446">#26446</a>)</li> 15010<li>filter out broken tests for astropy 7.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26449">#26449</a>)</li> 15011<li>add <code>--auto-servernum</code> to <code>preconfigopts</code> for <code>xvfb-run</code> in R-bundle-CRAN easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26450">#26450</a>)</li> 15012<li>add patch to fix scipy 1.17.1 tests for AOCL-BLAS in SciPy-bundle 2026.05 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26458">#26458</a>)</li> 15013<li>change source URL and homepage in libaec easyconfigs to official GitHub page (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26536">#26536</a>)</li> 15014<li>update acres patch to correct version in easyconfig for Nipype 1.10 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26560">#26560</a>)</li> 15015<li>add patch to fix broken test in Biopython 1.87 (rather than skipping it) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26567">#26567</a>)</li> 15016<li>fix source URL for Jena 5.6.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26568">#26568</a>)</li> 15017<li>make sure that correct Python headers and library are picked up for Arrow 22.0.0 + 24.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26569">#26569</a>)</li> 15018<li>add libiconv as direct dependency for R-bundle-CRAN + make sure that it's used for haven + readxl extensions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26573">#26573</a>)</li> 15019<li>fix pod5-file-format 0.3.x easyconfigs by avoiding that preconfigopts is inherited by extensions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26574">#26574</a>)</li> 15020<li>several fixes for SimNIBS 4.6.0 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26579">#26579</a>)</li> 15021<li>add patch to fix DistGeomHelpers test in RDKit v2026.03.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26580">#26580</a>)</li> 15022<li>limit parallelism during AOCL-BLAS tests via $OMP_NUM_THREADS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26590">#26590</a>)</li> 15023<li>add patch for QuantumESPRESSO 7.5 so wannier2pw.x is also installed (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26598">#26598</a>)</li> 15024<li>fix installation of mumax3 3.10 in case multiple CUDA compute capabilities are used (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26599">#26599</a>)</li> 15025<li>avoid duplicate build of cuda-bindings in CUDA-Python 12.8.0 & 12.9.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26606">#26606</a>)</li> 15026<li>
15026add patch for RStudio-server 2023.09.1+494 to use specific commit of dependency quarto (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26609">#26609</a>)</li> 15027<li>add alternative checksum for libcerf sources (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26612">#26612</a>)</li> 15028<li>add patch to deal with flaky test in LWP-Protocol-https extension in Perl-bundle-CPAN 5.42.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26622">#26622</a>)</li> 15029</ul> 15030</li> 15031<li>minor enhancements, including:<ul> 15032<li>install <code>*.tcl</code> files in Tcl 9.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26414">#26414</a>)</li> 15033<li>switch to https for Tcl source download (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26432">#26432</a>)</li> 15034<li>also install human-o package in HOMER 5.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26604">#26604</a>)</li> 15035</ul> 15036</li> 15037<li>enhancements and fixes for test suite:<ul> 15038<li>mention filename for failing use_pip check (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22638">#22638</a>)</li> 15039<li>update actions used in CI workflows to latest versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26328">#26328</a>)</li> 15040<li>refactor + fixes for tagbot 2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26336">#26336</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26335">#26335</a>)</li> 15041<li>update analysis workflow to include PR in artifact (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26346">#26346</a>)</li> 15042</ul> 15043</li> 15044<li>other changes:<ul> 15045<li>update jax 0.10.1 Easyconfig after MLIR patch for LLVM 21.1.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26359">#26359</a>)</li> 15046<li>remove <code>h11</code> extension already listed in PyPI-bundle from HTTPX 0.28.1 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26386">#26386</a>)</li> 15047<li>update homepage for <code>cutadapt</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26528">#26528</a>)</li> 15048<li>make systemd support in easyconfig for seatd 0.9.2 explicit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26556">#26556</a>)</li> 15049</ul> 15050</li> 15051</ul> 15052<h2 id="release_notes_eb531">EasyBuild v5.3.1 (19 Jun 2026)<a class="headerlink" href="#release_notes_eb531" title="Permanent link">¶</a></h2> 15053<p>bugfix/update release</p> 15054<p><strong>framework</strong></p> 15055<ul> 15056<li>bug fixes:<ul> 15057<li>don't call <code>render</code> when using <code>--dep-graph</code> to create <code>.dot</code> file (<a href="https://github.com/easybuilders/easybuild-framework/pull/5171">#5171</a>)</li> 15058<li>fix duplicate counting of download progress in <code>obtain_file</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5174">#5174</a>)</li> 15059<li>enhance <code>cmd.sh</code> so it works in non-interactive mode, like when passing <code>-c</code> to run a command (<a href="https://github.com/easybuilders/easybuild-framework/pull/5187">#5187</a>)</li> 15060</ul> 15061</li> 15062<li>enhancements:<ul> 15063<li>document where architecture dicts are allowed in easyconfig parameters & fix version templates for removed dependencies (<a href="https://github.com/easybuilders/easybuild-framework/pull/5150">#5150</a>)</li> 15064<li>add support for <code>--include-job-backends</code> and <code>--avail-job-backends</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5178">#5178</a>)</li> 15065<li>warn when using <code>get_cpu_arch_name</code> when <code>archspec</code> is not installed (<a href="https://github.com/easybuilders/easybuild-framework/pull/5193">#5193</a>)</li> 15066<li>remove repetition of shell command in log (<a href="https://github.com/easybuilders/easybuild-framework/pull/5195">#5195</a>)</li> 15067<li>add <code>get_ptrace_scope</code> function to <code>systemtools</code> to determine value for <code>ptrace_scope</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5199">#5199</a>)</li> 15068</ul> 15069</li> 15070<li>enhancements and fixes for test suite:<ul> 15071<li>add test to check how many <code>EasyConfig</code> instances are created when parsing a bunch of easyconfigs (<a href="https://github.com/easybuilders/easybuild-framework/pull/5168">#5168</a>)</li> 15072<li>
15072fix copy-paste error in <code>test_toy_cuda_sanity_check</code> and simplify (<a href="https://github.com/easybuilders/easybuild-framework/pull/5183">#5183</a>)</li> 15073<li>use flex instead of bzip2 for end-to-end tests in CI (+ update CI workflows) (<a href="https://github.com/easybuilders/easybuild-framework/pull/5196">#5196</a>)</li> 15074<li>fix <code>test_github_merge_pr</code> by using more recent easyconfig PR (<a href="https://github.com/easybuilders/easybuild-framework/pull/5197">#5197</a>)</li> 15075</ul> 15076</li> 15077</ul> 15078<p><strong>easyblocks</strong></p> 15079<ul> 15080<li>new easyblocks:<ul> 15081<li>add custom easyblock for ESPResSo (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4066">#4066</a>)</li> 15082</ul> 15083</li> 15084<li>bug fixes:<ul> 15085<li>fix location of <code>object_storage</code> for Dataset easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4128">#4128</a>)</li> 15086<li>enhance SAMtools easyblock to specify ncursesw libraries to link to via <code>CURSES_LIB</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4149">#4149</a>)</li> 15087<li>use <code>sanity_check_load_module</code> in sanity check step of custom easyblock for GROMACS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4151">#4151</a>)</li> 15088<li>fix incorrect plugins path in ABAQUS easyblock, which fixes long startup times (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4152">#4152</a>)</li> 15089<li>make sure that RPATH section for binaries in Rust 1.90.0+ installation includes path to runtime libraries of GCC compiler (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4156">#4156</a>)</li> 15090<li>trickle down modified build directory to bundle components in custom easyblock for gnupg-bundle (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4157">#4157</a>)</li> 15091<li>fix <code>--sanity-check-only</code> for netcdf4-python (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4161">#4161</a>)</li> 15092</ul> 15093</li> 15094<li>enhancements:<ul> 15095<li>add Arm support to NAMD easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3348">#3348</a>)</li> 15096<li>enable hwloc, cuFFTMp, and HeFFTe support in GROMACS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3531">#3531</a>)</li> 15097<li>enhance <code>run_pip_list</code> function to print warning for mismatched Python package names or versions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4109">#4109</a>)</li> 15098<li>adapt sanity checks in OpenMPI easyblock for AMD ROCm (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4119">#4119</a>)</li> 15099<li>add <code>$CUDNN_HOME</code> and <code>$CUDNN_PATH</code> as extra environment variables to be set by cuDNN easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4130">#4130</a>)</li> 15100<li>enhance custom easyblock for OpenMPI to add ROCm support (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4132">#4132</a>)</li> 15101<li>support <code>postinstallcmds</code> for <code>Dataset</code> generic easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4138">#4138</a>)</li> 15102<li>add logging if PyTorch tests were successful (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4140">#4140</a>)</li> 15103<li>enhance <code>PythonPackage</code> easyblock to limit ulimit stack size when unlimited (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4144">#4144</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4164">#4164</a>)</li> 15104<li>allow for either Mesa or OpenGL as dependency for VMD (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4147">#4147</a>)</li> 15105<li>improve error reporting for Python package without any close matches in output of <code>pip list</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4155">#4155</a>)</li> 15106<li>make custom easyblock for MRtrix aware of <code>configopts</code> easyconfig parameter (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4158">#4158</a>)</li> 15107<li>ignore compiler-rt and lldb test failure for <code>ptrace_scope</code> > 1 in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4159">#4159</a>)</li> 15108</ul> 15109</li> 15110<li>updates:<ul> 15111<li>update <code>Boost</code> sanity checks for versions 1.89 and newer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4088">#4088</a>)</li> 15112<li>update test command in custom easyblock for scipy easyblock for scipy >= 1.17 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4143">#4143</a>)</li> 15113</ul> 15114</li> 15115<li>code cleanup:<ul> 15116<li>pythonpackage: fix warning message for max ulimit (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4145">#4145</a>)</li> 15117</ul> 15118</li> 15119</ul> 15120<p><strong>easyconfigs</strong></p> 15121<ul> 15122<li>add easyconfigs for ROCm-based (sub)toolchains: <code>rocm-compilers/19.0.0-ROCm-6.4.1</code>, <code>rompi/2025a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25847">#25847</a>)</li> 15123<li>
15123add easyconfigs for update of (sub)toolchains based on LLVM + MPICH: <code>lmpich/2026.1</code>, <code>lmpflf/2026.1</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26040">#26040</a>)</li> 15124<li>added example easyconfig files for 96 new software packages:<ul> 15125<li>acl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25929">#25929</a>), AICD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25688">#25688</a>), Cabana (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25454">#25454</a>, 25455), CAFE5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26270">#26270</a>), cglm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25861">#25861</a>), composable_kernel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), 15126cppzmq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21125">#21125</a>), CUDA-wheel-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25266">#25266</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25558">#25558</a>), DeviceXlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23885">#23885</a>), dulwich (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25882">#25882</a>), EMOSLIB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25970">#25970</a>), 15127expected (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25939">#25939</a>), Firedrake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25157">#25157</a>), Flower (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26016">#26016</a>), Foldseek (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25786">#25786</a>), fresnel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22451">#22451</a>), freud (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22451">#22451</a>), 15128GPU-comcot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21041">#21041</a>), gwf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26073">#26073</a>), half (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), HIP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), hipBLAS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), hipBLAS-common (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), 15129hipBLASLt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), hipCUB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), hipFFT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), HIPIFY (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), hipRAND (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), hipSPARSE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), 15130hipSPARSELt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), hipTensor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), ittapi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26259">#26259</a>), jpeg4py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26045">#26045</a>), JuicerTools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22529">#22529</a>), level-zero (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26259">#26259</a>), 15131libccd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26044">#26044</a>), libcst (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25436">#25436</a>), libdecor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25804">#25804</a>), libdierckx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24419">#24419</a>), libsolv (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25941">#25941</a>), liftOver (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25709">#25709</a>), 15132LPJ-GUESS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26261">#26261</a>), msdf-atlas-gen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25874">#25874</a>), Orange3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25436">#25436</a>), PGDSpider (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25964">#25964</a>), PLplot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25949">#25949</a>), PovChem1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25688">#25688</a>), 15133projectaria-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25987">#25987</a>), pti-gpu (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26259">#26259</a>), PyFR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26184">#26184</a>), PyLipID (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25918">#25918</a>), Quickshell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25624">#25624</a>), random123 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22451">#22451</a>), 15134rapids-singlecell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25558">
15134#25558</a>), RCCL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), RepeatAfterMe (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26035">#26035</a>), rerun-sdk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25987">#25987</a>), rocBLAS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), ROCdbgapi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), 15135rocFFT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocm_bandwidth_test (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocm-cmake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocm-core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocminfo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocPRIM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), 15136rocprofiler-register (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocRAND (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocSOLVER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocSPARSE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocThrust (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), 15137rocTracer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rocWMMA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rowan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22451">#22451</a>), rpds-py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25997">#25997</a>), RPP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), rsync (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25929">#25929</a>), SDL3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25998">#25998</a>), 15138SDL3_image (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25998">#25998</a>), SDL3_ttf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25998">#25998</a>), seawater (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25976">#25976</a>), signac (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22451">#22451</a>), singularity-hpc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25831">#25831</a>), Spring (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25707">#25707</a>), 15139svtoolbox (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25706">#25706</a>), Tensile (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25576">#25576</a>), tibs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25769">#25769</a>), tig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26000">#26000</a>), tl-expected (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26068">#26068</a>), tMAE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26021">#26021</a>), unrar (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25829">#25829</a>), 15140uv-build (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25461">#25461</a>), Vesalius (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25783">#25783</a>), Victory-TCAD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25876">#25876</a>), watchfiles (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25865">#25865</a>), xopen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26221">#26221</a>), Yambo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23885">#23885</a>)</li> 15141</ul> 15142</li> 15143<li>
15143added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 15144<li>Abseil 20260107.1, ADMIXTURE 1.4.0, alsa-lib 1.2.15.3, amdahl 0.4.1, anndata 0.12.16, Armadillo 15.2.6 + 15.2.7, 15145Arrow 24.0.0, ASE 3.28.0, assimp 6.0.5, barrnap 1.10.5, BCFtools 1.23.1, BeautifulSoup 4.14.3, binutils 2.46.1, 15146Blosc2 3.1.2, Boost 1.90.0, Brotli 1.2.0, c-ares 1.34.6, cairomm 1.19.1, Catch2 3.14.0, cffi 2.0.0, CFITSIO 4.6.4, 15147CheckM 1.2.5, chopper 0.12.0b, CLHEP 2.4.7.2, code-cli 1.123.0, code-server 4.123.0, Compress-Raw-Zlib 2.222, 15148coverage 7.13.5, cryptography 47.0.0, CUDA 13.3.0, cuDNN 9.23.0.39, Cython 3.2.4, dav1d 1.5.3, DCMTK 3.7.0, 15149Delly 1.7.3, DIVEMesh 26.05, double-conversion 3.4.0, Doxygen 1.17.0, ecBuild 3.12.0, Eigen 5.0.0, EIGENSOFT 8.0.0, 15150elfutils 0.195, ESMF 8.9.1, Extrae 5.0.6, f90nml 1.5, FEniCS-DOLFINx-Python 0.10.0.post5, FFmpeg 8.1.1, 15151FHI-aims 260331, fontconfig 2.17.1, fonttools 4.63.0, ForceBalance 1.9.6, FOX-Toolkit 1.6.59, freeglut 3.8.0, 15152freetype 2.14.3, FUNAERO 1.6, GCC 15.3.0 + 16.1.0, gcloud 564.0.0, GDAL 3.13.0, Gdk-Pixbuf 2.44.6,, GDRCopy 2.5.2, 15153Geant4 11.4.1, Geant4-data 11.4, GenomeTools 1.6.6, gensim 4.4.0, GeoDict 2026-3-1.SP2, GEOS 3.14.1, gffread 0.12.9, 15154Ghostscript 10.07.1, giflib 6.1.3, git 2.54.0, GLib 2.89.0, Globus-CLI 3.42.0, glslang-SPIRV 16.3.0, gmpy2 2.3.0, 15155gnupg-bundle 20260518, GnuTLS 3.8.13, GObject-Introspection 1.86.0, googlebenchmark 1.9.5, graphite2 1.3.15, 15156GROMACS 2025.4 + 2026.2, grpcio 1.81.0, GTK3 3.24.52, h5py 3.16.0, HarfBuzz 14.2.0, hatchling 1.29.0, HDF5 2.1.1, 15157Highway 1.4.0, HPCToolkit 2026.0.1, HOOMD-blue 7.0.1, htop 3.5.0, HTSlib 1.23.1, hypothesis 6.153.2, ICU 78.3, 15158IGV 2.19.8, Imath 3.2.2, intel-mbuild 2026.03.18, intel-XED 2026.03.18, intervaltree-python 3.2.1, IPython 9.14.0, 15159ipywidgets 8.1.7, IQ-TREE 3.1.2, ISA-L 2.23.0, Jansson 2.15.0, JasPer 4.2.9, jedi 0.20.0, jemalloc 5.3.1, jiter 0.12.0, 15160json-fortran 9.3.1, JsonCpp 1.9.7, Julia 1.12.6, jupyter-server 2.19.0, Kalign 3.5.1, kallisto 0.52.0, Kokkos 5.1.1, 15161Kraken2 2.17.1, LAMMPS 22Jul2025_update4, LERC 4.1.0, libaom 3.14.0, libclc 21.1.8, libconfig 1.8.2, libde265 1.1.0, 15162libdeflate 1.25, libdrm 2.4.133, libgit2 1.9.4, libGridXC 2.0.3, libheif 1.22.2, libjpeg-turbo 3.1.4.1, libopus 1.6.1, 15163libpci 3.15.0, libpng 1.6.56, libsigc++ 3.8.1, LibSoup 3.6.6, libtasn1 4.21.0, LibTIFF 4.7.1, libtirpc 1.3.7, 15164libunwind 1.8.3, libuv 1.52.1, libvpx 1.16.0, libwebsockets 4.5.8, LittleCMS 2.19.1, libxslt 1.1.45, libwebp 1.6.0, 15165libxslt 1.1.45, lifelines 0.30.1, LMfit 1.3.3, Lua 5.5.0, lxml 6.1.1, M4 1.4.21, Mako 1.3.12, MariaDB 12.3.2, 15166MathWorksServiceHost 2026.3.0.6, matplotlib 3.10.9, maturin 1.13.1, MDTraj 1.11.1, meson-python 0.19.0, MetaBAT 2.18, 15167minimap2 2.31, MPC v1.4.1, MPICH 5.0.1, mpi4py 4.1.2, msgpack-c 7.0.1, msgpack-cxx 8.0.0, msprime 1.4.2, 15168NASM 3.01,, NCCL 2.30.4, networkx 3.6.1, ncbi-vdb 3.4.1, NCIPLOT 4.4-20260126, NCO 5.3.9, netCDF 4.10.0, 15169netcdf4-python 1.7.4, nettle 4.0, Nextflow 26.04.3, nghttp2 1.69.0, nghttp3 1.16.0, ngtcp2 1.23.0, NLopt 2.10.1, 15170nodejs 24.16.0, NSPR 4.39, NSS 3.119, occt 7.9.3, ollama 0.24.0, openai-python 1.65.1, OpenEXR 3.4.12, 15171OpenGL 2026.05, OpenJPEG 2.5.4, OpenMM 8.5.2, p11-kit 0.26.2, Pango 1.57.1, PCRE2 10.47, Perl-bundle-CPAN 5.42.0, 15172Pillow 12.2.0, PLUMED 2.10.0, PostgreSQL 18.4, PROJ 9.8.1, protobuf 35.0, protobuf-python 7.35.0, py3Dmol 2.5.5, 15173pybind 3.0.4, Pygments 2.20.0, pyproj 3.7.2, pysteps 1.10.0, PyTables 3.11.1, Python-bundle-PyPI 2026.04, 15174python-jellyfish 1.2.1, PyYAML 6.0.3, ratarmount 1.3.0, RAxML-NG 2.0.2, RE2 2025-11-05, re2c 4.5.1, RECON 1.10, 15175REEF3D 26.05, RepeatMasker 4.2.3, RepeatModeler 2.0.8, Rmath 4.5.1, RMBlast 2.17.1, RStudio-Server 2026.01.2, 15176Rust 1.94.1, SAMtools 1.23.1, SCons 4.10.1, scikit-bio 0.7.2, scikit-learn 1.8.0, SCOTCH 7.0.11, 15177SciPy-bundle 2026.05 (incl. numpy 2.4.6, scipy 1.17.1, pandas 3.0.3, ...), SDL2 2.32.10, SDL2_ttf 2.24.0, 15178setuptools-rust 1.12.1, SHAP 0.49.1, Shapely 2.1.2, SimNIBS 4.5.0 + 4.6.0, Simple-DFTD3 1.3.0, snakemake 9.22.0, 15179spin 0.18, spoa 4.1.5, SRA-Toolkit 3.4.1, statsmodels 0.14.6, SUMO 1.27.0, SVT-AV1 4.1.0, SWIG 4.4.1, 15180SymEngine-python 0.14.0, tbb 2022.3.0, tdb 1.4.15, test-drive 0.6.0, TEtrimmer 1.7.2, TINKER 26.1.2, 15181Tinker-HP 20260602, tinyxml2 11.0.0, Tk 9.0.3, Tkinter 3.14.2, tmux 3.6b, tornado 6.5.6, tqdm 4.67.3, Trilinos 16.2.0, 15182Trim_Galore 0.6.11, Visit v3.4.2, UCC-CUDA 1.7.0, UCX-CUDA 1.20.0, umap-learn 0.5.12, Unidecode 1.4.0, 15183util-linux 2.42, utf8proc 2.11.3, Virtuoso-opensource 7.2.17, VSEARCH 2.30.6, Vulkan 1.4.352, Wayland 1.25.0, 15184weblogo 3.9.0, wrapt 2.2.1, X11 20260518, x265 4.2, xxd 9.2.0612, yaml-cpp 0.9.0, zarr 3.2.1</li> 15185</ul> 15186</li> 15187<li>various bug fixes, including:<ul> 15188<li>update GROMACS easyconfigs to build with <code>gmxapi</code> distributed with GROMACS source code (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25188">#25188</a>)</li> 15189<li>
15189add patch for graniterapids support to OpenBLAS 0.3.27 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25730">#25730</a>)</li> 15190<li>add patch to ignore warning about avx10.1 when configuring for recent CMake easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25731">#25731</a>)</li> 15191<li>add patch to tbb 2022.2.0 easyconfig to avoid the use of <code>-fcf-protection=full</code> for riscv64 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25738">#25738</a>)</li> 15192<li>patch RStudio to correctly set <code>$R_HOME</code> when calculating <code>$LD_LIBRARY_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25745">#25745</a>)</li> 15193<li>update <code>$LD_LIBRARY_PATH</code> and <code>$LIBRARY_PATH</code> for <code>PySide6</code> + <code>shiboken6</code> shared libraries in easyconfig for PySide6 6.9.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25746">#25746</a>)</li> 15194<li>add alternative checksum for msigdbr in R-bundle-Bioconductor 3.22 w/ <code>foss/2025a</code> + R 4.5.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25796">#25796</a>)</li> 15195<li>remove Dyninst dependency for RISC-V in easyconfig for Extrae 5.0.0 w/ <code>gompi/2025b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25798">#25798</a>)</li> 15196<li>remove unnecessary gnupg-bundle dependency from easyconfig for poppler 25.12.0 w/ GCC/14.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25824">#25824</a>)</li> 15197<li>add googletest as build dependency for SPH-EXA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25827">#25827</a>)</li> 15198<li>use <code>julia.wrapper</code> + don't set <code>$JULIA_DEPOT_PATH</code> in multi-arch in easyconfigs for Julia 1.11.x + 1.12.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25836">#25836</a>)</li> 15199<li>apply patch to retain letter suffix of CUDA compute capability to GROMACS 2025.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25837">#25837</a>)</li> 15200<li>disable <code>opal_lifo</code> test for RISC-V in OpenMPI 5.0.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25838">#25838</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26252">#26252</a>)</li> 15201<li>Fix HIP hardcoded paths (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25846">#25846</a>)</li> 15202<li>enable <code>BUILD_LLVM_DYLIB</code> configure option to easyconfig for ROCm-LLVM 19.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25873">#25873</a>)</li> 15203<li>add missing (optional) dependencies as extension to easyconfig for RCall 0.13.17 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25903">#25903</a>)</li> 15204<li>fix InterProScan patches to properly pick up datasets (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25917">#25917</a>)</li> 15205<li>add missing Simple-DFTD3 dependency for CREST 3.0.2 w/ foss/2023a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25935">#25935</a>)</li> 15206<li>add patch for Underworld 2.16.4 to increase timeout in tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25960">#25960</a>)</li> 15207<li>add executable permission to binaries for ATAT 3.50 w/ <code>GCCcore/14.2.0</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25963">#25963</a>)</li> 15208<li>add alternate checksum for NAMD 3.0.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25984">#25984</a>)</li> 15209<li>fix pathspec extension version in easyconfig for scikit-build-core 0.12.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25996">#25996</a>)</li> 15210<li>add patch to fix bug in unittest-xml-reporting 3.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26030">#26030</a>)</li> 15211<li>fix sanity check of <code>ccache</code> with <code>system</code> toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26067">#26067</a>)</li> 15212<li>change RECON dependency to v1.10 in easyconfig for RepeatModeler 2.08 + fix RepeatAfterMe path in config file (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26069">#26069</a>)</li> 15213<li>
15213add missing <code>imp2importlib</code> extension for Cython 0.29.37 w/ GCCcore/13.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26082">#26082</a>)</li> 15214<li>add patch for worker 1.6.13 w/ <code>iimpi/2023a</code> to unset <code>$SLURM_EXPORT_ENV</code> in generated job script (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26093">#26093</a>)</li> 15215<li>fix compatibility with newer glibc and GCC for <code>GCCcore</code> 14.2.0, 14.3.0, and 15.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26126">#26126</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26138">#26138</a>)</li> 15216<li>disable URW fonts explicitly in groff v1.24.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26142">#26142</a>)</li> 15217<li>add Python as dependency for Wannier90 as some scripts are using "<code>/usr/bin/env python</code>" (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26166">#26166</a>)</li> 15218<li>add alternate package checksums for R-bundle-CRAN v2025.11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26170">#26170</a>)</li> 15219<li>add alternative checksum for msigdbr + add new URL for Illuminata package for R-bundle-Bioconductor v3.22 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26173">#26173</a>)</li> 15220<li>use <code>XORG_LIB_SOURCE</code> constant for libpciaccess and X11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26182">#26182</a>)</li> 15221<li>add missing googletest build dependency to easyconfig for spglib 2.5.0 (to avoid it being downloaded during the installation) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26186">#26186</a>)</li> 15222<li>add patch for Libint 2.11.1 to fix flaky test failure (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26194">#26194</a>)</li> 15223<li>add patch for scipy 1.17.1 to relax tolerance for tests failing on Arm Neoverse V1 system (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26223">#26223</a>)</li> 15224<li>fix linking issues with libiconv and fontconfig dependencies of gnuplot 6.0.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26224">#26224</a>)</li> 15225<li>fix homepage and source URL for magma: remove <code>.cs</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25925">#25925</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26242">#26242</a>)</li> 15226<li>add alternative checksum for metadat and metafor libraries in R-bundle-CRAN 2025.10 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26244">#26244</a>)</li> 15227<li>switch to <code>PythonBundle</code> easyblock for python-isal easyconfigs, to fix failing <code>pip list</code> sanity check (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26246">#26246</a>)</li> 15228<li>avoid that all cores are used for running MEME tests by patching <code>test_driver</code> script (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26253">#26253</a>)</li> 15229<li>add patch to M4 v1.4.20 to allow building with glibc v2.43 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26255">#26255</a>)</li> 15230<li>add <code>
15230-std=gnu89</code> to <code>$CFLAGS</code> for UnZip 6.0 to fix building on Ubuntu 26.06 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26258">#26258</a>)</li> 15231<li>add patch for SRA-Toolkit 3.4.1 so it does not fiddle with Python installations (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26285">#26285</a>)</li> 15232<li>use <code>netcdf4</code> as the extension name for <code>netcdf4-python</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26291">#26291</a>)</li> 15233<li>update source URL for xprop with new location (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26297">#26297</a>)</li> 15234</ul> 15235</li> 15236<li>minor enhancements, including:<ul> 15237<li>add HOIFCar extension to R-bundle-CRAN 2023.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25758">#25758</a>)</li> 15238<li>fix URL in comment to specific commit for ELPA eayconfigs using <code>lfoss</code> toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25794">#25794</a>)</li> 15239<li>add additional capabilities to Qt6 6.9.3 w/ GCCcore/14.3.0 by adding extra dependencies + use bundled libxml2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25901">#25901</a>)</li> 15240<li>add <code>alt_location</code> to NVHPC to use nvidia-compilers source files (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26122">#26122</a>)</li> 15241<li>update Python-bundle-PyPI 2026.04 to use wheel for <code>furo</code> extension, to avoid use of js/npm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26140">#26140</a>)</li> 15242</ul> 15243</li> 15244<li>enhancements and fixes for test suite:<ul> 15245<li>re-enable <code>test_dep_graph</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25700">#25700</a>)</li> 15246<li>handle arch-specific dependencies in tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25739">#25739</a>)</li> 15247</ul> 15248</li> 15249<li>other changes:<ul> 15250<li>remove easyconfig for ORCA-6.1.1 w/ <code>gompi/2025a</code> toolchain, as performance degradation is seen with OpenMPI-5, see issue <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25553">#25553</a> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/26084">#26084</a>)</li> 15251<li>remove (outdated) README & <code>sourceme</code> script in Lmod subdirectory (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25966">#25966</a>)</li> 15252</ul> 15253</li> 15254</ul> 15255<h2 id="release_notes_eb530">EasyBuild v5.3.0 (10 Apr 2026)<a class="headerlink" href="#release_notes_eb530" title="Permanent link">¶</a></h2> 15256<p>feature release</p> 15257<p><strong>framework</strong></p> 15258<ul> 15259<li>new features:<ul> 15260<li>make EasyBuild plugin-able through entrypoints (<a href="https://github.com/easybuilders/easybuild-framework/pull/4918">#4918</a>), see also <a href="https://docs.easybuild.io/entrypoints">https://docs.easybuild.io/entrypoints</a></li> 15261<li>add <code>--fetch-all</code> command line parameter (<a href="https://github.com/easybuilders/easybuild-framework/pull/5014">#5014</a>)</li> 15262<li>add support for ROCm-based toolchains (<code>rocm-compilers</code>, <code>rompi</code>, <code>rfbf</code>, <code>rfoss</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/5099">#5099</a>)</li> 15263<li>add (experimental) support for installing with <code>bwrap</code> (see <code>--bwrap</code> and <code>--bwrap-installpath</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/5130">#5130</a>)</li> 15264</ul> 15265</li> 15266<li>bug fixes:<ul> 15267<li>fix <code>check_checksums</code> when using templates, patch-dicts or <code>checksums.json</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5021">#5021</a>)</li> 15268<li>close stdout/stderr handles in <code>run_shell_cmd</code> and test teardown (<a href="https://github.com/easybuilders/easybuild-framework/pull/5050">#5050</a>)</li> 15269<li>fix setting <code>$OMPI_MCA_rmaps_base_oversubscribe</code> in sanity check (<a href="https://github.com/easybuilders/easybuild-framework/pull/5123">#5123</a>)</li> 15270<li>switch native flag from <code>-march=native</code> to <code>-mcpu=native</code> for LLVM compilers on Arm 64-bit (aarch64) (<a href="https://github.com/easybuilders/easybuild-framework/pull/5139">#5139</a>)</li> 15271<li>filter out NVHPC toolchains that share name from the toolchain hierarchy (<a href="https://github.com/easybuilders/easybuild-framework/pull/5140">#5140</a>)</li> 15272<li>fix handling of NVHPC toolchain with hierarchical module naming scheme (<a href="https://github.com/easybuilders/easybuild-framework/pull/5141">#5141</a>)</li> 15273<li>be a bit more forgiving with <code>copy_file</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5142">#5142</a>)</li> 15274<li>use fallback mechanism that relies on <code>$USER</code> or <code>$LOGNAME</code> when determining username via <code>
15274pwd.getpwuid</code> fails (<a href="https://github.com/easybuilders/easybuild-framework/pull/5151">#5151</a>)</li> 15275<li>raise error if <code>'filename'</code> is missing in source dict (<a href="https://github.com/easybuilders/easybuild-framework/pull/5152">#5152</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5156">#5156</a>)</li> 15276<li>be more careful when parsing output produced by rocm-smi command (+ add tests for <code>get_gpu_info</code> function) (<a href="https://github.com/easybuilders/easybuild-framework/pull/5155">#5155</a>)</li> 15277<li>enhance <code>get_cuda_object_dump_raw</code> to not run <code>cuobjdump</code> on shell scripts to determine CUDA architecture (<a href="https://github.com/easybuilders/easybuild-framework/pull/5161">#5161</a>)</li> 15278</ul> 15279</li> 15280<li>enhancements:<ul> 15281<li>add support for using list of values in <code>modulename</code> in extensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4716">#4716</a>)</li> 15282<li>add <code>return_conflicts</code> option to <code>check_conflicts</code> function and enhance tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/5000">#5000</a>)</li> 15283<li>hide output of module commands in log file by default + add <code>--debug-module-cmds</code> option to opt-in to keeping them (<a href="https://github.com/easybuilders/easybuild-framework/pull/5045">#5045</a>)</li> 15284<li>add script to gather git submodules (<a href="https://github.com/easybuilders/easybuild-framework/pull/5060">#5060</a>)</li> 15285<li>make sure that test commands used in <code>test_cases</code> step are executable (<a href="https://github.com/easybuilders/easybuild-framework/pull/5118">#5118</a>)</li> 15286<li>allow the use of extension specific <code>github_account</code> so <code>GITHUB_SOURCE</code> template constant can be used (<a href="https://github.com/easybuilders/easybuild-framework/pull/5121">#5121</a>)</li> 15287<li>add rich colors to <code>print_msg</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5125">#5125</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5149">#5149</a>)</li> 15288<li>only make use of graphviz to generate dependency graphs instead of pygraph (<a href="https://github.com/easybuilders/easybuild-framework/pull/5128">#5128</a>)</li> 15289</ul> 15290</li> 15291<li>enhancements and fixes for test suite:<ul> 15292<li>remove duplication in <code>toy_build</code> tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/5050">#5050</a>)</li> 15293<li>replace <code>assertTrue</code>/<code>assertFalse</code> with <code>assertRegex</code> in easyblock test (<a href="https://github.com/easybuilders/easybuild-framework/pull/5137">#5137</a>)</li> 15294<li>fix <code>test_github_merge_pr</code> by using more recent easyblocks PR (<a href="https://github.com/easybuilders/easybuild-framework/pull/5160">#5160</a>)</li> 15295</ul> 15296</li> 15297<li>code cleanup:<ul> 15298<li>remove deprecated 2-element list/tuple for specifying sources (<a href="https://github.com/easybuilders/easybuild-framework/pull/5153">#5153</a>)</li> 15299</ul> 15300</li> 15301</ul> 15302<p><strong>easyblocks</strong></p> 15303<ul> 15304<li>new easyblocks:<ul> 15305<li>add generic <code>ROCmComponent</code> easyblock to build & install ROCm components (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3861">#3861</a>)</li> 15306<li>custom easyblock for Sentaurus (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4001">#4001</a>)</li> 15307</ul> 15308</li> 15309<li>bug fixes:<ul> 15310<li>add guard to sanity check in custom easyblock for Stata to avoid running <code>ldd</code> on non ELF executable (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4077">#4077</a>)</li> 15311<li>take into account that no Python dependency may be provided when setting <code>$Python3_ROOT_DIR</code> in configure step of <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4079">#4079</a>)</li> 15312<li>also handle references to git tags in Cargo crates and download git repos recursively (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4081">#4081</a>)</li> 15313<li>make sure that netcdf easyblock picks up the provided libxml2 and bzip2 dependencies (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4086">#4086</a>)</li> 15314<li>set <code>$CIRCLECI</code> environment variable for torchvsion to work around flaky test (that requires downloading a file from <code>wikimedia.org</code>) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4094">#4094</a>)</li> 15315<li>include <code>/usr/local</code> Python package directory for system-level Python package installations (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4095">#4095</a>)</li> 15316<li>avoid crash in test step of custom easyblock for SuperLU if OpenMPI is not a dependency (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4099">#4099</a>)</li> 15317</ul> 15318</li> 15319<li>enhancements:<ul> 15320<li>use <code>clean_dir</code> instead of <code>remove_dir</code> on installation directory various easyblocks: <code>Binary</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3927">#3927</a>), <code>Tarball</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3926">#3926</a>), 15321Amber (+ AmberTools) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3935">#3935</a>), Anaconda (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3934">#3934</a>), FDTD_Solutions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3933">#3933</a>), GATE (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3932">#3932</a>), Go (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3931">#3931</a>), Java (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3928">#3928</a>), Molpro (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3930">#3930</a>), Tkinter (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3929">#3929</a>)</li> 15322<li>enhance <code>PythonPackage</code> and <code>PythonBundle</code> to verify Python package names and versions with <code>pip list</code> with <code>sanity_check_pip_list</code> parameter (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4049">#4049</a>)</li> 15323<li>
15323add ignore patterns for some RISC-V tests in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4059">#4059</a>)</li> 15324<li>enhance <code>PythonPackage</code> and <code>PythonBundle</code> easyblocks to add support to install dummy Python packages (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4063">#4063</a>)</li> 15325<li>enhance custom easyblocks for SCOTCH & MUMPS to add <code>lfoss</code> toolchain support (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4069">#4069</a>)</li> 15326<li>add search paths to CUPTI in installations of nvidia-compilers with CUDA (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4085">#4085</a>)</li> 15327<li>enhance custom easyblock for Amber easyblock to support installing <code>pmemd</code> only (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4093">#4093</a>)</li> 15328<li>limit number of parallel compile jobs in PyTorch tests by setting <code>$MAX_JOBS</code> + add support for using Arm Compute Library (ACL) as dependency (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4096">#4096</a>)</li> 15329<li>be more patient when running CPLEX interactive installer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4103">#4103</a>)</li> 15330<li>add mapping to LAMMPS easyblock for <code>9.0a</code>, <code>10.0f</code> and <code>12.0f</code> CUDA compute capabilities (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4105">#4105</a>)</li> 15331</ul> 15332</li> 15333<li>updates:<ul> 15334<li>update Conda easyblock to take into account that in Conda 24.3 <code>--force</code> was renamed to <code>--yes</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3573">#3573</a>)</li> 15335<li>update CPLEX easyblock for CPLEX v22.1.2 (which doesn't include Python bindings anymore) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3909">#3909</a>)</li> 15336<li>update jaxlib easyblock to support LLVM as alternative to Clang for CUDA builds (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4101">#4101</a>)</li> 15337</ul> 15338</li> 15339</ul> 15340<p><strong>easyconfigs</strong></p> 15341<ul> 15342<li>add easyconfigs for update of (common) toolchains: <code>foss/2026.1</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25615">#25615</a>), <code>intel/2026.1</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25621">#25621</a>), <code>lfoss/2026.1</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25634">#25634</a>)</li> 15343<li>added example easyconfig files for 85 new software packages:<ul> 15344<li>ADIOS2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24194">#24194</a>), ADOL-C (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24357">#24357</a>), ArmComputeLibrary (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21309">#21309</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25566">#25566</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25670">#25670</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25671">#25671</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25672">#25672</a>), ASTER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25405">#25405</a>), BamQuery (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25650">#25650</a>), 15345CaDiCaL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25404">#25404</a>), CasADi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23463">#23463</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24453">#24453</a>), cascadia (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25299">#25299</a>), coremltools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25432">#25432</a>), cvc5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25404">#25404</a>), docopt.cpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23464">#23464</a>), DRAM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25635">#25635</a>), 15346EasyOCR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25604">#25604</a>), ekg-intervaltree (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24616">#24616</a>), Entwine (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25151">#25151</a>), Eww (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25143">#25143</a>), fastobo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25299">#25299</a>), fMRIPrep (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22732">#22732</a>), FSL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25383">#25383</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22914">#22914</a>), 15347giotto-tda (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24743">#24743</a>), git-lfs-s3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25397">#25397</a>), gnome-common (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25143">#25143</a>), hwdata (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), IDR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25168">#25168</a>), Ipopt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23462">#23462</a>), JPype (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19880">#19880</a>), 15348jupyter-bash-kernel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25464">#25464</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25521">#25521</a>), JupyterLab-NVdashboard (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25497">#25497</a>), kraken-OCR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25432">#25432</a>), k-Wave-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25149">#25149</a>), labwc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), 15349LDhelmet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25516">#25516</a>), LDpop (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25517">#25517</a>), libdbusmenu (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25143">#25143</a>), libdisplay-info (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), libevdev (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), libinput (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), libliftoff (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), 15350libsfdo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), mango-auth (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25575">#25575</a>), MDBM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19536">#19536</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20677">#20677</a>), mycotools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25212">#25212</a>), Nipype (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22732">#22732</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25400">#25400</a>), OpenLB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24334">#24334</a>), 15351OpenSim (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23464">#23464</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24676">#24676</a>), pb-CpG-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25462">#25462</a>), Polyscope (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23108">#23108</a>), PyCBC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25187">#25187</a>), pyNVML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25395">#25395</a>), pyrho (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25517">#25517</a>), pyteomics (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25299">#25299</a>), 15352pytest-forked (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25574">#25574</a>), python-bidi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25432">#25432</a>), pytmatrix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25502">#25502</a>), qibo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19843">#19843</a>), qibojit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19843">#19843</a>), ratarmount (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25555">#25555</a>), RGI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25480">#25480</a>), 15353s9s (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25559">#25559</a>), scikit-multimodallearn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25438">#25438</a>), SCONE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23464">#23464</a>), seatd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>), Sentaurus (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24699">#24699</a>), sentieon-genomics (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25119">#25119</a>), 15354SHAPEIT5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25515">#25515</a>), Simbody (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23464">#23464</a>), SOD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25322">#25322</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25684">#25684</a>), SPAM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25156">#25156</a>), SPH-EXA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25606">#25606</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25584">#25584</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25585">#25585</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25693">#25693</a>), STREAmS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25219">#25219</a>), 15355SvABA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25561">#25561</a>), SWASH (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25638">#25638</a>), sway (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25412">#25412</a>), SymFPU (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25404">#25404</a>), SYSMOIC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25298">#25298</a>), table2asn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25039">#25039</a>), tangram-sc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25622">#25622</a>), 15356TIDDIT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25583">#25583</a>), tllist (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25412">#25412</a>), treePL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24357">#24357</a>), trove-classifiers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25526">#25526</a>), VCF2Dis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25460">#25460</a>), verifyBamID (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25164">#25164</a>), xraylib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25491">#25491</a>), 15357Xwayland (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25123">#25123</a>)</li> 15358</ul> 15359</li> 15360<li>
15360added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 15361<li>Alfred 0.5.3, ASAP3 3.13.11, AOCL-BLAS 5.2, BEDOPS 2.4.42, bin2cell 0.3.4, Braindecode 1.2.0, bx-python 0.14.0, Cantera 3.2.0, 15362CapnProto 1.4.0, Cassiopeia 2.1.0-2025-10-9, CellRank 2.0.7, CellTypist 1.7.1, Clarabel.rs 0.11.1, ColabFold 1.5.5, COBRApy 0.30.0, 15363code-cli 1.108.1, code-server 4.108.1, COLMAP 3.13.0, CPLEX 22.1.2, cramjam 2.11.0, CSBDeep 0.8.2, CUDA 13.1.1 + 13.2.0, CUTLASS 4.3.5, 15364CVXPY 1.5.1, cython-cmake 0.2.2, Dalton 2026, DFT-D4 4.0.2, DIA-NN 2.3.2, DIRAC 26.0, dm-haiku 0.0.16, DMTCP 4.1.0, Emacs 30.2, 15365Faiss 1.13.2, fastp 1.1.0, fastparquet 2026.3.0, Filtlong 0.3.1, fio 3.41, FlexiBLAS 3.5.0, GD 2.77, gemmi 0.7.4, gflags 2.3.0, 15366HF-Datasets 4.5.0, hwloc 2.13.0, igraph 1.0.0, inferCNV 1.22.0, infercnvpy 0.6.1, jax 0.8.1, json-fortran 9.2.1, jq 1.8.1, libdap 3.21.1, 15367libfabric 2.5.0, libgpg-error 1.59, libpciaccess 0.19, libxc 7.0.0, libzip 1.11.4, llama.cpp b8354, lpsolve 5.5.2.14, LLVM 21.1.8, 15368MAQAO 2026.0.0-b, MATLAB 2025b-r2, MEME 5.5.9, Meson 1.10.2, Miller 6.17.0, msprime 1.4.1, multicharge 0.5.0, nauty 2.9.3, ncdu 1.22, 15369NCO 5.3.6, NiBabel 5.3.3, Ninja 1.13.2, nvtop 3.3.2, Octave 11.1.0, ollama 0.15.6, OpenBLAS 0.3.32, OpenMolcas 26.02, OrfM 1.4.0, 15370panaroo 1.6.0, Parsnp 2.1.5, PMIx 6.1.0. pod5-file-format 0.3.23, PRANK 251117, prokka 1.15.6, PRRTE 4.1.0, psutil 7.2.1, 15371PyCharm 2025.3.2.1, pybedtools 0.12.0, pybind11-stubgen 2.5.5, pycocotools 2.0.11, pydot 4.0.1, pyfaidx 0.9.0.3, PyFrag 1.0.0, 15372Pylint 3.3.9, Pyomo 6.10.0, pyperf 2.10.0, PyQtGraph 0.14.0, PyRosetta 4.r420, pySCENIC 0.12.1-20250109, pyseer 1.4.0, python-docx 1.2.0, 15373python-igraph 1.0.0, python-irodsclient 3.2.0, python-isal 1.8.0, python-libsbml 5.21.0, QtPy 2.4.3, 15374QuantumESPRESSO 7.5 w/ NVHPC 25.3 + CUDA 12.8.0, QUAST 5.3.0, ReFrame 4.9.1, rioxarray 0.21.0, robin-map 1.4.1, rpy2 3.6.4, scib 1.1.7, 15375scib-metrics 0.5.9, scikit-bio 0.7.1.post1, scikit-misc 0.5.1, scVelo 0.3.4, SeqAn 2.5.2, Seurat 5.4.0, snpEff 5.4c, Spack 1.1.1, 15376Squidpy 1.6.6, STAR-CCM+ 2602, stardist 0.9.1, SUNDIALS 7.6.0, Transformers 5.0.0, TurboVNC 3.3, UCC 1.7.0, UCX 1.20.0, Umpire 2025.12.0, 15377unixODBC 2.3.14, vsc-mympirun 5.5.1, VTune 2025.9.0, waLBerla 7.2, wandb 0.25.1, XeniumRanger 4.0.0, XML-Compile 1.64, Z3 4.15.4</li> 15378</ul> 15379</li> 15380<li>various bug fixes, including:<ul> 15381<li>avoid test failures for netCDF with <code>iimpi</code> toolchain, by setting <code>$I_MPI_HYDRA_BOOTSTRAP</code> to <code>ssh</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24735">#24735</a>)</li> 15382<li>fix mpirun patch for CRYSTAL 23.1.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25023">#25023</a>)</li> 15383<li>don't specify KIND for search paths in RUSTFLAGS in easyconfig for librsvg 2.61.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25332">#25332</a>)</li> 15384<li>make sure that ReFrame script has executable permissions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25338">#25338</a>)</li> 15385<li>add (post-install) patch for libtool v2.5.4 to improve support for LLVM flang (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25345">#25345</a>)</li> 15386<li>make libdisplay-info proper dependency for Xfce 4.20, add Wayland build dependency to VTE 0.82.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25365">#25365</a>)</li> 15387<li>add patch to UCX v1.18.0 and v1.19.0 to fix build failure with glibc v2.43 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25399">#25399</a>)</li> 15388<li>fix wrong source URL for python-parasail 1.3.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25403">#25403</a>)</li> 15389<li>fix source URL in git-annex easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25426">#25426</a>)</li> 15390<li>make Python, Meson, Ninja, and CMake build dependencies in easyconfigs for btllib 1.7.0 + 1.7.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25456">#25456</a>)</li> 15391<li>add back patch to fix hardcoded paths in setup.py for libxml2-python 2.12.10 + 2.14.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25465">#25465</a>)</li> 15392<li>use <code>-fno-tree-ter</code> compiler option when building libaom and SVT-AV1 on Arm with GCC 14.2.0, to work around bug causing segmentation fault (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25466">#25466</a>)</li> 15393<li>fix extension name for SMC++-1.15.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25468">#25468</a>)</li> 15394<li>
15394fix pyiron 0.5.2-20251013 extension version (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25473">#25473</a>)</li> 15395<li>use <code>NETCDF_ENABLE_DAP_REMOTE_TESTS</code> instead of <code>ENABLE_DAP_REMOTE_TESTS</code> and prevent use of <code>srun</code> in netCDF 4.9.3 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25490">#25490</a>)</li> 15396<li>add additional patches for PyTorch 2.9.1 to fix problems with the tests + exclude <code>inductor/test_flex*</code> tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25492">#25492</a>)</li> 15397<li>add patch to reduce the number of used resources in scipy 1.16.1 test <code>test_import_cycles</code> + patch to disable failing test on RISC-V (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25495">#25495</a>)</li> 15398<li>don't depend on ScaFaCos in LAMMPS easyconfigs when building on Arm + add patch to disable failing test on Arm due to bug in kim-api (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25133">#25133</a>)</li> 15399<li>add patch to Mesa in 2025a and OpenGL in 2025b to fix build for glibc v2.43 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25505">#25505</a>)</li> 15400<li>add patch for DMTCP 4.0.0 to fix build on RHEL8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25530">#25530</a>)</li> 15401<li>add patch to fix using wrong OpenMP library in easyconfigs for PyTorch 2.3.0 + 2.6.0 + 2.7.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25541">#25541</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25542">#25542</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25543">#25543</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25544">#25544</a>)</li> 15402<li>add SQLite dependency to NSS 3.114 to avoid internal SQLite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25551">#25551</a>)</li> 15403<li>add pkconf build dependency to cargo-c 0.10.13 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25571">#25571</a>)</li> 15404<li>remove PyTorch (and CUDA) dependency for CellRank 2.0.2, since they're not actually needed (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25580">#25580</a>)</li> 15405<li>add patch to LAMMPS v22Jul2025 to fix failing test + make sure patches of CUDA version are consistent (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25593">#25593</a>)</li> 15406<li>correct homepage for Underworld 2.16.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25594">#25594</a>)</li> 15407<li>use gompi/2023b toolchain instead of gompi/2024a for ORCA v6.1.1 w/ avx2, since it doesn't work correctly on top of OpenMPI 5.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25607">#25607</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25691">#25691</a>)</li> 15408<li>add patch to pybind11 v3.0.0 to fix build failure with CUDA nvcc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25620">#25620</a>)</li> 15409<li>fix VESTA-gui by adding installation dir to <code>$LD_LIBRARY_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25633">#25633</a>)</li> 15410<li>add patch to fix implicit function declaration in OpenMPI 4.1.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25663">#25663</a>)</li> 15411<li>fix locale-dependent test failure in RCall 0.13.17 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25666">#25666</a>)</li> 15412<li>move netCDF to last dependency in <code>2022*</code> GDAL easyconfigs, to make sure correct <code>netcdf.h</code> is picked up (not the one included in HDF dependency) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25683">#25683</a>)</li> 15413<li>fix reported version for kiwisolver 1.4.5 extension in matplotlib easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25685">#25685</a>)</li> 15414<li>avoid requiring <code>glibc-static</code> for BEDOPS 2.4.41 by removing <code>-static</code> flag from <code>Makefile</code>s (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25686">#25686</a>)</li> 15415<li>
15415add alternate checksum for VSURF extension in R-bundle-CRAN 2023.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25687">#25687</a>)</li> 15416<li>fix homepage + description in lfoss easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25695">#25695</a>)</li> 15417</ul> 15418</li> 15419<li>minor enhancements, including:<ul> 15420<li>add jupyter-bash-kernel v0.9.3 dependency to recent Jupyter-bundle versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25464">#25464</a>)</li> 15421<li>add patch to support <code>$TRITON_HOME</code> In Triton 3.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25557">#25557</a>) and Triton 2.3.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25582">#25582</a>)</li> 15422<li>enable Wayland support in Qt6 6.9.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25611">#25611</a>)</li> 15423<li>also build serial library in recent easyconfigs for Wannier90 3.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25660">#25660</a>)</li> 15424</ul> 15425</li> 15426<li>enhancements and fixes for test suite:<ul> 15427<li>improve reported errors in easyconfigs test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23969">#23969</a>)</li> 15428<li>add GCC/GCCcore 15.2 based toolchains as 2026.1 to tagbot workflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24990">#24990</a>)</li> 15429<li>fix binutils build dependency test for BinariesTarball (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25305">#25305</a>)</li> 15430<li>reduce combinations for CI unit tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25413">#25413</a>)</li> 15431<li>add tagbot mapping for <code>2026.1</code> and add LLVM to toolchain map tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25639">#25639</a>)</li> 15432<li>install <code>graphviz</code> in CI workflow for easyconfigs test suite, required for <code>test_dep_graph</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25696">#25696</a>)</li> 15433<li>disable <code>test_dep_graph</code> for now, since it takes excessively long (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25699">#25699</a>)</li> 15434</ul> 15435</li> 15436<li>other changes:<ul> 15437<li>remove default PyPI URL from <code>PythonBundle</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21291">#21291</a>)</li> 15438<li>disable building BOLT in LLVM 20.1.x on RISC-V (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25218">#25218</a>)</li> 15439<li>bump OpenBLAS to v0.3.32 as dependency for FlexiBLAS 3.5.0 w/ GCC 15.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25603">#25603</a>)</li> 15440</ul> 15441</li> 15442<li>archiving of old easyconfigs:<ul> 15443<li>archive easyconfigs from 2021b generation (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25697">#25697</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25698">#25698</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25716">#25716</a>)</li> 15444</ul> 15445</li> 15446</ul> 15447<h2 id="release_notes_eb521">EasyBuild v5.2.1 (20 Feb 2026)<a class="headerlink" href="#release_notes_eb521" title="Permanent link">¶</a></h2> 15448<p>bugfix/update release</p> 15449<p><strong>framework</strong></p> 15450<ul> 15451<li>bug fixes:<ul> 15452<li>ignore stderr for <code>rocm-smi</code> during test report creation (<a href="https://github.com/easybuilders/easybuild-framework/pull/5087">#5087</a>)</li> 15453<li>use initially stored environment to determine GPU info for test reports (<a href="https://github.com/easybuilders/easybuild-framework/pull/5088">#5088</a>)</li> 15454<li>add back <code>easybuild.toolchains.compiler.nvhpc</code> as deprecated toolchain compiler (<a href="https://github.com/easybuilders/easybuild-framework/pull/5089">#5089</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5096">#5096</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5105">#5105</a>)</li> 15455<li>properly handle toolchains defining <code>openmp</code> toolchain opt as <code>dict</code> (relevant for NVHPC toolchain) (<a href="https://github.com/easybuilders/easybuild-framework/pull/5093">#5093</a>)</li> 15456<li>enhance <code>get_source_tarball_from_git</code> to ensure that Git repo URL does not contain double slashes due to trailing slash in source URL (<a href="https://github.com/easybuilders/easybuild-framework/pull/5097">#5097</a>)</li> 15457<li>fix crash with <code>MarkupError</code> in Rich when showing failed shell command containing special characters (<a href="https://github.com/easybuilders/easybuild-framework/pull/5098">#5098</a>)</li> 15458<li>fix sub-toolchains of NVHPC and NVHPCToolchain and load each one where appropriate (<a href="https://github.com/easybuilders/easybuild-framework/pull/5103">#5103</a>)</li> 15459<li>don't require installation prefix for toolchain dependencies that are an external module (<a href="https://github.com/easybuilders/easybuild-framework/pull/5108">#5108</a>)</li> 15460</ul> 15461</li> 15462<li>enhancements:<ul> 15463<li>
15463add support for injecting checksums for Rust crates (<a href="https://github.com/easybuilders/easybuild-framework/pull/4661">#4661</a>)</li> 15464<li>include full shell command that failed in raised error (<a href="https://github.com/easybuilders/easybuild-framework/pull/5074">#5074</a>)</li> 15465<li>improve error reporting for failures in <code>eb --merge-pr</code> and similar (<a href="https://github.com/easybuilders/easybuild-framework/pull/5076">#5076</a>)</li> 15466<li>add LLVM toolchains using ParaStationMPI (<a href="https://github.com/easybuilders/easybuild-framework/pull/5094">#5094</a>)</li> 15467</ul> 15468</li> 15469<li>enhancements and fixes for test suite:<ul> 15470<li>ignore output lines with skipped tests in check for unexpected output of test suite (<a href="https://github.com/easybuilders/easybuild-framework/pull/5082">#5082</a>)</li> 15471<li>import specific submodule <code>pygraph.classes.digraph</code> in <code>test_dep_graph*</code> so we can skip the test if import fails with setuptools >= 82.0.0 (<a href="https://github.com/easybuilders/easybuild-framework/pull/5111">#5111</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5116">#5116</a>)</li> 15472</ul> 15473</li> 15474<li>other changes:<ul> 15475<li>extend list of easyconfig parameters that extensions should not inherit: <code>sources</code>, <code>patches</code>, <code>checksums</code>, <code>skipsteps</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5075">#5075</a>)</li> 15476<li>deprecate <code>print_error</code> function and replace it with new <code>print_error_and_exit</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/5092">#5092</a>)</li> 15477<li>replace use of <code>datetime.utcfromtimestamp</code> which is deprecated since Python 3.12 (<a href="https://github.com/easybuilders/easybuild-framework/pull/5091">#5091</a>)</li> 15478</ul> 15479</li> 15480</ul> 15481<p><strong>easyblocks</strong></p> 15482<ul> 15483<li>new easyblocks:<ul> 15484<li>software-specific easyblocks for AOCL-LAPACK (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4042">#4042</a>) and ROCm-LLVM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3823">#3823</a>)</li> 15485</ul> 15486</li> 15487<li>bug fixes:<ul> 15488<li>avoid incorrect symlinks for NVHPC by force-setting selected CUDA version in install script (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4024">#4024</a>)</li> 15489<li>fix typo in description for <code>build_env_vars</code> easyconfig parameter of <code>BuildEnv</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4030">#4030</a>)</li> 15490<li>disable FlexiBLAS backends that are in the list of filtered dependencies (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4031">#4031</a>)</li> 15491<li>transfer dependencies in Bundle easyblock and fix sanity check for module only (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4037">#4037</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4057">#4057</a>)</li> 15492<li>fix missed sanity check in custom easyblock for GCC (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4041">#4041</a>)</li> 15493<li>set <code>$Python3_ROOT_DIR</code> in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4043">#4043</a>)</li> 15494<li>ensure AmberTools will find the correct Python library and include dir (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4045">#4045</a>)</li> 15495<li>fix setting Python variables in TensorRT easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4046">#4046</a>)</li> 15496<li>fix WIEN2k easyblock for newer toolchains (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4048">#4048</a>)</li> 15497<li>fix error reporting for number of checksums vs number of sources + patches in custom easyblock for Python (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4055">#4055</a>)</li> 15498<li>fix call to parent for static method <code>src_parameter_names</code> in <code>Cargo</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4062">#4062</a>)</li> 15499<li>fix limiting of threads for OpenBLAS tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4067">#4067</a>)</li> 15500</ul> 15501</li> 15502<li>enhancements:<ul> 15503<li>add support for detecting external MAGMA library for ELSI (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3536">#3536</a>)</li> 15504<li>create lockfile for Cargo package if missing (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3995">#3995</a>)</li> 15505<li>explictly call <code>PythonPackage</code> and <code>Cargo</code> configure step in <code>CargoPythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3996">#3996</a>)</li> 15506<li>allow oversubscription in sanity check for OpenFOAM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4019">
15506#4019</a>)</li> 15507<li>allow to enable more components in Extrae (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4027">#4027</a>)</li> 15508<li>add fallback architecture for zen5 to BLIS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4034">#4034</a>)</li> 15509<li>add LLVM support to ParaStationMPI easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4047">#4047</a>)</li> 15510<li>allow easier reuse of <code>compose_install_command</code> of <code>PythonPackage</code>, and add <code>%(python)s</code> template and default Python libdir in sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4050">#4050</a>) </li> 15511<li>update ELPA easyblock to make it aware of NVHPC toolchain compiler (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4051">#4051</a>)</li> 15512<li>add option to allow missing or additional detected PyTorch test suites (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4052">#4052</a>)</li> 15513<li>update QuantumESPRESSO easyblock - add pretestopts + GPU test cmd (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4053">#4053</a>)</li> 15514<li>enhance <code>PythonPackage</code> and <code>PythonBundle</code> to support updating module footers for click autocompletion for specified binaries (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4056">#4056</a>)</li> 15515</ul> 15516</li> 15517<li>updates:<ul> 15518<li>update custom easyblock for FDTD-Solutions so it can be used to install Lumerical-FDTD (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3362">#3362</a>)</li> 15519<li>changes to LLVM easyblock required for LLVM 21 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3902">#3902</a>)</li> 15520<li>update custom easyblock for Gurobi for version 13 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4060">#4060</a>)</li> 15521</ul> 15522</li> 15523<li>other changes:<ul> 15524<li>make <code>CargoPythonPackage</code> the default class for extensions/components of <code>CargoPythonBundle</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3993">#3993</a>)</li> 15525</ul> 15526</li> 15527<li>code cleanup: <ul> 15528<li>enable flake8-comprehension code style check and fix issues (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3989">#3989</a>)</li> 15529</ul> 15530</li> 15531</ul> 15532<p><strong>easyconfigs</strong></p> 15533<ul> 15534<li>added example easyconfig files for 65 new software packages:<ul> 15535<li>abTEM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24989">#24989</a>), AdaptiveCpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24894">#24894</a>), aiida-pseudo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20459">#20459</a>), aiida-quantumespresso (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20459">#20459</a>), AITW-microstructures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25220">#25220</a>), 15536 AITW-stiffness (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25220">#25220</a>), AITW-viscosity (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25220">#25220</a>), AOCL-LAPACK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25048">#25048</a>), BoTorch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24916">#24916</a>), Caliper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24985">#24985</a>), cargo-pgo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25205">#25205</a>), 15537 cfunits (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24953">#24953</a>), CGNS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24987">#24987</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25283">#25283</a>), CONCORD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25216">#25216</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25254">#25254</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25290">#25290</a>), davix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25040">#25040</a>), Dimemas (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24983">#24983</a>), Dynare (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19857">#19857</a>), 15538 earthkit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24954">#24954</a>), EPA-ng (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25163">#25163</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25154">#25154</a>), FAAD2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25020">#25020</a>), GPTL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25110">#25110</a>), GST-libav (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24992">#24992</a>), GST-plugins-good (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24950">#24950</a>), 15539 gtkmm3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25062">#25062</a>), gtkmm4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25057">#25057</a>), GtkSourceView4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24895">#24895</a>), hatch-nodejs-build (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25256">#25256</a>), HTTPX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25289">#25289</a>), Jena (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25067">#25067</a>), 15540 jsonschema (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20459">#20459</a>), jupyterview (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25256">#25256</a>), libs3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19541">#19541</a>), Lumerical-FDTD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20828">#20828</a>), McStas (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22833">#22833</a>), MedMNIST (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24006">#24006</a>), 15541 MERINGUE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25199">#25199</a>), metakernel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25155">#25155</a>), MinCED (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25037">#25037</a>), mpreal (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25184">#25184</a>), mypy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25236">#25236</a>), octave-kernel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25155">#25155</a>), OGGM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24805">#24805</a>), 15542 ONNX-IR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24965">#24965</a>), ONNX-Script (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24965">#24965</a>), OpenCoarrays (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24980">#24980</a>), OpenH264 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25029">#25029</a>), pangomm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25049">#25049</a>), pyEDFlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24934">#24934</a>), 15543 pylibxc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25084">#25084</a>), pyprep (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24837">#24837</a>), PyPSA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24782">#24782</a>), pyshtools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24952">#24952</a>), RELION (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19678">#19678</a>), ROCm-LLVM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23304">#23304</a>), SAW (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24904">#24904</a>),
15544 SKA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25152">#25152</a>), SpaceBF (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25199">#25199</a>), SpaGene (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25197">#25197</a>), torcheval (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24785">#24785</a>), uncrustify (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25211">#25211</a>), Underworld (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23365">#23365</a>), VisCello (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25216">#25216</a>), 15545 VTE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24895">#24895</a>), Xfce (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24369">#24369</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25261">#25261</a>), xmlschema (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20459">#20459</a>)</li> 15546</ul> 15547</li> 15548<li>added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 15549<li>accelerate 1.11.0, aiida-core 2.7.2, aiida-shell 0.8.2, amdsmi 26.2.1, AMRFinderPlus 4.0.23, any2fasta 0.8.1, AOCC 5.1.0, 15550 AOCL-BLAS 5.2, bakta 1.12.0, Bismark 0.25.1, bitsandbytes 0.46.1, black 26.1.0, BLIS 2.0, bwa-mem2 2.3, cairomm 1.19.0, 15551 casacore 3.7.1, clearml 2.0.2, CMake 4.2.1, CNVkit 0.9.12, CubeGUI 4.9.1, cURL 8.17.0, DeltaLake 1.2.1, DensPart 20251124, 15552 Dice 20250615, DiffBind 3.20.0, dlb 3.6.0, dorado 1.1.1, ELPA 2025.06.002, expat 2.7.3, Extrae 5.0.0, evince 48.1, 15553 FastQ_Screen 0.16.0, FDS 6.10.1, FlexiBLAS 3.5.0, FPM 1.17.0, GATE 9.4.1, gbasis 0.1.0, GeoDict 2026-2-1.SP1, gettext 0.26, 15554 gh 2.86.0, GHC 9.12.3, git 2.52.0, Go 1.25.7, GPyTorch 1.14.3, grpcio 1.76.0, gspell 1.14.2, Gubbins 3.4.3, Gurobi 13.0.1, 15555 huggingface-hub 1.2.4, imagecodecs 2024.12.30, InterProScan 5.77-108.0, kineto 20250715, libarchive 3.8.5, libreadline 8.3, 15556 libsigc++ 3.8.0, libunistring 1.4.1, libxml2 2.15.1, libxml2-python 2.14.3, Lightning 2.5.6, matlab-proxy 0.30.1, Miller 6.16.0, 15557 MLflow 2.22.4, MOPAC 23.2.2, NanoCaller 3.6.2, napari 0.6.6, ncurses 6.6, nodejs 24.12.0, nvidia-compilers 25.9, NVHPC 25.9, 15558 NVPL 25.11, Octave 10.3.0, ONNX-Runtime 1.23.2, OpenBLAS 0.3.31, OpenMM 8.4.0, packmol 21.2.0, pdsh 2.36, Perl 5.42.0, 15559 pkgconf 2.5.1, PLAMS 2025.105, plumpy 0.25.0, PyAMG 5.3.0, pybedtools 0.12.0, pyFFTW 0.15.1, PyHMMER 0.12.0, PyOpenGL 3.1.10, 15560 pyro-ppl 1.9.1, pytest-subtests 0.15.0, Python 3.14.2, python-xxhash 3.6.0, PyTorch 2.7.1 + 2.9.1, PyTorch-Lightning 2.5.2 + 2.5.6, 15561 qc-grid v0.0.9, Qtconsole 5.7.0, quarto 1.8.26, rasterio 1.5.0, Rgurobi 12.0.3, RStudio-Server 2025.09.2+418, rpy2 3.6.4, 15562 Safetensors 0.7.0, Score-P 9.4, scvi-tools 1.4.1, SeqKit 2.12.0, Siesta 5.4.2, SKA2 0.5.1, SMV 6.10.6, SQLite 3.51.1, 15563 SymEngine 0.14.0, tblis 1.3.0, Tcl 9.0.3, tensorboard 2.20.0, tiktoken 0.12.0, timm 1.0.20, tokenizers 0.22.2, Transformers 4.57.1, 15564 unittest-xml-reporting 3.2.0, Valgrind 3.26.0, ViennaRNA 2.7.2, VisPy 0.15.2, WCSLIB 8.5, zlib-ng 2.3.2</li> 15565</ul> 15566</li> 15567<li>various bug fixes, including:<ul> 15568<li>use <code>PORTABLE=ON</code> configure option for IDG 1.2.0 to set <code>-march=rv64gc</code> for RISCV to avoid using <code>-march=native</code> (which does not work) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22279">#22279</a>)</li> 15569<li>fix failing build for tensorstore 0.1.72 when using RPATH by passing <code>$TMPDIR</code> from host into Bazel sandbox (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23139">#23139</a>)</li> 15570<li>consistently use patch to correctly detect Slurm job environment for jax v0.6.2 and v0.7.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24447">#24447</a>)</li> 15571<li>add patch to fix <code>parfor</code> buildmap in numba v0.60.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24946">#24946</a>)</li> 15572<li>avoid librsvg build writing to $HOME (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24995">#24995</a>)</li> 15573<li>use C interface for google-crc32c in zarr v3.1.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25001">#25001</a>)</li> 15574<li>
15574add tcsh dependency to NCL 6.6.2 to avoid using system csh (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25027">#25027</a>)</li> 15575<li>add patch for RISC-V build issue to libfabric 2.0.0 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25035">#25035</a>)</li> 15576<li>fix value for <code>$HDF5_DIR</code> in easyconfigs for HDF5 1.14.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25041">#25041</a>)</li> 15577<li>add patches to hwloc v2.11.2 + v2.12.1 to better handle ACPI CPCC, fixes performance regression in MPI startup time (<code>MPI_Init</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25043">#25043</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25063">#25063</a>)</li> 15578<li>patch numpy so that f2py processes object files (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25082">#25082</a>)</li> 15579<li>add patch to Python 3.13.5 + 3.14.2 easyconfigs to fix <code>ctypes</code> when <code>$LD_LIBRARY_PATH</code> is not being set (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25106">#25106</a>)</li> 15580<li>use <code>-DPYTHON_LIBRARY</code> and <code>-DPYTHON_INCLUDE_DIR</code> in RDKit easyconfigs to fix deprecated <code>find_package(PythonLibs)</code> potentially finding wrong Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25109">#25109</a>)</li> 15581<li>add patch to use <code>https</code> instead of <code>http</code> to fix failing MDTraj tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25111">#25111</a>)</li> 15582<li>set <code>$ACLOCAL_PATH</code> in easyconfigs for gettext 0.25 + 0.26 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25136">#25136</a>)</li> 15583<li>add missing dependencies for PICRUSt2 2.6.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25139">#25139</a>)</li> 15584<li>update jupyter-core patch for recent jupyter-server versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25140">#25140</a>)</li> 15585<li>add missing <code>/</code> after <code>%(start_dir)s</code> template in PICRUSt2 2.5.2 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25141">#25141</a>)</li> 15586<li>add missing dependencies to easyconfig for PETSc 3.24.0: HDF5, netCDF, PnetCDF, hwloc, zlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25158">#25158</a>)</li> 15587<li>add patch for XZ 5.8.1 to fix "<code>Failed to enable the sandbox</code>" on certain RHEL9 kernel versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25178">#25178</a>)</li> 15588<li>fix shared-mime-info for systems with xmlto (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25182">#25182</a>)</li> 15589<li>remove unused configopt due to repetition in <code>Graphviz</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25189">#25189</a>)</li> 15590<li>add patch for AmberTools 23.6 to fix infinite loop of for <code>mdgx</code> on aarch64 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25193">#25193</a>)</li> 15591<li>add smoppix to R-bundle-Bioconductor-3.22 + bump <code>reactome.db</code> to 1.95.0 in easyconfig for R-bundle-Bioconductor 3.22 since 1.94.0 has disappeared (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25195">#25195</a>)</li> 15592<li>add patches to fix compilation of OpenBabel 3.1.1 on non-x86 targets (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25222">#25222</a>)</li> 15593<li>backport AVX512 SH-broadcast support to Clang 18 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25233">#25233</a>)</li> 15594<li>add patch to fix build of OpenBLAS 0.3.23 + 0.3.24 on AMD Turin (Zen 5) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25255">#25255</a>)</li> 15595<li>make <code>libiconv</code> a runtime dependency of (recent) <code>libarchive</code> versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25259">
15595#25259</a>)</li> 15596<li>add googletest build dependency to c-ares v1.34.5 and enable tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25260">#25260</a>)</li> 15597<li>fix incorrect homepage in existing JupyterLab-git easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25265">#25265</a>)</li> 15598<li>add missing fontconfig runtime dependency for Pango 1.57.0 + patch to effectively make fontconfig a link dependency of libpangocairo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25285">#25285</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25306">#25306</a>)</li> 15599<li>bump <code>RnBeads.hg38</code> extension from 1.42.0 to 1.42.1 in easyconfig for R-bundle-Bioconductor v3.22 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25303">#25303</a>)</li> 15600<li>give dependencies provided via EasyBuld priority over sysroot for Rust package in easyconfig for librsvg v2.61.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25317">#25317</a>)</li> 15601<li>fix potential CMake race condition in built files for Clang 18.1.8 + LLVM 18.1.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25319">#25319</a>)</li> 15602<li>add patch to work around failing test in <code>LWP::Protocol::https</code> extension due to problem with SSL certificate for <code>https://example.com</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25333">#25333</a>)</li> 15603</ul> 15604</li> 15605<li>minor enhancements, including:<ul> 15606<li>enable AV1, VP8, webp in older FFmpegs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24901">#24901</a>)</li> 15607<li>update <code>$GST_PLUGIN_PATH</code> for GST-plugins-base (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24927">#24927</a>) and GST-plugins-bad (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24928">#24928</a>)</li> 15608<li>add support for multiple paths for GDK pixbuf loaders (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24991">#24991</a>)</li> 15609<li>add KaHIP dependency for FEniCS-DOLFINx 0.9.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25004">#25004</a>)</li> 15610<li>enable yet more codecs in GST-plugins-bad 1.26.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25020">#25020</a>)</li> 15611<li>add dRiftDM v0.3.1 to R-bundle-CRAN 2025.11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25024">#25024</a>)</li> 15612<li>add xcb-error-utils component to X11 20250608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25026">#25026</a>)</li> 15613<li>enable all the things in GST-plugins-base (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25064">#25064</a>)</li> 15614<li>add kableExtra to R-bundle-CRAN 2024.06 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25072">#25072</a>)</li> 15615<li>add additional source URL for <code>pkgconf</code> in 2022b to 2025b (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25104">#25104</a>)</li> 15616<li>add GPTL support for ParallelIO 2.5.10 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25110">#25110</a>)</li> 15617<li>add EPA-ng-0.3.8 dependency to PICRUSt2-2.6.1-foss-2023a easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25163">#25163</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25154">#25154</a>)</li> 15618<li>add additional extensions to to R-bundle-CRAN 2025.10 and 2025.11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25179">#25179</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25181">#25181</a>)</li> 15619<li>enable static library in inih (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25185">#25185</a>)</li> 15620<li>add smoppix extension to R-bundle-Bioconductor v3.22 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25195">#25195</a>)</li> 15621<li>add dash to <code>mavx2</code> optarch specification for OpenBabel 3.1.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25196">#25196</a>)</li> 15622<li>use <code>click_autocomplete_bins</code> in aiida-core easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25198">#25198</a>)</li> 15623<li>fix warnings with <code>-O3</code> in recent jax easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25207">#25207</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25208">#25208</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25210">#25210</a>)</li> 15624<li>check for static libraries in elfutils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25209">#25209</a>)</li> 15625<li>
15625add missing fontconfig runtime dependency for all supported Pango versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25286">#25286</a>)</li> 15626</ul> 15627</li> 15628<li>other changes:<ul> 15629<li>use flit_core build dependency instead of license patch in easyconfig for typing-extensions 4.14.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23307">#23307</a>)</li> 15630<li>fix failing build for tensorstore 0.1.72 when using RPATH by passing <code>$TMPDIR</code> from host into Bazel sandbox (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24896">#24896</a>)</li> 15631<li>add versionsuffix for GENESPACE 1.2.3 that depends on OrthoFinder 2.5.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24973">#24973</a>)</li> 15632<li>use zlib v2.3.2 (zlib-ng configured with <code>--zlib-compat</code>) as dependency for binutils v2.45 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24999">#24999</a>)</li> 15633<li>set <code>$CONAN_USER_HOME</code> when installing CatBoost 1.2 and Qiskit 2.0.2 to avoid writing to <code>$HOME</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25016">#25016</a>)</li> 15634<li>set <code>$CARGO_HOME</code> for bcrypt extension in Python 3.10.8 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25017">#25017</a>)</li> 15635<li>remove (broken) easyconfigs for polars 0.15.6 + infercnvpy 0.4.2 w/ <code>foss/2022a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25066">#25066</a>)</li> 15636<li>rename <code>grid</code> 20220610 to <code>qc-grid</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25085">#25085</a>)</li> 15637<li>fix various easyconfigs not using <code>python -s</code> in sanity check commands (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25101">#25101</a>)</li> 15638<li>add patch to recent LAMMPS easyconfigs to ensure that system Python packages are used and not updated in Python virtual environment (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25127">#25127</a>)</li> 15639<li>update ignore target feature patch in Autoconf to upstream commit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25172">#25172</a>)</li> 15640<li>update ELPA 2025.06.001 to 2025.06.002 in easyconfigs for GPAW 25.7.0 and QuantunESPRESSO 7.5 using 2025b toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25201">#25201</a>)</li> 15641<li>add patch to skip <code>test_non_blocking_with_eager_init</code> in PyTorch 2.7.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25214">#25214</a>)</li> 15642<li>upgrade NCCL dependency from 2.26.6 to 2.27.7 in easyconfigs for CuPy 13.6.0, OSU-Micro-Benchmarks 7.5, UCC-CUDA 1.3.0 using a 2025a toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25249">#25249</a>)</li> 15643<li>move MultiQC down from foss to gfbf toolchain (where it belongs) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25270">#25270</a>)</li> 15644<li>separate HTTPX 0.28.1 into its own easyconfig, and use it as dependency for JupyterLab + PDM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25289">#25289</a>)</li> 15645<li>rename <code>huggingface_hub</code> to <code>huggingface-hub</code> (+ fix easyconfigs that depend on it) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25294">#25294</a>)</li> 15646</ul> 15647</li> 15648<li>archiving of old easyconfigs:<ul> 15649<li>removed archived easyconfigs using a toolchain from <code>2021*</code> era (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24944">#24944</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/25268">#25268</a>)<ul> 15650<li>this resulted in 113 fewer software projects being supported by EasyBuild</li> 15651</ul> 15652</li> 15653<li>archive SYSTEM level easyconfigs from before 2020-12-19 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24945">#24945</a>)</li> 15654</ul> 15655</li> 15656</ul> 15657<h2 id="release_notes_eb520">EasyBuild v5.2.0 (23 Dec 2025)<a class="headerlink" href="#release_notes_eb520" title="Permanent link">¶</a></h2> 15658<p>feature release</p> 15659<p><strong>framework</strong></p> 15660<ul> 15661<li>new features:<ul> 15662<li>
15662add support for NVHPC toolchain with nvidia-compilers, NVHPCX, NVBLAS, and NVScaLAPACK (<a href="https://github.com/easybuilders/easybuild-framework/pull/4927">#4927</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5073">#5073</a>)</li> 15663<li>add support for LLVM-based toolchains <code>lfoss</code> and <code>lmpflf</code> (+ subtoolchains <code>llvm-compilers</code>, <code>lfbf</code>, <code>lompi</code>, <code>lmpich</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4914">#4914</a>)</li> 15664</ul> 15665</li> 15666<li>various other enhancements, including:<ul> 15667<li>add support for <code>--disable-robot</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4781">#4781</a>)</li> 15668<li>make specifying <code>exts_defaultclass</code> optional (<a href="https://github.com/easybuilders/easybuild-framework/pull/4800">#4800</a>)</li> 15669<li>retry fetching source file for extensions from PyPI with alternative filename (with <code>-</code> replaced with <code>_</code> in extension name) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4943">#4943</a>)</li> 15670<li>handle <code>post_install_patches</code> in GitHub uploads (<a href="https://github.com/easybuilders/easybuild-framework/pull/5016">#5016</a>)</li> 15671<li>take into account alternative name <code>post_install_patches</code> when checking checksums (<a href="https://github.com/easybuilders/easybuild-framework/pull/5017">#5017</a>)</li> 15672<li>improve test report formatting (<a href="https://github.com/easybuilders/easybuild-framework/pull/5018">#5018</a>)</li> 15673<li>add <code>--keep-going</code> option to fail at the end not at first failing installation + use proper exit code as determined by <code>main</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/5022">#5022</a>)</li> 15674<li>add templates for source with just version numbers (like <code>VERSION_TAR_GZ</code> and <code>V_VERSION_TAR_GZ</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/5025">#5025</a>)</li> 15675<li>add templates for patch versions (<a href="https://github.com/easybuilders/easybuild-framework/pull/5028">#5028</a>)</li> 15676<li>add <code>search_path_vars_headers</code> and <code>search_path_vars_linker</code> properties to <code>Toolchain</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5031">#5031</a>)</li> 15677<li>print total runtime of all builds (<a href="https://github.com/easybuilders/easybuild-framework/pull/5032">#5032</a>)</li> 15678<li>unset <code>$PROMPT_COMMAND</code> in <code>cmd.sh</code> shell (<a href="https://github.com/easybuilders/easybuild-framework/pull/5034">#5034</a>)</li> 15679<li>add <code>runtime_only</code> options to <code>EasyConfig.dependency_names</code> method (<a href="https://github.com/easybuilders/easybuild-framework/pull/5044">#5044</a>)</li> 15680<li>remove superflous <code>module list</code> call in <code>ModulesTool.load</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5046">#5046</a>)</li> 15681<li>add backtrace to logged exception (<a href="https://github.com/easybuilders/easybuild-framework/pull/5047">#5047</a>)</li> 15682<li>add support for both <code>$VAR</code> and <code>${VAR}</code> variable formats in <code>modextravars</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5049">#5049</a>)</li> 15683<li>show more readable error message when uploading gist or posting comment failed (<a href="https://github.com/easybuilders/easybuild-framework/pull/5056">#5056</a>)</li> 15684<li>set <code>$___EASYBUILD___</code> environment variable to '<code>EasyBuild</code>' to indicate that you're in an EasyBuild session (<a href="https://github.com/easybuilders/easybuild-framework/pull/5058">#5058</a>)</li> 15685<li>vendor a copy of <code>tomli</code> in <code>easybuild.tools.tomllib</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5063">#5063</a>)</li> 15686<li>allow <code>f</code> suffix in CUDA compute capabilities (<a href="https://github.com/easybuilders/easybuild-framework/pull/5067">#5067</a>)</li> 15687<li>vendor copy of tomli-w 1.2.0, use it to implement <code>dump_toml</code> function in <code>easybuild.tools.filetools</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5071">#5071</a>)</li> 15688</ul> 15689</li> 15690<li>various bug fixes, including:<ul> 15691<li>pass correct <code>-march</code> option on RISC-V systems when <code>optarch</code> toolchain option is enabled (<a href="https://github.com/easybuilders/easybuild-framework/pull/5029">#5029</a>)</li> 15692<li>pass dependencies to <code>toolchain.prepare</code> when setting up build environment for extensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/5023">#5023</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5041">#5041</a>)</li> 15693<li>also pick up on toolchain components in <code>
15693Toolchain._add_dependency_variables</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5042">#5042</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5048">#5048</a>)</li> 15694<li>don't append empty component to <code>start_dir</code> in <code>EasyBlock.guess_start_dir</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5057">#5057</a>)</li> 15695</ul> 15696</li> 15697<li>enhancements and fixes for test suite:<ul> 15698<li>also with test Python 3.14 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4992">#4992</a>)</li> 15699<li>fix <code>test_gitrepo</code> in case global Git configuration is not in place (<a href="https://github.com/easybuilders/easybuild-framework/pull/5013">#5013</a>)</li> 15700<li>introduce <code>saved_env</code> context manager for restoring environment in tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/5015">#5015</a>)</li> 15701<li>add decorator to ignore PR test failures due to rate limit (<a href="https://github.com/easybuilders/easybuild-framework/pull/5019">#5019</a>)</li> 15702<li>also run tests with Lmod 9.0 (<a href="https://github.com/easybuilders/easybuild-framework/pull/5026">#5026</a>)</li> 15703<li>enable flake8-comprehension code style check and fix issues (<a href="https://github.com/easybuilders/easybuild-framework/pull/5043">#5043</a>)</li> 15704<li>disable trace output by default in tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/5053">#5053</a>)</li> 15705<li>add back CI for Python 3.6 by using <code>pyenv</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5064">#5064</a>)</li> 15706<li>fix <code>test_github_det_commit_status</code> by using more recent commits (<a href="https://github.com/easybuilders/easybuild-framework/pull/5066">#5066</a>)</li> 15707<li>fix ignoring of URLError in <code>test_copy_ec_from_commit</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5077">#5077</a>)</li> 15708</ul> 15709</li> 15710<li>other changes:<ul> 15711<li>deprecate support for running EasyBuild with Python < 3.9 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4966">#4966</a>)</li> 15712<li>make command environment of shell commands more discoverable in the log (<a href="https://github.com/easybuilders/easybuild-framework/pull/4999">#4999</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5078">#5078</a>)</li> 15713<li>don't show command string again when showing in which folder it runs (<a href="https://github.com/easybuilders/easybuild-framework/pull/5003">#5003</a>)</li> 15714<li>remove escaping when converting <code>EasyBuildError</code> to a string (<a href="https://github.com/easybuilders/easybuild-framework/pull/5009">#5009</a>)</li> 15715<li>add example hook for updating OpenSSL 1.x dependency to 3.x (<a href="https://github.com/easybuilders/easybuild-framework/pull/5035">#5035</a>)</li> 15716</ul> 15717</li> 15718</ul> 15719<p><strong>easyblocks</strong></p> 15720<ul> 15721<li>new easyblocks:<ul> 15722<li>generic: <code>NvidiaBase</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3788">#3788</a>)</li> 15723<li>software-specific: gnupg-bundle (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3972">#3972</a>), Kokkos (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3893">#3893</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4012">#4012</a>), nvidia-compilers (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3788">#3788</a>), pocl (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3978">#3978</a>), QEMU (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3976">#3976</a>)</li> 15724</ul> 15725</li> 15726<li>enhanced easyblocks for LLVM and NVHPC toolchains:<ul> 15727<li>enhance custom easyblock for ELPA, OpenMPI, QuantumESPRESSO to work with LLVM-based toolchain (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3759">#3759</a>)</li> 15728<li>refactor NVHPC easyblock into generic NvidiaBase easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3788">#3788</a>)</li> 15729<li>
15729add LLVM toolchain support for Boost (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3855">#3855</a>)</li> 15730<li>add LLVM toolchain support to Score-P easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3987">#3987</a>)</li> 15731<li>allow FlexiBLAS to link to MKL with LLVM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3997">#3997</a>)</li> 15732</ul> 15733</li> 15734<li>various other enhancements, including:<ul> 15735<li>add support for STAR-CCM+ installs with <code>.aol</code> installer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3510">#3510</a>)</li> 15736<li>fix issues with PyTorch test-results (XML files) parsing and add tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3803">#3803</a>)</li> 15737<li>add support to Python easyblock for conditionally applying extra patch to fix <code>ctypes</code> when EasyBuild is configured to filter <code>$LD_LIBRARY_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3860">#3860</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3965">#3965</a>)</li> 15738<li>enhance <code>Bundle</code> generic easyblock to support use of post-install patches (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3887">#3887</a>)</li> 15739<li>change LLVM EasyBlock to not apply concurrency workaround for pre-release LLVM 20 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3937">#3937</a>)</li> 15740<li>add <code>-DCACHE_SECTOR_SIZE_READONLY</code> when building BLIS for A64FX (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3938">#3938</a>)</li> 15741<li>enhance LAMMPS easyblock to make it possible to overide kokkos_arch for GENERIC ARM target (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3943">#3943</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3945">#3945</a>)</li> 15742<li>enhance <code>PythonPackage</code> & <code>PythonBundle</code> easyblock to consider <code>$EBPYTHONPREFIXES</code> for test installs and path configuration files (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3953">#3953</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3975">#3975</a>)</li> 15743<li>add support to <code>PythonPackage</code> easyblock to disable use of <code>--no-build-isolation</code> option for <code>pip install</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3954">#3954</a>)</li> 15744<li>mention expected path in Python site-hooks sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3957">#3957</a>)</li> 15745<li>show summary of relevant LLVM test failures (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3962">#3962</a>)</li> 15746<li>update binutils easyblock to handle libzstd in binutils 2.40+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3966">#3966</a>)</li> 15747<li>set verbosity level for CMake > 3.16 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3974">#3974</a>)</li> 15748<li>add missing question pattern to ABAQUS easyblock when building 2025 without hotfixes (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3980">#3980</a>)</li> 15749<li>enhance GROMACS easyblock to provide more control over building <code>gmxapi</code> Python package (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3982">#3982</a>)</li> 15750<li>honor <code>(pre)configopts</code>, <code>(pre)buildopts</code> and <code>(pre)testopts</code> in custom easyblock for HPCG (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3986">#3986</a>)</li> 15751<li>allow to enable/disable standard library C++ modules in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3994">#3994</a>)</li> 15752<li>enhance QuantumESPRESSO easyblock to bind to 1 socket by default in test step (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3998">#3998</a>)</li> 15753<li>add options to <code>CMakeMake.configure_step</code> to not fail on non-zero exit code of <code>cmake</code> command and to return full result of <code>cmake</code> shell command (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4000">#4000</a>)</li> 15754<li>extend ignore patterns for LLVM tests on aarch64 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4014">#4014</a>)</li> 15755<li>allow using <code>PythonPackage</code> as extension in <code>Conda</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4015">#4015</a>)</li> 15756<li>enhance Cargo easyblock to merge <code>Cargo.toml</code> file with workspace file (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4016">#4016</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4022">#4022</a>)</li> 15757<li>make NCL easyblock compatible with oneAPI intel compilers (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4017">#4017</a>)</li> 15758</ul> 15759</li> 15760<li>various updates:<ul> 15761<li>update TensorRT easyblock for TensorRT 10+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3554">#3554</a>)</li> 15762<li>update Mathematica easyblock to support versions > 14.1 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3707">#3707</a>)</li> 15763<li>update LAMMPS easyblock: v2025 fix + extra tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3894">#3894</a>)</li> 15764<li>update jaxlib easyblock for jax 0.6.2 with CUDA-12.6.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3951">#3951</a>)</li> 15765<li>update GAMESS easyblock for 20240715-R2 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3990">#3990</a>)</li> 15766<li>update WRF easyblock for Intel compilers >= 2024 (icx, ...) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3992">#3992</a>)</li> 15767<li>update custom easyblock for Trilinos to reflect changes in version 16 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4011">#4011</a>)</li> 15768<li>update OpenFOAM easyblock to skip build of plugins for OpenFOAM v2412, since it's missing in source tarball (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4025">#4025</a>)</li> 15769</ul> 15770</li> 15771<li>various bug fixes, including:<ul> 15772<li>unify handling of vendored crates in <code>Cargo</code> easyblock and add support for non-virtual workspaces (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3665">#3665</a>)</li> 15773<li>set required environment variables in Python sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3913">#3913</a>)</li> 15774<li>use <code>nvcc --version</code> to determine default CUDA version in NVHPC if not present (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3924">#3924</a>)</li> 15775<li>fix custom easyblock for bzip2 to ensure all versioned symlinks are created (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3948">#3948</a>)</li> 15776<li>tweak LLVM easyblock to only run dynamic linker check if clang is being built (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3952">#3952</a>)</li> 15777<li>move setting of <code>$PYTHON*</code> environment variables to <code>load_module</code> method in Python easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3958">#3958</a>)</li> 15778<li>fix MPIEXEC and improve handling of FlexiBLAS in GROMACS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3959">#3959</a>)</li> 15779<li>honor user-defined <code>configopts</code> in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3967">#3967</a>)</li> 15780<li>fix crash in LLVM easyblock when doing <code>module-only</code> or <code>sanity-check-only</code> rebuild (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3977">#3977</a>)</li> 15781<li>return result of configure/build/install step in <code>CMakeNinja</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3999">#3999</a>)</li> 15782<li>fix netCDF and netCDF-Fortran easyblock to take into account that <code>os.getenv('ENV_VAR')</code> returns <code>None</code> when <code>$ENV_VAR</code> is not defined (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4003">#4003</a>)</li> 15783<li>be more careful with PATH-like environment variables when using buildenv + use <code>pushenv</code> for other environment variables (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4007">#4007</a>)</li> 15784<li>enhance LLVM easyblock to fix tests not finding GCCcore libraries (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4010">#4010</a>)</li> 15785<li>enhance OpenBabel easyblock to re-create install dir (which may already exist) in prepare step (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4013">#4013</a>)</li> 15786<li>only consider stdout when checking <code>config.guess</code> in <code>ConfigureMake</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4020">#4020</a>)</li> 15787<li>fix <code>MesonNinja</code> easyblock to avoid ninja using all CPUs when only 1 is requested (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/4023">#4023</a>)</li> 15788</ul> 15789</li> 15790<li>enhancements and fixes for test suite:<ul> 15791<li>also run easyblocks test suite with Python 3.13 and 3.14 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3955">#3955</a>)</li> 15792</ul> 15793</li> 15794</ul> 15795<p><strong>easyconfigs</strong></p> 15796<ul> 15797<li>add easyconfigs for new toolchains: <code>lompi/2025b</code> + <code>lfbf/2025b</code> + <code>lfoss/2025b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24481">#24481</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24482">#24482</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24514">#24514</a>), <code>lmpich/2025b</code> + <code>lmpflf/2025b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24659">#24659</a>)</li> 15798<li>
15798added example easyconfig files for 174 new software packages:<ul> 15799<li>acpype (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24174">#24174</a>), aiida-shell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24252">#24252</a>), AMAS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24229">#24229</a>), antiword (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23924">#23924</a>), AptaSUITE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24242">#24242</a>), aqme (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23963">#23963</a>), 15800ATAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24672">#24672</a>), Autocycler (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23476">#23476</a>), autoplotly (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24360">#24360</a>), AWS-SDK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24443">#24443</a>), bacio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24846">#24846</a>), BBTools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24678">#24678</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24819">#24819</a>), 15801Bear (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24333">#24333</a>), BEAST-X (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24416">#24416</a>), bshoshany-thread-pool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24202">#24202</a>), caddy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24402">#24402</a>), camp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24778">#24778</a>), Capstone (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24214">#24214</a>), 15802CLI11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24136">#24136</a>), cnpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23943">#23943</a>), CodonTransformer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23379">#23379</a>), colour (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23524">#23524</a>), concurrentqueue (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24136">#24136</a>), cotainr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22775">#22775</a>), 15803CRYSTAL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23528">#23528</a>), cuBLASMp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24772">#24772</a>), cuFFTMp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24527">#24527</a>), cuSOLVERMp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24773">#24773</a>), dask-mpi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24717">#24717</a>), dav1d (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24836">#24836</a>), 15804debugpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21653">#21653</a>), deprecation (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22684">#22684</a>), DIVEMesh (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23475">#23475</a>), double-down (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23034">#23034</a>), dtc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24218">#24218</a>), dysco (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), 15805EasyPQP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24016">#24016</a>), EBSeq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24364">#24364</a>), EntrezDirect (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23465">#23465</a>), eumdac (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19114">#19114</a>), Excel-Writer-XLSX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24351">#24351</a>), fast_float (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24136">#24136</a>), 15806FEniCS-Basix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23838">#23838</a>), FEniCS-Basix-Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23838">#23838</a>), FEniCS-DOLFINx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23838">#23838</a>), FEniCS-DOLFINx-Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23838">#23838</a>), 15807FEniCS-FFCx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23838">#23838</a>), FEniCS-ufcx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23838">#23838</a>), FEniCS-UFL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23838">#23838</a>), FFTS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24584">#24584</a>), filecheck-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24077">#24077</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24665">#24665</a>), 15808Fluxbox (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24280">#24280</a>), fortranGIS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24650">#24650</a>), g-xtb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23865">#23865</a>), googleapis-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24781">#24781</a>), gtk-layer-shell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24354">#24354</a>), 15809HADDOCK3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24742">#24742</a>), helix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24219">#24219</a>), hictk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24138">#24138</a>), HPCViewer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24249">#24249</a>), hwloc-CUDA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24321">#24321</a>), IMAS-ParaView (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23010">#23010</a>), 15810intronProspector (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24704">#24704</a>), ip (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24846">#24846</a>), ipywidgets (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22684">#22684</a>), isONclust3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24175">#24175</a>), JCuda (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24727">#24727</a>), jgmenu (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24323">#24323</a>), 15811JPEG-NCCS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24640">#24640</a>), JUBE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24251">#24251</a>), juicer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24727">#24727</a>), jupyter_packaging (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22684">#22684</a>), JupyterLab-git (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24001">#24001</a>), k8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24734">#24734</a>), 15812Kokkos (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23723">#23723</a>), LAPACK++ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24135">#24135</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24246">#24246</a>), laspy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24079">#24079</a>), LavaVu (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23423">#23423</a>), lazrs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24079">#24079</a>), libaom (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24847">#24847</a>), 15813libclc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23764">#23764</a>), libnotify (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24228">#24228</a>), libproxy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24789">#24789</a>), libpthread-stubs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23887">#23887</a>), LibRaw (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21542">#21542</a>), libslirp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24214">#24214</a>), 15814liburing (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24218">
15814#24218</a>), LibVNCServer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24248">#24248</a>), libwebsockets (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24169">#24169</a>), libwnck (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24355">#24355</a>), LINC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), llnl-blt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24215">#24215</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24777">#24777</a>), 15815llvm-compilers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24481">#24481</a>), LofarStMan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), lohhla-mod (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24324">#24324</a>), LoSoTo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), LPC3D (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24703">#24703</a>), LSMTool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), 15816Meeko (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24682">#24682</a>), MGARD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24185">#24185</a>), MinIONQC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24385">#24385</a>), MOAB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23034">#23034</a>), Modeller (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23988">#23988</a>), MulticoreTSNE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20400">#20400</a>), mzmine (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24329">#24329</a>), 15817neko (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24438">#24438</a>), Neovim (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24130">#24130</a>), NEST (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24259">#24259</a>), ng-log (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24854">#24854</a>), numba-cuda (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24081">#24081</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24665">#24665</a>), nvidia-compilers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23125">#23125</a>), 15818nvidia-cutlass (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23606">#23606</a>), nvImageCodec (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24604">#24604</a>), OnTAD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23996">#23996</a>), Openbox (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24280">#24280</a>), OpenGL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23764">#23764</a>), opentelemetry-cpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24136">#24136</a>), 15819OTF-CPT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24041">#24041</a>), overpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24078">#24078</a>), Palantir (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24291">#24291</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24473">#24473</a>), ParaView-Catalyst (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24311">#24311</a>), PEFT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24302">#24302</a>), picom (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24279">#24279</a>), 15820Pixi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24615">#24615</a>), Pluto (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23032">#23032</a>), PyQt6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24757">#24757</a>), PySR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23412">#23412</a>), python-jellyfish (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21653">#21653</a>), pyunicore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24460">#24460</a>), PyVO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), 15821pyzstd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24802">#24802</a>), QEMU (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24371">#24371</a>), qsimcirq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23538">#23538</a>), Qutip (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24637">#24637</a>), R-crumble (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22766">#22766</a>), rav1e (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24836">#24836</a>), 15822readerwriterqueue (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24137">#24137</a>), REEF3D (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23475">#23475</a>), RELION (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19678">#19678</a>), RMextract (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), ruff (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23466">#23466</a>), (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23466">#23466</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24540">#24540</a>), 15823SAGECal (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), SDPR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24082">#24082</a>), ShapeMapper2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22922">#22922</a>), shared-mime-info (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24180">#24180</a>), simde (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24791">#24791</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24827">#24827</a>), SIONfwd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24103">#24103</a>), 15824SIRIUS-MS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24330">#24330</a>), slirp4netns (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24625">#24625</a>), SONIC-bio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23902">#23902</a>), spacexr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24386">#24386</a>), span-lite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24137">#24137</a>), SVT-AV1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24847">#24847</a>), 15825SWI-Prolog (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23003">#23003</a>), SYMPHONY (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20234">#20234</a>), tcping (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24403">#24403</a>), testsweeper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24135">#24135</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24246">#24246</a>), TGS-GapCloser (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23888">#23888</a>), 15826tint2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24280">#24280</a>), toil-cwl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23155">#23155</a>), tomlplusplus (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24138">#24138</a>), trame-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22505">#22505</a>), TRL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24302">#24302</a>), tslearn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24339">#24339</a>), ttyd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24169">
15826#24169</a>), 15827Twisted (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24625">#24625</a>), ucx-py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21933">#21933</a>), UDA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24444">#24444</a>), uthash (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24279">#24279</a>), VeloxChem (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24176">#24176</a>), ViTables (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24799">#24799</a>), Vulkan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24029">#24029</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24114">#24114</a>), 15828x11vnc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24662">#24662</a>), xterm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24280">#24280</a>), yq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24294">#24294</a>)</li> 15829</ul> 15830</li> 15831<li>added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 15832<li>ABAQUS 2025, ABINIT 10.4.7, accelerate 1.10.0, ANTs 2.6.2, Arriba 2.5.1 Arrow 22.0.0, arrow-R 22.0.0, ASAP3 3.13.10, 15833astropy 7.1.0, Autoconf-archive 2024.10.16, Avogadro2 1.101.0, awscli 2.32.16, Bazel 7.7.0, bcl-convert 4.4.4-2, 15834BDBag 1.8.0, BeautifulSoup 4.14.2, BgeeCall 1.26.0, BgeeDB 2.36.0, Biopython 1.86, black 25.9.0, BLAST+ 2.17.0, 15835Blender 4.4.0, Boost.MPI 1.88.0, Boost.Python 1.88.0, build 1.2.2.post1, captum 0.8.0, Cartopy 0.25.0, CCCL 3.0.2, 15836CellBender 0.3.2, CellRanger 10.0.0, CellRanger-ARC 2.1.0, CellRanger-ATAC 2.2.0, cfgrib 0.9.15.0, code-cli 1.105.1, 15837code-server 4.105.1, ConnectomeWorkbench 2.1.0, coverage 7.10.7, CubeGUI 4.9, CUDA 13.1.0, CUDA-Python 12.9.2, 15838cuDNN 9.15.0.57, CuPy 13.6.0, cuSPARSELt 0.8.0.4, cuTENSOR 2.3.1.0, dask 2025.9.1, DendroPy 5.0.8, Deprecated 1.3.1, 15839dotNET-Core 10.0.100, DIAMOND 2.1.16, DLPack 1.2, DMTCP 4.0.0, Emacs 30.2, enchant-2 2.8.12, ESMF 8.9.0, EVcouplings 0.2.1, 15840expecttest 0.3.0, EZC3D 1.6.0, fastp 1.0.1, FastTree 2.2, FFmpeg 7.1.2, Flux 0.80.0, Flye 2.9.6, FUNAERO 1.5, FUSE 3.17.4, 15841g2clib 2.3.0, g2lib 4.0.0, gcloud 548.0.0, genozip 15.0.74, GHC 9.12.2, git-lfs 3.7.1, GMAP-GSNAP 2025-08-31, gmsh 4.15.0, 15842gnuplot 6.0.3, gperftools 2.17.2, GraphDB 11.2.0, hifiasm 0.25.0, HPX 1.11.0, HyperQueue 0.24.0, IMAS-Data-Dictionary 4.1.0, 15843Julia 1.12.2, jxrlib 2019.10.9, Go 1.25.3, GPflow 2.10.0, GROMACS 2025.3, gRPC v1.76.0, GST-plugins-base 1.26.6, 15844GTK4 4.20.2, HEEDS 2504, HOOMD-blue 4.9.1, ichorCNA 0.5.1-20240609, IGMPlot 3.17, imbalanced-learn 0.14.0, 15845ImageMagick 7.1.2-7, intel-compilers 2025.3.0, IQ-TREE 2.4.0 + 3.0.1, ITK 5.4.5, Java 25, Jmol 16.3.33, JupyterHub 5.4.2, 15846KaHIP 3.19, Kent_tools 487, kma 1.6.6, libedit 20250104, libharu 2.4.5, Libint 2.11.1, libjxl 0.10.4, libRmath 4.5.1, 15847librosa 0.11.0, libSBML 5.20.5, libsupermesh 2025.4, libyuv 20251210, likwid 5.5.0, libxml2-python 2.12.7, MariaDB 11.8.3, 15848MATLAB 2025a, MATSim 2024.0, MCScanX 1.0.0, mctc-lib 0.5.0, MDAnalysis 2.10.0i, Miller 6.15.0, minimap2 2.30, MMseqs2 18-8cc5c, 15849MNE-Python 1.10.2, MOABB 1.2.0, modin 0.37.1, MoviePy 2.2.1, MPICH 4.3.2, MuJoCo 3.3.0, MUMmer 4.0.1, muparserx 4.0.12, 15850nanobind 2.9.2, Nextflow 25.10.2, nghttp3 1.13.1, nglview 4.0, ngtcp2 1.18.0, Nilearn 0.12.1, occt 7.9.1, OpenCV 4.12.0, 15851OpenFAST 4.1.2, OpenFOAM 13 + v2412_250814 + v2506, OpenImageIO 3.0.6.1, OptiX 9.0.0, optree 0.18.0, Optuna 4.6.0, 15852ORCA 6.1.1, orjson 3.11.4, OrthoFinder v3.1.0, Pandoc 3.8.2.1, Panoply 5.8.1, parallel 20250922, Parallel-Hashmap 2.0.0, 15853ParaView 6.0.1, PETSc 3.24.0, petsc4py 3.24.0, pfind 20250510, phono3py 3.16.0, phonopy 2.43.2, PhyloPhlAn 3.1.1, 15854picard 3.4.0, plotly.py 6.5.0, PnetCDF 1.14.1, pocl 7.1, poppler 25.12.0, pre-commit 4.3.0, PyAEDT 0.15.0, PyGObject 3.54.2, 15855pyiron 0.5.2-20251013, pymatgen 2025.10.7, PhyML 3.3.20250515, PyOpenCL 2025.2.7, PyPy 7.3.20, Pysam 0.23.3, PySide6 6.9.3, 15856pytest-rerunfailures 16.1, python-mujoco 3.3.0, python-xxhash 3.5.0, PyTorch-bundle 2.6.0, PyWavelets 1.9.0, PyZMQ 27.1.0, 15857PuLP 2.9.0 + 3.3.0, Qiskit 2.0.2, Qt6 6.9.3, QuPath 0.6.0, R 4.5.1 + 4.5.2, R-bundle-Bioconductor 3.22, 15858R-bundle-CRAN 2025.10 + 2025.11, Redis 8.2.2, redis-py 6.4.0, ReFrame 4.8.4, Regenie 4.1, RepeatMasker 4.2.1, rjags 4-17, 15859rnaQUAST 2.3.1, rpmrebuild v2.21, Rtree 1.4.1, Ruby v3.4.7, Rust v1.91.1, s3fs 2025.10.0, safestringlib 20250325, 15860Saxon-HE 12.9, Scalene 1.5.55, SciPy-bundle 2023.11 w/ iimkl/2023b, SciTools-Iris 3.13.0, Score-P 9.3, SCOTCH 7.0.10, 15861SentencePiece 0.2.1, seqtk 1.5, SimpleITK 2.5.3, SIP 6.13.1, skorch 1.3.0, SLEPc 3.24.0, slepc4py 3.23.2, snakemake 9.14.0, 15862Sniffles 2.7.1, SpaceRanger 4.0.1, Spack 1.0.2, SPAdes 4.2.0, Spark 4.0.1, SPEI 0.8.0, SRA-Toolkit 3.2.1, Stack 3.7.1, 15863Stata 19, SuiteSparse 7.11.0, TELEMAC-MASCARET v9.0.0, TensorFlow 2.18.1, tensorflow-probability 0.25.0, TensorRT 10.7.0, 15864TEtrimmer 1.5.4, tlparse v0.4.0, torchaudio v2.6.0, trame v3.12.0, Trilinos 16.1.0, trimesh 4.10.0, Trimmomatic 0.40, 15865Triton 3.5.0, TurboVNC 3.2, utf8proc 2.10.0, uv 0.7.13, VCFtools 0.1.17, VEP 115.2, Vim 9.1.1788, VirtualGL v3.1.4, 15866vsc-mympirun 5.5.0, VTK 9.5.2, WebDataset 1.0.2, wxWidgets 3.3.1, xarray 2025.10.0, xclim 0.58.1, XGBoost 3.0.4, 15867XlsxWriter 3.2.9, yt 4.4.1, zarr 3.1.1</li> 15868</ul> 15869</li> 15870<li>minor enhancements, including:<ul> 15871<li>replace <code>sed</code> command in Brunsli easyconfig by proper patch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21180">#21180</a>)</li> 15872<li>use <code>python -s</code> to ignore user-installed packages in sanity check for Python packages (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21362">#21362</a>)</li> 15873<li>
15873add patch for scikit-build to support newer CMake versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23895">#23895</a>)</li> 15874<li>enable FreeSASA support for recent RDKit versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23984">#23984</a>)</li> 15875<li>add patch to add Intel Meteor Lake and Emerald Rapids support for OpenBLAS 0.3.27 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24027">#24027</a>)</li> 15876<li>set environment variables to expose vulkan ICDs in Mesa 25.1.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24048">#24048</a>)</li> 15877<li>add missing dependencies needed by aiida-core for the RESTapi and for <code>atomic_tools</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24238">#24238</a>)</li> 15878<li>add hatch-docstring-description extension to hatchling 1.27.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24284">#24284</a>)</li> 15879<li>add patch for HMMER v3.4 to add support for <code>--seq_limit</code> option (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24301">#24301</a>)</li> 15880<li>build both shared + static libraries in existing spdlog easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24308">#24308</a>)</li> 15881<li>build both shared + static libraries in recent spdlog easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24310">#24310</a>)</li> 15882<li>enable plugin support for hwloc 2.11.2 + 2.12.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24321">#24321</a>)</li> 15883<li>add <code>iceauth</code> + <code>libXpresent</code> as components in easyconfig for X11 20250608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24367">#24367</a>)</li> 15884<li>enable running of tests for spdlog (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24400">#24400</a>)</li> 15885<li>enable OpenGL and jpeg-turbo in easyconfig for JasPer 4.2.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24456">#24456</a>)</li> 15886<li>enable ICO/BMP and more in Gdk-Pixbuf 2.42.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24470">#24470</a>)</li> 15887<li>update description of pytest patch in Python-bundle-PyPI-2024.06 to make it more discoverable (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24503">#24503</a>)</li> 15888<li>enable Quarto in RStudio 2024.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24542">#24542</a>)</li> 15889<li>add source URLs for NVSHMEM 3.3.20 instead of relying on manual download (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24558">#24558</a>)</li> 15890<li>add aarch64 checksum to easyconfg for Ray-project 2.47.1 w/ <code>foss/2025a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24578">#24578</a>)</li> 15891<li>add <code>cuda-binding</code>, <code>cuda-core</code>, <code>cuda-pathfinder</code> extensions to <code>CUDA-Python</code> v12.8.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24665">#24665</a>)</li> 15892<li>enable XYZ2MOL support in RDKit 2024.03.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24682">#24682</a>)</li> 15893<li>install python package using extensions in gemmi easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24690">#24690</a>)</li> 15894<li>add GLPK dependency to CVXOPT v1.3.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24719">#24719</a>)</li> 15895<li>add PnetCDF dependency for WRF 4.6.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24722">#24722</a>)</li> 15896<li>enable OPUS, VPX, AV1 in FFmpeg 7.1.2 + add NASM build dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24848">#24848</a>)</li> 15897<li>also build shared library for RE2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24902">#24902</a>)</li> 15898<li>use Easybuild-provided dependencies for recent FreeImage easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24905">#24905</a>)</li> 15899<li>enhance IMAS-Data-Dictionary easyconfigs to set <code>$IMAS_VERSION</code> environment variable (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24907">#24907</a>)</li> 15900</ul> 15901</li> 15902<li>various bug fixes, including:<ul> 15903<li>unset <code>$CONDA_PREFIX</code> in configure step for Arrow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20414">#20414</a>)</li> 15904<li>
15904add patch to Python easyconfigs to fix ctypes when <code>$LD_LIBRARY_PATH</code> is not being set (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23499">#23499</a>)</li> 15905<li>remove extensions that were added multiple times (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23806">#23806</a>)</li> 15906<li>add missing Autotools build dependency + add source URL for NAMD 3.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23979">#23979</a>)</li> 15907<li>explicitly disable Poppler in GDAL 3.9.0, 3.10.0, 3.11.1, 3.11.3 to not pick up system one (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24009">#24009</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24010">#24010</a>)</li> 15908<li>add patches to force use of the EasyBuild defined CUDA compute capabilities in LightGBM 4.5.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24023">#24023</a>)</li> 15909<li>enable introspection (GIR) in recent Pango easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24030">#24030</a>)</li> 15910<li>add patch to LLVM 20.1.5 + 20.1.7 to better support CUDA 13 and Blackwell GPUs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24039">#24039</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24040">#24040</a>)</li> 15911<li>use correct ptxas version in easyconfig for Triton 2.3.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24061">#24061</a>)</li> 15912<li>move definition of <code>$GENEMARK_PATH</code> to GeneMark-ET easyconfig (instead of funannotate) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24065">#24065</a>)</li> 15913<li>add post install commands for QCMaquis 4.0.0 to fix <code>MAQUIS_DMRGConfig.cmake</code> used by OpenMolcas (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24066">#24066</a>)</li> 15914<li>use QCMaquis v4.0.0 as dependency for OpenMolcas (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24069">#24069</a>)</li> 15915<li>add patch for GCCcore 10.3-13.2 to fix AVX-512 vectorizer bug (upstream PR 114566) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24073">#24073</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24157">#24157</a>)</li> 15916<li>add -lpthread to configure options for Parallel-Hashmap v2.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24094">#24094</a>)</li> 15917<li>fix CMake options for preCICE 3.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24123">#24123</a>)</li> 15918<li>add missing Python dep to <code>h5glance</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24125">#24125</a>)</li> 15919<li>update homepage of foss toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24127">#24127</a>)</li> 15920<li>switch source URL + add <code>preconfigopts</code> to generate configure for ABINIT 9.4.2, 9.6.2, 9.10.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24152">#24152</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24153">#24153</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24155">#24155</a>)</li> 15921<li>add missing M4 and Autotools build dependencies for ABINIT 9.10.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24158">#24158</a>)</li> 15922<li>add patch for libdeflate 1.20 to fix build on Arm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24171">#24171</a>)</li> 15923<li>add existing patches to fix failing tests for <code>Net::SSLeay</code> 1.94 and <code>Sys::Info::Driver::Linux</code> 0.7905 to relevant versions of Perl-bundle-CPAN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24186">#24186</a>)</li> 15924<li>add patch for Python 3.13 to fix test failure that may occur when collecting performance profile for profile-guided optimization (PGO) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24189">#24189</a>)</li> 15925<li>
15925add patch to link explicitly to protobuf libs using <code>pkgconf</code> to fix EL9 build error for harvest-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24197">#24197</a>)</li> 15926<li>add patches to fix CVEs in Redis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24201">#24201</a>)</li> 15927<li>add missing (direct) lz4 dependency in libarchive easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24203">#24203</a>)</li> 15928<li>add patch for OpenBLAS 0.3.29 to fix CPU detection on A64FX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24204">#24204</a>)</li> 15929<li>add <code>-Wno-error=int-conversion</code> as extra C compiler flag for BLIS 1.1, to fix build on A64FX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24205">#24205</a>)</li> 15930<li>symlink generic libraries for Tcl and Tk 9.0.1 for better library support (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24213">#24213</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24221">#24221</a>)</li> 15931<li>enable pic toolchain option for FreeImage v3.18.0 w/ GCCcore/14.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24216">#24216</a>)</li> 15932<li>set <code>$MAX_JOBS</code> when installing Triton 3.1.0 to control how many cores are used (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24222">#24222</a>)</li> 15933<li>drop ILP64 from lapacke in 2025b as flexiblas doesn't support it (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24231">#24231</a>)</li> 15934<li>add missing MPFR dependency for ViennaRNA v2.7.0 (and bump toolchain to gfbf/2024a) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24232">#24232</a>)</li> 15935<li>add patch to fix integer overflow bug in scikit-bio v0.6.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24233">#24233</a>)</li> 15936<li>avoid test failures due to concurrency issue in modkit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24234">#24234</a>)</li> 15937<li>fix test failure in juliaup-1.17.9 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24239">#24239</a>)</li> 15938<li>link explicitly to protobuf libs using pkgconf to fix EL9 build error for harvest-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24250">#24250</a>)</li> 15939<li>fix ASE test suite sometimes failing due to overly tight numerical tolerance (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24253">#24253</a>)</li> 15940<li>add Xvfb dependency for TurboVNC 3.1.2, it provides xkbcomp which is used at startup to compile keymap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24254">#24254</a>)</li> 15941<li>enable <code>precise</code> toolchain option in easyconfig for OpenMolcas 25.06 w/ <code>iomkl/2023a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24265">#24265</a>)</li> 15942<li>fix pkgconfig files of zstd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24274">#24274</a>)</li> 15943<li>don't run <code>autoreconf</code> for jq 1.7.1, as a release tarball is used as source (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24275">#24275</a>)</li> 15944<li>add missing libdrm dependency to Qt6 for 2025x toolchains (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24278">#24278</a>)</li> 15945<li>pull npm extensions compatible with nodejs version used in easyconfig for RStudio-Server v2023.09.1+494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24282">#24282</a>)</li> 15946<li>fix recent Arrow easyconfigs to not use system libraries + use <code>PythonPackage</code> easyblock for pyarrow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24283">#24283</a>)</li> 15947<li>fix python-igraph easyconfigs to actually use igraph dependency rather than build one + update easyconfig for synthcity 0.2.11 accordingly (changed ver
15947sion for ipython-igraph dependency) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24288">#24288</a>)</li> 15948<li>fix homepage + source URL for Gblocks 0.91b (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24297">#24297</a>)</li> 15949<li>fix <code>mlir-pdll-lsp-server</code> in Clang 18.1.8 by configuring with <code>-DLLVM_LINK_LLVM_DYLIB=OFF</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24327">#24327</a>)</li> 15950<li>fix Rust sysroot patch to properly skip libraries when setting the interpreter with <code>patchelf</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24331">#24331</a>)</li> 15951<li>rename <code>annovar</code> to use official software name <code>ANNOVAR</code> (+ fix sanity check commands for scNanoGPS) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24346">#24346</a>)</li> 15952<li>add source URL for extensions in pod5-file-format easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24349">#24349</a>)</li> 15953<li>fix source URL for PETSc 3.19.2 and older (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24352">#24352</a>)</li> 15954<li>add patch for Qt6 6.7.2 to fix issue with gperf>3.1, add build dependency on libglvnd (for <code>KHR/khrplatform.h</code>), add configure option to disable sysroot for CMake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24356">#24356</a>)</li> 15955<li>use custom easyblock for gnupg-bundle that ensures that UNIX sockets can be created for tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24359">#24359</a>)</li> 15956<li>add patch for Ruby 3.2.2 + 3.3.0 to fix support for PAC+BTI on 64-bit Arm systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24368">#24368</a>)</li> 15957<li>enhance RSEM easyconfigs to also install missing binaries and scripts required for EBSeq + add patch fix version info (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24373">#24373</a>)</li> 15958<li>use custom easyblock in recent pocl easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24375">#24375</a>)</li> 15959<li>add patches to easyconfig for EasyBuild v5.1.2 to fix known bugs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24376">#24376</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24556">#24556</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24608">#24608</a>)</li> 15960<li>avoid test failure on AVX512 systems by using <code>-O2</code> instead of <code>-O3</code> for CASTEP 24.1 + 25.1.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24378">#24378</a>)</li> 15961<li>update homepage URL for HTSeq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24384">#24384</a>)</li> 15962<li>add bistro fix to all UCX versions from 1.13.1 onwards (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24388">#24388</a>)</li> 15963<li>add missing dependencies in existing easyconfig for KaHIP 3.19 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24392">#24392</a>)</li> 15964<li>reset <code>$TCL_SRC_DIR</code> in <code>tclConfig.sh</code> created by Tcl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24397">#24397</a>)</li> 15965<li>add patch for UMI-tools 1.1.4 and 1.1.5 to resolve pandas incompatibility warning (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24405">#24405</a>)</li> 15966<li>make Z3 & zstd explicit dependency for numba to fix non-rpath build (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24406">#24406</a>)</li> 15967<li>add missing libglvnd dependency to GLFW (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24408">#24408</a>)</li> 15968<li>disable assembly tests for googlebenchmark (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24423">#24423</a>)</li> 15969<li>add patch to force use of OpenGL dependency in easyconfig for gmsh 4.12.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24449">#24449</a>)</li> 15970<li>fix ippicv component version for OpenCV v4.11.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24474">#24474</a>)</li> 15971<li>remove unneccessary environment variable <code>$MCXTRACE</code> which has nothing to do with mcpl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24476">#24476</a>)</li> 15972<li>
15972add (back) patch to make sure environment variables are defined for RStudio-Server v1.2.1335 terminal sessions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24490">#24490</a>)</li> 15973<li>update homepage URL for pycoQC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24494">#24494</a>)</li> 15974<li>add patch to LLVM 20.1.x easyconfig to fix bindc commonblocks in fortran compilation (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24495">#24495</a>)</li> 15975<li>add explicit dependencies for R-bundle-CRAN 2024.11 + add alternate checksum for VSURF 1.2.0 source tarball (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24524">#24524</a>)</li> 15976<li>add patch for RStudio 2024.12 to allow passing through environment (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24542">#24542</a>)</li> 15977<li>add patch with workaround for Arm SVE512 test failure to GROMACS 2024+2025 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24548">#24548</a>)</li> 15978<li>enable usempi toolchain option for MrBayes with <code>gompi/2025a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24552">#24552</a>)</li> 15979<li>add patch to make gmsh 4.12.2 + 4.14.0 use provided OpenGL dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24594">#24594</a>)</li> 15980<li>add patch for mctc-lib v0.5.0 to make mstore work (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24596">#24596</a>)</li> 15981<li>fix homepage URL for numsa v0.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24598">#24598</a>)</li> 15982<li>add patch for double precision SVE bug to GROMACS 2024.1 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24602">#24602</a>)</li> 15983<li>add patch to update sse2neon.h in RAxML 8.2.13 sources (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24627">#24627</a>)</li> 15984<li>use https for LibLZF homepage & source URL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24632">#24632</a>)</li> 15985<li>add missing ETE dependency for PICRUSt2 v2.6.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24655">#24655</a>)</li> 15986<li>add patch to LLVM 20.1.8 to always link <code>compiler-rt</code> to <code>flang</code> after <code>libgcc</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24661">#24661</a>)</li> 15987<li>add patch to Autoconf 2.71 + 2.72 to ignore <code>-target-feature</code> flags when determining Fortran libraries (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24669">#24669</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24693">#24693</a>)</li> 15988<li>add Python as build dependency for recent QuantumESPRESSO easyconfigs, to ensure pipes Python module is available (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24694">#24694</a>)</li> 15989<li>avoid using bundled HTSlib in Stacks 2.68 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24701">#24701</a>)</li> 15990<li>add missing pkgconf dependency to OpenSlide 4.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24714">#24714</a>)</li> 15991<li>add patch to libunwind 1.8.2 to fix off-by-one error on aarch64 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24716">#24716</a>)</li> 15992<li>fix homepage for DendroPy easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24725">#24725</a>)</li> 15993<li>fix location of ggml libraries for ollama v0.11.10 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24749">
15993#24749</a>)</li> 15994<li>consistently add patch to disable flaky <code>opal_path_nfs</code> test in recent OpenMPI easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24763">#24763</a>)</li> 15995<li>disable optarch for BLIS 2.0 w/ llvm-compilers toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24770">#24770</a>)</li> 15996<li>fix compatibility with Arm for recent Bowtie2 easyconfigs by adding simde header-only build dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24791">#24791</a>)</li> 15997<li>make NASM a build-only dependency for: cramjam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24843">#24843</a>), FFmpeg (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24845">#24845</a>), ISA-L (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24842">#24842</a>), libjpeg-turbo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24839">#24839</a>), Tensorflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24844">#24844</a>)</li> 15998<li>unset <code>$TERMINFO</code> when configuring ncurses 6.5 to avoid writing to system paths (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24868">#24868</a>)</li> 15999<li>fix source URL for HDF5 v1.14.0 + v1.14.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24873">#24873</a>)</li> 16000<li>move netCDF to last dependency in recent GDAL easyconfigs, to make sure correct <code>netcdf.h</code> is picked up (not the one included in HDF dependency) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24883">#24883</a>)</li> 16001<li>fix broken FreeImage 3.18.0 on aarch64 by disabling support for Neon (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24889">#24889</a>)</li> 16002<li>make SimpleITK pick the right Lua binary by using <code>-DSimpleITK_LUA_EXECUTABLE</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24908">#24908</a>)</li> 16003<li>fix source URL in Go easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24918">#24918</a>)</li> 16004<li>set <code>$DBUS_SESSION_SOCKET_DIR</code> to <code>/tmp</code> for DBus session config (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24925">#24925</a>)</li> 16005</ul> 16006</li> 16007<li>enhancements and fixes for test suite:<ul> 16008<li>add test for extensions being added multiple times (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23802">#23802</a>)</li> 16009<li>enhance easyconfig test suite to check that <code>pip_no_build_isolation</code> is not disabled (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24187">#24187</a>)</li> 16010<li>enhance tagbot workflow to ignore easyconfigs in PR when finding similar easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24217">#24217</a>)</li> 16011<li>remove <code>Kent_tools</code>, MATLAB, OpenFOAM-Extend from the checksum exclusion whitelist (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24223">#24223</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24225">#24225</a>)</li> 16012<li>fix failing <code>test_pr_python_packages</code> when extensions have templates (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24260">#24260</a>)</li> 16013<li>ignore comments in checks for 'python -s' (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24270">#24270</a>)</li> 16014<li>fix source distribution CI check (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24289">#24289</a>)</li> 16015<li>add <code>manual_download</code> automatic tagging to tagbot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24305">#24305</a>)</li> 16016<li>only check contents if files exist in tagbot workflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24484">#24484</a>)</li> 16017<li>add <code>[V_]VERSION</code> templates to known flake8 constants (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24795">#24795</a>)</li> 16018<li>
16018enable flake8-comprehension in CI and fix issues (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24567">#24567</a>)</li> 16019</ul> 16020</li> 16021<li>other changes:<ul> 16022<li>convert recent jupyter-resource-usage easyconfigs to use PythonPackage easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21863">#21863</a>)</li> 16023<li>unbundle some Python packages from jupyter-server 2.14.0: debugpy 1.8.1, deprecation 2.1.0, ipywidgets 8.1.2, <code>jupyter_packaging</code> 0.12.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22684">#22684</a>)</li> 16024<li>split NVHPC v25 easyconfigs into nvidia-compilers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23125">#23125</a>)</li> 16025<li>always add tbb and ScaFaCoS dependencies for recent LAMMPS versions, not just on <code>x86_64</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23719">#23719</a>)</li> 16026<li>remove license server from sources in easyconfig for ABAQUS v2024-hotfix-2441 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23754">#23754</a>)</li> 16027<li>use generic version of RAxML v8.2.13 as dependency for bcgTree, Gubbins, Parsnp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23975">#23975</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24607">#24607</a>)</li> 16028<li>in-place update of autoCAS v2.3.1 to v3.0.0 and OpenMolcas v25.02 to v25.06 + remove easyconfig for QCMaquis v3.1.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24069">#24069</a>) </li> 16029<li>use <code>GNU_SOURCE</code> as source URL for: cpio 2.14 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24116">#24116</a>), GMP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24122">#24122</a>), groff (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24118">#24118</a>), plotutils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24119">#24119</a>), screen 5.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24121">#24121</a>)</li> 16030<li>use <code>ftpmirror.gnu.org</code> as source URL for CVS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24120">#24120</a>), libidn2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24117">#24117</a>), libreadline (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24108">#24108</a>)</li> 16031<li>drop GSL from GStreamer and move them to GCCcore toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24179">#24179</a>)</li> 16032<li>change toolchain for aiida-core from <code>gfbf/2023a</code> to <code>foss/2023a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24238">#24238</a>)</li> 16033<li>use PythonPackage easyblock to install libpod5 wheel as extension in pod5-file-format easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24267">#24267</a>)</li> 16034<li>enhance tagbot workflow to add toolchain labels (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24439">#24439</a>)</li> 16035<li>enable <code>pic</code> toolchain option in pixman easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24448">#24448</a>)</li> 16036<li>remove <code>METIS</code> variant of SuiteSparse, since it's wrong (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24483">#24483</a>)</li> 16037<li>deal with case where the tagbot comment is too long (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24647">#24647</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24651">#24651</a>)</li> 16038<li>use non-minimal Graphviz as dependency for MUST (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24561">#24561</a>)</li> 16039<li>drop <code>build</code> easyconfigs from foss to GCCcore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24562">#24562</a>)</li> 16040<li>use <code>build</code> easyconfigs as a dependency for poetry (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24566">#24566</a>)</li> 16041<li>move Stacks 2.68 to GCC toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24701">#24701</a>)</li> 16042<li>unbundle Python bindings for zlib-ng 0.5.1 into a separate python-zlib-ng easyconfig file (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24718">#24718</a>)</li> 16043<li>
16043add LLVM-based toolchains to tagbot workflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24771">#24771</a>)</li> 16044<li>use <code>googleapis-python</code> as dependency in <code>qsimcirq</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24781">#24781</a>)</li> 16045<li>remove <code>PythonPackage</code> defaults from template easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/24796">#24796</a>)</li> 16046</ul> 16047</li> 16048<li>code cleanup:<ul> 16049<li>update and fix templates in cuDNN + NCCL easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23856">#23856</a>)</li> 16050<li>remove duplicate (explicit) versionsuffix from UCC-CUDA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20966">#20966</a>)</li> 16051</ul> 16052</li> 16053</ul> 16054<h2 id="release_notes_eb512">EasyBuild v5.1.2 (26 Sept 2025)<a class="headerlink" href="#release_notes_eb512" title="Permanent link">¶</a></h2> 16055<p>bugfix/update release</p> 16056<p><strong>framework</strong></p> 16057<ul> 16058<li>enhancements:<ul> 16059<li>show readable error message when applying patch without (extracted) source (<a href="https://github.com/easybuilders/easybuild-framework/pull/4738">#4738</a>)</li> 16060<li>add support for <code>amdgcn-capabilities</code> configuration option and <code>amdgcn_capabilities</code> easyconfig parameter + related templates, similar to <code>cuda-compute-capabilities</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4860">#4860</a>)</li> 16061<li>try to empty install dir if removing it fails (<a href="https://github.com/easybuilders/easybuild-framework/pull/4932">#4932</a>)</li> 16062<li>add support for "extensions" on Tcl modulefiles , but disable it for now (<a href="https://github.com/easybuilders/easybuild-framework/pull/4972">#4972</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4978">#4978</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4985">#4985</a>)</li> 16063<li>exit with appropriate error code for <code>--search</code> when no match is found (<a href="https://github.com/easybuilders/easybuild-framework/pull/4976">#4976</a>)</li> 16064<li>handle <code>post_install_patches</code> and <code>post_install_msgs</code> for extensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4980">#4980</a>)</li> 16065<li>skip RPATH sanity check for symlinks explicitely (<a href="https://github.com/easybuilders/easybuild-framework/pull/4988">#4988</a>)</li> 16066<li>take <code>--terse</code> into account for <code>--dry-run-short</code>/<code>-D</code> and <code>--dry-run</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4989">#4989</a>)</li> 16067</ul> 16068</li> 16069<li>bug fixes:<ul> 16070<li>
16070test if all extensions support parallel install before attempting parallel extension install (<a href="https://github.com/easybuilders/easybuild-framework/pull/4949">#4949</a>)</li> 16071<li>do not fail for read-only installation directory on <code>--module-only</code> (re)builds (<a href="https://github.com/easybuilders/easybuild-framework/pull/4958">#4958</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/5004">#5004</a>)</li> 16072<li>store all patches (incl. the ones for extensions) that need to be copied to a repo/reprod dir in an <code>all_patches</code> set (<a href="https://github.com/easybuilders/easybuild-framework/pull/4960">#4960</a>)</li> 16073<li>fix error when adding files to existing PR with <code>--update-pr</code> and refactor + fixes in <code>options</code> tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/4962">#4962</a>)</li> 16074<li>add back <code>OrderedDict</code> import in (deprecated) <code>easybuild.tools.py2vs3.py3</code> module (<a href="https://github.com/easybuilders/easybuild-framework/pull/4965">#4965</a>)</li> 16075<li>fixes for RPATH wrapper script:<ul> 16076<li>detect & replace <code>-Xlinker --enable-new-dtags</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4970">#4970</a>)</li> 16077<li>do not add RPATH (linking) flags when <code>-c</code> flag specified (<a href="https://github.com/easybuilders/easybuild-framework/pull/4981">#4981</a>)</li> 16078</ul> 16079</li> 16080<li>honor <code>--disable-module-extensions</code> configuration option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4971">#4971</a>)</li> 16081<li>fix f-string in rpath check and skip check for linked libs on symlinks (<a href="https://github.com/easybuilders/easybuild-framework/pull/4975">#4975</a>)</li> 16082<li>fix passing command as list of strings to <code>run_shell_cmd</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4977">#4977</a>)</li> 16083<li>add <code>f</code> for the f-string in a <code>git_config</code> error (<a href="https://github.com/easybuilders/easybuild-framework/pull/4982">#4982</a>)</li> 16084<li>keep <code>ModuleTool.mod_paths</code> in sync with <code>MODULEPATH</code> in <code>ModuleTool.load()</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4991">#4991</a>)</li> 16085<li>fix failure to resolve template in tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/4994">#4994</a>)</li> 16086<li>update regex used in <code>Lmod.get_setenv_value_from_modulefile</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4998">#4998</a>)</li> 16087</ul> 16088</li> 16089<li>enhancements and fixes for test suite:<ul> 16090<li>only run tests for <code>--from-commit</code> for subset of test configurations (those for which a GitHub token is available) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4967">#4967</a>)</li> 16091<li>adapt <code>module_extensions</code> disable test for Tcl modulefiles (<a href="https://github.com/easybuilders/easybuild-framework/pull/4973">#4973</a>)</li> 16092</ul> 16093</li> 16094<li>other changes:<ul> 16095<li>don't log variables (un)set + raw output of <code>module</code> command when cleaning up fake module (<a href="https://github.com/easybuilders/easybuild-framework/pull/4942">#4942</a>)</li> 16096<li>introduce <code>PYTHON_EXE</code> variable in template for RPATH wrapper script (to easily replace name of <code>python</code> command to use in <code>buildenv</code> easyblock) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4984">#4984</a>)</li> 16097<li>remove deprecated license classifier in <code>setup.py</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/5002">#5002</a>)</li> 16098</ul> 16099</li> 16100</ul> 16101<p><strong>easyblocks</strong></p> 16102<ul> 16103<li>new easyblocks:<ul> 16104<li>restore custom easyblock for ipp and update it for EasyBuild 5.0+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3890">#3890</a>)</li> 16105</ul> 16106</li> 16107<li>enhancements:<ul> 16108<li>improvements to custom easyblock for LLVM:<ul> 16109<li>fix build of LLVM on RISC-V systems and ignore a bunch of tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3676">#3676</a>)</li> 16110<li>make LLVM easyblock aware of <code>amdgcn_capabilities</code> build option (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3824">#3824</a>)</li> 16111<li>explicitely set OMPT options for LLVM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3853">#3853</a>)</li> 16112<li>run tests for LLVM in parallel (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3875">#3875</a>)</li> 16113<li>
16113add sanity check to link system libraries to LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3877">#3877</a>)</li> 16114<li>add custom easyconfig parameter for LLVM to ignore timed out tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3903">#3903</a>)</li> 16115</ul> 16116</li> 16117<li>enhance custom easyblock for NCCL so it defines <code>$NCCL_HOME</code> in generated module file (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3782">#3782</a>)</li> 16118<li>enhance <code>Bundle</code> easyblock to show status of component installation (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3783">#3783</a>)</li> 16119<li>enhance LAMMPS easyblock to use <code>FFT_KOKKOS</code> configure option (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3784">#3784</a>)</li> 16120<li>add option to <code>CMakeMake</code> to specify name of build directory (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3786">#3786</a>)</li> 16121<li>improve error message when CMake picked up invalid Python paths (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3833">#3833</a>)</li> 16122<li>enhance FlexiBLAS easyblock to support NVPL library (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3866">#3866</a>)</li> 16123<li>enhance Python easyblock to handle Tcl/Tk 9.0+ with external libtommath (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3867">#3867</a>)</li> 16124<li>avoid writes to $HOME from Triton during PyTorch tests by setting <code>$TRITON_HOME</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3876">#3876</a>)</li> 16125<li>update torchvision easyblock for libwebp support (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3882">#3882</a>)</li> 16126<li>allow oversubscription for FFTW tests, also for OpenMPI-5.X onwards (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3884">#3884</a>)</li> 16127<li>enhance custom easyblock for SuperLU to allow oversubscription when running tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3885">#3885</a>)</li> 16128<li>allow bypass of <code>update_amber</code> in custom easyblock for Amber/AmberTools (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3901">#3901</a>)</li> 16129<li>set required Python environment variables when installing <code>lammps</code> Python package (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3915">#3915</a>)</li> 16130</ul> 16131</li> 16132<li>updates:<ul> 16133<li>update TensorFlow easyblock for CUDA support in TensorFlow 2.18+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3765">#3765</a>)</li> 16134<li>update ORCA easyblock for version 6.1.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3796">#3796</a>)</li> 16135<li>update DualSPHysics sanity checks for newer version (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3850">#3850</a>)</li> 16136<li>update jaxlib easyblock for jax/jaxlib v0.6.2 and v0.7.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3852">#3852</a>)</li> 16137<li>update Amber easyblock for AmberTools >= 24.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3868">#3868</a>)</li> 16138<li>update sanity check in custom easyblock for MUMPS to support v5.8.0 and higher (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3879">#3879</a>)</li> 16139<li>update Mesa easyblock to remove <code>osmesa</code> part of the sanity check, since that's removed from Mesa 25.1 onwards (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3896">#3896</a>)</li> 16140</ul> 16141</li> 16142<li>bug fixes:<ul> 16143<li>various fixes for custom easyblock for LLVM:<ul> 16144<li>use property for <code>gcc_prefix</code>/<code>gcc_root</code> in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3793">#3793</a>)</li> 16145<li>move openmp to a runtime in newer versions of LLVM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3799">#3799</a>)</li> 16146<li>add explicit enabling/disabling of <code>libffi</code> with custom paths in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3849">#3849</a>)</li> 16147<li>fix missing <code>LIBOMPTARGET_DEVICE_ARCHITECTURES</code> in third stage of bootstrap build in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3851">#3851</a>)</li> 16148<li>allow sysroot for minimal builds for LLVM versions < 19 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3880">#3880</a>)</li> 16149<li>only consider explicit dependencies in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3881">#3881</a>)</li> 16150<li>disable LLVM OpenMP tests using Thread sanitizer if requested (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3883">#3883</a>)</li> 16151<li>fix sanity check step of LLVM by loading <code>binutils</code> as extra module (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3899">
16151#3899</a>)</li> 16152</ul> 16153</li> 16154<li>revert Python shebangs change for conda (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3760">#3760</a>)</li> 16155<li>disable UCX signal catching in Java by setting <code>$UCX_ERROR_SIGNALS</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3832">#3832</a>)</li> 16156<li>stop setting <code>separate_build_dir</code> to <code>True</code> and update GPU target in custom easyblock for DualSPhysics (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3835">#3835</a>)</li> 16157<li>remove use of deprecated <code>verbose</code> option in <code>build_step</code> methods (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3856">#3856</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3858">#3858</a>)</li> 16158<li>add back configure options for PETSc dependencies with generic <code>--with</code> options (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3857">#3857</a>)</li> 16159<li>remove duplicated output of test command from <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3859">#3859</a>)</li> 16160<li>use <code>--COPTFLAGS</code>/<code>--CXXOPTFLAGS</code>/<code>--FOPTFLAGS</code> instead of (undocumented) <code>--CFLAGS</code>/<code>--CXXFLAGS</code>/<code>--FFLAGS</code> as configure option for PETSc (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3863">#3863</a>)</li> 16161<li>use <code>sanity_check_load_module</code> in sanity check step of custom easyblock for pybind11 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3864">#3864</a>)</li> 16162<li>respect <code>--ignore-test-failure</code> and <code>--skip-test-step</code> for Perl extensions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3865">#3865</a>)</li> 16163<li>fix use of <code>--sanity-check-only</code> for custom easyblock for installing EasyBuild (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3871">#3871</a>)</li> 16164<li>explicitly set LAPACK/BLAS to FlexiBLAS if present in OpenCV (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3874">#3874</a>)</li> 16165<li>fix ELPA easyblock to not pass sm80 configure flag for newer NVIDIA GPUs (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3886">#3886</a>)</li> 16166<li>fix ignore test typo in PyTorch easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3898">#3898</a>)</li> 16167<li>accept arguments for <code>sanity_check_step</code> in HPL easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3904">#3904</a>)</li> 16168<li>load module in Bundle easyblock instead of components (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3905">#3905</a>)</li> 16169<li>change OpenFOAM easyblock to not use <code>cp -a</code>, might fail with NFS ACLs on install directory (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3916">#3916</a>)</li> 16170<li>make HPL easyblock intel-aware + allow running the <code>xhpl</code> benchmark as a test (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3917">#3917</a>)</li> 16171<li>resolve templates in <code>CmdCp</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3918">#3918</a>)</li> 16172<li>update WPS easyblock to patch CPP to replace the use of hardcoded <code>/usr/bin/cpp</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3919">#3919</a>)</li> 16173<li>fix <code>FATAL ERROR</code> regex to not match <code>printf</code> lines in OpenBLAS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3923">#3923</a>)</li> 16174<li>fix unresolved templates in <code>modextravars</code>/<code>modextrapaths</code> of components (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3940">#3940</a>)</li> 16175</ul> 16176</li> 16177<li>other changes:<ul> 16178<li>deprecate the Clang Easyblock in favor of the LLVM one for newer (>=18.1.6) versions of LLVM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3746">#3746</a>)</li> 16179<li>don't install libomp aliases by default in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3825">#3825</a>)</li> 16180<li>clean up GCC-related options for full-LLVM build (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3827">#3827</a>)</li> 16181<li>clean up ancient version support in custom easyblock for ROOT (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3841">#3841</a>)</li> 16182<li>increase the default for the maximum number of failed PyTorch tests to 10 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3869">#3869</a>)</li> 16183<li>change <code>buildenv</code> easyblock: use <code>python3</code> as default path to Python executable in RPATH wrapper scripts (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3910">#3910</a>)</li> 16184<li>limit parallelism of OpenBLAS tests with parallel property (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3936">#3936</a>)</li> 16185<li>remove deprecated license classifier in setup.py (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3942">#3942</a>)</li> 16186</ul> 16187</li> 16188<li>code cleanup: <ul> 16189<li>simplify use of <code>
16189self.cfg.dependencies()</code> in <code>PETSc</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3813">#3813</a>)</li> 16190<li>stop setting <code>separate_build_dir</code> to <code>True</code> in various custom easyblock for Geant4 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3836">#3836</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3837">#3837</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3838">#3838</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3839">#3839</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3840">#3840</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3842">#3842</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3843">#3843</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3844">#3844</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3845">#3845</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3846">#3846</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3847">#3847</a>)</li> 16191<li>remove disabling libunwind on aarch64 for Mesa (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3908">#3908</a>)</li> 16192</ul> 16193</li> 16194</ul> 16195<p><strong>easyconfigs</strong></p> 16196<ul> 16197<li>add easyconfigs for <code>foss/2025b</code> and <code>intel/2025b</code> common toolchains (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23480">#23480</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23468">#23468</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23586">#23586</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23589">#23589</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23708">#23708</a>)</li> 16198<li>added example easyconfig files for 81 new software packages:<ul> 16199<li>aiida-core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20456">#20456</a>), asv (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23724">#23724</a>), autoCAS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23201">#23201</a>), BigStitcher-Spark (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23726">#23726</a>), BPCells (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23441">#23441</a>), cargo-c (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23437">#23437</a>), Chargemol (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20885">#20885</a>), CHARM++ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22281">#22281</a>), Cling (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23388">#23388</a>), CPCM-X (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23575">#23575</a>), dpcpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22418">#22418</a>), Eclipse-IDE-java (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19621">#19621</a>), Eclipse-SDK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19621">#19621</a>), Elixir (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20441">#20441</a>), ErlangOTP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20441">#20441</a>), EvtGen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19135">#19135</a>), flit-core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23306">#23306</a>), Flux (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22979">#22979</a>), GAlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23862">#23862</a>), glslang-SPIRV (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23171">#23171</a>), GoPeaks (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20932">#20932</a>), gpaw-data (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23666">#23666</a>), heat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23857">#23857</a>), hpc-container-wrapper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23701">#23701</a>), HPCToolkit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23830">#23830</a>), huggingface_hub (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23656">#23656</a>), iGUIDE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23467">#23467</a>), IMAS-Validator (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23052">#23052</a>), ipp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23691">#23691</a>), ipyparallel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23300">#23300</a>), LCov (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23752">
16199#23752</a>), libecpint (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16172">#16172</a>), libGDSII (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23456">#23456</a>), libneurosim (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23481">#23481</a>), libosmium (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23768">#23768</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23788">#23788</a>), libspng (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23485">#23485</a>), libtecla (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19874">#19874</a>), libtommath (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23570">#23570</a>), libvpx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23486">#23486</a>), lru-dict (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20593">#20593</a>), luaposix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22979">#22979</a>), Ludwig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23348">#23348</a>), MACE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23210">#23210</a>), mcpl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23224">#23224</a>), McXtrace (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22834">#22834</a>), MDSplus (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23531">#23531</a>), MFEM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21023">#21023</a>), minizip-ng (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23522">#23522</a>), mirtrace (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18781">#18781</a>), MongoDB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17366">#17366</a>), mpiP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16796">#16796</a>), numdifftools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23342">#23342</a>), numsa (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23575">#23575</a>), nvbandwidth (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23653">#23653</a>), NVPL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20456">#20456</a>), OpenColorIO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23522">#23522</a>), OpenQP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22739">#22739</a>), opt-einsum (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23322">#23322</a>), OSM-Express (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23771">#23771</a>), osmium-tool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23768">#23768</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23788">#23788</a>), PennCNV (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21827">#21827</a>), Planet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21302">#21302</a>), plumpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23469">#23469</a>), PPM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23225">#23225</a>), protozero (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23768">#23768</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23788">#23788</a>), pyOpenRiverCam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23540">#23540</a>), pyrosm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23771">#23771</a>), pystring (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23522">#23522</a>), QCMaquis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23201">#23201</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23980">#23980</a>), r5py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23345">#23345</a>), RabbitMQ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20441">#20441</a>), RDP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23344">#23344</a>), rkcommon (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23504">#23504</a>), RSAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23706">#23706</a>), schemdraw (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23265">#23265</a>), simplification (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23344">#23344</a>), SnapATAC2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23314">#23314</a>), starfile (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20634">#20634</a>), websockify (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23596">#23596</a>
16199), wxMacMolPlt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22187">#22187</a>), xmlto (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20441">#20441</a>)</li> 16200</ul> 16201</li> 16202<li>added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 16203<li>AmberTools 24.10 + 25.2, ASE 3.26.0, BLIS 2.0, CASTEP 25.1.2, CDO 2.5.3, CENSO 2.1.4, CGAL 6.0.1, CUDA 12.9.1 + 13.0.0, CUDA-Python 12.8.0, CUDA-Samples 12.9, 16204 CUTLASS 4.1.0, deepdiff 8.5.0, DualSPHysics 5.4.0, ecCodes 2.43.0, ELPA 2025.06.001, Emacs 30.1, GATE 10.0.2, GCC 15.2.0, GDAL 3.11.1, Go 1.25.0, GPAW 25.7.0, 16205 GROMACS 2025.2, GTK4 4.17.1, Highway 1.3.0, HTSlib 1.22.1, iomkl 2023b + 2024a + 2025a, jax 0.6.2 + 0.7.0, libxc 7.0.0, likwid 5.4.1, LLVM 20.1.8, lxml 6.0.0, 16206 magma 2.9.0, matplotlib 3.10.5, MixMHC2pred 2.0, modkit 0.5.0, MUST 1.11.1, NAMD 3.0.2, networkx 3.5, NLTK 3.9.1, numba 0.62.0, NVSHMEM 3.3.20, Octave 10.1.0, 16207 ollama 0.11.10, OpenCV 4.11.0, OpenMM 8.3.0, ORCA 6.1.0, Perl-bundle-CPAN 5.40.2, PETSc 3.23.5, pocl 7.0, PyStan 3.10.0, PYTHIA 8.2.45, Python-bundle-PyPI 2025.07, 16208 PyTorch 2.6.0, pytorch-3dunet 1.9.1, QuantumESPRESSO 7.5, ROOT 6.32.10, SAMtools 1.22.1, scikit-learn 1.7.0, SciPy-bundle 2025.07, Score-P 9.2, 16209 segmentation-models-pytorch 0.5.0, SeqKit 2.10.1, Siesta 5.4.1, SLEPc 3.23.2, SLiM 5.0, SUNDIALS 7.0.0, torchvision 0.21.0, X11 20250608, xarray 2025.7.0</li> 16210<li>add CodePlay CUDA SYCL plug-in variants for oneAPI 2023.0.0 to 2025.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21582">#21582</a>)</li> 16211</ul> 16212</li> 16213<li>minor enhancements, including:<ul> 16214<li>also install Python bindings in recent tblite 0.4.0 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23998">#23998</a>)</li> 16215</ul> 16216</li> 16217<li>various bug fixes, including:<ul> 16218<li>switch to <code>CargoPythonBundle</code> easyblock for orjson 3.9.15 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21392">#21392</a>)</li> 16219<li>run the tests in the test step for OpenMolcas (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22230">#22230</a>)</li> 16220<li>add patch to enable installing GLib typelibs for GObject-Introspection 1.80.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22309">#22309</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23444">#23444</a>)</li> 16221<li>use patch to fix pkgconfig file for GraphicsMagick 1.3.45 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22930">#22930</a>)</li> 16222<li>remove default <code>separate_build_dir = True</code> from various easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23296">#23296</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23303">#23303</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23315">#23315</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23317">#23317</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23327">#23327</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23328">#23328</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23329">#23329</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23332">#23332</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23334">#23334</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23335">#23335</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23336">#23336</a>)</li> 16223<li>fix setting of <code>PYSCF_INC_DIR</code> in build options and Python packages in <code>PySCF</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23325">#23325</a>)</li> 16224<li>fix <code>source_urls</code> for <code>FLINT</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23333">#23333</a>)</li> 16225<li>add libiconv build dependency to libarchive 3.8.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23353">#23353</a>)</li> 16226<li>
16226add patch to build versioned shared libraries in ecCodes v2.38.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23360">#23360</a>)</li> 16227<li>fix missing <code>-lm -lpthread</code> for SQLite 3.50.1 by setting <code>$LIBS</code> to empty string value (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23374">#23374</a>)</li> 16228<li>add patch to re-enable <code>-rpath-link</code> for builds with Meson 1.8.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23375">#23375</a>)</li> 16229<li>replace broken source URL with download instructions in easyconfigs for bcl2fastq2 2.20.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23427">#23427</a>)</li> 16230<li>add pkgconf build dependency for Tkinter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23428">#23428</a>)</li> 16231<li>add missing libxml2, libffi, zstd dependencies for LLVM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23429">#23429</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23555">#23555</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23603">#23603</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23608">#23608</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23609">#23609</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23610">#23610</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23611">#23611</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23612">#23612</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23613">#23613</a>)</li> 16232<li>fix outdated source URL for <code>occt</code> v7.5.0p1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23430">#23430</a>)</li> 16233<li>add patch to EasyBuild 5.1.1 easyconfig for bug that causes failures when copying readonly patches (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23442">#23442</a>)</li> 16234<li>add <code>pkgconf</code> build dep for <code>SentencePiece</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23444">#23444</a>)</li> 16235<li>restore easyconfig for ADMIXTURE v1.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23449">#23449</a>)</li> 16236<li>add <code>Perl</code> and <code>pkgconf</code> build dependencies to easyconfigs for PMIx 5.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23495">#23495</a>)</li> 16237<li>fix broken source URLs for Mesa versions 23.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23516">#23516</a>)</li> 16238<li>explicitly disable libgsasl support in cURL easyconfigs avoid picking up system library (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23519">#23519</a>)</li> 16239<li>add missing dependencies libxml2 & zstd to libarchive easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23520">#23520</a>)</li> 16240<li>fix hardcoded path to java binary in canu v2.3 + add OpenSSL dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23529">#23529</a>)</li> 16241<li>add patch for ESM-2 2.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23532">#23532</a>)</li> 16242<li>add additional patches for OpenMPI 5.0.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23556">#23556</a>)</li> 16243<li>disable flaky <code>LWP::Simple</code> test in <code>Perl</code> * <code>Perl-bundle-CPAN</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23564">#23564</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23565">#23565</a>)</li> 16244<li>add libtommath dependency to Tcl v9.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23568">#23568</a>)</li> 16245<li>fix installation of xtb 6.7.1 w/ <code>gfbf/2023b</code> by adding missing dependencies (mctc-lib, tblite, mstore, numsa, CPCM-X, dftd4, Simple-DFTD3) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23575">#23575</a>)</li> 16246<li>disable <code>lseq</code> tests when building Tcl 9.0.1 on Arm and RISC-V systems (to avoid hang in test step) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23617">#23617</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23619">#23619</a>)</li> 16247<li>fix version information for <code>cppy</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23625">#23625</a>)</li> 16248<li>
16248add patch for dask v2024.9.1 to fix incorrect indexing with boolean arrays (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23634">#23634</a>)</li> 16249<li>skip flaky sanitizer tests in easyconfig for LLVM 18.1.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23636">#23636</a>)</li> 16250<li>ignore failing time formatter tests for LLVM 20.1.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23637">#23637</a>)</li> 16251<li>add missing ASE versionsuffix for MACE and remove redundant ASE exception from easyconfigs test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23660">#23660</a>)</li> 16252<li>fix source for PARI-GP 2.15.x + add missing Bison build dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23662">#23662</a>)</li> 16253<li>update extensions for OCaml 4.14.0 and 5.1.1 to nearest version that is still available (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23664">#23664</a>)</li> 16254<li>install <code>strmap.h</code> in easyconfig for mpifileutils 0.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23676">#23676</a>)</li> 16255<li>fix homepage in easyconfigs for <code>intel</code> toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23695">#23695</a>)</li> 16256<li>update <code>source_urls</code> for <code>WCSLIB</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23722">#23722</a>)</li> 16257<li>fix incorrect configopts for GOTCHA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23732">#23732</a>)</li> 16258<li>apply small fix in <code>simnibs_segmentation_utils.py</code> of SimNIBS v4.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23748">#23748</a>)</li> 16259<li>add patch to git easyconfigs to fix CVE-2025-48384 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23769">#23769</a>)</li> 16260<li>update source URL for CFITSIO v4.3.0 to use <code>https://</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23775">#23775</a>)</li> 16261<li>add patch to allow SymEngine v0.7 to compile with <code>glibc</code> >= 2.34 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23817">#23817</a>)</li> 16262<li>fix build of ncurses 5.9 with system compiler on RHEL9 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23820">#23820</a>)</li> 16263<li>fix patch for torchtext to use system libraries, to fix linking of RE2 in both PyTorch-bundle and torchtext (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23823">#23823</a>)</li> 16264<li>add Simple-DFTD3 as dependency for CREST to avoid it being downloaded during the build (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23831">#23831</a>)</li> 16265<li>use <code>%%(source)s</code> in <code>STREAM</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23841">#23841</a>)</li> 16266<li>add patch to fix UCX-18.0.0 compatibility with CUDA 12.9 (R575) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23843">#23843</a>)</li> 16267<li>fix typo in <code>%(version)s</code> template in easyconfig for AlphaFold v2.3.2 w/ CUDA 12.1.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23850">#23850</a>)</li> 16268<li>fix SuiteSparse options for CVXOPT 1.2.6 w/ <code>foss/2021a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23864">#23864</a>)</li> 16269<li>fix specifying meson options to pass via <code>--config-settings</code> in <code>pip install</code> for matplotlib 3.9+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23872">#23872</a>)</li> 16270<li>replace broken source URL with download instructions in easyconfigs for bcl-convert 4.3.13 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23878">#23878</a>)</li> 16271<li>add patch for Boost 1.85.0 to fix UB on flat_map/multimap containers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23890">#23890</a>)</li> 16272<li>add missing ICU dependency to Xerces-C++ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23896">#23896</a>)</li> 16273<li>consistently apply patch for OpenMPI 5.x to fix compatibility with recent GPFS versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23908">#23908</a>)</li> 16274<li>
16274add patch to fix compatibility of OpenMPI 4.x >= 4.1.1 with recent GPFS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23911">#23911</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23916">#23916</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23917">#23917</a>)</li> 16275<li>fix sources for librttopo 1.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23921">#23921</a>)</li> 16276<li>add patch to LLVM 20.1.8 to better support CUDA 13 and Blackwell GPUs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23940">#23940</a>)</li> 16277<li>add patch to fix failing tests for <code>Net::SSLeay</code> 1.92 and <code>IO::Socket::SSL</code> 2.083 in Perl-bundle-CPAN easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23967">#23967</a>)</li> 16278<li>add missing zlib + zstd dependencies for Clang 18.1.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23983">#23983</a>)</li> 16279</ul> 16280</li> 16281<li>enhancements and fixes for test suite:<ul> 16282<li>add RISC-V support to R-bundle-CRAN easyconfigs by adding/improving patches for <code>liquidSVM</code> and <code>ff</code> extensions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21726">#21726</a>)</li> 16283<li>add patches for LLVM 20.1.5 required for RISC-V compatibility (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22656">#22656</a>)</li> 16284<li>include <code>intel-compilers</code> in the toolchain multi-variant checks (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23187">#23187</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23594">#23594</a>)</li> 16285<li>remove unused whitelist items for non HTTPS URLs in test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23235">#23235</a>)</li> 16286<li>add RISC-V checksum to Java 17.0.15 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23448">#23448</a>)</li> 16287<li>add NVPL backend to FlexiBLAS v3.4.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23563">#23563</a>)</li> 16288<li>add RTree module to SQLite 3.50.1, required by GDAL-3.11.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23765">#23765</a>)</li> 16289<li>enhance patch file to show output when LAMMPS Python package failed to install (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23774">#23774</a>)</li> 16290<li>add patch for ESPResSo v4.2.2 to allow specifying target CUDA architectures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23795">#23795</a>)</li> 16291</ul> 16292</li> 16293<li>other changes:<ul> 16294<li>remove redundant <code>default_easyblock</code> in PyQt5 and ml-dtypes easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22449">#22449</a>)</li> 16295<li>add InterProScan_data dependency to easyconfig for InterProScan 5.73-104.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22747">#22747</a>)</li> 16296<li>use LLVM easyblock for Clang 18 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23055">#23055</a>)</li> 16297<li>add explicit <code>R-bundle-CRAN</code> dependency to <code>R-bundle-Bioconductor</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23127">#23127</a>)</li> 16298<li>switch to <code>CMakeMake</code> easyblock and remove unused dependencies in <code>Armadillo/14.0.3-foss-2024a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23261">#23261</a>)</li> 16299<li>cleanup <code>icc</code>, <code>iccifort</code>, and <code>ifort</code> directories (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23230">#23230</a>)</li> 16300<li>remove final links to gforge (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23233">#23233</a>)</li> 16301<li>use minimal Graphviz as dependency for MUST v1.10.0 + also install prebuilds (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23308">#23308</a>)</li> 16302<li>use available custom easyblock for DualSPHysics v5.0.175 w/ CUDA 11.4.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23382">#23382</a>)</li> 16303<li>remove <code>'sanity_pip_check': True</code> from easyconfig templates (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23418">
16303#23418</a>)</li> 16304<li>remove <code>max_failed_tests</code> in PyTorch easyconfigs where the used value was less or equal to the default (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23577">#23577</a>)</li> 16305<li>update Java/21 wrapper to Java v21.0.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23677">#23677</a>)</li> 16306<li>replace ASE v3.25.0 with v3.26.0 for 2025b generation of easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23758">#23758</a>)</li> 16307<li>remove duplicate Pygments package from Python-bundle-PyPI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23801">#23801</a>)</li> 16308<li>move Biopython down to gfbf toolchain level (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23870">#23870</a>)</li> 16309<li>Unify system-lib options for matplotlib < 3.9 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23873">#23873</a>)</li> 16310<li>explicitly disable building documentation in recent <code>HarfBuzz</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23922">#23922</a>)</li> 16311<li>disable building of documentation for Waylandpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23968">#23968</a>)</li> 16312<li>remove deprecated license classifier in <code>setup.py</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23991">#23991</a>)</li> 16313</ul> 16314</li> 16315</ul> 16316<h2 id="release_notes_eb511">EasyBuild v5.1.1 (6 July 2025)<a class="headerlink" href="#release_notes_eb511" title="Permanent link">¶</a></h2> 16317<p>bugfix/update release</p> 16318<p><strong>framework</strong></p> 16319<ul> 16320<li>enhancements:<ul> 16321<li>don't allow using <code>--pr-commit-msg</code> when only adding new files with <code>--new-pr</code> (unless <code>--force</code> is used) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4498">#4498</a>)</li> 16322<li>update <code>install-EasyBuild-develop.sh</code> script to allow installation without forking (<a href="https://github.com/easybuilders/easybuild-framework/pull/4899">#4899</a>)</li> 16323<li>add blue, cyan, purple as known colors that can be used in colorize function (<a href="https://github.com/easybuilders/easybuild-framework/pull/4907">#4907</a>)</li> 16324<li>trigger <code>post_run_shell_cmd_hook</code> before raising error if shell command failed + pass down full <code>RunShellCmdResult</code> instance (<a href="https://github.com/easybuilders/easybuild-framework/pull/4908">#4908</a>)</li> 16325<li>also pass value of <code>fail_on_error</code> and <code>hidden</code> options of <code>run_shell_cmd</code> call down to pre/post <code>run_shell_cmd</code> hook (<a href="https://github.com/easybuilders/easybuild-framework/pull/4911">#4911</a>)</li> 16326<li>add configuration option to ignore unversioned (0.0.0) Python packages (<a href="https://github.com/easybuilders/easybuild-framework/pull/4912">#4912</a>)</li> 16327<li>add <code>required</code> option to <code>EasyConfig.get_cuda_cc_template_value</code> method (<a href="https://github.com/easybuilders/easybuild-framework/pull/4913">#4913</a>)</li> 16328<li>add total iteration count to trace output (<a href="https://github.com/easybuilders/easybuild-framework/pull/4919">#4919</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4952">#4952</a>)</li> 16329<li>add support for pre/post <code>easyblock</code> hook (<a href="https://github.com/easybuilders/easybuild-framework/pull/4923">#4923</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4938">#4938</a>)</li> 16330<li>catch <code>HTTPException</code> when doing GitHub API request (<a href="https://github.com/easybuilders/easybuild-framework/pull/4926">#4926</a>)</li> 16331</ul> 16332</li> 16333<li>bug fixes:<ul> 16334<li>fix reporting of method name in <code>EasyBlock.run_step</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4920">#4920</a>)</li> 16335<li>fix handling of broken symlinks in <code>filetools.remove</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4921">#4921</a>)</li> 16336<li>keep symlinks when copying build dirs of failed installations (<a href="https://github.com/easybuilders/easybuild-framework/pull/4933">#4933</a>)</li> 16337<li>also copy patches of extensions to easybuild subdirectory of installation directory (<a href="https://github.com/easybuilders/easybuild-framework/pull/4939">#4939</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4946">#4946</a>)</li> 16338<li>also copy easyblocks of bundle components to reprod dir (<a href="https://github.com/easybuilders/easybuild-framework/pull/4944">#4944</a>)</li> 16339<li>take into account that forked repository may not have same name as origin <code>--sync-pr-with-develop</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4947">#4947</a>)</li> 16340</ul> 16341</li> 16342<li>enhancements and fixes for test suite:<ul> 16343<li>add support for passing valid unittest options to test suite (<a href="https://github.com/easybuilders/easybuild-framework/pull/3790">#3790</a>)</li> 16344<li>enhance <code>LooseVersion</code> test to add cases with leading alphabetical characters (<a href="https://github.com/easybuilders/easybuild-framework/pull/4901">#4901</a>)</li> 16345<li>prefer using <code>importlib.metadata</code> over the deprecated <code>pkg_resources</code> in <code>det_pypkg_version</code> + switch container tests to Rocky Linux 8.10 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4904">#4904</a>)</li> 16346<li>fix <code>TypeError</code>
16346 for Python version comparison in <code>test_fetch_sources_git</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4934">#4934</a>)</li> 16347<li>fix broken tests for GitHub integration features (<a href="https://github.com/easybuilders/easybuild-framework/pull/4954">#4954</a>)</li> 16348</ul> 16349</li> 16350<li>other changes:<ul> 16351<li>change value of architectures constants RISCV32 and RISCV64 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4915">#4915</a>)</li> 16352<li>remove some superflous Python 2 checks (<a href="https://github.com/easybuilders/easybuild-framework/pull/4917">#4917</a>)</li> 16353<li>remove use of unsupported <code>source</code> key in patch spec (<a href="https://github.com/easybuilders/easybuild-framework/pull/4924">#4924</a>)</li> 16354<li>remove super() arguments from mk_tmpl_easyblock_for (<a href="https://github.com/easybuilders/easybuild-framework/pull/4936">#4936</a>)</li> 16355</ul> 16356</li> 16357</ul> 16358<p><strong>easyblocks</strong></p> 16359<ul> 16360<li>new easyblocks:<ul> 16361<li>add custom easyblock for BLIS, which can also be used for AOCL-BLAS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3773">#3773</a>)</li> 16362</ul> 16363</li> 16364<li>enhancements:<ul> 16365<li>add support for iterative build of OpenBLAS with 64-bit integers (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2753">#2753</a>)</li> 16366<li>add Kokkos mapping for AMD zen4 and NVIDIA Grace to LAMMPS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3742">#3742</a>)</li> 16367<li>enhance LLVM easyblock to use <code>dlopen</code> for AMDGPU/CUDA libomptarget / offload target libraries (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3747">#3747</a>)</li> 16368<li>enhance Rust easyblock to allow specifying channel to use (stable vs nightly) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3749">#3749</a>)</li> 16369<li>enhance <code>run_pip_check</code> function to respect EasyBuild configuration option to ignore unversioned (0.0.0) Python packages (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3753">#3753</a>)</li> 16370<li>enhance SuperLU easyblock to set configure options for ParMETIS (or disable it if ParMETIS is not a dependency) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3767">#3767</a>)</li> 16371<li>symlink CUPTI files to standard locations in CUDA installation (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3791">#3791</a>)</li> 16372<li>enhance <code>PythonPackage</code> to allow specifying location to temporary installation used in test step + also update <code>$PATH</code> to pick up on binaries/scripts from it (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3797">#3797</a>)</li> 16373<li>add support for <code>UCX</code>, <code>CUDA</code> and <code>mpi_abi</code> directly in MPICH easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3807">#3807</a>)</li> 16374<li>refactor LLVM easyblock and install OpenMP library symlinks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3815">#3815</a>)</li> 16375<li>enhance <code>Bundle</code> generic easyblock to also run test step for each bundle component (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3748">#3748</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3752">#3752</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3775">#3775</a>)</li> 16376</ul> 16377</li> 16378<li>updates:<ul> 16379<li>remove <code>2to3</code> file from sanity check in Anaconda easyblock (no longer there in recent versions) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3761">#3761</a>)</li> 16380<li>update numpy easyblock to support installing numpy >= 2.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3777">#3777</a>)</li> 16381<li>update Mesa easyblock to use not use removed <code>swrast</code> as gallium driver for Mesa versions >= 25.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3790">#3790</a>)</li> 16382</ul> 16383</li> 16384<li>bug fixes:<ul> 16385<li>bug fixes for custom easyblock for LLVM:</li> 16386<li>ensure sysroot dynamic linker is used + add ignore patterns for failing tests that can be ignored in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3741">#3741</a>)</li> 16387<li>fix configuration option for OpenMP offload target + logic in sanity check step in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3755">#3755</a>)</li> 16388<li>use <code>self.start_dir</code> in LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3770">#3770</a>)</li> 16389<li>moved logic from the constructor to <code>configure_step</code> in LLVM easyblock (so it can be used to install bundle component) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3781">#3781</a>)</li> 16390<li>fix LLVM easyblock to allow building with multiple versions at once (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3812">#3812</a>)</li> 16391<li>do not create compiler configs for LLVM < 19 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3817">#3817</a>)</li> 16392<li>fix condition to ignore failed LLVM GPU tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3819">#3819</a>)</li> 16393<li>fix/simplify use of <code>
16393self.cfg.dependencies()</code> in various easyblocks: <code>CMake</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3810">#3810</a>), <code>OpenFOAM</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3814">#3814</a>), <code>PETSc</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3813">#3813</a>), <code>SLEPc</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3811">#3811</a>), <code>Term::ReadLine::Gnu</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3808">#3808</a>)</li> 16394<li>take into account that <code>f90wrap_version</code> may be <code>None</code> in MetalWalls easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3468">#3468</a>)</li> 16395<li>fix <code>enhance_sanity_check</code> for <code>PythonPackage</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3477">#3477</a>)</li> 16396<li>improve reliability of PyTorch test reporting (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3723">#3723</a>)</li> 16397<li>also install OpenCOSMORS for ORCA versions >= 6.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3726">#3726</a>)</li> 16398<li>fix missed f-string in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3729">#3729</a>)</li> 16399<li>use <code>--enable-install-libiberty</code> to enable <code>libiberty</code> for <code>binutils</code> + move <code>libiberty.a</code> binutils library to <code>lib</code> subdirectory if it's the only file in <code>lib64</code> subdirectory (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3736">#3736</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3822">#3822</a>)</li> 16400<li>make sure RPATH wrappers shipped via <code>buildenv</code> are world executable (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3743">#3743</a>)</li> 16401<li>take into account that <code>$PYTHONPATH</code> and <code>$PATH</code> may be unset in configure step of custom easyblock for scipy (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3744">#3744</a>)</li> 16402<li>set <code>$HOME</code> to temporary folder for TensorFlow build and tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3751">#3751</a>)</li> 16403<li>fix unbound variable <code>install_args</code> in Conda easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3763">#3763</a>)</li> 16404<li>set <code>$CARGO_NET_OFFLINE</code> to <code>true</code> in <code>set_cargo_vars</code> method of <code>Cargo</code> easyblock (only if <code>offline</code> mode is used), so it's set for every extension when <code>CargoPythonBundle</code> easyblock is used (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3764">#3764</a>)</li> 16405<li>fix test step for <code>CMakeNinja</code> easyblock by customizing <code>test_cmd</code> and <code>runtest</code> easyconfig parameters (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3771">#3771</a>)</li> 16406<li>use <code>parallel</code> property rather than value of (deprecated) <code>parallel</code> easyconfig parameter in ORCA easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3772">#3772</a>)</li> 16407<li>(re)set environment variables used by <code>cargo</code> in prepare step of <code>Cargo</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3774">#3774</a>)</li> 16408<li>don't forcibly set <code>$LD_LIBRARY_PATH</code> in LAMMPS sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3776">#3776</a>)</li> 16409<li>add missing call to <code>make_module_step</code> for components in <code>Bundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3801">#3801</a>)</li> 16410<li>add support for hwloc to MPICH easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3821">#3821</a>)</li> 16411</ul> 16412</li> 16413<li>enhancements and fixes for test suite:<ul> 16414<li>allow test case filtering and other <code>unittest</code> arguments (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3653">#3653</a>)</li> 16415</ul> 16416</li> 16417<li>other changes:<ul> 16418<li>disable trace output when unpacking crates in Cargo easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3750">#3750</a>)</li> 16419<li>update Rust easyblock to disable installations of docs via <code>--disable-docs</code> configure option (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3768">#3768</a>)</li> 16420<li>simplify remaining <code>super()</code> calls (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3780">#3780</a>)</li> 16421<li>handle <code>$PATH</code> environment variable with <code>module_load_environment</code> in init of <code>Binary</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3787">#3787</a>)</li> 16422<li>change ABAQUS easyblock to use <code>LM_LICENSE_FILE</code> instead of <code>ABAQUSLM_LICENSE_FILE</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3794">#3794</a>)</li> 16423</ul> 16424</li> 16425</ul> 16426<p><strong>easyconfigs</strong></p> 16427<ul> 16428<li>added example easyconfig files for 105 new software packages:<ul> 16429<li>amdsmi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23279">#23279</a>), ANTx2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13819">#13819</a>), ASAGI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21065">#21065</a>), bipartite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21623">#21623</a>), BLAKE3-C (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22476">#22476</a>), btop (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21373">#21373</a>), climate-indices (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22015">#22015</a>), 16430 ClustalW (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21973">#21973</a>), cowsay (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22976">#22976</a>), CrossMap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22089">#22089</a>), csvtk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15305">#15305</a>), DiffDRR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20656">#20656</a>), dssp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22155">#22155</a>), Dyninst (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22946">#22946</a>), 16431 easi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21065">#21065</a>), EMD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22734">#22734</a>), etils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22642">#22642</a>), evaluate (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22809">
16431#22809</a>), EvoDiff (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19939">#19939</a>), Extra-P (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22907">#22907</a>), FEBio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22999">#22999</a>), 16432 fineSTRUCTURE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19817">#19817</a>), ForceBalance (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22978">#22978</a>), FUNAERO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23067">#23067</a>), GADGET (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21625">#21625</a>), GENESPACE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21973">#21973</a>), Gephi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13231">#13231</a>), 16433 GIBBON (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23044">#23044</a>), Ginkgo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22719">#22719</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23078">#23078</a>), googlebenchmark (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22641">#22641</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23176">#23176</a>), GTKWave-GTK3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23020">#23020</a>), h5glance (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23243">#23243</a>), h5pyd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21743">#21743</a>), 16434 HiCTools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22528">#22528</a>), huggingface-hub (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19991">#19991</a>), IcarusVerilog (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23021">#23021</a>), IMAS-Data-Dictionary (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22933">#22933</a>), IMAS-Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22630">#22630</a>), 16435 ImpalaJIT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21065">#21065</a>), Infomap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21296">#21296</a>), intel-mbuild (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23189">#23189</a>), intel-XED (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23189">#23189</a>), ITK-SNAP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13232">#13232</a>), JACUSA2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23095">#23095</a>), 16436 Juicebox (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22530">#22530</a>),KITE-Tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17138">#17138</a>), Kornia (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22938">#22938</a>), levmar (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22999">#22999</a>), libbacktrace (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20738">#20738</a>), libcifpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22155">#22155</a>), 16437 libetsf_io (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23170">#23170</a>), libmcfp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22155">#22155</a>), MagicVLSI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23018">#23018</a>), MCScanX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21973">#21973</a>), mdocfile (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20610">#20610</a>), MetaGeneMark-2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22531">#22531</a>), 16438 metaMDBG (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22014">#22014</a>), MIGEC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22989">#22989</a>), Minimac3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22382">
16438#22382</a>), mOTUlizer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22524">#22524</a>), mrc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22155">#22155</a>), MRIcron (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13819">#13819</a>), msgpack-cxx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23098">#23098</a>), 16439 mumax3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20743">#20743</a>), NAGlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22184">#22184</a>), nanobind (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22414">#22414</a>), Netgen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23019">#23019</a>), PeptideShaker (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23070">#23070</a>), pybigtools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22800">#22800</a>), 16440 Pychopper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22943">#22943</a>), pycomlink (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22974">#22974</a>), pyiron-gpl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23122">#23122</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23154">#23154</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23220">#23220</a>), PyMDE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19713">#19713</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19715">#19715</a>), python-gdcm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20664">#20664</a>), 16441 python-glfw (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22642">#22642</a>), rmats2sashimiplot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19659">#19659</a>), robin-map (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22413">#22413</a>), scalescape (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23038">#23038</a>), scatac_fragment_tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22800">#22800</a>), 16442 SdfLib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22642">#22642</a>), SEACR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22526">#22526</a>), SearchGUI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23309">#23309</a>), SeisSol (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21065">#21065</a>), SLICOT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19860">#19860</a>), snipit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22266">#22266</a>), snp-dists (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20996">#20996</a>), 16443 soapcheckr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22939">#22939</a>), spacyr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22803">#22803</a>), spin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23023">#23023</a>), TBProfiler (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23014">#23014</a>), tdb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22911">#22911</a>), tinyobjloader (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22642">#22642</a>), TinyXML-2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22642">#22642</a>), 16444 tinyxml2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22476">#22476</a>), tmpi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22949">#22949</a>), trame (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20993">#20993</a>), TRIQS-som (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23242">#23242</a>), tueplots (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21335">#21335</a>), USalign (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22463">#22463</a>), vireoSNP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22660">#22660</a>), 16445 WarpX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19784">#19784</a>), WebDataset (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22062">#22062</a>), XeniumRanger (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20135">#20135</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20974">#20974</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21751">#21751</a>), xschem (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23017">#23017</a>), yMMSL-dot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20906">#20906</a>)</li> 16446</ul> 16447</li> 16448<li>
16448added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 16449<li>Abseil 20250512.1, ABySS 2.3.10, Amber 24.3 + AmberTools 24.10, aria2 1.37.0, ASE 3.25.0, Autotools 20250527, 16450 BindCraft 1.5.1, Blender 4.3.2, Boost 1.88.0, BUSCO 5.8.2, CMake 4.0.3, code-server 4.100.2, CUDA-Python 12.4.0, 16451 cuDNN 9.10.1.4 , cutadapt 5.1, Dakota 6.22.0, DaliLite 5.0, datamash 1.9, DeltaLake 0.25.5, DFTB+ 24.1, DGL 1.1.3, 16452 ELFIO 3.12, Embree 4.4.0, FFmpeg 7.1.1, FHI-aims 240920, Fiona 1.10.1, FLAC 1.5.0, flatbuffers-python 24.3.25, 16453 Flink 2.0.0, FLTK 1.4.3, FLUENT 2024R1, GDB 16.3, Geant4 11.3.0, git-lfs 3.6.1, GLib 2.85.1, Globus-CLI 3.34.0, 16454 googletest 1.17.0, gperf 3.3, GPyTorch 1.11, Gradle 8.14.2, h5py 3.14.0, HDF5 1.14.6, humann 3.9, intel-compilers 2025.2.0, 16455 IPython 9.3.0, Jupyter-bundle 20250530, JupyterHub 5.3.0, Levenshtein 0.25.1, libfabric 2.1.0, libjpeg-turbo 3.1.0, 16456 libpng 1.6.48, MAQAO 2025.1.0, matlab-proxy 0.25.1, matplotlib 3.10.3, MDAnalysis 2.9.0, Meson 1.8.2, mpi4py 4.1.0, 16457 MUSCLE3 0.8.0, MUST 1.10.0, Nextflow 25.04.6, ngspice 44.2, Ninja 1.13.0, NLopt 2.10.0, nodejs 22.16.0, nsync 1.29.2, 16458 openCARP 18.0, OpenFAST 3.5.2, OSPRay 3.2.0, OVITO 3.11.0, oxDNA 3.6.0, panaroo 1.5.1, PAPI 7.2.0, phonopy 2.40.0, 16459 Pillow 11.3.0, pkgconf 2.4.3, polars 1.28.1, poppunk 2.6.7, PostgreSQL 17.5, preCICE 3.2.0, PROJ 9.5.1, py3Dmol 2.5.0, 16460 Python 3.13.5, PyZMQ 27.0.0, Ray-project 2.47.1, RDKit 2025.03.3, re2c 4.2, RevBayes 1.3.0, rMATS-turbo 4.3.0, 16461 rocm-smi 7.6.0 w/ ROCm 6.4.1, scNanoGPS 2.0, Siesta 5.4.0, SNAP-ESA 12.0.0, Sniffles 2.4, strace 6.14, Tcl 9.0.1, 16462 TensorFlow 2.18.1, tensorflow-probability 0.23.0, Triton 3.1.0, ViennaRNA 2.7.0, X11 20250521, XZ 5.8.1</li> 16463</ul> 16464</li> 16465<li>minor enhancements, including:<ul> 16466<li>add libheif dependency to JasPer easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22055">#22055</a>)</li> 16467<li>add ggpicrust2 and required dependencies to R-bundle-Bioconductor v3.20 and R-bundle-CRAN v2024.11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23026">#23026</a>)</li> 16468</ul> 16469</li> 16470<li>various bug fixes, including:<ul> 16471<li>use patch to fix finding libraries when linking ImageMagick (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21640">#21640</a>)</li> 16472<li>build CORSIKA v77550 in installation directory (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21868">#21868</a>)</li> 16473<li>add missing Python dependency to Bowtie easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22277">#22277</a>)</li> 16474<li>add patch for ParaView 5.12.0 to fix VTK HDF5 mangling (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22501">#22501</a>)</li> 16475<li>add patch for RISC-V architecture detection to easyconfig for ncbi-vdb 3.1.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22543">#22543</a>)</li> 16476<li>fix beagle-lib dependency for MrBayes 3.2.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22959">#22959</a>)</li> 16477<li>inject missing RPATH entries for QuPath (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22964">#22964</a>)</li> 16478<li>guide OpenFOAM to find the correct Python by patching <code>CMakeLists.txt</code> and setting <code>$Python3_ROOT_DIR</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22969">#22969</a>)</li> 16479<li>use Rust with nightly channel as build dependency for polars 0.19.19 + 0.20.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22984">#22984</a>)</li> 16480<li>add missing f-string in mixed component bundle easyconfig templates (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22996">#22996</a>)</li> 16481<li>fix build failure in M4 1.4.19 when C standard is set (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22998">#22998</a>)</li> 16482<li>add patch to fix failing OCSP stapling test for <code>IO::Socket::SSL</code> extension in Perl-bundle-CPAN easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23030">#23030</a>)</li> 16483<li>fix source URL for c-ares (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23057">#23057</a>)</li> 16484<li>ensure that configure step of Zoltan uses an up-to-date <code>config.guess</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23068">#23068</a>)</li> 16485<li>
16485add patch for porefoam 2023-12-01 to make sure that case directory has user write permissions after copying (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23071">#23071</a>)</li> 16486<li>add patch to fix support for non-x86_64 architectures for MEGAHIT 1.2.9 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23073">#23073</a>)</li> 16487<li>fix failing contourpy installation in matplotlib-3.7.2-iimkl-2023a with RPATH (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23079">#23079</a>)</li> 16488<li>update colabdesign extension to required version 1.1.3 in easyconfig for BindCraft 1.5.1 + add modloadmsg (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23087">#23087</a>)</li> 16489<li>update homepage URL for IsoSeq to correct repository link (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23094">#23094</a>)</li> 16490<li>add missing zlib dependency to <code>Serf</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23118">#23118</a>)</li> 16491<li>add Perl build dependency for groff 1.23.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23123">#23123</a>)</li> 16492<li>add missing Perl dependency for OpenPGM + make sure Perl scripts use it (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23126">#23126</a>)</li> 16493<li>also make <code>dssp</code> and <code>DAlphaBall.gcc</code> scripts and binaries in functions subdirectory executable for BindCraft v1.5.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23136">#23136</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23195">#23195</a>)</li> 16494<li>fix sanity check commands for MinPath 1.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23151">#23151</a>)</li> 16495<li>update homepage for Pango 1.54.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23185">#23185</a>)</li> 16496<li>enable <code>-fPIC</code> (and OpenMP) for phono3py 2.7.0 using standard <code>toolchainopts</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23198">#23198</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23207">#23207</a>)</li> 16497<li>update <code>source_urls</code> in <code>PDT</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23234">#23234</a>)</li> 16498<li>switch homepage for <code>libxml2</code>, <code>libxml2-python</code>, and <code>libxslt</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23236">#23236</a>)</li> 16499<li>drop incorrect Java dependency from Gephi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23241">#23241</a>)</li> 16500<li>add hwloc dependency to MPICH easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23260">#23260</a>)</li> 16501<li>switch to correct Pillow dep (non SIMD as its not actually updated) for matplotlib in 2024a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23264">#23264</a>)</li> 16502<li>switch to using Pillow 10.2.0 instead of incorrect Pillow-SIMD 10.4.0 for 2023b easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23266">#23266</a>)</li> 16503<li>make Mesa 24.1.3 use standard LLVM to avoid dependency conflicts (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23267">#23267</a>)</li> 16504<li>add missing Python dependency to rocm-smi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23301">#23301</a>)</li> 16505<li>add G4CHANNELING to Geant4-data v11.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23321">#23321</a>)</li> 16506</ul> 16507</li> 16508<li>enhancements and fixes for test suite:<ul> 16509<li>improve check for multi-variant dependencies per generation of easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12687">#12687</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23177">#23177</a>)</li> 16510<li>improve output of styletest on failure (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22515">#22515</a>)</li> 16511<li>clean up <code>alt_dep_versions</code> in test to check for dependency variants (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23179">#23179</a>)</li> 16512<li>set a <code>User-Agent</code> for the https/http check (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23245">#23245</a>)</li> 16513<li>cleanup old items in whitelists in test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23297">#23297</a>)</li> 16514<li>also check on post-install patches in easyconfigs test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23331">#23331</a>)</li> 16515</ul> 16516</li> 16517<li>other changes:<ul> 16518<li>fix order of easyconfig parameters in enchant-2 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22050">#22050</a>)</li> 16519<li>only build static libraries for googletest 1.14.0 and 1.15.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22641">#22641</a>)</li> 16520<li>archive old easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22954">#22954</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22955">#22955</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22960">#22960</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23005">#23005</a>)</li> 16521<li>archive Java 1.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22968">#22968</a>)</li> 16522<li>make Rust a build dependency for maturin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22980">#22980</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22981">#22981</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22982">#22982</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22983">#22983</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22985">#22985</a>)</li> 16523<li>use <code>Binary</code> easyblock instead of <code>JAR</code> in <code>HiCTools</code> + <code>Juicebox</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22995">#22995</a>)</li> 16524<li>migrate pre-2021 easyconfigs and Java 1.8 into archive repo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23005">#23005</a>)</li> 16525<li>replace deprecated <code>usepolly</code> with <code>use_polly</code> in LLVM easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23033">
16525#23033</a>)</li> 16526<li>update SuperLU_DIST easyconfigs to rely on updated SuperLU easyblock for configure options for ParMETIS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23075">#23075</a>)</li> 16527<li>update <code>nvptx-tools</code> version to fix compatibility with CUDA 12 in easyconfigs for GCCcore 12.x and 13.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23077">#23077</a>)</li> 16528<li>use BLIS easyblock for recent BLIS and AOCL-BLAS easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23088">#23088</a>)</li> 16529<li>move toolchain from <code>foss</code> to <code>gfbf</code> for bx-python v0.13.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23101">#23101</a>)</li> 16530<li>clarify use of download_instructions parameter in test_downloadable_or_instructions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23103">#23103</a>)</li> 16531<li>remove dependency on Python-bundle-PyPI from pytest v8.3.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23109">#23109</a>)</li> 16532<li>use <code>c-ares</code> 1.34.5 dependency for <code>tensorstore</code> 0.1.72 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23132">#23132</a>)</li> 16533<li>use newer version of <code>pydantic</code> dependency in 2023b toolchain generation (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23137">#23137</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23138">#23138</a>)</li> 16534<li>switch <code>CESM-deps</code> to use latest <code>git-lfs</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23115">#23115</a>)</li> 16535<li>delete all old <code>git-lfs</code> easyconfigs (CVE-2024-53263) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23116">#23116</a>)</li> 16536<li>skip building the docs to avoid <code>ImageMagick</code> (<code>convert</code>) build dependency for <code>giflib</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23182">#23182</a>)</li> 16537<li>clean up old patches (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23231">#23231</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23330">#23330</a>)</li> 16538<li>switch to https for homepage/source for ITSTool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23237">#23237</a>)</li> 16539<li>update MPICH easyconfigs to rely on enhanced custom easyblock for MPICH (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23239">#23239</a>)</li> 16540<li>remove <code>packaging</code> extension from easyconfigs for <code>scikit-build</code> 0.17.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23258">#23258</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23259">#23259</a>)</li> 16541<li>remove default <code>separate_build_dir = True</code> from various easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23273">#23273</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23274">#23274</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23275">#23275</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23277">#23277</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23278">#23278</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23284">#23284</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23285">#23285</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23286">#23286</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23287">#23287</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23294">#23294</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23310">#23310</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23311">#23311</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23316">#23316</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23318">#23318</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23319">#23319</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23324">#23324</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23326">#23326</a>)</li> 16542<li>update <code>dotNET-Core/8.0</code> to dotNET-Core v8.0.411 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/23289">#23289</a>)</li> 16543</ul> 16544</li> 16545</ul> 16546<h2 id="release_notes_eb510">EasyBuild v5.1.0 (26 May 2025)<a class="headerlink" href="#release_notes_eb510" title="Permanent link">¶</a></h2> 16547<p>feature release</p> 16548<p><strong>framework</strong></p> 16549<ul> 16550<li>various enhancements, including:<ul> 16551<li>add support for data installations (<a href="https://github.com/easybuilders/easybuild-framework/pull/4474">#4474</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4873">#4873</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4874">#4874</a>)</li> 16552<li>allow specifying location for RPATH wrapper scripts via <code>rpath_wrappers_dir</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4596">#4596</a>)</li> 16553<li>
16553add a CUDA device code sanity check (<a href="https://github.com/easybuilders/easybuild-framework/pull/4692">#4692</a>)</li> 16554<li>add support for <code>check_readelf_rpath</code> easyconfig parameter to optionally skip RPATH checks (<a href="https://github.com/easybuilders/easybuild-framework/pull/4768">#4768</a>)</li> 16555<li>add support for using environment variables in value used in <code>modextravars</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4855">#4855</a>)</li> 16556<li>print summary after the build in trace output (<a href="https://github.com/easybuilders/easybuild-framework/pull/4861">#4861</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4875">#4875</a>)</li> 16557<li>avoid leaking keys by mistake with <code>--upload-test-report</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4877">#4877</a>)</li> 16558<li>obtain PR/commit diff via GitHub API rather than downloading <code>*.diff</code> file via github.com (<a href="https://github.com/easybuilders/easybuild-framework/pull/4878">#4878</a>)</li> 16559<li>support options for <code>patch</code> command (<a href="https://github.com/easybuilders/easybuild-framework/pull/4886">#4886</a>)</li> 16560<li>replace full trace message for extension check command with simple pass/fail message (<a href="https://github.com/easybuilders/easybuild-framework/pull/4892">#4892</a>)</li> 16561</ul> 16562</li> 16563<li>various bug fixes, including:<ul> 16564<li>also pass <code>rpath_include_dirs</code> when preparing build environment for extensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4596">#4596</a>)</li> 16565<li>fix <code>check_checksums</code> when <code>nosource: True</code> is used (<a href="https://github.com/easybuilders/easybuild-framework/pull/4806">#4806</a>)</li> 16566<li>fix help string of <code>findPythonDeps.py</code> script (<a href="https://github.com/easybuilders/easybuild-framework/pull/4821">#4821</a>)</li> 16567<li>take into account <code>job-output-dir</code> option in Slurm job backend (<a href="https://github.com/easybuilders/easybuild-framework/pull/4842">#4842</a>)</li> 16568<li>fix unbound variable in error case in <code>build_and_install_software</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4843">#4843</a>)</li> 16569<li>avoid failure when only some passed easyconfigs exist (<a href="https://github.com/easybuilders/easybuild-framework/pull/4847">#4847</a>)</li> 16570<li>restore original value for non-list easyconfig parameter values that are considered for iterating over (<a href="https://github.com/easybuilders/easybuild-framework/pull/4848">#4848</a>)</li> 16571<li>add <code>-</code> before <code>DMKL_ILP64</code> in <code>$CFLAGS</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4850">#4850</a>)</li> 16572<li>enhance RPATH sanity check to skip anything whose absolute path resolves to outside the install dir (<a href="https://github.com/easybuilders/easybuild-framework/pull/4854">#4854</a>)</li> 16573<li>use new <code>ModEnvVarType.STRICT_PATH_WITH_FILES</code> with <code>CMAKE_LIBRARY_PATH</code> environment variable (<a href="https://github.com/easybuilders/easybuild-framework/pull/4858">#4858</a>)</li> 16574<li>fix <code>is_patch_for</code> for patch dicts (<a href="https://github.com/easybuilders/easybuild-framework/pull/4865">#4865</a>)</li> 16575<li>update fake module for each extension installed (<a href="https://github.com/easybuilders/easybuild-framework/pull/4868">#4868</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4888">#4888</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4895">#4895</a>)</li> 16576<li>implement exponential backoff in <code>download_file</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4870">#4870</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4880">#4880</a>)</li> 16577<li>use <code>develop</code> branch for PRs that target removed <code>5.0.x</code> branch in <code>fetch_files_from_pr</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4879">#4879</a>)</li> 16578<li>also ignore errors raised during test step when <code>--ignore-test-failure</code> is used (<a href="https://github.com/easybuilders/easybuild-framework/pull/4881">#4881</a>)</li> 16579<li>fix download progress bar (<a href="https://github.com/easybuilders/easybuild-framework/pull/4885">#4885</a>)</li> 16580<li>fix <code>--dep-graph</code> by using <code>graphviz</code> Python package (<a href="https://github.com/easybuilders/easybuild-framework/pull/4891">#4891</a>)</li> 16581</ul> 16582</li> 16583<li>fixes for test suite:<ul> 16584<li>fix <code>test_github_preview_pr</code> which got broken because there's no more easyconfigs for bzip2 1.0.6 in easyconfigs repo (<a href="https://github.com/easybuilders/easybuild-framework/pull/4827">#4827</a>)</li> 16585<li>fix tests after removal of 5.0.x branch (<a href="https://github.com/easybuilders/easybuild-framework/pull/4830">#4830</a>)</li> 16586<li>fix missed message in trivial equal-asserts (<a href="https://github.com/easybuilders/easybuild-framework/pull/4831">#4831</a>)</li> 16587<li>
16587fix wrong variable name used for Python version in linting CI (<a href="https://github.com/easybuilders/easybuild-framework/pull/4839">#4839</a>)</li> 16588<li>fix failing GitHub integration CI tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/4841">#4841</a>)</li> 16589<li>fix testsuite badge in README (<a href="https://github.com/easybuilders/easybuild-framework/pull/4845">#4845</a>)</li> 16590</ul> 16591</li> 16592<li>other changes:<ul> 16593<li>go back to using <code>develop</code> branch rather than <code>5.0.x</code> branch in GitHub Actions workflows (<a href="https://github.com/easybuilders/easybuild-framework/pull/4820">#4820</a>)</li> 16594<li>remove source tarball for Python 3.7.2 from test sources (<a href="https://github.com/easybuilders/easybuild-framework/pull/4828">#4828</a>)</li> 16595<li>delete <code>.coveragerc</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4833">#4833</a>)</li> 16596<li>remove Python 2 constructs (<a href="https://github.com/easybuilders/easybuild-framework/pull/4834">#4834</a>)</li> 16597<li>remove superflous assignment in <code>_sanity_check_step</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4851">#4851</a>)</li> 16598<li>replace deprecation warning about reproducible tarballs on Python older than 3.9 with a regular warning (<a href="https://github.com/easybuilders/easybuild-framework/pull/4852">#4852</a>)</li> 16599<li>move <code>EasyBlock.expand_module_search_path</code> into <code>ModuleEnvironmentVariable.expand_paths</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4859">#4859</a>)</li> 16600</ul> 16601</li> 16602</ul> 16603<p><strong>easyblocks</strong></p> 16604<ul> 16605<li>new easyblocks:<ul> 16606<li>add generic <code>Dataset</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3246">#3246</a>)</li> 16607<li>add custom easyblock for VSCode (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3638">#3638</a>)</li> 16608<li>add back easyblock for fastStructure which was removed in EasyBuild v5.0.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3642">#3642</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3692">#3692</a>)</li> 16609<li>add custom easyblock for <code>Term::ReadLine::Gnu</code> Perl module (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3712">#3712</a>)</li> 16610</ul> 16611</li> 16612<li>various enhancements, including:<ul> 16613<li>generate version from the source files for LAMMPS when using <code>software-commit</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3485">#3485</a>)</li> 16614<li>add support for <code>optarch</code> to <code>GoPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3503">#3503</a>)</li> 16615<li>add support for <code>neoverse_n1</code> instances of Azure (cortex-a72) to LAMMPs easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3580">#3580</a>)</li> 16616<li>enhance <code>BuildEnv</code> generic easyblock to copy RPATH wrapper scripts from build environment to installation directory (if available) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3661">#3661</a>)</li> 16617<li>add option to impi easyblock to rebuild Fortran 2008 bindings (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3678">#3678</a>)</li> 16618<li>also install <code>easybuild</code> package for <code>EasyBuild >= 5</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3700">#3700</a>)</li> 16619<li>enhance <code>Cargo</code> easyblock to handle single-line members in workspaces (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3705">#3705</a>)</li> 16620<li>generate an egg-info file for the <code>easybuild</code> meta package (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3725">#3725</a>)</li> 16621<li>produce clean trace message for '<code>pip check</code>' (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3732">#3732</a>)</li> 16622</ul> 16623</li> 16624<li>various updates:<ul> 16625<li>minor updates to ABAQUS easyblock to make hotfixes 2441 and 2424 working (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3512">#3512</a>)</li> 16626<li>update easyblock for AEDT 2025R1 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3644">#3644</a>)</li> 16627<li>update Amber easyblock for version 24.x and newer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3685">#3685</a>)</li> 16628<li>update TensorFlow easyblock for v2.18.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3699">#3699</a>)</li> 16629<li>do not build <code>ld.gold</code> with binutils 2.44 or newer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3703">#3703</a>)</li> 16630</ul> 16631</li> 16632<li>various bug fixes, including:<ul> 16633<li>run <code>pip check</code> only once for <code>PythonBundle</code> and <code>Python</code> installations (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3432">#3432</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3730">#3730</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3731">#3731</a>)</li> 16634<li>avoid failure in Python package installation and sanity check when <code>$PIP_REQUIRE_VIRTUALENV</code>
16634 is set (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3460">#3460</a>)</li> 16635<li>fix handling of maximum Python version in <code>pick_python_cmd</code> function in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3478">#3478</a>)</li> 16636<li>unset PMIX environment variables when configuring OpenMPI (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3511">#3511</a>)</li> 16637<li>various fixes for LLVM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3674">#3674</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3690">#3690</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3695">#3695</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3706">#3706</a>)</li> 16638<li>enhance LLVM EasyBlock to better handle offload builds (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3675">#3675</a>)</li> 16639<li>fix <code>make_module_extra</code> methods for easyblocks that derive from <code>ExtensionEasyBlock</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3681">#3681</a>)</li> 16640<li>fix access to unassigned variable when installing Python < 3.9.1 with using sysroot (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3686">#3686</a>)</li> 16641<li>update QuantumESPRESSO easyblock to use <code>cfg.parallel</code> property (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3688">#3688</a>)</li> 16642<li>configure Rust to use <code>stable</code> channel (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3691">#3691</a>)</li> 16643<li>don't use non-existing <code>--enable-sve</code> configure option when building FFTW on Arm system that supports SVE (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3696">#3696</a>)</li> 16644<li>specify path to <code>gcc</code> RPATH wrapper to linker option of Rust compiler (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3698">#3698</a>)</li> 16645<li>avoid leaking file handles in <code>PythonPackage</code> by using <code>read_file</code> and <code>write_file</code> functions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3704">#3704</a>)</li> 16646<li>rebuild C++ API for Gurobi (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3714">#3714</a>)</li> 16647<li>fix Python shebangs for scripts in Python and Conda-like installations (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3717">#3717</a>)</li> 16648<li>fix dry run for <code>openssl_wrapper</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3719">#3719</a>)</li> 16649<li>allow downloaded Python packages if implicitely requested (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3722">#3722</a>)</li> 16650<li>replace deprecated <code>expand_module_search_path</code> with <code>ModuleEnvironmentVariable.expand_paths()</code> in <code>Bundle</code> and <code>Java</code> easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3727">#3727</a>)</li> 16651<li>add <code>-std=c++11</code> to <code>$CXXFLAGS</code> when building binutils 2.42+ with system GCC 4.8.1 to 5.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3728">#3728</a>)</li> 16652</ul> 16653</li> 16654<li>other changes:<ul> 16655<li>require that maximum major Python version is specified if maximum minor Python version is specified in <code>pick_python_cmd</code> function (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3478">#3478</a>)</li> 16656<li>remove Python 2.7 and 3.5 from list of classifiers in <code>setup.py</code> + add Python 3.12 & 3.13 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3669">#3669</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3673">#3673</a>)</li> 16657<li>code cleanup: remove Python2 style <code>super()</code>-calls (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3681">#3681</a>)</li> 16658<li>fix testsuite badge in README (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3687">#3687</a>)</li> 16659<li>delete <code>.travis.yml</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3679">#3679</a>)</li> 16660<li>remove superflous assignment of sanity check module data in custom easyblock for torchvision (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3701">#3701</a>)</li> 16661<li>deprecate JAR easyblock, <code>Binary</code> easyblock should be used instead (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3721">#3721</a>)</li> 16662</ul> 16663</li> 16664</ul> 16665<p><strong>easyconfigs</strong></p> 16666<ul> 16667<li>add easyconfigs for <code>foss/2025a</code> and <code>intel/2025a</code> common toolchains (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22879">#22879</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22941">#22941</a>)</li> 16668<li>
16668added example easyconfig files for 64 new software packages:<ul> 16669<li>ADMIXTURE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22813">#22813</a>), bcgTree (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22540">#22540</a>), BOLT-LMM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22771">#22771</a>), Boltz-1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22473">#22473</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22475">#22475</a>), bwtool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22925">#22925</a>), CAESES (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20542">#20542</a>), cellsnp-lite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22632">#22632</a>), 16670 clisops (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22635">#22635</a>), compleasm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21837">#21837</a>), cooltools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22536">#22536</a>), cramjam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22465">#22465</a>), CrystFEL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22863">#22863</a>), Evo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22746">#22746</a>), FALL3D (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22610">#22610</a>), fastStructure 16671 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22423">#22423</a>), FCM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17115">#17115</a>), GCTB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22710">#22710</a>), grackle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21185">#21185</a>), greedy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22755">#22755</a>), HEEDS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20545">#20545</a>), jupyterlab-h5web (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22374">#22374</a>), koopmans (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22372">#22372</a>), koopmans-kcp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22372">#22372</a>), 16672 koopmans-qe-utils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22372">#22372</a>), KrakenTools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22617">#22617</a>), Lep-MAP3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22794">#22794</a>), libbeato (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22925">#22925</a>), LM-Studio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22712">#22712</a>), lsb_release (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22721">#22721</a>), 16673 LST-AI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22755">#22755</a>), Mamba-SSM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22670">#22670</a>), MAQAO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22860">#22860</a>), momepy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22131">#22131</a>), MOPAC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22662">#22662</a>), ninja-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22669">#22669</a>), pairix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22600">#22600</a>), PFLOTRAN_OGS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18141">#18141</a>), 16674 porefoam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22915">#22915</a>), ProLaTherm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22194">#22194</a>), ProTstab2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22302">#22302</a>), PyEphem (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22783">#22783</a>), pyet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22668">#22668</a>), PySAL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22316">#22316</a>), PySide6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22906">#22906</a>), 16675 pytest-subtests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22849">#22849</a>), quaqc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22872">#22872</a>), RFdiffusion-models (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20019">#20019</a>), RFdiffusion-schedules (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20019">#20019</a>), SQUID (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22637">#22637</a>), SQuIRE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22356">#22356</a>), 16676 STITCH (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22525">#22525</a>), stpipeline (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17127">#17127</a>), tblite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19219">#19219</a>), TEtrimmer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22252">#22252</a>), THOP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22762">#22762</a>), timezonefinder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22783">#22783</a>), Tinker-HP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22224">#22224</a>), 16677 tlparse (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20489">#20489</a>), tree-sitter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22776">#22776</a>), TSEBRA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21837">#21837</a>), UFCG (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22223">#22223</a>), uv (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21637">#21637</a>), xclim (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22635">#22635</a>), yacrd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22812">#22812</a>)</li> 16678</ul> 16679</li> 16680<li>
16680added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 16681<li>AFNI 25.1.01, AlphaPulldown 2.0.3, Amber 24.0, AUGUSTUS 3.5.0, binutils 2.44, Bracken 3.1, CUDA 12.9.0, GCC 14.3.0 + 15.1.0, 16682 geopandas 1.0.1, <code>iimkl/2024a</code>, 16683 LLVM 20.1.5, metaWRAP 1.4-20230728, MPICH 4.3.0, MultiQC 1.28, 16684 Nektar++ 5.7.0, NVHPC 25.3, nvtop 3.2.0, openCARP 17.0, OpenFold 2.0.0, OpenMolcas 24.10, PETSc 3.22.5, poetry 2.1.2, PyOpenGL 3.1.9, PyTensor 2.30.3, PyTorch 16685 2.3.0, Python-bundle-PyPI 2025.04, RepeatModeler 2.0.6, Rust 1.85.1, QIIME2 16686 2024.10.1, Qt5 5.15.16, scikit-learn 1.6.1, scikit-optimize 0.10.2, Score-P 9.0, StringTie 16687 3.0.0, SuiteSparse 7.10.1, tiktoken 0.9.0, trimAl 1.5.0, Valgrind 3.25.0, VTK 9.3.1, WhatsHap 2.6</li> 16688</ul> 16689</li> 16690<li>minor enhancements, including:<ul> 16691<li>add modsem extension + its dependencies to recent R-bundle-CRAN easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22594">#22594</a>)</li> 16692<li>add sgdGMF extension to recent R-bundle-CRAN easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22709">#22709</a>)</li> 16693<li>also build static libraries of Abseil (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22805">#22805</a>)</li> 16694<li>also install Python bindings for zlib-ng v2.1.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22818">#22818</a>)</li> 16695<li>add patch to add zen5 support to OpenBLAS 0.3.27 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22850">#22850</a>)</li> 16696<li>incorporate more detailed description in MAQAO easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22864">#22864</a>)</li> 16697<li>add kableExtra extension to R-bundle-CRAN 2023.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22874">#22874</a>)</li> 16698<li>add hiAnnotator extension to recent R-bundle-Bioconductor easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22873">#22873</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22897">#22897</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22898">#22898</a>)</li> 16699</ul> 16700</li> 16701<li>various bug fixes, including:<ul> 16702<li>add JsonCpp dependency to recent BamTools easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21612">#21612</a>)</li> 16703<li>add missing dependencies (TSEBRA, compleasm) + use more recent AUGUSTUS version for BRAKER v3.0.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21837">#21837</a>)</li> 16704<li>add patch for OpenMPI v5.0.3 to fix C90 compliance (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22006">#22006</a>)</li> 16705<li>add an egg-info file to make RDKit findable by pip (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22018">#22018</a>)</li> 16706<li>disable check for RPATH section in git-lfs easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22346">#22346</a>)</li> 16707<li>add patch for astropy 7.0.0 to make one of the tests pass on ARM architectures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22469">#22469</a>)</li> 16708<li>add patch to fix broken test for Siesta v5.2.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22562">#22562</a>)</li> 16709<li>control number of parallel processes used by Ninja and add fix for aarch64 in easyconfig for Qt6 6.7.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22588">#22588</a>)</li> 16710<li>add patch to fix regression in pytest 8.2.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22602">#22602</a>)</li> 16711<li>remove Python 2.7 + Python 3.5 from classifiers in <code>setup.py</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22605">#22605</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22621">#22621</a>)</li> 16712<li>update homepage and source URLs in libGLU easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22625">#22625</a>)</li> 16713<li>fix statsmodels 0.14.4 version by replacing incorrect patch with sed command in preinstallopts (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22628">#22628</a>)</li> 16714<li>use HTTP rather than FTP in source URLs of 'file' easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22685">#22685</a>)</li> 16715<li>
16715add patch in occt easyconfig to fix OpenCASCADEConfig.cmake to correctly deal with <code>lib64</code> directory (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22689">#22689</a>)</li> 16716<li>add patch to fix OSHA1stream.H in OpenFOAM 6-20190620 w/ foss/2023a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22694">#22694</a>)</li> 16717<li>make Python a dependency of GObject-Introspection 1.80.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22701">#22701</a>)</li> 16718<li>update version of pRolocdata and RnBeads.hg38 extensions in R-bundle-Bioconductor 3.20 (since source tarball for previous versions are no longer available) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22706">#22706</a>)</li> 16719<li>add patch to make bcgTree 1.2.1 compatible with MUSCLE 5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22707">#22707</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22852">#22852</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22861">#22861</a>)</li> 16720<li>re-add build of shared libs for LLVM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22720">#22720</a>)</li> 16721<li>add <code>lsb_release</code> as build dependency to recent ABAQUS easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22721">#22721</a>)</li> 16722<li>add patch to fix dependency check in OPERA-MS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22725">#22725</a>)</li> 16723<li>patch Siesta in order to let EasyBuild control optimization flags (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22731">#22731</a>)</li> 16724<li>add patch to avoid OpenCV searching for Python 2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22742">#22742</a>)</li> 16725<li>ensure <code>Infernal</code> is built with MPI support, and drop toolchain to gompi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22753">#22753</a>)</li> 16726<li>ensure <code>Proteinortho</code> links against <code>FlexiBLAS</code>, and bump to <code>foss</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22754">#22754</a>)</li> 16727<li>fix <code>get_good_inter_pae.py</code> script in AlphaPulldown v2.0.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22758">#22758</a>)</li> 16728<li>use proper dependency for tokenizers in Uni-Core v0.0.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22758">#22758</a>)</li> 16729<li>add patch to fix installation of MUSCLE 5.1.0 on aarch64 systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22780">#22780</a>)</li> 16730<li>use "standard" variant of RAxML dependency for bcgTree on aarch64 systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22781">#22781</a>)</li> 16731<li>add patch to fix bug in unittest-xml-reporting on Python 3.11+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22787">#22787</a>)</li> 16732<li>copy tests to minimap2 install dir to fix --sanity-check-only and --module only (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22791">#22791</a>)</li> 16733<li>fix installing recent <code>minimap2</code> easyconfigs on ARM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22791">#22791</a>)</li> 16734<li>add groff build dependency to enchant-2 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22804">#22804</a>)</li> 16735<li>set C standard to <code>c99</code> for ncurses 6.5 and M 1.4.19 with system toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22807">#22807</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22798">#22798</a>)</li> 16736<li>add optional patch file for OpenMPI 4.1.5 to disable OPAL path NFS test (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22817">#22817</a>)</li> 16737<li>add missing groff build dependency for Graphviz 12.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22837">#22837</a>)</li> 16738<li>use <code>Java/21</code> wrapper instead of specific version for Bazel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22839">#22839</a>), Turbovnc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22838">#22838</a>), GraphViz (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22837">#22837</a>)</li> 16739<li>
16739add patch to fix PyTorch 2.3 on systems with disabled SMT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22843">#22843</a>)</li> 16740<li>use <code>modextravars</code> to set <code>$GENEMARK_PATH</code> in funannotate easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22851">#22851</a>)</li> 16741<li>use <code>CargoPythonBundle</code> easyblock for Python-bundle-PyPI 2024.06 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22853">#22853</a>)</li> 16742<li>don't update <code>$PYTHONPATH</code> via <code>modextrapaths</code> in easyconfig for OTF2 3.1.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22854">#22854</a>)</li> 16743<li>add ICU dependency for Xerces-C++ 3.2.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22866">#22866</a>)</li> 16744<li>use mimalloc instead of jemalloc for Arrow 17.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22858">#22858</a>)</li> 16745<li>fix LM Studio AppImage permission (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22867">#22867</a>)</li> 16746<li>disable XPMEM in recent libfabric easyconfigs (v1.21.0, v2.0.0) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22880">#22880</a>)</li> 16747<li>port ReFrame easyconfigs to EasyBuild 5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22883">#22883</a>)</li> 16748<li>fix MKL ILP64 flags for Global Arrays 5.8.2 w/ <code>intel/2024a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22894">#22894</a>)</li> 16749<li>disable libxpmem explicitely in OpenMPI 5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22902">#22902</a>)</li> 16750<li>stick to QIIME2 2024.2.0 with foss/2023a, since recent versions (like 2024.10.0) require a more recent version of <code>pandas</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22904">#22904</a>)</li> 16751<li>add patch for PMIx 5.0.2 to fix support for IPv6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22909">#22909</a>)</li> 16752<li>don't fix shebang line in mympirun script, to make sure it uses system Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22916">#22916</a>)</li> 16753<li>define <code>$CONDA_PREFIX</code> via <code>modextravars</code> in QIIME2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22918">#22918</a>)</li> 16754<li>add patch to fix ml_dtypes 0.5.0 on AVX512 CPUs with FP16 support (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22919">#22919</a>)</li> 16755<li>stick to torchrl 0.3.0 in PyTorch-bundle 2.1.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22937">#22937</a>)</li> 16756</ul> 16757</li> 16758<li>other changes:<ul> 16759<li>stick to <code>gfbf/2023b</code> toolchain for SuiteSparse 7.7.0 and remove <code>METIS</code> dependency + corresponding <code>versionsuffix</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21199">#21199</a>)</li> 16760<li>change default data location in snpEff v5.2c to be a user-writable directory (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21910">#21910</a>)</li> 16761<li>update easyconfigs according to defaults in EasyBuild 5.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22629">#22629</a>)</li> 16762<li>improve failure message for download instruction CI check (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22648">#22648</a>)</li> 16763<li>delete <code>.pre-commit-config.yaml</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22665">#22665</a>)</li> 16764<li>use <code>PythonPackage</code> easyblock for coverage v7.4.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22672">#22672</a>)</li> 16765<li>use <code>SHLIB_EXT</code> in <code>TinyXML</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22703">#22703</a>)</li> 16766<li>use Python rather than CMake as dependency in easyconfig templates for <code>PythonBundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22760">#22760</a>)</li> 16767<li>replace <code>setenv</code> commands with environment variables in module footers with <code>modextravars</code> in easyconfigs for HIP, JupyterLab, mujoco-py, Triton (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22801">#22801</a>)</li> 16768<li>fix missing space in missing-patch CI error (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22826">#22826</a>)</li> 16769<li>update to latest Java versions for <code>Java/8</code>, <code>Java/11</code>, <code>Java/17</code>, <code>Java/21</code>, <code>Java/23</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22840">#22840</a>)</li> 16770<li>use Java 17 as default Java version in all 2024a generation easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22862">#22862</a>)</li> 16771<li>disable building documentation for jemalloc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22869">#22869</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22870">#22870</a>)</li> 16772<li>
16772add missing extension curly brackets and parentheses to template easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22892">#22892</a>)</li> 16773<li>update easyconfigs to use <code>Binary</code> instead of (deprecated) <code>JAR</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22900">#22900</a>)</li> 16774</ul> 16775</li> 16776</ul> 16777<h2 id="release_notes_eb500">EasyBuild v5.0.0 (18 Mar 2025)<a class="headerlink" href="#release_notes_eb500" title="Permanent link">¶</a></h2> 16778<p>major release</p> 16779<p><strong>framework</strong></p> 16780<ul> 16781<li>remove support for Python 2.7 and 3.5 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4229">#4229</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4270">#4270</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4306">#4306</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4473">#4473</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4477">#4477</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4476">#4476</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4478">#4478</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4524">#4524</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4607">#4607</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4756">#4756</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4810">#4810</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4811">#4811</a>) <ul> 16782<li>also run unit test suite with Python 3.12 + 3.13 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4484">#4484</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4674">#4674</a>)</li> 16783</ul> 16784</li> 16785<li>changed defaults in EasyBuild configuration:<ul> 16786<li>enable --trace by default (<a href="https://github.com/easybuilders/easybuild-framework/pull/4250">#4250</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4310">#4310</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4311">#4311</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4491">#4491</a>)</li> 16787<li>enable RPATH linking by default (<a href="https://github.com/easybuilders/easybuild-framework/pull/4448">#4448</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4515">#4515</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4779">#4779</a>)<ul> 16788<li>disable strict RPATH sanity check by default, allow re-enabling it via <code>--strict-rpath-sanity-check</code> configuration option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4475">#4475</a>)</li> 16789</ul> 16790</li> 16791<li>enable <code>module-depends-on</code> by default (<a href="https://github.com/easybuilders/easybuild-framework/pull/4500">#4500</a>)</li> 16792<li>enable <code>module-extensions</code> by default (<a href="https://github.com/easybuilders/easybuild-framework/pull/4501">#4501</a>)</li> 16793<li>set default maximum level of parallellism to <code>16</code> via <code>max-parallel</code> configuration option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4606">#4606</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4777">#4777</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4816">#4816</a>)</li> 16794<li>use Slurm as the default job backend (<a href="https://github.com/easybuilders/easybuild-framework/pull/4659">#4659</a>)</li> 16795<li>enable keeping of symbolic links by default when copying (set <code>keepsymlinks</code> easyconfig parameter to <code>True</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4773">#4773</a>)</li> 16796</ul> 16797</li> 16798<li>changed behaviour:<ul> 16799<li>change default for <code>change_into_dir</code> option in <code>extract_file</code> function to to <code>False</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4246">#4246</a>)</li> 16800<li>enforce correct <code>.patch(.*)</code>
16800 extension for patch files (<a href="https://github.com/easybuilders/easybuild-framework/pull/4247">#4247</a>)</li> 16801<li>create <code>lib</code> -> <code>lib64</code> symlink (or vice versa) <em>before</em> running <code>postinstallcmds</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4435">#4435</a>)</li> 16802<li>don't allow unresolved templates in easyconfig parameters by default + add support for <code>--allow-unresolved-templates</code> configuration option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4516">#4516</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4725">#4725</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4726">#4726</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4727">#4727</a>)</li> 16803<li>switch default checksum to <code>sha256</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4523">#4523</a>)</li> 16804<li>only allow use of <code>rpath</code> toolchain option when <code>system</code> toolchain is used (<a href="https://github.com/easybuilders/easybuild-framework/pull/4585">#4585</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4808">#4808</a>)</li> 16805<li>use default value <code>$XDG_CONFIG_DIRS</code> from XDG basedir spec: <code>/etc/xdg</code> (instead of <code>/etc</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4591">#4591</a>)</li> 16806<li>reverse order for parsing files in <code>XDG_CONFIG_DIRS</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4630">#4630</a>)</li> 16807<li>move verifying of checksums from <code>source</code> to <code>fetch</code> step, to include it with <code>--fetch</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4624">#4624</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4729">#4729</a>)</li> 16808<li>drop support for pep8 package (was used for <code>--check-contrib</code> + <code>--check-style</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4634">#4634</a>)</li> 16809<li>specify changes that should be made by generated module files via <code>module_load_environment</code> attribute of <code>EasyBlock</code> class (<a href="https://github.com/easybuilders/easybuild-framework/pull/4653">#4653</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4754">#4754</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4761">#4761</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4774">#4774</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4799">#4799</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4784">#4784</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4801">#4801</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4802">#4802</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4803">#4803</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4809">#4809</a>)</li> 16810<li>let jobs retweak easyconfigs themselves by passing down <code>--try-*</code> options (<a href="https://github.com/easybuilders/easybuild-framework/pull/4669">#4669</a>)</li> 16811<li>refactor <code>make_extension_string</code> method in <code>EasyBlock</code> class (<a href="https://github.com/easybuilders/easybuild-framework/pull/4690">#4690</a>)</li> 16812<li>change <code>Toolchain.get_flag</code> so it doesn't automatically prepend a dash (<code>-</code>) to compiler flags (<a href="https://github.com/easybuilders/easybuild-framework/pull/4698">#4698</a>)</li> 16813<li>rename <code>Compiler.COMPILER*_FLAGS</code> to <code>Compiler.COMPILER*_OPTIONS</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4698">#4698</a>)</li> 16814<li>change semantics of <code>--dry-run</code>, so it doesn't imply <code>--robot</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4704">#4704</a>)</li> 16815<li>run sanity checks commands from an empty temporary directory (rather than the softw
16815are install directory) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4723">#4723</a>)</li> 16816<li>add context manager for allowing unresolved templates and make the state members private (<a href="https://github.com/easybuilders/easybuild-framework/pull/4735">#4735</a>)<ul> 16817<li>also remove support for directly setting <code>enable_templating</code> and <code>expect_resolved_template_values</code></li> 16818</ul> 16819</li> 16820</ul> 16821</li> 16822<li>various enhancements:<ul> 16823<li><code>run_shell_cmd</code> function to run shell commands which replaces both the (now deprecated) <code>run_cmd</code> and <code>run_cmd_qa</code> functions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4284">#4284</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4314">#4314</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4321">#4321</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4322">#4322</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4327">#4327</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4334">#4334</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4335">#4335</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4336">#4336</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4351">#4351</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4356">#4356</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4378">#4378</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4380">#4380</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4383">#4383</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4390">#4390</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4422">#4422</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4423">#4423</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4427">#4427</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4428">#4428</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4430">#4430</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4431">#4431</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4432">#4432</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4441">#4441</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4443">#4443</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4444">#4444</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4453">#4453</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4454">#4454</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4471">#4471</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4504">#4504</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4509">#4509</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4544">#4544</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4612">#4612</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4617">#4617</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4664">#4664</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4721">#4721</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4728">#4728</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4731">#4731</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4755">#4755</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4757">#4757</a>)</li> 16824<li>detect Fortran <code>.mod</code> files for installations using <code>GCCcore</code> toolchain (<a href="https://github.com/easybuilders/easybuild-framework/pull/4389">#4389</a>)</li> 16825<li>create <code>env.sh</code> and <code>cmd.sh</code> helper scripts in <code>run_shell_cmd</code> to allow starting interactive shell to debug failing shell commands (<a href="https://github.com/easybuilders/easybuild-framework/pull/4486">#4486</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4611">#4611</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4662">#4662</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4666">#4666</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4685">#4685</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4792">#4792</a>)</li> 16826<li>
16826add support for alternate easyconfig parameters/templates/constants (<a href="https://github.com/easybuilders/easybuild-framework/pull/4511">#4511</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4514">#4514</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4549">#4549</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4555">#4555</a>)</li> 16827<li>create reproducible tarballs for sources created via <code>git_config</code> (requires <code>.tar.xz</code> + Python 3.9+) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4248">#4248</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4517">#4517</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4522">#4522</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4660">#4660</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4733">#4733</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4797">#4797</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4798">#4798</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4813">#4813</a>)</li> 16828<li>use more granular exit codes when <code>EasyBuildError</code> is raised (<a href="https://github.com/easybuilders/easybuild-framework/pull/4534">#4534</a>)</li> 16829<li>prepend to <code>$PYTHONPATH</code> or <code>$EBPYTHONPREFIXES</code> in generated module files by automatically scanning for Python site package directories (as configured via <code>prefer-python-search-path</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4539">#4539</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4686">#4686</a>)</li> 16830<li>copy build directory and/or log file(s) if installation failed to path specified via <code>--failed-install-build-dirs-path</code> or <code>--failed-install-logs-path</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4601">#4601</a>)</li> 16831<li>add <code>--search-path-cpp-headers</code> configuration option to control how EasyBuild sets paths to headers at build time (<a href="https://github.com/easybuilders/easybuild-framework/pull/4645">#4645</a>)</li> 16832<li>add <code>module-search-path-headers</code> configuration option to control how modules set search paths to header files (<a href="https://github.com/easybuilders/easybuild-framework/pull/4655">#4655</a>)</li> 16833<li>add <code>--keep-debug-symbols</code> configuration option to set default value of '<code>debug</code>' toolchain option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4688">#4688</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4764">#4764</a>)</li> 16834<li>add <code>--search-path-linker</code> option to control linker options at build time (<a href="https://github.com/easybuilders/easybuild-framework/pull/4697">#4697</a>)</li> 16835<li>don't raise error when required extensions are not found when installing extensions in parallel (<a href="https://github.com/easybuilders/easybuild-framework/pull/4671">#4671</a>)</li> 16836<li>mark support for installing extensions in parallel as being mature, since it's no longer experimental (<a href="https://github.com/easybuilders/easybuild-framework/pull/4672">#4672</a>)</li> 16837<li>mark easystack support as being mature, since it's no longer experimental (<a href="https://github.com/easybuilders/easybuild-framework/pull/4673">#4673</a>)</li> 16838<li>several additional small enhancements:<ul> 16839<li>enhance download instructions by mentioning active source path (<a href="https://github.com/easybuilders/easybuild-framework/pull/4459">#4459</a>)</li> 16840<li>add CUDA compute capability integer format templates (<code>cuda_int_*_sep</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4463">#4463</a>)</li> 16841<li>add new <code>get_cwd</code> function to <code>tools.filetools</code> to retrieve current working directory (<a href="https://github.com/easybuilders/easybuild-framework/pull/4525">#4525</a>)</li> 16842<li>use <code>dict.items()</code> instead of repeatedly getting the value (<a href="https://github.com/easybuilders/easybuild-framework/pull/4533">#4533</a>)</li> 16843<li>set <code>usedforsecurity</code> to <code>False</code> when calling <code>hashlib.md5</code> with Python >= 3.9 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4550">#4550</a>)</li> 16844<li>
16844add <code>GNU_FTP_SOURCE</code> template constant (<a href="https://github.com/easybuilders/easybuild-framework/pull/4598">#4598</a>)</li> 16845<li>allow using <code>amend/try-amend</code> multiple times in an easystack file entry (<a href="https://github.com/easybuilders/easybuild-framework/pull/4667">#4667</a>)</li> 16846<li>add support for <code>%(rpath_enabled)s</code> template value (<a href="https://github.com/easybuilders/easybuild-framework/pull/4670">#4670</a>)</li> 16847<li>add <code>resolve_template</code> method to <code>EasyConfig</code> class (<a href="https://github.com/easybuilders/easybuild-framework/pull/4677">#4677</a>)</li> 16848<li>allow templates in <code>custom_paths</code> & <code>custom_commands</code> sanity-check arguments (<a href="https://github.com/easybuilders/easybuild-framework/pull/4679">#4679</a>)</li> 16849<li>updates and fixes for <code>findPythonDeps</code> script (<a href="https://github.com/easybuilders/easybuild-framework/pull/4682">#4682</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4740">#4740</a>)</li> 16850<li>allow use of custom delimiter for paths in module generator (<a href="https://github.com/easybuilders/easybuild-framework/pull/4687">#4687</a>)</li> 16851<li>enhance <code>get_software_libdir</code> to return full paths if requested (<a href="https://github.com/easybuilders/easybuild-framework/pull/4699">#4699</a>)</li> 16852<li>enhance <code>EasyBlock</code> class to allow passing in <code>logfile</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4707">#4707</a>)</li> 16853<li>avoid checking loaded module twice in <code>findUpdatedEcs.sh</code> script (<a href="https://github.com/easybuilders/easybuild-framework/pull/4710">#4710</a>)</li> 16854<li>allow nesting values in checksum dicts (<a href="https://github.com/easybuilders/easybuild-framework/pull/4711">#4711</a>) Flamefire:non-dict MERGED 2024-12-02T12:14:12Z</li> 16855<li>use <code>enumerate</code> where applicable + fix for <code>ModuleGenerator._generate_multi_deps_list</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4720">#4720</a>)</li> 16856<li>faster <code>nub</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/4737">#4737</a>)</li> 16857<li>enhance <code>apply_regex_substitutions</code> to support use of multi-line patterns, requiring matching all patterns in each file, and use pre-compiled regular expressions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4758">#4758</a>)</li> 16858<li>ignore other classes if software specific easyblock class was found (<a href="https://github.com/easybuilders/easybuild-framework/pull/4769">#4769</a>)</li> 16859<li>also allow trailing whitespaces for <code>examples</code> and <code>citing</code> easyconfig parameters (<a href="https://github.com/easybuilders/easybuild-framework/pull/4796">#4796</a>)</li> 16860<li>enhance <code>get_gpu_info</code> to also use <code>amd-smi</code> for AMD GPUs if possible (<a href="https://github.com/easybuilders/easybuild-framework/pull/4805">#4805</a>)</li> 16861</ul> 16862</li> 16863</ul> 16864</li> 16865<li>various changes, improvemnents, and fixes for the supported modules tools (Environment Modules + Lmod)<ul> 16866<li>drop load storm safe guard for Environment Modules v4.2.4+ (<a href="https://github.com/easybuilders/easybuild-framework/pull/4373">#4373</a>)</li> 16867<li>run unit tests on an updated versions of Environment Modules: v4.5.3 + v5.3.1 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4415">#4415</a>)</li> 16868<li>add <code>check_group</code> support for module files in Tcl syntax (<a href="https://github.com/easybuilders/easybuild-framework/pull/4418">#4418</a>)</li> 16869<li>bump minimum required Lmod to 8.0.0 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4424">#4424</a>)</li> 16870<li>bump minimum required Tmod (4.x) to 4.3.0 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4425">#4425</a>)</li> 16871<li>use <code>getenv</code> modulefile command with <code>EnvironmentModules</code> >= 4.2.0 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4614">#4614</a>)</li> 16872<li>
16872add module cache build support in <code>EnvironmentModules</code> class (<a href="https://github.com/easybuilders/easybuild-framework/pull/4615">#4615</a>)</li> 16873<li>derive <code>EnvironmentModules</code> class directly from <code>ModulesTool</code> rather than from to be deprecated <code>EnvironmentModulesTcl</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4625">#4625</a>)</li> 16874<li>adapt <code>module show</code> command run to cope with non-zero exit code for non-existing module (required for Environment Modules v5.5+ and Lmod 8.7.56+) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4739">#4739</a>)</li> 16875</ul> 16876</li> 16877<li>various improvements for the framework test suite:<ul> 16878<li>allow test case filtering by class name (<a href="https://github.com/easybuilders/easybuild-framework/pull/4788">#4788</a>)</li> 16879<li>improve test failure output for <code>assertEqual</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4807">#4807</a>)</li> 16880<li>fix <code>test_modulerc</code> by taking into account that wrapper module may also be shown as being loaded (<a href="https://github.com/easybuilders/easybuild-framework/pull/4778">#4778</a>)</li> 16881<li>(temporarily) use 5.0.x branch for easyblocks + easyconfigs in CI workflows (<a href="https://github.com/easybuilders/easybuild-framework/pull/4358">#4358</a>)</li> 16882<li>fix GitHub Actions for CentOS 7.9 container (<a href="https://github.com/easybuilders/easybuild-framework/pull/4712">#4712</a>)</li> 16883<li>stop using Ubuntu 20.4 in GitHub Actions workflows, use Ubuntu 22.04 instead (<a href="https://github.com/easybuilders/easybuild-framework/pull/4783">#4783</a>)</li> 16884<li>update GitHub actions workflows to use <code>ubuntu-24.04</code> where possible (<a href="https://github.com/easybuilders/easybuild-framework/pull/4795">#4795</a>)</li> 16885</ul> 16886</li> 16887<li>various small bug fixes:<ul> 16888<li>silence output of included easyblocks for <code>--terse</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4765">#4765</a>)</li> 16889<li>avoid processing the same EasyConfig multiple times (<a href="https://github.com/easybuilders/easybuild-framework/pull/4767">#4767</a>)</li> 16890<li>fix easyconfig parameter deprecation (<a href="https://github.com/easybuilders/easybuild-framework/pull/4479">#4479</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4480">#4480</a>)</li> 16891<li>switch from <code>ls</code> to <code>bash</code> in tests that are expecting this to be a binary (<a href="https://github.com/easybuilders/easybuild-framework/pull/4492">#4492</a>)</li> 16892<li>fix the checksum type check (<a href="https://github.com/easybuilders/easybuild-framework/pull/4578">#4578</a>)</li> 16893<li>fix <code>to_checksums</code> with <code>None</code> values in dicts and recursion (<a href="https://github.com/easybuilders/easybuild-framework/pull/4579">#4579</a>)</li> 16894<li>fix <code>test_toy_lock_cleanup_signals</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4600">#4600</a>)</li> 16895<li>resolve symlink when making log dir writable (<a href="https://github.com/easybuilders/easybuild-framework/pull/4658">#4658</a>)</li> 16896<li>fix typo in <code>veryloose</code> toolchain option for RISC-V (<a href="https://github.com/easybuilders/easybuild-framework/pull/4668">#4668</a>)</li> 16897<li>fix dry-run output when using <code>multi_deps</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4678">#4678</a>)</li> 16898<li>make <code>LooseVersion('1.0') == LooseVersion('1')</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4691">#4691</a>)</li> 16899<li>fix FFT entry in <code>--list-toolchains</code> output for Cray toolchains (<a href="https://github.com/easybuilders/easybuild-framework/pull/4719">#4719</a>)</li> 16900<li>avoid making build directory read-only (<a href="https://github.com/easybuilders/easybuild-framework/pull/4736">#4736</a>)</li> 16901</ul> 16902</li> 16903<li>deprecated functionality:<ul> 16904<li><code>easybuild.tools.py2vs3</code> module (<a href="https://github.com/easybuilders/easybuild-framework/pull/4229">#4229</a>)</li> 16905<li>rename unclear <code>*run*</code> methods to <code>*install_extension*</code> + rename <code>install_extensions</code> to <code>install_all_extensions</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4400">#4400</a>)</li> 16906<li>deprecate <code>run_cmd</code> and <code>run_cmd_qa</code> & co, move them to <code>easybuild._deprecated</code> module (<a href="https://github.com/easybuilders/easybuild-framework/pull/4433">#4433</a>)</li> 16907<li>deprecate support for <code>EnvironmentModulesC</code> and <code>EnvironmentModulesTcl</code> module tools (<a href="https://github.com/easybuilders/easybuild-framework/pull/4439">#4439</a>)</li> 16908<li>deprecate old checksum types (incl. md5) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4526">#4526</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4545">#4545</a>)</li> 16909<li>deprecate use of <code>parallel</code> easyconfig parameter and fix updating the template value (<a href="https://github.com/easybuilders/easybuild-framework/pull/4580">#4580</a>)</li> 16910<li>convert template constant lists to dicts and export the constants by name (<a href="https://github.com/easybuilders/easybuild-framework/pull/4595">#4595</a>)</li> 16911<li>rename '<code>source</code>' step to '<code>extract</code>' (affects <code>skipsteps</code> easyconfig parameter + <code>--stop</code> option) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4629">
16911#4629</a>)</li> 16912<li>deprecate <code>make_module_req_guess</code> method in <code>EasyBlock</code> class (<a href="https://github.com/easybuilders/easybuild-framework/pull/4653">#4653</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4763">#4763</a>)</li> 16913<li>deprecate support for GC3Pie as job backend (<a href="https://github.com/easybuilders/easybuild-framework/pull/4659">#4659</a>)</li> 16914<li>add deprecation warning for <code>optarch</code> value without leading dash (<a href="https://github.com/easybuilders/easybuild-framework/pull/4698">#4698</a>)</li> 16915<li>deprecate <code>post_install_step</code> method in <code>EasyBlock</code>, was renamed to <code>post_processing_step</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4715">#4715</a>)</li> 16916</ul> 16917</li> 16918<li>remove functionality that was deprecated in EasyBuild v4.x, including:<ul> 16919<li>EasyBuild bootstrap script (<a href="https://github.com/easybuilders/easybuild-framework/pull/4233">#4233</a>)</li> 16920<li>support for YAML-based easyconfig format (.yeb) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4237">#4237</a>)</li> 16921<li><code>wait-on-lock</code> configuration setting (<a href="https://github.com/easybuilders/easybuild-framework/pull/4239">#4239</a>)</li> 16922<li><code>dummy</code> toolchain (<a href="https://github.com/easybuilders/easybuild-framework/pull/4240">#4240</a>)</li> 16923<li><code>accept-eula</code> configuration setting (<a href="https://github.com/easybuilders/easybuild-framework/pull/4242">#4242</a>)</li> 16924<li><code>is_generic_easyblock</code> function from <code>easybuild.framework.easyconfig.easyconfig</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4243">#4243</a>)</li> 16925<li><code>use_git_am</code> option for <code>apply_patch</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/4244">#4244</a>)</li> 16926<li><code>fetch_extension_sources</code> method in <code>EasyBlock</code> class (<a href="https://github.com/easybuilders/easybuild-framework/pull/4245">#4245</a>)</li> 16927<li>support for 32-bit targets (<a href="https://github.com/easybuilders/easybuild-framework/pull/4272">#4272</a>)</li> 16928<li><code>descr</code> option for <code>simple_option</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/4273">#4273</a>)</li> 16929<li><code>Toolchain.add_dependencies</code> method (<a href="https://github.com/easybuilders/easybuild-framework/pull/4274">#4274</a>)</li> 16930<li><code>copytree</code>, <code>rmtree2</code> functions from <code>easybuild.filetools</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4275">#4275</a>)</li> 16931<li><code>skip_symlinks</code> option for <code>adjust_permissions</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/4275">#4275</a>)</li> 16932<li><code>log_error</code> option from <code>which</code> function (<a href="https://github.com/easybuilders/easybuild-framework/pull/4276">#4276</a>)</li> 16933<li><code>skip_lower</code> option from <code>template_constant_dict</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4277">#4277</a>)</li> 16934<li><code>disable_templating</code> + <code>default_fallback</code> options in <code>get_easyblock_class</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4278">#4278</a>)</li> 16935<li><code>mod_exists_regex_template</code> options in <code>ModulesTool.exist</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4279">#4279</a>)</li> 16936</ul> 16937</li> 16938<li>other changes<ul> 16939<li>take into account that <code>VERBOSE_VERSION</code> imported from <code>easybuild.easyblocks</code> is now a string value (<a href="https://github.com/easybuilders/easybuild-framework/pull/4357">#4357</a>)</li> 16940</ul> 16941</li> 16942</ul> 16943<p><strong>easyblocks</strong></p> 16944<ul> 16945<li>use <code>run_shell_cmd</code> rather than <code>run_cmd</code> and/or <code>run_cmd_qa</code> in all easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3046">#3046</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3074">#3074</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3090">#3090</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3091">#3091</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3092">#3092</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3093">#3093</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3094">#3094</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3098">#3098</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3099">#3099</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3100">#3100</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3101">#3101</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3102">#3102</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3105">#3105</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3106">#3106</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3107">#3107</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3109">#3109</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3110">#3110</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3112">#3112</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3113">#3113</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3115">#3115</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3120">#3120</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3122">#3122</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3123">#3123</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3124">#3124</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3127">#3127</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3128">#3128</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3129">#3129</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3130">#3130</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3131">#3131</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3132">#3132</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3133">#3133</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3134">#3134</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3135">#3135</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3136">#3136</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3137">#3137</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3139">#3139</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3140">#3140</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3141">#3141</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3142">#3142</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3143">#3143</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3144">#3144</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3145">#3145</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3146">#3146</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3147">#3147</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3149">#3149</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3150">#3150</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3153">#3153</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3156">#3156</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3158">#3158</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3159">#3159</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3162">#3162</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3163">#3163</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3164">
16945#3164</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3165">#3165</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3166">#3166</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3167">#3167</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3168">#3168</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3169">#3169</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3171">#3171</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3179">#3179</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3180">#3180</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3187">#3187</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3188">#3188</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3189">#3189</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3190">#3190</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3192">#3192</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3193">#3193</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3195">#3195</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3197">#3197</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3198">#3198</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3199">#3199</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3200">#3200</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3201">#3201</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3203">#3203</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3204">#3204</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3206">#3206</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3207">#3207</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3209">#3209</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3210">#3210</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3212">#3212</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3213">#3213</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3214">#3214</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3215">#3215</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3217">#3217</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3218">#3218</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3219">#3219</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3242">#3242</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3243">#3243</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3244">#3244</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3270">#3270</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3274">#3274</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3286">#3286</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3288">#3288</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3289">#3289</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3290">#3290</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3291">#3291</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3293">#3293</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3295">#3295</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3297">#3297</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3298">#3298</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3299">#3299</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3308">#3308</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3327">#3327</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3342">#3342</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3411">#3411</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3413">#3413</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3414">#3414</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3415">#3415</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3426">#3426</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3664">#3664</a>)</li> 16946<li>adopt <code>module_load_environment</code> in all easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3513">#3513</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3529">#3529</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3530">#3530</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3550">#3550</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3551">#3551</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3552">
16946#3552</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3553">#3553</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3555">#3555</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3556">#3556</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3559">#3559</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3560">#3560</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3561">#3561</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3562">#3562</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3577">#3577</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3578">#3578</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3579">#3579</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3585">#3585</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3586">#3586</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3587">#3587</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3592">#3592</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3593">#3593</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3594">#3594</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3596">#3596</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3597">#3597</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3598">#3598</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3600">#3600</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3601">#3601</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3602">#3602</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3603">#3603</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3604">#3604</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3606">#3606</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3607">#3607</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3608">#3608</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3609">#3609</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3610">#3610</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3611">#3611</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3612">#3612</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3613">#3613</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3615">#3615</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3616">#3616</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3618">#3618</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3619">#3619</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3620">#3620</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3622">#3622</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3625">#3625</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3626">#3626</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3627">#3627</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3628">#3628</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3629">#3629</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3630">#3630</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3631">#3631</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3634">#3634</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3647">#3647</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3635">#3635</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3641">#3641</a>)</li> 16947<li>enable <code>download_dep_fail</code>, <code>
16947use_pip</code>, <code>sanity_pip_check</code> by default in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3022">#3022</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3079">#3079</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3221">#3221</a>)</li> 16948<li>enhance <code>ConfigureMake</code> easyblock to error out on unknown configure options (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3025">#3025</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3563">#3563</a>)</li> 16949<li>adopt to changes in EasyBuild framework:<ul> 16950<li>stop testing with Python 3.5 and Lmod 6.x, stop using <code>toolchain.DUMMY</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3014">#3014</a>)</li> 16951<li>stop importing from deprecated easybuild.tools.py2vs3 module + stop testing with Python 2.7 and 3.5 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2916">#2916</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3015">#3015</a>)</li> 16952<li>use <code>LooseVersion</code> from <code>easybuild.tools</code> in all easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3018">#3018</a>)</li> 16953<li>rename <code>run</code> method to <code>install_extension</code>, and likewise for <code>prerun</code> to <code>pre_install_extension</code>, <code>postrun</code> to <code>post_install_extension</code>, and <code>run_async</code> to <code>install_extension_async</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3064">#3064</a>)</li> 16954<li>disable check for <code>.mod</code> files in Clang, AOCC, AOMP, and CPLEX easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3067">#3067</a>)</li> 16955<li>stop running easyblocks test suite with Lmod 7.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3083">#3083</a>)</li> 16956<li>use <code>sysconfig.get_config_vars</code> from Python standard library in <code>PythonPackage</code> easyblock (instead of <code>distutils.sysconfig.get_config_vars</code>) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3264">#3264</a>)</li> 16957<li>also run easyblocks test suite with Python 3.12 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3266">#3266</a>)</li> 16958<li>use <code>ERROR</code> global from tools.config in Clang (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3318">#3318</a>) and TensorFlow (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3320">#3320</a>) easyblocks</li> 16959<li>update easyblocks to let EasyBuild framework take care of prepend to <code>$PYTHONPATH</code> or <code>$EBPYTHONPREFIXES</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3343">#3343</a>)</li> 16960<li>use <code>PYPI_SOURCE</code> constant in generic <code>PythonPackage</code> easyblock + custom easyblock for Python (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3410">#3410</a>)</li> 16961<li>use non-system toolchain for testing <code>--module-only</code> for ELPA and FFTW easyblocks, since they rely on toolchain options like 'pic' being set (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3425">#3425</a>)</li> 16962<li>take into account that '<code>pic</code>' toolchain option may not be defined in <code>CMakeMake</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3470">#3470</a>)</li> 16963<li>remove use of deprecated <code>parse_log_for_error</code> in <code>RPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3515">#3515</a>)</li> 16964<li>rename <code>post_install_step</code> to <code>post_processing_step</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3525">#3525</a>)</li> 16965<li>be more careful when getting value of particular easyconfig parameter in <code>PythonBundle</code> and <code>PythonPackage</code> easyblock, to avoid trouble with unresolved template values (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3537">#3537</a>)</li> 16966<li>remove use of deprecated <code>extract_errors_from_log</code> in <code>ConfigureMake</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3540">#3540</a>)</li> 16967<li>remove Python 2 fallback in <code>openssl_wrapper</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3544">#3544</a>)</li> 16968<li>update easyblocks to use <code>EasyConfig.parallel</code> property (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3557">#3557</a>)</li> 16969<li>honor <code>--module-search-path-headers</code> in easyblocks that hardcode CPATH (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3584">#3584</a>)</li> 16970<li>remove hardcoded CPLUS_INCLUDE_PATH in favor of module-search-path-headers in custom easyblock for Eigen (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3599">#3599</a>)</li> 16971</ul> 16972</li> 16973<li>various updates:<ul> 16974<li>update version of <code>config.guess</code> used by <code>ConfigureMake</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3013">#3013</a>)</li> 16975<li>enhance Score-P EasyBlock for future releases and better oneAPI support (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3548">#3548</a>)</li> 16976<li>enhance AOCC easyblock to work with LLVM 16 and newer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3458">#3458</a>)</li> 16977<li>update VTune easyblock to work with v2024 and newer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3465">#3465</a>)</li> 16978<li>enhance NAMD easyblock to support NAMD v3.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3494">#3494</a>)</li> 16979<li>fix oneAPI sanity check for ifort removal in 2025.0 and newer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3495">#3495</a>)</li> 16980</ul> 16981</li> 16982<li>various other enhancements:<ul> 16983<li>set CMake installation <code>LIBDIR</code> to <code>lib</code> by default in <code>CMakeMake</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3227">#3227</a>)</li> 16984<li>
16984add warning if <code>.Renviron</code> detected during install of RPackage (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3263">#3263</a>)</li> 16985<li>make <code>PythonBundle</code> and <code>PythonPackage</code> aware of <code>--prefer-python-search-path</code> EasyBuild configuration option (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3343">#3343</a>)</li> 16986<li>enhance <code>LLVM</code> easyblock for compilation of clang/flang + other llvm-projects (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3373">#3373</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3657">#3657</a>)</li> 16987<li>enhance <code>CMakeMake</code> easyblock to check whether correct <code>Python</code> installation was picked up by <code>CMake</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3399">#3399</a>)</li> 16988<li>enhance Qt5 easyblock to support building on RISC-V (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3462">#3462</a>)</li> 16989<li>let <code>CMakeMake</code> easyblock also set <code>Python_EXECUTABLE</code> option, as well as <code>Python3_EXECUTABLE</code> and <code>Python2_EXECUTABLE</code> derivatives (when appropriate) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3463">#3463</a>)</li> 16990<li>update ROOT easyblock to support sysroot (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3467">#3467</a>)</li> 16991<li>enhance generic <code>Bundle</code> easyblock to transfer module requirements of components, but do not create logfile in components (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3472">#3472</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3504">#3504</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3509">#3509</a>)</li> 16992<li>enhance cuDNN easyblock to verify that EULA is accepted before installing it (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3473">#3473</a>)</li> 16993<li>enhance AOCC easyblock to correctly pass GCC toolchain and compiler driver (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3480">#3480</a>)</li> 16994<li>enhance Cargo easyblock for sources from git repositories (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3483">#3483</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3654">#3654</a>)</li> 16995<li>enhance Cargo easyblock to print message for generating <code>Cargo.lock</code> if it's missing (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3491">#3491</a>)</li> 16996<li>let <code>PythonPackage</code> easyblock fix python shebangs by default (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3499">#3499</a>)</li> 16997<li>make it possible to disable single precision as build target in GROMACS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3501">#3501</a>)</li> 16998<li>pass netCDF-Fortran path via <code>$NETCDFF_DIR</code> in WPS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3522">#3522</a>)</li> 16999<li>set <code>CMAKE_CUDA_HOST_COMPILER</code>, <code>CMAKE_CUDA_COMPILER</code>, and <code>CMAKE_CUDA_ARCHITECTURES</code> when using CUDA in <code>CMakeMake</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3523">#3523</a>)</li> 17000<li>show path of output file produced by MATLAB installer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3532">#3532</a>)</li> 17001<li>make path to temporary install directory used in test step of <code>PythonPackage</code> easyblock available through environment variable so that it may be used in easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3565">#3565</a>)</li> 17002<li>add support for Sapphire Rapids in LAMMPS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3569">#3569</a>)</li> 17003<li>allow installing from commit for LAMMPS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3582">#3582</a>)</li> 17004<li>add support to OpenFOAM easyblock for custom <code>sanity_check_motorbike</code> easyconfig parameter to opt out of running motorBike tutorial example during sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3595">#3595</a>)</li> 17005<li>enhance FlexiBLAS easyblock to add support for AOCL-BLAS backend (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3589">#3589</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3605">#3605</a>)</li> 17006<li>enhance handling of <code>PETSC_ARCH</code> in SLEPc easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3629">#3629</a>)</li> 17007<li>use unittest XML files to parse PyTorch test results (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3633">#3633</a>)</li> 17008</ul> 17009</li> 17010<li>various bug fixes:<ul> 17011<li>don't change <code>installopts</code> easyconfig parameter value in-place in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3080">#3080</a>)</li> 17012<li>fail on non-zero exit code in command to run Perl test suite (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3170">#3170</a>)</li> 17013<li>fix <code>--module-only</code> + cleanup for custom easyblock for Geant4 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3302">#3302</a>)</li> 17014<li>consider both <code>easybuild-easyblocks*.tar.gz</code> and <code>easybuild_easyblocks*tar.gz</code> in CI workflows (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3309">#3309</a>)</li> 17015<li>make <code>CMakeMake</code> respect <code>debug</code> and <code>noopt</code> toolchain options when selecting build type (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3452">#3452</a>)</li> 17016<li>make <code>MesonNinja</code> respect the <code>debug</code>/<code>noopt</code>/<code>lowopt</code>/<code>opt</code> toolchain options to correctly set build type and use <code>--debug</code> and <code>--optimization</code> flags (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3454">#3454</a>)</li> 17017<li>strip leading <code>local/</code> from pylibdir where appropriate in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3464">#3464</a>)</li> 17018<li>remove X11 flag for GROMACS 2023+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3466">#3466</a>)</li> 17019<li>fix setting of <code>CMAKE_OPTIONS</code> for SuiteSparse versions between 5.1.2 and 6.0.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3471">#3471</a>)</li> 17020<li>
17020add missing <code>return</code> for customised <code>install_extension_async</code> methods in Rserve and Rmpi easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3474">#3474</a>)</li> 17021<li>disable CPU-specific optimizations for generic builds (by using a custom <code>processor_arch</code>) in LAMMPS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3484">#3484</a>)</li> 17022<li>also add path to <code>libtorch.so</code> & co to <code>$LIBRARY_PATH</code> in generated module file for PyTorch (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3488">#3488</a>)</li> 17023<li>use <code>*DESCRIPTION</code> rather than <code>*/DESCRIPTION</code> in <code>RPackage.requires_deps</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3490">#3490</a>)</li> 17024<li>use <code>DYNAMIC_ARCH=1</code> when building OpenBLAS with <code>--optarch=GENERIC</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3492">#3492</a>)</li> 17025<li>fix check in Score-P's configure scripts that may fail if the path to certain dependencies include <code>yes</code> or <code>no</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3496">#3496</a>)</li> 17026<li>let internal easyblock not create a log file in QuantumESPRESSO easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3505">#3505</a>)</li> 17027<li>update CUDA easyblock to add CUPTI and nvvm library directories to <code>$LIBRARY_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3516">#3516</a>)</li> 17028<li>force use of <code>bash</code> for <code>Allwmake</code> scripts in OpenFOAM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3519">#3519</a>)</li> 17029<li>fix detection of math library in numpy build (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3520">#3520</a>)</li> 17030<li>retain custom easyconfig parameters supported by <code>MesonNinja</code> easyblock in custom easyblock for <code>scipy</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3526">#3526</a>)</li> 17031<li>inject custom '<code>%(python)s</code>' template value before getting value of '<code>buildcmd</code>' custom easyconfig parameter in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3539">#3539</a>)</li> 17032<li>import from other easyblocks without the single folder letter (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3543">#3543</a>)</li> 17033<li>fix <code>$PYTHONPATH</code> for hermetic Python in TensorFlow builds (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3568">#3568</a>)</li> 17034<li>fix building PyTorch when using <code>setup.py</code> as the build command (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3574">#3574</a>)</li> 17035<li>set Cargo variables also for extensions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3576">#3576</a>)</li> 17036<li>use bash for compiler wrapper in AOCC easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3648">#3648</a>)</li> 17037<li>fix compatibility of Molpro easyblock with <code>--module-only</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3615">#3615</a>)</li> 17038<li>specify tmpdir for ANSYS installations (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3646">#3646</a>)</li> 17039<li>update + fixes in GitHub Actions workflows to use Ubuntu 22.04 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3651">#3651</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3655">#3655</a>)</li> 17040<li>make AOCC compiler wrappers aware of keepsymlinks option (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3659">#3659</a>)</li> 17041<li>convert RUNPATH into RPATH for Rust binaries in recent Rust versions (> 1.79.0) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3660">#3660</a>)</li> 17042<li>update configuration options for version 4+ of MPICH (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3663">#3663</a>)</li> 17043</ul> 17044</li> 17045<li>various minor changes:<ul> 17046<li>don't auto-enable use of <code>-DSCOTCH_PTHREAD</code> when using MPI library other than Intel MPI in SCOTCH easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3019">#3019</a>)</li> 17047<li>replace <code>
17047log.warn</code> with <code>log.warning</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3245">#3245</a>)</li> 17048<li>refactor search for <code>python_cmd</code> in <code>PythonPackage</code> and <code>PythonBundle</code> easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3475">#3475</a>)</li> 17049<li>update <code>Python</code> easyblock to move <code>sitecustomize.py</code> into <code>site-packages</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3514">#3514</a>)</li> 17050<li>switch default to <code>install_pip=True</code> in custom Python easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3546">#3546</a>)</li> 17051<li>use context managers for templating changes in <code>Bundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3547">#3547</a>)</li> 17052<li>use <code>PythonPackage</code> as the <code>default_easyblock</code> for <code>PythonBundle</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3649">#3649</a>)</li> 17053</ul> 17054</li> 17055<li>cleanup of dead code<ul> 17056<li>drop support for versions < 2.0 in custom easyblock for ScaLAPACK (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3106">#3106</a>)</li> 17057<li>drop support for versions < 9.5 in custom easyblock for Geant4 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3296">#3296</a>)</li> 17058<li>remove code supporting obsolete versions from <code>IntelBase</code> family of easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3533">#3533</a>)</li> 17059<li>clean up custom easyblock for Paraver, only support Paravar >= v4.7 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3535">#3535</a>)</li> 17060<li>set minimum supported version of PETSc to v3.9 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3627">#3627</a>)</li> 17061</ul> 17062</li> 17063<li>remove unused software-specific easyblocks for ACML (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3172">#3172</a>), ALADIN (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3173">#3173</a>), Allinea (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), ARB (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3096">#3096</a>), ATLAS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3103">#3103</a>), BamTools (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3424">#3424</a>), Bioconductor (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), BiSearch (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3174">#3174</a>), BLACS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3104">#3104</a>), Blender (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), BWISE (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), CFDEMcoupling (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3151">#3151</a>), Chapel (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), CHARMM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3108">#3108</a>), cppcheck (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3111">#3111</a>), DL_POLY_Classic (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3152">#3152</a>), DOLFIN (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3154">#3154</a>), Doris (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3175">#3175</a>), Doxygen (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3114">#3114</a>), EggLib (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3066">#3066</a>), EPD (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), ESPResSo (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3117">#3117</a>), fastStructure (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3155">#3155</a>), FoldX (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), FreeFEM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3157">#3157</a>), HEALPix (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3285">#3285</a>), IMOD (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3126">#3126</a>), IPP (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3533">#3533</a>), IronPython (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3125">#3125</a>), libsmm (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3216">#3216</a>), MetaVelvet (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), Modeller (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3292">#3292</a>), Mono (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3211">#3211</a>), Mothur (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), MSM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3208">#3208</a>), MTL4 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3617">#3617</a>), MyMediaLite (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3205">#3205</a>), mutil (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), MVAPICH2 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), ncurses (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3265">#3265</a>), NEMO (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3202">#3202</a>), OpenIFS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3194">#3194</a>), Pasha (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), pbdMPI (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), pbdSLAP (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), PGI (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3181">#3181</a>), picard (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), pplacer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3185">#3185</a>), Primer3 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3621">#3621</a>), PyQuante (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), python_meep (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3182">#3182</a>), Samcef (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3176">#3176</a>), SAS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3177">#3177</a>), Scalasca v1.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), SHRiMP (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), SNPhylo (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3178">#3178</a>), SOAPdenovo (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), TAU (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3535">#3535</a>), TotalView (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3191">#3191</a>), UFC (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3423">#3423</a>), VSC-tools (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3138">#3138</a>), WRF-Fire (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3271">#3271</a>)</li> 17064</ul> 17065<p><strong>easyconfigs</strong></p> 17066<ul> 17067<li>added example easyconfig files for 148 new software packages:<ul> 17068<li>AOCL-BLAS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22291">#22291</a>), astropy-testing (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22198">#22198</a>), Atomsk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22312">#22312</a>), Auto-WEKA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17172">#17172</a>), bakta (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21861">#21861</a>), Baysor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22286">#22286</a>), 17069bin2cell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21869">#21869</a>), BindCraft (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21791">#21791</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21958">#21958</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22039">#22039</a>), black (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21684">#21684</a>), Cellformer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21621">#21621</a>), CellProfiler (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21949">#21949</a>), 17070Ceres-Solver (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19104">#19104</a>), CIRCE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21703">#21703</a>), cisDIVERSITY (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21692">#21692</a>), clearml (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21937">#21937</a>), cmcrameri (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21567">#21567</a>), cnvpytor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22479">#22479</a>), 17071COAWST-deps (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22458">#22458</a>
17071), COLMAP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19104">#19104</a>), columba (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21706">#21706</a>), cookiecutter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21684">#21684</a>), cp2k-input-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21550">#21550</a>), 17072CTranslate2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22134">#22134</a>), CUDA-Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21058">#21058</a>), cuQuantum (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21355">#21355</a>), cython-cmake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22176">#22176</a>), Dask-ML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21729">#21729</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21731">#21731</a>), 17073DECAF-synthetic-data (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21141">#21141</a>), DeepDRR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21069">#21069</a>), dm-control (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21956">#21956</a>), draco (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22159">#22159</a>), elfx86exts (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22145">#22145</a>), 17074EVidenceModeler (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21569">#21569</a>), face-recognition (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21459">#21459</a>), FastK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22065">#22065</a>), fastText (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22239">#22239</a>), FloPy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21680">#21680</a>), GOTCHA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21399">#21399</a>), 17075Gradio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20349">#20349</a>), GraphAligner (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22246">#22246</a>), GROMACS-LS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21800">#21800</a>), gym-pybullet-drones (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21488">#21488</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21500">#21500</a>), harvest-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22027">#22027</a>), 17076hatch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22074">#22074</a>), HNOCA-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22165">#22165</a>), HOLE2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21514">#21514</a>), HolisticTraceAnalysis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21987">#21987</a>), HPX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21570">#21570</a>), ISCE2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21520">#21520</a>), 17077JACUSA2helper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21730">#21730</a>), juliaup (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21895">#21895</a>), kaggle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21854">#21854</a>), KMCLib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21555">#21555</a>), kyber (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21649">#21649</a>), libvips (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20854">#20854</a>), 17078libyuv (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21929">#21929</a>), LightGBM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21699">#21699</a>), LIME (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21630">#21630</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21682">#21682</a>), LIQA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22033">#22033</a>), llama-cpp-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21959">#21959</a>), llama.cpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22243">#22243</a>), 17079LOBSTER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22295">#22295</a>), MashMap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22246">#22246</a>), MathWorksServiceHost (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22226">#22226</a>), MDStress (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21800">#21800</a>), MFiX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22212">#22212</a>), MitoFinder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22017">#22017</a>), 17080mlst (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21942">#21942</a>), modin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21667">#21667</a>), modkit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21725">#21725</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21727">#21727</a>), MOLGW (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21029">#21029</a>), MoloVol (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21480">#21480</a>), mpl-ascii (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21679">#21679</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21707">#21707</a>), 17081msisensor-pro (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22202">#22202</a>), Mustache (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21783">#21783</a>), NanoPack (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21649">#21649</a>), netket (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21760">#21760</a>), NextDenovo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21264">#21264</a>), ngmlr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21517">#21517</a>), 17082numpydoc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21684">#21684</a>), ollama (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22424">#22424</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22559">#22559</a>), omp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22307">#22307</a>), OPEN-SURFEX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21975">#21975</a>), OpenMM-Torch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21251">#21251</a>), OpenNMT-py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21976">#21976</a>), 17083optree (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22403">#22403</a>), pairtools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22262">#22262</a>), PALM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20684">#20684</a>), Panoply (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21455">#21455</a>), Parsnp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22027">#22027</a>), pathos (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22132">#22132</a>), PDAL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22159">#22159</a>), 17084PennyLane (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21353">#21353</a>), Phonopy-Spectroscopy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21024">#21024</a>), phylo-treetime (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21677">#21677</a>), PoPoolation-TE2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21757">#21757</a>), pre-commit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22198">#22198</a>), 17085pyannote.audio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22259">#22259</a>), pybind11_abseil (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22153">#22153</a>), python-lsp-server (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21684">#21684</a>), python-slugify (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21684">#21684</a>), python-zlib-ng (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22379">
17085#22379</a>), 17086pyvips (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20854">#20854</a>), quarto (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21738">#21738</a>), RAPIDS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21058">#21058</a>), rDock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22012">#22012</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22056">#22056</a>), read2tree (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21517">#21517</a>), REViewer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22518">#22518</a>), 17087SciANN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21710">#21710</a>), SciKeras (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21734">#21734</a>), scNanoGPS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22033">#22033</a>), screen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22282">#22282</a>), SCRIPro (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20388">#20388</a>), scTIE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21694">#21694</a>), sensormotion (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22218">#22218</a>), 17088sisl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22132">#22132</a>), skani (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21518">#21518</a>), Slideflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20857">#20857</a>), SlurmViewer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21899">#21899</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22045">#22045</a>), SNPTEST (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21708">#21708</a>), Solids4foam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21606">#21606</a>), 17089Spectre (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21881">#21881</a>), sPyRMSD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21037">#21037</a>), squashfs-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22213">#22213</a>), starcode (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21486">#21486</a>), Stellarscope (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21602">#21602</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22585">#22585</a>), Suppressor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20106">#20106</a>), 17090tblis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21616">#21616</a>), tensorstore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19942">#19942</a>), test-drive (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22292">#22292</a>), TestU01 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21284">#21284</a>), text-unidecode (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21684">#21684</a>), treeseg (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21624">#21624</a>), 17091trusTEr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21855">#21855</a>), tsai (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21845">#21845</a>), unittest-xml-reporting (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22205">#22205</a>), VASPKIT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20846">#20846</a>), Verkko (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22246">#22246</a>), vLLM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21901">#21901</a>), vRhyme (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22163">#22163</a>), 17092webvtt-py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22238">#22238</a>), Wengan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21986">#21986</a>), Whisper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21470">#21470</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22031">#22031</a>), whisper-ctranslate2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22135">#22135</a>), WhisperX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22259">#22259</a>), wurlitzer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21684">#21684</a>), 17093xformers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21901">#21901</a>), YaHS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22199">#22199</a>)</li> 17094</ul> 17095</li> 17096<li>
17096added additional easyconfigs for various supported software packages, including (but not limited to):<ul> 17097<li>ABINIT 10.2.5, ASE 3.24.0, astropy 7.0.0, Beast 2.7.7, BLAST+ 2.16.0, Bonito 0.8.1, BRAKER 3.0.8, CASTEP 24.1, CDO 2.4.4, CellRanger 9.0.0, CUDA 12.8.0, deepTools 3.5.5, dorado 0.9.1, ELPA 2024.05.001, FDS 6.9.1, funannotate 1.8.17, h5py 3.12.1,HDF5 1.14.5, Extrae 4.2.5, GATK 4.6.0.0, GDAL 3.10.0, gnuplot 6.0.1, GPAW 25.1.0, Graphviz 12.2.0, GRASS 8.4.0, GROMACS 2024.4, GSL 2.8, Gurobi 12.0.0, HyperQueue 0.20.0, HMMER 3.4, LAMMPS 28Oct2024, Longshot 1.0.0, MONAI 1.4.0, mpi4py 4.0.1, NAMD 3.0, NCCL 2.22.3, NEURON 8.2.6, NVHPC 25.1, ONNX-Runtime 1.19.2, ont-remora 3.3.0, OpenImageIO 2.5.15.0, OpenMPI 5.0.7, Optuna 4.1.0, Paraver 4.12.0 ParaView 5.13.2, PSI4 1.9.1, psutil 6.0.0, pymatgen 2024.5.1, PySCF 2.7.0, Python 3.13.1, QuantumESPRESSO 7.4, R 4.4.2, R-bundle-CRAN 2024.11, R-bundle-Bioconductor 3.20, Scalene 1.5.51, Siesta 5.2.2, SMV 6.9.5, SPAdes 4.1.0, spaln 3.0.6b, Spyder 6.0.1, sympy 1.13.3, synthcity 0.2.11, Unicycler 0.5.1, WebKitGTK+ 2.41.4, WIEN2k 24.1, WRF 4.6.1, WPS 4.6.0</li> 17098</ul> 17099</li> 17100<li>minor enhancements, including:<ul> 17101<li>add <code>download_instructions</code> to easyconfigs for which download can not be done automatically (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19881">#19881</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19882">#19882</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19883">#19883</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19884">#19884</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19885">#19885</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19887">#19887</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19888">#19888</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19889">#19889</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19890">#19890</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19894">#19894</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19895">#19895</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19896">#19896</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19897">#19897</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19898">#19898</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19899">#19899</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19900">#19900</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19901">#19901</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19903">#19903</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19904">#19904</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19905">#19905</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19907">#19907</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19908">#19908</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19909">#19909</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19910">#19910</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19911">#19911</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19912">#19912</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19918">#19918</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19919">#19919</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19920">#19920</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19923">#19923</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19924">#19924</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19926">#19926</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19927">#19927</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19928">#19928</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19929">#19929</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19931">#19931</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19932">#19932</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19934">#19934</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19935">#19935</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19936">#19936</a>)</li> 17102<li>
17102add <code>source_urls</code> to cuDNN easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19902">#19902</a>)</li> 17103<li>add goldilocks + gsDesign extensions to R-bundle-CRAN v2024.06 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21583">#21583</a>)</li> 17104<li>enable tblite support in easyconfig for DFTB+ 24.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21947">#21947</a>)</li> 17105<li>add seqPattern, genomation, ChIPseeker, SimBu extensions to recent R-bundle-Bioconductor easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21474">#21474</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21948">#21948</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22151">#22151</a>)</li> 17106<li>add missing (optional) pyabpoa dependency as extension to medaka 1.11.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21983">#21983</a>)</li> 17107<li>add collection of easyconfig templates organized per generation (and remove <code>TEMPLATE.eb</code> poor mans template easyconfig) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21984">#21984</a>)</li> 17108<li>add frbs + gcmr extensions to recent R-bundle-CRAN easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21993">#21993</a>)</li> 17109<li>add TorchRL extension to PyTorch-bundle v2.1.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22000">#22000</a>)</li> 17110<li>Set <code>$PKG_CONFIG</code> in pkgconf modules (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22005">#22005</a>)</li> 17111<li>add wayland-utils component to Wayland 1.23.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22009">#22009</a>)</li> 17112<li>add patch for Autoconf to improve handling for 'llc' flags appearing e.g. with NVHPC on aarch64 systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22173">#22173</a>)</li> 17113<li>enable plugins that require HDF5 + Boost dependencies for Visit v3.4.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22334">#22334</a>)</li> 17114<li>use reproducible archives on easyconfigs with sources from git repos without a <code>.git</code> dir (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22575">#22575</a>)</li> 17115</ul> 17116</li> 17117<li>various bug fixes, including:<ul> 17118<li>remove executable flag from easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19059">#19059</a>)</li> 17119<li>fix some typos found in software descriptions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19142">#19142</a>)</li> 17120<li>fix source definition for dialog (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19906">#19906</a>)</li> 17121<li>use proper dependencies for Safetensors and tokenizers in Transformers easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20868">#20868</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20869">#20869</a>)</li> 17122<li>remove ignored <code>toolchainopts</code> from <code>SYSTEM</code> toolchain easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21035">#21035</a>)</li> 17123<li>add patch to fix compilation of HPDBSCAN 20210826 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21467">#21467</a>)</li> 17124<li>use <code>-lncurses</code> rather than <code>-ltermcap</code> for <code>Term::ReadLine::GNU</code> Perl extension (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21469">#21469</a>)</li> 17125<li>use skani rather than FastANI as dependency for GTDB-Tk v2.4.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21518">#21518</a>)</li> 17126<li>add patch for ROOT v6.24.06, v6.26.06, v6.26.10, v6.30.6 to disable sysroot for cling at runtime (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21526">#21526</a>)</li> 17127<li>link <code>libOpenCL.so.1</code> to the <code>lib</code> directory for NextGenMap (required when using RPATH linking) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21528">#21528</a>)</li> 17128<li>
17128add patch for bug/typo in RISC-V toolchain options to EasyBuild 4.9.4 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21547">#21547</a>)</li> 17129<li>strip out '<code>-minsize 1</code>' option from <code>umi_binning.sh</code> in longread_umi 0.3.2, since it's not supported by VSEARCH (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21557">#21557</a>)</li> 17130<li>add patch to SciPy-bundle 2024.05 that fixes test failure on aarch64 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21559">#21559</a>)</li> 17131<li>promote pybind11 to runtime dependency for CPPE (to fix <code>pip check</code> failure) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21564">#21564</a>)</li> 17132<li>fix installation of NextPolish v1.4.1 when RPATH linking is used (+ move to <code>GCC</code> toolchain) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21588">#21588</a>)</li> 17133<li>remove explicit use of <code>ld.gold</code> in recent PLUMED easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21613">#21613</a>)</li> 17134<li>stop using <code>--buildtype=release</code> in easyconfigs using <code>MesonNinja</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21619">#21619</a>)</li> 17135<li>demote hatchling to build-only dependency in various easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21657">#21657</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21809">#21809</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21844">#21844</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22039">#22039</a>)</li> 17136<li>add pyproject-metadata to scikit-build-core v0.9.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21671">#21671</a>)</li> 17137<li>fix failing RPATH sanity check for recent dorado easyconfigs using <code>foss/2023a</code> toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21673">#21673</a>)</li> 17138<li>add patch to fix alignment bug in patchelf 0.18.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21674">#21674</a>)</li> 17139<li>ignore user Python packages when running custom sanity check command <code>pip check</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21675">#21675</a>)</li> 17140<li>add patch for SciPy-bundle 2023.07 + 2023.11 to fix vectorization bug in scipy 1.11.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21693">#21693</a>)</li> 17141<li>fix the zero division bug of <code>networkx-3.1</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21702">#21702</a>)</li> 17142<li>add <code>trimmomatic</code> wrapper script for recent Trimmomatic 0.39 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21704">#21704</a>)</li> 17143<li>switch to using new spaces as delimiters for TCLLIBPATH (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21724">#21724</a>)</li> 17144<li>use new checksum for source tarball of SIONlib 1.7.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21748">#21748</a>)</li> 17145<li>remove <code>-m64</code> compiler flag for non-x86-64 CPU architectures in SIONlib 1.7.7 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21752">#21752</a>)</li> 17146<li>add missing Perl-bundle-CPAN dependency to recent parallel easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21776">#21776</a>)</li> 17147<li>update libvdwxc webpage as old URL has been taken over by evildoers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21797">#21797</a>)</li> 17148<li>add path to Faiss shared libraries to $LD_LIBRARY_PATH (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21799">#21799</a>)</li> 17149<li>add patch to fix vectorization bug in scipy 1.11.1 also to SciPy-bundle 2023.07 w/ iimkl/2023a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21805">#21805</a>)</li> 17150<li>fix bug in HTSplotter 2.11 through runtime patching via <code>sed</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21812">#21812</a>)</li> 17151<li>fix conflict for platformdirs dependency in easyconfig Pylint 3.2.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21873">#21873</a>)</li> 17152<li>fix parallel for cppyy-cling in easyconfig for cppyy v3.1.2 + don't specify to use C++14 by setting <code>$STDCXX</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21900">#21900</a>)</li> 17153<li>use original sources for enchant-2 v2.6.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21944">#21944</a>)</li> 17154<li>fix Boost 1.85 build on POWER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21950">#21950</a>)</li> 17155<li>
17155add missing cutadapt dependency for decona 1.4-20240731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21982">#21982</a>)</li> 17156<li>fix typo in <code>configopts</code> for ParaView v5.11.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21894">#21894</a>)</li> 17157<li>add patch to fix use of RPATH wrappers in LASTZ-1.04.22 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22016">#22016</a>)</li> 17158<li>fix test failure due to unresolved template (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22061">#22061</a>)</li> 17159<li>expand templates in checksum keys (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22091">#22091</a>)</li> 17160<li>fix incorrect keys in checksums for jaxlib component in jax 0.4.25 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22092">#22092</a>)</li> 17161<li>update homepage and source_urls for libxsmm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22164">#22164</a>)</li> 17162<li>fix setuptools issue by sticking to a single version in ReFrame 4.3.3 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22183">#22183</a>)</li> 17163<li>detect use of deprecated behavior in test runs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21885">#21885</a>)</li> 17164<li>move download of data files to source step for Casacore v3.5.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22201">#22201</a>)</li> 17165<li>add MathWorksServiceHost dependency to MATLAB 2024b easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22226">#22226</a>)</li> 17166<li>add patch for WIEN2k 24.1 to fix bug in symmetry determination (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22234">#22234</a>)</li> 17167<li>change <code>source_urls</code> for Boost from <code>boostorg.jfrog.io</code> to <code>archives.boost.io</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22157">#22157</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22240">#22240</a>)</li> 17168<li>avoid using <code>$HOME/.cargo</code> when installing poetry by using <code>CargoPythonBundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22257">#22257</a>)</li> 17169<li>unset <code>$BUILD_VERSION</code> set by <code>torchvision</code> easyblock in <code>preinstallopts</code> for <code>torchaudio</code> in easyconfigs for <code>PyTorch-bundle</code> 2.1.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22258">#22258</a>)</li> 17170<li>{chem}[foss/2023a] LAMMPS v28Oct2024 w/ kokkos CUDA 12.1.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22268">#22268</a>)</li> 17171<li>add missing dependency on pybind11 for contourpy in matplotlib v3.9.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22294">#22294</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22301">#22301</a>)</li> 17172<li>fix warning in jax 0.3.x that fails the build by using <code>-Wno-maybe-uninitialized</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22325">#22325</a>)</li> 17173<li>add patch for QuantumESPRESSO 7.4 to fix parallel symmetrization glitch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22345">#22345</a>)</li> 17174<li>use all same checksums of libxc v6.2.2 in its easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22348">#22348</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22580">#22580</a>)</li> 17175<li>fix checksum for Miniforge3 24.1.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22366">#22366</a>)</li> 17176<li>fix <code>python-zlib-ng</code> dependency for pytest-workflow 2.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22379">#22379</a>)</li> 17177<li>add missing Doxygen build dependency for bcl2fastq2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22429">#22429</a>) and libheif (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22054">#22054</a>)</li> 17178<li>fix NSS easyconfigs by not keeping symlinks when copying files to installation (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22471">#22471</a>)</li> 17179<li>
17179add multiple checksoms to Pandoc easyconfigs supporting multiple archs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22493">#22493</a>)</li> 17180<li>disable <code>rpath</code> toolchain option in older NCCL easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22520">#22520</a>)</li> 17181<li>use <code>PerlBundle</code> easyblock for XML-LibXML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22521">#22521</a>)</li> 17182<li>fix download source for PDT/3.25.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22523">#22523</a>)</li> 17183<li>fix MPICH with-device configuration option (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22555">#22555</a>)</li> 17184<li>don't use unknown configure options <code>--with-gmp</code> and <code>--with-givaro</code> in easyconfig for FFLAS-FFPACK 2.5.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22558">#22558</a>)</li> 17185<li>add <code>$TMPDIR</code> to sandbox mounts for Bazel 7.4.1 tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22564">#22564</a>)</li> 17186<li>disable <code>keepsymlinks</code> in libStatGen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22565">#22565</a>)</li> 17187<li>use <code>.tar.xz</code> archive for <code>jsonpath_lib</code> sources in polars easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22566">#22566</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22450">#22450</a>)</li> 17188<li>add build dependency on git to Scalene (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22567">#22567</a>)</li> 17189<li>don't use unknown configure options in LinBox easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22569">#22569</a>)</li> 17190<li>add patch to fix build failure due to too long filenames in Qt6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22570">#22570</a>)</li> 17191<li>consistently use patch in easyconfigs for PRSice 2.3.5 to stop relying on sysctl.h (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22571">#22571</a>)</li> 17192<li>make CMake a runtime dependency of gemmi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22572">#22572</a>)</li> 17193<li>switch download source for ffnvcodec (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22574">#22574</a>)</li> 17194<li>replace source URLs of Mesa to new location in archive.mesa3d.org (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22576">#22576</a>)</li> 17195<li>remove unknown configure options for GRASS 8.4.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22577">#22577</a>)</li> 17196<li>update homepage and sources of METIS and ParMETIS with new home at kaypis.github.io (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22579">#22579</a>)</li> 17197<li>add new checksum for tantan v50 tarball (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22581">#22581</a>)</li> 17198<li>update homepage and sources of MUMPS with new home at mumps-solver.org (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22582">#22582</a>)</li> 17199<li>ensure that sanity check command for ExpressBetaDiversity v1.0.10 is run from <code>bin</code> subdirectory of installation directory (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22586">#22586</a>)</li> 17200<li>add new checksums for R packages of PEcAn v1.8.0.9000 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22587">#22587</a>)</li> 17201</ul> 17202</li> 17203<li>other changes:<ul> 17204<li>archive easyconfigs for old software versions or using unsupported toolchain in <code>easybuild-easyconfigs-archive</code> repository (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18934">#18934</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18958">#18958</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18968">#18968</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18976">#18976</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18978">#18978</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18982">#18982</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18984">#18984</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18989">#18989</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18990">#18990</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18991">#18991</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18992">#18992</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18993">#18993</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19002">#19002</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19004">#19004</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19005">#19005</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19008">#19008</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19013">#19013</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19494">#19494</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19656">#19656</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19827">#19827</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19834">#19834</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19933">#19933</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19937">#19937</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20006">#20006</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20259">#20259</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20435">#20435</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22051">#22051</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22069">#22069</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22175">#22175</a>)</li> 17205<li>use more recent easyconfigs in checks for <code>--search</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18995">#18995</a>)</li> 17206<li>clean up easyconfigs that explicitly set <code>
17206use_pip</code>, <code>sanity_pip_check</code> and <code>download_dep_fail</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19265">#19265</a>)</li> 17207<li>replace use of <code>parallel</code> easyconfig parameter with <code>maxparallel</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19375">#19375</a>)</li> 17208<li>bypass <code>.mod</code> file in GeneMark-ET (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19500">#19500</a>)</li> 17209<li>move <code>setuptools_scm</code> from <code>hatchling</code> to Python easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19651">#19651</a>)</li> 17210<li>replace usage of <code>easybuild.tools.py2vs3</code> in easyconfigs test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19744">#19744</a>)</li> 17211<li>add check to make sure that <code>download_dep_fail</code>, <code>sanity_pip_check</code>, <code>use_pip</code> are not explicitly set to <code>True</code> in easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19830">#19830</a>)</li> 17212<li>replace <code>run_cmd</code> with <code>run_shell_cmd</code> in easyconfigs testsuite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19818">#19818</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19886">#19886</a>)</li> 17213<li>remove trailing whitespace from easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20082">#20082</a>)</li> 17214<li>cleanup Python < 2.6 test skip (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20253">#20253</a>)</li> 17215<li>remove <code>CMAKE_INSTALL_LIBDIR</code> settings from <code>configopts</code> + add test to enfore use of <code>install_libdir</code> instead (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20487">#20487</a>)</li> 17216<li>fix LLVM easyconfigs as required by revamped custom easyblock for LLVM + add <code>lit</code> and <code>git</code> as build dependencies (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20902">#20902</a>)</li> 17217<li>stop using <code>modextrapaths</code> to update <code>$PYTHONPATH</code> with standard path to installed Python packages (<code>lib/python%(pyshortver)s/site-packages</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20960">#20960</a>)</li> 17218<li>use <code>CMakeMake</code> easyblock for BamTools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21263">#21263</a>)</li> 17219<li>use pycodestyle for code style check + stop using <code>l</code> in list comprehensions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21502">#21502</a>)</li> 17220<li>move jedi package from IPython 8.14.0 to own easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21650">#21650</a>)</li> 17221<li>fix CI check for extension patches using <code>alt_location</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21700">#21700</a>)</li> 17222<li>remove <code>install_pip=True</code> from Python easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22103">#22103</a>)</li> 17223<li>add a github workflow that tags PRs with new/update/change + add diffs in comments (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21758">#21758</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21779">#21779</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21793">#21793</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21795">#21795</a>)</li> 17224<li>test suite changes required for changes in EasyBuild v5.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22116">#22116</a>)</li> 17225<li>move pybind11 dependency from SciPy-bundle v2024.05 to builddependencies (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22170">#22170</a>)</li> 17226<li>swicth GCC-system and GCCcore-system to SystemCompilerGCC easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22174">#22174</a>)</li> 17227<li>use latest version (0.2.5) of archspec for LAMMPS 2Aug2023 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22235">#22235</a>)</li> 17228<li>Remove explicit C++ standard from Bowtie2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22278">#22278</a>)</li> 17229<li>migrate easyconfig for NEURON v8.2.6 to use custom easyblock for NEURON (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22324">#22324</a>)</li> 17230<li>avoid using <code>buildcmd</code> in PySide2 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22380">#22380</a>)</li> 17231<li>remove deprecated <code>
17231allow_prepend_abs_path</code> from libglvnd and SpaceRanger (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22416">#22416</a>)</li> 17232<li>replace hardcoded <code>'CPATH'</code> in <code>modextravars</code> with <code>MODULE_LOAD_ENV_HEADERS</code> constant (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22417">#22417</a>)</li> 17233<li>update GitHub actions workflows to use Ubuntu 22.04 or 24.04 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22457">#22457</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22459">#22459</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22472">#22472</a>)</li> 17234<li>clean up easyconfigs so they don't explicitly enable <code>keepsymlinks</code>, since it's now enabled by default (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/22573">#22573</a>)</li> 17235</ul> 17236</li> 17237</ul> 17238<h2 id="release_notes_eb494">EasyBuild v4.9.4 (22 Sept 2024)<a class="headerlink" href="#release_notes_eb494" title="Permanent link">¶</a></h2> 17239<p>bugfix/update release</p> 17240<p><strong>framework</strong></p> 17241<ul> 17242<li>various enhancements, including:<ul> 17243<li>set <code>$LMOD_TERSE_DECORATIONS</code> to '<code>no</code>' to avoid additional info in output produced by '<code>ml --terse avail</code>' (<a href="https://github.com/easybuilders/easybuild-framework/pull/4648">#4648</a>)</li> 17244</ul> 17245</li> 17246<li>various bug fixes, including:<ul> 17247<li>implement workaround for permission error when copying read-only files that have extended attributes set and using Python 3.6 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4642">#4642</a>)</li> 17248<li>take into account alternate sysroot for <code>/bin/bash</code> used by <code>run_cmd</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4646">#4646</a>)</li> 17249</ul> 17250</li> 17251</ul> 17252<p><strong>easyblocks</strong></p> 17253<ul> 17254<li>various enhancements, including:<ul> 17255<li>ignore Python from virtualenvs in GROMACS configure via <code>-DPython3_FIND_VIRTUALENV=STANDARD</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3283">#3283</a>)</li> 17256<li>enhance custom easyblock for NCCL: add licence to NCCL installation (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3451">#3451</a>)</li> 17257</ul> 17258</li> 17259<li>various bug fixes, including:<ul> 17260<li>allow Python bundles and packages to specify a maximum Python version for the system toolchain (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3431">#3431</a>)</li> 17261<li>copy <code>EasyConfig</code> instance in constructor of <code>Bundle</code> and <code>Cargo</code> easyblocks before making changes to it (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3448">#3448</a>)</li> 17262<li>fix crash in GCC easyblock when <code>cuda-compute-capabilities</code> EasyBuild configuration option is not set (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3449">#3449</a>)</li> 17263</ul> 17264</li> 17265</ul> 17266<p><strong>easyconfigs</strong></p> 17267<ul> 17268<li>added example easyconfig files for 14 new software packages:<ul> 17269<li>Biotite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21026">#21026</a>), chopper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21418">#21418</a>), CLUMPP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21329">#21329</a>), cramino (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21382">#21382</a>), dub (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21378">#21378</a>), ESM3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21026">#21026</a>), GOMC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21008">#21008</a>), 17270MOKIT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21352">#21352</a>), nanoQC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21371">#21371</a>), phasius (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21389">#21389</a>), PyBullet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21356">#21356</a>), rnamotif (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21336">#21336</a>), versioningit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21424">#21424</a>), 17271xskillscore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21351">#21351</a>)</li> 17272</ul> 17273</li> 17274<li>
17274added additional easyconfigs for various supported software packages, including:<ul> 17275<li>awscli 2.17.54, BiG-SCAPE-1.1.9, ccache 4.10.2, CLHEP 2.4.7.1, CREST 3.0.2, decona 1.4-2024073, dftd4 3.7.0, 17276GATE 9.4, Gdk-Pixbuf 2.42.11, Geant4 11.2.2, Geant4-data 11.2, Ghostscript 10.03.1, GitPython 3.1.43, 17277GObject-Introspection 1.80.1, HarfBuzz 9.0.0, ImageMagick 7.1.1-38, JasPer 4.2.4, joypy 0.2.6, Julia 1.10.4, 17278LDC 1.39.0, Leptonica 1.84.1, Markdown 3.7, MPICH 4.2.2, NanoComp 1.24.0, nanoget 1.19.3, nanomath 1.4.0, 17279NanoPlot 1.43.0, Pango 1.54.0, PCAngsd 1.2, Pillow 10.4.0, python-isal 1.7.0, pocl 6.0, PROJ 9.4.1, protobuf 28.0, 17280protobuf-python 5.28.0, R-tesseract 5.2.1, RepeatMasker 4.1.7-p1, RHEIA 1.1.11, RMBlast 2.14.1, 17281scikit-build-core 0.10.6, sleuth 0.30.1, SNAP-ESA 10.0.0, tesseract 5.3.4, Triton 2.1.0, TurboVNC 3.1.2, 17282VirtualGL 3.1.1, zlib-ng 2.2.1</li> 17283</ul> 17284</li> 17285<li>minor enhancements, including:<ul> 17286<li>enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21056">#21056</a>)</li> 17287<li>use proper dependency for tensorboard in easyconfigs for TensorFlow v2.15.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21337">#21337</a>)</li> 17288</ul> 17289</li> 17290<li>various bug fixes, including:<ul> 17291<li>account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches in easyconfigs test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21419">#21419</a>)</li> 17292<li>avoid missing symbol in <code>mclust</code> extension of R-4.0.3 w/ foss/2020b (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21429">#21429</a>)</li> 17293<li>fix build of librosa 0.10.1 in some environments by removing "python -m build" for soxr extension (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21434">#21434</a>)</li> 17294<li>fix repeated sanity check runs in manta easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21435">#21435</a>)</li> 17295<li>fix <code>test_easyconfig_locations</code> when easyconfigs index is present (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21394">#21394</a>)</li> 17296<li>use proper dependency for libnsl in git-annex (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21441">#21441</a>)</li> 17297<li>avoid writing into <code>~/.stack</code> directory during build for git-annex (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21452">#21452</a>)</li> 17298</ul> 17299</li> 17300<li>other changes:<ul> 17301<li>remove <code>exts_default_options</code> from TensorFlow 2.3.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21290">#21290</a>)</li> 17302</ul> 17303</li> 17304</ul> 17305<h2 id="release_notes_eb493">EasyBuild v4.9.3 (14 Sept 2024)<a class="headerlink" href="#release_notes_eb493" title="Permanent link">¶</a></h2> 17306<p>bugfix/update release</p> 17307<p><strong>framework</strong></p> 17308<ul> 17309<li>various enhancements, including:<ul> 17310<li>add support for <code>--extra-source-urls</code> to fetch sources from additional URLs (<a href="https://github.com/easybuilders/easybuild-framework/pull/4079">#4079</a>)</li> 17311<li>add definition for gmpflf toolchain (<a href="https://github.com/easybuilders/easybuild-framework/pull/4566">#4566</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4571">#4571</a>)</li> 17312<li>reuse pre-computed checksums (<a href="https://github.com/easybuilders/easybuild-framework/pull/4569">#4569</a>)</li> 17313<li>add <code>cuda_cc_space_sep</code> variant that does not have periods (<a href="https://github.com/easybuilders/easybuild-framework/pull/4583">#4583</a>)</li> 17314<li>add <code>--skip-sanity-check</code> option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4590">#4590</a>)</li> 17315<li>add <code>GNU_FTP_SOURCE</code> template constant (<a href="https://github.com/easybuilders/easybuild-framework/pull/4597">#4597</a>)</li> 17316<li>improve error messages for empty easyconfigs (<a href="https://github.com/easybuilders/easybuild-framework/pull/4603">#4603</a>)</li> 17317<li>improve help string for <code>--dep-graph</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4610">#4610</a>)</li> 17318<li>only call <code>_sanity_check_step_extensions</code> if <code>--skip-extensions</code> is not set (<a href="https://github.com/easybuilders/easybuild-framework/pull/4620">#4620</a>)</li> 17319<li>
17319add support for <code>--software-commit</code> and an associated template <code>%(software_commit)s</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4628">#4628</a>)</li> 17320</ul> 17321</li> 17322<li>various bug fixes, including:<ul> 17323<li>correctly evaluate result for <code>--dep-graph</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4554">#4554</a>)</li> 17324<li>fix fetch progress bar showing too many files (<a href="https://github.com/easybuilders/easybuild-framework/pull/4568">#4568</a>)</li> 17325<li>resolve internal for imkl>=2021 version subdir via "latest" symlink (<a href="https://github.com/easybuilders/easybuild-framework/pull/4570">#4570</a>)</li> 17326<li>fix typo in message about including an easyblock from a commit (<a href="https://github.com/easybuilders/easybuild-framework/pull/4575">#4575</a>)</li> 17327<li>don't use special flags for <code>strict</code>, <code>precise</code>, <code>loose</code>, <code>veryloose</code> toolchain options on RISC-V (<a href="https://github.com/easybuilders/easybuild-framework/pull/4576">#4576</a>)</li> 17328<li>fix help text for <code>cuda_compute_capabilities</code> template (<a href="https://github.com/easybuilders/easybuild-framework/pull/4589">#4589</a>)</li> 17329<li>fix help message for <code>--http-headers-fields-urlpat</code> configuration option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4594">#4594</a>)</li> 17330<li>fix <code>test_compiler_cache</code> in case <code>gcc</code> is available multiple times (<a href="https://github.com/easybuilders/easybuild-framework/pull/4599">#4599</a>)</li> 17331<li>handle post-install patches in check_checksums_for (<a href="https://github.com/easybuilders/easybuild-framework/pull/4605">#4605</a>)</li> 17332<li>fix <code>copy_file</code> with a folder as the target (<a href="https://github.com/easybuilders/easybuild-framework/pull/4609">#4609</a>)</li> 17333<li>allow for case where <code>homepage = None</code> when generating the docs (<a href="https://github.com/easybuilders/easybuild-framework/pull/4626">#4626</a>)</li> 17334<li>fix <code>test_github_det_commit_status</code> by using more recent commits (<a href="https://github.com/easybuilders/easybuild-framework/pull/4636">#4636</a>)</li> 17335</ul> 17336</li> 17337<li>other changes:<ul> 17338<li>clean up code that was only there to support Python 2.6 + avoid syntax warnings when parsing py2vs3/py.p2 with Python 3.x (<a href="https://github.com/easybuilders/easybuild-framework/pull/3788">#3788</a>)</li> 17339<li>use Intel's oneAPI Fortran compiler by default for version 2024.0.0 and newer (<code>oneapi_fortran</code> toolchain option set to <code>True</code>) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4567">#4567</a>)</li> 17340<li>allow using Node 16 actions in CI (<a href="https://github.com/easybuilders/easybuild-framework/pull/4574">#4574</a>)</li> 17341<li>remove a superflous check in <code>EasyBlock.run_all_steps</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4623">#4623</a>)</li> 17342<li>remove trailing dots from backup message produced by --inject-checksums (<a href="https://github.com/easybuilders/easybuild-framework/pull/4632">#4632</a>)</li> 17343</ul> 17344</li> 17345</ul> 17346<p><strong>easyblocks</strong></p> 17347<ul> 17348<li>minor updates, including:<ul> 17349<li>update custom easyblock for Tensorflow for versions 2.14 + 2.15 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3303">#3303</a>)</li> 17350<li>add support for versions >= 2024a to MCR easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3369">#3369</a>)</li> 17351<li>update custom easyblock for Bazel for versions >= 7.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3370">#3370</a>)</li> 17352<li>don't consider lib/release for impi >= 2021.11 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3375">#3375</a>)</li> 17353<li>update ORCA easyblock for version 6 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3395">#3395</a>)</li> 17354<li>update custom easyblock for psmpi to support the renaming of a couple of options in 5.10.0-1 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3420">#3420</a>)</li> 17355<li>update sanity check in OpenFOAM easyblock, since there's no <code>modifyMesh</code> in OpenFOAM 12 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3434">#3434</a>)</li> 17356<li>fix sanity check for Geant4 >= v11.2 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3439">#3439</a>)</li> 17357</ul> 17358</li> 17359<li>minor enhancements, including:<ul> 17360<li>enhance psmpi easyblock to activate CUDA support when it is a dependency + make check for static libs in MPICH easyblock optional (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2787">#2787</a>)</li> 17361<li>make a project environment and manage LOAD_PATH for JuliaPackage (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3239">#3239</a>)</li> 17362<li>set build type for PyTorch explicitely (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3332">#3332</a>)</li> 17363<li>
17363add <code>sanity_check_test_inputs</code> custom easyconfig parameter, mapping for zen4, and support building of non-stable versions to LAMMPS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3336">#3336</a>)</li> 17364<li>add RISCV64 support and update config options of new versions of Extrae (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3339">#3339</a>)</li> 17365<li>set <code>$ESMFMKFILE</code> environment variable in environment module for ESMF (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3368">#3368</a>)</li> 17366<li>use build dir for big files/folders while building TensorFlow (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3371">#3371</a>)</li> 17367<li>update <code>PythonPackage</code> easyblock to allow installation of Python packages with <code>$PIP_REQUIRE_VIRTUALENV</code> set + move temporary pip folder into build dir (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3374">#3374</a>)</li> 17368<li>add RISC-V support to Boost easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3376">#3376</a>)</li> 17369<li>add support for generating <code>.gem</code> files from <code>.gemspec</code> files and support for <code>preinstallopts</code> in the <code>RubyGem</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3381">#3381</a>)</li> 17370<li>simplify install step in custom easyblock for <code>Tkinter</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3382">#3382</a>)</li> 17371<li>add MSA and specially PMIx support for ParaStationMPI (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3383">#3383</a>)</li> 17372<li>update custom easyblock for PETSc to consider <code>include/suitesparse</code> subdirectory for SuiteSparse headers (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3391">#3391</a>)</li> 17373<li>enhance custom easyblock for GCC to use <code>with-arch</code> option for nvptx with 13.1+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3396">#3396</a>)</li> 17374<li>support revisions in crates extraction of cargo packages (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3405">#3405</a>)</li> 17375<li>set <code>$R_LIBS_USER</code> in <code>RPackage</code> easyblock to avoid picking up on R packages installed in home directory (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3407">#3407</a>)</li> 17376<li>update custom easyblock for QuantumESPRESSO to be aware of MPI tests being disabled in EasyBuild configuration (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3412">#3412</a>)</li> 17377<li>disable the version check of pip in Python packages by defining <code>$PIP_DISABLE_PIP_VERSION_CHECK</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3427">#3427</a>)</li> 17378<li>make sure user packages are not used in sanity check of PythonBundle (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3435">#3435</a>)</li> 17379<li>enhance OpenFOAM easyblock to also build the plugins for OpenFOAM >= v2406 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3436">#3436</a>)</li> 17380<li>enhance binutils easyblock to explicitely pass msgpack configure option (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3438">#3438</a>)</li> 17381</ul> 17382</li> 17383<li>various bug fixes, including:<ul> 17384<li>patch <code>ctypes</code> for Python installations when filtering <code>LD_LIBRARY_PATH</code> + fix path to <code>ldconfig</code> when using alternate sysroot (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3352">#3352</a>)</li> 17385<li>also consider 'normalised' package name with underscore rather than dash in EasyBuild easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3358">#3358</a>)</li> 17386<li>use PRRTE MCA environment variable for oversubscription in OpenMPI easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3360">#3360</a>)</li> 17387<li>fix import of <code>parse</code> in <code>openssl_wrapper.py</code> for Python 2.7 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3364">#3364</a>)</li> 17388<li>make sure that OpenFOAM's wmake can find MPFR and GMP if CGAL >= 5.0 (header-only) is used (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3366">#3366</a>)</li> 17389<li>remove dummy license server info from ANSYS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3377">#3377</a>)</li> 17390<li>explicitly call <code>csh</code> in custom easyblock for WPS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3384">#3384</a>)</li> 17391<li>use relative paths to object files when compiling shared libraries in the OpenFOAM easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3388">#3388</a>)</li> 17392<li>change extra <code>$PATH</code> entry for OCaml to use <code>opam/default</code> rather than <code>opam/system</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3390">#3390</a>)</li> 17393<li>force <code>--without-unwind</code> for ARM and add <code>--with-libz</code> option for all architectures in custom easyblock for Extrae (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3393">#3393</a>)</li> 17394<li>fix <code>--sanity-check-only</code> for impi (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3403">#3403</a>)</li> 17395<li>fix crash in Cargo easyblock when no crates are specified (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3404">#3404</a>)</li> 17396<li>fix double initialization of <code>Cargo</code> by <code>CargoPythonPackage</code> by removing incorrect custom <code>__init__</code> implementation + fix use of <code>super()</code> in PALM easyblock (since that doesn't work with Python 2.7) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3406">#3406</a>)</li> 17397<li>fix typo in log message in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3408">#3408</a>)</li> 17398<li>make sure to raise an error if <code>pick_python_cmd</code> returns <code>False</code> for Python bundles/packages (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3430">#3430</a>)</li> 17399<li>don't wipe build environment before building opam in install step of OCaml easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3443">#3443</a>)</li> 17400</ul> 17401</li> 17402<li>other changes:<ul> 17403<li>merge of the <code>ConfigureMake</code> and <code>CMakeMake</code> versions of the easyblock for QuantumESPRESSO (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3338">#3338</a>)</li> 17404<li>remove redundant backslashes in GEANT easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3394">#3394</a>)</li> 17405</ul> 17406</li> 17407</ul> 17408<p><strong>easyconfigs</strong></p> 17409<ul> 17410<li>added easyconfigs for <code>foss/2024a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21100">#21100</a>) and <code>intel/2024a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21101">#21101</a>) common toolchains</li> 17411<li>new toolchain: <code>gmpflf/2024.06</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20882">#20882</a>)</li> 17412<li>
17412added example easyconfig files for 107 new software packages:<ul> 17413<li>absl-py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21039">#21039</a>), accelerate (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21107">#21107</a>), affogato (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), APOST3D (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21133">#21133</a>), bayesian-optimization (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21301">#21301</a>), 17414BayesOpt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21261">#21261</a>), BGEN-enkre (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15752">#15752</a>), bitsandbytes (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21248">#21248</a>), bliss (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21206">#21206</a>), cfgrib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21113">#21113</a>), CLANS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21099">#21099</a>), 17415colorize (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20964">#20964</a>), CORSIKA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20693">#20693</a>), COSTA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20989">#20989</a>), coxeter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21254">#21254</a>), Critic2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20833">#20833</a>), crypt4gh (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20870">#20870</a>), 17416dblatex (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21207">#21207</a>), dictys (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21166">#21166</a>), DL_POLY_Classic_GUI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20819">#20819</a>), EGA-QuickView (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20870">#20870</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20888">#20888</a>), EMMAX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21174">#21174</a>), 17417empanada-dl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20454">#20454</a>), empanada-napari (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20454">#20454</a>), ESIpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21006">#21006</a>), fastfilters (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21003">#21003</a>), fish (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21345">#21345</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21381">#21381</a>), 17418flash-attention (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21083">#21083</a>), Flax (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21039">#21039</a>), fonttools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21363">#21363</a>), fsm-lite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20503">#20503</a>), GDMA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21171">#21171</a>), GeoDict (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20650">#20650</a>), 17419GPflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21172">#21172</a>), gtk-doc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21207">#21207</a>), Gubbins (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20413">#20413</a>), Gymnasium (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20420">#20420</a>), HERRO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21252">#21252</a>), IEntropy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20808">#20808</a>), 17420ilastik-napari (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21003">#21003</a>), IMAGE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20994">#20994</a>), junos-eznc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21166">#21166</a>), jupyter-collaboration (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20741">#20741</a>), 17421jupyter-vscode-proxy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20876">#20876</a>), langchain-mistralai (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20759">#20759</a>), langchain-openai (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20711">#20711</a>), LRBinner (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21310">#21310</a>), 17422lrcalc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21339">#21339</a>), MAGIC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20900">#20900</a>), mallard-ducktype (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21127">#21127</a>), MATES (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21229">#21229</a>), MBX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21155">#21155</a>), mcqd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21283">#21283</a>), 17423MeshLab (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20806">#20806</a>), meteogrid (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20921">#20921</a>), micro-sam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), miniprot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21157">#21157</a>), napari-denoiseg (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20934">#20934</a>), 17424NECAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21359">#21359</a>), nellie (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21267">#21267</a>), NextPolish (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21265">#21265</a>), nifty (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), ome-types (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21256">#21256</a>), openai-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20711">#20711</a>), 17425OpenForceField-Toolkit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20852">#20852</a>), orjson (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20880">#20880</a>), PEcAn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21227">#21227</a>), PretextMap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20790">#20790</a>), PyBEL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20953">#20953</a>), 17426pyMBE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21034">#21034</a>), pystencils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20889">#20889</a>), python-blosc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), python-elf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), rankwidth (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20788">#20788</a>), Rasqal (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21207">#21207</a>), 17427Redland (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21227">#21227</a>), Regenie (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15752">#15752</a>), rMATS-long (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20916">#20916</a>), Sagemath (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21365">#21365</a>), scCustomize (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20907">#20907</a>), SCENICplus (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21085">#21085</a>), 17428scFEA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20777">#20777</a>), sdsl-lite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20503">#20503</a>), SharedMeatAxe (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21303">#21303</a>), Single-cell-python-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20116">#20116</a>), SIRIUS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20989">#20989</a>), 17429sirocco (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21304">#21304</a>), SKA2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20411">#20411</a>), SpFFT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20989">#20989</a>), spla (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11607">#11607</a>), Stable-Baselines3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20884">#20884</a>), submitit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21103">#21103</a>), 17430SVDSS2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20855">#20855</a>), tdlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21305">#21305</a>), torch-em (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), Umpire (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20989">#20989</a>), Uni-Core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21182">#21182</a>), vigra (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), 17431Visit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20981">#20981</a>), weblogo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20800">#20800</a>), wradlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21110">#21110</a>), xtb-IFF (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20783">#20783</a>), yell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20964">#20964</a>), yelp-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21127">#21127</a>), 17432yelp-xsl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21127">#21127</a>), z5py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20636">#20636</a>), Zoltan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21324">#21324</a>)</li> 17433</ul> 17434</li> 17435<li>
17435added additional easyconfigs for various supported software packages, including:<ul> 17436<li>AGAT 1.4.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, 17437AmberTools 26.3, Arrow 16.1.0, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BayesTraits 4.1.2, BeautifulSoup 4.12.3, 17438Biopython 1.84, Boost.MPI 1.83.0, bcl-convert 4.2.7-2, beagle-lib 4.0.1, biom-format 2.1.16, byacc 2.0.20240109, 17439CDO 2.3.0, CFITSIO 4.4.1, CUDA-Samples 12.2, CUDA 12.5.0 + 12.6.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, 17440Clang 18.1.8, Coreutils 9.5, chewBBACA 3.3.9, code-server 4.90.2, connected-components-3d 3.14.1, cooler 0.10.2, 17441cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, dorado 0.7.3, dtcmp 1.1.5, ESMF 8.6.1, EvidentialGene 2023.07.15, 17442Extrae 4.2.0, ecBuild 3.8.5, elfutils 0.191, FFmpeg 7.0.2, FLAC 1.4.3, FUSE 3.16.2, Flask 3.0.3, Flye 2.9.4, 17443FriBidi 1.0.15, ffnvcodec 12.2.72.0, flatbuffers-python 24.3.25, flatbuffers 24.3.25, fmt 10.2.1, fpylll 0.6.1, 17444GCC 14.2.0, GDAL 3.9.0, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1 + 2.75.0 + 2.77.0 + 2.78.1, 17445GPAW 24.6.0, GetOrganelle 1.7.7.1, Guile 2.0.14 + 3.0.10, Gurobi 11.0.2, gap 4.13.0, genomepy 0.16.1, gensim 4.3.2, 17446gffutils 0.13, gh 2.52.0, git-annex 10.20240731, gmpy2 2.2.0, googletest 1.15.2, graph-tool 2.59, HDBSCAN 0.8.38.post1, 17447HOMER 4.11.1, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, histolab 0.7.0, 17448hypothesis 6.103.1, IQ-TREE 2.3.5, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, imageio 2.34.1, 17449imbalanced-learn 0.12.3, inferCNV 1.21.0, intervaltree 0.1, JsonCpp 1.9.5, Julia 1.10.4, jax 0.4.25, json-fortran 8.5.2, 17450Kent_tools 468, LLVM 18.1.8, LittleCMS 2.16, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, 17451libgit2 1.8.1, libopus 1.5.2, libsigc++ 3.6.0, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libwebp 1.4.0, 17452libxslt 1.1.42, libzip 1.10.1, lwgrp 1.0.6, lxml 5.3.0, MCR R2024a, MPICH 4.2.1, MUMPS 5.7.2, MariaDB 11.6.0, 17453Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, Miniconda3 23.10.0-1, MultiQC 1.22.3, makedepend 1.0.9, matplotlib 3.9.2, 17454maturin 1.6.0, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, mm-common 1.0.6, NanoCaller 3.6.0, Normaliz 3.10.3, 17455n2v 0.3.3, nano 8.1, ncbi-vdb 3.1.1, nettle 3.10, nsync 1.29.2, numexpr 2.9.0, ORCA 6.0.0, OpenEXR 3.2.4, OpenFOAM 12, 17456OpenFOAM v2406, OpenJPEG 2.5.2, Optax 0.2.2, Optuna 3.6.1, PaStiX 6.3.2, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, 17457Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PyAEDT 0.9.9, PyCharm 2024.1.6, PyRosetta 4.release-384, 17458PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, 17459pagmo 2.19.0, parallel 20240722, pixman 0.43.4, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, 17460primecount 7.14, psycopg 3.2.1, pyGenomeTracks 3.9, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pygmo 2.19.5, 17461pyperf 2.7.0, pyseer 1.3.12, pysteps 1.10.0, QuantumESPRESSO 7.3.1, Qwt 6.3.0, R-bundle-CRAN 2024.06, R 4.4.1, 17462RDKit 2024.03.3, RapidJSON 1.1.0-20240409, Ray-project 2.9.1, ReFrame 4.6.2, Rust 1.79.0, redis-py 5.0.9, 17463regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, SDL2 2.30.6, SHAP 0.43.0, SIP 6.8.3, SRA-Toolkit 3.1.1, 17464STAR 2.7.11b_alpha_2024-02-09, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Salmon 1.10.3, 17465SciPy-bundle 2024.05, SeqKit 2.8.2, SingleM 0.16.0, Sphinx-RTD-Theme 2.0.0, Stack 3.1.1, SuiteSparse 7.7.0, 17466SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scib-metrics 0.5.1, scvi-tools 1.1.2, sdsl-lite 2.0.3, 17467setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, 17468spglib-python 2.5.0, spglib 2.5.0, TELEMAC-MASCARET 8p5r0, Tk 8.6.14, Tkinter 3.12.3, Trycycler 0.5.5, tiktoken 0.7.0, 17469timm 1.0.8, UCX-CUDA 1.16.0, unixODBC 2.3.12, utf8proc 2.9.0, VSEARCH 2.28.1, virtualenv 20.26.2, WRF 4.5.1, 17470Wayland 1.23.0, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, 17471xtb 6.7.1, xtensor 0.24.7, yelp-xsl 42.1</li> 17472</ul> 17473</li> 17474<li>minor enhancements, including:<ul> 17475<li>add internal CUDA header patch for PSM2 v12.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20804">#20804</a>)</li> 17476<li>
17476add patch for JupyterHub support to recent tensorboard easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20823">#20823</a>)</li> 17477<li>make sure that recent ImageMagick versions pick up the right pkgconf + improve sanity check for ImageMagick (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20900">#20900</a>)</li> 17478<li>also install utilities for recent versions of FUSE 3.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20918">#20918</a>)</li> 17479<li>add RISC-V support to x264 v20231019 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20968">#20968</a>)</li> 17480<li>add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20970">#20970</a>)</li> 17481<li>enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20971">#20971</a>)</li> 17482<li>add extensions to R-bundle-CRAN: missmDA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21167">#21167</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21183">#21183</a>). insight (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21260">#21260</a>), performance + datwizard + bayestestR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21272">#21272</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21285">#21285</a>)</li> 17483<li>add Qt support to VTK 9.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21221">#21221</a>)</li> 17484<li>add <code>helper_scripts</code> to <code>$PATH</code> in easyconfig for ProteinMPNN v1.0.1-20230627 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21289">#21289</a>)</li> 17485<li>also build & install the plugins with OpenFOAM v2406 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21332">#21332</a>)</li> 17486</ul> 17487</li> 17488<li>various bug fixes, including:<ul> 17489<li>fix easyconfigs for recent versions of QuantumESPRESSO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20070">#20070</a>)</li> 17490<li>add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20103">#20103</a>)</li> 17491<li>fix typo in description of SuiteSparse v7.7.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20567">#20567</a>)</li> 17492<li>add 'pic' flag to IML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20789">#20789</a>)</li> 17493<li>add patch to recent SciPy-bundle easyconfigs to fix build error with numpy with some Fortran compilers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20817">#20817</a>)</li> 17494<li>rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '<code>--install-latest-eb-release</code>' works with older EasyBuild versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20818">#20818</a>)</li> 17495<li>fix build of OpenBLAS 0.3.24 on A64FX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20820">#20820</a>)</li> 17496<li>remove maturin build dependency from langchain-antropic (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20825">#20825</a>)</li> 17497<li>add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20841">#20841</a>)</li> 17498<li>add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20847">#20847</a>)</li> 17499<li>skip unreliable memory leak test in PyTorch 2.1.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20874">#20874</a>)</li> 17500<li>use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions to fix problem with Cython 3.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20879">#20879</a>)</li> 17501<li>use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20881">#20881</a>)</li> 17502<li>
17502add fix for failing test on zen4 to Highway 1.0.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20942">#20942</a>)</li> 17503<li>add patch to fix implicit function declaration in OpenMPI 4.1.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20949">#20949</a>)</li> 17504<li>only use libxsmm as dependency for CP2K 2023.1 w/ <code>foss/2023a</code> on x86_64 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20951">#20951</a>)</li> 17505<li>copy missing <code>rsem_perl_utils.pm</code> in DETONATE, since it's required by <code>rsem-eval-calculate-score</code> command (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20956">#20956</a>)</li> 17506<li>set <code>$SATSUMA2_PATH</code> so Satsuma2 can locate executables (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20957">#20957</a>)</li> 17507<li>disable auto-vectorizer (<code>-ftree-vectorize</code>) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20958">#20958</a>)</li> 17508<li>disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20969">#20969</a>)</li> 17509<li>add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21002">#21002</a>)</li> 17510<li>update homepage in phonopy easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21014">#21014</a>)</li> 17511<li>make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21017">#21017</a>)</li> 17512<li>add <code>OPENSSL_ENABLE_SHA1_SIGNATURES</code> for building <code>ansys-pythonnet</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21028">#21028</a>)</li> 17513<li>fix download URLs for old Intel software (2018-2023) by using <code>IRC_NAS</code> instead of <code>irc_nas</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21108">#21108</a>)</li> 17514<li>update source and homepage URLs in Szip easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21129">#21129</a>)</li> 17515<li>rename source URL in HDF v4.2.16-2 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21130">#21130</a>)</li> 17516<li>consistently fix homeage + source URL for <code>HDF</code> + <code>h4toh5</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21134">#21134</a>)</li> 17517<li>ensure that recent BioPerl easyconfigs use <code>Bundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21136">#21136</a>)</li> 17518<li>fix checksum checks for easyconfigs using a <code>Bundle</code>-like easyblock in easyconfigs test suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21143">#21143</a>)</li> 17519<li>add pkgconf build dependency to scikit-misc v0.3.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21144">#21144</a>)</li> 17520<li>explicitly disable use of MySQL in recent GDAL easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21156">#21156</a>)</li> 17521<li>fix easyconfig tensorflow-probability v0.20.0 to pass <code>pip check</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21172">#21172</a>)</li> 17522<li>stop RStudio-Server 2023.09 from installing R packages (+ move to <code>foss/2023a</code> toolchain) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21175">#21175</a>)</li> 17523<li>remove <code>Time::HiRes</code> from <code>Perl-bundle-CPAN</code> since there's newer version in <code>Perl</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21198">#21198</a>)</li> 17524<li>fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of <code>-maxv2</code> + add missing <code>xxd</code> build dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21200">#21200</a>)</li> 17525<li>
17525add missing cairo dependency for python-igraph v0.10.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21211">#21211</a>)</li> 17526<li>add patch for xtb 6.7.0 to fix build failure due to changes in tblite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21255">#21255</a>)</li> 17527<li>add patch for HDF5 v1.14.3 to suppress fp exceptions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21280">#21280</a>)</li> 17528<li>update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21297">#21297</a>)</li> 17529<li>use proper Python dependency for OTF2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21325">#21325</a>)</li> 17530<li>use source tarballs from GitHub for recent libdap easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21334">#21334</a>)</li> 17531<li>remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21366">#21366</a>)</li> 17532<li>add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21370">#21370</a>)</li> 17533</ul> 17534</li> 17535<li>other changes:<ul> 17536<li>archive outdated example easyconfigs for Fujitsu toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20781">#20781</a>)</li> 17537<li>upgrade rpmrebuild build dependency to version 2.18 in bcl-convert 4.2.7 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20861">#20861</a>)</li> 17538<li>use proper dependency for Safetensors in easyconfig for Transformers v4.39.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20864">#20864</a>)</li> 17539<li>remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20905">#20905</a>)</li> 17540<li>whitelist <code>ConfigureMakePythonPackage</code> for <code>sanity_check_paths</code> CI check (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20963">#20963</a>)</li> 17541<li>rename <code>gubbins-2.4.0.eb</code> to <code>Gubbins-2.4.0.eb</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20995">#20995</a>)</li> 17542<li>make pytest v7.4.2 independent of Python-bundle-PyPI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21004">#21004</a>)</li> 17543<li>reorganize Flax/JAX stack in 2023a: move <code>jax</code> + <code>Optax</code> to <code>gfbf/2023a</code> toolchain + use standalone <code>Flax</code> + <code>absl-py</code> as dependencies (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21038">#21038</a>)</li> 17544<li>use stand-alone absl-py as dependency for jax w/ <code>gfbf/2023a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21039">#21039</a>)</li> 17545<li>remove Cython dependency from Python-bundle-PyPI 2024.06 + add standalone easyconfig for Cython 3.0.10 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21233">#21233</a>)</li> 17546<li>add Cython build dependency for SciPy-bundle v2024.05 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21235">#21235</a>)</li> 17547<li>use top-level parameters for <code>use_pip</code> & co instead of <code>exts_default_options</code> for <code>PythonBundle</code> easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/21292">#21292</a>)</li> 17548</ul> 17549</li> 17550</ul> 17551<h2 id="release_notes_eb492">EasyBuild v4.9.2 (12 June 2024)<a class="headerlink" href="#release_notes_eb492" title="Permanent link">¶</a></h2> 17552<p>bugfix/update release</p> 17553<p><strong>framework</strong></p> 17554<ul> 17555<li>various enhancements, including:<ul> 17556<li>improve behavior when using extension which has <code>nosource</code> enabled (<a href="https://github.com/easybuilders/easybuild-framework/pull/4506">#4506</a>)</li> 17557<li>enhance <code>get_software_libdir</code> to return <code>lib</code> or <code>lib64</code> if only one of them contains library files (<a href="https://github.com/easybuilders/easybuild-framework/pull/4513">#4513</a>)</li> 17558<li>implement version checks to avoid mixing major versions across the EasyBuild components (<a href="https://github.com/easybuilders/easybuild-framework/pull/4520">#4520</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4553">#4553</a>)</li> 17559<li>
17559add support for easyconfig parameter <code>module_only</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4537">#4537</a>)</li> 17560</ul> 17561</li> 17562<li>various bug fixes, including:<ul> 17563<li>fix typo in <code>patch_step</code> logging (<a href="https://github.com/easybuilders/easybuild-framework/pull/4505">#4505</a>)</li> 17564<li>consider both <code>easybuild-framework*.tar.gz</code> and <code>easybuild_framework*.tar.gz</code> in CI workflows (<a href="https://github.com/easybuilders/easybuild-framework/pull/4507">#4507</a>)</li> 17565<li>don't delete existing environment module files when using <code>--dump-env-script</code> with <code>--force</code> or <code>--rebuild</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4512">#4512</a>)</li> 17566<li>fix resolved (template) values in case of failure (<a href="https://github.com/easybuilders/easybuild-framework/pull/4532">#4532</a>)</li> 17567<li>also consider <code>$CRAY_PE_LIBSCI_PREFIX_DIR</code> to determine installation prefix for <code>cray-libsci</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4551">#4551</a>)</li> 17568<li>symlink downloaded repo at specified commit when using <code>--from-commit</code> so easyconfigs for dependencies are found (<a href="https://github.com/easybuilders/easybuild-framework/pull/4552">#4552</a>)</li> 17569</ul> 17570</li> 17571<li>other changes:<ul> 17572<li>code cleanup in <code>easyblock.py</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4519">#4519</a>)</li> 17573<li>stop running unit tests on Python 3.5 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4530">#4530</a>)</li> 17574</ul> 17575</li> 17576</ul> 17577<p><strong>easyblocks</strong></p> 17578<ul> 17579<li>4 new software-specific easyblocks: QuantumESPRESSO with CMake (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3257">#3257</a>), AEDT (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3281">#3281</a>), optiSLang (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3300">#3300</a>), MetalWalls (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3311">#3311</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3331">#3331</a>)</li> 17580<li>minor enhancements and updates, including:<ul> 17581<li>refactor GAMESS-US easyblock to directly write <code>install.info</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3047">#3047</a>)</li> 17582<li>add ABAQUS license server to generated module (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3277">#3277</a>)</li> 17583<li>allow <code>nosource: True</code> in PythonPackage extensions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3305">#3305</a>)</li> 17584<li>auto-disable FFTW quad precision on RISC-V (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3314">#3314</a>)</li> 17585<li>use regular <code>configure</code> instead of wrapper script in easyblock for UCX plugins (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3315">#3315</a>)</li> 17586<li>add libjpeg-turbo to include dir for torchvision easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3322">#3322</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3353">#3353</a>)</li> 17587<li>add RISC-V support to custom easyblocks for Clang (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3325">#3325</a>), Java (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3323">#3323</a>), Mesa (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3324">#3324</a>)</li> 17588<li>add a sanity check for OpenFOAM's <code>wmake</code> to make sure it finds the compiler commands (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3328">#3328</a>)</li> 17589<li>always override the compiler version check for CUDA installations (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3329">#3329</a>)</li> 17590<li>allow version mismatchs between OpenSSL components in host system as long as they fulfill version requirements (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3340">#3340</a>)</li> 17591<li>allow external PRRTE in OpenMPI easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3347">#3347</a>)</li> 17592</ul> 17593</li> 17594<li>various bug fixes, including:<ul> 17595<li>don't manipulate setup.py for Python 3.12+ when using alternate sysroot (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3313">#3313</a>)</li> 17596<li>do not run unit tests on Python 3.5 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3326">#3326</a>)</li> 17597<li>
17597avoid sanity check on the software itself for <code>CargoPythonBundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3341">#3341</a>)</li> 17598<li>fix malformed <code>$CPATH</code> for <code>intel-compilers</code> on Debian/Ubuntu (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3346">#3346</a>)</li> 17599</ul> 17600</li> 17601<li>other changes:<ul> 17602<li>Binary easyblock already adds top level directory to <code>PATH</code>, so no need to do it in the Stata easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3307">#3307</a>)</li> 17603</ul> 17604</li> 17605</ul> 17606<p><strong>easyconfigs</strong></p> 17607<ul> 17608<li>added easyconfigs for <code>foss/2024.05</code> toolchain (candidate for <code>foss/2024a</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20646">#20646</a>)</li> 17609<li>added example easyconfig files for 82 new software packages:<ul> 17610<li>AEDT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20357">#20357</a>), amdahl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20346">#20346</a>), AMGX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20255">#20255</a>), assembly-stats (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20281">#20281</a>), Bio-FeatureIO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20461">#20461</a>), 17611bitshuffle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20661">#20661</a>), Cassiopeia (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20289">#20289</a>), CCCL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20255">#20255</a>), charm-gems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20327">#20327</a>), CheckM2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20399">#20399</a>), 17612chromVARmotifs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20402">#20402</a>), cmph (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20278">#20278</a>), COMEBin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20717">#20717</a>), Compass (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20500">#20500</a>), ctffind5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20669">#20669</a>), currentNe (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20791">#20791</a>), 17613CVX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20231">#20231</a>), deepfold (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20247">#20247</a>), dotNET-Core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20256">#20256</a>), EasyMocap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20446">#20446</a>), ensmallen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20485">#20485</a>), EVcouplings (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20744">#20744</a>), 17614Faiss (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19669">#19669</a>), FDMNES (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20321">#20321</a>), gnupg-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20406">#20406</a>), grpcio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20191">#20191</a>), hatch-jupyter-builder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20606">#20606</a>), 17615hevea (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20597">#20597</a>), HiGHS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20186">#20186</a>), hmmcopy_utils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20472">#20472</a>), HOMER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20590">#20590</a>), ICON (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20573">#20573</a>), jiter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20746">#20746</a>),
17616LangChain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20746">#20746</a>), langchain-anthropic (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20746">#20746</a>), libabigail (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20539">#20539</a>), libbraiding (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20655">#20655</a>), libhomfly (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20482">#20482</a>), 17617libsupermesh (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20470">#20470</a>), LIBSVM-MATLAB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20752">#20752</a>), Lightning (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19964">#19964</a>), lil-aretomo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20696">#20696</a>), makefun (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20619">#20619</a>), 17618MetalWalls (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20403">#20403</a>), MICOM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20186">#20186</a>), ml-collections (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20247">#20247</a>), ml_dtypes (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20707">#20707</a>), mlpack (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20485">#20485</a>), MOFA2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20538">#20538</a>), 17619mumott (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20719">#20719</a>), nvitop (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20512">#20512</a>), ocamlbuild (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20552">#20552</a>), optiSLang (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20320">#20320</a>), orthAgogue (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20278">#20278</a>), pdf2docx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20416">#20416</a>), 17620planarity (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20753">#20753</a>), plantri (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20467">#20467</a>), plmc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20744">#20744</a>), PortAudio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20307">#20307</a>), premailer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20348">#20348</a>), ProteinMPNN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20705">#20705</a>), 17621PRRTE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20698">#20698</a>), PSM2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20496">#20496</a>), PyAEDT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20357">#20357</a>), pybind11-stubgen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20518">#20518</a>), PyEXR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19983">#19983</a>), pyGAM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20385">#20385</a>), 17622PyHMMER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20544">#20544</a>), pyseer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20502">#20502</a>), PyVista (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20649">#20649</a>), qmflows (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20384">#20384</a>), SciTools-Iris (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20767">#20767</a>), SCReadCounts (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20455">#20455</a>), 17623SDL2_gfx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20466">#20466</a>), subunit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20412">#20412</a>), TF-COMB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20666">#20666</a>), tiktoken (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20336">#20336</a>), TorchIO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20648">#20648</a>), t-SNE-CUDA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19669">#19669</a>), 17624VAMPIRE-ASM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20368">#20368</a>), wfdb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20521">#20521</a>), WGDgc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20367">#20367</a>)</li> 17625</ul> 17626</li> 17627<li>
17627added additional easyconfigs for various supported software packages, including:<ul> 17628<li>4ti2 1.6.10, AFNI 24.0.02, Autoconf 2.72, Autotools 20231222, adjustText 1.1.1, aiohttp 3.9.5, alevin-fry 0.9.0, 17629alsa-lib 1.2.9, atropos 1.1.32, autopep8 2.2.0, BCFtools 1.19, BLIS 1.0, BWA 0.7.18, Boost 1.85.0, bcrypt 4.1.3, 17630binutils 2.42, bokeh 3.4.1, CGAL 5.6.1, CREST 3.0.1, CellRanger-ARC 2.0.2, CellRanger 8.0.1, CellRank 2.0.2, 17631Clang 17.0.6, CoCoALib 0.99850, Cython 3.0.10, cURL 8.7.1, cffi 1.16.0, code-server 4.89.1, 17632configurable-http-proxy 4.6.1, coverage 7.4.4, cpio 2.15, cppyy 3.1.2, cysignals 1.11.4, Doxygen 1.11.0, 17633dask-labextension 7.0.0, dask 2024.5.1, deal.II 9.5.2, dorado 0.5.3, dotNET-Core 8.0.203, E-ANTIC 2.0.2, 17634ECL 24.5.10, ESPResSo 4.2.2, eclib 20240408, expat 2.6.2, FLTK 1.3.9, FMM3D 1.0.4, FlexiBLAS 3.4.4, f90wrap 0.2.13, 17635fgbio 2.2.1, fontconfig 2.15.0, freetype-py 2.4.0, GAMESS-US 20220930-R2 + 20230930-R2, GCC 13.3.0 + 14.1.0, 17636GDB 14.2, GDRCopy 2.4.1, GOATOOLS 1.4.5, GTDB-Tk 2.4.0, Giza 1.4.1, gc 8.2.6, gcloud 472.0.0, gemmi 0.6.5, 17637gettext 0.22.5, giac 1.9.0-99, git 2.45.1, gmsh 4.12.2, gsutil 5.29, HDDM 0.9.9, HTSlib 1.19.1, HyPhy 2.5.60, 17638h5py 3.11.0, hwloc 2.10.0, ICU 75.1, IOR 4.0.0, imagecodecs 2024.1.1, imgaug 0.4.1, ipympl 0.9.4, 17639Jupyter-bundle 20240522, JupyterHub 4.1.5, JupyterLab 4.2.0, JupyterNotebook 7.2.0, jupyter-matlab-proxy 0.12.2, 17640jupyter-resource-usage 1.0.2, jupyter-rsession-proxy 2.2.0, jupyter-server-proxy 4.1.2, jupyter-server 2.14.0, 17641Kalign 3.4.0, KrakenUniq 1.0.4, kallisto 0.50.1, LAPACK 3.12.0, libarchive 3.7.4, libde265 1.0.15, libdeflate 1.20, 17642libdwarf 0.9.2, libfabric 1.21.0, libffi 3.4.5, libgcrypt 1.10.3, libgpg-error 1.48, libheif 1.17.6, libidn2 2.3.7, 17643libnsl 2.0.1, libpciaccess 0.18.1, libpng 1.6.43, libuv 1.48.0, libxml2 2.12.7, line_profiler 4.1.2, MATSim 15.0, 17644MDTraj 1.9.9, Mako 1.3.5, Meson 1.4.0, MetaMorpheus 1.0.5, Molpro 2024.1.0, MuJoCo 3.1.4, matlab-proxy 0.18.1, 17645mold 2.31.0, mpmath 1.3.0, NASM 2.16.03, NanoPlot 1.42.0, Nextflow 24.04.2, Ninja 1.12.1, nanoget 1.19.1, 17646napari 0.4.19.post1, nauty 2.8.8, ncurses 6.5, nghttp2 1.58.0, nghttp3 1.3.0, nglview 3.1.2, ngtcp2 1.2.0, 17647nodejs 20.13.1, numactl 2.0.18, nvtop 3.1.0, OCaml 5.1.1, OSU-Micro-Benchmarks 7.4, OpenBLAS 0.3.27, OpenMPI 5.0.3, 17648PARI-GP 2.15.5, PCRE2 10.43, PMIx 5.0.2, Perl 5.38.2, PhyML 3.3.20220408, PnetCDF 1.13.0, PyAMG 5.1.0, 17649PyQtGraph 0.13.7, PyTorch-Geometric 2.5.0, PyTorch-bundle 2.1.2, PycURL 7.45.3, Pysam 0.22.0, Python 3.12.3, 17650p11-kit 0.25.3, p4est 2.8.6, parallel 20240322, pauvre 0.2.3, petsc4py 3.20.3, pkgconf 2.2.0, plc 3.10, polars 0.20.2, 17651poppler 24.04.0, psutil 5.9.8, py3Dmol 2.1.0, pybedtools 0.9.1, pygame 2.5.2, pyiron 0.5.1, pyro-ppl 1.9.0, 17652python-mujoco 3.1.4, ROOT 6.30.06, RPostgreSQL 0.7-6, RStudio-Server 2023.12.1+402, Rtree 1.2.0, Rust 1.78.0, 17653SAMtools 1.19.2, SCOTCH 7.0.4, SDL2_image 2.8.2, SDL2_mixer 2.8.0, SDL2_ttf 2.22.0, SQLite 3.45.3, SWIG 4.2.1, 17654SentencePiece 0.2.0, Seurat 5.1.0, SeuratDisk 20231104, SimNIBS 4.0.1, Singular 4.4.0, Spack 0.21.2, Squidpy 1.4.1, 17655SymEngine-python 0.11.0, SymEngine 0.11.2, sbt 1.6.2, scikit-build-core 0.9.3, scikit-learn 1.4.2, TOBIAS 0.16.1, 17656Tcl 8.6.14, TensorFlow 2.15.1, Transformers 4.39.3, texlive 20230313, tmux 3.4, tokenizers 0.15.2, 0.2.5.20231120, 17657tornado 6.4, UCC 1.3.0, UCX 1.16.0, util-linux 2.40, VSCode 1.88.1, Valgrind 3.23.0, VisPy 0.14.1, wget 1.24.5, 17658XZ 5.4.5, xorg-macros 1.20.1, xprop 1.2.7, xtb 6.7.0, xxd 9.1.0307, yaml-cpp 0.8.0, zarr 2.17.1, zfp 1.0.1, 17659zlib-ng 2.1.6, zlib 1.3.1, zstd 1.5.6</li> 17660</ul> 17661</li> 17662<li>minor enhancements, including:<ul> 17663<li>add missing (optional) dependency pyproject-metadata to scikit-build-core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20391">#20391</a>)</li> 17664<li>add <code>hatch-requirements-txt</code> extension to hatchling easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20389">#20389</a>)</li> 17665<li>install pkg-config files for ncurses 6.4 when using <code>GCCcore</code> toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20405">#20405</a>)</li> 17666<li>use regular <code>configure</code> instead of wrapper script for recent UCX easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20428">#20428</a>)</li> 17667<li>
17667add RISC-V support to UCX 1.15.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20429">#20429</a>), UCC 1.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20432">#20432</a>), BLIS 0.9.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20468">#20468</a>), PAPI 7.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20659">#20659</a>)</li> 17668<li>add extensions to R-bundle-CRAN v2023.12: cmna (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20445">#20445</a>), rhandsontable (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20614">#20614</a>), XBRL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20506">#20506</a>)</li> 17669<li>add checksum for RISC-V version to easyconfig for Java 21.0.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20495">#20495</a>)</li> 17670<li>remove <code>TORCHVISION_INCLUDE</code> from PyTorch-bundle easyconfigs, now handled by custom easyblock for torchvision (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20504">#20504</a>)</li> 17671<li>add dependencies required for GUI in Cellpose 2.2.2 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20620">#20620</a>)</li> 17672<li>add <code>build_info_msg</code> about kernel modules to GDRCopy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20641">#20641</a>)</li> 17673<li>build both static and shared libs for Brotli 1.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20757">#20757</a>)</li> 17674</ul> 17675</li> 17676<li>various bug fixes, including:<ul> 17677<li>add missing dependencies for funannotate (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17690">#17690</a>)</li> 17678<li>fix path to SuiteSparse include/lib in easyconfig for CVXopt v1.3.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20232">#20232</a>)</li> 17679<li>fix Highway 1.0.3 on some systems by disabling <code>AVX3_DL</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20298">#20298</a>)</li> 17680<li>replace incorrect scikit-bio 0.5.9 with scikit-bio 0.6.0 as dependency for scCODA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20300">#20300</a>)</li> 17681<li>add alternate checksum to OpenMolcas v23.06 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20301">#20301</a>)</li> 17682<li>change arrow-R dependency of Bioconductor v3.18 to v14.0.1 (which depends on required matching Arrow v14.0.1) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20324">#20324</a>)</li> 17683<li>fix hardcoded <code>/bin/mv</code> path in Rhdf5lib extension included in R-bundle-Bioconductor v3.16 + v3.18 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20378">#20378</a>)</li> 17684<li>remove dependency on HDF5 in recent Bioconductor easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20379">#20379</a>)</li> 17685<li>make sure that libjpeg-turbo libraries are installed in <code>lib</code> subdirectory (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20386">#20386</a>)</li> 17686<li>add patch for Libint 2.7.2 to fix compiler error with glibc >= 2.34 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20396">#20396</a>)</li> 17687<li>use <code>bash</code> rather than <code>sh</code> to run PLINK-2.00a3.7 tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20404">#20404</a>)</li> 17688<li>add patch to fix "<code>UNPACK-OPAL-VALUE: UNSUPPORTED TYPE 33 FOR KEY</code>" error in OpenMPI 4.1.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20422">#20422</a>)</li> 17689<li>add patch to increase compatibility with AVX512 platforms for bwa-mem2 v2.2.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20434">#20434</a>)</li> 17690<li>add patch for GROMACS 2024.1 to fix filesystem race in tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20439">#20439</a>)</li> 17691<li>demote poetry to build dependency for nanocompore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20453">#20453</a>)</li> 17692<li>
17692add patch to fix CVE-2024-27322 in R v3.6.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20464">#20464</a>), v4.0.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20463">#20463</a>), and v4.1.x + v4.2.x + v4.3.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20462">#20462</a>)</li> 17693<li>disable test that fetches from the web for torchtext extension in PyTorch-bundle v2.1.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20484">#20484</a>)</li> 17694<li>fix sanity check paths for JupyterLab 4.0.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20514">#20514</a>)</li> 17695<li>fix detection of CC/CXX compilers for <code>wmake</code> in OpenFOAM v2306 + v2312 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20517">#20517</a>)</li> 17696<li>use the included gmxapi for GROMACS 2024.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20522">#20522</a>)</li> 17697<li>add new checksum for <code>signal_1.8-0</code> to R-bundle-CRAN-2023.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20527">#20527</a>)</li> 17698<li>fix test in <code>Cwd</code> extension of Perl-bundle-CPAN 5.36.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20536">#20536</a>)</li> 17699<li>fix patch name in easyconfig for Perl-bundle-CPAN 5.36.1 + add also use it for Perl-bundle-CPAN 5.38.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20540">#20540</a>)</li> 17700<li>fix <code>cwd_enoent</code> test in Perl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20541">#20541</a>)</li> 17701<li>move dependency on BeasutifulSoup in IPython v8.14.0 to jupyter-server (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20547">#20547</a>)</li> 17702<li>remove dependency on BeasutifulSoup from IPython v8.17.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20548">#20548</a>)</li> 17703<li>add alternative checksum for source tarball of MONAI 1.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20618">#20618</a>)</li> 17704<li>add cpio as build dependency to recent BLAST+ versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20674">#20674</a>)</li> 17705<li>add <code>--disable-htmlpages</code> to recent FFmpeg easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20686">#20686</a>)</li> 17706<li>remove duplicate crates from easyconfig for timm-0.9.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20687">#20687</a>)</li> 17707<li>add missing HDF5 dependency in recent Armadillo easyconfigs (>= 11.4.3) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20710">#20710</a>)</li> 17708<li>add patches for failing LAPACK tests and RISC-V test segfaults to OpenBLAS 0.3.27 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20745">#20745</a>)</li> 17709<li>move all easyconfigs for libavif to GCCcore toolchain + fix dependencies (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20747">#20747</a>)</li> 17710<li>make sure mummerplot can use gnuplot if available for recent MUMmer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20749">#20749</a>)</li> 17711<li>prevent configure script of recent BLAST+ versions from prepending system paths to <code>$PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20751">#20751</a>)</li> 17712<li>fix fastparquet v2023.4.0 using <code>CargoPythonBundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20775">#20775</a>)</li> 17713<li>remove <code>--with-64</code> from configopts for recent BLAST+ versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20784">#20784</a>)</li> 17714<li>add patch to fix build of pdsh 2.34 with Slurm 23.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20795">#20795</a>)</li> 17715</ul> 17716</li> 17717<li>other changes:<ul> 17718<li>move <code>build</code> from extensions to dependencies in easyconfig for napari 0.4.18 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20433">#20433</a>)</li> 17719<li>update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20477">#20477</a>)</li> 17720<li>
17720add commented out PSM2 dependency, relevant for x86_64 systems with OmniPath, to recent libfabric easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20501">#20501</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20585">#20585</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20794">#20794</a>)</li> 17721<li>replace SQLAlchemy extension with regular dependency in easyconfig for Optuna v3.5.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20510">#20510</a>)</li> 17722<li>replace SQLAlchemy extension in JupyterHub v4.0.2 easyconfig with regular dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20511">#20511</a>)</li> 17723<li>bump Cython to v3.0.8 in Cartopy v0.22.0 easyconfig for foss/2023a toolchain, to avoid dependency version conflict with sckit-learn v1.4.2, which requires Cython >= v3.0.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20525">#20525</a>)</li> 17724<li>change dependency on hatchling of BeautifulSoup v4.12.2 to a build dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20546">#20546</a>)</li> 17725<li>bump async-timeout to 4.0.3 in aiohttp 3.8.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20553">#20553</a>)</li> 17726<li>stick to <code>gfbf/2023a</code> as toolchain for ipympl v0.9.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20586">#20586</a>)</li> 17727<li>rename <code>tornado-timeouts.patch</code> to <code>tornado-6.1_increase-default-timeouts.patch</code> + add missing authorship (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20587">#20587</a>)</li> 17728<li>remove easyconfigs for CellBender v0.3.1, since this version has been redacted due to a serious bug (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20722">#20722</a>)</li> 17729</ul> 17730</li> 17731</ul> 17732<h2 id="release_notes_eb491">EasyBuild v4.9.1 (5 April 2024)<a class="headerlink" href="#release_notes_eb491" title="Permanent link">¶</a></h2> 17733<p>bugfix/update release</p> 17734<p><strong>framework</strong></p> 17735<ul> 17736<li>various enhancements, including:<ul> 17737<li>make <code>is_rpath_wrapper</code> faster by only checking file contents if file is not located in subdirectory of RPATH wrapper subdirectory (<a href="https://github.com/easybuilders/easybuild-framework/pull/4406">#4406</a>)</li> 17738<li>add terse support to <code>--missing-modules</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4407">#4407</a>)</li> 17739<li>adapt version pattern for <code>EnvironmentModules</code> to allow using development version (<a href="https://github.com/easybuilders/easybuild-framework/pull/4416">#4416</a>)</li> 17740<li>use <code>--all</code> option with <code>EnvironmentModules</code> v4.6+ to get available hidden modules (<a href="https://github.com/easybuilders/easybuild-framework/pull/4417">#4417</a>)</li> 17741<li>add support for appending to path environment variables via <code>modextrapaths_append</code> + add corresponding <code>allow_append_abs_path</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4436">#4436</a>)</li> 17742<li>improve output produced by <code>--check-github</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4437">#4437</a>)</li> 17743<li>add script for updating local git repos with <code>develop</code> branch (<a href="https://github.com/easybuilders/easybuild-framework/pull/4438">#4438</a>)</li> 17744<li>show error when multiple PR options are passed (<a href="https://github.com/easybuilders/easybuild-framework/pull/4440">#4440</a>)</li> 17745<li>improve <code>findPythonDeps</code> script to recognize non-canonical package names (<a href="https://github.com/easybuilders/easybuild-framework/pull/4445">#4445</a>)</li> 17746<li>add support for <code>--from-commit</code> and <code>--include-easyblocks-from-commit</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4468">#4468</a>)</li> 17747<li>improve logging & handling of (empty) <code>--optarch</code> values (<a href="https://github.com/easybuilders/easybuild-framework/pull/4481">#4481</a>)</li> 17748<li>
17748add <code>--short</code> option to <code>findUpdatedEcs</code> script (<a href="https://github.com/easybuilders/easybuild-framework/pull/4488">#4488</a>)</li> 17749<li>add generic GCC and Clang compiler flags for RISC-V (<a href="https://github.com/easybuilders/easybuild-framework/pull/4489">#4489</a>)</li> 17750</ul> 17751</li> 17752<li>various bug fixes, including:<ul> 17753<li>clean up log file of <code>EasyBlock</code> instance in <code>check_sha256_checksums</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4452">#4452</a>)</li> 17754<li>fix description of <code>backup-modules</code> configuration option (<a href="https://github.com/easybuilders/easybuild-framework/pull/4456">#4456</a>)</li> 17755<li>replace <code>'</code> with <code>"</code> for <code>printf</code> in CI workflow for running test suite to have bash replace a variable (<a href="https://github.com/easybuilders/easybuild-framework/pull/4461">#4461</a>)</li> 17756<li>use <code>cp -dR</code> instead of <code>cp -a</code> for shell script "extraction" (<a href="https://github.com/easybuilders/easybuild-framework/pull/4465">#4465</a>)</li> 17757<li>fix link to documentation in <code>close_pr</code> message (<a href="https://github.com/easybuilders/easybuild-framework/pull/4466">#4466</a>)</li> 17758<li>fix <code>test_github_merge_pr</code> by using more recent easyconfigs PR (<a href="https://github.com/easybuilders/easybuild-framework/pull/4470">#4470</a>)</li> 17759<li>add workaround for 404 error when installing packages in CI workflow for testing Apptainer integration (<a href="https://github.com/easybuilders/easybuild-framework/pull/4472">#4472</a>)</li> 17760</ul> 17761</li> 17762<li>other changes:<ul> 17763<li>clean up & speed up environment checks (<a href="https://github.com/easybuilders/easybuild-framework/pull/4409">#4409</a>)</li> 17764<li>use more performant and concise dict construction by using dict comprehensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4410">#4410</a>)</li> 17765<li>remove superflous string formatting (<a href="https://github.com/easybuilders/easybuild-framework/pull/4411">#4411</a>)</li> 17766<li>clean up uses of <code>getattr</code> and <code>hasattr</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4412">#4412</a>)</li> 17767<li>update copyright lines to 2024 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4494">#4494</a>)</li> 17768</ul> 17769</li> 17770</ul> 17771<p><strong>easyblocks</strong></p> 17772<ul> 17773<li>1 new software-specific easyblock: DualSPHysics (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3050">#3050</a>)</li> 17774<li>minor enhancements and updates, including:<ul> 17775<li>use proxy in sanity check of custom easyblock to install OpenSSL wrapper (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2922">#2922</a>)</li> 17776<li>update Clang-AOMP easyblock for ROCm 5.6 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2958">#2958</a>)</li> 17777<li>consider both <code>$EBROOTGCC</code> and <code>$EBROOTGCCCORE</code> in Clang-AOMP easyblock to specify <code>-DGCC_INSTALL_PREFIX</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2958">#2958</a>)</li> 17778<li>update WIEN2k easyblock for v23.2 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3035">#3035</a>)</li> 17779<li>enhance LAMMPS easyblock to dynamically add <code>ARMV81</code> and <code>A64FX</code> to Kokkos CPU mapping based on LAMMPS version (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3036">#3036</a>)</li> 17780<li>add <code>pip_verbose</code> option to PythonPackage and set it to True in PyTorch easyblock, to show build output when using pip (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3065">#3065</a>)</li> 17781<li>also support OpenSSL 3 in OpenSSL wrapper easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3081">#3081</a>)</li> 17782<li>improve error checking in PyTorch easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3085">#3085</a>)</li> 17783<li>update MCR easyblock for compatibility with versions >= R2022b (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3119">#3119</a>)</li> 17784<li>
17784add <code>species</code> easyconfig parameter to VEP easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3121">#3121</a>)</li> 17785<li>only install Gurobi Python bindings via <code>setup.py</code> for Gurobi v10.x and older (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3225">#3225</a>)</li> 17786<li>consistently honor <code>pretestopts</code> & <code>testopts</code> in <code>PerlModule</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3231">#3231</a>)</li> 17787<li>fix OCaml easyblock for recent versions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3235">#3235</a>)</li> 17788<li>improve QuantumESPRESSO easyblock by cleaning up and extending configure step + running test suite (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3241">#3241</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3258">#3258</a>)</li> 17789<li>allow overriding <code>testinstall</code> in PyTorch easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3250">#3250</a>)</li> 17790<li>enhance GCC easyblock to set <code>$LIBRARY_PATH</code> and disable building of NVPTX offload support on RISC-V systems (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3256">#3256</a>)</li> 17791<li>add support for conda provided by Miniforge (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3260">#3260</a>)</li> 17792<li>set <code>$GOPATH</code> in configure step of <code>GoPackage</code> easyblock to avoid polluting <code>$HOME/go</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3262">#3262</a>)</li> 17793</ul> 17794</li> 17795<li>various bug fixes, including:<ul> 17796<li>set <code>$BGW_TEST_MPI_NPROCS</code> in BerkeleyGW test step (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2950">#2950</a>)</li> 17797<li>fix installation of Python bindings for LAMMPS >= 2Aug2023 + fix sanity check by doing <code>MPI_Finalize</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3036">#3036</a>)</li> 17798<li>fix ELPA preprocessor flag for QuantumESPRESSO >= 7 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3063">#3063</a>)</li> 17799<li>fix link order in PETSc easyblock for SCOTCH >= 7.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3069">#3069</a>)</li> 17800<li>update PyTorch easyblock to avoid configure warnings by disabling some options (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3070">#3070</a>)</li> 17801<li>pick Tcl/Tk lib directory correctly in R easyblock, may be either <code>lib</code> or <code>lib64</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3072">#3072</a>)</li> 17802<li>use <code>(=|:=)</code> in regex because OpenFOAM rule files use <code>:=</code> instead of <code>=</code> since v2212 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3073">#3073</a>)</li> 17803<li>add Clang <code>opt</code> binary to RPATH wrapper dir (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3076">#3076</a>)</li> 17804<li>improve <code>generate_crate_list</code> + parsing of crates in <code>Cargo</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3084">#3084</a>)</li> 17805<li>remove trailing slash in <code>PETSC_DIR</code> set by custom easyblock for PETSc (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3086">#3086</a>)</li> 17806<li>use correct TCL configure options for Python 3.11+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3087">#3087</a>)</li> 17807<li>tweak <code>CMakeMake</code> easyblock to apply CMake policy to select <code>python</code> based on <code>$PATH</code> order, instead of highest version (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3088">#3088</a>)</li> 17808<li>update <code>Cargo</code> easyblock to extract crates into a vendor subdir and overwrite git repo URLs with local paths (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3118">#3118</a>)</li> 17809<li>only add <code>--with-ucc</code> for OpenMPI 4.1.4+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3223">#3223</a>)</li> 17810<li>remove trailing slash in <code>SLEPC_DIR</code> in configure step of custom easyblock for SLEPc (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3229">#3229</a>)</li> 17811<li>fix OpenFOAM easyblock to fix <code>motorBike</code> example in sanity check for versions >=11 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3232">#3232</a>)</li> 17812<li>only run CUDA sanity check command for torchvision if GPU is present (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3236">#3236</a>)</li> 17813<li>ensure localrc is created in the correct subdir for NVHPC v22.9+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3240">#3240</a>)</li> 17814<li>remove wrong configure option for LibInt 2.6.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3249">#3249</a>)</li> 17815<li>do not rename GCC's <code>include-fixed</code> directory by default + add script to regenerate it (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3254">#3254</a>)</li> 17816</ul> 17817</li> 17818<li>other changes:<ul> 17819<li>
17819update copyright lines to 2024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3268">#3268</a>)</li> 17820</ul> 17821</li> 17822</ul> 17823<p><strong>easyconfigs</strong></p> 17824<ul> 17825<li>added example easyconfig files for 101 new software packages:<ul> 17826<li>AMICA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19842">#19842</a>), AreTomo2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19681">#19681</a>), btllib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19779">#19779</a>), bwa-mem2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20217">#20217</a>), CENSO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19826">#19826</a>), Circlator (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19847">#19847</a>), Clarabel.rs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20149">#20149</a>), 17827code-cli (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19645">#19645</a>), Concorde (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19768">#19768</a>), contextily (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19807">#19807</a>), CUTLASS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19304">#19304</a>), DeepLoc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19514">#19514</a>), Delft3D (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19869">#19869</a>), DeltaLake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19758">#19758</a>), 17828denseweight (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20139">#20139</a>), desktop-file-utils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), devbio-napari (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19586">#19586</a>), DjVuLibre (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), Elmer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19448">#19448</a>), 17829EnergyPlus (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19565">#19565</a>), EpiSCORE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18618">#18618</a>), evince (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), ExpressBetaDiversity (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19938">#19938</a>), ExtremeLy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19870">#19870</a>), f90nml (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19171">#19171</a>), 17830FFAVES (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19822">#19822</a>), fugue (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19694">#19694</a>), gcsfs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20042">#20042</a>), GenomeComb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19749">#19749</a>), GI-DocGen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), GKlib-METIS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20096">#20096</a>), GRASP-suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19665">#19665</a>), 17831gspell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), GUIDANCE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20063">#20063</a>), hdWGCNA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20124">#20124</a>), HF-Datasets (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20166">#20166</a>), IDG (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18924">#18924</a>), igvShiny (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19714">#19714</a>), inflection (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20036">#20036</a>), 17832InterOp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19303">#19303</a>), IonQuant (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19812">#19812</a>), Lab-Streaming-Layer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19945">#19945</a>), Levenshtein (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19771">#19771</a>), libfyaml (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19856">#19856</a>), libgxps (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), 17833libhandy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), libspectre (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19701">#19701</a>), lit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20252">#20252</a>), lmoments3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19870">#19870</a>), Markdown (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20239">#20239</a>), MetaDecoder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20123">#20123</a>), mfqe (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19781">#19781</a>), 17834Miniforge3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20227">#20227</a>), MLflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19893">#19893</a>), MODFLOW (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20142">#20142</a>), morphosamplers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20000">#20000</a>), MotionCor3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19681">#19681</a>), MSFragger (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19811">#19811</a>), 17835multiprocess (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19986">#19986</a>), nf-core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19107">#19107</a>), noise (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20048">#20048</a>), OpenMEEG (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19853">#19853</a>), OpenSlide-Java (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19962">#19962</a>), PAGAN2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19618">#19618</a>), PASA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19570">#19570</a>), 17836pblat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19570">#19570</a>), PBZIP2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19677">#19677</a>), PDM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20012">#20012</a>), Philosopher (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19383">
17836#19383</a>), phyluce (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19779">#19779</a>), poppunk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17402">#17402</a>), PSASS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20160">#20160</a>), psycopg (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19107">#19107</a>), 17837PyInstaller (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19519">#19519</a>), PyQt-builder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16703">#16703</a>), pytest-workflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19107">#19107</a>), python-casacore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20089">#20089</a>), pytorch-3dunet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19290">#19290</a>), pyXDF (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19916">#19916</a>), 17838q2-krona (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19633">#19633</a>), QuPath (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19962">#19962</a>), radian (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19484">#19484</a>), remake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19581">#19581</a>), rethinking (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19755">#19755</a>), RHEIA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19496">#19496</a>), s3fs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19576">#19576</a>), 17839safestringlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20217">#20217</a>), scikit-extremes (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19870">#19870</a>), SemiBin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19767">#19767</a>), semla (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19747">#19747</a>), Sentence-Transformers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19509">#19509</a>), sinto (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13846">#13846</a>), 17840sktime (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19692">#19692</a>), SQLAlchemy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20242">#20242</a>), tiny-cuda-nn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19304">#19304</a>), tox (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16178">#16178</a>), Vamb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17457">#17457</a>), xpdf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20024">#20024</a>), yt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20263">#20263</a>), Zeo++ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19555">#19555</a>), 17841zUMIs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19949">#19949</a>)</li> 17842</ul> 17843</li> 17844<li>added additional easyconfigs for various supported software packages, including:<ul> 17845<li>Abseil 20240116.1, ABySS 2.3.7, AMS 2023.104, Anaconda3 2024.02, anndata 0.10.5.post1, anvio 8, ArchR 1.0.2, 17846 archspec 0.2.2, Armadillo 12.8.0, arpack-ng 3.9.1, arrow-R 14.0.0.2, ASAP3 3.13.3, assimp 5.3.1, autopep8 2.0.4, 17847 basemap 1.3.9, BerkeleyGW 3.1.0 + 4.0, BiG-SCAPE 1.1.5, Biopython 1.83, Blosc 1.21.5, Blosc2 2.13.2, Boost.MPI 1.82.0, 17848 Boost.Python 1.83.0, Braindecode 0.8.1, Brotli-python 1.1.0, build 1.0.3, buildenv-default foss-2023b + intel-2023b, 17849 bx-python 0.10.0, CapnProto 1.0.1.1, c-ares 1.27.0, Cartopy 0.22.0, casacore 3.5.0, Cbc 2.10.11, ccache 4.9, cclib 1.8, 17850 CellBender 0.3.1, CellTypist 1.6.2, CFITSIO 4.3.1, Cgl 0.60.8, Clang-Python-bindings 16.0.6, Clp 1.17.9, CmdStanR 0.7.1, 17851 COBRApy 0.29.0, code-server 4.22.1, CoinUtils 2.11.10, CoordgenLibs 3.0.2, CREST 2.12, cryoCARE 0.3.0, CSBLAST 2.2.4, 17852 CUDA 12.3.2 + 12.4.0, cuDNN 8.9.7.29, CuPy 13.0.0, cuSPARSELt 0.6.0.6, cuTENSOR 2.0.1.2, CVXPY 1.4.2, Cython 3.0.8, 17853 dask 2023.12.1, datalad 0.19.5, DB_File 1.859, deepdiff 6.7.1, DeepLabCut 2.3.6, DendroPy 4.6.1, Deprecated 1.2.14, 17854 DFT-D4 3.6.0, DIAMOND 2.1.9, Dice 20240101, dlb 3.4, DLPack 0.8, dorado 0.5.1, EggLib 3.3.0, einops 0.7.0, ELPA 2023.11.001, 17855 enchant-2 2.6.5, ESMF 8.4.2, eSpeak-NG 1.51, ETE 3.1.3, expecttest 0.2.1, fastjet 3.4.2, fastjet-contrib 1.053, FDS 6.8.0, 17856 fineRADstructure 20210514, fio 3.36, Fiona 1.9.5, Flask 3.0.0, FLINT 3.1.1, Flye 2.9.3, fmt 10.2.0, freebayes 1.3.7, 17857 GATK 4.5.0.0, gawk 5.3.0, geocube 0.4.3, geopandas 0.14.2, geopy 2.4.1, GHC 9.4.6, Ghostscript 10.02.1, GIMIC 2.2.1, 17858 git-lfs 3.5.1, GitPython 3.1.42, GLFW 3.4, Go 1.22.1, GPAW 24.1.0, GPAW-setups 24.1.0, gperftools 2.14, Gradle 8.6, 17859 graph-tool 2.55, Greenlet 3.0.3, GROMACS 2024.1, gRPC 1.62.1, GTK3 3.24.39, Gurobi 11.0.0, HDF5 1.14.3, HeFFTe 2.4.0, 17860 HepMC3 3.2.6, hunspell 1.7.2, igraph 0.10.10, infercnvpy 0.4.3, iperf 3.16, IQ-TREE 2.2.2.7, ISA-L 2.31.0, Java/19 (19.0.2), 17861 Java/21 (21.0.2), json-c 0.17, Julia 1.10.0, KaHIP 3.16, LAMMPS 2Aug2023_update2, LASTZ 1.04.22, LDC 1.36.0, leiden
17861alg 0.10.2, 17862 libcint 5.5.0, libgit2 1.7.2, librosa 0.10.1, librsvg 2.58.0, libSBML 5.19.7, libsigsegv 2.14, libtirpc 1.3.4, 17863 libxml2-python 2.11.4, likwid 5.3.0, LLVM 14.0.6, MACS3 3.0.1, maeparser 1.3.1, Mamba 23.11.0-0, MATIO 1.5.26, 17864 matplotlib 3.8.2, maturin 1.5.0, MCR R2023a, MDAnalysis 2.7.0, MDI 1.4.26, medaka 1.11.3, Meson 1.3.1, MiXCR 4.6.0, 17865 MNE-Python-1.6., MOABB 1.0.0, molmod 1.4.8, MONAI 1.3.0, mpi4py 3.1.5, mrcfile 1.5.0, NCCL 2.20.5, NCO 5.1.9, NECI 20230620, 17866 netcdf4-python-1.6.5, networkx 3.2.1, NGSpeciesID 0.3.0, NiBabel 5.2.0, nichenetr 2.0.4, Nilearn 0.10.3, 17867 nlohmann_json 3.11.3, NLTK 3.8.1, ntCard 1.2.2, numba 0.58.1, NVHPC 24.1, OBITools3 3.0.1b26, OCaml 4.14.0, occt 7.8.0, 17868 onedrive 2.4.25, ONNX 1.15.0, ONNX-Runtime 1.16.3, ont-fast5-api 4.1.2, OPARI2 2.0.8, OpenFOAM v2306 + v2312, OpenSSL/3, 17869 Optuna 3.5.0, Osi 0.108.9, PAPI 7.1.0, Parallel-Hashmap 1.3.12, ParaView 5.12.0, PDT 3.25.2, PETSc 3.20.3, PGPLOT 5.2.2, 17870 phonemizer 3.2.1, phono3py 2.7.0, Pillow 10.2.0, Pint 0.23, plotly.py 5.18.0, poetry 1.7.1, presto-1.0.0 20230501, 17871 PROJ 9.3.1, prompt-toolkit 3.0.36, protobuf 25.3, protobuf-python 4.25.3, psmc 0.6.5_20221121, pstoedit 3.78, 17872 psycopg2 2.9.9, PuLP 2.8.0, PyCheMPS2 1.8.12, pycodestyle 2.11.1, pydantic 1.10.13 + 2.5.3 2.6.4, pydicom 2.4.4, pydot 2.0.0, 17873 pyfaidx 0.8.1.1, PyFrag 2023-dev.20240220, pymatgen 2023.12.18, PyOpenCL 2023.1.4, PyOpenGL 3.1.7, pyparsing 3.1.1, 17874 PyQt5 5.15.10, Pysam 0.22.0, PySCF 2.4.0, pyspoa 0.2.1, PyTables 3.9.2, pytest-rerunfailures 14.0, python-igraph 0.11.4, 17875 python-irodsclient 2.0.0, python-isal 1.6.1, python-libsbml 5.20.2, python-xxhash 3.4.1, PyTorch-Ignite 0.4.13, 17876 PyTorch-Lightning 2.2.1, PyZMQ 25.1.2, QIIME2 2023.7.0, Qt5 5.15.13, Qt6 6.6.3, Qtconsole 5.5.1, QtPy 2.4.1, 17877 QuantumESPRESSO 7.3, R 4.3.3, rasterio 1.3.9, R-bundle-Bioconductor 3.18, rclone 1.66.0, RE2 2024-03-01, Redis 7.2.4, 17878 redis-py 5.0.1, rioxarray 0.15.0, Rivet 3.1.9, rMATS-turbo 4.2.0, RNA-Bloom 2.0.1, rocm-smi 5.6.0, rpy2 3.5.15, 17879 ruamel.yaml 0.18.6, Ruby 3.3.0, Rust 1.75.0 + 1.76.0, Salmon 1.10.1, Sambamba 1.0.1, Saxon-HE 12.4, SBCL 2.4.1, 17880 ScaFaCoS 1.0.4, Scalene 1.5.35, scanpy 1.9.8, scib 1.1.4, scikit-bio 0.5.9, scikit-learn 1.4.0, scikit-lego 0.7.4, 17881 scikit-misc 0.3.1, SCons 4.6.0, Score-P 8.4, scVelo 0.3.1, Seaborn 0.13.2, SentencePiece 0.1.99, Seqmagick 0.8.6, 17882 Seurat 5.0.1, SIP 6.8.1, siscone 3.0.6, skorch 0.15.0, SLEPc 3.20.1, snakemake 8.4.2, SNAPE-pooled 20150707, 17883 SOAPdenovo-Trans 1.0.5, Spark 3.5.1, spdlog 1.12.0, spoa 4.1.0, SRA-Toolkit 3.0.10, Stack 2.13.1, STAR 2.7.11b, 17884 statsmodels 0.14.1, tensorboard 2.15.1, tensorboardX 2.6.2.2, tensorflow-probability 0.20.0, texinfo 7.1, timm 0.9.7, 17885 torchvision 0.16.0, tqdm 4.66.2, TRIQS 3.2.0, TRIQS-cthyb 3.2.1, TRIQS-dft_tools 3.2.0, TRIQS-tprf 3.2.1, 17886 typing-extensions 4.9.0, UCX 1.16.0, UDUNITS 2.2.28, umap-learn 0.5.5, UMI-tools 1.1.4, Vala 0.56.14, VEP 111, 17887 Vim 9.1.0004, vsc-mympirun 5.4.0, WFA2 2.3.4, wget 1.21.4, WhatsHap 2.2, WIEN2k 23.2, wrf-python 1.3.4.1, 17888 Xerces-C++ 3.2.5, XlsxWriter 3.1.9, XML-LibXML v2.0209, xxHash 0.8.2, yaff 1.6.0, YAXT 0.10.0, Yices 2.6.4, YODA 1.9.9</li> 17889</ul> 17890</li> 17891<li>minor enhancements, including:<ul> 17892<li>add build info message to easyconfig for NLTK 3.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18550">#18550</a>)</li> 17893<li>enable KLU and CUDA solvers in SUNDIALS v6.6.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19490">#19490</a>)</li> 17894<li>add extensions to R-bundle-CRAN v2023.12: tidybayes (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19712">#19712</a>), spdep (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19729">#19729</a>), fixest (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20055">#20055</a>)</li> 17895<li>add plyranges extension to R-bundle-Bioconductor (for zUMIs) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19949">#19949</a>)</li> 17896<li>add PyOpenGL-accelerate extension to PyOpenGL v3.1.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20007">#20007</a>)</li> 17897<li>use system architecture template in DB_File (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20014">#20014</a>), GD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20015">#20015</a>), and GDGraph (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20016">#20016</a>)</li> 17898<li>
17898add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20069">#20069</a>)</li> 17899<li>add MODIStsp extension (+ required dependencies) to R 4.2.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20113">#20113</a>)</li> 17900<li>enable LittleCMS2 and WebP support in recent Pillow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20195">#20195</a>)</li> 17901<li>improve test for validity of easyconfig files (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20205">#20205</a>)</li> 17902<li>add easyconfig test that checks if backdoored XZ versions are introduced (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20267">#20267</a>)</li> 17903</ul> 17904</li> 17905<li>various bug fixes, including:<ul> 17906<li>add patch for Bison 3.7.1 to fix build error on old OS versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12291">#12291</a>)</li> 17907<li>add missing pkg-config build dependency for recent p11-kit easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16318">#16318</a>)</li> 17908<li>fix dependencies and configure flags of GnuTLS 3.7.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19070">#19070</a>)</li> 17909<li>remove numa configure option from hwloc 2.5+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19085">#19085</a>)</li> 17910<li>add patches for OpenBLAS v0.3.21 to disable -ftree-vectorize for netlib LAPACK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19280">#19280</a>)</li> 17911<li>add patch to fix flaky scipy build in SciPy-bundle v2023.11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19481">#19481</a>)</li> 17912<li>add missing SciPy-bundle dependency to TensorRT easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19486">#19486</a>)</li> 17913<li>fix lapack test failures in OpenBLAS 0.3.23/24 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19495">#19495</a>)</li> 17914<li>add patch for Arrow v8.0.0 - v11.0.0 to add missing <code>__arrow_ext_class__</code> method to <code>BaseExtensionType</code> class (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19532">#19532</a>)</li> 17915<li>change homepage for argtable (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19551">#19551</a>)</li> 17916<li>add patches for PyTorch v2.1.2 with <code>foss/2022a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19571">#19571</a>), <code>foss/2022b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19572">#19572</a>), and <code>foss/2023a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19573">#19573</a>) to fix test failures on non-x86 platforms</li> 17917<li>use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19584">#19584</a>)</li> 17918<li>remove <code>osdependencies</code> from ccache easyconfigs using GCCcore toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19600">#19600</a>)</li> 17919<li>use https source URL for alsa-lib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19628">#19628</a>)</li> 17920<li>add missing dm-tree dependency for dm-reverb 0.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19653">#19653</a>)</li> 17921<li>add libyaml import check to PyYAML and fix builds since split to minimal Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19662">#19662</a>)</li> 17922<li>demote meson-python to a build dependency in recent matplotlib easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19670">#19670</a>)</li> 17923<li>add patch to fix upb CopyFrom error in protobuf-python 4.24.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19671">#19671</a>)</li> 17924<li>demote poetry to build dep in expecttest (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19675">#19675</a>)</li> 17925<li>
17925add zlib dependency to YODA and Rivet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19679">#19679</a>)</li> 17926<li>fix missing spaces in Graphviz configure options (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19687">#19687</a>)</li> 17927<li>strip iconv from pkgconfig file for libarchive v3.6.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19698">#19698</a>)</li> 17928<li>use separate bcrypt easyconfig (using <code>CargoPythonPackage</code>) as dependency for JupyterHub v4.0.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19703">#19703</a>)</li> 17929<li>use maturin easyconfig using <code>CargoPythonPackage</code> as a dependency for fastparquet v2023.4.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19704">#19704</a>)</li> 17930<li>add patches for Perl-bundle-CPAN v5.36.1 to fix installation of <code>Sys::Info::Driver::Linux*</code> extensions on Debian Bookworm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19727">#19727</a>)</li> 17931<li>explicitly specify Fortran compiler for recent CDO versions to fix issues on non-x86_64 architectures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19735">#19735</a>)</li> 17932<li>add patch for <code>jupyter_core</code> extension in <code>jupyter-server</code> to set jupyter path by <code>$EB_ENV_JUPYTER_ROOT</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19737">#19737</a>)</li> 17933<li>add Python build dependency to 1.9.x Doxygen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19743">#19743</a>)</li> 17934<li>fix Arrow v14.0.1 to install pyarrow as an extension (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19758">#19758</a>)</li> 17935<li>fix homepage + source URL for Gblocks 0.91b (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19797">#19797</a>)</li> 17936<li>make sure that Brunsli libraries are installed into <code>lib</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19805">#19805</a>)</li> 17937<li>fix dependency with <code>libidn.so.11</code> in tbl2asn v20220427 and v20230713 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19821">#19821</a>)</li> 17938<li>add missing dependencies for fslpy in easyconfig for FSL v6.0.5.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19829">#19829</a>)</li> 17939<li>remove numa configure option from hwloc 2+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19833">#19833</a>)</li> 17940<li>avoid spurious test failure when enabling RPATH for Perl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19835">#19835</a>)</li> 17941<li>add missing Python deps and packages in PSI4 1.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19836">#19836</a>)</li> 17942<li>add patch to fix <code>MS_RDONLY</code> error in OpenMPI 3.1.x and 4.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20140">#20140</a>), 4.0.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19944">#19944</a>), and 4.0.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19837">#19837</a>)</li> 17943<li>demote meson-python to build dependency for matplotlib v3.7.2 w/ <code>iimkl/2023a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19892">#19892</a>)</li> 17944<li>demote hatchling to build dependency in easyconfig for einops 0.7.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19915">#19915</a>)</li> 17945<li>add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19940">#19940</a>)</li> 17946<li>stop using non-existent <code>--disable-libdeflate</code> option for LibTIFF 4.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19951">#19951</a>)</li> 17947<li>add patch to remove git version check and fix test command for molmod 1.4.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19952">#19952</a>)</li> 17948<li>replace SYSTEM-level GCC dependency in git-annex with binutils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19956">#19956</a>)</li> 17949<li>stop using non-existing <code>--with-doc</code> configure option for groff 1.23 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19969">#19969</a>)</li> 17950<li>fix test failures of Perl-bundle-CPAN-5.38 in non-English locales (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19971">#19971</a>)</li> 17951<li>
17951add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19974">#19974</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20218">#20218</a>)</li> 17952<li>drop checksum from easyconfig for VSCode 1.85.0 since tarball are not stable (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19995">#19995</a>)</li> 17953<li>respect <code>sysroot</code> in recent Pillow-SIMD easyconfigs, when in use (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19996">#19996</a>)</li> 17954<li>remove <code>--disable-docs</code> configure option from FriBidi 1.0.5+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19998">#19998</a>)</li> 17955<li>fix geotiff configure option in GDAL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19999">#19999</a>)</li> 17956<li>unpack SCG database to <code>db</code> subdirectory for DAS_Tool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20008">#20008</a>)</li> 17957<li>remove Jasper dependency and configure option from GDAL 3.5+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20009">#20009</a>)</li> 17958<li>update homepage and source URLs for SPAdes (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20018">#20018</a>)</li> 17959<li>fix GDAL 3.5.0 install on high-core-count machines (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20027">#20027</a>)</li> 17960<li>remove disable-visibility configure flag from GTK3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20028">#20028</a>)</li> 17961<li>remove mpi configure option from libfdf 0.2.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20034">#20034</a>)</li> 17962<li>add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20035">#20035</a>)</li> 17963<li>fix invocation typo and unneeded folder change on invocation in fgbio 1.3.0 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20039">#20039</a>)</li> 17964<li>remove hdf5 configure option from MDSplus 7.96.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20041">#20041</a>)</li> 17965<li>fix python configure option of MEME (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20043">#20043</a>)</li> 17966<li>fix configure options of FFLAS-FFPACK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20052">#20052</a>)</li> 17967<li>find the correct Python in xtensor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20056">#20056</a>)</li> 17968<li>fix geotiff configure option in GDAL 2.2.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20057">#20057</a>)</li> 17969<li>fix configure option and remove gperftools dependency for MIRA 5.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20061">#20061</a>)</li> 17970<li>fix confgure options in GRASS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20062">#20062</a>)</li> 17971<li>fix configure of LinBox 1.7.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20064">#20064</a>)</li> 17972<li>remove unknown configure option from GnuTLS 3.7.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20065">#20065</a>)</li> 17973<li>use 32-bit indexing for SUNDIALS 6.6.0 (with foss/2023a) to enable sunmatrix-cusparse (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20075">#20075</a>)</li> 17974<li>find correct Python for MDI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20083">#20083</a>)</li> 17975<li>add <code>pixman</code> and <code>FriBidi</code> dependencies to recent ImageMagick easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20086">#20086</a>)</li> 17976<li>add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20090">#20090</a>) and v5.38.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20118">#20118</a>)</li> 17977<li>
17977add patches for minimus2 in AMOS-3.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20114">#20114</a>)</li> 17978<li>fix download url for cuSPARSELt 0.3.0.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20129">#20129</a>)</li> 17979<li>add patches to fix test issues for PyTorch 2.1.2 with <code>foss/2023a</code> + CUDA 12.1.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20156">#20156</a>)</li> 17980<li>remove easyconfig for UCX-CUDA 1.15.0 using incompatible combo of CUDA 12.3.0 + GCC 13.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20158">#20158</a>)</li> 17981<li>remove flake8 suppressions for invalid escape sequences (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20161">#20161</a>)</li> 17982<li>fix post-install command for SuperLU_DIST in case library prefix is <code>lib</code> instead of <code>lib64</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20162">#20162</a>)</li> 17983<li>switch to gitlab source URL for libxc + add alternative checksum (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20163">#20163</a>)</li> 17984<li>enable <code>download_dep_fail</code> in Pythonpackage easyconfigs where it was wrongly disabled (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20174">#20174</a>)</li> 17985<li>add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20176">#20176</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20177">#20177</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20178">#20178</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20179">#20179</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20180">#20180</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20181">#20181</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20182">#20182</a>)</li> 17986<li>disable tests for <code>Time::HiRes</code> extension in Perl-bundle-CPAN v5.36.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20187">#20187</a>)</li> 17987<li>fix several typos in GlobalArrays 5.8 configure step (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20188">#20188</a>)</li> 17988<li>fix broken homepage from older SCOTCH easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20192">#20192</a>)</li> 17989<li>remove dead URL for ISL from <code>source_urls</code> in easyconfigs for GCCcore 10.3.0, 11.1.0, 11.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20193">#20193</a>)</li> 17990<li>fix package installation in easyconfigs for Python 2.7.15 and 3.7.2 (using <code>GCCcore/8.2.0</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20194">#20194</a>)</li> 17991<li>add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20214">#20214</a>)</li> 17992<li>fix cuSPARSELt easyconfigs for aarch64 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20216">#20216</a>)</li> 17993<li>fix python shebang in napari easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20219">#20219</a>)</li> 17994<li>add patch to fix scipy test failure for SciPy-bundle 2023.02 with <code>gfbf/2022b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20235">#20235</a>)</li> 17995<li>fix <code>incompatible types</code> errors when building the R extension <code>dbarts</code> on Arm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20238">#20238</a>)</li> 17996<li>add patch to fix for libarchive to fix error reporting in tar (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20254">#20254</a>)</li> 17997<li>add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20260">#20260</a>)</li> 17998<li>fix download for python-parasail 1.3.4 by adding missing source URL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20263">#20263</a>)</li> 17999</ul> 18000</li> 18001<li>other changes:<ul> 18002<li>update DualSPHysics easyconfig to use custom easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19400">#19400</a>)</li> 18003<li>fix name for DETONATE in existing easyconfig (was <code>detonate</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19569">#19569</a>)</li> 18004<li>rename <code>VSCode</code> to <code>code-cli</code> (to match with existing <code>code-server</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19585">#19585</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19645">#19645</a>)</li> 18005<li>remove urllib3 extension from wandb easyconfig, not neeed since P
18005ython-bundle-PyPI dependency already provides it (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19725">#19725</a>)</li> 18006<li>stop using custom easyblock for Doxygen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19742">#19742</a>)</li> 18007<li>move <code>setuptools_scm</code> extension from hatchling to Python easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19777">#19777</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20200">#20200</a>)</li> 18008<li>move xtb v6.6.1 to gfbf/2023a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19826">#19826</a>)</li> 18009<li>unify Z3 4.12.2 easyconfigs into a single one with Python bindings (and fix Z3 dependency for PyTorch 2.1.2 accordingly) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20050">#20050</a>)</li> 18010<li>use GPAW-setups v24.1.0 in existing GPAW easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20117">#20117</a>)</li> 18011<li>fix duplicate dict entries and enable fatal error checking for easyconfigs via <code>flake8</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20173">#20173</a>)</li> 18012<li>move Greenlet 2.0.2 to GCCcore toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20241">#20241</a>)</li> 18013<li>update Java/8 wrapper to Java 8.402 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20261">#20261</a>)</li> 18014<li>update copyright lines to 2024 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/20276">#20276</a>)</li> 18015</ul> 18016</li> 18017</ul> 18018<h2 id="release_notes_eb490">EasyBuild v4.9.0 (29 Dec 2023)<a class="headerlink" href="#release_notes_eb490" title="Permanent link">¶</a></h2> 18019<p>feature release</p> 18020<p><strong>framework</strong></p> 18021<ul> 18022<li>various enhancements, including:<ul> 18023<li>allow tweaking of easyconfigs from different toolchains (<a href="https://github.com/easybuilders/easybuild-framework/pull/3669">#3669</a>)</li> 18024<li>add support for <code>--list-software --output-format=json</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4152">#4152</a>)</li> 18025<li>add <code>--module-cache-suffix</code> configuration setting to allow multiple (Lmod) caches (<a href="https://github.com/easybuilders/easybuild-framework/pull/4403">#4403</a>)</li> 18026</ul> 18027</li> 18028<li>various bug fixes, including:<ul> 18029<li>deduplicate warnings & errors found in logs and add initial newline + tab in output (<a href="https://github.com/easybuilders/easybuild-framework/pull/4361">#4361</a>)</li> 18030<li>fix support for Environment Modules as modules tool to pass unit tests with v4.2+ (<a href="https://github.com/easybuilders/easybuild-framework/pull/4369">#4369</a>)</li> 18031<li>adapt module function check for Environment Modules v4+ (<a href="https://github.com/easybuilders/easybuild-framework/pull/4371">#4371</a>)</li> 18032<li>only install GitHub token when testing with Lmod 8.x + Python 3.6 or 3.9 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4375">#4375</a>)</li> 18033<li>use <code>-qopenmp</code> instead of <code>-fiopenmp</code> for OpenMP in Intel compilers (<a href="https://github.com/easybuilders/easybuild-framework/pull/4377">#4377</a>)</li> 18034<li>fix <code>LIBBLAS_MT</code> for FlexiBLAS, ensure <code>-lpthread</code> is included (<a href="https://github.com/easybuilders/easybuild-framework/pull/4379">#4379</a>)</li> 18035<li>relax major version match regex in <code>find_related_easyconfigs</code> using for <code>--review-pr</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4385">#4385</a>)</li> 18036<li>eliminate duplicate multideps from generated module files (<a href="https://github.com/easybuilders/easybuild-framework/pull/4386">#4386</a>)</li> 18037<li>resolve templated values in extension names in <code>_make_extension_list</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4392">#4392</a>)</li> 18038<li>use source toolchain version when passing only <code>--try-toolchain</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4395">#4395</a>)</li> 18039<li>fix writing spider cache for Lmod >= 8.7.12 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4402">#4402</a>)</li> 18040<li>fix <code>--inject-checksums</code> when extension specifies patch file in tuple format (<a href="https://github.com/easybuilders/easybuild-framework/pull/4405">#4405</a>)</li> 18041<li>fix <code>LooseVersion</code> when running with Python 2.7 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4408">#4408</a>)</li> 18042<li>use more recent easyblocks PR in <code>test_github_merge_pr</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4414">#4414</a>)</li> 18043</ul> 18044</li> 18045<li>other changes:<ul> 18046<li>extend test that checks build environment to recent <code>foss/2023a</code> toolchain (<a href="https://github.com/easybuilders/easybuild-framework/pull/4391">#4391</a>)</li> 18047</ul> 18048</li> 18049</ul> 18050<p><strong>easyblocks</strong></p> 18051<ul> 18052<li>add generic <code>CargoPythonBundle</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2964">#2964</a>)</li> 18053<li>3 new software-specific easyblocks: flook (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3034">#3034</a>), HPCC (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3009">#3009</a>), PALM (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3020">#3020</a>)</li> 18054<li>minor enhancements and updates, including:<ul> 18055<li>add custom easyconfig parameter <code>cmake_options</code> to SuiteSparse easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3031">#3031</a>)</li> 18056<li>update custom intel-compilers easyblock for versions >= 2024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3037">#3037</a>)</li> 18057<li>update custom easyblock for Intel MPI easyblock for v2021.11 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3039">#3039</a>)</li> 18058<li>update numpy easyblock for v1.26+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3041">#3041</a>)</li> 18059<li>update custom easyblock for Intel MKL for v2024.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3042">#3042</a>)</li> 18060<li>update Ferret easyblock to be compatible with v7.6.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3052">#3052</a>)</li> 18061</ul> 18062</li> 18063<li>various bug fixes, including:<ul> 18064<li>add support for allowing version mismatch + consider versionsuffix when creating <code>.modulerc</code> in <code>ModuleRC</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3028">#3028</a>)</li> 18065<li>update error detection for PyTorch tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3033">
18065#3033</a>)</li> 18066<li>disable LLVM build downloads from CI in Rust (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3038">#3038</a>)</li> 18067<li>add requirement for EULA acceptance to CUDA easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3045">#3045</a>)</li> 18068<li>make various fixes and enhancements to NWChem easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3049">#3049</a>)</li> 18069<li>add binutils symlinks when building TensorFlow with <code>--rpath</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3054">#3054</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3058">#3058</a>)</li> 18070<li>fix specifying path to SuiteSparse header files and libraries in numpy, Trilinos, PETSc easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3056">#3056</a>)</li> 18071<li>fix <code>det_pylibdir</code> provided by <code>PythonPackage</code> easyblock for Python 3.12+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3057">#3057</a>)</li> 18072<li>fix nvptx sanity check for Clang >= 14.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3059">#3059</a>)</li> 18073</ul> 18074</li> 18075<li>other changes:<ul> 18076<li>update SuiteSparse easyblock to only install SuiteSparse libraries with <code>make install</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3004">#3004</a>)</li> 18077<li>also consider <code>$EB_COMSOL_LICENSE_FILE</code> environment variable in custom easyblock for COMSOL (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3044">#3044</a>)</li> 18078<li>import <code>LooseVersion</code> from <code>easybuild.tools</code> instead of <code>distutils.version</code> in easyblocks (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3048">#3048</a>)</li> 18079</ul> 18080</li> 18081</ul> 18082<p><strong>easyconfigs</strong></p> 18083<ul> 18084<li>added easyconfigs for <code>foss/2023b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19449">#19449</a>) and <code>intel/2023b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19450">#19450</a>) common toolchains</li> 18085<li>added example easyconfig files for 77 new software packages:<ul> 18086<li>AICSImageIO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19315">#19315</a>), ANTIC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19203">#19203</a>), BiasAdjustCXX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19341">#19341</a>), BOPTEST (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19295">#19295</a>), BRiAl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19208">#19208</a>), castor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19176">#19176</a>), 18087CellBender (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19296">#19296</a>), cliquer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19210">#19210</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19323">#19323</a>), CPMD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19387">#19387</a>), cppyy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19204">#19204</a>), CUDD (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19208">#19208</a>), datalad (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18675">#18675</a>), 18088Demystify (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17990">#17990</a>), dftd4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19223">#19223</a>), dialog (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17696">#17696</a>), DIA-NN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19454">#19454</a>), dynesty (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19091">#19091</a>), ebGSEA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19447">#19447</a>), 18089ECL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19211">#19211</a>), eclib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19209">#19209</a>), epct (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19298">#19298</a>), EUKulele (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19217">#19217</a>), FACE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14840">#14840</a>), fastml (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19357">#19357</a>), forbear (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14840">#14840</a>), 18090fplll (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19371">#19371</a>), fpylll (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19371">#19371</a>), ftfy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19353">#19353</a>), Gdspy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19458">#19458</a>), GFF3-toolkit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19071">#19071</a>), giac (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19323">#19323</a>), GMP-ECM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19323">#19323</a>), 18091HepMC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19139">
18091#19139</a>), hic-straw (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19309">#19309</a>), HPCC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18892">#18892</a>), iced (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19309">#19309</a>), IML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19201">#19201</a>), iperf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19259">#19259</a>), jedi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19269">#19269</a>), 18092jedi-language-server (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19269">#19269</a>), jupyter-rsession-proxy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19311">#19311</a>), lcalc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19329">#19329</a>), libaed2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14840">#14840</a>), 18093LoopTools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19397">#19397</a>), m4ri (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19208">#19208</a>), m4rie (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19208">#19208</a>), MDI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19417">#19417</a>), mdust (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19106">#19106</a>), MitoHiFi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19263">#19263</a>), MPFI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19323">#19323</a>), 18094multicharge (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19221">#19221</a>), OMERO.insight (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19337">#19337</a>), OMERO.py (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19338">#19338</a>), PFFT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19255">#19255</a>), primecount (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19370">#19370</a>), 18095primecountpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19370">#19370</a>), PyAV (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19359">#19359</a>), pycubescd (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19302">#19302</a>), pylipid (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19428">#19428</a>), PySINDy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19306">#19306</a>), 18096pythermalcomfort (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19285">#19285</a>), PyTorchVideo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19359">#19359</a>), R-bundle-CRAN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19170">#19170</a>), Restrander (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19232">#19232</a>), scikit-lego (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19064">#19064</a>), 18097scrublet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19215">#19215</a>), SEACells (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18724">#18724</a>), simanneal (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19347">#19347</a>), Simstrat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14840">#14840</a>), solo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19216">#19216</a>), SPEI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19441">#19441</a>), 18098SUPPA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19181">#19181</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19275">#19275</a>), SYMMETRICA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19328">#19328</a>), Triton (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19381">#19381</a>), vaeda (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19214">#19214</a>), VSCode (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19418">#19418</a>), waLBerla (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18932">
18098#18932</a>)</li> 18099</ul> 18100</li> 18101<li>added additional easyconfigs for various supported software packages, including:<ul> 18102<li>ANTs 2.5.0, Arriba 2.4.0, Arrow 14.0.1, at-spi2-core 2.50.0, Autoconf-archive 2023.02.20, awscli 2.15.2, 18103Blender 3.6.5 + 4.0.1, Boost 1.83.0, boto3 1.28.70, Bracken 2.9, BUStools 0.43.1, cairo 1.18.0, cairomm 1.16.2, 18104CASTEP 23.1, cddlib 0.94m, cdo-bindings 1.6.0, CellRanger 7.2.0, CoCoALib 0.99818, COMSOL 6.2.0.290, Coreutils 9.1, 18105cryptography 41.0.5, CubeLib 4.8.2, CubeWriter 4.8.2, CUDA 12.3.0, CVXPY 1.3.0, cysignals 1.11.2, DBus 1.15.8, 18106dftd4 3.4.0, E-ANTIC 1.3.0, elfutils 0.190, f90wrap 0.2.11, FastQC 0.12.1, Ferret 7.6.0, FFLAS-FFPACK 2.5.0, 18107ffnvcodec 12.1.14.0, FPM 1.15.1, FriBidi 1.0.13, gap 4.12.2, git-lfs 3.4.0, GitPython 3.1.40, Givaro 4.2.0, 18108GLib 2.78.1, glog 0.6.0, GObject-Introspection 1.78.1, gperftools 2.13, GPyTorch 1.10, GROMACS 2023.3, 18109HarfBuzz 8.2.2, HiC-Pro 3.1.0, hifiasm 0.19.7, hypothesis 6.90.0, ICU 74.1, imageio 2.33.1, imkl 2024.0.0, 18110impi 2021.11.0, intel-compilers 2024.0.0, IPython 8.17.2, ITK 5.3.0, Kent_tools 457, KyotoCabinet 1.2.80, 18111LHAPDF 6.5.4, libfdf 0.5.0, libjxl 0.8.2, LinBox 1.7.0, lrslib 7.2, lxml 4.9.3, magma 2.7.2, maturin 1.3.1, 18112MEME 5.5.4, meson-python 0.15.0, Miniconda3 23.9.0, Mmg 5.7.2, Molden 7.3, mrcfile 1.4.3, nanoflann 1.5.0, 18113nauty 2.8.6, Nextflow 23.10.0, nodejs 20.9.0, Normaliz 3.10.1, NSS 3.94, NWChem 7.2.2, Oases 20180312, Pango 1.51.0, 18114Parallel-Hashmap 1.36, parameterized 0.9.0, phonopy 2.20.0, pigz 2.8, pmt 1.2.0, poetry 1.6.1, PostgreSQL 16.1, 18115pplpy 0.8.9, PyCairo 1.25.1, pypmt 1.2.0, PyQt5 5.15.7, pytest 7.4.2, pytest-xdist 3.3.1, 18116Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, RASPA2 2.0.47, SBCL 2.3.11, SCENIC 1.3.0, scikit-image 0.22.0, 18117SciPy-bundle 2023.11, SDL2 2.28.5, setuptools-rust 1.8.0, Seurat 4.4.0, SimpleITK 2.3.1, Singular 4.3.2p10, 18118Spark 3.5.0, STAR 2.7.11a, STAR-CCM+ 2310, strace 6.6, SuiteSparse 7.1.0, tbb 2021.11.0, TOML-Fortran 0.4.1, 18119TRAVIS-Analyzer 220729, UCX-CUDA 1.15.0, VirSorter 1.0.6, virtualenv 20.24.6, VSEARCH 2.25.0, VTK 9.3.0, 18120wandb 0.16.1, XGBoost 2.0.2, xprop 1.2.6, xtb 6.6.1, Xvfb 21.1.9, xxd 9.0.2112</li> 18121</ul> 18122</li> 18123<li>minor enhancements, including:<ul> 18124<li>add sanity check commands for recent GDB versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19102">#19102</a>)</li> 18125<li>add aarch64 and ppc64le checksums to NVHPC 23.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19249">#19249</a>)</li> 18126<li>allow Python version of Z3 to be used as a dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19354">#19354</a>)</li> 18127</ul> 18128</li> 18129<li>various bug fixes, including:<ul> 18130<li>use <code>CargoPythonBundle</code> generic easyblock for timm to install required Rust packages in a controlled way (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18332">#18332</a>)</li> 18131<li>add alternate checksum for OpenImageIO v2.4.14.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19090">#19090</a>)</li> 18132<li>only set flag <code>--enable-asmjit</code> for PLUMED when installing on <code>x86_64</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19110">#19110</a>)</li> 18133<li>ensure right Python version is used in DP3, WSClean and dependencies by specifying <code>-DPython3_EXECUTABLE</code> CMake option (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19119">#19119</a>)</li> 18134<li>add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19133">#19133</a>)</li> 18135<li>add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19141">#19141</a>)</li> 18136<li>remove outdated <code>--disable-docs</code> configure option from FriBidi-1.0.12 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19147">#19147</a>)</li> 18137<li>add libiconv dependency to gettext 0.22 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19155">#19155</a>)</li> 18138<li>fix OpenBLAS 0.3.20+ on newer Intel CPUs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19159">#19159</a>)</li> 18139<li>only use ScaFaCos as dependency for LAMMPS 23Jun2022 on <code>x86_64</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19164">#19164</a>)</li> 18140<li>
18140add patch to fix regression in GCC 12.x on AVX512 systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19180">#19180</a>)</li> 18141<li>add pkgconf build dependency to libGLU (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19186">#19186</a>)</li> 18142<li>sidestep some build issues with CUDA-Samples 12.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19189">#19189</a>)</li> 18143<li>make Pillow easyconfigs aware of sysroot template (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19226">#19226</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19267">#19267</a>)</li> 18144<li>fix possible error/crash in NCCL on x86 due to cpuid (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19231">#19231</a>)</li> 18145<li>reduce timestep to fix sanity check commands in LAMMPS 23Jun2022 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19246">#19246</a>)</li> 18146<li>add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19253">#19253</a>)</li> 18147<li>replace format tag with explicit extension name in Optuna v3.0.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19256">#19256</a>)</li> 18148<li>enhance easyconfigs for gnuplot 5.4.x to make sure that Lua dependency is always used (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19261">#19261</a>)</li> 18149<li>patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19268">#19268</a>)</li> 18150<li>avoid indirect dependency on old CMake version built with GCCcore/10.2.0 via Catch2 build dependency using system toolchain in recent pybind11 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19270">#19270</a>)</li> 18151<li>use existing patch in pybind11 2.6.2 and 2.7.1 to fix failing test due to extra whitespace (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19279">#19279</a>)</li> 18152<li>change toolchain in <code>json-fortran</code> easyconfigs to <code>GCC</code>, since it includes Fortran modules (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19283">#19283</a>)</li> 18153<li>remove Unicode character in description of SMRT-Link easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19312">#19312</a>)</li> 18154<li>don't use <code>%(namelower)s</code> template in extension name in IPython v8.14.0 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19330">#19330</a>)</li> 18155<li>add patch to fix <code>[cz]asums</code> in OpenBLAS 0.3.24 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19331">#19331</a>)</li> 18156<li>fix failing tokenizers with <code>CargoPythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19333">#19333</a>)</li> 18157<li>define <code>$GTKDOCIZE</code> as '<code>echo</code>' before generating configure script for new HarfBuzz versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19339">#19339</a>)</li> 18158<li>fix PAPI test step hanging on some systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19372">#19372</a>)</li> 18159<li>compile LERC test binary in <code>postinstallcmds</code> to fix sanity check error when RPATH linking is enabled (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19386">#19386</a>)</li> 18160<li>use <code>GCC</code> toolchain in <code>kim-api</code>, since it includes Fortran modules (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19399">#19399</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19401">#19401</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19402">#19402</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19403">#19403</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19404">#19404</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19405">#19405</a>)</li> 18161<li>fix wrong handling of floats in z3-solver (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19414">#19414</a>)</li> 18162<li>Fix numpy build on Sapphire Rapids CPUs in SciPy-bundle-2023.07-gfbf-2023a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19419">#19419</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19425">#19425</a>)</li> 18163<li>allow ITK legacy code and Python wrappers in ITK v5.2.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19431">#19431</a>)</li> 18164<li>link to xxHash library provided via EasyBuild in python-xxhash v3.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19432">#19432</a>)</li> 18165<li>include MPFR 4.1.0 patch in MPFR 4.2.0 easyconfigs to fix failing tsprintf test with glibc >= 2.37 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19438">#19438</a>)</li> 18166<li>skip <code>Test::Sys::Info</code> test that expects <code>/etc/fstab</code> in Perl-bundle-CPAN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19440">#19440</a>)</li> 18167<li>exclude <code>cdp*</code> CUDA samples that fail to build on aarch64 in CUDA-Samples v12.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19451">#19451</a>)</li> 18168</ul> 18169</li> 18170<li>other changes:<ul> 18171<li>let SuiteSparse easyblock set <code>CMAKE_OPTIONS</code> for SuiteSparse v7.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19177">#19177</a>)</li> 18172<li>
18172add versionsuffix <code>-param</code> to easyconfig for ReaxFF 2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19307">#19307</a>)</li> 18173<li>use <code>LooseVersion</code> from <code>easybuild.tools</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19376">#19376</a>)</li> 18174</ul> 18175</li> 18176</ul> 18177<h2 id="release_notes_eb482">EasyBuild v4.8.2 (29 Oct 2023)<a class="headerlink" href="#release_notes_eb482" title="Permanent link">¶</a></h2> 18178<p>bugfix/update release</p> 18179<p><strong>framework</strong></p> 18180<ul> 18181<li>various enhancements, including:<ul> 18182<li>add support for <code>%(sysroot)s</code> template value (<a href="https://github.com/easybuilders/easybuild-framework/pull/4359">#4359</a>)</li> 18183<li>add <code>dependency_names</code> method to <code>EasyConfig</code> class to get set of names of (direct) dependencies (<a href="https://github.com/easybuilders/easybuild-framework/pull/4360">#4360</a>)</li> 18184</ul> 18185</li> 18186<li>various bug fixes, including:<ul> 18187<li>add CI workflow to run unit tests with Python 2 (again) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4333">#4333</a>)</li> 18188<li>fix typo in help message for <code>--silence-hook-trigger</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4343">#4343</a>)</li> 18189<li>include major version (<code>*majver</code>) templates in auto-generated documentation (<a href="https://github.com/easybuilders/easybuild-framework/pull/4347">#4347</a>)</li> 18190<li>reset <code>tempfile.tempdir</code> to <code>None</code> to avoid that tmpdir path gets progressively deeper with each easystack item (<a href="https://github.com/easybuilders/easybuild-framework/pull/4350">#4350</a>)</li> 18191<li>fix <code>findPythonDeps.py</code> script when called with an (absolute or relative) path to an easyconfig instead of a filename (<a href="https://github.com/easybuilders/easybuild-framework/pull/4365">#4365</a>)</li> 18192<li>fix broken test for <code>reasons_for_closing</code>, which fails because commit status of easyconfigs PR is no longer available (<a href="https://github.com/easybuilders/easybuild-framework/pull/4366">#4366</a>)</li> 18193</ul> 18194</li> 18195<li>other changes:<ul> 18196<li>reduce number of CI jobs by testing for Lua and Tcl module syntax in a single CI job (<a href="https://github.com/easybuilders/easybuild-framework/pull/4192">#4192</a>)</li> 18197</ul> 18198</li> 18199</ul> 18200<p><strong>easyblocks</strong></p> 18201<ul> 18202<li>minor enhancements and updates, including:<ul> 18203<li>allow use of <code>test_cmd</code> without <code>runtest</code> for <code>ConfigureMake</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2837">#2837</a>)</li> 18204<li>enhance <code>CMakeMake</code> easyblock to run <code>ctest</code> command if <code>runtest</code> is <code>True</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2838">#2838</a>)</li> 18205<li>enhance <code>Conda</code> easyblock: add support for using custom <code>conda</code> command (like <code>mamba</code>), and clean up after installation (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2996">#2996</a>)</li> 18206<li>update WRF easyblock to correctly determine <code>WRF*</code> subdirectory for WRF versions >= 4.5.1 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2997">#2997</a>)</li> 18207<li>update numpy easyblock to be able to use FlexiBLAS with MKL as dependency (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2999">#2999</a>)</li> 18208<li>add error regexp for PyTorch tests run in subprocess and enhance error message (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3003">#3003</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3005">#3005</a>)</li> 18209<li>don't blindly overwrite <code>-Dccflags</code> + honour <code>preconfigopts</code> in Perl easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3010">#3010</a>)</li> 18210<li>use more test programs in sanity check step of OpenMPI easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3016">#3016</a>)</li> 18211<li>fix <code>CMAKE_PREFIX_PATH</code> in imkl easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3021">#3021</a>)</li> 18212<li>update sanity check in wxPython easyblock for version 4.2.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3023">#3023</a>)</li> 18213</ul> 18214</li> 18215<li>various bug fixes, including:<ul> 18216<li>fix creation of symlink for libraries in TBB easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2927">#2927</a>)</li> 18217<li>fix <code>--sanity-check-only</code> and <code>--module-only</code> for UCX plugins (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3007">#3007</a>)</li> 18218<li>replace umlaut in docstring of PerlBundle easyblock (to fix Non-ASCII character error when using Python 2.7) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3008">#3008</a>)</li> 18219<li>enhance TensorFlow easyblock to avoid use of <code>-mcpu=native</code> for XNNPACK component when building on aarch64 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3011">#3011</a>)</li> 18220<li>only use <code>-DCMAKE_SKIP_RPATH=ON</code>
18220 for CMake < 3.5.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3012">#3012</a>)</li> 18221<li>fix the blas/lapack name passed to meson when building recent scipy versions (>= 1.9.0) on top of Intel MKL (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/3024">#3024</a>)</li> 18222</ul> 18223</li> 18224</ul> 18225<p><strong>easyconfigs</strong></p> 18226<ul> 18227<li>added example easyconfig files for 48 new software packages:<ul> 18228<li>ALL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18971">#18971</a>), anadama2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18688">#18688</a>), AOFlagger (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19010">#19010</a>), bases2fastq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18866">#18866</a>), BgeeCall (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18784">#18784</a>), 18229 biobakery-workflows (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18688">#18688</a>), BMTK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18863">#18863</a>), CIRIquant (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18815">#18815</a>), Clair3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18748">#18748</a>), CLEAR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16357">#16357</a>), 18230 cpio (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14728">#14728</a>), DP3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19010">#19010</a>), EveryBeam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19010">#19010</a>), fasta-reader (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18936">#18936</a>), git-annex (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18673">#18673</a>), GSD (#6453), 18231 imutils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18920">#18920</a>), Jblob (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18478">#18478</a>), Jmol (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18988">#18988</a>), kneaddata (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18688">#18688</a>), libbaseencode (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12319">#12319</a>), 18232 libcotp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12319">#12319</a>), MACS3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18354">#18354</a>), Mashtree (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19019">#19019</a>), mpath (#5029), MUSCLE3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18287">#18287</a>), plotutils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16196">#16196</a>), 18233 ProBiS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18830">#18830</a>), PyMC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10399">#10399</a>), PyPy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18847">#18847</a>), PyTensor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18928">#18928</a>), Qt6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18683">#18683</a>), QuickTree (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19019">#19019</a>), 18234 Raptor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18919">#18919</a>), RCall (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18933">#18933</a>), ResistanceGA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18933">#18933</a>), scCODA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18949">#18949</a>), scikit-build-core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18777">#18777</a>), 18235 segmentation-models-pytorch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18930">#18930</a>), SNAP-ESA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19031">#19031</a>), SNAP-ESA-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19031">#19031</a>), starparser (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18965">#18965</a>), 18236 synapseclient (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19016">#19016</a>), uncertainties (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18923">#18923</a>), WSClean (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19010">#19010</a>), XBeach (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18849">#18849</a>), XOOPIC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15269">#15269</a>), 18237 zeus-mcmc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19033">#19033</a>)</li> 18238</ul> 18239</li> 18240<li>
18240added additional easyconfigs for various supported software packages, including:<ul> 18241<li>alleleCount 4.3.0, Amber 22.4, ant 1.10.14, ArviZ 0.16.1, ASAP3 3.13.2, biobambam2 2.0.185, BLAST+ 2.14.1, 18242bokeh 3.2.2, Brotli 1.1.0, Cantera 3.0.0, CapnProto 1.0.1, casacore 3.5.0, Catch2 2.13.9, CGAL 5.6, 18243Chemaxon-Marvin 23.9, CMake 3.27.6, code-server 4.16.1, Coot 0.9.8.92, CSBDeep 0.7.4, CUDA-Samples 12.1.1, 18244CuPy 12.1.0, cURL 8.3.0, dask 2023.9.2, DL_POLY_4 5.1.0, DoubletFinder 2.0.3-20230131, Doxygen 1.9.8, dxpy 0.345.0, 18245EDirect 20.5.20231006, FastANI 1.34, FastME 2.1.6.3, Flask 2.3.3, Flye 2.9.2, fmt 10.1.0, foss/2023.09, 18246freetype 2.13.2, GDAL 3.7.1, GDRCopy 2.4, git 2.42.0, GMP 6.3.0, Go 1.21.1, googletest 1.14.0, GPAW 23.9.1, 18247groff 1.23.0, GTDB-Tk 2.3.2, GTK4 4.13.1, gzip 1.13, harmony 0.1.0, HDF 4.2.16, HighFive 2.7.1, Highway 1.0.7, 18248HMMER 3.4, hmmlearn 0.3.0, Imath 3.1.9, Inspector 2023.2.0, intel/2023.07, IsoSeq 4.0.0, itac 2021.10.0, 18249JupyterNotebook 7.0.3, libarchive 3.7.2, libcint 5.4.0, libdeflate 1.19, libdrm 2.4.117, libglvnd 1.7.0, 18250libjpeg-turbo 3.0.1, libmaus2 2.0.813, libpng 1.6.40, libsigc++ 2.12.1, libsodium 1.0.19, LibTIFF 4.6.0, 18251libwebp 1.3.2, libxc 6.2.2, line_profiler 4.1.1, LMDB 0.9.31, MAFFT 7.520, makeinfo 7.1, MATLAB 2023b, 18252MEGAN 6.25.3, Mesa 23.1.9, Meson 1.2.3, mold 2.3.1, MPFR 4.2.1, msgpack-c 6.0.0, nanopolish 0.14.0, 18253NBO 7.0.10, netcdf4-python 1.6.4, OpenBLAS 0.3.24, OpenCV 4.8.1, OpenEXR 3.2.0, OpenMolcas 23.06, OpenMPI 4.1.6, 18254openslide-python 1.3.1, OrthoFinder 2.5.5, OSU-Micro-Benchmarks 7.2, ParaView 5.11.2, Perl-bundle-CPAN 5.38.0, 18255PETSc 3.19.2, PMIx 4.2.6, poppler 23.09.0, preCICE 2.5.0, pretty-yaml 23.9.5, PyCairo 1.25.0, pyEGA3 5.0.2, 18256PyGObject 3.46.0, pygraphviz 1.11, pytest-rerunfailures 12.0, Python 3.11.5, PyTorch 2.0.1, PyTorch-bundle 1.13.1, 18257PyTorch-Ignite 0.4.12, PyYAML 6.0.1, RagTag 2.1.0, rapidcsv 8.62, rasterstats 0.19.0, RAxML-NG 1.2.0, 18258RDFlib 7.0.0, RDKit 2023.03.3, ReFrame 4.3.3, RMBlast 2.14.0, ruamel.yaml 0.17.32, Rust 1.73.0, scikit-learn 1.3.1, 18259SCons 4.5.2, SHAP 0.42.1, SignalP 6.0h, SMRT-Link 12.0.0.177059, spglib-python 2.1.0, SQLite 3.43.1, 18260TensorRT 8.6.1, texlive 20230313, Tkinter 3.11.5, UCX 1.15.0, VBZ-Compression 1.0.3, VCFtools 0.1.16, 18261VTune 2023.2.0, X11 20231019, x264 20231019, xarray 2023.9.0, XlsxWriter 3.1.3, xtb 6.6.0, ZeroMQ 4.3.5</li> 18262</ul> 18263</li> 18264<li>minor enhancements, including:<ul> 18265<li>also run easyconfigs test suite with Python 3.11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18009">#18009</a>)</li> 18266<li>don't disable building of third and fourth derivates in libxc 6.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18467">#18467</a>)</li> 18267<li>add easyconfigs cache file to <code>.gitignore</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18797">#18797</a>)</li> 18268<li>add patch to improve CUDA 11 compatibility of <code>GCCcore/12.2.0</code> and <code>GCCcore/12.3.0</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18854">#18854</a>)</li> 18269<li>also build Python bindings for ITK 5.2.1 with <code>foss/2022a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18922">#18922</a>)</li> 18270<li>add ridge extension to R 4.2.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18924">#18924</a>)</li> 18271<li>add MSstatsLiP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19009">#19009</a>) and escape (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19027">#19027</a>) to Bioconductor 3.16 bundle</li> 18272<li>add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19045">#19045</a>)</li> 18273</ul> 18274</li> 18275<li>various bug fixes, including:<ul> 18276<li>rename ACT to Artemis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18382">#18382</a>)</li> 18277<li>backport lchown patch to PMIx 3.1.x + 3.2.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18759">#18759</a>)</li> 18278<li>also copy scripts directory for Clair3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18783">#18783</a>)</li> 18279<li>rename isoseq3 after download for IsoSeq 3.8.2 + fix permissions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18785">#18785</a>)</li> 18280<li>
18280add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18789">#18789</a>)</li> 18281<li>add patch for OpenBLAS 0.3.23 to fix hanging tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18790">#18790</a>)</li> 18282<li>add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18833">#18833</a>)</li> 18283<li>fix permission issues when copying xvfb-run script in Xvfb easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18834">#18834</a>)</li> 18284<li>statically link Boost 1.75 in Cufflinks v20190706 installed with <code>GCC/11.2.0</code>, so Boost can be changed to build dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18843">#18843</a>)</li> 18285<li>add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18847">#18847</a>)</li> 18286<li>add patch to fix build of util-linux 2.39 on CentOS 7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18855">#18855</a>)</li> 18287<li>add patch to fix finding of tk.tcl for Tk 8.6.13 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18864">#18864</a>)</li> 18288<li>add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18870">#18870</a>)</li> 18289<li>fix source URL for segemehl 0.3.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18878">#18878</a>)</li> 18290<li>avoid use of hardcoded paths for Pillow by using <code>--disable-platform-guessing</code> option (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18881">#18881</a>)</li> 18291<li>add patch to disable flaky DDRGES3 LAPACK test in OpenBLAS 0.3.23 + 0.3.24 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18887">#18887</a>)</li> 18292<li>add alternate checksum for NCCL v2.18.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18906">#18906</a>)</li> 18293<li>add missing dependencies for MONAI to support extras required by MONAI-Label (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18921">#18921</a>)</li> 18294<li>make sure Python dependency included for ESPResSo is actually used by specifying <code>-DPYTHON_EXECUTABLE</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18963">#18963</a>)</li> 18295<li>only add tbb as dependency in recent LAMMPS easyconfigs when installing on x86_64 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19000">#19000</a>)</li> 18296<li>detect the correct Python for vcflib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19001">#19001</a>)</li> 18297<li>fix invalid pointer access in UCX 1.11-1.14 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19023">#19023</a>)</li> 18298<li>disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19024">#19024</a>)</li> 18299<li>add missing GSL dependency for casacore 3.4.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19042">#19042</a>)</li> 18300<li>fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19047">#19047</a>)</li> 18301<li>enable <code>-fPIC</code> in easyconfig for libwebp 1.3.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19098">#19098</a>)</li> 18302</ul> 18303</li> 18304<li>other changes:<ul> 18305<li>remove <code>'cstd': 'c++17'</code> as that's the default in GCC 11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18941">#18941</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18942">#18942</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18943">#18943</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18944">#18944</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18945">#18945</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18946">#18946</a>)</li> 18306<li>rename CVS to ConcurrentVersionsSystem, to avoid problems with recent setuptools versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18985">#18985</a>)</li> 18307<li>use <code>sysroot</code> template in wget easyconfigs to define <code>PKG_CONFIG_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/19080">#19080</a>)</li> 18308</ul> 18309</li> 18310</ul> 18311<hr /> 18312<h2 id="release_notes_eb481">EasyBuild v4.8.1 (11 Sept 2023)<a class="headerlink" href="#release_notes_eb481" title="Permanent link">¶</a></h2> 18313<p>bugfix/update release</p> 18314<p><strong>framework</strong></p> 18315<ul> 18316<li>various enhancements, including:<ul> 18317<li>
18317add end-to-end test for running EasyBuild in different Linux distros using containers (<a href="https://github.com/easybuilders/easybuild-framework/pull/3968">#3968</a>)</li> 18318<li>suggest default title in <code>--review-pr</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4287">#4287</a>)</li> 18319<li>add <code>build_and_install_loop</code> hooks to run before and after the install loop for individual easyconfigs (<a href="https://github.com/easybuilders/easybuild-framework/pull/4304">#4304</a>)</li> 18320<li>implement support for <code>cancel_hook</code> and <code>fail_hook</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4315">#4315</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4325">#4325</a>)</li> 18321<li>add postiter hook to the list of steps so the corresponding hook can be used (<a href="https://github.com/easybuilders/easybuild-framework/pull/4316">#4316</a>)</li> 18322<li>add <code>run_shell_cmd</code> hook (<a href="https://github.com/easybuilders/easybuild-framework/pull/4323">#4323</a>)</li> 18323<li>add <code>build_info_msg</code> easyconfig parameter to print message during installation of an easyconfig (<a href="https://github.com/easybuilders/easybuild-framework/pull/4324">#4324</a>)</li> 18324<li>add <code>--silence-hook-trigger</code> configuration option to supress printing of debug message every time a hook is triggered (<a href="https://github.com/easybuilders/easybuild-framework/pull/4329">#4329</a>)</li> 18325<li>add support for using fine grained Github tokens (<a href="https://github.com/easybuilders/easybuild-framework/pull/4332">#4332</a>)</li> 18326<li>add definitions for <code>ifbf</code> and <code>iofbf</code> toolchain (<a href="https://github.com/easybuilders/easybuild-framework/pull/4337">#4337</a>)</li> 18327<li>add support for submodule filtering and specifying extra Git configuration in <code>git_config</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4338">#4338</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4339">#4339</a>)</li> 18328</ul> 18329</li> 18330<li>various bug fixes, including:<ul> 18331<li>improve error when checksum dict has no entry for a file (<a href="https://github.com/easybuilders/easybuild-framework/pull/4150">#4150</a>)</li> 18332<li>avoid error being logged when <code>checksums.json</code> is not found (<a href="https://github.com/easybuilders/easybuild-framework/pull/4261">#4261</a>)</li> 18333<li>don't fail in <code>mkdir</code> if path gets created while processing it (<a href="https://github.com/easybuilders/easybuild-framework/pull/4300">#4300</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4328">#4328</a>)</li> 18334<li>ignore request for external module (meta)data when no modules tool is active (<a href="https://github.com/easybuilders/easybuild-framework/pull/4308">#4308</a>)</li> 18335<li>use <code>sys.executable</code> to obtain path to <code>python</code> command in tests, rather than assuming that <code>python</code> command is available in <code>$PATH</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4309">#4309</a>)</li> 18336<li>fix <code>test_add_and_remove_module_path</code> by replacing string comparison of paths by checking whether they point to the same path (since symlinks may cause trouble) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4312">#4312</a>)</li> 18337<li>enhance <code>Toolchain.get_flag</code> to handle lists (<a href="https://github.com/easybuilders/easybuild-framework/pull/4319">#4319</a>)</li> 18338<li>only add extensions in module file if there are extensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4331">#4331</a>)</li> 18339</ul> 18340</li> 18341</ul> 18342<p><strong>easyblocks</strong></p> 18343<ul> 18344<li>new custom easyblock for sympy (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2949">#2949</a>) and tensorflow-compression (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2990">#2990</a>)</li> 18345<li>minor enhancements and updates, including:<ul> 18346<li>drop unnecessary CUDA stub libraries from <code>$LIBRARY_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2793">#2793</a>)</li> 18347<li>update Score-P easyblock to use <code>--with-nocross-compiler-suite=nvhpc</code> for recent software versions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2928">#2928</a>)</li> 18348<li>unset <code>$CPPFLAGS</code>, <code>$LDFLAGS</code>, <code>$LIB</code> which may interfere with Score-P configure magic (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2928">#2928</a>)</li> 18349<li>update Clang easyblock for versions >= 16 + run tests only for final stage of bootstrap build (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2929">#2929</a>)</li> 18350<li>handle new directory structure for Intel Advisor (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2942">#2942</a>)</li> 18351<li>use <code>DCPU_BASELINE=DETECT</code> for OpenCV when default optarch compiler option is used (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2954">#2954</a>)</li> 18352<li>update MXNet easyblock + don't try to install R extension by default for MXNet >= 1.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2955">#2955</a>)</li> 18353<li>use <code>checkMCR.sh</code> to determine if we have the correct MCR for FreeSurfer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2962">#2962</a>)</li> 18354<li>
18354add options to <code>MesonNinja</code> easyblock to customize <code>build_cmd</code>, <code>install_cmd</code>, <code>builddir</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2963">#2963</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2993">#2993</a>)</li> 18355<li>add support for building CP2K with libvori support (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2967">#2967</a>)</li> 18356<li>enable system <code>pybind11</code> for PyTorch 1.10+ to make sure <code>pybind11</code> provided as dependency is used (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2968">#2968</a>)</li> 18357<li>update LLVM easyblock for LLVM v16: symlink <code>third-party</code> to <code>third-party-<version>.src</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2970">#2970</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2994">#2994</a>)</li> 18358<li>update scipy easyblock for scipy >= 1.11.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2971">#2971</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2980">#2980</a>)</li> 18359<li>update sanity check for Mesa >= 22.3 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2973">#2973</a>)</li> 18360<li>update sanity check for OpenFOAM 11 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2978">#2978</a>)</li> 18361<li>add support to <code>PerlModule</code> easyblock to customize prefix option used in installation command (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2979">#2979</a>)</li> 18362<li>update TensorFlow easyblock for v2.13 since LMDB is no longer a dependency (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2982">#2982</a>)</li> 18363<li>enhance PyTorch easyblock to print individual failed tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2983">#2983</a>)</li> 18364<li>enhance PETSc easyblock to support using custom <code>$PETSC_ARCH</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2987">#2987</a>)</li> 18365</ul> 18366</li> 18367<li>various bug fixes, including:<ul> 18368<li>correctly determine path to active binutils in TensorFlow easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2218">#2218</a>)</li> 18369<li>patch Java binaries/libraries when using alternate sysroot to ensure correct glibc & co are picked up + add custom sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2557">#2557</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2995">#2995</a>)</li> 18370<li>update OpenMPI easyblock to fix sanity check for Clang-based compilers (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2774">#2774</a>)</li> 18371<li>improve depot management in <code>JuliaPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2935">#2935</a>)</li> 18372<li>disable disk space check in STAR-CCM+ installer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2956">#2956</a>)</li> 18373<li>fix type check for <code>optarch</code> value in <code>Cargo</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2969">#2969</a>)</li> 18374<li>conditionally add <code>-Wno-unused-command-line-argument</code> to <code>$CFLAGS</code> to fix error when installing <code>imkl-FFTW</code> with RPATH (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2975">#2975</a>)</li> 18375<li>enhance <code>PythonPackage</code> easyblock to deal with <code>posix_local</code> installation scheme used by Python in recent Debian/Ubuntu versions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2977">#2977</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2988">#2988</a>)</li> 18376<li>don't add MATLAB libraries to <code>$LD_LIBRARY_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2981">#2981</a>)</li> 18377<li>enhance Mesa easyblock to append EGL vendor library directory path to <code>$__EGL_VENDOR_LIBRARY_DIRS</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2985">#2985</a>)</li> 18378<li>fix typo in TensorFlow easyblock when finding libdir of OpenSSL (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2989">#2989</a>)</li> 18379</ul> 18380</li> 18381</ul> 18382<p><strong>easyconfigs</strong></p> 18383<ul> 18384<li>added example easyconfig files for 83 new software packages:<ul> 18385<li>ALAMODE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18733">#18733</a>), AMRFinderPlus (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18559">#18559</a>), Ax (#68), bcrypt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18208">
18385#18208</a>), bench (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18656">#18656</a>), BgeeDB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18743">#18743</a>), 18386Boost.Python-NumPy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18505">#18505</a>), CatBoost (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18591">#18591</a>), centerline (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18273">#18273</a>), cffi (#7105), ChIPseeker (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18662">#18662</a>), 18387connected-components-3d (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18289">#18289</a>), cryptography (#8495), CVglasso (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18657">#18657</a>), DiffBind (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18663">#18663</a>), drmaa-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18614">#18614</a>), 18388e3nn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18304">#18304</a>), flit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18208">
18388#18208</a>), GAPPadder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18692">#18692</a>), GenerativeModels (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18451">#18451</a>), geosphere (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18659">#18659</a>), gffutils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18331">#18331</a>), 18389gkmSVM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18660">#18660</a>), hampel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18409">#18409</a>), hatchling (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18208">#18208</a>), HDF-EOS2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18297">#18297</a>), Hybpiper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18414">#18414</a>), inih (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18516">#18516</a>), 18390IsoformSwitchAnalyzeR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18664">#18664</a>), IsoQuant (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18331">#18331</a>), Jupyter-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18634">#18634</a>), JupyterNotebook (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18735">#18735</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18735">#18735</a>), 18391leafcutter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18615">#18615</a>), libleidenalg (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18548">#18548</a>), LIBSVM-Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18455">#18455</a>), libvori (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18379">#18379</a>), maturin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18405">#18405</a>), 18392meboot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18658">#18658</a>), mgen (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18402">#18402</a>), Mikado (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18614">#18614</a>), NanoCaller (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18726">#18726</a>), nbclassic (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18617">#18617</a>), ncolor (#7146), 18393nose3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18234">#18234</a>), novaSTA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18601">#18601</a>), Omnipose (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18402">#18402</a>), Optax (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18610">#18610</a>), paramiko (#1504), Parsl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18408">#18408</a>), 18394peakdetect (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18402">#18402</a>), PICRUSt2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18333">#18333</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18459">#18459</a>), Platypus-Opt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18291">#18291</a>), PortMidi (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18252">#18252</a>), pv (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16439">#16439</a>), 18395py-c3d (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18409">#18409</a>), pygame (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18252">#18252</a>), pyodbc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18334">#18334</a>), Python-bundle-PyPI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18208">
18395#18208</a>), qforce (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18456">#18456</a>), 18396RFdiffusion (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18304">#18304</a>), Rhodium (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18291">#18291</a>), ruptures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18306">#18306</a>), Sabre (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18342">#18342</a>), scGSVA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18401">#18401</a>), scib-metrics (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18734">#18734</a>), 18397scikit-plot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18377">#18377</a>), SDL2_mixer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18252">#18252</a>), SDL2_ttf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18252">#18252</a>), segment-anything (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18290">#18290</a>), sentinelsat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18367">#18367</a>), 18398setuptools-rust (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18208">
18398#18208</a>), slurm-drmaa (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18614">#18614</a>), SuAVE-biomat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18678">#18678</a>), T-Coffee (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17916">#17916</a>), 18399tensorflow-compression (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18676">#18676</a>), torchvf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18637">#18637</a>), tornado (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18511">#18511</a>), tseriesEntropy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18661">#18661</a>), TXR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18665">#18665</a>), 18400unifdef (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18427">#18427</a>), UniFrac (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18407">#18407</a>), virtualenv (#2660), WFA2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18636">#18636</a>)</li> 18401</ul> 18402</li> 18403<li>added additional easyconfigs for various supported software packages, including:<ul> 18404<li>ABINIT 9.10.3, Advisor 2023.2.0, aiohttp 3.8.5, AMD-uProf 4.1.424, Anaconda3 2023.07-2, anndata 0.9.2, 18405APR 1.7.4, APR-util 1.6.3, Arcade-Learning-Envionment 0.8.1, archspec 0.2.1, Armadillo 12.6.2, arpack-ng 3.9.0, 18406assimp 5.2.5, BAGEL 1.2.2, bam-readcount 1.0.1, Bazel 6.3.1, BCFtools 1.18, BeautifulSoup 4.12.2, BEDTools 2.31.0, 18407biom-format 2.1.15, bokeh 3.2.1, Boost 1.82.0, cairo 1.17.8, c-ares 1.19.1, ccache 4.8.3, CDO 2.2.2, CFITSIO 4.3.0, 18408Cgl 0.60.7, CharLS 2.4.2, cicero 1.3.8, Clang 16.0.6, Clp 1.17.8, Cluster-Buster 20200507, CoinUtils 2.11.9, 18409conan 1.60.2, configurable-http-proxy 4.5.5, coverage 7.2.7, CP2K 2023.1, CubeLib 4.8.1, CubeWriter 4.8.1, 18410CUDA 12.2.2, dask 2023.7.1, dcm2niix 1.0.20230411, Delly 1.1.6, dill 0.3.7, ecBuild 3.8.0, ecCodes 2.31.0, 18411ELPA 2023.05.001, exiv2 0.28.0, expecttest 0.1.5, fastparquet 2023.4.0, FFmpeg 6.0, ffnvcodec 12.0.16.0, 18412flatbuffers 23.5.26, flatbuffers-python 23.5.26, FreeSurfer 7.4.1, fsom 20151117, gc 8.2.4, GCC 13.2.0, GDB 13.2, 18413GEOS 3.12.0, gettext 0.22, GHC 9.2.2, Ghostscript 10.01.2, GLib 2.77.1, gmpy2 2.1.5, gnuplot 5.4.8, 18414GObject-Introspection 1.76.1, gperftools 2.12, Graphviz 8.1.0, gRPC 1.57.0, GST-plugins-base 1.22.5, 18415GStreamer 1.22.5, GTK3 3.24.37, GTK4 4.11.3, h4toh5 2.2.5, h5netcdf 1.2.0, h5py 3.9.0, hiredis 1.2.0, 18416Horovod 0.28.1, htop 3.2.2, HTSlib 1.18, hwloc 2.9.2, Hydra 1.3.2, hypothesis 6.82.0, Hypre 2.29.0, ICU 73.2, 18417igraph 0.10.6, iimkl/2023a, imageio 2.31.1, ImageMagick 7.1.1-15, inferCNV 1.14.2, IPython 8.14.0, ISL 0.26, 18418Julia 1.9.3, JupyterLab 4.0.5, jupyter-resource-usage 1.0.0, kma 1.4.12a, KMC 3.2.2, leidenalg 0.10.1, 18419libdrm 2.4.115, libdwarf 0.7.0, libfabric 1.19.0, libgit2 1.7.1, libGLU 9.0.3, libsndfile 1.2.2, libwpe 1.14.1, 18420libxml2 2.11.5, LittleCMS 2.15, LLVM 16.0.6, Lua 5.4.6, MACS2 2.2.9.1, magma 2.7.1, mahotas 1.4.13, makeinfo 7.0.3, 18421Mamba 23.1.0, matplotlib 3.7.2, medaka 1.8.1 + 1.9.1, Mercurial 6.4.5, Mesa 23.1.4, meson-python 0.13.2, 18422Miniconda3 23.5.2, Monocle3 1.3.1, MPC 1.3.1, MRtrix 3.0.4, MUMPS 5.6.1, MXNet 1.9.1, napari 0.4.18, ncdu 1.18, 18423netCDF 4.9.2, netCDF-Fortran 4.6.1, nettle 3.9.1, networkx 3.1, nodejs 18.17.1, nsync 1.26.0, NVHPC 23.7, 18424OpenAI-Gym 0.26.2, OpenCV 4.8.0, OpenFOAM 11, OpenImageIO 2.4.14.0, Osi 0.108.8, OTF2 3.0.3, Pango 1.50.14, 18425PAPI 7.0.1, parallel 20230722, Perl 5.38.0, Pillow 10.0.0, Pillow-SIMD 9.5.0, Pint 0.22, pkgconf 2.0.3, 18426plotly.py 5.16.0, PLUMED 2.9.0, pocl 4.0, poetry 1.5.1, protobuf 24.0, protobuf-python 4.24.0, psutil 5.9.5, 18427PuLP 2.7.0, pyBigWig 0.3.22, pybind11 2.11.1, PyCairo 1.24.0, PyGObject 3.44.1, Pylint 2.17.4, pyproj 3.6.0, 18428pyro-ppl 1.8.4, python-igraph 0.10.6, PyZMQ 25.1.1, QIIME2 2023.5.1, Qt5 5.15.10, QuantumESPRESSO 7.2, 18429rclone 1.63.1, RE2 2023-08-01, re2c 3.1, RegTools 1.0.0, RnBeads 2.14.0, RTG-Tools 3.12.1, SAMtools 1.18, 18430Scalene 1.5.26, scikit-build 0.17.6, scikit-image 0.21.0, SciPy-bundle 2023.07, Score-P 8.1, SCOTCH 7.0.3, 18431SDL2 2.28.2, SDL2_image 2.6.3, setuptools 64.0.3, SeuratWrappers 20221022, snakemake 7.32.3, SpaceRanger 2.1.0,
18432SpiecEasi 1.1.1, Stack 2.11.1, STAR 2.7.11a, SUNDIALS 6.6.0, SWIG 4.1.1, sympy 1.12, tabixpp 1.1.2, tbb 2021.10.0, 18433tbl2asn 20230713, tcsh 6.24.10, TensorFlow 2.13.0, tensorflow-probability 0.19.0, Tk 8.6.13, Tkinter 3.11.3, 18434tqdm 4.66.1, unixODBC 2.3.11, Valgrind 3.21.0, vcflib 1.0.9, VirtualGL 3.1, VisPy 0.12.2, Wayland 1.22.0, 18435WebKitGTK+ 2.40.4, wpebackend-fdo 1.14.1, wxPython 4.2.1, Xvfb 21.1.8, xxd 9.0.1696, XZ 5.4.4, Yambo 5.1.2, 18436Z3 4.12.2, zarr 2.16.0</li> 18437</ul> 18438</li> 18439<li>minor enhancements, including:<ul> 18440<li>add extensions to recent R-bundle-Bioconductors easyconfigs: UCell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18281">#18281</a>), decoupleR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18399">#18399</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18552">#18552</a>), RnBeads (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18682">#18682</a>)</li> 18441<li>add extensions to recent R easyconfigs: tabletools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18510">#18510</a>), flextables (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18719">#18719</a>)</li> 18442<li>add test for easyconfig file permissions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18647">#18647</a>)</li> 18443<li>simplify build and install options for Ghostscript (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18750">#18750</a>)</li> 18444</ul> 18445</li> 18446<li>various bug fixes, including:<ul> 18447<li>set <code>$JULIA_DEPOT_PATH</code> in Julia easyconfigs with default value (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17976">#17976</a>)</li> 18448<li>remove superflous dependencies from Horovod easyconfig on top of PyTorch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18262">#18262</a>)</li> 18449<li>disable building documentation for libsigc++ 2.10.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18301">#18301</a>)</li> 18450<li>use MCR dependency in FreeSurfer 7.3.2 and 7.4.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18303">#18303</a>)</li> 18451<li>add <code>hpctestlib</code> to the <code>$PYTHONPATH</code> in ReFrame 4.2.0 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18320">#18320</a>)</li> 18452<li>fix installation of Python bindings for recent Arrow easyconfigs by adding <code>--no-build-isolation</code> to <code>pip install</code> command (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18348">#18348</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18432">#18432</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18440">#18440</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18441">#18441</a>)</li> 18453<li>add/fix patches for PyTorch 1.13.1 w/ foss/2022a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18371">#18371</a>)</li> 18454<li>add missing nbclassic extension to jupyter-server 1.21.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18389">#18389</a>)</li> 18455<li>fix batchspawner for JupyterHub 3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18390">#18390</a>)</li> 18456<li>fix compiler flags and toolchain options for ScaLAPACK 2.1.0 + 2.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18396">#18396</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18397">#18397</a>)</li> 18457<li>add patch to fix CUDA race condition problem for Score-P v8.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18411">#18411</a>)</li> 18458<li>add <code>-DABSL_PROPAGATE_CXX_STD=ON</code> to recent Abseil easyconfigs (required for PyTorch) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18413">#18413</a>)</li> 18459<li>add missing patches for PyTorch 1.12.0 w/ foss/2022a (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18430">#18430</a>)</li> 18460<li>fix regression in GCC 12.1 + 12.2 with wrong warnings (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18434">#18434</a>)</li> 18461<li>
18461add patch for LIBSVM 3.30 to pass <code>$CFLAGS</code> + <code>$LDFLAGS</code> and run tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18454">#18454</a>)</li> 18462<li>add patch for Automake 1.16.5 to fix help2man error (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18468">#18468</a>)</li> 18463<li>consistently use ON/OFF for -DBUILD_SHARED_LIBS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18484">#18484</a>)</li> 18464<li>add missing patches for PyTorch 1.12.0 w/ <code>foss/2022a</code> + CUDA 11.7.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18491">#18491</a>)</li> 18465<li>add patches to fix PyTorch 1.12.1 + 1.13.1 on POWER on POWER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18489">#18489</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18490">#18490</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18492">#18492</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18493">#18493</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18494">#18494</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18500">#18500</a>)</li> 18466<li>add patch to fix flaky <code>test_jit_legacy</code> test for PyTorch 1.13.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18500">#18500</a>)</li> 18467<li>add alternative checksum for Extrae v4.0.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18564">#18564</a>)</li> 18468<li>remove appending of <code>$__EGL_VENDOR_LIBRARY_DIRS</code> in recent Mesa easyconfigs, since Mesa easyblock now appends to it (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18630">#18630</a>)</li> 18469<li>correct <code>dirs</code> in <code>sanity_check_paths</code> in template easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18635">#18635</a>)</li> 18470<li>set <code>$MUJOCO_PY_FORCE_CPU</code> to avoid that mujoco-py checks for nvidia-smi and aborts installation because <code>/usr/lib/nvidia</code> is not in <code>$LD_LIBRARY_PATH</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18641">#18641</a>)</li> 18471<li>fix sanity check for ccache by setting <code>LC_ALL=C</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18677">#18677</a>)</li> 18472<li>make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18680">#18680</a>)</li> 18473<li>strip out hardcoded <code>-march=native</code> used by RapidJSON 1.1.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18725">#18725</a>)</li> 18474<li>disable detection of Dbus broker for <code>at-spi2-core</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18727">#18727</a>)</li> 18475<li>make sure that <code>moduleclass</code> is set in all easyconfig files (and is not set to default <code>base</code> module class) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18739">#18739</a>)</li> 18476<li>add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18746">#18746</a>)</li> 18477<li>add patch for PMIx 4.x to use <code>lchown</code> so links are not followed (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18755">#18755</a>)</li> 18478</ul> 18479</li> 18480<li>other changes:<ul> 18481<li>update <code>Java/11</code> wrapper to Java/11.0.20 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18435">#18435</a>)</li> 18482<li>use custom easyblock for recent sympy easyconfigs to prevent test failures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18428">#18428</a>)</li> 18483<li>use <code>GCC/12.2.0</code> toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with <code>GCCcore/12.2.0</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18501">#18501</a>)</li> 18484<li>disable wx support in gnuplot 5.4.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18648">#18648</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18691">#18691</a>)</li> 18485<li>filter out template + archived easyconfigs when determining changed easyconfigs in PRs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18753">
18485#18753</a>)</li> 18486</ul> 18487</li> 18488</ul> 18489<h2 id="release_notes_eb480">EasyBuild v4.8.0 (7 July 2023)<a class="headerlink" href="#release_notes_eb480" title="Permanent link">¶</a></h2> 18490<p>feature release</p> 18491<p><strong>framework</strong></p> 18492<ul> 18493<li>various enhancements, including:<ul> 18494<li>use version suffixes in PR title instead of Python versions when using <code>--new-pr</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4253">#4253</a> + <a href="https://github.com/easybuilders/easybuild-framework/pull/4286">#4286</a>)</li> 18495<li>add script to find updated ECs for installed module (<a href="https://github.com/easybuilders/easybuild-framework/pull/4271">#4271</a>)</li> 18496</ul> 18497</li> 18498<li>various bug fixes, including:<ul> 18499<li>fix regex for extracting glibc version from output of '<code>ldd --version</code>' in Gentoo Linux (<a href="https://github.com/easybuilders/easybuild-framework/pull/4290">#4290</a>)</li> 18500<li>allow versionsuffix to be set to None in <code>det_full_ec_version</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4292">#4292</a>)</li> 18501</ul> 18502</li> 18503<li>other changes:<ul> 18504<li>stop running tests with Python 2.7 since it is no longer supported in GitHub Action (<a href="https://github.com/easybuilders/easybuild-framework/pull/4267">#4267</a>)</li> 18505<li>replace <code>imp.load_source</code> by leveraging <code>importlib.util.module_from_spec</code> when using Python 3 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4280">#4280</a>)</li> 18506</ul> 18507</li> 18508</ul> 18509<p><strong>easyblocks</strong></p> 18510<ul> 18511<li>add <code>PerlBundle</code> generic easyblock for installing a bundle of Perl modules (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2945">#2945</a>)</li> 18512<li>add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if <code>--rpath</code> is used (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2952">#2952</a>)</li> 18513<li>minor enhancements and updates, including:<ul> 18514<li>add support for NVIDIA Hopper CC 9.0 in LAMMPS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2941">#2941</a>)</li> 18515<li>add support for <code>install_cmds</code> in <code>Binary</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2953">#2953</a>)</li> 18516</ul> 18517</li> 18518<li>various bug fixes, including:<ul> 18519<li>patch CMake's <code>UnixPaths.cmake</code> script if <code>--sysroot</code> is set (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2248">#2248</a>)</li> 18520<li>fix incorrect <code>sanity_check_step</code> for torchvision (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2938">#2938</a>)</li> 18521<li>update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2944">#2944</a>)</li> 18522<li>improve handling of <code>optarch</code> in <code>Cargo</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2947">#2947</a>)</li> 18523<li>reset modules loaded by <code>PythonPackage</code> to let <code>ExtensionEasyBlock</code> handle <code>multi_deps</code> correctly (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2951">#2951</a>)</li> 18524</ul> 18525</li> 18526<li>other changes:<ul> 18527<li>stop running tests with Python 2.7 since it is no longer supported in GitHub Actions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2943">#2943</a>)</li> 18528</ul> 18529</li> 18530</ul> 18531<p><strong>easyconfigs</strong></p> 18532<ul> 18533<li>added easyconfigs for <code>foss/2023a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18264">#18264</a>) and <code>intel/2023a</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18275">#18275</a>) common toolchains</li> 18534<li>added example easyconfig files for 76 new software packages:<ul> 18535<li>3d-dna (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9258">#9258</a>), affinity (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18051">#18051</a>), AIMAll (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13153">#13153</a>), alleleIntegrator (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17923">#17923</a>), AlphaPulldown (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17774">#17774</a>), 18536 ASCAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17923">#17923</a>), ASF-SearchAPI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18179">#18179</a>), ATAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18213">#18213</a>), AutoDockSuite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9678">#9678</a>), axel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10961">#10961</a>), BayesPrism (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17885">#17885</a>), 18537 BGC-Bayesian-genomic-clines (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18005">#18005</a>), CalculiX-CrunchiX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16805">#16805</a>), CASA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18055">#18055</a>), cctbx-base (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17774">#17774</a>), 18538 Circuitscape (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16720">
18538#16720</a>), CppHeaderParser (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18272">#18272</a>), CuCLARK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9482">#9482</a>), cuteSV (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18077">#18077</a>), DALI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18204">#18204</a>), DaliLite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17989">#17989</a>), 18539 DEICODE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18181">#18181</a>), dm-haiku (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18013">#18013</a>), dominate (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18086">#18086</a>), dx-toolkit (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18232">#18232</a>), easel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18156">#18156</a>), ecFlow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15719">#15719</a>), 18540 EDirect (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17479">#17479</a>), FragPipe (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18161">#18161</a>), GEM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18120">#18120</a>), gemelli (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18120">#18120</a>), GLIMPSE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18163">#18163</a>), GRIDSS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18170">#18170</a>), 18541 HOOMD-blue (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18224">#18224</a>), KerasTuner (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18197">#18197</a>), LayoutParser (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18220">#18220</a>), LISFLOOD-FP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18194">#18194</a>), LuaRocks (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18073">#18073</a>), 18542 mannkendall (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18043">#18043</a>), MOB-suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16798">#16798</a>), molecularGSM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13150">#13150</a>), MONAI-Label (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18180">#18180</a>), MView (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18198">#18198</a>), 18543 NanoStat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18201">#18201</a>), oxDNA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18175">#18175</a> + <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18214">#18214</a>), pastml (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15336">#15336</a>), pbipa (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18229">#18229</a>), Perl-bundle-CPAN (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17970">#17970</a>), PheWeb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10951">#10951</a>), 18544 plinkliftover (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18136">#18136</a>), pmt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18052">#18052</a>), PyBioLib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18124">#18124</a>), Pychopper (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10344">#10344</a>), pydicom-seg (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18180">#18180</a>), 18545 pyMannKendall (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18044">#18044</a>), pypmt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18045">#18045</a>), python-mujoco (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18253">#18253</a>), pytorch-CycleGAN-pix2pix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18086">#18086</a>), 18546 PyTorch-Image-Models (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18220">#18220</a>), PyWBGT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17980">#17980</a>), Safetensors (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18220">#18220</a>), Sniffles (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18048">#18048</a>), strace (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14381">#14381</a>), 18547 Structure_threader (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18219">#18219</a>), subset-bam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18032">#18032</a>), SVclone (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18084">#18084</a>), SVIM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18071">#18071</a>
18547), Tapenade (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18109">#18109</a>), 18548 TensorFlow-Graphics (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17465">#17465</a>), timm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17787">#17787</a>), Trinotate (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18124">#18124</a>), Ultralytics (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17894">#17894</a>), visdom (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18086">#18086</a>), 18549 wrapt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18125">#18125</a>), xclip (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17055">#17055</a>), xdotool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17055">#17055</a>)</li> 18550</ul> 18551</li> 18552<li>added additional easyconfigs for various supported software packages, including:<ul> 18553<li>AGAT 1.1.0, alleleCount 4.2.1, AMS 2023.101, ANSYS 2023R1, BayesTraits 3.0.2, Bismark 0.24.1, BLAST+ 2.14.0, 18554 boto3 1.26.163, Bowtie2 2.5.1, BUSCO 5.4.7, Cellpose 2.2.2, CHERAB 1.4.0, CmdStanR 0.5.2, CNVkit 0.9.10,
18555 corner 2.2.2, CUDA 12.1.1 + 12.2.0, cuDNN 8.9.2.26, cutadapt 4.4, cuTENSOR 1.7.0.1, CVXOPT 1.3.1, Dalton 2020.1, 18556 datamash 1.8, deepTools 3.5.2, DIAMOND 2.1.8, DMTCP 3.0.0, dorado 0.3.0 + 0.3.1, dtcmp 1.1.4, duplex-tools 0.3.3, 18557 elastix 5.0.0, Emacs 28.2, emcee 3.1.4, Extrae 4.0.4, fastp 0.23.4, FlexiBLAS 3.3.1, fontconfig 2.14.2, 18558 FreeSurfer 7.4.0, freetype 2.13.0, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0, GCTA 1.94.1, GDRCopy 2.3.1, 18559 Geant4 11.1.2, Geant4-data 11.1, GetOrganelle 1.7.7.0, git 2.41.0, GMAP-GSNAP 2023-04-20, GROMACS 2023.1, 18560 hifiasm 0.19.5, Horovod 0.25.0, hwloc 2.9.1, InterProScan 5.62, IQ-TREE 2.2.2.3, ITSTool 2.0.7, JAGS 4.3.2, 18561 Julia 1.9.0, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, LMfit 1.2.1, LSD2 2.4.1, LuaJIT 2.1.0, 18562 lwgrp 1.0.5, MAGeCK 0.5.9.5, MATLAB 2023a, MaxQuant 2.4.2.0.eb, MCR R2022a.5, meshio 5.3.4, Meson 1.1.1, 18563 minimap2 2.26, MMseqs2 14-7e284, mpifileutils 0.11.1, MuJoCo 2.2.2, nanomath 1.3.0, ncbi-vdb 3.0.5, NCCL 2.18.3, 18564 Nextflow 23.04.2, ngspice 39, ont-fast5-api 4.1.1, OpenBLAS 0.3.23, OpenMPI 4.1.5, openpyxl 3.1.2, 18565 OSU-Micro-Benchmarks 7.1-1, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, patchelf 0.18.0, Perl 5.36.1, 18566 PMIx 4.2.4, POT 0.9.0, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyCalib 20230531, pycocotools 2.0.6, 18567 pyfaidx 0.7.2.1, pyiron 0.3.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, Python 3.11.3, 18568 python-parasail 1.3.4, PyTorch 1.13.1, rasterio 1.3.8, regionmask 0.10.0, Ruby 3.2.2, Rust 1.70.0, ScaFaCoS 1.0.4, 18569 seqtk 1.4, SRA-Toolkit 3.0.5, statsmodels 0.14.0, strace 5.14, Subversion 1.14.2, SUNDIALS 6.5.1, tidymodels 1.1.0, 18570 tokenizers 0.13.3, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2 + 4.30.2, UCC 1.2.0, UCC-CUDA 1.2.0, 18571 UCX 1.14.1, UCX-CUDA 1.14.1, util-linux 2.39, VASP 6.3.2, VTK 9.2.6, WhatsHap 1.7, X11 20230603, xarray 2023.4.2, 18572 XlsxWriter 3.1.2, XML-LibXML 2.0208, xorg-macros 1.20.0, zlib-ng 2.0.7</li> 18573</ul> 18574</li> 18575<li>minor enhancements, including:<ul> 18576<li>add CI check for <code>-DCMAKE_BUILD_TYPE</code>, should use <code>build_type</code> instead (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14008">#14008</a>)</li> 18577<li>enhance sanity check for recent LibTIFF easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17975">#17975</a>)</li> 18578<li>update JupyterLab v3.5.0 to set <code>$JUPYTERLAB_SETTINGS_DIR</code> and <code>$JUPYTERLAB_WORKSPACES_DIR</code> on loading of module (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17982">#17982</a>)</li> 18579<li>use custom easyblock for Rust 1.65.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18174">#18174</a>) and Rust 1.70.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18167">#18167</a>)</li> 18580<li>update easyconfig for Nextflow 23.04.2 to use <code>install_cmds</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18173">#18173</a>)</li> 18581<li>add extra packages to recent R easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18029">#18029</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18063">#18063</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18122">#18122</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18195">#18195</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18245">#18245</a>)</li> 18582<li>add extra packages to recent R-bundle-Bioconductor easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18196">#18196</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18246">#18246</a>)</li> 18583</ul> 18584</li> 18585<li>various bug fixes, including:<ul> 18586<li>add patches to fix TensorFlow 2.7.1 on POWER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16795">#16795</a>)</li> 18587<li>fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ <code>foss/2021b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17058">#17058</a>)</li> 18588<li>stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17998">#17998</a>)</li> 18589<li>
18589add pkgconfig as build dependency for nodejs , required for finding ICU dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18007">#18007</a>)</li> 18590<li>fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18030">#18030</a>)</li> 18591<li>update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18041">#18041</a>)</li> 18592<li>fix <code>--sanity-check-only</code> for MAGeCK v0.5.9.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18047">#18047</a>)</li> 18593<li>enable building static libs and check for <code>libexslt.*</code> in libxslt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18064">#18064</a>)</li> 18594<li>add <code>-pthread</code> flag for dorado (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18072">#18072</a>)</li> 18595<li>add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18087">#18087</a>)</li> 18596<li>add missing pkgconf build dependency for XML-LibXML v2.0208 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18159">#18159</a>)</li> 18597<li>update homepage for NWChem 7.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18184">#18184</a>)</li> 18598<li>update homepage for SUNDIALS 5.x and 6.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18186">#18186</a>)</li> 18599<li>add missing <code>source_urls</code> for SimpleITK (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18212">#18212</a>)</li> 18600<li>use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18230">#18230</a>)</li> 18601<li>fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18231">#18231</a>)</li> 18602<li>fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18235">#18235</a>)</li> 18603<li>use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18236">#18236</a>)</li> 18604<li>update <code>source_urls</code> for Velvet 1.2.10 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18237">#18237</a>)</li> 18605<li>use upstream patch for symbol compatibility in XZ 5.2.5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18250">#18250</a>)</li> 18606<li>update source url for pkgconf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18271">#18271</a>)</li> 18607</ul> 18608</li> 18609<li>other changes:<ul> 18610<li>stop running easyconfig unit tests with Python 2.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18006">#18006</a>)</li> 18611<li>fix toolchain for networkx-3.0 (<code>foss/2022b</code> -> <code>gfbf/2022b</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18061">#18061</a>)</li> 18612<li>remove unused PyTorch patch (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18062">#18062</a>)</li> 18613<li>allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18098">#18098</a>)</li> 18614<li>bump OpenSSL 1.1 wrapper fallback to 1.1.1u (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18188">#18188</a>)</li> 18615<li>remove default <code>separate_build_dir = True</code> and <code>build_type = 'Release'</code> from double-conversion (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18222">#18222</a>)</li> 18616<li>remove default <code>separate_build_dir = True</code> and <code>CMAKE_BUILD_TYPE=Release</code> from MariaDB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18223">#18223</a>)</li> 18617<li>
18617remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18260">#18260</a>)</li> 18618<li>change base compiler for <code>intel/2023.03</code> to <code>GCCcore/12.3.0</code> (required to use it as intel/2023a) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/18263">#18263</a>)</li> 18619</ul> 18620</li> 18621</ul> 18622<h2 id="release_notes_eb472">EasyBuild v4.7.2 (27 May 2023)<a class="headerlink" href="#release_notes_eb472" title="Permanent link">¶</a></h2> 18623<p>bugfix/update release</p> 18624<p><strong>framework</strong></p> 18625<ul> 18626<li>various enhancements, including:<ul> 18627<li>extend (experimental) support for generating container images with Apptainer (<a href="https://github.com/easybuilders/easybuild-framework/pull/3975">#3975</a>)</li> 18628<li>add default download timeout (<a href="https://github.com/easybuilders/easybuild-framework/pull/4226">#4226</a>)</li> 18629<li>make the RPATH section check with <code>readelf -d</code> in sanity check optional (<a href="https://github.com/easybuilders/easybuild-framework/pull/4249">#4249</a>)</li> 18630</ul> 18631</li> 18632<li>various bug fixes, including:<ul> 18633<li>add <code>make_extension_string</code> and <code>_make_extension_list</code> methods to <code>EasyBlock</code> class, so easyblocks can customize them (<a href="https://github.com/easybuilders/easybuild-framework/pull/3697">#3697</a>)</li> 18634<li>fix typo in condition guarding installation of GitHub token in CI workflow to run unit tests + fix broken tests related to GitHub integration features (<a href="https://github.com/easybuilders/easybuild-framework/pull/4216">#4216</a>)</li> 18635<li>fix <code>--check-github</code> as gist url now includes username (<a href="https://github.com/easybuilders/easybuild-framework/pull/4231">#4231</a>)</li> 18636<li>switch to Ubuntu 22.04 in GitHub Actions workflow to run container tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/4238">#4238</a>)</li> 18637<li>use "<code>/usr/bin/env python</code>" in <code>test_run_cmd_script</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4241">#4241</a>)</li> 18638</ul> 18639</li> 18640<li>other changes:<ul> 18641<li>print potential errors after running a command only once (<a href="https://github.com/easybuilders/easybuild-framework/pull/4065">#4065</a>)</li> 18642<li>change <code>github_*</code> template descriptions to be somewhat clearer (<a href="https://github.com/easybuilders/easybuild-framework/pull/4251">#4251</a>)</li> 18643<li>remove workflow to test bootstrap script (<a href="https://github.com/easybuilders/easybuild-framework/pull/4255">#4255</a>)</li> 18644</ul> 18645</li> 18646</ul> 18647<p><strong>easyblocks</strong></p> 18648<ul> 18649<li>new generic easyblock for installing Rust crates with cargo: <code>Cargo</code> and <code>CargoPythonPackage</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2902">#2902</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2934">#2934</a>)</li> 18650<li>minor enhancements and updates, including:<ul> 18651<li>let MATLAB easyblock raise an error if the MATLAB installation key is not provided (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2905">#2905</a>)</li> 18652<li>print message to inform that GPU package (instead of Kokkos) is used for LAMMPS (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2906">#2906</a>)</li> 18653<li>enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2915">#2915</a>)</li> 18654</ul> 18655</li> 18656<li>various bug fixes, including:<ul> 18657<li>use custom RPATH sanity check for Go packages that doesn't actually check for an RPATH section in the binary (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2913">
18657#2913</a>)</li> 18658<li>use string <code>'0'</code> to avoid problems when openssl version is not determined (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2914">#2914</a>)</li> 18659<li>update GCC easyblock to ensure that <code>--sysroot</code> is passed to linker (but only when it needs to be) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2921">#2921</a>)</li> 18660<li>add output log to MATLAB installs, actually parse for common errors (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2924">#2924</a>)</li> 18661<li>enhance Gurobi easyblock to allow using <code>$EB_GUROBI_LICENSE_FILE</code> environment variable (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2926">#2926</a>)</li> 18662<li>force building <code>torchvision</code> with CUDA support if CUDA is included as dependency by setting <code>$FORCE_CUDA</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2931">#2931</a>)</li> 18663<li>fix exec permission on files in arch bindir for COMSOL (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2932">#2932</a>)</li> 18664</ul> 18665</li> 18666</ul> 18667<p><strong>easyconfigs</strong></p> 18668<ul> 18669<li>added easyconfigs for <code>intel/2023.03</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17676">#17676</a>)</li> 18670<li>added example easyconfig files for 89 new software packages:<ul> 18671<li>AGeNT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17864">#17864</a>), anndata (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17677">#17677</a>), Annocript (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17910">#17910</a>), avro-cpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17527">#17527</a>), batchgenerators (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17833">#17833</a>), 18672 BoltzTraP2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17742">#17742</a>), Braindecode (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17913">#17913</a>), build (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17776">#17776</a>), casacore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15499">#15499</a>), Casanovo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17735">#17735</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17736">#17736</a>), 18673 CASPR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17606">#17606</a>), CellChat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17856">#17856</a>), CellOracle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17507">#17507</a>), CLIP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17782">#17782</a>), CodingQuarry (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17682">#17682</a>), ColabFold (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17751">#17751</a>), 18674 CopyKAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17646">#17646</a>), CPC2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17849">#17849</a>), cppzmq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17601">#17601</a>), dask-labextension (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17882">#17882</a>), DIALOGUE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17696">#17696</a>), DiCE-ML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17591">#17591</a>), 18675 ESPResSo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17709">#17709</a>), Evcxr-REPL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17831">#17831</a>), EZC3D (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17832">#17832</a>), funannotate (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17588">#17588</a>), FunGAP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17652">#17652</a>), GATB-Core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17635">#17635</a>), 18676 GenMap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17746">#17746</a>), GimmeMotifs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17507">#17507</a>), GLI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17793">#17793</a>), GOBNILP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17639">#17639</a>), h5netcdf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17835">#17835</a>), HD-BET (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17833">#17833</a>), 18677 HTSplotter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17369">#17369</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17586">#17586</a>), ipympl (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17613">#17613</a>), IsoSeq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17791">#17791</a>), KrakenUniq (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17569">
18677#17569</a>), LIANA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17928">#17928</a>), 18678 libWallModelledLES (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17480">#17480</a>), LoRDEC (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17635">#17635</a>), M3GNet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17555">#17555</a>), mandrake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17394">#17394</a>), mctc-lib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16760">#16760</a>), MOABB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17913">#17913</a>), 18679 MRPRESSO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17925">#17925</a>), ont-guppy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17477">#17477</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17828">#17828</a>), OptaDOS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17777">#17777</a>), PALEOMIX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17912">#17912</a>), PGPLOT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15496">#15496</a>), 18680 PICI-LIGGGHTS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17710">#17710</a>), pod5-file-format (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17776">#17776</a>), powerlaw (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17647">#17647</a>), pp-sketchlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17397">#17397</a>), 18681 py3Dmol (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17752">#17752</a>), pytesseract (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17898">#17898</a>), pytest-cpp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17966">#17966</a>), pytest-flakefinder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17966">#17966</a>), Python-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17626">#17626</a>), 18682 python-xxhash (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17844">#17844</a>), PyTorch-bundle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17540">#17540</a>), qnorm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17507">#17507</a>), R-MXM (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17667">#17667</a>), R-transport (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17642">#17642</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17968">#17968</a>), 18683 Raven (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15833">#15833</a>), ReaxFF (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17780">#17780</a>), ripunzip (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17959">#17959</a>), RPostgreSQL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17739">#17739</a>), rustworkx (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17857">#17857</a>), Scalene (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16472">#16472</a>), 18684 sceasy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17677">#17677</a>), SCIP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17639">#17639</a>), Simple-DFTD3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16760">#16760</a>), SMAP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17672">#17672</a>), SoPlex (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17639">#17639</a>), SoupX (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17851">#17851</a>), 18685 spektral (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15551">#15551</a>), synthcity (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17623">#17623</a>), sysbench (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17643">#17643</a>), tantan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17681">#17681</a>), thirdorder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17703">#17703</a>), TOPAS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17553">#17553</a>), 18686 Triplexator (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17866">#17866</a>), tRNAscan-SE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17680">#17680</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17800">#17800</a>), turbinesFoam (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17917">#17917</a>), unicore-uftp (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17665">#17665</a>), vispr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17606">#17606</a>), 18687 WCSLIB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15497">#15497</a>), ZIMPL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17639">#17639</a>)</li> 18688</ul> 18689</li> 18690<li>
18690added additional easyconfigs for various supported software packages, including:<ul> 18691<li>Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21, 18692 Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1, 18693 bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11, 18694 Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1, 18695 CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0, 18696 Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0, 18697 freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4, 18698 googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0, 18699 Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5, 18700 L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1, 18701 libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12, 18702 libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4, 18703 libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6, 18704 mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4, 18705 netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0, 18706 Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1, 18707 pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0, 18708 pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0, 18709 pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01, 18710 ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4, 18711 ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1, 18712 ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0, 18713 Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0, 18714 Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5</li> 18715</ul> 18716</li> 18717<li>minor enhancements, including:<ul> 18718<li>add <code>local::lib</code> extension to Perl 5.34.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17679">#17679</a>)</li> 18719<li>install shared libraries for tesseract (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17721">#17721</a>)</li> 18720<li>add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17738">#17738</a>)</li> 18721<li>add extensions to R-bundle-Bioconductor 3.15: deepSNV (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17852">#17852</a>)</li> 18722<li>add extensions to R 4.2.x: dlm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17640">#17640</a>), PMA + unikn + ppcor (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17695">#17695</a>), tvem (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17729">#17729</a>), epitools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17852">#17852</a>)</li> 18723</ul> 18724</li> 18725<li>various bug fixes, including:<ul> 18726<li>add patch for UCC 1.1.0 for multiple component paths (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17255">#17255</a>)</li> 18727<li>fix configure step for ELSI 2.5.0+ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17288">#17288</a>)</li> 18728<li>switch bamtofastq to <code>Cargo</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17595">#17595</a>)</li> 18729<li>
18729add missing OpenJPEG dependency for recent GDAL versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17599">#17599</a>)</li> 18730<li>fix CodAn <code>bin/*</code> executable permissions for all users #(<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17607">#17607</a>)</li> 18731<li>upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade <code>jupyterlab_widgets</code> extensions in IPython v8.5.0 to fix known issues (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17612">#17612</a>)</li> 18732<li>add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17618">#17618</a>)</li> 18733<li>add alternative checksum for MONAI 1.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17628">#17628</a>)</li> 18734<li>fix paths to Perl modules in MAKER v3.01.04 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17629">#17629</a>)</li> 18735<li>add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17631">#17631</a>)</li> 18736<li>explicitely disable mpi/python in Boost (<code>intel-compilers/2021.4.0</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17638">#17638</a>)</li> 18737<li>remove LLVM build dependency from TensorFlow easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1764
187371">#17641</a>)</li> 18738<li>update easyconfig for Longshot 0.4.5 to use <code>Cargo</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17666">#17666</a>)</li> 18739<li>fix homepage in ELPA easyconfigs (due to switch to new domain) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17697">#17697</a>)</li> 18740<li>add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17713">#17713</a>)</li> 18741<li>use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17717">#17717</a>)</li> 18742<li>exclude flaky <code>test_optim</code> for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17726">#17726</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17730">#17730</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17731">#17731</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17737">#17737</a>)</li> 18743<li>add missing PCRE dependency for InterProScan 5.55-88.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17762">#17762</a>)</li> 18744<li>fix building Python bindings of DGL, requires static libs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17764">#17764</a>)</li> 18745<li>only use QEF gitlab source url for QuantumESPRESSO itself (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17766">#17766</a>)</li> 18746<li>add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17779">#17779</a>)</li> 18747<li>fix broken source URL for AOCC 4.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17794">#17794</a>)</li> 18748<li>specify <code>source_urls</code> inside <code>exts_default_options</code> in Seurat easyconfigs to ensure correct name expansion for the archived packages (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17830">#17830</a>)</li> 18749<li>add Doxygen build dependency to X11 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17842">#17842</a>)</li> 18750<li>FLINT needs BLAS so move it up from GCC level (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17868">#17868</a>)</li> 18751<li>fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17875">#17875</a>)</li> 18752<li>add dependency on PycURL to easyconfig for JupyterHub 3.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17887">#17887</a>)</li> 18753<li>add historical repo paths to install command for old versions of texlive (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17893">#17893</a>)</li> 18754<li>add missing FastTreeMP binary for FastTree (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17897">#17897</a>)</li> 18755<li>add checksum for arm64 source tarball for Go 1.18.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17903">#17903</a>)</li> 18756<li>add patch to fix <code>test_quantization</code> in PyTorch 1.12.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17908">#17908</a>)</li> 18757<li>add make 4.3 as build dependency for recent OpenBLAS versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17924">#17924</a>)</li> 18758</ul> 18759</li> 18760<li>other changes:<ul> 18761<li>bump versions in Java wrappers to latest builds that include <code>ppc64le</code>: <code>Java/8.362</code>, <code>Java/11.0.8</code>, <code>Java/17.0.6</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17775">#17775</a>)</li> 18762<li>move Arb and polymake to <code>gfbf</code>/<code>foss</code> since FLINT is now at <code>gfbf</code>/<code>foss</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17869">#17869</a>)</li> 18763</ul> 18764</li> 18765</ul> 18766<h2 id="release_notes_eb471">EasyBuild v4.7.1 (20 March 2023)<a class="headerlink" href="#release_notes_eb471" title="Permanent link">¶</a></h2> 18767<p>bugfix/update release</p> 18768<p><strong>framework</strong></p> 18769<ul> 18770<li> 18771<p>various enhancements, including:</p> 18772<ul> 18773<li>add option to make <code>sanity_check_paths</code> arch dependent (<a href="https://github.com/easybuilders/easybuild-framework/pull/3845">#3845</a>)</li> 18774<li>
18774add support for <code>%(start_dir)s</code> easyconfig template (<a href="https://github.com/easybuilders/easybuild-framework/pull/4073">#4073</a>)</li> 18775<li>add Ubuntu friendly package naming scheme <code>EasyBuildDebFriendlyPNS</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4115">#4115</a>)</li> 18776<li>allow to directly import constants from <code>easybuild.framework.easyconfig.constants</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4144">#4144</a>)</li> 18777<li>accept single source as dict and single checksum in <code>check_checksums_for</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4180">#4180</a>)</li> 18778<li>add pre/post extension hook that is triggered before/after individual extension installations (<a href="https://github.com/easybuilders/easybuild-framework/pull/4193">#4193</a>)</li> 18779<li>enforce absolute paths as start dir of extensions (<a href="https://github.com/easybuilders/easybuild-framework/pull/4196">#4196</a>)</li> 18780<li>print warning when non-existing <code>start_dir</code> is specified for extension (<a href="https://github.com/easybuilders/easybuild-framework/pull/4201">#4201</a>)</li> 18781<li>add support to silence deprecation warning for easyconfigs and toolchains (<a href="https://github.com/easybuilders/easybuild-framework/pull/4207">#4207</a>)</li> 18782<li>skip directories when fixing shebangs (<a href="https://github.com/easybuilders/easybuild-framework/pull/4209">#4209</a>)</li> 18783<li>add support for <code>modunloadmsg</code> easyconfig parameter (<a href="https://github.com/easybuilders/easybuild-framework/pull/4223">#4223</a>)</li> 18784</ul> 18785</li> 18786<li> 18787<p>various bug fixes, including:</p> 18788<ul> 18789<li>fix use of <code>locate</code> in <code>check_os_dependency</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4166">#4166</a>)</li> 18790<li>add <code>VERSION</code> to <code>easybuild.easyblocks</code> namespace in test sandbox (<a href="https://github.com/easybuilders/easybuild-framework/pull/4171">#4171</a>)</li> 18791<li>also apply filter to asyncprocess test subsuite (<a href="https://github.com/easybuilders/easybuild-framework/pull/4172">#4172</a>)</li> 18792<li>don't use deprecated <code>SafeConfigParser</code> when running with Python 3.x (<a href="https://github.com/easybuilders/easybuild-framework/pull/4173">#4173</a>)</li> 18793<li>update CI workflows to run <code>apt-get update</code> if installation of packages via <code>apt-get install</code> failed, likely due to stale apt cache (<a href="https://github.com/easybuilders/easybuild-framework/pull/4176">#4176</a>)</li> 18794<li>fixes for <code>findPythonDeps</code> script (<a href="https://github.com/easybuilders/easybuild-framework/pull/4179">#4179</a>)</li> 18795<li>check type of <code>versionsuffix</code> value in <code>det_full_ec_version</code>, and raise useful error message if it's not a string (<a href="https://github.com/easybuilders/easybuild-framework/pull/4184">#4184</a>)</li> 18796<li>avoid GC3Pie deprecation warning (<a href="https://github.com/easybuilders/easybuild-framework/pull/4185">#4185</a>)</li> 18797<li>correctly restore <code>sys.path</code> in tests (<a href="https://github.com/easybuilders/easybuild-framework/pull/4186">#4186</a>)</li> 18798<li>suppress output of <code>--skip-test-step</code> test (<a href="https://github.com/easybuilders/easybuild-framework/pull/4187">#4187</a>)</li> 18799<li>fix flaky <code>test_search_file</code> due to accidental matches for <code>.*C++</code> search pattern (<a href="https://github.com/easybuilders/easybuild-framework/pull/4190">#4190</a>)</li> 18800<li>silence <code>distutils</code> deprecation warnings (<a href="https://github.com/easybuilders/easybuild-framework/pull/4204">#4204</a>)</li> 18801<li>improve handling of <code>start_dir</code> and add tests for cases where either <code>ext_dir</code> or initial <code>start_dir</code> or both are unset or <code>None</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4206">#4206</a>)</li> 18802<li>restore initial environment before processing each easystack item (<a href="https://github.com/easybuilders/easybuild-framework/pull/4213">#4213</a>)</li> 18803<li>make <code>test_help_long</code> work on small terminals (<a href="https://github.com/easybuilders/easybuild-framework/pull/4218">#4218</a>)</li> 18804</ul> 18805</li> 18806<li> 18807<p>other changes:</p> 18808<ul> 18809<li>use better test assertions by replacing use of <code>assertFalse</code>/<code>assertTrue</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4170">#4170</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4205">#4205</a>)</li> 18810<li>remove Travis CI configuration file (<a href="https://github.com/easybuilders/easybuild-framework/pull/4174">#4174</a>)</li> 18811<li>filter out deprecation warnings for platform.dist in <code>get_os_version</code> and <code>platform.linux_distribution</code> in <code>get_os_name</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4175">#4175</a>)</li> 18812<li>only give read permissions in GitHub Actions workflows (<a href="https://github.com/easybuilders/easybuild-framework/pull/4182">#4182</a>)</li> 18813<li>fix website/docs links in <code>README</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4199">#4199</a>)</li> 18814<li>only print "<code>default:</code>" for configuration option of <code>strlist</code> type if default is not empty (<a href="https://github.com/easybuilders/easybuild-framework/pull/4220">#4220</a>)</li> 18815</ul> 18816</li> 18817</ul> 18818<p><strong>easyblocks</strong></p> 18819<ul> 18820<li> 18821<p>minor enhancements and updates, including:</p> 18822<ul> 18823<li>fix TensorFlow easyblock for new versions of Bazel & TensorFlow (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2854">#2854</a>)</li> 18824<li>make NAMD easyblock aware of <code>(pre)testopts</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2856">#2856</a>)</li> 18825<li>update <code>MesonNinja</code> easyblock for Meson >=0.64.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2861">#2861</a>)</li> 18826<li>update scipy easyblock for scipy >= 1.9.0 to use <code>meson</code>/<code>ninja</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2862">#2862</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2903">#2903</a>)</li> 18827<li>modify logic in QScintilla easyblock to find the PyQt5 <code>sipdir</code> in more places (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2868">#2868</a>)</li> 18828<li>
18828add <code>testinstall</code> custom easyconfig parameter to <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2872">#2872</a>)</li> 18829<li>use <code>-x</code> option for "<code>go install</code>" in <code>GoPackage</code> generic easyblock, to print commands as they are executed (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2878">#2878</a>)</li> 18830<li>allow disabling pybind11 tests with <code>runtest = False</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2892">#2892</a>)</li> 18831<li>call parent <code>post_install_step</code> in <code>EasyBuildMeta</code> easyblock (so <code>postinstallcmds</code> are taken into account) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2893">#2893</a>)</li> 18832<li>update and enhance Maple easyblock for recent versions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2895">#2895</a>)</li> 18833<li>relax glob pattern to find Mathematica install script (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2896">#2896</a>)</li> 18834<li>implement CUDA support in the ELPA EasyBlock & fix <code>$CPP</code> configure issue on newer ELPA versions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2898">#2898</a>)</li> 18835<li>update Trilinos easyblock to allow disabling of building tests and forward deps + support Trilinos v13.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2900">#2900</a>)</li> 18836<li>enhance Python easyblock to create non-versioned symlink for <code>python-config</code> + check for <code>bin/python</code> and <code>bin/python-config</code> in sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2904">#2904</a>)</li> 18837</ul> 18838</li> 18839<li> 18840<p>various bug fixes, including:</p> 18841<ul> 18842<li>do not use <code>-g77</code>
18842 option when installing NVHPC 22.9+ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2819">#2819</a>)</li> 18843<li>check that <code>sanity_check_module_loaded</code> attribute exists before querying it in <code>PythonPackage</code> easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2865">#2865</a>)</li> 18844<li>fix <code>$JULIA_DEPOT_PATH</code> in installation of multiple <code>JuliaPackage</code> extensions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2869">#2869</a>)</li> 18845<li>fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2873">#2873</a>)</li> 18846<li>show template values of <code>exts_default_options</code> in <code>PythonBundle</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2874">#2874</a>)</li> 18847<li>fix missing initialization of <code>CMakeMake</code> in <code>CMakePythonPackage</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2876">#2876</a>)</li> 18848<li>fix error when failing <code>pip</code> version check during <code>PythonPackage</code> sanity check (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2877">#2877</a>)</li> 18849<li>handle templating correctly in <code>CMakeMake</code> when playing with <code>configopts</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2882">#2882</a>)</li> 18850<li>avoid crash in test step of PyTorch easyblock if <code>runtest</code> is not a command (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2883">#2883</a>)</li> 18851<li>fix check configure option in FlexiBLAS easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2886">#2886</a>)</li> 18852<li>use older <code>ncgen -H</code> for older netCDF (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2889">#2889</a>)</li> 18853<li>fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2897">#2897</a>)</li> 18854</ul> 18855</li> 18856<li> 18857<p>other changes:</p> 18858<ul> 18859<li>only give read permissions in GitHub Actions workflows (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2863">#2863</a>)</li> 18860<li>use start dir of extension to install R packages (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2867">#2867</a>)</li> 18861<li>fix website/docs links in <code>README</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2870">#2870</a>)</li> 18862<li>add deprecation notice to <code>RPackage</code> extensions with relative paths in <code>start_dir</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2879">#2879</a>)</li> 18863</ul> 18864</li> 18865</ul> 18866<p><strong>easyconfigs</strong></p> 18867<ul> 18868<li> 18869<p>added example easyconfig files for 99 new software packages:</p> 18870<ul> 18871<li>astro-tulips (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17263">#17263</a>), BA3-SNPS-autotune (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17248">#17248</a>), BayesAss3-SNPs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17247">#17247</a>), Block (#27), CatLearn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14940">#14940</a>), 18872CDFlib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17133">#17133</a>), Cellpose (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13703">#13703</a>), CheckM-Database (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17462">#17462</a>), chemprop (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17261">#17261</a>), cimfomfa (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17268">#17268</a>), conan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17326">#17326</a>), 18873cooler (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17328">#17328</a>), crossguid (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16207">#16207</a>), cuSPARSELt (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17141">#17141</a>), cython-blis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17544">#17544</a>), DBCSR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17170">#17170</a>), dclone (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17225">#17225</a>), 18874DensPart (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17473">#17473</a>), Deprecated (#1248), DLPack (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17311">#17311</a>), DMLC-Core (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17311">#17311</a>), dorado (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17195">#17195</a>), duplex-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17497">#17497</a>), 18875eQuilibrator (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16812">#16812</a>), fastai (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16985">#16985</a>), fastjet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17367">#17367</a>), fastjet-contrib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17377">#17377</a>), ffnvcodec (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17271">#17271</a>), 18876finder (#1917), flowFDA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17495">#17495</a>), gbasis (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17473">#17473</a>), genomepy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17506">#17506</a>), Giotto-Suite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17207">#17207</a>), GKeyll (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16044">#16044</a>), 18877GraphDB (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17280">#17280</a>), graphviz-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17352">#17352</a>), grid (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17473">#17473</a>), GUSHR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16905">#16905</a>), Health-GPS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17434">#17434</a>), HepMC3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17341">#17341</a>), 18878HiCMatrix (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17330">#17330</a>), Inferelator (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17223">#17223</a>), iodata (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17473">#17473</a>), irodsfs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17486">#17486</a>), jupyter-contrib-nbextensions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17270">#17270</a>), 18879jupyterlab-lmod (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16563">#16563</a>), jupyterlmod (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16563">#16563</a>), kb-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17260">#17260</a>), kineto (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17194">#17194</a>), KMCP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17267">#17267</a>), 18880krbalancing (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17325">#17325</a>), Lace (#954), LASSO-Python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17510">#17510</a>), libemf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16188">#16188</a>), loomR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14518">#14518</a>), MAKER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17345">#17345</a>), 18881methylartist (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17264">#17264</a>), nanoflann (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17311">#17311</a>), netMHCII (#9741), NEXUS-CL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17350">#17350</a>), nichenetr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17524">#17524</a>), 18882Parallel-Hashmap (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17311">#17311</a>), pdsh (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17139">#17139</a>), Perseus (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17210">#17210</a>), PfamScan (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17530">#17530</a>), Phenoflow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17495">#17495</a>), PIRATE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17275">#17275</a>), 18883PLAMS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17473">#17473</a>), plot1cell (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17498">#17498</a>), pybinding (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17137">#17137</a>), pyperf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17063">#17063</a>), pyslim (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17150">#17150</a>), 18884pytest-rerunfailures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17295">#17295</a>), pytest-shard (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17295">#17295</a>), python-louvain (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17207">#17207</a>), PyTorch-Ignite (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15491">#15491</a>), 18885PyVCF3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17519">#17519</a>), R2jags (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17226">#17226</a>), rapidcsv (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16211">#16211</a>), rapidNJ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17399">#17399</a>), Rivet (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17380">#17380</a>), rmarkdown (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17189">#17189</a>), 18886scArches (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17069">#17069</a>), scHiCExplorer (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17334">#17334</a>), scib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17142">#17142</a>), SeaView (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17385">#17385</a>), silhouetteRank (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17207">#17207</a>), 18887siscone (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17342">#17342</a>), smfishHmrf (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17207">#17207</a>), sparse-neighbors-search (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17329">#17329</a>), SpatialDE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17207">#17207</a>), sradownloader (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17188">
18887#17188</a>), 18888stardist (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17215">#17215</a>), Strainberry (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17522">#17522</a>), toil (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17098">#17098</a>), vConTACT2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17372">#17372</a>), VirSorter2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17371">#17371</a>), 18889vitessce-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17472">#17472</a>), vitessceR (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17525">#17525</a>), YODA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17343">#17343</a>)</li> 18890</ul> 18891</li> 18892<li> 18893<p>added additional easyconfigs for various supported software packages, including:</p> 18894<ul> 18895<li>AlphaFold 2.3.0, Anaconda3 2022.10, angsd 0.940, archspec 0.2.0, Armadillo 11.4.3, AUGUSTUS 3.5.0, bcbio-gff 0.7.0, 18896BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Biopython 1.81, BLAT 3.7, Blender 3.4.1, 18897Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0, 18898Cereal 1.3.2, CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8, 18899CUDA 12.1.0, cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6, 18900DIRAC 23.0, dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0, 18901FabIO 0.14.0, FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4, 18902GDAL 3.6.2, GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1, 18903googletest 1.12.1, GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1, 18904h5py 3.8.0, HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2, 18905Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0, 18906imkl-FFTW 2023.0.0, impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5, 18907JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2, 18908Kent_tools 442, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0, 18909libtirpc 1.3.3, libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0, 18910MATIO 1.5.23, MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, MDAnalysis 2.4.2, 18911Miniconda3 22.11.1, mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14, 18912mygene 3.2.2, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1, 18913networkx 3.0, Nextflow 22.10.6, nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0, 18914OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0, 18915PIPITS 3.0, PLINK 2.00a3.7, plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0, 18916presto 1.0.0-20230113, PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2, 18917py-cpuinfo 9.0.0, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0, 18918PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1, 18919QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, R 4.2.2, Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1, 18920ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0, 18921SAMtools 1.17, Scalasca 2.6.1, scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0, 18922snakemake 7.22.0, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1, 18923SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3, 18924Tkinter 3.10.8, tqdm 4.64.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only,
18925Unidecode 1.3.6, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226, 18926Xerces-C++ 3.2.4, XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6</li> 18927</ul> 18928</li> 18929<li> 18930<p>minor enhancements, including:</p> 18931<ul> 18932<li>add additional extensions to R 4.2.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17043">#17043</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17125">#17125</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17224">#17224</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17493">#17493</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17523">#17523</a>)</li> 18933<li>add additional extensions to Bioconductor 3.15 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17126">#17126</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17315">#17315</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17494">#17494</a>)</li> 18934<li>add sanity check command to OpenMolcas v22.10 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17128">#17128</a>)</li> 18935<li>add <code>Set::Object</code> and <code>Heap::Fibonacci</code> extensions to Perl 5.32.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17151">#17151</a>)</li> 18936<li>add additional extensions to Python 3.10.8 (required for scipy test suite) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17159">#17159</a>)</li> 18937<li>enhance OpenFold 1.0.1 for standalone usage (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17206">#17206</a>)</li> 18938<li>add SDL2 dependency for FFmpeg 5.0.1 to build <code>ffplay</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17213">#17213</a>)</li> 18939<li>set <code>$JULIA_DEPOT_PATH</code> and <code>$JULIA_HISTORY</code> in Julia easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17216">#17216</a>)</li> 18940<li>add <code>Devel::Size</code> + <code>Math::Utils</code> extension to recent Perl easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17246">#17246</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17466">#17466</a>)</li> 18941<li>combine errors of extension patch check into a single failure (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17286">#17286</a>)</li> 18942<li>add case-insensitive name clash test (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17303">#17303</a>)</li> 18943<li>add ffnvcodec build dependency to all recent FFmpeg easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17316">#17316</a>)</li> 18944<li>use '<code>import deap.base</code>' in sanity check for deap extension in <code>SciPy-bundle</code> 2022.05 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17429">#17429</a>)</li> 18945<li>add source URL to cuDNN 8.8 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17439">#17439</a>)</li> 18946<li>add missing zstd dep to Boost (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17482">#17482</a>)</li> 18947</ul> 18948</li> 18949<li> 18950<p>various bug fixes, including:</p> 18951<ul> 18952<li>fix <code>postinstallcmds</code> and clarify download instructions for netMHC + netMHCpan 4.0a (#9739, #9740)</li> 18953<li>fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15845">#15845</a>)</li> 18954<li>add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17077">#17077</a>)</li> 18955<li>fix build of TensorFlow 2.5+ on <code>aarch64</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17101">#17101</a>)</li> 18956<li>explictely download <code>qe-gipaw</code> source tarball from <code>qe-gipaw</code> GitHub repository in QuantumESPRESSO 7.1 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17129">#17129</a>)</li> 18957<li>
18957add patch for <code>GCCcore</code> 11.1.0 + 11.2.0 to fix AVX2 bug (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17135">#17135</a>)</li> 18958<li>add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17140">#17140</a>)</li> 18959<li>fix source URL for p7zip v17.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17144">#17144</a>)</li> 18960<li>add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17165">#17165</a>)</li> 18961<li>remove dependency on Pillow from scikit-bio v0.5.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17178">#17178</a>)</li> 18962<li>correctly specify path to libfabric installation prefix in PMIx 4.1.0 easyconfig (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17204">#17204</a>)</li> 18963<li>use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17221">#17221</a>)</li> 18964<li>fix CMake print summary for long hostnames for NECI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17230">#17230</a>)</li> 18965<li>add missing pmix patch to OpenMPI 4.1.1 easyconfig used in <code>iomkl/2021a</code> and <code>iomkl/2021b</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17240">#17240</a>)</li> 18966<li>include required <code>stereo_chemical_props.txt</code> for OpenFold 1.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17242">#17242</a>)</li> 18967<li>add patch for PAPI 7.0.0 to fix compilation error (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17244">#17244</a>)</li> 18968<li>also update <code>$PERL5LIB</code> for RepeatMasker v4.1.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17245">#17245</a>)</li> 18969<li>add alternative <code>source_url</code> for MariaDB > 10.4 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17250">#17250</a>)</li> 18970<li>remove use of rysnc in building <code>Kent_tools</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17252">#17252</a>)</li> 18971<li>add missing pkgconf build dependency in recent libxslt easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17254">#17254</a>)</li> 18972<li>add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17257">#17257</a>)</li> 18973<li>fix <code>postinstallcmds</code> in shovill easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17279">#17279</a>)</li> 18974<li>allow multiple easyconfigs with same name if they differ by CUDA version included in <code>versionsuffix</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17289">#17289</a>)</li> 18975<li>remove duplicate SlamDunk easyconfig using lowercase name (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17301">#17301</a>)</li> 18976<li>use <code>https</code> in homepage + source URL for GenomeThreader 1.7.3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17338">#17338</a>)</li> 18977<li>consistently use Check capitailisation (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17351">#17351</a>)</li> 18978<li>add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17356">#17356</a>)</li> 18979<li>fix homepage + source URL for ELPA (due to switch to new domain) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17357">#17357</a>)</li> 18980<li>fix homepage in ELPA easyconfigs (due to switch to new domain) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17358">#17358</a>)</li> 18981<li>rename libpsml for consistency with libPSML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17359">#17359</a>)</li> 18982<li>replace obsolete <code>pycrypto</code> with <code>pycryptodome</code> in Python 3.10.x easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17412">#17412</a>)</li> 18983<li>update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17413">#17413</a>)</li> 18984<li>
18984add patch for Qt5 5.12.2 with <code>GCCcore/11.2.0</code> to fix template bug (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17464">#17464</a>)</li> 18985<li>replace src include path with installation dir for HDF5 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17469">#17469</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17488">#17488</a>)</li> 18986<li>disable Python support for OTF2 v2.2, since we're not including Python 2.x as dependency (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17499">#17499</a>)</li> 18987<li>update homepage and source urls of DFT-D3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17528">#17528</a>)</li> 18988<li>use <code>Binary</code> easyblock for ANIcalculator to prevent RPATH sanity check failures (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17536">#17536</a>)</li> 18989</ul> 18990</li> 18991<li> 18992<p>other changes:</p> 18993<ul> 18994<li>fix invalid escape sequences in easyconfigs by using raw strings (<code>r"..."</code>) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11149">#11149</a>)</li> 18995<li>add exception for ncbi-vdb 3.0.0 dependency variant (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17131">#17131</a>)</li> 18996<li>use proper source tarball instead of cloning GitHub repository for wxWidgets v3.2.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17167">#17167</a>)</li> 18997<li>enable <code>-fPIC</code> in GEOS 3.11.1 (required by GDAL) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17196">#17196</a>)</li> 18998<li>fix website/docs links in <code>README</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17232">#17232</a>)</li> 18999<li>remove commented out line and delete unused patch for TALON (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17298">#17298</a>)</li> 19000<li>re-enable disabled tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17304">#17304</a>)</li> 19001<li>rename MAGMA to MAGMA-gene-analysis to avoid name collision (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17345">#17345</a>)</li> 19002<li>Archive ARB and blasr patch files (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17346">#17346</a>)</li> 19003<li>Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17348">#17348</a>)</li> 19004<li>consistently use NanoFilt capitalisation (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17349">#17349</a>)</li> 19005<li>rename ncl to NEXUS-CL to avoid case-insensitive name clash (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17350">#17350</a>)</li> 19006<li>rename python graphviz to graphviz-python to avoid case-insensitive name clash (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17352">#17352</a>)</li> 19007<li>archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17364">#17364</a>)</li> 19008</ul> 19009</li> 19010</ul> 19011<h2 id="release_notes_eb470">EasyBuild v4.7.0 (January 9th 2023)<a class="headerlink" href="#release_notes_eb470" title="Permanent link">¶</a></h2> 19012<p>feature release</p> 19013<p><strong>framework</strong></p> 19014<ul> 19015<li> 19016<p>print deprecation warning with running EasyBuild with Python 2 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4136">#4136</a>)</p> 19017</li> 19018<li> 19019<p>various enhancements, including:</p> 19020<ul> 19021<li>add support for checksums specified in external <code>checksums.json</code> file (<a href="https://github.com/easybuilders/easybuild-framework/pull/3749">#3749</a>)</li> 19022<li>vendor <code>distutils.version.LooseVersion</code> as <code>easybuild.tools.LooseVersion</code> (since distutils is deprecated in Python 3.10) (<a href="https://github.com/easybuilders/easybuild-framework/pull/3794">#3794</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4156">#4156</a>)</li> 19023<li>take into account custom configuration options specified in easystack file (<a href="https://github.com/easybuilders/easybuild-framework/pull/4057">#4057</a>)</li> 19024<li>
19024add support for using <code>--output-format=md</code> (MarkDown) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4117">#4117</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4155">#4155</a>)</li> 19025<li>add support for <code>--filter-rpath-sanity-libs</code> to skip RPATH sanity check for designated libraries (<a href="https://github.com/easybuilders/easybuild-framework/pull/4119">#4119</a>)</li> 19026<li>add sanity_check_load_module method to EasyBlock to provide control over when module is loaded during sanity check step (<a href="https://github.com/easybuilders/easybuild-framework/pull/4125">#4125</a>)</li> 19027<li>add <code>eb_bash_completion_local.bash</code> script to <code>setup.py</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4127">#4127</a>)</li> 19028<li>check whether <code>nvidia-smi/rocm-smi</code> command is available before trying to run it in <code>get_gpu_info</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4131">#4131</a>)</li> 19029<li>add <code>gfbf</code> as subtoolchain of foss (<a href="https://github.com/easybuilders/easybuild-framework/pull/4143">#4143</a>)</li> 19030<li>add support for <code>postinstallmsgs</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4145">#4145</a>)</li> 19031<li>make <code>iimkl</code> toolchain aware of <code>intel-compilers</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4146">#4146</a>)</li> 19032<li>add definition for <code>nvofbf</code> toolchain (<a href="https://github.com/easybuilders/easybuild-framework/pull/4157">#4157</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4163">#4163</a>)</li> 19033</ul> 19034</li> 19035<li> 19036<p>various bug fixes, including:</p> 19037<ul> 19038<li>also use EasyConfig instances cache in process_easyconfig when <code>build_specs</code> is empty dict (<a href="https://github.com/easybuilders/easybuild-framework/pull/4107">#4107</a>)</li> 19039<li>fix build options that should have empty list as default value (<a href="https://github.com/easybuilders/easybuild-framework/pull/4108">#4108</a>)</li> 19040<li>catch easyconfig parsing failure so we can generate and post a test report (<a href="https://github.com/easybuilders/easybuild-framework/pull/4109">#4109</a>)</li> 19041<li>add explicit return when no checksums match those specified in a tuple (<a href="https://github.com/easybuilders/easybuild-framework/pull/4112">#4112</a>)</li> 19042<li>tweak <code>findPythonDeps.py</code> script to use canonical package names (<a href="https://github.com/easybuilders/easybuild-framework/pull/4118">#4118</a>)</li> 19043<li>add <code>-fdefault-double-8</code> to <code>r8</code> toolchain compiler option for GCC (to be consistent with Intel) (<a href="https://github.com/easybuilders/easybuild-framework/pull/4121">#4121</a>)</li> 19044<li>always start with empty list for banned/requires libraries to avoid that corresponding build option is updated in-place (<a href="https://github.com/easybuilders/easybuild-framework/pull/4137">#4137</a>)</li> 19045<li>fix container tests by using EPEL archive URL for downloading Singularity RPM (<a href="https://github.com/easybuilders/easybuild-framework/pull/4138">#4138</a>)</li> 19046<li>use <code>-march=x86-64 -mtune=generic</code> instead of <code>-xSSE2</code> when using Intel oneAPI compilers (<a href="https://github.com/easybuilders/easybuild-framework/pull/4147">#4147</a>)</li> 19047<li>partially <code>skip test_det_copy_ec_specs</code> if no GitHub token is available (<a href="https://github.com/easybuilders/easybuild-framework/pull/4149">#4149</a>)</li> 19048</ul> 19049</li> 19050<li> 19051<p>other changes:</p> 19052<ul> 19053<li>drop support for easystack files using <code>'software'</code> top-level key (<a href="https://github.com/easybuilders/easybuild-framework/pull/4057">#4057</a>)</li> 19054<li>also run unit tests with Python 3.11 + add Python 3.11 to classifiers in <code>setup.py</code> (<a href="https://github.com/easybuilders/easybuild-framework/pull/4092">#4092</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4141">#4141</a>)</li> 19055<li>use new EasyBuild logo in README (<a href="https://github.com/easybuilders/easybuild-framework/pull/4123">#4123</a>)</li> 19056<li>automatically cancel Github Action workflow runs for outdated commits (<a href="https://github.com/easybuilders/easybuild-framework/pull/4132">#4132</a>)</li> 19057<li>auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4135">#4135</a>)</li> 19058<li>trim CI test configurations to avoid hitting GitHub rate limits (<a href="https://github.com/easybuilders/easybuild-framework/pull/4148">#4148</a>)</li> 19059<li>various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format (<a href="https://github.com/easybuilders/easybuild-framework/pull/4129">#4129</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4130">#4130</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4154">#4154</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4160">#4160</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4162">#4162</a>, <a href="https://github.com/easybuilders/easybuild-framework/pull/4168">#4168</a>)</li> 19060<li>update copyright lines for 2023 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4161">#4161</a>)</li> 19061</ul> 19062</li> 19063</ul> 19064<p><strong>easyblocks</strong></p> 19065<ul> 19066<li> 19067<p>add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2816">#2816</a>) and JuliaBundle (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2830">#2830</a>)</p> 19068</li> 19069<li> 19070<p>minor enhancements and updates, including:</p> 19071<ul> 19072<li>enhance TensorFlow easyblock to take into account provided OpenSSL dependency (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2575">#2575</a>)</li> 19073<li>
19073add fix_shebang to <code>install_step</code> of PythonPackage easyblock so that we can fix shebangs when installing extensions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2680">#2680</a>)</li> 19074<li>update PETSc easyblock for newer versions (>= 3.17) (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2796">#2796</a>)</li> 19075<li>update Clang easyblock to add support for new directory structure in Clang versions >= 14 + support Flang (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2800">#2800</a>)</li> 19076<li>update Xmipp easyblock since versions >= 3.20.07 use <code>noAsk</code> option to configure (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2809">#2809</a>)</li> 19077<li>add <code>include/opencv4</code> to <code>$CPATH</code> for OpenCV versions >= 4.0 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2818">#2818</a>)</li> 19078<li>add extra option for disabling LAPACK in ESMF (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2821">#2821</a>)</li> 19079<li>enable building of static libraries for libxml2 >= 2.10 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2825">#2825</a>)</li> 19080<li>update Xmipp easyblock to handle effects of CUDA at SYSTEM level and newer CUDA version requirements for stdc++ (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2831">#2831</a>)</li> 19081<li>update LLVM easyblock to put <code>'cmake'</code> symlink in place so separate CMake modules required for LLVM 15+ can be found (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2832">#2832</a>)</li> 19082<li>set <code>$TEMPDIRPATH</code> for testsuite in the BerkeleyGW easyblock, to avoid polluting <code>/tmp</code> (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2836">#2836</a>)</li> 19083<li>add <code>configure_no_prefix</code> option to skip addition of prefix to configure command in ConfigureMake easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2842">#2842</a>)</li> 19084<li>update <code>qscintilla.py</code> to be compatible with EB install of PyQt5 >= 5.15 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2845">#2845</a>)</li> 19085<li>add UCC to known_dependencies in OpenMPI EasyBlock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2847">#2847</a>)</li> 19086<li>update Clang-AOMP easyblock to handle version 5.2 and newer (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2851">#2851</a>)</li> 19087</ul> 19088</li> 19089<li> 19090<p>various bug fixes, including:</p> 19091<ul> 19092<li>fix installing of Clang with RPATH linking (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2799">#2799</a>)</li> 19093<li>fix <code>--module-only</code> for Clang + fix sanity check for Clang 11.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2800">#2800</a>)</li> 19094<li>create <code>$XDG_CACHE_HOME</code> for PyTorch tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2806">#2806</a>)</li> 19095<li>make PythonPackage easyblock compatible with <code>--sanity-check-only</code> by loading module early during sanity check step (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2828">#2828</a>)</li> 19096<li>fix docstring of PythonBundle generic easyblock (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2833">#2833</a>)</li> 19097<li>fix counting of failures in PyTorch tests (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2834">#2834</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2840">#2840</a>)</li> 19098<li>make sure that ANSYS INSTALL script has execute permissions (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2852">#2852</a>, <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2853">#2853</a>)</li> 19099</ul> 19100</li> 19101<li> 19102<p>other changes:</p> 19103<ul> 19104<li>remove useless <code>-openmp</code> build option for MRtrix v3.x (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2822">#2822</a>)</li> 19105<li>update HDF5 easyblock to use <code>--enable-threadsafe</code> configure option to make C API thread safe (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2824">#2824</a>)</li> 19106<li>use new EasyBuild logo in README (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2827">#2827</a>)</li> 19107<li>automatically cancel Github Action workflow runs for outdated commits (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2835">#2835</a>)</li> 19108<li>use fixed names for <code>bazel/wrapper</code> subdirectories used when building TensorFlow, to make debugging easier (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2841">#2841</a>)</li> 19109<li>also run unit tests with Python 3.11 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2844">#2844</a>)</li> 19110<li>tweak docstring in some generic easyblocks so it renders nicely in auto-generated documentation (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2849">#2849</a>)</li> 19111<li>update copyright lines for 2023 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2850">#2850</a>)</li> 19112</ul> 19113</li> 19114</ul> 19115<p><strong>easyconfigs</strong></p> 19116<ul> 19117<li> 19118<p>added easyconfigs for <code>foss/2022b</code>, <code>intel/2022b</code> common toolchains (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16961">#16961</a> and <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16962">#16962</a>)</p> 19119<ul> 19120<li>see also <a href="https://docs.easybuild.io/en/latest/Common-toolchains.html">https://docs.easybuild.io/en/latest/Common-toolchains.html</a></li> 19121</ul> 19122</li> 19123<li> 19124<p>added easyconfigs for NVHPC-based toolchains <code>nvompi/2022.07</code> and <code>nvofbf/2022.07</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16724">#16724</a>)</p> 19125</li> 19126<li> 19127<p>added example easyconfig files for 107 new software packages:</p> 19128<ul> 19129<li>Alfred (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16780">#16780</a>), attrdict3 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16856">#16856</a>), bamFilters (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16735">#16735</a>), bcl-convert (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16351">#16351</a>), Beagle (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/346">#346</a>), Boost.MPI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15757">#15757</a>), 19130captum (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16477">#16477</a>), CAT-BAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16577">#16577</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16634">#16634</a>), cdo-bindings (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16669">#16669</a>), Chemaxon-Marvin (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13954">#13954</a>), CliMetLab (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16842">#16842</a>), 19131CloudCompare (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16944">#16944</a>), cmocean (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16659">#16659</a>), COBRApy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16616">#16616</a>), CodAn (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16902">#16902</a>), CoSymLib (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17049">#17049</a>), CPPE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16749">#16749</a>), 19132cryoCARE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16534">
19132#16534</a>), CTPL (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16498">#16498</a>), CUDA-Samples (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16914">#16914</a>), cwltool (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16503">#16503</a>), Cytoscape (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16682">#16682</a>), DeepLabCut (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16391">#16391</a>), 19133DeepMod2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17008">#17008</a>), Dice (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16752">#16752</a>), dlb (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16845">#16845</a>), DRAGMAP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16532">#16532</a>), ecBuild (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16842">#16842</a>), EGTtools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16704">#16704</a>), 19134ESM-2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16528">#16528</a>), flair-NLP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15588">#15588</a>), FMS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16965">#16965</a>), Godon (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16574">#16574</a>), gsw (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16643">#16643</a>), HighFive (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16737">#16737</a>), humann (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16853">#16853</a>), 19135HyperQueue (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16753">#16753</a>), IJulia (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16494">#16494</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16665">#16665</a>), infercnvpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16712">#16712</a>), InParanoid (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16572">#16572</a>), jupyter-server (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14844">#14844</a>), 19136KaHIP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16861">#16861</a>), KITE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16550">#16550</a>), lagrangian-filtering (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16654">#16654</a>), LHAPDF (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17028">#17028</a>), librttopo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16856">#16856</a>), libwpe (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16088">#16088</a>), 19137Magics (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16842">#16842</a>), matlab-proxy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14270">#14270</a>), mcu (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16566">#16566</a>), MEMOTE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16772">#16772</a>), memtester (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16763">#16763</a>), meson-python (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16911">#16911</a>), 19138minizip (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16856">#16856</a>), MITgcmutils (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16623">#16623</a>), MONAI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16519">#16519</a>), MOOSE (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13824">#13824</a>), mstore (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16892">#16892</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17029">#17029</a>), 19139MultilevelEstimators (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15630">#15630</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16665">#16665</a>), n2v (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16535">#16535</a>), NanoLyse (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16575">#16575</a>), napari (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16468">#16468</a>), NECI (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16751">#16751</a>), 19140nf-core-mag (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16613">#16613</a>), oceanspy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16640">#16640</a>), olego (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16909">#16909</a>), OmegaFold (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16698">#16698</a>), OVITO (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16811">#16811</a>), Panedr (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16564">#16564</a>), 19141Parcels (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16838">#16838</a>), polars (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16989">#16989</a>), PsiCLASS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16906">#16906</a>), pyccel (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16823">#16823</a>), PyCheMPS2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16710">#16710</a>), PyDamage (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16576">#16576</a>), 19142PyImageJ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16757">#16757</a>), pysteps (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16783">#16783</a>), python-libsbml (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16610">#16610</a>), python-telegram-bot (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16442">#16442</a>), pyWannier90 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16447">#16447</a>), 19143resolos (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16649">#16649</a>), RLCard (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16695">#16695</a>), SAP (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5200">#5200</a>), scikit-misc (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16457">#16457</a>), scvi-tools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16457">#16457</a>), SELFIES (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17032">#17032</a>), 19144SeuratDisk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16951">#16951</a>), sfftk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16466">#16466</a>), simint (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16886">#16886</a>), SISSO++ (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15759">#15759</a>), slamdunk (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15197">#15197</a>), spaCy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17027">#17027</a>), 19145Sphinx-RTD-Theme (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16736">#16736</a>), SPOOLES (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16756">#16756</a>), Squidpy (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16880">#16880</a>), svist4get (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16505">#16505</a>
19145), task-spooler (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17048">#17048</a>), 19146TBA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16497">#16497</a>), TensorFlow-Datasets (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16421">#16421</a>), TFEA (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16476">#16476</a>), TinyXML (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16992">#16992</a>), tokenizers (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15587">#15587</a>), 19147torchsampler (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16464">#16464</a>), trimesh (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16858">#16858</a>), UCX-ROCm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17033">#17033</a>), wpebackend-fdo (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16093">#16093</a>), xmitgcm (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16637">#16637</a>)</li> 19148</ul> 19149</li> 19150<li> 19151<p>added additional easyconfigs for various supported software packages, including:</p> 19152<ul> 19153<li>Albumentations 1.3.0, ANSYS 2022R2, AOCC 4.0.0, archspec 0.1.4, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, 19154basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, Blender 3.3.1, Blosc 1.21.3, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, 19155boto3 1.26.37, BRAKER 2.1.6, CDO 2.1.1, cdsapi 0.5.1, CharLS 2.4.1, CheMPS2 1.8.12, CMake 3.24.3, CubeGUI 4.8, 19156CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0 + 12.0.0, cuDNN 8.6.0.163 + 8.7.0.84, cURL 7.86.0, cutadapt 4.2, 19157cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, 19158dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, ecCodes 2.27.0, exiv2 0.27.5, Fiji 2.9.0, Filtlong 0.2.1, 19159FLANN 1.9.1, FlexiBLAS 3.2.1, fontconfig 2.14.1, FreeXL 1.0.6, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, 19160Gdk-Pixbuf 2.42.10, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, 19161git 2.38.1, GLib 2.75.0, GlobalArrays 5.8.2, GnuTLS 3.7.8, GObject-Introspection 1.74.0, GRASS 8.2.0, GTK3 3.24.35, 19162HarfBuzz 5.3.1, HTSeq 2.0.2, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, imagecodecs 2022.9.26, imageio 2.22.2, 19163ImageMagick 7.1.0-53, imbalanced-learn 0.9.0, JasPer 4.0.0, jax 0.3.23, JupyterLab 3.5.0, Leptonica 1.83.0, 19164libavif 0.11.1, libdap 3.20.11, libdeflate 1.15, libdrm 2.4.114, libfabric 1.16.1, libffi 3.4.4, libglvnd 1.6.0, 19165libgpg-error 1.46, libidn 1.41, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, librsvg 2.55.1, 19166LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libxml2 2.10.3, 19167libxml2-python 2.9.13, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, makedepend 1.0.7, Mako 1.2.4, 19168MATLAB-Engine 2021b, Mesa 22.2.4, Meson 0.64.0, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, 19169MotionCor2 1.5.0, MoviePy 1.0.3, MRChem 1.1.1, MRCPP 1.4.1, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, 19170nanomath 1.2.1, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.3, nglview 3.0.3, NiBabel 4.0.2, 19171Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.7.0, Octave 7.1.0, OPARI2 2.0.7, 19172OpenFOAM 10, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.10, openpyxl 3.0.10, openslide-python 1.2.0, 19173OpenStackClient 6.0.0, OSU-Micro-Benchmarks 6.2, OTF2 3.0.2, Pango 1.50.12, PAPI 7.0.0, pauvre 0.2.3, PETSc 3.17.4, 19174phonopy 2.16.3, pigz 2.7, Pillow 9.2.0, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, psutil 5.9.3, 19175pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, pyproj 3.4.0, PyQt5 5.15.5, pytest 7.1.3, 19176Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, QCA 2.3.5, 19177QGIS 3.28.1, QIIME2 2022.8, QScintilla 2.11.6, Qt5 5.15.7, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, 19178rasterio 1.3.4, re2c 3.0, ReFrame 3.12.0, RStudio-Server 2022.07.2+576, Ruby 3.0.5, Rust 1.65.0, SAP 1.1.3, 19179scanpy 1.9.1, scikit-image 0.19.3, SCons 4.4.0, Score-P 8.0, Seaborn 0.12.1, SentencePiece 0.1.97, Seurat 4.3.0, 19180SignalP 6.0g, SimPEG 0.18.1, SLEPc 3.17.2, SNAP 2.0.1, SpaceRanger 2.0.0, SQLite 3.39.4, STAR-CCM+ 17.06.007, 19181SuperLU_DIST 8.1.0, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, 19182texinfo 6.8, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, Transformers 4.24.0, 19183typing-extensions 4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, util-linux 2.38.1, Valgrind 3.20.0, Vim 9.0.0950, VTK 9.2.2, 19184wandb 0.13.6, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.9.0, 19185XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, XZ 5.2.7, yaml-cpp 0.7.0, zarr 2.13.3, zlib-ng 2.0.6</li> 19186</ul> 19187</li> 19188<li> 19189<p>minor enhancements, including:</p> 19190<ul> 19191<li>enable building of dev tools in recent PyQt5 easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16469">#16469</a>)</li> 19192<li>
19192add extensions to R v4.2.1: LMERConvenienceFunctions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16512">#16512</a>), HGNChelper 4.2.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16744">#16744</a>)</li> 19193<li>add extensions to R-bundle-Bioconductor 3.15: SPOTlight (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16569">#16569</a>), HiCcompare (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16581">#16581</a>), ROntoTools (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16636">#16636</a>), 19194scDblFinder (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16686">#16686</a>), numbat (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16777">#16777</a>), HiCBricks (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16913">#16913</a>), zellkonverter (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16952">#16952</a>)</li> 19195<li>add libmad dependency to SoX v14.4.2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16758">#16758</a>)</li> 19196<li>also install subtree support in recent git easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16784">#16784</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16785">#16785</a>)</li> 19197<li>add extensions to ESM-2 to enhance it for esmfold (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16841">#16841</a>)</li> 19198<li>add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16844">#16844</a>)</li> 19199<li>add KaHIP dependency to OpenFOAM v2206 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16974">#16974</a>)</li> 19200<li>enable dataset support for recent versions of Arrow (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16956">#16956</a>)</li> 19201</ul> 19202</li> 19203<li> 19204<p>various bug fixes, including:</p> 19205<ul> 19206<li>define <code>$JUPYTER_PATH</code> via modextrapaths rather than modextravars for IRkernel 1.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15776">#15776</a>)</li> 19207<li>add patches to fix PyTorch 1.10.0 build on POWER (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15904">#15904</a>)</li> 19208<li>fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16485">#16485</a>)</li> 19209<li>add patch for M4 1.4.18 to fix glibc v2.34 <code>SIGSTKSZ</code> compatibility (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16486">#16486</a>)</li> 19210<li>add patch for pybind11 2.6.0 to fix failing test due to extra whitespace (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16487">#16487</a>)</li> 19211<li>work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16490">#16490</a>)</li> 19212<li>fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16502">#16502</a>)</li> 19213<li>add OpenBLAS patches to disable FMA in <code>[cz]cal</code> and fix crash in <code>zdot</code> (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16510">#16510</a>)</li> 19214<li>add missing Perl build dependency GStreamer + add patch to skip trying to make files suid (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16516">#16516</a>)</li> 19215<li>build nodejs with OpenSSL and ICU provided as proper dependencies (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16529">#16529</a>)</li> 19216<li>also define <code>$JUPYTER_CONFIG_PATH</code> in IPython and JupyterLab easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16556">#16556</a>)</li> 19217<li>define <code>$GTKDOCIZE</code> as <code>'echo'</code> before generating configure script for recent HarfBuzz versions (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16570">#16570</a>)</li> 19218<li>disable use of <code>-Werror</code> in recent NSS easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16571">#16571</a>)</li> 19219<li>use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16611">#16611</a>)</li> 19220<li>avoid that zlib + htslib are downloaded and built during installation of MetaBAT (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16624">#16624</a>)</li> 19221<li>
19221add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16633">#16633</a>)</li> 19222<li>add missing pyWannier90 dependency for mcu + enhance sanity check (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16667">#16667</a>)</li> 19223<li>fix <code>source_urls</code> for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo) (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16693">#16693</a>)</li> 19224<li>add patches to fix or skip PyTorch 1.12.1 tests (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16793">#16793</a>)</li> 19225<li>fix checksum for cell2location 0.05-alpha and add missing build dependency on flex (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16819">#16819</a>)</li> 19226<li>upgrade dependency on libdeflate to common v1.8 in fastp and vt easyconfigs using GCC(core)/10.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16839">#16839</a>)</li> 19227<li>fix checksum for dlllogger extension in OpenFold v1.0.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16694">#16694</a>)</li> 19228<li>make sure that Python dependency is actually used for VTK 9.0.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16741">#16741</a>)</li> 19229<li>fix homepage for pocl v1.8 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16857">#16857</a>)</li> 19230<li>fix source_urls in MUMPS easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16931">#16931</a>, <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16932">#16932</a>)</li> 19231<li>fix installation of Bowtie2 v2.4.4+ on non-x86_64 systems (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16946">#16946</a>)</li> 19232<li>add missing OpenSSL dependency to DCMTK 3.6.7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16979">#16979</a>)</li> 19233<li>fix source URL for PCRE2 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16987">#16987</a>)</li> 19234<li>add pkgconf dependency for ICU and add patch to avoid trouble with long path names for nodejs-16.15.1/GCCcore-11.3.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16990">#16990</a>)</li> 19235<li>add patch for libwpe 1.13.3 to avoid build issues on CentOS 7 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17001">#17001</a>)</li> 19236<li>add missing zlib and zstd to GnuTLS (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17013">#17013</a>)</li> 19237<li>add missing pkgconf build dependency to Transformers v4.24.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17020">#17020</a>)</li> 19238<li>fix checksums for <code>xxx-rocm-4.5.0.tar.gz</code> source tarballs for Clang-AOMP 4.5.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17042">#17042</a>)</li> 19239<li>replace useless test step for simint 0.7 with (lightweight) sanity check command (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/17044">#17044</a>)</li> 19240</ul> 19241</li> 19242<li> 19243<p>other changes:</p> 19244<ul> 19245<li>only give read permissions in GitHub Actions workflows (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16263">#16263</a>)</li> 19246<li>remove ExomeDepth from recent R-bundle-Bioconductor easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16492">#16492</a>)</li> 19247<li>include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16578">#16578</a>)</li> 19248<li>use new EasyBuild logo in README (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16641">#16641</a>)</li> 19249<li>rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16697">#16697</a>)</li> 19250<li>automatically cancel Github Action workflow runs for outdated commits (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16754">#16754</a>)</li> 19251<li>use geo moduleclass for SimPEG 0.14.1 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16847">#16847</a>)</li> 19252</ul> 19253</li> 19254</ul> 19255<h2 id="release_notes_eb462">EasyBuild v4.6.2 (October 21st 2022)<a class="headerlink" href="#release_notes_eb462" title="Permanent link">¶</a></h2> 19256<p>bugfix/update release</p> 19257<p><strong>framework</strong></p> 19258<ul> 19259<li>various enhancements, including:<ul> 19260<li>add support for easystack file that contains easyconfig 19261 filenames + implement parsing of configuration options 19262 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4021">#4021</a>)</li> 19263<li>skip over unset <code>$EB_PYTHON</code>/<code>$EB_INSTALLPYTHON</code> in eb wrapper 19264 script 19265 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4080">#4080</a>)</li> 19266<li>
19266add <code>GITHUB_RELEASE</code> and <code>GITHUB_LOWER_RELEASE</code> templates 19267 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4084">#4084</a>)</li> 19268<li>add <code>%(cuda_cc_cmake)s</code> template 19269 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4087">#4087</a>)</li> 19270</ul> 19271</li> 19272<li>various bug fixes, including:<ul> 19273<li>make <code>check_sha256_checksums</code> verify all checksums if they're 19274 specified as a dict value 19275 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4076">#4076</a>)</li> 19276<li>replace use of symlink with copied files in <code>alt_location</code> tests 19277 to fix failing EasyBuild installation on BeeGFS 19278 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4083">#4083</a>)</li> 19279<li>fix trying to generate RPATH wrappers for Clang 19280 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4088">#4088</a>)</li> 19281<li>make sure that GitPython version is a proper version before 19282 checking minimal required version 19283 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4090">#4090</a>, 19284 <a href="https://github.com/easybuilders/easybuild-framework/pull/4091">#4091</a>)</li> 19285<li>first look for patch in <code>alt_location</code> when it is specified 19286 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4093">#4093</a>)</li> 19287</ul> 19288</li> 19289<li>other changes:<ul> 19290<li>make scripts executable 19291 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4081">#4081</a>)</li> 19292<li>make <code>--inject-checksums</code> inject dictionary value for checksums 19293 which maps filename to SHA256 checksum 19294 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4085">#4085</a>)</li> 19295<li>update to v3 of actions/checkout and actions/setup-python in CI 19296 workflows 19297 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4089">#4089</a>)</li> 19298<li>use <code>SYSTEM</code> template constant in dependencies instead of <code>True</code> 19299 in framework tests 19300 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4094">#4094</a>)</li> 19301</ul> 19302</li> 19303</ul> 19304<p><strong>easyblocks</strong></p> 19305<ul> 19306<li>2 new software-specific easyblock:<ul> 19307<li>CUDA compatibility libraries 19308 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2764">#2764</a>) 19309 and mamba 19310 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2808">#2808</a>)</li> 19311</ul> 19312</li> 19313<li>minor enhancements and updates, including:<ul> 19314<li>update OpenFOAM easyblock to support OpenFOAM 10 + clean up 19315 variant/version checks 19316 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2766">#2766</a>)</li> 19317<li>added support for ESMPy in ESMF 19318 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2789">#2789</a>)</li> 19319<li>enhance OpenBLAS easyblock to support running LAPACK test 19320 suite + checking how many tests fail 19321 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2801">#2801</a>)</li> 19322<li>make numexpr easyblock aware of toolchain with GCC + imkl 19323 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2810">#2810</a>)</li> 19324<li>add sanity check commands for netCDF 19325 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2811">#2811</a>)</li> 19326</ul> 19327</li> 19328<li>various bug fixes, including:<ul> 19329<li>handle problems copying symlink that points to CUDA folder that 19330 is not created for non CUDA builds of SuiteSparse 19331 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2790">#2790</a>)</li> 19332<li>don't install docs (to avoid trouble with Java) + add Rocky 19333 support for ABAQUS 19334 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2792">#2792</a>)</li> 19335<li>correctly count the number of failing tests (not failing test 19336 suites) in PyTorch builds 19337 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2794">#2794</a>, 19338 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2803">#2803</a>)</li> 19339<li>fix docstring for PyTorch easyblock 19340 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2795">#2795</a>)</li> 19341<li>handle iterative builds with MakeCp easyblock 19342 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2798">#2798</a>)</li> 19343<li>accept both <code>None</code> and empty value for optarch to let OpenCV 19344 detect host CPU 19345 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2804">#2804</a>)</li> 19346<li>enhance EasyBuildMeta easyblock: auto-enable installing with 19347 pip + fix setup.py of easyconfigs package so installation with 19348 setuptools >= 61.0 works 19349 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2805">#2805</a>)</li> 19350<li>use <code>python -m pip</code> instead of <code>pip</code> in PythonPackage easyblock 19351 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2807">#2807</a>)</li> 19352</ul> 19353</li> 19354<li>other changes:<ul> 19355<li>make the test output from PythonPackage less verbose by 19356 disabling default search for error patterns done by <code>run_cmd</code> 19357 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2797">#2797</a>)</li> 19358</ul> 19359</li> 19360</ul> 19361<p><strong>easyconfigs</strong></p> 19362<ul> 19363<li>add easyconfig for intel/2022.09 toolchain 19364 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16435">#16435</a>)</li> 19365<li>
19365added example easyconfig files for 25 new software packages:<ul> 19366<li>AGAT 19367 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16261">#16261</a>), 19368 AMAPVox 19369 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16438">#16438</a>), 19370 Avogadro2 19371 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16257">#16257</a>), 19372 buildingspy 19373 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16308">#16308</a>), 19374 CDBtools 19375 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16436">#16436</a>), 19376 Compress-Raw-Zlib 19377 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16307">#16307</a>), 19378 CUDAcompat 19379 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15892">#15892</a>), 19380 CWIPI 19381 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16342">#16342</a>), 19382 enchant-2 19383 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16082">#16082</a>, 19384 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16319">#16319</a>), 19385 f90wrap 19386 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16346">#16346</a>), 19387 Imath 19388 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16276">#16276</a>), 19389 Mamba 19390 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16432">#16432</a>), 19391 Miller 19392 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16221">#16221</a>), 19393 nghttp2 19394 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16096">#16096</a>), 19395 ngtcp2 19396 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16098">#16098</a>), 19397 NVSHMEM 19398 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16254">#16254</a>), 19399 pairsnp 19400 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16331">#16331</a>), 19401 paladin 19402 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16320">#16320</a>), 19403 PyMOL 19404 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16394">#16394</a>), 19405 python-irodsclient 19406 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16328">#16328</a>), 19407 ruffus 19408 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16428">#16428</a>), 19409 TELEMAC-MASCARET 19410 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16274">#16274</a>), 19411 torchdata 19412 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16344">#16344</a>), 19413 Waylandpp 19414 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16092">#16092</a>), 19415 x13as 19416 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16163">#16163</a>)</li> 19417</ul> 19418</li> 19419<li>added additional easyconfigs for various supported software 19420 packages, including:<ul> 19421<li>Amber 22.0, AMS 2022.102, ASE 3.22.1, atools 1.5.1, Beast 2.6.7, 19422 biogeme 3.2.10, Boost.Python 1.79.0, ccache 4.6.3, dbus-glib 19423 0.112, Delly 1.1.5, ESMF 8.3.0, expat 2.4.9, FDS 6.7.9, file 19424 5.43, FLTK 1.3.8, FTGL 2.4.0, gc 8.2.2, GitPython 3.1.27, Go 19425 1.18.3, GPAW 22.8.0, Guile 3.0.8, htop 3.2.1, hunspell 1.7.1, 19426 IPython 8.5.0, jq 1.6, Julia 1.8.2, LDC 1.30.0, libcint 5.1.6, 19427 libconfig 1.7.3, libreadline 8.2, LibSoup 3.0.7, LIBSVM 3.30, 19428 libwebp 1.2.4, likwid 5.2.2, MariaDB 10.9.3, matplotlib 3.5.2, 19429 ncdu 1.17, netcdf4-python 1.6.1, Nextflow 22.10.0, NFFT 3.5.3, 19430 Nipype 1.8.5, numactl 2.0.16, onedrive 2.4.21, OpenCV 4.6.0, 19431 OpenEXR 3.1.5, OpenJPEG 2.5.0, OpenMM 7.7.0, OpenPGM 5.2.122, 19432 OpenSSL 1.1.1q, Perl 5.36.0, Pillow-SIMD 9.2.0, pkgconf 1.9.3, 19433 PostgreSQL 14.4, PyCharm 2022.2.2, PyTorch 1.12.0, PyTorch 19434 1.12.0, PyTorch-Lightning 1.7.7, RDFlib 6.2.0, SAMtools 1.16.1, 19435 scikit-learn 1.1.2, Score-P 7.1, SDL2 2.0.22, spaln 2.4.12, 19436 spglib-python 2.0.0, SuiteSparse 5.13.0, SUNDIALS 6.3.0, sympy 19437 1.11.1, tensorboard 2.10.0, torchvision 0.13.1, TRIQS 3.1.1, 19438 TRIQS-cthyb 3.1.0, TRIQS-dft_tools 3.1.0, TRIQS-tprf 3.1.1, 19439 TRUST4 1.0.7, TurboVNC 3.0.1, typing-extensions 4.3.0, UCX 19440 1.13.1, umap-learn 0.5.3, VEP 107, VMD 1.9.4a57, Wayland 1.21.0, 19441 wxWidgets 3.2.1, xprop 1.2.5</li> 19442</ul> 19443</li> 19444<li>minor enhancements, including:<ul> 19445<li>configure recent pocl versions with <code>-DLLC_HOST_CPU=native</code> to 19446 avoid CPU auto-detection 19447 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16246">#16246</a>)</li> 19448<li>
19448add multi-dep exception to easyconfigs test suite for 19449 ncbi-vdb-3.0.0 which requires HDF5 1.10.x 19450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16316">#16316</a>)</li> 19451<li>enable running of LAPACK tests for recent OpenBLAS easyconfigs + 19452 add patch to fix failing LAPACK tests due to use of 19453 <code>-ftree-vectorize</code> 19454 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16406">#16406</a>)</li> 19455<li>add <code>GITHUB_(LOWER_)RELEASE</code> to known constants in <code>setup.cfg</code> 19456 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16422">#16422</a>)</li> 19457<li>add AMAPVox extension to R v4.2.1 19458 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16439">#16439</a>)</li> 19459<li>add OpenEXR dependency to POV-Ray 3.7.0.10 19460 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16408">#16408</a>)</li> 19461</ul> 19462</li> 19463<li>various bug fixes, including:<ul> 19464<li>add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on 19465 POWER 19466 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16199">#16199</a>)</li> 19467<li>skip flaky test in PyTorch 1.9.0 19468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16258">#16258</a>)</li> 19469<li>add <code>--with-versioned-syms</code> to ncurses 6.2 and 6.3 19470 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16270">#16270</a>)</li> 19471<li>add missing pkg-config build dependency to Guile 19472 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16317">#16317</a>)</li> 19473<li>add patches to fix incompatibilites between ASE and other 19474 packages in 2022a toolchain 19475 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16332">#16332</a>)</li> 19476<li>add patches to fix PyTorch 1.11 on POWER 19477 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16339">#16339</a>)</li> 19478<li>add patches for Ambertools 21 to Amber 20.11 to work with 19479 updated Amber easyblock 19480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16343">#16343</a>)</li> 19481<li>use Intel MPI from EasyBuild toolchain in AMS 19482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16363">#16363</a>)</li> 19483<li>fix execution permissions for <code>bin/ngm*</code> for NextGenMap v0.5.5 19484 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16383">#16383</a>)</li> 19485<li>fix using provided Qhull and freetype dependencies for 19486 matplotlib 3.5.2 by creating <code>mplsetup.cfg</code> rather than 19487 <code>setup.cfg</code> 19488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16396">#16396</a>)</li> 19489<li>fix GitHub download link in for libpsl 0.21.1 19490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16397">#16397</a>)</li> 19491<li>stick to http in source URL for <code>stride.tar.gz</code> in VMD 1.9.4a51 19492 easyconfigs due to problems with SSL certificate 19493 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16403">#16403</a>)</li> 19494<li>add patch to detect available cores and remove unneeded deps for 19495 Unicycler 0.5.0 19496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16407">#16407</a>)</li> 19497<li>add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ 19498 GCCcore/10.3.0 19499 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16410">#16410</a>)</li> 19500<li>add patch to GCC 11.x + 12.x to fix vectorizer bug 19501 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16411">#16411</a>)</li> 19502<li>fix checksum for GULP 6.1 19503 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16423">#16423</a>)</li> 19504<li>add bzip2 and libxml2 as dependencies for netCDF 4.9.0 19505 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16450">#16450</a>)</li> 19506</ul> 19507</li> 19508<li>other changes:<ul> 19509<li>drop Java dep from ABAQUS 2022 19510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16314">#16314</a>)</li> 19511<li>deprecate use of <code>True</code> in favour of <code>SYSTEM</code> for 19512 system-toolchain dependencies in easyconfigs using a recent 19513 toolchain version (>2019b) 19514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16384">#16384</a>)</li> 19515<li>update easyconfigs to use <code>SYSTEM</code> template constant instead of 19516 <code>True</code> in dependencies 19517 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16386">#16386</a>, 19518 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16418">#16418</a>)</li> 19519<li>update libxml2 + libxslt easyconfigs to use <code>gnome.org</code> source 19520 URL 19521 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16429">#16429</a>)</li> 19522</ul> 19523</li> 19524</ul> 19525<h2 id="release_notes_eb461">EasyBuild v4.6.1 (September 12th 2022)<a class="headerlink" href="#release_notes_eb461" title="Permanent link">¶</a></h2> 19526<p>bugfix/update release</p> 19527<p><strong>framework</strong></p> 19528<ul> 19529<li>various enhancements, including:<ul> 19530<li>add script to find dependencies of Python packages 19531 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3839">#3839</a>)</li> 19532<li>
19532add <code>ai</code> default module class 19533 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4053">#4053</a>)</li> 19534</ul> 19535</li> 19536<li>various bug fixes, including:<ul> 19537<li>fix code style issues reported by recent flake8 linter 19538 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4049">#4049</a>)</li> 19539<li>stick to autopep8 < 1.7.0 with Python 2.7 19540 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4055">#4055</a>)</li> 19541<li>ensure we call <code>EasyBlock.patch_step</code> for <code>postinstallpatches</code> 19542 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4063">#4063</a>)</li> 19543<li>fix leaked handles in <code>set_columns</code>, <code>complete_cmd</code>, 19544 <code>run_cmd_qa</code>, <code>det_terminal_size functions</code> + tests 19545 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4066">#4066</a>)</li> 19546<li>fix <code>quote_str</code> when string with both <code>'</code> and <code>"</code> ends with a 19547 double quote 19548 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4068">#4068</a>)</li> 19549<li>fix type-checking of patches to allow dict values + correctly 19550 handle patches specified as dict values in <code>--new-pr</code> 19551 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4070">#4070</a>)</li> 19552<li>relax toolchain test by accepting both <code>-march=native</code> (x86_64) 19553 and <code>-mcpu=native</code> (aarch64) 19554 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4071">#4071</a>)</li> 19555</ul> 19556</li> 19557<li>other changes:<ul> 19558<li>run python in the same process as <code>eb</code> wrapper script by using 19559 <code>exec</code> 19560 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4048">#4048</a>)</li> 19561<li>add <code>get_linked_libs_raw</code> function, and use it from both 19562 <code>check_linked_shared_libs</code> and <code>sanity_check_rpath</code> 19563 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4051">#4051</a>)</li> 19564<li>update CI workflows (except container tests) to use Ubuntu 19565 20.04, since Ubuntu 18.04 is deprecated 19566 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4064">#4064</a>)</li> 19567<li>use <code>SYSTEM</code> constant for dependency that uses system toolchain 19568 in dumped easyconfig 19569 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4069">#4069</a>)</li> 19570</ul> 19571</li> 19572</ul> 19573<p><strong>easyblocks</strong></p> 19574<ul> 19575<li>minor enhancements and updates, including:<ul> 19576<li>update LAMMPS easyblock for LAMMPS/23Jun22 19577 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2213">#2213</a>)</li> 19578<li>reduce the number of command line options for <code>cmake</code> command in 19579 CMakeMake generic easyblock 19580 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2514">#2514</a>)</li> 19581<li>update libQGLViewer easyblock to take into account changes in 19582 the shared library names depending on Qt versions they are 19583 compiled with 19584 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2730">#2730</a>)</li> 19585<li>improve PLUMED detection in GROMACS easyblock 19586 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2749">#2749</a>)</li> 19587<li>make <code>$LD_LIBRARY_PATH</code> detection more robust for LAMMPS 19588 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2765">#2765</a>)</li> 19589<li>enhance NVHPC easyblock to avoid superfluous warning 19590 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2767">#2767</a>)</li> 19591<li>enhance PyTorch easyblock to also capture tests failing with 19592 signal 19593 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2768">#2768</a>)</li> 19594<li>enhance PythonPackage easyblock to make sure all test command 19595 output makes it to the EasyBuild log, also when 19596 <code>return_output_ec=True</code> 19597 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2770">#2770</a>)</li> 19598<li>set <code>$NVHPC_CUDA_HOME</code> for NVHPC 22.7+ 19599 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2776">#2776</a>)</li> 19600</ul> 19601</li> 19602<li>various bug fixes, including:<ul> 19603<li>make Amber easyblock aware of FlexiBLAS 19604 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2720">#2720</a>)</li> 19605<li>update PyTorch easyblock to configure without breakpad support 19606 on POWER 19607 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2763">#2763</a>)</li> 19608<li>use <code>lib*</code> in <code>post_install</code> step of FFTW.MPI easyblock to fix
19609 paths not being found on Linux distros favouring lib64 (like 19610 Suse/SLES) 19611 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2771">#2771</a>)</li> 19612<li>use <code>det_cmake_version</code> function to determine CMake version in 19613 CMakeMake generic easyblock 19614 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2772">#2772</a>)</li> 19615<li>don't enable building of <code>ld.gold</code> when installing binutils on 19616 a RISC-V system + don't configure GCC to use gold as default 19617 linker on a RISC-V system 19618 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2780">#2780</a>)</li> 19619<li>tweak Amber(Tools) easyblock to run tests from top-level 19620 directory 19621 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2781">#2781</a>)</li> 19622<li>fix version check for NVPTX library in sanity check of Clang 19623 easyblock 19624 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2783">#2783</a>)</li> 19625</ul> 19626</li> 19627<li>other changes:<ul> 19628<li>update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is 19629 deprecated) 19630 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2779">#2779</a>)</li> 19631</ul> 19632</li> 19633</ul> 19634<p><strong>easyconfigs</strong></p> 19635<ul> 19636<li>added example easyconfig files for 37 new software packages:<ul> 19637<li>AptaSUITE 19638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8583">#8583</a>), 19639 BigDFT 19640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15860">#15860</a>), 19641 colossalai 19642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15971">#15971</a>), 19643 CrystFEL 19644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8407">#8407</a>), 19645 Dakota 19646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15883">#15883</a>, 19647 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16210">#16210</a>), 19648 FastFold 19649 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15972">#15972</a>), 19650 fastparquet 19651 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15020">#15020</a>), 19652 FOX-Toolkit 19653 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15986">#15986</a>), 19654 GLM-AED 19655 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15879">#15879</a>), 19656 hiredis 19657 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16071">#16071</a>), 19658 how_are_we_stranded_here 19659 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16220">#16220</a>, 19660 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16227">#16227</a>), 19661 indicators 19662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16209">#16209</a>), 19663 JavaFX 19664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8583">#8583</a>), 19665 json-fortran 19666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15979">#15979</a>), 19667 jupyter-resource-usage 19668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15834">#15834</a>), 19669 libev 19670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16086">#16086</a>), 19671 libmad 19672 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16067">#16067</a>), 19673 libplinkio 19674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13040">#13040</a>), 19675 LuaJIT2-OpenResty 19676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16047">#16047</a>), 19677 MetaMorpheus 19678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15825">#15825</a>), 19679 mgltools 19680 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16226">#16226</a>), 19681 miniasm 19682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15858">#15858</a>), 19683 muMerge 19684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16115">#16115</a>), 19685 nano 19686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16198">#16198</a>), 19687 nghttp3 19688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16097">#16097</a>), 19689 olaFlow 19690 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16021">#16021</a>), 19691 OpenFAST 19692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15983">#15983</a>, 19693 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15983">#15983</a>), 19694 OpenFold 19695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15971">#15971</a>), 19696 Phantompeakqualtools 19697 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15871">#15871</a>), 19698 pyGenomeTracks 19699 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16143">#16143</a>), 19700 QuickPIC 19701 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15978">#15978</a>), 19702 RheoTool 19703 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16077">#16077</a>), 19704 Satsuma2 19705 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16068">#16068</a>), 19706 SMC++ 19707 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16017">#16017</a>), 19708 stripy 19709 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15866">#15866</a>), 19710 UCC-CUDA 19711 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15956">#15956</a>), 19712 VESTA 19713 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16217">#16217</a>)</li> 19714</ul> 19715</li> 19716<li>
19716added additional easyconfigs for various supported software 19717 packages, including:<ul> 19718<li>alevin-fry 0.6.0, AmberTools 22.3, arrow-R 8.0.0, ASE 3.22.1, 19719 BBMap 38.98, BCFtools 1.15.1, binutils 2.39, BLAST+ 2.13.0, 19720 Bowtie2 2.4.5, BUSCO 5.4.3, CapnProto 0.10.2, Cartopy 0.20.3, 19721 ccache 4.6.1, cclib 1.7.2, CDO 2.0.5, CellRanger-ATAC 2.1.0, 19722 CoordgenLibs 3.0.1, cURL 7.84.0, cuTENSOR 1.6.0.3, einops 0.4.1, 19723 Elk 8.5.2, Emacs 28.1, Embree 3.13.4, FFmpeg 4.4.2 + 5.0.1, fio 19724 3.32, Flask 2.2.2, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, 19725 FreeSurfer 7.3.2, GATE 9.2, GATK 4.2.6.1, GCC(core) 12.2.0, GDB 19726 12.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, GLFW 19727 3.3.8, glib-networking 2.72.1, Globus-CLI 3.6.0, gnuplot 5.4.4, 19728 gperftools 2.10, Graphviz 5.0.0, Gurobi 9.5.2, HDF5 1.12.2, 19729 HTSlib 1.15.1, Hypre 2.25.0, Jansson 2.14, jax 0.3.14, Kalign 19730 3.3.2, kim-api 2.3.0, LAMMPS 23Jun2022, libcerf 2.1, libdwarf 19731 0.4.1, Libint 2.7.2, libQGLViewer 2.8.0, LibSoup 2.74.0, libzip 19732 1.9.2, Lua 5.4.4, lxml 4.9.1, maeparser 1.3.0, matplotlib 3.5.2, 19733 MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, 19734 Mercurial 6.2, MetaEuk 6, Mini-XML-3.3.1, MUMmer 4.0.0rc1, MUMPS 19735 5.5.1, netCDF-Fortran 4.6.0, NGSpeciesID 0.1.2.1, ont-remora 19736 1.0.0, OpenFOAM v2206, OTF2 3.0, parallel 20220722, ParaView 19737 5.10.1, patchelf 0.15.0, Perl 5.36.0, pftoolsV3 3.2.12, PLINK 19738 2.00a3.6, pretty-yaml 21.10.1, PRSice 2.3.5, pugixml 1.12.1, 19739 Pyomo 6.4.2, PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 3.5.0, 19740 PyYAML 6.0, RDKit 2022.03.5, scikit-bio 0.5.7, scikit-build 19741 0.15.0, scikit-learn 1.1.2, scikit-optimize 0.9.0, SCOTCH 7.0.1, 19742 SIONlib 1.7.7, SISSO 3.1, spglib-python 2.0.0, Stacks 2.62, 19743 Stata 17, SUMO 1.14.1, tbb 2021.5.0, tqdm 4.64.0, Transformers 19744 4.21.1, Trycycler 0.5.3, Unicycler 0.5.0, Valgrind 3.19.0, 19745 ViennaRNA 2.5.1, VTune 2022.3.0.eb, wxPython 4.1.1, x264 19746 20220620, Z3 4.10.2, zfp 1.0.0</li> 19747</ul> 19748</li> 19749<li>minor enhancements, including:<ul> 19750<li>add alternate download URL for Voro++ 19751 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15898">#15898</a>)</li> 19752<li>add extra symlinks and sanity checks for libtinfo in ncurses 19753 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15903">#15903</a>)</li> 19754<li>include some easyconfig constants in flake8 configuration file 19755 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16040">#16040</a>)</li> 19756<li>add pigz dependency for cutadapt v3.4 + v3.5 19757 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16056">#16056</a>)</li> 19758<li>add sanity check commands for recent gettext versions (>= 19759 0.20.x) 19760 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16091">#16091</a>)</li> 19761</ul> 19762</li> 19763<li>various bug fixes, including:<ul> 19764<li>use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 19765 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13375">#13375</a>)</li> 19766<li>fix set-alias statements for MaxQuant v2.0.3.0 19767 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15743">#15743</a>)</li> 19768<li>add Autotools build dependency to R 4.2.0 w/ foss 2021b 19769 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15822">#15822</a>)</li> 19770<li>add patch for BLIS to fix auto-detection of POWER 19771 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15826">#15826</a>)</li> 19772<li>downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since 19773 v3.15.3 is too new 19774 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15840">#15840</a>)</li> 19775<li>explicitly enable HDF5 from kallisto v0.46.2 onwards 19776 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15843">#15843</a>)</li> 19777<li>add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all 19778 OSs 19779 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15856">#15856</a>)</li> 19780<li>use build environment set by EasyBuild and add missing 19781 dependency on zlib to minimap2 19782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15859">#15859</a>)</li> 19783<li>
19783add missing dependencies and execute tests on Trycycler v0.5.2 19784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15864">#15864</a>)</li> 19785<li>add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 19786 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15874">#15874</a>)</li> 19787<li>exclude (flaky) <code>fault_tolerance_test</code> and fix non-x86 build for 19788 TensorFlow 2.7.1 19789 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15882">#15882</a>)</li> 19790<li>work around miscompilation of OpenBLAS on POWER by compiling 19791 with <code>-fstack-protector-strong</code> 19792 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15885">#15885</a>)</li> 19793<li>fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 19794 for BLIS (AMD) v2.0 + v3.0 19795 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15889">#15889</a>)</li> 19796<li>add and fix patches for PyTorch 1.9.0 on POWER 19797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15919">#15919</a>)</li> 19798<li>exclude Binary, PackedBinary and JAR easyblocks from binutils 19799 build requirements 19800 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15932">#15932</a>)</li> 19801<li>consistently add libffi + elfutils dependencies to recent Clang 19802 easyconfigs 19803 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16935">#15935</a>, 19804 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16225">#16225</a>)</li> 19805<li>add patch to fix broken test on POWER for numpy in SciPy-bundle 19806 2022.05 19807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15968">#15968</a>)</li> 19808<li>refactor checksum test for extensions to use 19809 <code>collect_exts_file_info</code> 19810 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15973">#15973</a>)</li> 19811<li>fix dependency on FOX Toolkit in SUMO 19812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15986">#15986</a>)</li> 19813<li>add missing SciPy-bundle dependency for rMATS-turbo 19814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15988">#15988</a>)</li> 19815<li>explicitly download wannier90 source tarball from wannier90 19816 GitHub repository in QuantumESPRESSO 7.1 easyconfigs 19817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15993">#15993</a>)</li> 19818<li>restore ploteig in EIGENSOFT 7.2.1 19819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15996">#15996</a>)</li> 19820<li>add alternative checksum for plot3Drgl extension in R v4.1.x + 19821 v4.2.0 easyconfigs 19822 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16011">#16011</a>)</li> 19823<li>add patch to fix missing sync in LINCS and SETTLE CUDA kernels 19824 for GROMACS 2020 19825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16027">#16027</a>) 19826 and 2021 19827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16026">#16026</a>)</li> 19828<li>exclude failing test in TensorFlow 2.4.1 19829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16042">#16042</a>)</li> 19830<li>skip NASA performance and remote server tests in netCDF v4.9.0 19831 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16050">#16050</a>, 19832 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16158">#16158</a>)</li> 19833<li>use versioned symbols in ncurses built with system toolchain (by 19834 adding <code>--with-versioned-syms</code> configure option) 19835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16064">#16064</a>)</li> 19836<li>add patch to fix pkgconfig file for Blitz++ v1.0.2 19837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16102">#16102</a>)</li> 19838<li>
19838add missing BCFtools dependency for recent medaka versions 19839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16107">#16107</a>)</li> 19840<li>add GTK2 v2.24.33 as a dependency for Ghostscript v9.56.1 19841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16112">#16112</a>)</li> 19842<li>fix checksum for Stacks v2.62 (due to silent re-release without 19843 version bump) 19844 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16134">#16134</a>)</li> 19845<li>fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 19846 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16145">#16145</a>)</li> 19847<li>fix top level Makefile for AmberTools 20 and enable tests 19848 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16150">#16150</a>)</li> 19849<li>add missing patches + enable running tests for AmberTools 21 19850 with intel/2021a 19851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16151">#16151</a>) 19852 and intel/2021b 19853 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16152">#16152</a>)</li> 19854<li>replace HDF5 v1.13.1 with v1.12.1 as dependency, since we 19855 shouldn't use odd minor versions of HDF5 which are not stable 19856 releases 19857 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16153">#16153</a>)</li> 19858<li>remove modextrapaths to add top-level install directory to 19859 <code>$PATH</code>for recent InterProScan easyconfigs (now done by default 19860 by Binary easyblock) 19861 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16167">#16167</a>)</li> 19862<li>fix sources + source URL + homepage for Molekel v5.4.0 19863 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16219">#16219</a>)</li> 19864<li>consistently add maeparser + CoordgenLibs dependencies to 19865 OpenBabel 3.1.1 easyconfigs 19866 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16231">#16231</a>)</li> 19867<li>fix checksum for CUDA 11.4.1 aarch64 installer 19868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16234">#16234</a>)</li> 19869<li>remove incorrect comment for Boost dependency in OpenBabel 3.1.1 19870 easyconfigs 19871 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16238">#16238</a>)</li> 19872<li>add direct Pango dependency in recent ImageMagick easyconfigs 19873 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16237">#16237</a>)</li> 19874</ul> 19875</li> 19876<li>other changes:<ul> 19877<li>remove superfluous <code>-DCMAKE_BUILD_TYPE=Release</code>, use of 19878 <code>build_type = Release</code>, or enabling <code>separate_build_dir</code> from 19879 easyconfigs using CMakeMake easyblock 19880 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13384">#13384</a>)</li> 19881<li>synchronize ncurses easyconfigs using system toolchain 19882 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15903">#15903</a>)</li> 19883<li>stick to Java/11 as dependency for Bazel 5.1.1 (which is 19884 available for x86_64, aarch64, ppc64le) 19885 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15906">#15906</a>)</li> 19886<li>speed up OpenMPI 4.1.4 configure by not running 19887 <code>autogen.pl --force</code>, but only running required Autotools 19888 commands 19889 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15957">#15957</a>)</li> 19890<li>replace sed commands by upstreamed patches for BLIS built with 19891 intel-compilers toolchain 19892 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15958">#15958</a>)</li> 19893<li>simplify AlphaFold foss/2021a easyconfigs by using a fleshed out 19894 patched OpenMM dependency 19895 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15981">#15981</a>)</li> 19896<li>update Java/11 to 11.0.16 and Java/17 to 17.0.4 19897 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16001">#16001</a>)</li> 19898<li>remove unnecessary patch in recent JupyterLab 19899 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16030">#16030</a>)</li> 19900<li>update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is 19901 deprecated) 19902 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16070">#16070</a>)</li> 19903<li>make check for toolchain value in dependency spec in easyconfigs 19904 test suite aware that dumped easyconfig uses <code>SYSTEM</code> constant 19905 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/16126">#16126</a>)</li> 19906</ul> 19907</li> 19908</ul> 19909<h2 id="release_notes_eb460">EasyBuild v4.6.0 (July 8th 2022)<a class="headerlink" href="#release_notes_eb460" title="Permanent link">¶</a></h2> 19910<p>feature release</p> 19911<p><strong>framework</strong></p> 19912<ul> 19913<li>various enhancements, including:<ul> 19914<li>allow searching for sources/patches in alternative location by 19915 specifying '<code>alt_location</code>' in source/patch spec 19916 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3994">#3994</a>)</li> 19917<li>show URLs used for download attempts in trace output 19918 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4026">#4026</a>)</li> 19919<li>
19919add support for setting environment variables via '<code>pushenv</code>' 19920 with <code>modextravars</code> 19921 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4030">#4030</a>)</li> 19922<li>add support for OneAPI compilers using toolchain option 19923 '<code>oneapi</code>' 19924 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4031">#4031</a>, 19925 <a href="https://github.com/easybuilders/easybuild-framework/pull/4032">#4032</a>, 19926 <a href="https://github.com/easybuilders/easybuild-framework/pull/4039">#4039</a>)</li> 19927<li>make <code>check_linked_shared_libs</code> more robust by taking into 19928 account that '<code>ldd</code>' may fail 19929 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4033">#4033</a>)</li> 19930<li>fall back to sequential extension install if parallel install is 19931 not implemented 19932 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4034">#4034</a>)</li> 19933<li>add support for using template values in name/version of 19934 extensions 19935 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4036">#4036</a>)</li> 19936</ul> 19937</li> 19938<li>various bug fixes, including:<ul> 19939<li>make sure that <code>ARCH</code> constant has '<code>aarch64</code>' (rather than 19940 '<code>arm64</code>') as value on macOS ARM 19941 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4018">#4018</a>)</li> 19942<li>tweak '<code>eb</code>' wrapper script to correctly handle errors when 19943 python command being considered fails to run 19944 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4019">#4019</a>)</li> 19945<li>tweak <code>is_patch_for</code> function to make it more robust 19946 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4028">#4028</a>)</li> 19947</ul> 19948</li> 19949<li>other changes:<ul> 19950<li>update Lmod used to run tests to version 8.7.6 19951 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4027">#4027</a>, 19952 <a href="https://github.com/easybuilders/easybuild-framework/pull/4030">#4030</a>)</li> 19953<li>tweak <code>apply_patch</code> to not create <code>.orig files</code> (by default) 19954 when applying patch files 19955 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4038">#4038</a>)</li> 19956</ul> 19957</li> 19958</ul> 19959<p><strong>easyblocks</strong></p> 19960<ul> 19961<li>new software-specific easyblock for STAR-CCM+ 19962 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1613">#1613</a>)</li> 19963<li>minor enhancements and updates, including:<ul> 19964<li>update Siesta EasyBlock to support GCC 10+ by adding 19965 <code>-fallow-argument-mismatch</code> Fortran compiler option 19966 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2690">#2690</a>)</li> 19967<li>enable building of shared library for Libint 2.7+ 19968 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2738">#2738</a>)</li> 19969<li>allow some PyTorch tests to fail + print warning if one or more 19970 tests fail 19971 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2742">#2742</a>)</li> 19972<li>also support OpenSSL 3.0 in OpenSSL wrapper easyblock 19973 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2746">#2746</a>)</li> 19974<li>add more logging to <code>install_pc_files</code> method of OpenSSL wrapper 19975 easyblock 19976 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2752">#2752</a>)</li> 19977<li>make WPS easyblock aware of <code>(pre)buildopts</code> 19978 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2754">#2754</a>)</li> 19979<li>add Abseil system dependency for TensorFlow 2.9+ 19980 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2757">#2757</a>)</li> 19981<li>disable altivec when building FFTW versions < 3.4 with 19982 single-precision with GCC on POWER 19983 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2758">#2758</a>)</li> 19984</ul> 19985</li> 19986<li>various bug fixes, including:<ul> 19987<li>make VEP easyblock compatible with <code>--sanity-check-only</code> 19988 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2743">#2743</a>)</li> 19989<li>update Rosetta easyblock to take into account that 19990 <code>$LD_LIBRARY_PATH</code>, <code>$CPATH</code>, <code>$PATH</code> may not be defined 19991 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2744">#2744</a>)</li> 19992<li>only load temporary module file during sanity check for pybind11 19993 for stand-alone installations, so it can be installed as 19994 extension 19995 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2747">#2747</a>)</li> 19996<li>make sure that <code>CMakeMakeCp</code> uses correct build dir 19997 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2748">#2748</a>)</li> 19998<li>enhance Bazel easyblock to avoid writing to <code>$HOME</code> in sanity 19999 check 20000 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2756">#2756</a>)</li> 20001</ul> 20002</li> 20003</ul> 20004<p><strong>easyconfigs</strong></p> 20005<ul> 20006<li> 20007<p>added easyconfigs for <code>foss/2022a</code>, <code>intel/2022a</code> common toolchains 20008 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15755">#15755</a>)</p> 20009<ul> 20010<li>see also 20011 <a href="https://docs.easybuild.io/en/latest/Common-toolchains.html">https://docs.easybuild.io/en/latest/Common-toolchains.html</a></li> 20012</ul> 20013</li> 20014<li> 20015<p>add easyconfig for <code>gfbf/2022a</code> toolchain 20016 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15653">#15653</a>, 20017 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15755">#15755</a>)</p> 20018</li> 20019<li> 20020<p>added example easyconfig files for 24 new software packages:</p> 20021<ul> 20022<li>BLT 20023 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15624">#15624</a>), 20024 category_encoders 20025 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15638">#15638</a>), 20026 fio 20027 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10321">#10321</a>), 20028 FSON 20029 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15721">#15721</a>), 20030 G-PhoCS 20031 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7619">#7619</a>), 20032 GCTA 20033 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15649">#15649</a>), 20034 Gibbs2 20035 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15702">#15702</a>), 20036 InterProScan_data 20037 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15717">#15717</a>), 20038 Jorg 20039 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15346">#15346</a>), 20040 libopus 20041 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15682">#15682</a>), 20042 Minipolish 20043 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15713">#15713</a>), 20044 mm-common 20045 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15764">#15764</a>), 20046 MONA 20047 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15696">#15696</a>), 20048 NetPyNE 20049 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15606">#15606</a>), 20050 pfind 20051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15685">#15685</a>), 20052 regionmask 20053 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15786">#15786</a>), 20054 samplot 20055 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15686">#15686</a>), 20056 SISSO 20057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15766">#15766</a>), 20058 sklearn-pandas 20059 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15637">#15637</a>), 20060 STAR-CCM+ 20061 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7398">#7398</a>), 20062 SWIPE 20063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6795">#6795</a>), 20064 topaz 20065 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15739">
20065#15739</a>), 20066 uncertainty-calibration 20067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15612">#15612</a>), 20068 Virtuoso-opensource 20069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14102">#14102</a>)</li> 20070</ul> 20071</li> 20072<li> 20073<p>added additional easyconfigs for various supported software 20074 packages, including:</p> 20075<ul> 20076<li>AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, Bracken 2.7, 20077 CellRanger 7.0.0, Clp 1.17.7, CoinUtils 2.11.6, cppy 1.2.1, 20078 deal.II 9.3.3, double-conversion 3.2.0, Doxygen 1.9.4, FLAC 20079 1.3.4, fmt 7.1.1, FSL 6.0.5.1, GDAL 3.5.0, gdbm 1.21, geopandas 20080 0.11.0, GEOS 3.10.3, Ghostscript 9.56.1, GLibmm 2.66.4, Groovy 20081 4.0.3, GULP 6.1, h5py 3.7.0, HDF5 1.13.1, hifiasm 0.16.1, 20082 IGMPlot 2.6.9b, ImageMagick 7.1.0-37, InterProScan 5.55-88.0, 20083 IRkernel 1.3, jemalloc 5.3.0, JsonCpp 1.9.5, Julia 1.7.3, 20084 Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 20085 1.17, libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, libxc 20086 5.2.3, libxml++ 2.42.1, line_profiler 3.5.1, LittleCMS 2.13.1, 20087 MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, NCCL 20088 2.12.12, netCDF 4.9.0, nettle 3.8, networkx 2.8.4, NEURON 7.8.2, 20089 NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, 20090 nvtop 2.0.2, Osi 0.108.7, p4est 2.8, parasail 2.5, Pillow 9.1.1, 20091 PLUMED 2.8.0, PnetCDF 1.12.3, PRISMS-PF 2.2, PROJ 9.0.0, 20092 protobuf 3.19.4, protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 20093 3.1.6, pyproj 3.3.1, PyTorch 1.11.0, Qhull 2020.2, Qt5 5.15.5, 20094 QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, rasterio 1.2.10, 20095 Ray-project 1.13.0, RE2 2022-06-01, redis-py 4.3.3, ReFrame 20096 3.11.2, rioxarray 0.11.1, RNA-SeQC 2.4.2, Schrodinger 2022-2, 20097 Shapely 1.8.2, Siesta 4.1.5, SimpleITK 2.1.1.2, SpectrA 1.0.1, 20098 TensorFlow 2.7.1, Tk 8.6.12, Tkinter 3.10.4, Transformers 20099 4.20.1, UCX-CUDA 1.12.1, utf8proc 2.7.0, WhatsHap 1.4, WPS 20100 3.9.1, Xvfb 21.1.3</li> 20101</ul> 20102</li> 20103<li> 20104<p>minor enhancements, including:</p> 20105<ul> 20106<li>add extensions to R v4.2.0: hypergeo 20107 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15701">#15701</a>), 20108 rtdists 20109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15734">#15734</a>), 20110 geeM 20111 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15810">#15810</a>)</li> 20112<li>add patch for GCCcore 11.3.0 to support using <code>-fuse-ld=mold</code> 20113 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15715">#15715</a>)</li> 20114<li>add patch for porefoam to fix hardcoded <code>mpirun</code> command and 20115 take into account <code>$POREFOAM_MPIRUN_CMD</code> 20116 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15730">#15730</a>)</li> 20117</ul> 20118</li> 20119<li> 20120<p>various bug fixes, including:</p> 20121<ul> 20122<li>switch to Rust 1.60.0 build dependency for bamtofastq, since 20123 build fails with Rust 1.52.1 20124 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15636">#15636</a>)</li> 20125<li>avoid that pygmo v2.18.0 installs stuff in Python installation 20126 directory + add custom sanity check paths to pygmo easyconfigs 20127 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15657">#15657</a>)</li> 20128<li>add patch for Mmg v5.6.0 to remove library CI tests that point 20129 to external sources 20130 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15691">#15691</a>)</li> 20131<li>correct configopts in deal.II v9.1.1 easyconfig 20132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15692">#15692</a>)</li> 20133<li>add missing Python dependency for HPDBSCAN to fix unresolved 20134 <code>%(pyshortver)s</code> template 20135 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15694">#15694</a>)</li> 20136</ul> 20137</li> 20138<li> 20139<p>other changes:</p> 20140<ul> 20141<li>disable flaky GPU test for TensorFlow 2.6.0 20142 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15824">#15824</a>)</li> 20143</ul> 20144</li> 20145</ul> 20146<h2 id="release_notes_eb455">EasyBuild v4.5.5 (June 8th 2022)<a class="headerlink" href="#release_notes_eb455" title="Permanent link">¶</a></h2> 20147<p>bugfix/update release</p> 20148<p><strong>framework</strong></p> 20149<ul> 20150<li>various enhancements, including:<ul> 20151<li>add toolchain definitions for <code>nvompi</code> (NVHPC + OpenMPI) 20152 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3969">#3969</a>), 20153 <code>nvpsmpi</code> (NVHPC + ParaStationMPI) 20154 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3970">#3970</a>), 20155 <code>gfbf</code> (GCC, FlexiBLAS, FFTW) 20156 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4006">#4006</a>)</li> 20157<li>
20157add support for <code>FFTW.MPI</code> toolchain component (<code>$FFT*DIR</code> 20158 variables) 20159 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4012">#4012</a>)</li> 20160<li>add support for customizing EasyBuild command used in jobs via 20161 <code>--job-eb-cmd</code> 20162 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4016">#4016</a>)</li> 20163</ul> 20164</li> 20165<li>various bug fixes, including:<ul> 20166<li>fix copying of easyconfig file with <code>--copy-ec</code> without 20167 <code>--rebuild</code> if module is already installed 20168 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3993">#3993</a>)</li> 20169<li>ignore deprecation warnings regarding cryptography in Python 20170 3.6 + Blowfish with Python 3.10 in test suite output 20171 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3999">#3999</a>)</li> 20172<li>fix typo in debug log message in <code>easyblock.py</code> 20173 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4000">#4000</a>)</li> 20174<li>fix printing of list of attempted download URLs when url-encoded 20175 characters are used in URL 20176 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4005">#4005</a>)</li> 20177<li>set <code>$FFT(W)_LIB_DIR</code> to imkl-FFTW's lib path in build 20178 environment if usempi toolchain option is enabled 20179 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4011">#4011</a>)</li> 20180<li>correctly identify Apple Silicon M1 as Arm 64-bit by also 20181 considering arm64 next to aarch64 20182 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4014">#4014</a>)</li> 20183<li>fix '<code>eb --show-system-info</code>' on Apple M1 system 20184 (<a href="https://github.com/easybuilders/easybuild-framework/pull/4015">#4015</a>)</li> 20185</ul> 20186</li> 20187<li>other changes:<ul> 20188<li>change '<code>eb</code>' command to <code>import easybuild.framework</code> to check 20189 if EasyBuild framework is available 20190 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3995">#3995</a>, 20191 <a href="https://github.com/easybuilders/easybuild-framework/pull/3998">#3998</a>)</li> 20192</ul> 20193</li> 20194</ul> 20195<p><strong>easyblocks</strong></p> 20196<ul> 20197<li>new software-specific easyblock for FFTW.MPI 20198 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2724">#2724</a>)</li> 20199<li>minor enhancements and updates, including:<ul> 20200<li>update NEURON easyblock to use CMakeMake for recent versions 20201 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2304">#2304</a>)</li> 20202<li>enhance Clang easyblock to add support for building with AMDGPU 20203 offload 20204 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2684">#2684</a>, 20205 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2729">#2729</a>)</li> 20206<li>update sanity check in OpenMPI easyblock to support OpenMPI 20207 v5.0.0 20208 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2709">#2709</a>)</li> 20209<li>don't use <code>gold</code> linker by default for GCC >= 11.3 20210 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2711">#2711</a>)</li> 20211<li>update sanity check in R easyblock for versions >= 4.2.0, since 20212 S.h is not included anymore 20213 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2713">#2713</a>)</li> 20214<li>update ABAQUS easyblock for ABAQUS 2022 20215 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2716">#2716</a>)</li> 20216<li>update LLVM easyblock for LLVM v14.0.x 20217 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2718">#2718</a>)</li> 20218<li>update Mesa easyblock to remove swr driver configopts for 20219 versions 22+ 20220 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2719">#2719</a>)</li> 20221<li>enhance Clang easyblock to support also installing Python 20222 bindings 20223 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2721">#2721</a>, 20224 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2725">#2725</a>)</li> 20225<li>enhance SuperLU easyblock to support building on top of 20226 FlexiBLAS and be compatible with SuperLU v5.3 20227 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2722">#2722</a>)</li> 20228<li>update TensorFlow easyblock for version 2.8.0 20229 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2723">#2723</a>)</li> 20230<li>modify FFTW's sanity check step to allow checking only for MPI 20231 parts of FFTW installation 20232 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2724">#2724</a>)</li> 20233<li>
20233add support to ConfigureMake for tweaking (first part of) test 20234 command via '<code>test_cmd</code>' 20235 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2726">#2726</a>, 20236 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2737">#2737</a>)</li> 20237<li>enhance MrBayes easyblock with custom sanity check command 20238 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2727">#2727</a>)</li> 20239<li>update cudnnarch string templates used to compose source tarball 20240 names from cuDNN 8.3.3 onwards 20241 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2728">#2728</a>)</li> 20242<li>add sanity check command to OpenSSL wrapper easyblock to verify 20243 that system certificates are available to OpenSSL 20244 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2735">#2735</a>)</li> 20245<li>ignore exit code of <code>pkg-config</code> command in OpenSSL wrapper 20246 easyblock, since with <code>pkgconf</code> they exit with a non-zero exit 20247 code if the OS package is not installed 20248 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2736">#2736</a>)</li> 20249</ul> 20250</li> 20251<li>various bug fixes, including:<ul> 20252<li>remove system-compiled binutils dirs from <code>$LDFLAGS</code> in binutils 20253 easyblock 20254 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2712">#2712</a>)</li> 20255<li>fix for FreeSurfer easyblock: define <code>$FREESURFER</code> needed by 20256 recon_all 20257 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2717">#2717</a>)</li> 20258<li>also symlink <code>cert.pem</code> in from-source OpenSSL installation (if 20259 it exists) 20260 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2735">#2735</a>)</li> 20261</ul> 20262</li> 20263</ul> 20264<p><strong>easyconfigs</strong></p> 20265<ul> 20266<li>add candidates for 2022a common toolchains: <code>foss/2022.05</code> 20267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15561">#15561</a>), 20268 intel/2022.05 20269 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15485">#15485</a>)</li> 20270<li>added example easyconfig files for 35 new software packages:<ul> 20271<li>Albumentations 20272 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15302">#15302</a>), 20273 AMPtk 20274 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15435">#15435</a>), 20275 arosics 20276 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15249">#15249</a>), 20277 CellTypist 20278 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15530">#15530</a>), 20279 detectron2 20280 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15442">#15442</a>), 20281 EigenExa 20282 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15234">#15234</a>), 20283 Fastaq 20284 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15332">#15332</a>), 20285 FFTW.MPI 20286 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15561">#15561</a>), 20287 FreeBarcodes 20288 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15350">#15350</a>), 20289 gcloud 20290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15443">#15443</a>), 20291 GST-plugins-bad 20292 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15446">#15446</a>), 20293 gsutil 20294 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15507">#15507</a>), 20295 GTK4 20296 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15447">#15447</a>), 20297 hector 20298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15397">#15397</a>), 20299 i7z 20300 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15236">#15236</a>), 20301 libde265 20302 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15395">#15395</a>), 20303 libheif 20304 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15395">#15395</a>), 20305 ModelTest-NG 20306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15448">#15448</a>), 20307 num2words 20308 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15473">#15473</a>), 20309 OGDF 20310 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15407">#15407</a>), 20311 panito 20312 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15314">#15314</a>), 20313 parameterized 20314 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15481">#15481</a>), 20315 purge_dups 20316 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15385">#15385</a>), 20317 redis-py 20318 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15475">#15475</a>), 20319 ruamel.yaml 20320 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15531">#15531</a>), 20321 SCGid 20322 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15065">#15065</a>), 20323 scPred 20324 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15575">#15575</a>), 20325 slow5tools 20326 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15457">#15457</a>), 20327 smooth-topk 20328 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15506">#15506</a>), 20329 SPOTPY 20330 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15326">#15326</a>), 20331 tmap 20332 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14601">#14601</a>), 20333 UCC 20334 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14291">#14291</a>), 20335 Wayland 20336 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11107">#11107</a>), 20337 XGrafix 20338 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15268">#15268</a>), 20339 XPLOR-NIH 20340 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15479">#15479</a>)</li> 20341</ul> 20342</li> 20343<li>
20343added additional easyconfigs for various supported software 20344 packages, including:<ul> 20345<li>ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 20346 5.0.4, ATK 2.38.0, Autotools 20220317, Bader 1.04, Bazel 4.2.2 + 20347 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 20348 0.9.0, Boost 1.79.0, breseq 0.36.1, bx-python 0.8.13, cairo 20349 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0, CUDA 20350 11.7.0, cuDNN 8.4.1.50, cURL 7.83.0, DBus 1.14.0, eggnog-mapper 20351 2.1.7, elfutils 0.187, EvidentialGene 2022.01.14, expat 2.4.8, 20352 FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, freebayes 20353 1.3.6, freeglut 3.2.2, freetype 2.12.1, FriBidi 1.0.12, GCC 20354 9.5.0 + 11.3.0 + GCC 12.1.0, Gdk-Pixbuf 2.42.8, geopandas 20355 0.10.2, git 2.36.0, GLib 2.72.1, GMAP-GSNAP 2021-21-17, Go 20356 1.18.1, GObject-Introspection 1.72.0, Graphene 1.10.8, 20357 GST-plugins-base 1.20.2, GStreamer 1.20.2, GTDB-Tk 2.0.0, GTK3 20358 3.24.33, gzip 1.12, HarfBuzz 4.2.1, help2man 1.49.2, hwloc 20359 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, ICU 71.1, IGV 2.12.3, 20360 IMB 2021.3, inferCNV 1.10.1, InterProScan 5.52, IQ-TREE 2.2.1, 20361 jax 0.3.9, json-c 0.16, LAPACK 3.10.1, libarchive 3.6.1, 20362 libdeflate 1.10, libdrm 2.4.110, libedit 20210910, libepoxy 20363 1.5.10, libfabric 1.15.1, libglvnd 1.4.0, libjpeg-turbo 2.1.3, 20364 libreadline 8.1.2, librsb 1.3.0.1, librsvg 2.52.8, libtool 20365 2.4.7, libunwind 1.6.2, libxml2 2.9.13, LLVM 14.0.3, LocARNA 20366 1.9.2.3, MACS2 2.2.7.1, magma 2.6.2, Mako 1.2.0, Mathematica 20367 13.0.0, MCL 14.137, MCR R2022a.1, Mesa 22.0.3, Meson 0.62.1, 20368 MIRA 5.0rc2, Mmg 5.6.0, mold 1.2.1, mosdepth 0.3.3, MrBayes 20369 3.2.7a, MultiQC 1.12, MUMPS 5.5.0, muParser 2.3.3, ncurses 6.3, 20370 neptune-client 0.16.2, Nextflow 22.04.0, Nim 1.6.6, NTPoly 20371 2.7.1, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSSL 1.1.1n, 20372 OpenStackClient 5.8.0, OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, 20373 Pango 1.50.7, parallel-fastq-dump 0.6.7, PCRE2 10.40, Perl 20374 5.34.1, Pillow 9.1.0, PLINK 2.00a3.1, PMIx 4.1.2, PyAMG 4.2.3, 20375 pybind11 2.9.2, PyCairo 1.21.0, pygmo 2.18.0, PyGObject 3.42.1, 20376 Python 3.10.4, R 4.2.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 20377 3.15, ReFrame 3.11.0, RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Rust 20378 1.60.0, Sambamba 0.8.2, SAMtools 1.15.1, ScaLAPACK 2.2.0, 20379 SciPy-bundle 2022.05, SeqKit 2.2.0, Shapely 1.8.1.post1, 20380 SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, SQLite 3.38.3, 20381 StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, 20382 Tcl 8.6.12, TCLAP 1.2.5, tcsh 6.24.01, texlive 20220321, ToFu 20383 1.5.0, UCX 1.12.1, util-linux 2.38, VEP 105, ViennaRNA 2.5.0, 20384 vsc-mympirun 5.2.11, worker 1.6.13, X11 2022050, YAXT 0.9.2.1, 20385 Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2</li> 20386</ul> 20387</li> 20388<li>minor enhancements, including:<ul> 20389<li>use OpenSSL wrapper dependency for CMake 3.18.4 with system 20390 toolchain 20391 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15227">#15227</a>)</li> 20392<li>also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 20393 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15347">#15347</a>)</li> 20394<li>add extensions to R v4.1.2 + v4.2.0 easyconfigs:<ul> 20395<li>Hmsc 20396 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15393">#15393</a>), 20397 MonteCarlo + RhpcBLASctl 20398 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15438">#15438</a>), 20399 chkptstanr 20400 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15540">#15540</a>), 20401 chkptstanr + MLmetrics + renv 20402 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15573">#15573</a>)</li> 20403</ul> 20404</li> 20405<li>add extensions to R-bundle-Bioconductor 3.14 easyconfig: 20406 DNABarcodes 20407 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15405">#15405</a>)</li> 20408<li>use redist source_urls for cuDNN > 7.5 20409 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15411">#15411</a>)</li> 20410<li>add download_instructions to Java 1.8 > 200 20411 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15412">
20411#15412</a>)</li> 20412<li>update Arrow to use EB versions of some dependencies and enable 20413 all compression codecs 20414 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15512">#15512</a>)</li> 20415<li>add csh -> tcsh symlink in recent tcsh easyconfigs 20416 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15571">#15571</a>)</li> 20417<li>allow external tools to be located elsewhere for ETE 20418 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15578">#15578</a>)</li> 20419<li>add additional sanity check commands for IQ-TREE v2.2.1 20420 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15596">#15596</a>)</li> 20421</ul> 20422</li> 20423<li>various bug fixes, including:<ul> 20424<li>fix source URL for freetype 2.6.5 with <code>foss/2016b</code> 20425 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14204">#14204</a>)</li> 20426<li>fix installation of easybuild-easyconfigs with setuptools>=61 20427 by explicitly declaring there are no Python packages 20428 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15206">#15206</a>)</li> 20429<li>use x.py to bootstrap Rust so that build options are properly 20430 passed through 20431 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15211">#15211</a>)</li> 20432<li>fix RepeatMasker-4.1.2-p1 easyconfig by moving the database 20433 configure command to postinstallcmds 20434 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15280">#15280</a>, 20435 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15615">#15615</a>)</li> 20436<li>add hwloc dependency to tbb v2021.4.0 20437 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15294">#15294</a>)</li> 20438<li>tweak find command used in preconfigopts in easyconfig for 20439 pkg-config v0.29.2 with system toolchain to avoid descending 20440 into other filesystems 20441 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15313">#15313</a>)</li> 20442<li>remove pkg-config use from SeqLib configure patch (avoids 20443 problem due to faulty autoconf macro) 20444 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15316">#15316</a>)</li> 20445<li>update source URL for isl in GCCcore easyconfigs 20446 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15320">#15320</a>)</li> 20447<li>update source URLs for YAXT 0.9.x to fix download 20448 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15323">#15323</a>)</li> 20449<li>define <code>$HHLIB</code> as path to HH-suite installation directory, 20450 required by Perl scripts 20451 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15324">#15324</a>)</li> 20452<li>add missing parallel and tbl2asn dependencies for prokka 1.14.5 20453 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15360">#15360</a>, 20454 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15381">#15381</a>)</li> 20455<li>add missing dependencies for libheif (libpng, libjpeg-turbo) 20456 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15408">#15408</a>)</li> 20457<li>switch to configuring build of libheif with CMake so libde265 20458 dependency is picked up 20459 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15408">#15408</a>)</li> 20460<li>disable use of <code>-ftree-vectorize</code> for OpenFOAM v2112 with 20461 <code>foss/2021b</code> 20462 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15495">#15495</a>)</li> 20463<li>add patch for OpenMPI 4.1.1 to support building using 20464 <code>--with-cuda=internal</code> 20465 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15528">#15528</a>, 20466 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15589">#15589</a>)</li> 20467<li>add patch to fix support for external PMIx v3.1 in OpenMPI 20468 v3.1.3 20469 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15566">#15566</a>)</li> 20470<li>also build shared library + fix <code>$PYTHONPATH</code> for gmsh 4.9.0 20471 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15579">#15579</a>)</li> 20472<li>
20472add patch for GLib 2.68.2 to fix use of close_range 20473 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15594">#15594</a>)</li> 20474<li>fix download of thrift 0.12.0 for Arrow 0.16.0 20475 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15597">#15597</a>)</li> 20476<li>add Bison and flex build dependencies to SCOTCH 6.1.x 20477 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15618">#15618</a>)</li> 20478<li>add alternative checksums for class, nnet, spatial extensions in 20479 R v4.2.0 easyconfig 20480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15619">#15619</a>)</li> 20481<li>add missing dependencies + switch to non-static build for Arriba 20482 v2.1.0 20483 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15623">#15623</a>)</li> 20484</ul> 20485</li> 20486<li>other changes:<ul> 20487<li>add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to 20488 <code>foss/2021b</code> toochain 20489 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15216">#15216</a>)</li> 20490<li>update fallback version for OpenSSL 1.1 wrapper to v1.1.1o 20491 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15592">#15592</a>)</li> 20492<li>install sklearn meta-package with scikit-learn v1.0.1 20493 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15613">#15613</a>)</li> 20494<li>switch from <code>pkg-config</code> to <code>pkgconf</code> as build dependency for 20495 OpenSSL wrapper easyconfigs 20496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15616">#15616</a>, 20497 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15617">#15617</a>)</li> 20498</ul> 20499</li> 20500</ul> 20501<h2 id="release_notes_eb454">EasyBuild v4.5.4 (March 31st 2022)<a class="headerlink" href="#release_notes_eb454" title="Permanent link">¶</a></h2> 20502<p>bugfix/update release</p> 20503<p><strong>framework</strong></p> 20504<ul> 20505<li>various enhancements, including:<ul> 20506<li>warn about potentially missing patches in <code>--new-pr</code> 20507 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3759">#3759</a>, 20508 <a href="https://github.com/easybuilders/easybuild-framework/pull/3966">#3966</a>)</li> 20509<li>add support for '<code>clone_into</code>' field in git_config source spec 20510 to specify different name for top-level directory 20511 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3949">#3949</a>)</li> 20512<li>add bash completion for easyconfigs from local dir but not robot 20513 search path 20514 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3953">#3953</a>)</li> 20515<li>add a 'sync pr' message when the PR has a mergeable state but 20516 is showing a failed status for the test suite on the last commit 20517 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3967">#3967</a>)</li> 20518<li>add <code>gmpit</code> toolchain definition (GCC + MPItrampoline) 20519 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3971">#3971</a>)</li> 20520<li>use '<code>zypper search -i</code>' to check whether specified OS 20521 dependency is installed on openSUSE + make sure that rpm is 20522 considered for checking OS dependencies on RHEL8 20523 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3973">#3973</a>)</li> 20524<li>add support for post-install patches 20525 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3974">#3974</a>)</li> 20526<li>add support for '<code>download_instructions</code>' easyconfig parameter 20527 key to specify some download or installation steps for user in 20528 case of complicated way of obtaining needed files 20529 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3976">#3976</a>, 20530 <a href="https://github.com/easybuilders/easybuild-framework/pull/3981">#3981</a>)</li> 20531<li>also try collecting AMD GPU info (via <code>rocm-smi</code>) for 20532 <code>--show-system-info</code> 20533 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3978">#3978</a>, 20534 <a href="https://github.com/easybuilders/easybuild-framework/pull/3982">#3982</a>)</li> 20535</ul> 20536</li> 20537<li>various bug fixes, including:<ul> 20538<li>ensure <code>--review-pr</code> can find dependencies included in PR 20539 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3979">#3979</a>)</li> 20540<li>run '<code>apt-get update</code>' in GitHub Actions workflow for 20541 container tests to update container package list before 20542 installing anything 20543 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3985">#3985</a>)</li> 20544</ul> 20545</li> 20546<li>other changes:<ul> 20547<li>
20547enable code linting check for all supported Python versions 20548 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3725">#3725</a>)</li> 20549<li>update copyright lines for 2022 20550 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3986">#3986</a>)</li> 20551</ul> 20552</li> 20553</ul> 20554<p><strong>easyblocks</strong></p> 20555<ul> 20556<li>minor enhancements and updates, including:<ul> 20557<li>update Clang-AOMP easyblock to add support for ROCm v5.0 20558 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2681">#2681</a>)</li> 20559<li>enable system SSL certificates in OpenSSL installations 20560 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2683">#2683</a>)</li> 20561<li>enhance MRtrix easyblock: build in parallel + enable OpenMP 20562 support for MRtrix >= 3.0 20563 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2685">#2685</a>)</li> 20564<li>avoid dependency on '<code>which</code>' command in sanity check for 20565 Python, use '<code>command -v</code>' instead 20566 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2687">#2687</a>)</li> 20567<li>enhance Tarball easyblock to support using it for installing 20568 extensions 20569 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2688">#2688</a>)</li> 20570<li>update wxPython easyblock to support wxPython v4.1 20571 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2689">#2689</a>)</li> 20572<li>enhance Gurobi easyblock to also update <code>$MATLABPATH</code> 20573 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2691">#2691</a>)</li> 20574<li>build single-file shared libraries for imkl so it can be used as 20575 FlexiBLAS backend via <code>$FLEXIBLAS_LIBRARY_PATH</code> 20576 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2694">#2694</a>)</li> 20577</ul> 20578</li> 20579<li>various bug fixes, including:<ul> 20580<li>added regex to replace /lib/cpp with cpp in OpenFOAM's wmake 20581 rules file 20582 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2331">#2331</a>)</li> 20583<li>set <code>$NINJAFLAGS</code> to make sure Ninja doesn't use all visible 20584 cores when building Qt5 20585 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2338">#2338</a>)</li> 20586<li>update Siesta EasyBlock to use serial FFTW 20587 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2662">#2662</a>)</li> 20588<li>fix support for imkl for numexpr 2.8.0+ in numexpr easyblock 20589 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2678">#2678</a>)</li> 20590<li>make sure TensorFlow doesn't see the <code>nvptx-none</code> dir when 20591 searching for <code>gcc</code> include dir 20592 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2682">#2682</a>)</li> 20593<li>force use of bash for Anaconda install script 20594 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2692">#2692</a>)</li> 20595<li>add guess for path to add to <code>$MANPATH</code> for intel-compilers 20596 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2696">#2696</a>)</li> 20597<li>change permissions of the Java build directory to avoid 20598 permission denied error 20599 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2698">#2698</a>)</li> 20600<li>also consider <code>$MKLROOT/lib/pkgconfig</code> for <code>$PKG_CONFIG_PATH</code> 20601 for imkl 20602 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2701">#2701</a>)</li> 20603<li>close log after installing Bundle component 20604 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2702">#2702</a>)<ul> 20605<li>fixes problem of log leaking across installations 20606 (<a href="https://github.com/easybuilders/easybuild-framework/issues/3533">framework issue 20607 #3533</a>)</li> 20608</ul> 20609</li> 20610<li>replace hardcoded /tmp to make sure that Bazel build respects 20611 <code>$TMPDIR</code> 20612 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2703">#2703</a>)</li> 20613</ul> 20614</li> 20615<li>other changes:<ul> 20616<li>minor code cleanup in numexpr easyblock 20617 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2679">#2679</a>)</li> 20618<li>update copyright lines for 2022 20619 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2705">#2705</a>)</li> 20620</ul> 20621</li> 20622</ul> 20623<p><strong>easyconfigs</strong></p> 20624<ul> 20625<li>added example easyconfig files for 29 new software packages:<ul> 20626<li>Abseil 20627 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15102">#15102</a>), 20628 AMS 20629 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13155">#13155</a>), 20630 ArchR 20631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15119">#15119</a>), 20632 CMAverse 20633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14963">#14963</a>), 20634 CmdStanR 20635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15198">#15198</a>), 20636 CONN 20637 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15052">#15052</a>), 20638 Devito 20639 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14984">#14984</a>, 20640 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15009">#15009</a>), 20641 GraphMap 20642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10299">#10299</a>), 20643 gRPC 20644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14728">#14728</a>), 20645 Hydra 20646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15025">#15025</a>), 20647 jupyter-server-proxy 20648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14844">#14844</a>), 20649 M1QN3 20650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15002">#15002</a>), 20651 MAGeCK 20652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15082">#15082</a>), 20653 matplotlib-inline 20654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15084">#15084</a>), 20655 MEGAN 20656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15064">#15064</a>), 20657 MNE-Python 20658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15174">#15174</a>), 20659 ONNX 20660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15158">#15158</a>), 20661 ONNX-Runtime 20662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15158">#15158</a>), 20663 ont-remora 20664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15162">#15162</a>), 20665 Optuna 20666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15021">#15021</a>), 20667 patch 20668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15035">#15035</a>), 20669 porefoam 20670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15067">#15067</a>), 20671 presto 20672 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15119">#15119</a>), 20673 PyFrag 20674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15184">#15184</a>), 20675 skorch 20676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15175">#15175</a>), 20677 SlamDunk 20678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15197">#15197</a>), 20679 SPM 20680 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15050">#15050</a>), 20681 STRique 20682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14980">#14980</a>), 20683 XML-Compile 20684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15177">#15177</a>)</li> 20685</ul> 20686</li> 20687<li>
20687added additional easyconfigs for various supported software 20688 packages, including:<ul> 20689<li>ABAQUS 2021, AlphaFold 2.1.2, AmberTools 21, archspec 0.1.3, 20690 Bandage 0.9.0, BLIS 3.1, c-ares 1.18.1, CCL 1.12.1, CharLS 20691 2.3.4, Clang-Python-bindings 13.0.1, dcm2niix 1.0.20211006, 20692 DFTB+ 21.1, DIRAC 22.0, ELPA 2021.11.001, FlexiBLAS 3.1.3, 20693 FLUENT 2021R2, GATK 4.2.5.0, GetOrganelle 1.7.5.3, IgBLAST 20694 1.18.0, IntelClusterChecker 2021.5.0, intervaltree-python 3.1.0, 20695 ITSx 1.1.3, Julia 1.7.2, kallisto 0.48.0, KMC 3.2.1, libobjcryst 20696 2021.1.2, libtree 3.0.3, loompy 3.0.7, matplotlib 3.5.1, MCR 20697 R2022a, MDAnalysis 1.1.1+ 2.0.0, MDTraj 1.9.7, medaka 1.5.0, 20698 meshalyzer 20200308, MRtrix 3.0.3, NiBabel 3.2.2, NLTK 3.7, 20699 numexpr 2.8.1, ont-fast5-api 4.0.2, OpenAI-Gym 0.21.0, OpenBLAS 20700 0.3.20, ORCA 5.0.3, parallel-fastq-dump 0.6.6, PIPITS 2.8, pocl 20701 1.8, pycocotools 2.0.4, pyEGA3 4.0.0, pyobjcryst 2.2.1, RE2 20702 2022-02-01, SAMtools 1.15, SBCL 2.2.1, shovill 1.1.0, SKESA 20703 2.4.0, SOCI 4.0.3, sympy 1.9, TensorFlow 2.5.3, VirtualGL 3.0, 20704 vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, 20705 XGBoost 1.5.0</li> 20706</ul> 20707</li> 20708<li>minor enhancements, including:<ul> 20709<li>add Flask-Session to Flask v1.1.4 and Flask v2.0.2 20710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15027">#15027</a>)</li> 20711<li>add check to verify that patch files touched in PRs have a 20712 description in place 20713 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15061">#15061</a>)</li> 20714<li>add extensions to R v4.1.2 easyconfig: hash 20715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15098">#15098</a>), 20716 nabor + harmony 20717 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15117">#15117</a>), 20718 apluster, DataCombine, docstring, gdalUtils, openair, mstate, 20719 SNFtool, and deps 20720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15141">#15141</a>)</li> 20721<li>also install rMATS_P commands in rMATS-turbo easyconfig 20722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15113">#15113</a>)</li> 20723<li>add extensions to Bioconductor v3.14 easyconfig: chromVAR 20724 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15118">#15118</a>), 20725 EnsDb.Hsapiens.v79 20726 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15154">#15154</a>), 20727 WGCNA 20728 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15178">#15178</a>)</li> 20729<li>add extensions to Perl v5.34.0 easyconfigs: Sys::Info, 20730 HTML::Template, Log::Report 20731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15176">#15176</a>), 20732 Sys::<Info::Driver>::Unknown, Sys::<Info::Driver>::Linux, 20733 Unix::Processors 20734 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15190">#15190</a>)</li> 20735<li>enable running of tests for MEME with <code>gompi/2021b</code> 20736 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15191">#15191</a>, 20737 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15199">#15199</a>)</li> 20738</ul> 20739</li> 20740<li>various bug fixes, including:<ul> 20741<li>add missing xxd build dependency for recent PLUMED versions 20742 (2.6.2, 2.7.x) 20743 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14847">#14847</a>)</li> 20744<li>downgrade dependency on nodejs + use jupyter-server-proxy in 20745 jupyter-matlab-proxy and configurable-http-proxy easyconfigs 20746 using <code>GCCcore/10.3.0</code> toolchain 20747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14942">#14942</a>)</li> 20748<li>add additional valid checksum for extensions in R 4.1.0 and 20749 4.1.2 easyconfigs: norm 20750 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14987">#14987</a>), 20751 optmatch 20752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14993">#14993</a>)</li> 20753<li>avoid pollution in the tmp directory when running the AlphaFold 20754 tests 20755 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14989">#14989</a>)</li> 20756<li>consistently enable usempi toolchain option in 20757 OSU-Micro-Benchmarks easyconfigs 20758 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15039">#15039</a>)</li> 20759<li>fix GBprocesS easyconfig by switching to source tarball created 20760 using <code>git_config</code> 20761 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15048">#15048</a>)</li> 20762<li>
20762add patches for mauveAligner to fix build on RHEL8 20763 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15049">#15049</a>)</li> 20764<li>fix installation of RDKit by using <code>-DBoost_NO_BOOST_CMAKE=ON</code> 20765 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15051">#15051</a>)</li> 20766<li>add patch to fix linking error for imread extension in 20767 scikit-image easyconfigs using intel toolchain 20768 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15054">#15054</a>)</li> 20769<li>avoid excessively long shebang in Autoconf/Automake Perl 20770 scripts + promote Perl to runtime dependency + fix Perl shebang 20771 for intltool 20772 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15055">#15055</a>)</li> 20773<li>fix <code>python</code> shebang in cutadapt script for cutadapt 1.18 w/ 20774 <code>GCCcore/8.3.0</code> 20775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15059">#15059</a>)</li> 20776<li>don't use v2.1.0rc1 release candidate of gmpy2, stick to proper 20777 release v2.1.2 20778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15060">#15060</a>)</li> 20779<li>add M4 as build dependency for CCL-1.12 20780 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15075">#15075</a>)</li> 20781<li>configure libffi 3.4.2 with <code>--disable-exec-static-tramp</code> to 20782 prevent segfaults 20783 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15086">#15086</a>)</li> 20784<li>set <code>XLA_PYTHON_CLIENT_ALLOCATOR=platform</code> for running tests in 20785 jax CUDA easyconfigs 20786 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15097">#15097</a>)</li> 20787<li>remove disable flag for RTTI in snappy v1.1.9 20788 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15099">#15099</a>)</li> 20789<li>fix grconvert build for Grace 5.1.25 with <code>foss/2021a</code> by adding 20790 libtirpc dependency + related patch 20791 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15121">#15121</a>)</li> 20792<li>clean up PSolver and futile easyconfigs and add dynamic libs 20793 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15148">#15148</a>)</li> 20794<li>enhance vcflib easyconfigs to also install scripts 20795 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15181">#15181</a>)</li> 20796<li>add patch to fix shared linking in vcflib 20797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15203">#15203</a>)</li> 20798<li>fix failing sanity check for PRINSEQ 20799 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15205">#15205</a>)</li> 20800</ul> 20801</li> 20802<li>other changes:<ul> 20803<li>use typing-extensions from Python v3.9.6 easyconfig in ArviZ and 20804 PyMC3 20805 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15003">#15003</a>)</li> 20806<li>disable building of documentation for DBus 1.13.18 20807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15010">#15010</a>)</li> 20808<li>consistently use system toolchain in EasyBuild easyconfigs 20809 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15126">#15126</a>)</li> 20810<li>use EasyBuild hwloc in likwid and move to GCC/intel-compiler 20811 level due to Fortran modules 20812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/15149">#15149</a>)</li> 20813</ul> 20814</li> 20815</ul> 20816<h2 id="release_notes_eb453">EasyBuild v4.5.3 (February 11th 2022)<a class="headerlink" href="#release_notes_eb453" title="Permanent link">¶</a></h2> 20817<p>bugfix/update release</p> 20818<p><strong>framework</strong></p> 20819<ul> 20820<li>various enhancements, including:<ul> 20821<li>also check for git in <code>--check-eb-deps</code> 20822 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3954">#3954</a>)</li> 20823<li>add end2end test for <code>eb --containerize</code> 20824 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3958">#3958</a>)</li> 20825</ul> 20826</li> 20827<li>various bug fixes, including:<ul> 20828<li>take into account that patch files can also be zipped when 20829 checking filename extension for patches 20830 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3936">#3936</a>)</li> 20831<li>initialize <code>BACKUP_PKG_URL</code> with empty string in 20832 <code>install_eb_dep.sh</code> script 20833 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3939">#3939</a>)</li> 20834<li>fix <code>get_os_name</code> and <code>get_os_version</code> to avoid reporting 20835 <code>UNKNOWN</code> in output of <code>eb --show-system-info</code> 20836 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3942">#3942</a>)</li> 20837<li>consistently use <code>actions/setup-python@v2</code> in CI workflows 20838 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3944">#3944</a>)</li> 20839<li>switch to using <code>pip3</code> for installing EasyBuild in container 20840 recipes generated by EasyBuild 20841 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3945">#3945</a>)</li> 20842<li>specify <code>easybuild.io</code> as EasyBuild homepage in <code>setup.py</code> 20843 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3947">#3947</a>)</li> 20844<li>avoid crash in <code>get_os_version</code> on modern SLES-based OSs 20845 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3955">#3955</a>)</li> 20846</ul> 20847</li> 20848<li>other changes:<ul> 20849<li>indicate compatibility with Python 3.10 in <code>setup.py</code> 20850 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3940">#3940</a>)</li> 20851</ul> 20852</li> 20853</ul> 20854<p><strong>easyblocks</strong></p> 20855<ul> 20856<li>new software-specific easyblock for reticulate R package 20857 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2668">#2668</a>)</li> 20858<li>minor enhancements and updates, including:<ul> 20859<li>set CUDA target architecture(s) for GROMACS based on 20860 <code>cuda_cc_semicolon_sep</code> template value 20861 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2655">#2655</a>)</li> 20862<li>
20862add support to NAMD easyblock to opt out of building with CUDA 20863 support even if CUDA is included as dependency 20864 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2666">#2666</a>)</li> 20865<li>update sanity check in CUDA easyblock: CUDA 11.6 no longer 20866 includes samples 20867 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2669">#2669</a>)</li> 20868</ul> 20869</li> 20870<li>various bug fixes, including:<ul> 20871<li>also run easyblocks test suite with Python 3.8-3.10 + 20872 consistently use <code>actions/setup-python@v2</code> in CI workflows 20873 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2664">#2664</a>)</li> 20874<li>specify <code>easybuild.io</code> as EasyBuild homepage in <code>setup.py</code> 20875 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2667">#2667</a>)</li> 20876</ul> 20877</li> 20878<li>other changes:<ul> 20879<li>remove vulnerable binaries from sanity check of HDF5, no longer 20880 installed by default with HDF5 1.10.8 20881 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2670">#2670</a>)</li> 20882</ul> 20883</li> 20884</ul> 20885<p><strong>easyconfigs</strong></p> 20886<ul> 20887<li>added example easyconfig files for 25 new software packages:<ul> 20888<li>Arcade-Learning-Environment 20889 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14753">#14753</a>), 20890 Bambi 20891 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14811">#14811</a>), 20892 CASTEP 20893 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14420">#14420</a>), 20894 Crumble 20895 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14785">#14785</a>), 20896 deepmedic 20897 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14953">#14953</a>), 20898 FoBiS 20899 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14771">#14771</a>), 20900 histolab 20901 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14945">#14945</a>), 20902 Iris 20903 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14788">#14788</a>), 20904 Jasmine 20905 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14789">#14789</a>), 20906 libexif 20907 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14823">#14823</a>), 20908 libgdiplus 20909 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14823">#14823</a>), 20910 MuJoCo 20911 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14965">#14965</a>), 20912 mujoco-py 20913 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14776">#14776</a>, 20914 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14965">#14965</a>), 20915 namedlist 20916 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14814">#14814</a>), 20917 OpenCensus-python 20918 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14837">#14837</a>), 20919 PyEVTK 20920 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14911">#14911</a>), 20921 pyradiomics 20922 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14851">#14851</a>), 20923 PyTorch-Lightning 20924 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14933">#14933</a>), 20925 Redis 20926 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14783">#14783</a>), 20927 rising 20928 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14952">#14952</a>), 20929 SoXt 20930 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14803">#14803</a>), 20931 SURVIVOR 20932 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14786">#14786</a>), 20933 tensorboard 20934 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14926">#14926</a>), 20935 xtensor 20936 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14944">#14944</a>), 20937 xxd 20938 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14846">#14846</a>)</li> 20939</ul> 20940</li> 20941<li>added additional easyconfigs for various supported software 20942 packages, including:<ul> 20943<li>aiohttp 3.8.1, AOCC 3.2.0, ArviZ 0.11.4, BeautifulSoup 4.10.0, 20944 bokeh 2.4.2, Boost.Python 1.77.0, Bowtie 1.3.1, CheMPS2 1.8.11, 20945 Clang 13.0.1, CLHEP 2.4.5.1, ConnectomeWorkbench 1.5.0, Crumble 20946 0.8.3, CUDA 11.5.1 + 11.6.0, cutadapt 3.5, dask 2022.1.0, 20947 deepdiff 5.7.0, deepTools 3.5.0, dm-tree 0.1.6, DROP 1.1.1, 20948 ecCodes 2.24.2, Emacs 27.2, FDS 6.7.7, file 5.41, Flask 2.0.2, 20949 FORD 6.1.6, GATE 9.1, Geant4 11.0.0, GEMMA 0.98.5, GnuTLS 3.7.3, 20950 Go 1.17.6, gpustat 1.0.0b1, Graphviz 2.50.0, GROMACS 2021.5, 20951 Guile 3.0.7, HDF5 1.10.8, imageio 2.13.5, JupyterLab 3.2.8, lftp 20952 4.9.2, libBigWig 0.4.6, libpsml 1.1.10, libRmath 4.1.2, librsb 20953 1.3.0.0, libtasn1 4.18.0, libunistring 1.0, likwid 5.2.1, 20954 MaxQuant 2.0.3.0, MEGA 11.0.10.eb, MethylDackel 0.6.1, methylpy 20955 1.2.9, minimap2 2.24, Mono 6.12.0.122, MUSCLE 5.1, 20956 nanomax-analysis-utils 0.4.3, ncbi-vdb 2.11.2, NCIPLOT-4.0 20957 20200624, Nextflow 21.10.6, NGS 2.11.2, nvtop 1.2.2, OpenCV 20958 4.5.5, openslide-python 1.1.2, pftoolsV3 3.2.11, picard 2.26.10, 20959 pydicom 2.2.2, pyFAI 0.20.0, Pysam 0.18.0, pytest-xdist 2.5.0, 20960 Racon 1.5.0, RAxML 8.2.12, ReFrame 3.10.1, ROOT 6.24.06, 20961 scikit-image 0.19.1, SDL2 2.0.20, SeqKit 2.1.0, Siesta 4.1.5,
20962 SimpleITK 2.1.1, SqueezeMeta 1.5.0, tMAE 1.0.1, torchvision 20963 0.11.3, Trim_Galore 0.6.7, typing-extensions 3.10.0.2</li> 20964</ul> 20965</li> 20966<li>minor enhancements, including:<ul> 20967<li>also install Python bindings for SHTns 3.5.1 20968 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14893">#14893</a>)</li> 20969<li>add catlearn extension to easyconfig for R v4.1.2 20970 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14940">#14940</a>)</li> 20971</ul> 20972</li> 20973<li>various bug fixes, including:<ul> 20974<li>update TALYS sources to (hopefully) ensure constant checksums 20975 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14797">#14797</a>)</li> 20976<li>add missing graphite2 + HarfBuzz dependencies to Qt5 v5.15.2 20977 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14802">#14802</a>)</li> 20978<li>add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1 20979 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14859">#14859</a>)</li> 20980<li>specify <code>easybuild.io</code> as EasyBuild homepage in <code>setup.py</code> 20981 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14870">#14870</a>)</li> 20982<li>add alternative checksum for MASS, class, nnet, spatial 20983 extensions in R 4.1.0 20984 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14873">#14873</a>) 20985 and R 4.1.2 20986 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14880">#14880</a>) 20987 easyconfigs</li> 20988<li>add patch to fix Kraken2 ncbi <code>ftp</code>/<code>https</code> check in 20989 <code>rsync_from_ncbi.pl</code> for versions 2.0.9-2.1.1 20990 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14889">#14889</a>)</li> 20991<li>disable building of tests/benchmarks for snappy 1.1.8 to avoid 20992 failing build 20993 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14923">#14923</a>)</li> 20994<li>disable use of <code>-Werror</code> for recent NSS versions 20995 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14924">#14924</a>)</li> 20996<li>fix download URL in UDUNITS v2.2.28 easyconfigs 20997 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14954">#14954</a>)</li> 20998<li>remove unnecessary CUDAcore dependency from nvtop v1.2.1 20999 easyconfig 21000 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14957">#14957</a>)</li> 21001<li>consistently apply patch for mapDamage 2.2.1 to use external 21002 seqtk 21003 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14961">#14961</a>)</li> 21004<li>fix typo in templated source URL in RcppGSL 0.3.8 easyconfig: 21005 <code>$(name)s</code> should be <code>%(name)s</code> 21006 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14962">#14962</a>)</li> 21007</ul> 21008</li> 21009<li>other changes:<ul> 21010<li>update Java/17 wrapper to Java 17.0.2 21011 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14868">#14868</a>)</li> 21012<li>use <code>actions/setup-python@v2</code> in CI workflows + trim test 21013 configurations for easyconfigs test suite: only test with Python 21014 2.7 + 3.6 and Lmod 7.x + 8.x 21015 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14857">#14857</a>, 21016 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14881">#14881</a>)</li> 21017</ul> 21018</li> 21019</ul> 21020<h2 id="release_notes_eb452">EasyBuild v4.5.2 (January 24th 2022)<a class="headerlink" href="#release_notes_eb452" title="Permanent link">¶</a></h2> 21021<p>bugfix/update release</p> 21022<p><strong>framework</strong></p> 21023<ul> 21024<li>various enhancements, including:<ul> 21025<li>automatically prepend value for <code>env-for-shebang</code> configuration 21026 setting with sysroot 21027 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3919">#3919</a>)</li> 21028<li>enhance <code>update_build_option</code> to return original value + add 21029 support for <code>update_build_options</code> 21030 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3923">#3923</a>)</li> 21031<li>fix compatibility with Python 3.10 21032 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3926">#3926</a>, 21033 <a href="https://github.com/easybuilders/easybuild-framework/pull/3933">#3933</a>)</li> 21034<li>also take <code>/etc/os-release</code> into account in <code>get_os_name</code> and 21035 <code>get_os_version</code> 21036 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3930">#3930</a>)</li> 21037<li>enhance <code>get_cpu_architecture</code> and <code>get_cpu_family</code> to be aware 21038 of RISC-V 21039 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3931">#3931</a>)</li> 21040</ul> 21041</li> 21042<li>various bug fixes, including:<ul> 21043<li>relax pattern checks in <code>test_toy_exts_parallel</code> 21044 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3921">#3921</a>)</li> 21045<li>use <code>sources.easybuild.io</code> as backup URL for downloading 21046 Environment Modules sources to run test suite 21047 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3928">#3928</a>)</li> 21048<li>make intelfftw toolchain component aware of GCCcore 21049 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3929">#3929</a>)</li> 21050</ul> 21051</li> 21052<li>other changes:<ul> 21053<li>deprecate use of (actual) patch files that don't have a 21054 filename ending with <code>.patch</code> 21055 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3920">#3920</a>)</li> 21056<li>remove version restriction for keyring in <code>requirements.txt</code> to 21057 test with latest version 21058 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3925">#3925</a>)</li> 21059<li>simplify <code>requirements.txt</code> by removing Python 2.6 support 21060 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3927">#3927</a>)</li> 21061<li>only run GitHub tests when testing with Lua module syntax, to 21062 avoid hitting GitHub rate limit when running tests 21063 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3938">#3938</a>)</li> 21064</ul> 21065</li> 21066</ul> 21067<p><strong>easyblocks</strong></p> 21068<ul> 21069<li>minor enhancements and updates, including:<ul> 21070<li>remove necessity for license for oneAPI versions (>= 2021.x) in 21071 itac easyblock 21072 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2492">#2492</a>)</li> 21073<li>
21073add CUDA support in SuiteSparse easyblock 21074 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2627">#2627</a>)</li> 21075<li>use all available cores for running Perl test suite 21076 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2637">#2637</a>)</li> 21077<li>add option to not copy the license file for Gurobi 21078 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2639">#2639</a>, 21079 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2641">#2641</a>)</li> 21080<li>update AOCC easyblock to support version 3.2.0 21081 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2643">#2643</a>)</li> 21082<li>don't grep for specific version in <code>--version</code> output of Intel 21083 compiler commands for versions 2022.x 21084 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2644">#2644</a>)</li> 21085<li>add support for enabling sanity checks for specific components 21086 in the Bundle easyblock 21087 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2649">#2649</a>)</li> 21088<li>update Libint easyblock for LibInt v2.7.0 which requires 21089 configuring via CMake 21090 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2650">#2650</a>)</li> 21091<li>update Mathematica easyblock for version 13 21092 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2652">#2652</a>)</li> 21093<li>add sanity check command for Bazel 21094 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2653">#2653</a>)</li> 21095<li>update NAMD easyblock to allow non-system csh 21096 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2654">#2654</a>)</li> 21097<li>enhance CUDA easyblock to create version independent pkgconfig 21098 files 21099 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2656">#2656</a>)</li> 21100<li>add <code>util</code> subdirectory to <code>$PATH</code> for WPS 21101 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2658">#2658</a>)</li> 21102</ul> 21103</li> 21104<li>various bug fixes, including:<ul> 21105<li>convert version numbers to strictly numerical in Siesta 21106 easyblock 21107 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2553">#2553</a>)</li> 21108<li>fix shebang of scripts in Perl installation if installation 21109 prefix is too long 21110 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2640">#2640</a>)</li> 21111<li>enhance IntelBase easyblock to avoid crash when <code>$USER</code> is not 21112 set 21113 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2642">#2642</a>)</li> 21114<li>fix quotes in definition of default platform macro and enhance 21115 sanity check in GATE easyblock 21116 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2645">#2645</a>)</li> 21117<li>avoid excessively long shebang line in compile script for WRF 21118 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2648">#2648</a>)</li> 21119<li>fix checking of Intel Fortran compiler version in CP2K easyblock 21120 for recent toolchains 21121 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2651">#2651</a>)</li> 21122</ul> 21123</li> 21124</ul> 21125<p><strong>easyconfigs</strong></p> 21126<ul> 21127<li>added easyconfig for intel/2022.00 toolchain 21128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14620">#14620</a>)</li> 21129<li>added example easyconfig files for 48 new software packages:<ul> 21130<li>alevin-fry 21131 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14617">#14617</a>), 21132 AMD-uProf 21133 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14626">#14626</a>), 21134 ANGEL 21135 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11857">#11857</a>), 21136 atropos 21137 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7580">#7580</a>), 21138 Austin 21139 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14596">#14596</a>), 21140 AutoDock-GPU 21141 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14671">#14671</a>), 21142 AutoDock-Vina 21143 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14675">#14675</a>), 21144 boost_histogram 21145 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14516">#14516</a>), 21146 CAFE5 21147 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14603">#14603</a>), 21148 Calcam 21149 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7488">#7488</a>), 21150 Carma 21151 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14527">#14527</a>), 21152 Cogent 21153 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14278">#14278</a>), 21154 dlib 21155 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14556">#14556</a>), 21156 DualSPHysics 21157 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14632">#14632</a>), 21158 dune-core 21159 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14693">#14693</a>), 21160 dune-fem 21161 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14693">#14693</a>), 21162 DyMat 21163 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14615">#14615</a>), 21164 elbencho 21165 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14548">#14548</a>), 21166 Embree 21167 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7471">#7471</a>), 21168 ExaML 21169 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14530">#14530</a>), 21170 FMPy 21171 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14481">#14481</a>), 21172 genozip 21173 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14583">#14583</a>), 21174 hivtrace 21175 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14691">#14691</a>), 21176 intervaltree-python 21177 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8995">#8995</a>), 21178 IsoNet 21179 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14075">#14075</a>), 21180 MACSE 21181 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14709">#14709</a>), 21182 MetaPhlAn 21183 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12917">#12917</a>), 21184 MicrobeAnnotator 21185 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14549">#14549</a>), 21186 mold 21187 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14595">#14595</a>), 21188 numdiff 21189 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14609">#14609</a>), 21190 OpenFace 21191 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14556">#14556</a>), 21192 PhyloPhlAn 21193 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14564">#14564</a>),
21194 PREQUAL 21195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14722">#14722</a>), 21196 PuLP 21197 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14581">#14581</a>), 21198 PyCalib 21199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14616">#14616</a>), 21200 PyTorch3D 21201 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13240">#13240</a>), 21202 QCG-PilotJob 21203 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14337">#14337</a>), 21204 RaGOO 21205 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8995">#8995</a>), 21206 RAPSearch2 21207 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13199">#13199</a>), 21208 SCopeLoomR 21209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14518">#14518</a>), 21210 ShengBTE 21211 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14557">#14557</a>), 21212 SHTns 21213 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14682">#14682</a>), 21214 STRUMPACK 21215 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14560">#14560</a>), 21216 TALYS 21217 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14716">#14716</a>), 21218 TN93 21219 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14691">#14691</a>), 21220 xxHash 21221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14251">#14251</a>), 21222 yaml-cpp 21223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14547">#14547</a>), 21224 Zgoubi 21225 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14516">#14516</a>)</li> 21226</ul> 21227</li> 21228<li>added additional easyconfigs for various supported software 21229 packages, including:<ul> 21230<li>annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, Arrow 21231 6.0.1, Bismark 0.23.1, BLAST+ 2.12.0, cDNA_Cupcake 26.0.0, 21232 CHERAB 1.3.0, CMake 3.22.1, CP2K 8.2, DIAMOND 2.0.13, 21233 dotNET-Core-Runtime 6.0.1, dotNET-SDK 6.0.101, Extrae 3.8.3, 21234 fastp 0.23.2, FreeSurfer 7.2.0, GffCompare 0.12.6, gmsh 4.9.0, 21235 GTK3 3.24.31, h5py 3.6.0, igraph 0.9.5, Inspector 2022.0.0, 21236 IQ-TREE 2.1.3, itac 2021.5.0.eb, Java/15 + Java/17, JUBE 2.4.2, 21237 libdeflate 1.8, libxsmm 1.17, LSD2 2.3, MAGMA 1.09b, MATLAB 21238 2021b, MinPath 1.6, MultiQC 1.11, MUSCLE 5.0.1428, numba 0.54.1, 21239 NVHPC 21.11, OBITools 1.2.13, occt 7.5.0p1, openCARP 8.2, OpenCV 21240 3.4.1, OpenFOAM v2112, ORCA 5.0.2, phonopy 2.12.0, Pillow 8.3.2, 21241 Pillow-SIMD 8.3.2, PLUMED 2.7.3, poppler 22.01.0, PyQtGraph 21242 0.12.3, python-igraph 0.9.8, PyZMQ 22.3.0, Raysect 0.7.1, 21243 Rgurobi 9.5.0, scanpy 1.8.2, Schrodinger 2021, SqueezeMeta 21244 1.0.0, statsmodels 0.13.1, texlive 20210324, VTune 2022.0.0</li> 21245</ul> 21246</li> 21247<li>minor enhancements, including:<ul> 21248<li>add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b 21249 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14547">#14547</a>)</li> 21250<li>include output of failing code style check in message produced 21251 by failing easyconfigs style test 21252 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14578">#14578</a>)</li> 21253<li>bundle LAPACKE with FlexiBLAS 3.0.4 21254 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14591">#14591</a>), 21255 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14769">#14769</a>)</li> 21256<li>add extensions to R v4.1.2 easyconfig: semTools, mirt, OpenMX 21257 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14634">#14634</a>), 21258 FactorCopula 21259 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14648">#14648</a>), 21260 rpact, ldbounds 21261 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14750">#14750</a>)</li> 21262<li>add extensions to R-bundle-Bioconductor 3.14: ExomeDepth 21263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14684">#14684</a>), 21264 DSS 21265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14748">#14748</a>), 21266 pathview 21267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14806">#14806</a>)</li> 21268</ul> 21269</li> 21270<li>various bug fixes, including:<ul> 21271<li>fix <code>homepage</code> and <code>source_urls</code> for GLIMMER 3.02b 21272 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7945">#7945</a>)</li> 21273<li>fix source URL for Trilinos 12.12.1 with foss/2019b 21274 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14547">#14547</a>)</li> 21275<li>use proper Perl dependency for worker 1.6.12 with foss/2019a 21276 (fixes installation on RHEL8 OS) 21277 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14565">#14565</a>)</li> 21278<li>fix checksum and versions of annovar v20191024 21279 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14579">#14579</a>)</li> 21280<li>
21280add patch for Rust 1.52.2 and 1.54.0 to fix build when using 21281 alternate sysroot 21282 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14584">#14584</a>)</li> 21283<li>retain version in filename for cromwell sources 21284 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14586">#14586</a>)</li> 21285<li>specify compiler to use in WildMagic easyconfig 21286 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14594">#14594</a>)</li> 21287<li>avoid need for git build dependency for recent x265 easyconfigs 21288 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14605">#14605</a>)</li> 21289<li>fix broken patch file for recent GPAW versions 21290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14619">#14619</a>)</li> 21291<li>add alternative checksum for Siesta-4.1-MaX-1.0 21292 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14643">#14643</a>)</li> 21293<li>add missing PCRE dependency for pullseq + add sanity check 21294 commands 21295 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14650">#14650</a>)</li> 21296<li>use <code>%(arch)s</code> template to avoid hardcoding <code>x86_64</code> in recent 21297 XML-LibXML easyconfigs 21298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14655">#14655</a>)</li> 21299<li>fix name for (binary) AutoDock-Vina v1.1.2 21300 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14675">#14675</a>)</li> 21301<li>add patch to fix memory leak in OpenMPI that heavily affects 21302 CP2K, SIESTA, QuantumESPRESSO, VASP, ... 21303 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14726">#14726</a>)</li> 21304<li>set <code>$GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS</code> for installing grcpio 21305 extension included with:<ul> 21306<li>TensorFlow 2.2.3-2.4.1 with 2020* toolchain 21307 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14729">#14729</a>) 21308 and 2.5.0+ 21309 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14728">#14728</a>)</li> 21310<li>Ray-project 21311 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14730">#14730</a>)</li> 21312</ul> 21313</li> 21314<li>enforce using internal boost for bcl2fastq2 with a GCC 10.x 21315 toolchain 21316 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14741">#14741</a>)</li> 21317<li>add patch for hard-coded checksum value of downloaded source 21318 file in the source code of RDKit 2021.03.4 21319 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14743">#14743</a>)</li> 21320<li>also install <code>libaio.so.1</code> symlink in easyconfigs for libaio 21321 v0.3.112 21322 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14745">#14745</a>)</li> 21323<li>do not use external libgcrypt or python for libxslt with recent 21324 toolchains 21325 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14756">#14756</a>)</li> 21326<li>
21326add patches to fix CVE-2021-23437 for Pillow 21327 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14765">#14765</a>) 21328 and Pillow-SIMD 21329 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14792">#14792</a>)</li> 21330<li>add libXfont2 patch to fix build when libbsd is present 21331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14821">#14821</a>)</li> 21332</ul> 21333</li> 21334<li>other changes:<ul> 21335<li>update Java 1.8 wrapper to 1.8.0_311 for x86_64 21336 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14644">#14644</a>)</li> 21337<li>bring gffread back down to GCCcore level for toolchain version 21338 10.3.0 21339 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14660">#14660</a>)</li> 21340<li>update build dependencies for recent binutils + GCCcore 21341 easyconfigs to avoid depending on M4 1.4.18 with system 21342 toolchain 21343 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14731">#14731</a>), 21344 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14755">#14755</a>)</li> 21345<li>bump nbconvert extension in recent IPython easyconfigs to 21346 version 6.4.0 21347 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14738">#14738</a>)</li> 21348</ul> 21349</li> 21350</ul> 21351<h2 id="release_notes_eb451">EasyBuild v4.5.1 (December 13th 2021)<a class="headerlink" href="#release_notes_eb451" title="Permanent link">¶</a></h2> 21352<p>bugfix/update release</p> 21353<p><strong>framework</strong></p> 21354<ul> 21355<li>various enhancements, including:<ul> 21356<li>also dump environment to reprod directory 21357 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3374">#3374</a>)</li> 21358<li>determine which extensions can be skipped in parallel (if 21359 <code>--parallel-extensions-install</code> is enabled) 21360 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3890">#3890</a>)</li> 21361<li>fall back to sequential installation for extensions with unknown 21362 dependencies when using <code>--parallel-extensions-install</code> 21363 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3906">#3906</a>)</li> 21364<li>allow oversubscription in sanity check for OpenMPI-based 21365 toolchains 21366 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3909">#3909</a>)</li> 21367</ul> 21368</li> 21369<li>various bug fixes, including:<ul> 21370<li>don't try to ensure absolute path for path part of 21371 <code>repositorypath</code> 21372 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3893">#3893</a>, 21373 <a href="https://github.com/easybuilders/easybuild-framework/pull/3899">#3899</a>)</li> 21374<li>fix typo in EULA agreement error message 21375 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3894">#3894</a>)</li> 21376<li>only remove lock if it was created in the same EasyBuild session 21377 (not if it existed already) 21378 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3889">#3889</a>)</li> 21379<li>introduce <code>EasyBlock.post_init</code> method to correctly define 21380 <code>builddir</code> variable when <code>build-in-installdir</code> mode is enabled 21381 in easyconfig or easyblock 21382 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3900">#3900</a>)</li> 21383<li>also show download progress bar when using <code>--inject-checksums</code> 21384 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3905">#3905</a>)</li> 21385<li>pick up custom <code>extract_cmd</code> specified for extension 21386 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3907">#3907</a>)</li> 21387<li>make <code>test_run_cmd_async</code> more robust against fluke failures 21388 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3908">#3908</a>)</li> 21389</ul> 21390</li> 21391</ul> 21392<p><strong>easyblocks</strong></p> 21393<ul> 21394<li>new software-specific easyblock for Clang-AOMP 21395 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2617">#2617</a>)</li> 21396<li>minor enhancements and updates, including:<ul> 21397<li>enhance Rpm generic easyblock to support installing tarball of 21398 RPMs (by unpacking it first) + take into account 21399 <code>(pre)installopts</code> 21400 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2580">#2580</a>)</li> 21401<li>
21401add option to control use of MKL-DNN in jaxlib easyblock 21402 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2619">#2619</a>)</li> 21403<li>update SAMtools easyblock to support installation of SAMtools 21404 1.14 21405 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2620">#2620</a>)</li> 21406<li>add option to ignore PLUMED version check for GROMACS 21407 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2621">#2621</a>)</li> 21408<li>update Inspector easyblock for recent versions (>= 2021, oneAPI 21409 versions) 21410 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2624">#2624</a>)</li> 21411<li>enhance tbb easyblock by adding option to build Python bindings 21412 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2626">#2626</a>)</li> 21413<li>fix patching of <code>CMakeLists.txt</code> for Eigen v3.4 21414 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2633">#2633</a>)</li> 21415</ul> 21416</li> 21417<li>various bug fixes, including:<ul> 21418<li>update CP2K easyblock to use <code>-D__MKL</code> for CP2K versions newer 21419 than 2.3 21420 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2586">#2586</a>)</li> 21421<li>set OpenMPI configuration for ORCA sanity check 21422 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2596">#2596</a>)</li> 21423<li>allow oversubscription in OpenMPI sanity check 21424 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2611">#2611</a>)</li> 21425<li>set <code>wm_*</code> class variables in OpenFOAM easyblock constructor (to 21426 fix <code>--sanity-check-only</code>) 21427 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2616">#2616</a>)</li> 21428<li>remove newline from easybuild-easyblocks package description 21429 (required to avoid installation error with setuptools>=59.0.0) 21430 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2623">#2623</a>)</li> 21431<li>avoid patching binary files + other enhancements for MUMmer 21432 easyblock 21433 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2630">#2630</a>)</li> 21434<li>enable <code>build-in-installdir</code> mode in constructor of PETSc and 21435 SLEPc easyblocks 21436 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2631">#2631</a>)</li> 21437<li>skip netcdf4-python tests that require network connectivity 21438 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2634">#2634</a>)</li> 21439</ul> 21440</li> 21441</ul> 21442<p><strong>easyconfigs</strong></p> 21443<ul> 21444<li>added example easyconfig files for 71 new software packages:<ul> 21445<li>ANIcalculator 21446 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14478">#14478</a>, 21447 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14494">#14494</a>, 21448 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14510">#14510</a>), 21449 arrow-R 21450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14267">#14267</a>), 21451 ASAP 21452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14367">#14367</a>), 21453 BabelStream 21454 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14503">#14503</a>), 21455 bamtofastq 21456 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14391">#14391</a>), 21457 bcbio-gff 21458 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14322">#14322</a>), 21459 biom-format 21460 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13205">#13205</a>), 21461 Blosc2 21462 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14247">#14247</a>), 21463 boto3 21464 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14452">#14452</a>), 21465 Brotli-python 21466 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14528">#14528</a>), 21467 Brunsli 21468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14247">#14247</a>), 21469 Clang-AOMP 21470 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14327">#14327</a>), 21471 CLEASE 21472 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14413">#14413</a>), 21473 CMSeq 21474 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14326">#14326</a>), 21475 cpu_features 21476 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14385">#14385</a>), 21477 cromwell 21478 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12125">#12125</a>), 21479 cxxopts 21480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14487">#14487</a>, 21481 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14504">#14504</a>), 21482 dRep 21483 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14479">#14479</a>), 21484 DUBStepR 21485 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14495">#14495</a>), 21486 eht-imaging 21487 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14239">#14239</a>), 21488 einops 21489 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14373">#14373</a>), 21490 ELFIO 21491 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14488">#14488</a>, 21492 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14504">#14504</a>), 21493 elprep 21494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14422">#14422</a>), 21495 epiScanpy 21496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14447">#14447</a>), 21497 FMM3D 21498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14257">#14257</a>), 21499 FORD 21500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13653">#13653</a>), 21501 GPy 21502 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14380">#14380</a>), 21503 HIP 21504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14339">#14339</a>), 21505 idemux 21506 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14499">#14499</a>), 21507 imagecodecs 21508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14247">#14247</a>), 21509 InChI 21510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13902">#13902</a>), 21511 jupyter-matlab-proxy 21512 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14270">#14270</a>), 21513 jxrlib 21514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14247">#14247</a>), 21515 LBFGS++ 21516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14230">#14230</a>), 21517 LERC 21518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14247">#14247</a>), 21519 libaec 21520 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14247">#14247</a>), 21521 libavif 21522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14246">#14246</a>), 21523 LibLZF 21524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14246">#14246</a>), 21525 libnsl 21526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14494">#14494</a>), 21527 libtree 21528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14501">#14501</a>), 21529 LPeg 21530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14157">#14157</a>), 21531 Megalodon 21532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14256">#14256</a>), 21533 nnU-Net 21534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14249">#14249</a>), 21535 PAL2NAL 21536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14430">#14430</a>), 21537 photontorch 21538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14410">#14410</a>), 21539 pkgconf 21540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14426">#14426</a>), 21541 pmx 21542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14319">#14319</a>), 21543 PPanGGOLiN 21544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14449">
21544#14449</a>), 21545 ProFit 21546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14340">#14340</a>), 21547 pugixml 21548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14367">#14367</a>, 21549 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14492">#14492</a>), 21550 PySide2 21551 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13460">#13460</a>), 21552 Relate 21553 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14443">#14443</a>), 21554 ROCm 21555 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14355">#14355</a>), 21556 rocm-cmake 21557 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14327">#14327</a>), 21558 ROCm-CompilerSupport 21559 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14327">#14327</a>), 21560 rocminfo 21561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14327">#14327</a>), 21562 rocm-smi 21563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14354">#14354</a>), 21564 ROCR-Runtime 21565 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14327">#14327</a>), 21566 ROCT-Thunk-Interface 21567 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14327">#14327</a>), 21568 SCENIC 21569 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14260">#14260</a>), 21570 Shasta 21571 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14385">#14385</a>), 21572 SimNIBS 21573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14257">#14257</a>), 21574 SMV 21575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14157">#14157</a>), 21576 SRST2 21577 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14253">#14253</a>), 21578 STACEY 21579 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14293">#14293</a>), 21580 termcolor 21581 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14489">#14489</a>, 21582 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14504">#14504</a>), 21583 ThemisPy 21584 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14231">#14231</a>), 21585 TOBIAS 21586 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14452">#14452</a>, 21587 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14458">#14458</a>), 21588 zfp 21589 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14246">#14246</a>), 21590 zlib-ng 21591 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14246">#14246</a>), 21592 Zopfli 21593 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14246">#14246</a>)</li> 21594</ul> 21595</li> 21596<li>added additional easyconfigs for various supported software 21597 packages, including:<ul> 21598<li>ABINIT 9.6.2, ABRicate 1.0.0, AlphaFold 2.1.1, antiSMASH 6.0.1, 21599 Arrow 6.0.0, astropy 4.3.1, BCFtools 1.14, BeautifulSoup 4.9.3, 21600 Boost 1.77.0, bpp 4.4.0, Bracken 2.6.2, CapnProto 0.9.1, 21601 CellRanger 6.1.2, Eigen 3.4.0, enaBrowserTool 1.6, ESMF 8.2.0, 21602 Flye 2.9, FMRIprep 1.4.1, FSL 6.0.4, GATK 4.2.3.0, gc 8.2.0, GDB 21603 11.1, git 2.33.1, Go 1.17.3, Gurobi 9.5.0, Horovod 0.23.0, 21604 HTSlib 1.14, HyPhy 2.5.33, Infernal 1.1.4, Inspector 2021.4.0 21605 ITK 5.2.1, jax 0.2.24, Julia 1.7.0, Kent_tools 422, king 2.2.7, 21606 libdwarf 20210528, MAFFT 7.490, makeinfo 6.8, Mash 2.3, 21607 matplotlib 3.4.3, MCR R2021b, minimap2 2.22, MUST 1.7.2, NCO 21608 5.0.3, NCO 5.0.3, nlohmann_json 3.10.4, NVHPC 21.9, OpenMPI 21609 4.0.7 + 4.1.2, panaroo 1.2.9, pangolin 3.1.16, pkgconfig 1.5.5, 21610 plotly.py 5.4.0, pyfaidx 0.6.3.1, Pysam 0.17.0, PyTorch 1.10.0, 21611 R 4.1.2, R-bundle-Bioconductor 3.14, ReFrame 3.9.1, rpy2 3.4.5, 21612 scikit-image 0.18.3, scikit-learn 1.0.1 SimpleITK 2.1.0, 21613 snakemake 6.10.0, SPAdes 3.15.3, tbb 2021.4.0, torchtext 0.10.0, 21614 torchvision 0.11.1, tqdm 4.62.3, TRUST4 1.0.6, Trycycler 0.5.2, 21615 Unicycler 0.4.9, UShER 0.5.0, WPS 4.3.1, xarray 0.20.1, 21616 XlsxWriter 3.0.2, Yambo 5.0.4</li> 21617</ul> 21618</li> 21619<li>minor enhancements, including:<ul> 21620<li>add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 21621 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14259">#14259</a>)</li> 21622<li>
21622add extensions for R v4.1.x:<ul> 21623<li>geex + momentfit 21624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14299">#14299</a>); 21625 StatMatch, leaflet, tmap + collapse 21626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14328">#14328</a>), 21627 genoPlotR + penfa 21628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14433">#14433</a>), 21629 adcovsim 21630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14484">#14484</a>)</li> 21631</ul> 21632</li> 21633<li>add M3Drop extension to R-bundle-Bioconductor 3.14 21634 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14436">#14436</a>)</li> 21635</ul> 21636</li> 21637<li>various bug fixes, including:<ul> 21638<li>specify to use Python provided as dependency, remove 21639 <code>separate_build_dir</code>, and fix URL in comment for Arrow 0.17.1 21640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14263">#14263</a>)</li> 21641<li>fix <code>gettid</code> nameclash with glibc 2.30 in Bazel 0.25.2, 0.26.1, 21642 0.29.1, and 1.1.0 21643 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14269">#14269</a>)</li> 21644<li>restore and fix sanity check commands in RStudio-Server 1.4 21645 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14275">#14275</a>)</li> 21646<li>add pkg-config build dependency to Python easyconfigs, to ensure 21647 OpenSSL wrapper is detected 21648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14316">#14316</a>)</li> 21649<li>add patch for UCX v1.11.2 to fix missing include statement for 21650 <code>string.h</code> 21651 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14317">#14317</a>)</li> 21652<li>set <code>$DALTON_TMPDIR</code> to build directory to run Dalton tests 21653 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14341">#14341</a>)</li> 21654<li>add patch for libfabric v1.12.1 to fix <code>unknown link width 0x10</code> 21655 warning 21656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14387">#14387</a>)</li> 21657<li>add missing Automake dependency to PhyML 3.3.20200621 21658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14397">#14397</a>)</li> 21659<li>add git as build dependency to Python 3.8.x and 3.9.x 21660 easyconfigs (required for pbr extension) 21661 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14421">#14421</a>)</li> 21662<li>add missing XZ dependency to recent PROJ easyconfigs 21663 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14429">#14429</a>)</li> 21664<li>fix homepage/source URL for king v2.2.4 21665 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14444">#14444</a>)</li> 21666<li>add patch for GCCcore 9.1-9.3 to fix compatibility with recent 21667 kernel headers 21668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14453">#14453</a>)</li> 21669<li>add patch for GCCcore 10.1-11.1 to fix compatibility with recent 21670 kernel headers 21671 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14454">#14454</a>)</li> 21672<li>
21672add patch to fix CVE-2021-43527 in NSS 21673 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14497">#14497</a>)</li> 21674<li>pass tests on A* GPUs by setting <code>NVIDIA_TF32_OVERRIDE=0</code> in 21675 jax 0.2.19 21676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14502">#14502</a>)</li> 21677<li>add patch to fix broken (hanging) Mash binaries 21678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14511">#14511</a>)</li> 21679<li>add missing Perl build dependency for Longshot 21680 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14535">#14535</a>)</li> 21681<li>add googletest build dependency for Highway 21682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14536">#14536</a>)</li> 21683<li>seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 21684 easyconfigs 21685 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14537">#14537</a>)</li> 21686</ul> 21687</li> 21688<li>other changes:<ul> 21689<li>rename R bindings for Arrow to arrow-R, so it can be used in a 21690 lowercase module naming scheme 21691 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14262">#14262</a>)</li> 21692<li>comment out imkl build dependency for FlexiBLAS 3.0.4 with 21693 GCC/11.2.0 21694 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14335">#14335</a>)</li> 21695<li>don't add <code>bin</code> subdir to <code>$PATH</code> via <code>modextrapaths</code> in 21696 ReFrame easyconfigs 21697 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14415">#14415</a>)</li> 21698<li>consistently use 'Grace' software name + sync 21699 <code>homepage</code>/<code>source_urls</code> 21700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14493">#14493</a>)</li> 21701<li>move cxxopts, termcolor and ELFIO header only libraries to 21702 <code>SYSTEM</code> toolchain 21703 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14504">#14504</a>)</li> 21704</ul> 21705</li> 21706</ul> 21707<h2 id="release_notes_eb450">EasyBuild v4.5.0 (October 29th 2021)<a class="headerlink" href="#release_notes_eb450" title="Permanent link">¶</a></h2> 21708<p>feature release</p> 21709<p><strong>framework</strong></p> 21710<ul> 21711<li>various enhancements, including:<ul> 21712<li>add <code>--review-pr-max</code> and <code>--review-pr-filter</code> options to limit 21713 easyconfigs used by <code>--review-pr</code> + retain order of easyconfigs 21714 being compared with 21715 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3754">#3754</a>)</li> 21716<li>use Rich (if available) to show progress bars when installing 21717 easyconfigs 21718 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3823">#3823</a>, 21719 <a href="https://github.com/easybuilders/easybuild-framework/pull/3826">#3826</a>, 21720 <a href="https://github.com/easybuilders/easybuild-framework/pull/3833">#3833</a>, 21721 <a href="https://github.com/easybuilders/easybuild-framework/pull/3835">#3835</a>, 21722 <a href="https://github.com/easybuilders/easybuild-framework/pull/3844">#3844</a>, 21723 <a href="https://github.com/easybuilders/easybuild-framework/pull/3864">#3864</a>, 21724 <a href="https://github.com/easybuilders/easybuild-framework/pull/3867">#3867</a>, 21725 <a href="https://github.com/easybuilders/easybuild-framework/pull/3882">#3882</a>)<ul> 21726<li>see also 21727 <a href="https://docs.easybuild.io/en/latest/Progress_bars.html">https://docs.easybuild.io/en/latest/Progress_bars.html</a></li> 21728</ul> 21729</li> 21730<li>add support for checking required/optional EasyBuild 21731 dependencies via <code>eb --check-eb-deps</code> 21732 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3829">#3829</a>)</li> 21733<li>add support for collecting GPU info (via <code>nvidia-smi</code>), and 21734 include it in <code>--show-system-info</code> and test report 21735 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3851">#3851</a>)</li> 21736<li>added support for <code>--insecure-download</code> configuration option 21737 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3859">#3859</a>)</li> 21738<li>make intelfftw toolchain component aware of imkl-FFTW module 21739 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3861">#3861</a>)</li> 21740<li>make sure the contrib/hooks tree is included in the source 21741 tarball for easybuild-framework 21742 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3862">#3862</a>)</li> 21743<li>
21743add <code>check_async_cmd</code> function to facilitate checking on 21744 asynchronously running commands 21745 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3865">#3865</a>, 21746 <a href="https://github.com/easybuilders/easybuild-framework/pull/3881">#3881</a>)</li> 21747<li>add initial/experimental support for installing extensions in 21748 parallel 21749 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3667">#3667</a>, 21750 <a href="https://github.com/easybuilders/easybuild-framework/pull/3878">#3878</a>)<ul> 21751<li>see also 21752 <a href="https://docs.easybuild.io/en/latest/Installing_extensions_in_parallel.html">https://docs.easybuild.io/en/latest/Installing_extensions_in_parallel.html</a></li> 21753</ul> 21754</li> 21755<li>filter out duplicate paths added to module files, and print 21756 warning when they occur 21757 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3770">#3770</a>, 21758 <a href="https://github.com/easybuilders/easybuild-framework/pull/3874">#3874</a>)</li> 21759</ul> 21760</li> 21761<li>various bug fixes, including:<ul> 21762<li>ensure that path configuration options have absolute path values 21763 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3832">#3832</a>)</li> 21764<li>fix broken test by taking into account changed error raised by 21765 Python 3.9.7 when copying directory via <code>shutil.copyfile</code> 21766 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3840">#3840</a>)</li> 21767<li>ensure newer location of CUDA stubs is taken into account by 21768 RPATH filter 21769 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3850">#3850</a>)</li> 21770<li>replace <code>which</code> by <code>command -v</code> in <code>eb</code> wrapper script to avoid 21771 dependency on <code>which</code> command 21772 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3852">#3852</a>)</li> 21773<li>refactor EasyBlock to decouple collecting of information on 21774 extension source/patch files from downloading them 21775 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3860">#3860</a>)<ul> 21776<li>in this context, the <code>EasyBlock.fetch_extension_sources</code> 21777 method was deprecated, and replaced by 21778 <code>EasyBlock.collect_exts_file_info</code></li> 21779</ul> 21780</li> 21781<li>fix library paths to add to <code>$LDFLAGS</code> for intel-compilers 21782 toolchain component 21783 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3866">#3866</a>)</li> 21784<li>remove <code>--depth 1</code> from git clone when <code>commit</code> specified 21785 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3871">#3871</a>, 21786 <a href="https://github.com/easybuilders/easybuild-framework/pull/3872">#3872</a>)</li> 21787<li>make sure correct include directory is used for FlexiBLAS 21788 toolchain component 21789 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3875">#3875</a>)</li> 21790<li>explicitly disable rebase when pulling develop branch to create 21791 a merge commit, since not specifying how to reconcile divergent 21792 branches is an error with Git 2.33.1 and newer 21793 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3879">#3879</a>)</li> 21794<li>tweak <code>test_http_header_fields_urlpat</code> to download from 21795 <code>sources.easybuild.io</code> rather than <code>https://ftp.gnu.org</code> 21796 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3883">#3883</a>)</li> 21797</ul> 21798</li> 21799<li>other changes:<ul> 21800<li>change <code>copy_file</code> function to raise an error when trying to 21801 copy non-existing file 21802 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3836">#3836</a>, 21803 <a href="https://github.com/easybuilders/easybuild-framework/pull/3855">#3855</a>, 21804 <a href="https://github.com/easybuilders/easybuild-framework/pull/3877">#3877</a>)</li> 21805<li>only print the hook messages if EasyBuild is running in debug 21806 mode 21807 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3843">#3843</a>)</li> 21808<li>deprecate old toolchain versions (pre-2019a common toolchains) 21809 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3876">#3876</a>, 21810 <a href="https://github.com/easybuilders/easybuild-framework/pull/3884">#3884</a>)<ul> 21811<li>see also 21812 <a href="https://docs.easybuild.io/en/latest/Deprecated-easyconfigs.html#deprecated-toolchains">https://docs.easybuild.io/en/latest/Deprecated-easyconfigs.html#deprecated-toolchains</a></li> 21813</ul> 21814</li> 21815</ul> 21816</li> 21817</ul> 21818<p><strong>easyblocks</strong></p> 21819<ul> 21820<li>new software-specific easyblock for imkl-FFTW 21821 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2599">#2599</a>)</li> 21822<li>minor enhancements and updates, including:<ul> 21823<li>add support for installing R extensions in parallel 21824 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2408">#2408</a>)</li> 21825<li>update MotionCor2 easyblock to consider to locations for built 21826 binary 21827 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2541">#2541</a>, 21828 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2598">#2598</a>)</li> 21829<li>let GROMACS runtime logs show EasyBuild was used by setting 21830 <code>-DGMX_VERSION_STRING_OF_FORK</code> configuration option 21831 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2571">#2571</a>)</li> 21832<li>
21832adjust qa list in WIEN2k easyblock to handle new questions + fix 21833 sanity check for v21.1 21834 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2572">#2572</a>)</li> 21835<li>enhance GCC easyblock to add support for AMD GPU offloading 21836 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2578">#2578</a>)</li> 21837<li>add support for specifying subdirectory for target installation 21838 directory in CMakeMake 21839 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2579">#2579</a>)</li> 21840<li>enhance COMSOL easyblock to change permission on build directory 21841 during extract step (to allow using patches) 21842 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2584">#2584</a>)</li> 21843<li>enhance FlexiBLAS easyblock to support building with Intel MKL 21844 (imkl) as backend 21845 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2588">#2588</a>)</li> 21846<li>update MATLAB easyblock for 2021b (jre is no longer included) 21847 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2589">#2589</a>)</li> 21848<li>update OpenCV easyblock to detect GTK3 and GTK2 dependencies 21849 (next to GTK+) 21850 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2591">#2591</a>)</li> 21851<li>avoid that path to CUDA install directory is added to <code>$PATH</code> 21852 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2593">#2593</a>)</li> 21853<li>enhance imkl easyblock to add support for installing with NVHPC 21854 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2595">#2595</a>)</li> 21855<li>enhance PETSc easyblock to run tests in parallel 21856 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2601">#2601</a>)</li> 21857<li>update ELSI easyblock to support two new external dependencies 21858 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2602">#2602</a>)</li> 21859<li>add custom custom easyconfig parameter <code>backends</code> in FlexiBLAS 21860 easyblock to specify backends 21861 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2605">#2605</a>)</li> 21862<li>detect problem with compiling CPU detection code in configure 21863 output in GROMACS easyblock 21864 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2609">#2609</a>)</li> 21865<li>use correct include directory for FlexiBLAS 21866 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2610">#2610</a>)</li> 21867</ul> 21868</li> 21869<li>various bug fixes, including:<ul> 21870<li>unset <code>$EASYBUILD_*</code> environment variables when running sanity 21871 check in EasyBuildMeta easyblock + also unset 21872 <code>$MODULES_LMCONFLICT</code> to avoid conflict when loading EasyBuild 21873 module 21874 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2568">#2568</a>)</li> 21875<li>ensure that all ABAQUS components get installed for ABAQUS 21876 2021.x (+ add support for enabling/disabling fe-safe) 21877 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2569">#2569</a>)</li> 21878<li>fix subdir path in VTune easyblock for 2021.x versions + add 21879 sanity check command 21880 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2576">#2576</a>)</li> 21881<li>make sure custom easyblock for installing EasyBuild respects 21882 requested version of Python (like <code>$EB_PYTHON</code>) 21883 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2581">#2581</a>)</li> 21884<li>restore RPATH wrappers for OpenMPI sanity check 21885 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2582">#2582</a>)</li> 21886<li>fix installation of libcp2k for recent CP2K versions 21887 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2585">#2585</a>)</li> 21888<li>make version regex in OpenSSL wrapper easyblock less strict 21889 (version string does not always end with a letter) 21890 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2597">#2597</a>)</li> 21891<li>redefine <code>collect_exts_file_info</code> instead of now deprecated 21892 fetch_extension_sources in OCaml easyblock 21893 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2603">#2603</a>)</li> 21894</ul> 21895</li> 21896<li>other changes:<ul> 21897<li>don't use <code>--config=mkl</code> for TensorFlow 2.4+ 21898 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2583">#2583</a>)<ul> 21899<li>this fixes some performance related issues for TensorFlow, 21900 see 21901 <a href="https://github.com/easybuilders/easybuild-easyblocks/issues/2577">https://github.com/easybuilders/easybuild-easyblocks/issues/2577</a> 21902 and 21903 <a href="https://github.com/easybuilders/easybuild-easyconfigs/issues/14120">https://github.com/easybuilders/easybuild-easyconfigs/issues/14120</a></li> 21904</ul> 21905</li> 21906<li>fix support for recent imkl version in numexpr easyblock 21907 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2606">#2606</a>)</li> 21908<li>derive custom easyblock from MotionCor2 from PackedBinary 21909 instead of EasyBlock 21910 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/260
219107">#2607</a>)</li> 21911</ul> 21912</li> 21913</ul> 21914<p><strong>easyconfigs</strong></p> 21915<ul> 21916<li>added easyconfigs for foss/2021b 21917 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14217">#14217</a>) 21918 and intel/2021b 21919 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14218">#14218</a>) 21920 common toolchains<ul> 21921<li>see also 21922 <a href="https://docs.easybuild.io/en/latest/Common-toolchains.html">https://docs.easybuild.io/en/latest/Common-toolchains.html</a></li> 21923</ul> 21924</li> 21925<li>add easyconfig for gobff/2021a toolchain 21926 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14019">#14019</a>, 21927 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14038">#14038</a>)</li> 21928<li>added example easyconfig files for 39 new software packages:<ul> 21929<li>abTEM 21930 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13974">#13974</a>), 21931 ARTS 21932 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9651">#9651</a>), 21933 AutoGeneS 21934 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13903">#13903</a>), 21935 bashplotlib 21936 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13942">#13942</a>), 21937 CIRI-long 21938 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13985">#13985</a>), 21939 DFT-D4 21940 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12803">#12803</a>), 21941 ELSI-RCI 21942 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14147">#14147</a>), 21943 ESL-Bundle 21944 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14179">#14179</a>), 21945 expecttest 21946 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14106">#14106</a>), 21947 fdict 21948 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14161">#14161</a>), 21949 flook 21950 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14161">#14161</a>), 21951 FreeTDS 21952 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13952">#13952</a>), 21953 HDBSCAN 21954 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14062">#14062</a>), 21955 imkl-FFTW 21956 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14195">#14195</a>), 21957 isoCirc 21958 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13982">#13982</a>), 21959 libfdf 21960 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14173">#14173</a>), 21961 libmbd 21962 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14129">#14129</a>), 21963 libpspio 21964 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14173">#14173</a>), 21965 libSBML 21966 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14050">#14050</a>), 21967 longread_umi 21968 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13987">#13987</a>), 21969 Mesa-demos 21970 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14123">#14123</a>), 21971 MixMHC2pred 21972 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14041">#14041</a>), 21973 NTPoly 21974 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14183">#14183</a>), 21975 OpenSceneGraph 21976 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14197">#14197</a>), 21977 panaroo 21978 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14203">#14203</a>), 21979 PEPT 21980 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14077">#14077</a>), 21981 pycoQC 21982 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14012">#14012</a>), 21983 python-docx 21984 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13930">#13930</a>), 21985 QD 21986 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14122">#14122</a>), 21987 radeontop 21988 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14124">#14124</a>), 21989 Rgurobi 21990 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14188">#14188</a>), 21991 RInChI 21992 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14049">#14049</a>), 21993 scGeneFit 21994 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13963">#13963</a>), 21995 swifter 21996 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14114">#14114</a>), 21997 TOML-Fortran 21998 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13929">#13929</a>), 21999 TRUST4 22000 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14035">#14035</a>), 22001 ucx-py 22002 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14051">#14051</a>), 22003 vawk 22004 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14040">#14040</a>), 22005 VMTK 22006 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14023">#14023</a>)</li> 22007</ul> 22008</li> 22009<li>
22009added additional easyconfigs for various supported software 22010 packages, including:<ul> 22011<li>AlphaFold 2.0.1, artic-ncov2019 2021.06.24, BerkeleyGW 3.0.1, 22012 bokeh 2.4.1, Boost.Python 1.76.0, canu 2.2, Cartopy 0.20.0, CP2K 22013 8.2, CUDA 11.4.2, Dalton 2020.0, dask 2021.9.1, edlib 1.3.9, 22014 ELSI 2.7.1, FFTW 3.3.10, GD 2.73, GDAL 3.3.2, GTDB-Tk 1.7.0, 22015 ImageJ 1.52q, jax 0.2.20, Kraken2 2.1.2, leidenalg 0.8.7, 22016 libfabric 1.13.2, libspatialindex 1.9.3, libxc 5.1.6, libxsmm 22017 1.16.2, lifelines 0.26.3, Longshot 0.4.3, LSD2 2.2, MAFFT 7.487, 22018 MEME 5.4.1, MotionCor2 1.4.4, NCCL 2.11.4, netCDF 4.8.1, 22019 networkx 2.6.3, Nextflow 21.08.0, OpenBLAS 0.3.18, OpenCV 4.5.3, 22020 OrthoFinder 2.5.4, OSU-Micro-Benchmarks 5.8, PhyML 3.3.20200621, 22021 PostgreSQL 13.4, pygraphviz 1.7, pyproj 3.1.0, 22022 python-Levenshtein 0.12.1, PyTorch-Geometric 2.0.1, QIIME2 22023 2021.8.eb, Qiskit 0.31.0, QuantumESPRESSO 6.8, Racon 1.4.21, 22024 rampart 1.2.0, rclone 1.56.0, RDKit 2021.03.4, SAMtools 1.13, 22025 scanpy 1.8.1, scikit-allel 1.3.3, SciPy-bundle 2021.10, Seaborn 22026 0.11.2, SHAPEIT4 4.2.2, spglib 1.16.2, UCX 1.11.2, UCX-CUDA 22027 1.11.2, VSEARCH 2.18.0, Z3 4.8.12, zarr 2.10.1</li> 22028</ul> 22029</li> 22030<li>minor enhancements, including:<ul> 22031<li>add JASPAR2020 to R-bundle-Bioconductor 3.13 22032 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13962">#13962</a>)</li> 22033<li>add Autotools as build dependency for CubeGUI-4.6 22034 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14109">#14109</a>)</li> 22035<li>add compiler/parallel/tcltk R libraries included in base 22036 installation to extensions in recent R easyconfigs 22037 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14189">#14189</a>, 22038 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14190">#14190</a>, 22039 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14194">#14194</a>)<ul> 22040<li>required for parallel installation of extensions for these R 22041 easyconfigs</li> 22042</ul> 22043</li> 22044<li>also add location to MPI startup tests to <code>$PATH</code> in 22045 OSU-Micro-Benchmarks easyconfigs 22046 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14126">#14126</a>)</li> 22047</ul> 22048</li> 22049<li>various bug fixes, including:<ul> 22050<li>add missing Brotli dependency to freetype 22051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13915">#13915</a>, 22052 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14002">#14002</a>)</li> 22053<li>add patch for OpenBLAS 0.3.15 to fix failing numpy tests on 22054 aarch64 22055 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13923">#13923</a>)</li> 22056<li>fix source URL + add alternate checksum for ADMIXTURE 1.3.0 22057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13933">#13933</a>)</li> 22058<li>just use <code>cp</code> to copy <code>stereo_chemical_props.txt</code> to AlphaFold 22059 installation directory 22060 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13938">#13938</a>)</li> 22061<li>add UnZip build dependency to TensorFlow 2.4.1 22062 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13958">#13958</a>), 22063 2.5.0 22064 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13959">#13959</a>) 22065 and 2.6.0 easyconfigs 22066 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13960">#13960</a>)</li> 22067<li>add missing Python dependency for WIEN2k 21.1 + patch to fix 22068 build failure for <code>lapw0_mpi</code> with libxc 22069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13961">#13961</a>)</li> 22070<li>add additional valid checksum for lhs 1.1.1 extension in recent 22071 R 4.0.x and 4.1.0 easyconfigs 22072 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13969">#13969</a>)</li> 22073<li>fix Fortran system call stdout/err redirection for WIEN2k v21.1 22074 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13972">#13972</a>)</li> 22075<li>add OpenSSL dependency to Kent_tools 418 easyconfig to fix a 22076 link error 22077 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13989">#13989</a>)</li> 22078<li>
22078make binutils a build-only dependency for Brotli + add sanity 22079 check command 22080 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14004">#14004</a>)</li> 22081<li>fix installation of Racon v1.4.7 with gcccuda/2019b after move 22082 of ClaraGenomicsAnalysis repository 22083 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14010">#14010</a>)</li> 22084<li>fix source URL for KEGG.db extension in R-bundle-Bioconductor 22085 3.13 easyconfig (since it's a deprecated library now) 22086 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14013">#14013</a>)</li> 22087<li>add patch for BLIS 0.8.1 to fix dgemm FPE signalling on 22088 Broadwell 22089 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14018">#14018</a>)</li> 22090<li>add patch to fix installation of TensorFlow 2.2.3 on POWER 22091 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14025">#14025</a>)</li> 22092<li>fix AmberTools v20 easyconfig using intel/2020a toolchain 22093 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14028">#14028</a>)</li> 22094<li>fix download + permissions of binary for USEARCH v11.0.667 22095 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14036">#14036</a>)</li> 22096<li>remove h5py 3.x dependency for Keras with 2020b toolchain, since 22097 TensorFlow provides (and requires) h5py 2.x 22098 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14052">#14052</a>)</li> 22099<li>correctly specify install prefix for CUDA in 22100 OSU-Micro-Benchmarks after renaming CUDAcore to CUDA for 2021a 22101 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14063">#14063</a>)</li> 22102<li>add patch to fix failing file system cache test for jax on 22103 recent Linux kernels 22104 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14067">#14067</a>), 22105 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14070">#14070</a>)</li> 22106<li>fix compilation of BWA 0.7.17 with GCC/10.2.0 on POWER 22107 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14073">#14073</a>)</li> 22108<li>add missing dependencies for recent LibTIFF versions: XZ, 22109 jbigkit, zstd 22110 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14079">#14079</a>)</li> 22111<li>add missing header file to existing versions of jbigkit 22112 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14081">#14081</a>)</li> 22113<li>fix source URL for SUNDIALS 5.x 22114 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14092">#14092</a>, 22115 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14096">#14096</a>)</li> 22116<li>add Perl and Python runtime dependencies to Bowtie2 2.4.4 22117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14097">#14097</a>)</li> 22118<li>fix source URL for SCOTCH 6.1.0 22119 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14099">#14099</a>)</li> 22120<li>drop tcmalloc from SymEngine as it causes crashes with scipy 22121 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14119">#14119</a>)</li> 22122<li>fix homepage + description in SimpleITK easyconfigs 22123 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14125">#14125</a>)</li> 22124<li>add missing scripts from <code>utils</code> and <code>analysis_scripts</code> to <code>bin</code> 22125 for cryoDRGN 22126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14137">#14137</a>)</li> 22127<li>patch <code>rsync_from_ncbi.pl</code> in Kraken2 v2.1.2 to allow syncing 22128 with NCBI servers over HTTPS 22129 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14148">#14148</a>)</li> 22130<li>skip <code>mkl_fused_batch_norm_op_test</code> test (broken on AMD EPYC 22131 systems) for TensorFlow 2.5.0 and 2.6.0 22132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14151">#14151</a>, 22133 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14153">#14153</a>)</li> 22134<li>fix incorrect module load message and update morphology plugin 22135 of ImageJ 1.51k 22136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14152">#14152</a>)</li> 22137<li>fix XCrySDen v1.6.2 linking to libdl and Togl 22138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14160">#14160</a>)</li> 22139<li>
22139add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, 22140 v4.1.0 22141 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14177">#14177</a>)</li> 22142<li>add patch for OpenBLAS 0.3.17 + 0.3.18 to fix segfault triggered 22143 by scipy tests 22144 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14178">#14178</a>)</li> 22145<li>fix spatstat.* downloads for Seurat v4.0.1 22146 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14199">#14199</a>)</li> 22147<li>add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to 22148 fix CPU detection 22149 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14212">#14212</a>)</li> 22150</ul> 22151</li> 22152<li>other changes:<ul> 22153<li>remove help2man build dependency for flex using system toolchain 22154 (because it requires Perl) 22155 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13922">#13922</a>)</li> 22156<li>use proper dependency for python-Levenshtein in CIRI-long 22157 easyconfig 22158 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13985">#13985</a>)</li> 22159<li>in-place updates for foss/2021b and intel/2021b common 22160 toolchains<ul> 22161<li>update to UCX(-CUDA) 1.11.2 as dependency for OpenMPI 22162 v4.1.1 + NCCL v2.10.3 22163 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14090">#14090</a>)</li> 22164<li>update libfabric to 1.13.1 in OpenMPI and add it as a 22165 dependency in PMIx for the upcoming foss 2021b toolchain 22166 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14164">#14164</a>)</li> 22167<li>update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 22168 3.0.4 with GCCcore/11.2.0 toolchain 22169 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14167">#14167</a>)</li> 22170<li>update libfabric to 1.13.2 in OpenMPI v4.1.1 + PMIx 4.1.0 22171 for the upcoming foss/2021b toolchain 22172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14176">#14176</a>)</li> 22173</ul> 22174</li> 22175<li>remove format mapping from homepage of Subread easyconfigs 22176 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14145">#14145</a>)</li> 22177<li>add BLIS and imkl (x86_64 only) builddependencies to FlexiBLAS 22178 0.3.4 with GCC/11.2.0 toolchain 22179 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/14225">#14225</a>)</li> 22180</ul> 22181</li> 22182</ul> 22183<h2 id="release_notes_eb442">EasyBuild v4.4.2 (September 7th 2021)<a class="headerlink" href="#release_notes_eb442" title="Permanent link">¶</a></h2> 22184<p>bugfix/update release</p> 22185<p><strong>framework</strong></p> 22186<ul> 22187<li>various enhancements, including:<ul> 22188<li>add per-extension timing in output produced by <code>eb</code> command 22189 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3734">#3734</a>)</li> 22190<li>add definition for new toolchain <code>nvpsmpic</code> (NVHPC + 22191 ParaStationMPI + CUDA) 22192 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3736">#3736</a>)</li> 22193<li>include list of missing libraries in warning about missing FFTW 22194 libraries in <code>imkl</code> toolchain component 22195 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3776">#3776</a>)</li> 22196<li>check for recursive symlinks by default before copying a folder 22197 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3784">#3784</a>)</li> 22198<li>add <code>--filter-ecs</code> configuration option to filter out 22199 easyconfigs from set of easyconfigs to install 22200 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3796">#3796</a>)</li> 22201<li>check type of <code>source_tmpl</code> value for extensions, ensure it's a 22202 string value (not a list) 22203 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3799">#3799</a>)</li> 22204<li>also define <code>$BLAS_SHARED_LIBS</code> & co in build environment 22205 (analogous to <code>$BLAS_STATIC_LIBS</code>) 22206 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3800">#3800</a>)</li> 22207<li>report use of <code>--ignore-test-failure</code> in success message in 22208 output 22209 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3806">#3806</a>)</li> 22210<li>
22210add <code>get_cuda_cc_template_value</code> method to <code>EasyConfig</code> class 22211 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3807">#3807</a>)</li> 22212<li>add support for <code>fix_bash_shebang_for</code> 22213 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3808">#3808</a>)</li> 22214<li>pick up <code>$MODULES_CMD</code> to facilitate using Environment Modules 22215 4.x as modules tool 22216 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3816">#3816</a>)</li> 22217<li>use more sensible branch name for creating easyblocks PR with 22218 <code>--new-pr</code> 22219 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3817">#3817</a>)</li> 22220</ul> 22221</li> 22222<li>various bug fixes, including:<ul> 22223<li>remove Python 2.6 from list of supported Python versions in 22224 <code>setup.py</code> 22225 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3767">#3767</a>)</li> 22226<li>don't add directory that doesn't include any files to <code>$PATH</code> 22227 or <code>$LD_LIBRARY_PATH</code> 22228 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3769">#3769</a>)</li> 22229<li>make logdir writable also when <code>--stop</code>/<code>--fetch</code> is used and 22230 <code>--read-only-installdir</code> is enabled 22231 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3771">#3771</a>)</li> 22232<li>fix forgotten renaming of <code>l</code> to <code>char</code> in <code>__init__.py</code> that is 22233 created for included Python modules 22234 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3773">#3773</a>)</li> 22235<li>fix <code>verify_imports</code> by deleting all imported modules before 22236 re-importing them one by one 22237 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3780">#3780</a>)</li> 22238<li>fix <code>ignore_test_failure</code> not set for Extension instances 22239 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3782">#3782</a>)</li> 22240<li>update <code>iompi</code> toolchain to <code>intel-compiler</code> subtoolchain for 22241 oneAPI versions (>= <code>iompi</code> 2020.12) 22242 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3785">#3785</a>)</li> 22243<li>
22243don't parse patch files as easyconfigs when searching for where 22244 patch file is used 22245 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3786">#3786</a>)</li> 22246<li>make sure git clone with a tag argument actually downloads a tag 22247 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3795">#3795</a>)</li> 22248<li>fix CI by excluding GC3Pie 2.6.7 (which is broken with Python 2) 22249 and improve error reporting for option parsing 22250 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3798">#3798</a>)</li> 22251<li>correctly resolve templates for patches in extensions when 22252 uploading to GitHub 22253 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3805">#3805</a>)</li> 22254<li>add <code>--easystack</code> to ignored options when submitting job 22255 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3813">#3813</a>)</li> 22256</ul> 22257</li> 22258<li>other changes:<ul> 22259<li>speed up tests by caching checked paths in <code>set_tmpdir</code> + less 22260 test cases for <code>test_compiler_dependent_optarch</code> 22261 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3802">#3802</a>)</li> 22262<li>speed up <code>set_parallel</code> method in <code>EasyBlock</code> class 22263 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3812">#3812</a>)</li> 22264</ul> 22265</li> 22266</ul> 22267<p><strong>easyblocks</strong></p> 22268<ul> 22269<li>4 new software-specific easyblocks:<ul> 22270<li>CRISPR-DAV 22271 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2487">#2487</a>), 22272 jaxlib 22273 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2545">#2545</a>), 22274 ORCA 22275 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2504">#2504</a>), 22276 RepeatModeler 22277 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2470">#2470</a>)</li> 22278</ul> 22279</li> 22280<li>minor enhancements, including:<ul> 22281<li>update ABAQUS easyblock to support installation of v2020 22282 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2034">#2034</a>)</li> 22283<li>enable make check and sanity check exec for OpenMPI 22284 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2444">#2444</a>)</li> 22285<li>fixed sanity check for later versions of Molpro 22286 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2499">#2499</a>)</li> 22287<li>add Ampere to known GPU architectures for Kokkos in LAMMPS 22288 easyblock 22289 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2510">#2510</a>)</li> 22290<li>update sanity check in ESMF easyblock to take into account new 22291 binary names from version 8.1.0 onwards 22292 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2512">#2512</a>)</li> 22293<li>use <code>report_test_failure</code> in TensorFlow easyblock 22294 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2519">#2519</a>)</li> 22295<li>add support for imkl 2021.x in easyblocks for<ul> 22296<li>Amber 22297 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2527">#2527</a>), 22298 BerkeleyGW 22299 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2528">#2528</a>), 22300 CP2K 22301 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2529">#2529</a>), 22302 FreeFEM 22303 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2530">#2530</a>), 22304 GROMACS 22305 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2531">#2531</a>), 22306 numexpr 22307 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2532">#2532</a>)</li> 22308</ul> 22309</li> 22310<li>add <code>install_src</code> option and enhance <code>buildcmd</code> option in 22311 PythonPackage easyblock 22312 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2534">#2534</a>)</li> 22313<li>make sure AOCC commands like clang/flang pick up <code>GCCcore</code> as 22314 GCC toolchain 22315 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2538">#2538</a>)</li> 22316<li>create <code>CMakeConfig</code> files for tbb >= 2020 22317 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2539">#2539</a>)</li> 22318<li>find source dir for libunwind when building ldd for Clang 22319 versions >= 12.0.1 22320 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2540">#2540</a>)</li> 22321<li>fix motorBike test in sanity check for OpenFOAM 9 22322 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2544">#2544</a>)</li> 22323<li>generate and install pkg-config files for OpenSSL wrapper 22324 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2549">#2549</a>)</li> 22325<li>don't run <code>setup.py config</code> for numpy >= 1.21, since it's no 22326 longer supported 22327 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2554">#2554</a>)</li> 22328<li>update WIEN2k easyblock to handle new Intel versions, WIEN2k 22329 v21, Perl dependency, and tuning of dimension parameters 22330 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2558">#2558</a>)</li> 22331<li>remove PCRE from list of system libraries for TensorFlow 2.6.0 22332 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2559">#2559</a>)</li> 22333<li>
22333add support for also installing Tosca component in ABAQUS 22334 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2560">#2560</a>)</li> 22335<li>update ABAQUS easyblock to support installing of version 2021 22336 with hot fixes 22337 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2562">#2562</a>)</li> 22338<li>update sanity check in VTune easyblock for 2021.x versions 22339 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2563">#2563</a>)</li> 22340</ul> 22341</li> 22342<li>various bug fixes, including:<ul> 22343<li>handle failure of running <code>nvidia-smi</code> in TensorFlow tests 22344 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2506">#2506</a>)</li> 22345<li>remove Python 2.6 from list of supported Python versions in 22346 <code>setup.py</code> 22347 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2507">#2507</a>)</li> 22348<li>clean up installation of Tkinter 22349 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2509">#2509</a>)</li> 22350<li>remove redundant <code>$CPATH</code> entry of tbb modules + fix 22351 <code>--module-only</code> 22352 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2511">#2511</a>)</li> 22353<li>honor <code>--ignore-test-failure</code> in PythonPackage 22354 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2516">#2516</a>)</li> 22355<li>use correct GTK+ version for OpenCV based on dependencies 22356 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2520">#2520</a>)</li> 22357<li>ensure Python prep is done in sanity check + support debug 22358 builds in TensorFlow easyblock 22359 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2522">#2522</a>)</li> 22360<li>correct cleanup of single-letter local variable in <code>__init__</code> of 22361 <code>easybuild.easyblocks</code> 22362 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2524">#2524</a>)</li> 22363<li>reset runtest to <code>None</code> in CMakePythonPackage 22364 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2536">#2536</a>)</li> 22365<li>set <code>$I_MPI_ROOT</code> correctly for 2021.x in impi easyblock 22366 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2537">#2537</a>)</li> 22367<li>let Bundle easyblock pick up custom easyblock for components 22368 based on name if no easyblock is specified explicitly 22369 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2543">#2543</a>, 22370 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2547">#2547</a>)</li> 22371<li>explicitly use only OpenBLAS for PyTorch if MKL is not used 22372 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2448">#2448</a>)</li> 22373<li>keep symlinks in cuDNN installations 22374 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2550">#2550</a>)</li> 22375<li>use <code>${BLAS,LAPACK}_SHARED_LIBS</code> in GROMACS easyblock for 22376 FlexiBLAS-based toolchains 22377 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2552">#2552</a>)</li> 22378<li>copy the list to avoid changing the original lists in 22379 <code>DEFAULT_TARGETS_MAP</code> for Clang and LLVM 22380 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2556">#2556</a>)</li> 22381<li>fix <code>pathsep</code> <code>join</code> bug that breaks installation of CUDA 22382 versions < 10.1 if <code>$PERL5LIB</code> is defined 22383 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2561">#2561</a>)</li> 22384</ul> 22385</li> 22386<li>other changes:<ul> 22387<li>simplify Boost easyblock 22388 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2513">#2513</a>)</li> 22389<li>remove deprecated options from PythonPackage 22390 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2535">#2535</a>)</li> 22391</ul> 22392</li> 22393</ul> 22394<p><strong>easyconfigs</strong></p> 22395<ul> 22396<li>added easyconfig for foss/2021.07 (candidate for foss/2021b) 22397 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13788">#13788</a>) 22398 and iomkl/2021a 22399 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13521">#13521</a>) 22400 toolchains</li> 22401<li>
22401added example easyconfig files for 79 new software packages:<ul> 22402<li>AlphaFold 22403 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13867">#13867</a>), 22404 andi 22405 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13768">#13768</a>), 22406 aria2 22407 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13709">#13709</a>), 22408 AUTO-07p 22409 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13831">#13831</a>), 22410 babl 22411 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13216">#13216</a>), 22412 BAli-Phy 22413 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13484">#13484</a>), 22414 biogeme 22415 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13735">#13735</a>), 22416 Bio-SearchIO-hmmer 22417 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13419">#13419</a>), 22418 BuDDy 22419 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13907">#13907</a>), 22420 c-ares 22421 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13709">#13709</a>), 22422 CellRank 22423 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13408">#13408</a>), 22424 Coin 22425 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13818">#13818</a>), 22426 Co-phylog 22427 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13769">#13769</a>), 22428 cppy 22429 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13823">#13823</a>), 22430 CREST 22431 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13648">#13648</a>), 22432 CRISPR-DAV 22433 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13139">#13139</a>), 22434 CSBLAST 22435 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13794">#13794</a>), 22436 DGL 22437 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13793">#13793</a>), 22438 DistributedStream 22439 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13659">#13659</a>), 22440 Excel-Writer-XLSX 22441 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13139">#13139</a>), 22442 FBPIC 22443 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13500">#13500</a>), 22444 freebayes 22445 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12859">#12859</a>), 22446 freud-analysis 22447 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13354">#13354</a>), 22448 fumi_tools 22449 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13517">#13517</a>), 22450 GEGL 22451 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13216">#13216</a>), 22452 GIMP 22453 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13216">#13216</a>), 22454 glib-networking 22455 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13216">#13216</a>), 22456 GOATOOLS 22457 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13364">#13364</a>, 22458 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13629">#13629</a>), 22459 gofasta 22460 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13651">#13651</a>), 22461 GTK2 22462 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13900">#13900</a>), 22463 GTK3 22464 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13900">#13900</a>), 22465 Highway 22466 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13453">#13453</a>), 22467 hipSYCL 22468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13837">#13837</a>), 22469 ISA-L 22470 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13663">#13663</a>), 22471 jax 22472 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13760">#13760</a>), 22473 JSON-GLib 22474 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13216">#13216</a>), 22475 Kalign 22476 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13463">#13463</a>), 22477 LADR 22478 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13351">#13351</a>), 22479 lDDT 22480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13794">#13794</a>), 22481 libdivsufsort 22482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13768">#13768</a>), 22483 libjxl 22484 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13453">#13453</a>, 22485 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13829">
22485#13829</a>), 22486 libmypaint 22487 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13216">#13216</a>), 22488 libtecla 22489 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13908">#13908</a>), 22490 lie_learn 22491 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13793">#13793</a>), 22492 longestrunsubsequence 22493 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13800">#13800</a>), 22494 Maude 22495 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13909">#13909</a>), 22496 mimalloc 22497 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13726">#13726</a>), 22498 MINPACK 22499 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13802">#13802</a>), 22500 Mish-Cuda 22501 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13759">#13759</a>, 22502 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13784">#13784</a>), 22503 muparserx 22504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13779">#13779</a>), 22505 nlohmann_json 22506 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13777">#13777</a>), 22507 OpenStackClient 22508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13644">#13644</a>), 22509 OSPRay 22510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12852">#12852</a>), 22511 pandapower 22512 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13687">#13687</a>), 22513 pangolin 22514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13733">#13733</a>, 22515 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13848">#13848</a>), 22516 PSIPRED 22517 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13794">#13794</a>), 22518 PYPOWER 22519 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13689">#13689</a>), 22520 PyPSA 22521 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13673">#13673</a>), 22522 PyRosetta 22523 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13793">#13793</a>), 22524 pysamstats 22525 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13139">#13139</a>), 22526 pytest-benchmark 22527 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13622">#13622</a>), 22528 python-isal 22529 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13663">#13663</a>), 22530 QCxMS 22531 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13650">#13650</a>), 22532 RepeatModeler 22533 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13126">#13126</a>), 22534 Schrodinger 22535 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11698">#11698</a>), 22536 sklearn-som 22537 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13699">#13699</a>), 22538 SoQt 22539 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13818">#13818</a>), 22540 spdlog 22541 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13778">#13778</a>), 22542 SpectrA 22543 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13743">#13743</a>), 22544 SymEngine-python 22545 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13652">#13652</a>), 22546 SyRI 22547 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13800">#13800</a>), 22548 torchinfo 22549 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13662">#13662</a>), 22550 TRAVIS-Analyzer 22551 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13503">#13503</a>), 22552 UShER 22553 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13708">#13708</a>), 22554 Vampire 22555 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13352">#13352</a>), 22556 VBZ-Compression 22557 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13536">#13536</a>), 22558 VisPy 22559 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13468">#13468</a>), 22560 wgsim 22561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1347
225615">#13475</a>), 22562 Yices 22563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13906">#13906</a>)</li> 22564</ul> 22565</li> 22566<li>added additional easyconfigs for various supported software 22567 packages, including:<ul> 22568<li>ABAQUS 2020.eb, ANTs 2.3.5, AOCC 3.1.0, Arb 2.19.0, archspec 22569 0.1.2, Armadillo 10.5.3, ASE 3.22.0, Autotools 20210726, 22570 BamTools 2.5.2, bgen 4.1.3, Biopython 1.79, bitarray 1.5.3, 22571 Boost 1.76.0, Bowtie2 2.4.4, bpytop 1.0.67, Cartopy 22572 0.19.0.post1, Centrifuge 1.0.4, Clang 12.0.1, CMake 3.21.1, 22573 CRISPResso2 2.2.1, CUDA 11.4.1, cuDNN 8.2.2.26, cURL 7.78.0, 22574 cutadapt 3.4, DIAMOND 2.0.11, DROP 1.1.0, Dsuite 20210718, dtcmp 22575 1.1.2, ecCodes 2.22.1, Elk 7.2.42, ESMF 8.1.1, expat 2.4.1, 22576 fastq-tools 0.8.3, Fiona 1.8.20, FLINT 2.7.1, g2clib 1.6.3, 22577 g2lib 3.2.0, GCC(core) 11.2.0, GDCM 3.0.8, GDRCopy 2.3, 22578 GenomeTools 1.6.2, GffCompare 0.12.2, gffread 0.12.7, GLib 22579 2.69.1, GMT 6.2.0, Go 1.16.6, GPAW 21.6.0, Gradle 6.9.1.eb, 22580 GROMACS 2021.3, HarfBuzz 2.8.2, HDF5 1.12.1, Horovod 0.22.1, 22581 hwloc 2.5.0, hypothesis 6.14.6, igraph 0.9.4, ImageMagick 7.1.0, 22582 IMOD 4.11.5, IPython 7.26.0, Java 16, Julia 1.6.2, JupyterHub 22583 1.4.1, JupyterLab 3.1.6, Kent_tools 418, lavaan 0.6-9, libfabric 22584 1.13.0, libffcall 2.4, libffi 3.4.2, libgeotiff 1.7.0, libRmath 22585 4.1.0, LIBSVM 3.25, LibTIFF 4.3.0, likwid 5.2.0, LLVM 12.0.1, 22586 LMDB 0.9.29, magma 2.6.1, MariaDB 10.6.4, MATIO 1.5.21, 22587 matplotlib 3.4.2, MEGA 10.0.5, Mesa 21.1.7, Meson 0.59.1, Metal 22588 2020-05-05, Mini-XML 3.2, molmod 1.4.8, MPICH 3.4.2, nanopolish 22589 0.13.3, NCCL 2.10.3, ncdu 1.16, NCO 5.0.1, neptune-client 22590 0.10.5, netcdf4-python 1.5.7, networkx 2.5.1, nodejs 14.17.6, 22591 NSPR 4.32, NSS 3.69, NVHPC 21.7, OpenBLAS 0.3.17, OpenEXR 3.1.1, 22592 OpenFOAM 9, OpenFOAM v2106, OpenMM 7.5.1, OpenMolcas 21.06, 22593 openpyxl 3.0.7, Pango 1.48.8, parallel 20210722, Paraver 4.9.2, 22594 ParaView 5.9.1, patchelf 0.13, PCRE2 10.37, PCRE 8.45, Perl 22595 5.34.0, PETSc 3.15.1, petsc4py 3.15.0, Pillow 8.3.1, Pillow-SIMD 22596 8.3.1, plotly.py 5.1.0, PLUMED 2.7.2, PMIx 4.1.0, poppler 22597 21.06.1, PostgreSQL 13.3, preseq 3.1.2, pybind11 2.7.1, pyFFTW 22598 0.12.0, PyGEOS 0.10.2, Pyomo 6.0.1, PyQt5 5.15.4, pyshp 2.1.3, 22599 Python 3.9.6, python-igraph 0.9.6, QTLtools 1.3.1, RAxML-NG 22600 1.0.3, R-bundle-Bioconductor 3.13, re2c 2.2, ReFrame 3.8.0., 22601 RStudio-Server 1.4.1717, Rust 1.54.0, Scalasca 2.6, scVelo 22602 0.2.3, Shapely 1.8a1, shrinkwrap 1.1.0, SLEPc 3.15.1, slepc4py 22603 3.15.1, snakemake 6.6.1, snappy 1.1.9, snippy 4.6.0, snpEff 22604 5.0e, SOCI 4.0.2, SpaceRanger 1.3.0, Spack 0.16.2, spatialreg 22605 1.1-8, spglib-python 1.16.1, SQLite 3.36, STAR 2.7.9a, 22606 statsmodels 0.12.2, StringTie 2.1.7, Subread 2.0.3, SymEngine 22607 0.7.0, TensorFlow 2.6.0, TetGen 1.6.0, Tkinter 3.9.6, torchtext 22608 0.9.1, tqdm 4.61.2, UCX 1.11.0, UCX-CUDA 1.11.0, unrar 6.0.2, 22609 util-linux 2.37, VTune 2021.6.0, WIEN2k 21.1, WPS 4.2, WRF 4.3, 22610 X11 20210802, x264 20210613, xarray 0.19.0, XlsxWriter 1.4.4, 22611 XML-Parser 2.46, zstd 1.5.0</li> 22612</ul> 22613</li> 22614<li>minor enhancements, including:<ul> 22615<li>add extensions to recent R v4.x easyconfigs: PCAmatchR 22616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13448">#13448</a>), 22617 hal9001 22618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13451">#13451</a>), 22619 cobalt 22620 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13544">#13544</a>), 22621 CBPS 22622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13549">#13549</a>), 22623 SBdecomp 22624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13565">#13565</a>), 22625 lwgeom 22626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13674">#13674</a>), 22627 naturalsort 22628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13762">
22628#13762</a>), 22629 finalfit + gtsummary 22630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13766">#13766</a>)</li> 22631<li>add VBZ compress capability to nanopolish 0.13.3 (for fast5 22632 files) 22633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13536">#13536</a>)</li> 22634<li>add CMake build dependency to easyconfig for tbb 2020.03 22635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13704">#13704</a>)</li> 22636<li>also build shared libs for MUMPS 5.3.5 22637 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13702">#13702</a>) 22638 and 5.4.0 22639 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13705">#13705</a>)</li> 22640<li>add dependency on pkg-config to OpenSSL wrappers 22641 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13765">#13765</a>)</li> 22642</ul> 22643</li> 22644<li>various bug fixes, including:<ul> 22645<li>fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD 22646 CPUs by patching out hardcoded <code>-xHost</code> 22647 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11577">#11577</a>)</li> 22648<li>fix sanity check error for OpenCV v4.5.1 by adding (and using) 22649 freetype and HarfBuzz dependencies 22650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12517">#12517</a>)</li> 22651<li>add patches for TensorFlow 1.13.1 to fix installation 22652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13326">#13326</a>)</li> 22653<li>remove Python 2.6 from list of supported Python versions in 22654 <code>setup.py</code> 22655 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13349">#13349</a>)</li> 22656<li>switch back to Bundle easyblock for PyQt5 5.15.1 + add back 22657 source URLs for components 22658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13371">#13371</a>)</li> 22659<li>add pkg-config build dependency for GDAL 3.2.1 22660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13383">#13383</a>, 22661 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13808">#13808</a>), 22662 Rust 22663 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13538">#13538</a>), 22664 GenomeTools 22665 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13805">#13805</a>), 22666 x264 22667 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13834">#13834</a>)</li> 22668<li>add missing Python 3 build dependency for Rust v1.52.1 22669 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13399">#13399</a>)</li> 22670<li>fix order of cffi extension in old Python easyconfigs 22671 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13400">#13400</a>)</li> 22672<li>patch out <code>__asm__</code> use in ctffind to avoid build failure on 22673 ppc64le 22674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13409">#13409</a>)</li> 22675<li>disable building man pages in Gdk-Pixbuf 22676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13410">#13410</a>)</li> 22677<li>add missing Bio-Search-hmmer dependency for prokka 22678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13419">#13419</a>)</li> 22679<li>avoid downloading old numpy version during install for h5py 22680 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13428">#13428</a>)</li> 22681<li>add patch for Qt5 5.8.0 to fix compilation failure in webkit 22682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13434">#13434</a>)</li> 22683<li>avoid downloading and building freetype and qhull for matplotlib 22684 3.4.2 22685 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13437">#13437</a>)</li> 22686<li>fix order of components in recent GTK+ easyconfigs to avoid 22687 dependency on system GTK+ in GTK+ themes 22688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13449">#13449</a>)</li> 22689<li>fix Python 2.7.13 easyconfigs by adding missing extensions 22690 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13456">#13456</a>)</li> 22691<li>add TensorFlow patch to fix crash on shutdown 22692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13462">#13462</a>)</li> 22693<li>allow for non-x86_64 in <code>postinstallcmds</code> for CuPy 22694 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13501">#13501</a>)</li> 22695<li>disable default EULA acceptance in easyconfig for NVHPC v21.5 22696 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13516">#13516</a>)</li> 22697<li>fix error with p7zip's 7z command not finding <code>7z.dll</code> 22698 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13542">#13542</a>)</li> 22699<li>patch MaxBin2 Perl script to use provided Perl dependency 22700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13551">#13551</a>)</li> 22701<li>
22701add missing zlib dependency to libarchive 22702 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13579">#13579</a>)</li> 22703<li>fix pkgconfig version in patch for bzip 1.0.8 (+ add easyconfig 22704 with GCCcore/11.2.0 toolchain) 22705 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13581">#13581</a>)</li> 22706<li>fix build of DIRAC 19.0 easyconfig with high compiler 22707 optimizations 22708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13613">#13613</a>)</li> 22709<li>fix source URLs and add alternative checksum for Hypre 2.15.1 22710 (since it moved to a different GitHub repo) 22711 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13616">#13616</a>)</li> 22712<li>add new source URL for Mesa easyconfigs using 2017b toolchain 22713 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13617">#13617</a>)</li> 22714<li>avoid <code>MPICXX</code> dependency in SimpleElastics ITK 22715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13623">#13623</a>)</li> 22716<li>add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE 22717 on avx512 (affects UCX) 22718 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13628">#13628</a>)</li> 22719<li>add patch for ctffind 4.1.14 to declare functions without return 22720 as void (fixes segfault) 22721 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13665">#13665</a>)</li> 22722<li>enable EGL in recent libepoxy ECs 22723 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13684">#13684</a>)</li> 22724<li>remove unused <code>buildcmd</code> from libgpuarray easyconfigs 22725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13720">#13720</a>)</li> 22726<li>add patch to fix building Qt5.10.1 against newer glibc 22727 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13730">#13730</a>)</li> 22728<li>add Python 3 as a builddependency to recent fontconfig 22729 easyconfigs 22730 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13731">#13731</a>)</li> 22731<li>update source_URL in BLAST 2.2.26 easyconfig 22732 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13732">#13732</a>)</li> 22733<li>restore error message on failing easyconfigs test suite, 22734 required by bot to determine end of output of test suite 22735 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13745">#13745</a>, 22736 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13770">#13770</a>)</li> 22737<li>add Perl build dependency to recent Clang easyconfigs 22738 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13746">#13746</a>)</li> 22739<li>disable using system Valgrind in the json-c tests 22740 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13750">#13750</a>)</li> 22741<li>use Archive source URL for spatstat.geom extension in Seurat 22742 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13761">#13761</a>)</li> 22743<li>add ld.gold relocts patch to binutils 2.30 22744 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13785">#13785</a>)</li> 22745<li>add missing Python + Zip build dependencies for old Bazel 22746 versions used as build dep for TensorFlow 1.12.0 + 1.13.1 22747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13786">#13786</a>)</li> 22748<li>add alternative checksum for AFNI 18.3.00 22749 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13790">#13790</a>)</li> 22750<li>update tensorflow-probability easyconfigs to include <code>--release</code> 22751 flag in <code>installopts</code> 22752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13810">#13810</a>)</li> 22753<li>fix source URL for DB 18.1.32 22754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13813">#13813</a>)</li> 22755<li>add missing cppy build dependency for matplotlib 3.4.2 22756 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13823">#13823</a>)</li> 22757<li>disable bash completion in recent x264 easyconfigs 22758 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13834">#13834</a>)</li> 22759<li>
22759add Perl as build dependency for ELPA 2021.05.001 + patch to fix 22760 hardcoded <code>/usr/bin/perl</code> 22761 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13835">#13835</a>)</li> 22762<li>add archive source URL to Spark 3.x easyconfigs to fix broken 22763 download 22764 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13842">#13842</a>)</li> 22765<li>fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2 22766 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13861">#13861</a>)</li> 22767<li>add Perl build dependency for HMMER 3.3.2 + patch to ensure it 22768 is used 22769 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13870">#13870</a>)</li> 22770<li>stick to intel-compilers toolchain for DFT-D3 v3.2.0 22771 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13878">#13878</a>)</li> 22772<li>add missing flex build dependency for leidenalg 22773 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13884">#13884</a>)</li> 22774<li>update CMake build dependency for Eigen 3.3.4 + 3.3.5 22775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13889">#13889</a>)</li> 22776<li>fix source URL for Yasm 1.3.0 (+ add missing checksum) 22777 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13901">#13901</a>)</li> 22778<li>update to more recent Meson build dependency for GCCcore/8.3.0 22779 easyconfigs to fix failing RPATH sanity check 22780 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13910">#13910</a>)</li> 22781<li>fix shebang for RepeatMasker 4.1.2-p1 Perl script 22782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13911">#13911</a>)</li> 22783</ul> 22784</li> 22785<li>other changes:<ul> 22786<li>use custom ORCA easyblock in easyconfigs for ORCA v4.x 22787 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13348">#13348</a>)</li> 22788<li>move archived easyconfig files to correct <code>__archive__</code> folder 22789 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13422">#13422</a>)</li> 22790<li>rename NINJA to TWL-NINJA to avoid nameclash 22791 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13529">#13529</a>)</li> 22792<li>remove superfluous <code>configopts</code> and add sanity checks/checksums 22793 in CLHEP easyconfigs 22794 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13614">#13614</a>)</li> 22795<li>remove superfluous <code>-DCMAKE_BUILD_TYPE</code> configuration option in 22796 Arrow easyconfigs 22797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13615">#13615</a>)</li> 22798<li>switch ITK easyconfigs to CMakePythonPackage easyblock, also 22799 enable <code>-DITK_USE_SYSTEM_HDF5</code> configuration option, fix 22800 download URLs 22801 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13619">#13619</a>)</li> 22802<li>use <code>build_type</code> instead of <code>-DCMAKE_BUILD_TYPE=RELEASE</code> in 22803 <code>configopts</code> in MMseqs2 easyconfigs 22804 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13620">#13620</a>)</li> 22805<li>avoid using system GTK+3 and remove <code>-DCMAKE_BUILD_TYPE=RELEASE</code> 22806 configure option in OpenCV easyconfigs 22807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13621">#13621</a>)</li> 22808<li>remove <code>-DCMAKE_BUILD_TYPE=RELEASE</code> configure option and add 22809 checksums in LLVM easyconfigs 22810 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13624">#13624</a>)</li> 22811<li>create libtinfo symlinks in easyconfigs for ncurses with system 22812 toolchain 22813 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13658">#13658</a>), 22814 6.1 22815 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13661">#13661</a>) 22816 and 6.2 22817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13660">#13660</a>)</li> 22818<li>increase test timeouts for PyTorch 1.8.1 and 1.9.0 22819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13700">#13700</a>)</li> 22820<li>rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging 22821 foss/fosscuda, to ensure that <code>get_software_root('CUDA')</code> used 22822 in easyblocks works 22823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13874">#13874</a>)</li> 22824<li>use CUDA instead of CUDAcore in recent NVHPC comments 22825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13875">#13875</a>)</li> 22826</ul> 22827</li> 22828</ul> 22829<h2 id="release_notes_eb441">EasyBuild v4.4.1 (July 6th 2021)<a class="headerlink" href="#release_notes_eb441" title="Permanent link">¶</a></h2> 22830<p>bugfix/update release</p> 22831<p><strong>framework</strong></p> 22832<ul> 22833<li>various enhancements, including:<ul> 22834<li>
22834enhance detection of patch files supplied to <code>eb</code> command with 22835 better error messages 22836 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3709">#3709</a>)</li> 22837<li>add per-step timing information 22838 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3716">#3716</a>)</li> 22839<li>add <code>module-write hook</code> 22840 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3728">#3728</a>)</li> 22841<li>add <code>ignore-test-failure</code> configuration option to ignore failing 22842 test step 22843 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3732">#3732</a>)</li> 22844<li>add toolchain definition for nvompic (NVHPC + OpenMPI) 22845 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3735">#3735</a>)</li> 22846<li>warn about generic milestone in <code>--review-pr</code> and <code>--merge-pr</code> 22847 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3751">#3751</a>)</li> 22848</ul> 22849</li> 22850<li>various bug fixes, including:<ul> 22851<li>don't override <code>COMPILER_MODULE_NAME</code>, inherited from <code>Ffmpi</code>, 22852 in Fujitsu toolchain definition 22853 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3721">#3721</a>)</li> 22854<li>avoid overwriting <code>pr_nr</code> in <code>post_pr_test_report</code> for reports 22855 with <code>--include-easyblocks-from-pr</code> 22856 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3724">#3724</a>, 22857 <a href="https://github.com/easybuilders/easybuild-framework/pull/3726">#3726</a>)</li> 22858<li>fix crash in <code>get_config_dict</code> when copying modules that were 22859 imported in easyconfig file (like <code>import os</code>) 22860 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3729">#3729</a>)</li> 22861<li>parse C standard flags in <code>CFLAGS</code> for Fujitsu compiler 22862 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3731">#3731</a>)</li> 22863<li>fix error message for <code>--use-ccache</code> 22864 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3733">#3733</a>)</li> 22865<li>error out when passing a list to <code>run_cmd*</code> to avoid running 22866 wrong command unintended, unless <code>shell=True</code> is used 22867 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3737">#3737</a>)</li> 22868<li>minor fixes to output of test reports when using multiple PRs 22869 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3741">#3741</a>)</li> 22870<li>fix location for modules installed with intel-compilers 22871 toolchain in HierarchicalMNS by always checking toolchain 22872 compiler name against template map 22873 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3745">#3745</a>)</li> 22874<li>avoid checking <code>msg</code> attribute of <code>GitCommandError</code> 22875 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3756">#3756</a>)</li> 22876<li>consider sources provided as dict in 22877 <code>EasyBlock.check_checksums_for</code> 22878 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3758">#3758</a>)</li> 22879<li>don't make changes to software installation directory when 22880 using <code>--sanity-check-only</code> 22881 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3761">#3761</a>)</li> 22882<li>honor specified easyblock for extensions 22883 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3762">#3762</a>)</li> 22884</ul> 22885</li> 22886<li>other changes:<ul> 22887<li>make sure that tests requiring a github token have <code>github</code> in 22888 the test name so that they can be easily filtered 22889 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3730">#3730</a>)</li> 22890<li>deprecate EasyBuild bootstrap script 22891 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3742">#3742</a>)</li> 22892<li>use temporary download folder in 22893 <code>test_http_header_fields_urlpat</code> 22894 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3755">#3755</a>)</li> 22895</ul> 22896</li> 22897</ul> 22898<p><strong>easyblocks</strong></p> 22899<ul> 22900<li>5 new software-specific easyblocks:<ul> 22901<li>AOMP 22902 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2435">#2435</a>, 22903 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2462">#2462</a>, 22904 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2464">#2464</a>), 22905 FreeFEM 22906 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1969">#1969</a>), 22907 NCCL (built from source) 22908 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2337">#2337</a>, 22909 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2460">#2460</a>), 22910 torchvision 22911 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2467">#2467</a>), 22912 UCX plugins 22913 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2491">#2491</a>)</li> 22914</ul> 22915</li> 22916<li>minor enhancements, including:<ul> 22917<li>enhance Amber easyblock to support installing Amber via CMake 22918 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2445">#2445</a>)</li> 22919<li>enhance ConfigureMake generic easyblock to add support for 22920 building multiple build targets 22921 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2449">#2449</a>, 22922 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2479">#2479</a>, 22923 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2480">#2480</a>)</li> 22924<li>enhance sanity check for Clang to verify if CUDA offload library 22925 was produced 22926 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2454">#2454</a>)</li> 22927<li>update custom easyblock for Boost to always build single and 22928 multi threaded versions 22929 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2456">#2456</a>)</li> 22930<li>enhance <code>sitecustomize.py</code> in Python easyblock to support 22931 overriding core Python packages, and allowing overriding in 22932 virtualenv 22933 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2458">#2458</a>, 22934 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2483">#2483</a>)</li> 22935<li>update CMakeMake to handle old and new Boost/Boost.Python builds 22936 using custom easyblock for Boost 22937 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2461">#2461</a>)</li> 22938<li>
22938add file prefix option to XALT easyblock 22939 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2463">#2463</a>)</li> 22940<li>enhance Java easyblock to define <code>%(jdkarch)s</code> template 22941 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2472">#2472</a>)</li> 22942<li>adjust Perl easyblock to only check for a <code>man</code> subdirectory if 22943 groff is a dependency 22944 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2474">#2474</a>)</li> 22945<li>support arbitrary version strings in OpenSSL wrapper and add 22946 <code>minimum_openssl_version</code> option 22947 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2475">#2475</a>)</li> 22948<li>enhance Python easyblock to explicitly disable installing 22949 core-pip when <code>install_pip</code> is not <code>True</code> 22950 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2476">#2476</a>)</li> 22951<li>enhance intel-compiler easyblock to include multipath include 22952 dir in <code>$CPATH</code> 22953 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2477">#2477</a>)</li> 22954<li>enhance Hypre easyblock to enable CUDA support 22955 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2482">#2482</a>)</li> 22956<li>update Xmipp easyblock for new version (v3.20.07) 22957 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2486">#2486</a>)</li> 22958<li>enhance FFTW easyblock to skip tests if <code>--mpi-tests</code> EasyBuild 22959 configuration option is disabled 22960 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2490">#2490</a>)</li> 22961<li>use <code>PYPI_SOURCE</code> as the default for <code>source_urls</code> of extensions 22962 of Python easyconfigs 22963 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2493">#2493</a>)</li> 22964</ul> 22965</li> 22966<li>various bug fixes, including:<ul> 22967<li>only use siterc fix for NVHPC < 21.3 22968 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2453">#2453</a>)</li> 22969<li>fix CPU-only runtime for dpcpp-generated executables in custom 22970 easyblock for intel-compilers 22971 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2457">#2457</a>)</li> 22972<li>always add <code>distinct_host_configuration=false</code> to build command 22973 for TensorFlow 22974 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2459">#2459</a>)</li> 22975<li>disable installation of bundled BioPerl and HTSLib if they are 22976 dependencies of VEP 22977 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2468">#2468</a>)</li> 22978<li>don't use list value for command to detect installed Python 22979 packages in TensorFlow easyblock 22980 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2469">#2469</a>)</li> 22981<li>change Bundle easyblock to also collect <code>altroot</code> and 22982 <code>altversion</code> in the module step so they are set when running 22983 <code>--module-only</code> 22984 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2485">#2485</a>)</li> 22985<li>always strip output from <code>gcc -print-multiarch</code> in 22986 intel-compilers easyblock 22987 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2489">#2489</a>)</li> 22988<li>don't overwrite all of <code>exts_default_options</code> in TensorFlow 22989 easyblock 22990 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2494">#2494</a>)</li> 22991<li>enhance GCC easyblock to make sure that system GCC provides LTO 22992 support, and disable LTO when building MPFR if not 22993 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2498">#2498</a>)</li> 22994<li>rework the dependency handling of OpenMPI to use explicit 22995 configure options to disable features if required dependency is 22996 not provided 22997 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2500">#2500</a>, 22998 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2501">#2501</a>)</li> 22999</ul> 23000</li> 23001</ul> 23002<p><strong>easyconfigs</strong></p> 23003<ul> 23004<li>added example easyconfig files for 39 new software packages:<ul> 23005<li>AMPHORA2 23006 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13003">#13003</a>), 23007 AOMP 23008 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12909">#12909</a>), 23009 CAMPARI 23010 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13152">#13152</a>), 23011 CSB 23012 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12877">#12877</a>), 23013 dijitso 23014 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10719">#10719</a>),
23015 DosageConvertor 23016 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13278">#13278</a>), 23017 dSFMT 23018 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12971">#12971</a>), 23019 exiv2 23020 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13204">#13204</a>), 23021 FEniCS 23022 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10719">#10719</a>), 23023 FreeFEM 23024 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9902">#9902</a>), 23025 futhark 23026 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12921">#12921</a>), 23027 futile 23028 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12864">#12864</a>), 23029 gappa 23030 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13186">#13186</a>), 23031 GenomeWorks 23032 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13083">#13083</a>, 23033 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13092">#13092</a>), 23034 gexiv2 23035 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13204">#13204</a>), 23036 HAL 23037 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13267">#13267</a>), 23038 hipify-clang 23039 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12961">#12961</a>), 23040 inline 23041 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12029">#12029</a>), 23042 libcint 23043 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13214">#13214</a>), 23044 LTR_retriever 23045 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13125">#13125</a>), 23046 mapDamage 23047 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13172">#13172</a>), 23048 MbedTLS 23049 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13061">#13061</a>), 23050 microctools 23051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13010">#13010</a>), 23052 Nektar++ 23053 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12664">#12664</a>), 23054 NINJA 23055 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13125">#13125</a>), 23056 OBITools3 23057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12969">#12969</a>), 23058 ont-fast5-api 23059 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13033">#13033</a>), 23060 OpenMM-PLUMED 23061 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13268">#13268</a>), 23062 phototonic 23063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13241">#13241</a>), 23064 PyFoam 23065 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12675">#12675</a>), 23066 RagTag 23067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13247">#13247</a>), 23068 RcppGSL 23069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13172">#13172</a>), 23070 RECON 23071 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13123">#13123</a>), 23072 RepeatScout 23073 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13124">#13124</a>), 23074 retworkx 23075 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13228">#13228</a>), 23076 UCX-CUDA 23077 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13260">#13260</a>), 23078 unimap 23079 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13247">#13247</a>), 23080 Vala 23081 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13204">#13204</a>), 23082 WhatsHap 23083 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12989">#12989</a>)</li> 23084</ul> 23085</li> 23086<li>added additional easyconfigs for various supported software 23087 packages, including:<ul> 23088<li>Amber 20.11, BBMap 38.90, Beast 2.6.4, BLIS 3.0 (AMDo fork), 23089 Bonito 0.4.0, CellRanger-ARC 2.0.0, CellRanger-ATAC 2.0.0, Check 23090 0.15.2, CubeGUI 4.6, CubeLib 4.6, CubeWriter 4.6, cuDNN 23091 8.2.1.32, CVXOPT 1.2.6, DOLFIN 2019.1.0.post0, eggnog-mapper 23092 2.1.4, ELPA 2021.05.001, FDS 6.7.6, FFC 2019.1.0.post0, FFmpeg 23093 4.3.2, FIAT 2019.1.0, flatbuffers 2.0.0, flatbuffers-python 2.0, 23094 FLTK 1.3.6, gc 8.0.4, GCC 8.4.0 + 9.4.0, GDAL 3.3.0, Gdk-Pixbuf 23095 2.42.6, geopy 2.1.0, Ghostscript 9.54.0, git 2.32.0, GitPython 23096 3.1.18, GLFW 3.3.4, gmsh 4.8.4, gnuplot 5.4.2, GnuTLS 3.7.2, Go 23097 1.16.5, GObject-Introspection 1.68.0, gperftools 2.9.1, 23098 GraphicsMagick 1.3.36, Graphviz 2.47.2, GSL 2.7, GTK+ 2.24.33, 23099 Guile 2.2.7, h5py 3.2.1, HarfBuzz 2.8.1, Horovod 0.22.0, Hypre 23100 2.21.0, ICU 69.1, ImageMagick 7.0.11-14, IOR 3.3.0, IPython 23101 7.25.0, IRkernel 1.2, ispc 1.16.0, JupyterLab 3.0.16, LDC 23102 1.26.0, libcerf 1.17, libepoxy 1.5.8, libgd 2.3.1, libStatGen 23103 1.0.15, libxc 5.1.5, LittleCMS 2.12, LMfit 1.0.2, Lua 5.4.3, M4 23104 1.4.19, MCR R2021a.3, medaka 1.4.3, Mercurial 5.8, minimap2 23105 2.20, MMseqs2 13, MrBayes 3.2.7, MUMPS 5.4.0, NCCL 2.9.9, netCDF 23106 4.8.0, Nim 1.4.8, nodejs 14.17.0, Nsight-Compute 2021.2.0, numba 23107 0.53.1, NVHPC 21.5.eb, nvtop 1.2.1, Octave 6.2.0, OPARI2 2.0.6, 23108 openkim-models 20210128, OpenMPI 4.0.6, OTF2 2.3, p11-kit 23109 0.24.0, Pango 1.48.5, parallel 20210622, petsc4py 3.12.0, picard 23110 2.25.5, Pillow 8.2.0, PROJ 8.0.1, protobuf 3.17.3, 23111 protobuf-python 3.17.3, PSolver 1.8.3, PySCF 1.7.6, pyspoa 23112 0.0.8, pytest-xdist 2.3.0, PyTorch 1.9.0, PyYAML 5.4.1, Qhull 23113 2020.2, Quandl 3.6.1, R 4.0.5 + R 4.1.0, Ragout 2.3, RE2 23114 2021-06-01, ReFrame 3.6.2, RepeatMasker 4.1.2, rgdal 1.5-23, 23115 RMBlast 2.11.0, Ruby 3.0.1, scikit-learn 0.24.2, Score-P 7.0, 23116 Seurat 4.0.3, slepc4py 3.12.0, spoa 4.0.7, Subread 2.0.2, 23117 Subversion 1.14.1, SuiteSparse 5.10.1, sympy 1.8, tensorboardX 23118 2.2, TensorFlow 2.5.0, Tk 8.6.11, tmux 3.2a, torchtext 0.8.1, 23119 torchvision 0.9.1, UDUNITS 2.2.28, UFL 2019.1.0, utf8proc 2.6.1, 23120 VEP 103.1, VMD 1.9.4a51, vsc-mympirun 5.2.6, XCFun 2.1.1, Xvfb 23121 1.20.11, Z3 4.8.11, ZeroMQ 4.3.4</li> 23122</ul> 23123</li> 23124<li>minor enhancements, including:<ul> 23125<li>update cuDNN 8.0.x easyconfigs with a download location 23126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12368">#12368</a>)</li> 23127<li>
23127add extensions to recent R easyconfigs: GxEScanR 23128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13039">#13039</a>), 23129 cSEM 23130 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13208">#13208</a>), 23131 cubelyr + broom.mixed 23132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13252">#13252</a>), 23133 grf 23134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13261">#13261</a>), 23135 twang + xgboost 23136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13284">#13284</a>), 23137 neuralnet 23138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13330">#13330</a>)</li> 23139<li>add check to easyconfigs test suite to ensure OpenSSL wrapper is 23140 used in easyconfigs using a recent toolchain 23141 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13079">#13079</a>)</li> 23142<li>add gipaw to QuantumESPRESSO/6.7 23143 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13087">#13087</a>)</li> 23144<li>add checksum for aarch64 installation file for CUDAcore 23145 easyconfigs 23146 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13014">#13014</a>, 23147 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13097">#13097</a>)</li> 23148<li>add Perl dependency to makeinfo easyconfigs 23149 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13166">#13166</a>)</li> 23150<li>set minimal OpenSSL version to 1.1.1 for OpenSSL v1.1 wrapper 23151 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13188">#13188</a>)</li> 23152<li>add JIT support for CUDA 11 to PyTorch 1.7.1 23153 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13207">#13207</a>)</li> 23154<li>add <code>ninja --version</code> as sanity check command in Ninja 23155 easyconfigs 23156 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13222">#13222</a>)</li> 23157<li>code cleanup + improvements for easyconfigs test suite 23158 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13257">#13257</a>)</li> 23159</ul> 23160</li> 23161<li>various bug fixes, including:<ul> 23162<li>download sources via git for XGBoost 20171120 easyconfig due to 23163 use of submodules 23164 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6880">#6880</a>)</li> 23165<li>add elfutils as build dependency for Clang 8.0.x and 9.0.1 23166 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13015">#13015</a>) 23167 and Clang 11.0.1 23168 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13008">#13008</a>) 23169 easyconfigs that have a CUDA dependency</li> 23170<li>add missing CMake option to Geant4 v10.7.1 in order to actually 23171 use external CLHEP 23172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13019">#13019</a>)</li> 23173<li>add new checksum for mvabund extension to R v4.0.4 eaysconfigs 23174 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13020">#13020</a>, 23175 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13021">#13021</a>)</li> 23176<li>add patch to fix numpy <code>test_ccompiler_opt</code> in SciPy-bundle 23177 v2021.05 23178 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13042">#13042</a>)</li> 23179<li>add patch to fix installation of HDF 4.2.15 on aarch64 23180 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13059">#13059</a>)</li> 23181<li>make sure that MbedTLS' Makefile uses <code>python</code> rather than 23182 <code>python2</code> 23183 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13061">#13061</a>)</li> 23184<li>fix checksum for snpEff 5.0 23185 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13062">#13062</a>)</li> 23186<li>fix source URL for LIBSVM 3.24 by downloading from GitHub 23187 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13076">#13076</a>)</li> 23188<li>add <code>preinstallopts</code> for minimap2 to fix installation on aarch64 23189 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13080">#13080</a>)</li> 23190<li>
23190add patch for GCC 10.2.0 to fix internal compiler error on 23191 aarch64 23192 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13086">#13086</a>)</li> 23193<li>switch to NCCL 2.8.3 built from source for CuPy, Horovod, 23194 libgpuarray, PyTorch and TensorFlow using fosscuda/2020b 23195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13103">#13103</a>)</li> 23196<li>add astor to dependencies of TensorFlow with 2019b 23197 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13111">#13111</a>) 23198 and 2020b 23199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13103">#13103</a>, 23200 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13112">#13112</a>) 23201 toolchains</li> 23202<li>break cyclic dependency between groff, makeinfo and Perl by 23203 adding Perl-minimal and makeinfo-minimal easyconfigs 23204 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13163">#13163</a> - 23205 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13165">#13165</a>)</li> 23206<li>add missing rgdal dep to R-INLA 23207 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13179">#13179</a>)</li> 23208<li>add patch to fix <code>uniq</code> operation in TensorFlow 2.4.1 23209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13181">#13181</a>)</li> 23210<li>add Perl build dependency for PnetCDF 1.12.1 23211 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13183">#13183</a>)</li> 23212<li>disable own avx detection of libfabric v1.12.1 23213 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13215">#13215</a>)</li> 23214<li>add GCCcore-[1-9][0-9].x to 23215 <code>test_dep_versions_per_toolchain_generation</code> 23216 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13243">#13243</a>, 23217 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13249">#13249</a>, 23218 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13251">#13251</a>)</li> 23219<li>add patch to fix installation of TensorFlow 2.0.x 23220 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13248">#13248</a>)</li> 23221<li>add patch for recent GCCcore versions to fix compatibility with 23222 CUDA 11 23223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13290">#13290</a>)</li> 23224<li>fix install step for glew 23225 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13297">#13297</a>)</li> 23226<li>update Boost 1.74.0 easyconfigs to use <code>tagged_layout</code> rather 23227 than <code>boost_multi_thread</code> 23228 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13300">#13300</a>)</li> 23229<li>avoid using PMIx from system instead of PMIx dependency 23230 specified via <code>--with-pmix</code> for OpenMPI 4.x 23231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13307">#13307</a>)</li> 23232<li>add patch for GCCcore 10.3.0 to prevent issues when compiling 23233 with nvcc 23234 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13310">#13310</a>)</li> 23235<li>add patch for OpenMPI 4.0.x to fix building against (system) UCX 23236 version > 1.7 23237 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13329">#13329</a>)</li> 23238<li>fix build of manta 1.6.0 on top of Boost 1.74.0 23239 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13338">#13338</a>)</li> 23240<li>fix recent taxator-tk easyconfigs by adding (back) 23241 <code>-DBoost_NO_BOOST_CMAKE=ON</code> configure option 23242 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13342">#13342</a>)</li> 23243</ul> 23244</li> 23245<li>other changes:<ul> 23246<li>disable <code>debuginfod</code> for elfutils to minimize required 23247 dependencies 23248 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13034">#13034</a>)</li> 23249<li>add bare Python 3.9.5 easyconfig and use that as builddep for 23250 LLVM 11.1.0 23251 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13035">#13035</a>)</li> 23252<li>remove misleading comment from Python >= 3.7 easyconfigs, 23253 libffi is now also required for Python itself (no longer 23254 bundled) 23255 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13041">#13041</a>)</li> 23256<li>use new custom easyblock in torchvision easyconfigs 23257 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13102">#13102</a>)</li> 23258<li>remove superfluous TensorFlow patch 23259 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13223">#13223</a>)</li> 23260<li>cleanup of easyconfigs for (bundles) of Python packages: remove 23261 default <code>PYPI_SOURCE</code> source URLs + use <code>PythonBundle</code> rather 23262 than <code>Bundle</code> easyblock 23263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13253">#13253</a>, 23264 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13295">#13295</a>, 23265 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13336">#13336</a>)</li> 23266<li>update <code>README</code> with instructions for MATLAB easyconfigs 23267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12597">#12597</a>)</li> 23268</ul> 23269</li> 23270</ul> 23271<h2 id="release_notes_eb440">EasyBuild v4.4.0 (June 2nd 2021)<a class="headerlink" href="#release_notes_eb440" title="Permanent link">¶</a></h2> 23272<p>feature release</p> 23273<p><strong>framework</strong></p> 23274<ul> 23275<li>various enhancements, including:<ul> 23276<li>enhance <code>apply_regex_substitutions</code> to allow specifying action 23277 to take in case there are no matches 23278 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3440">#3440</a>)</li> 23279<li>performance improvements for easyconfig parsing and eb startup 23280 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3555">#3555</a>)</li> 23281<li>
23281add support for downloading easyconfigs from multiple PRs with 23282 <code>--from-pr</code> 23283 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3605">#3605</a>, 23284 <a href="https://github.com/easybuilders/easybuild-framework/pull/3707">#3707</a>, 23285 <a href="https://github.com/easybuilders/easybuild-framework/pull/3708">#3708</a>)</li> 23286<li>add support for prepending custom library paths in RPATH section 23287 via <code>--rpath-override-dirs</code> 23288 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3650">#3650</a>)</li> 23289<li>allow amending easyconfig parameters which are not the default 23290 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3651">#3651</a>)</li> 23291<li>update HierarchicalMNS for Intel OneAPI compilers 23292 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3653">#3653</a>)</li> 23293<li>add support for <code>--sanity-check-only</code> 23294 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3655">#3655</a>)</li> 23295<li>add support for running commands asynchronously via <code>run_cmd</code> + 23296 <code>complete_cmd</code> functions 23297 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3656">#3656</a>)</li> 23298<li>add support for using oneAPI versions of 'intel' toolchain 23299 components 23300 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3665">#3665</a>)</li> 23301<li>add toolchain definition for gofbf (foss with FlexiBLAS rather 23302 than OpenBLAS) 23303 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3666">#3666</a>)</li> 23304<li>add support for using <code>ARCH</code> constant in easyconfig files 23305 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3670">#3670</a>)</li> 23306<li>honor keyboard interrupt in <code>eb</code> command 23307 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3674">#3674</a>)</li> 23308<li>add toolchain definition for Fujitsu toolchain 23309 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3677">#3677</a>, 23310 <a href="https://github.com/easybuilders/easybuild-framework/pull/3704">#3704</a>, 23311 <a href="https://github.com/easybuilders/easybuild-framework/pull/3712">#3712</a>, 23312 <a href="https://github.com/easybuilders/easybuild-framework/pull/3713">#3713</a>, 23313 <a href="https://github.com/easybuilders/easybuild-framework/pull/3714">#3714</a>, 23314 <a href="https://github.com/easybuilders/easybuild-framework/pull/3717">#3717</a>)</li> 23315<li>extend sanity check step to check whether specific libraries are 23316 not linked into installed binaries/libraries 23317 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3678">#3678</a>)<ul> 23318<li>via <code>banned-linked-shared-libs</code> and 23319 <code>required-linked-shared-libs</code> EasyBuild configuration 23320 options</li> 23321<li>via <code>banned_linked_shared_libs</code> and 23322 <code>required_linked_shared_libs</code> methods in toolchain support</li> 23323<li>via <code>banned_linked_shared_libs</code> and 23324 <code>required_linked_shared_libs</code> methods in easyblock</li> 23325<li>via <code>banned_linked_shared_libs</code> and 23326 <code>required_linked_shared_libs</code> easyconfig parameters</li> 23327</ul> 23328</li> 23329<li>add <code>locate_solib</code> function to locate Linux shared libraries 23330 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3682">#3682</a>)</li> 23331<li>add system agnostic function to locate shared libraries 23332 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3683">#3683</a>)</li> 23333<li>add <code>update_build_option</code> function to update specific build 23334 options after initializing the EasyBuild configuration 23335 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3684">#3684</a>)</li> 23336<li>allow opting out of recursively unloaded of modules via 23337 recursive_module_unload easyconfig parameter 23338 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3689">#3689</a>)</li> 23339<li>check for correct version values when parsing easystack file 23340 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3693">#3693</a>)</li> 23341<li>
23341run post-install commands specified for a specific extension 23342 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3696">#3696</a>)</li> 23343<li>add support for <code>--skip-extensions</code> 23344 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3702">#3702</a>)</li> 23345<li>include PR title in output produced by <code>--merge-pr</code> 23346 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3706">#3706</a>)</li> 23347</ul> 23348</li> 23349<li>various bug fixes, including:<ul> 23350<li>avoid metadata greedy behaviour when probing for external module 23351 metadata (mostly relevant for integration with Cray Programming 23352 Environment) 23353 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3559">#3559</a>)</li> 23354<li>catch problems early on if <code>--github-user</code> is not specified for 23355 <code>--new-pr</code> & co 23356 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3644">#3644</a>)</li> 23357<li>re-enable write permissions when installing with 23358 <code>read-only-installdir</code> 23359 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3649">#3649</a>)</li> 23360<li>also run sanity check for extensions when using <code>--module-only</code> 23361 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3655">#3655</a>)</li> 23362<li>improve logging when failing to load class from <code>exts_classmap</code> 23363 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3657">#3657</a>)</li> 23364<li>fix use of <code>--module-only</code> on existing installations without 23365 write permissions 23366 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3659">#3659</a>)</li> 23367<li>correct help text for <code>subdir-user-modules</code> 23368 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3660">#3660</a>)</li> 23369<li>avoid picking up easyblocks outside of sandbox in framework 23370 tests 23371 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3680">#3680</a>)</li> 23372<li>use unload/load in <code>ModuleGeneratorLua.swap_module</code>, since 23373 <code>swap</code> is not supported by Lmod 23374 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3685">#3685</a>)</li> 23375<li>update HierarchicalMNS to also return 23376 'Toolchain/<name>/<version>' as <code>$MODULEPATH</code> extension 23377 for cpe* Cray toolchains 23378 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3686">#3686</a>)</li> 23379<li>make <code>EasyConfigParser.get_config_dict</code> return a copy rather 23380 than a reference 23381 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3692">#3692</a>)</li> 23382<li>make sure that <code>$TAPE</code> is unset when using piped tar 23383 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3698">#3698</a>)</li> 23384<li>fix extending message for changed files in <code>new_pr_from_branch</code> 23385 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3699">#3699</a>)</li> 23386<li>enhance <code>sched_getaffinity</code> function to avoid early crash when 23387 counting available cores on systems with more than 1024 cores 23388 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3701">#3701</a>)</li> 23389<li>correctly strip extension from filename in <code>extract_cmd</code> and 23390 <code>back_up_file</code> functions 23391 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3705">#3705</a>)</li> 23392</ul> 23393</li> 23394<li>other changes:<ul> 23395<li>deprecate adding a non-existing path to <code>$MODULEPATH</code> 23396 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3637">#3637</a>)</li> 23397<li>bump cryptography requirement from 3.2.1 to 3.3.2 23398 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3643">#3643</a>, 23399 <a href="https://github.com/easybuilders/easybuild-framework/pull/3648">#3648</a>)</li> 23400<li>test bootstrap script in separate workflow, and limit test 23401 configurations a bit 23402 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3646">#3646</a>)</li> 23403<li>update <code>setup.py</code> to indicate compatibility with Python 3.8 and 23404 3.9 23405 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3647">#3647</a>)</li> 23406<li>replace <code>log_error</code> parameter of <code>which()</code> by <code>on_error</code> 23407 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3661">#3661</a>, 23408 <a href="https://github.com/easybuilders/easybuild-framework/pull/3664">#3664</a>)</li> 23409<li>don't skip sanity check for <code>--module-only --rebuild</code> 23410 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3645">#3645</a>)</li> 23411<li>move <code>disable_templating</code> function into the EasyConfig class 23412 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3668">#3668</a>)</li> 23413<li>
23413pin GitPython version for Python<3.6, don't test bootstrap 23414 script against Python 3.8/3.9 23415 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3675">#3675</a>)</li> 23416<li>tweak foss toolchain definition to switch from OpenBLAS to 23417 FlexiBLAS in foss/2021a 23418 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3679">#3679</a>)</li> 23419<li>suggest missing SSH key when not able to read from remote 23420 repository in <code>--check-github</code> 23421 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3681">#3681</a>)</li> 23422<li>drop support for Python 2.6 23423 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3715">#3715</a>)</li> 23424</ul> 23425</li> 23426</ul> 23427<p><strong>easyblocks</strong></p> 23428<ul> 23429<li>3 new software-specific easyblocks:<ul> 23430<li>FlexiBLAS 23431 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2369">#2369</a>, 23432 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2422">#2422</a>, 23433 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2424">#2424</a>, 23434 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2426">#2426</a>)</li> 23435<li>dm-reverb 23436 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2413">#2413</a>)</li> 23437<li>custom easyblock to install OpenSSL wrapper for OpenSSL 23438 installed in OS, with fallback to build and install OpenSSL from 23439 source if not available in OS 23440 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2429">#2429</a>)</li> 23441</ul> 23442</li> 23443<li>minor enhancements, including:<ul> 23444<li>also add <code>-pthread</code> to <code>prebuildopts</code> of cryptography 23445 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2270">#2270</a>)</li> 23446<li>don't unpack Python wheel (*.whl) files by default in generic 23447 PythonPackage easyblock 23448 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2366">#2366</a>, 23449 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2442">#2442</a>)</li> 23450<li>enable installation of samples for CUDA > 10.1 23451 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2374">#2374</a>)</li> 23452<li>add option to disable pip connecting to PyPi (enable use of 23453 <code>--no-index</code>) 23454 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2390">#2390</a>)</li> 23455<li>update MotionCor2 easyblock to handle new version and be aware 23456 of CUDAcore 23457 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2394">#2394</a>)</li> 23458<li>make it possible to force disabling kernel features in Qt 23459 easyblock 23460 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2403">#2403</a>)</li> 23461<li>update imkl easyblock to support oneAPI versions (>= 2021.x) 23462 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2407">#2407</a>)</li> 23463<li>add<code>"gurobi_cl --help</code> as default sanity check command for 23464 Gurobi 23465 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2411">#2411</a>)</li> 23466<li>enhance BWA easyblock to copy includes and libraries 23467 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2417">#2417</a>)</li> 23468<li>allow <code>default</code> versions to be defined by ModuleRC easyblock 23469 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2418">#2418</a>)</li> 23470<li>enhance MesonNinja and CMakeMake easyblocks to create unused 23471 build dir when <code>separate_build_dir</code> is set 23472 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2419">#2419</a>)</li> 23473<li>enable <code>sanity_pip_check</code> by default for Python easyconfigs if 23474 pip >= 9.0 will be installed 23475 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2423">#2423</a>)</li> 23476<li>enhance FFTW easyblock to support SVE CPU feature and building 23477 with Fujitsu compiler 23478 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2425">#2425</a>)</li> 23479<li>make ScaLAPACK easyblock aware of FlexiBLAS 23480 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2427">#2427</a>)</li> 23481<li>update imkl easyblock to unpack example tarballs and set 23482 <code>$MKL_EXAMPLES</code> (+ some code cleanup) 23483 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2430">#2430</a>)</li> 23484<li>update list of system libs for TensorFlow 2.5 23485 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2432">#2432</a>)</li> 23486<li>allow disabling MPI tests when installing Intel MPI (impi) via 23487 <code>--disable-mpi-tests</code> 23488 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2440">#2440</a>)</li> 23489<li>exclude bottleneck tests in PyTorch 23490 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2450">#2450</a>)</li> 23491</ul> 23492</li> 23493<li>various bug fixes, including:<ul> 23494<li>ensure lib subdirectory is found in stage 2 of GCC 23495 installation + fall back to lib64 23496 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2339">#2339</a>)</li> 23497<li>fix permission on MATLAB installer config file so it can be 23498 written to 23499 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2385">#2385</a>)</li> 23500<li>fix problem with installing older CUDA versions that uses the 23501 Perl based installer 23502 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2387">#2387</a>)</li> 23503<li>enhance Python easyblock: add option to install pip with core 23504 Python, tweak defaults, create unversioned pip symlink 23505 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2388">#2388</a>)</li> 23506<li>fix <code>installopts</code> before installing the extension in GROMACS 23507 easyblock 23508 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2391">#2391</a>)</li> 23509<li>updated numpy easyblock to use <code>
23509read_file</code> for patch 23510 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2395">#2395</a>)</li> 23511<li>use explicit build toolset and compiler path in Boost easyblock 23512 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2402">#2402</a>)</li> 23513<li>replace hardcoded <code>2021.1.1</code> with <code>self.version</code> in impi 23514 easyblock 23515 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2405">#2405</a>)</li> 23516<li>set <code>$SANDCASTLE</code> when running PyTorch tests to disable some 23517 tests as-if we are on Facebook's CI 23518 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2412">#2412</a>)</li> 23519<li>make GROMACS easyblock work with <code>--module-only</code> 23520 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2414">#2414</a>)</li> 23521<li>make sure OpenFOAM sanity checks don't require builddir write 23522 permissions 23523 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2415">#2415</a>)</li> 23524<li>make Tkinter easyblock work with <code>--module-only</code> 23525 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2416">#2416</a>)</li> 23526<li>also disable altivec with FFTW 3.3.9 on POWER 23527 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2437">#2437</a>)</li> 23528<li>make sure that <code>self.python_cmd</code> is set before using it in 23529 <code>PythonPackage.sanity_check_step</code> 23530 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2447">#2447</a>)</li> 23531</ul> 23532</li> 23533<li>other changes, including:<ul> 23534<li>update <code>setup.py</code> to indicate compatibility with Python 3.8 and 23535 3.9 23536 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2384">#2384</a>)</li> 23537<li>use <code>on_error</code> rather than deprecated <code>log_error</code> named argument 23538 for <code>which</code> function 23539 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2406">#2406</a>)</li> 23540<li>remove <code>cuda_compute_capabilities</code> from custom easyconfig 23541 parameters for Clang, LAMMPS and TensorFlow (now supported as 23542 general easyconfig parameter) 23543 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2433">#2433</a>)</li> 23544</ul> 23545</li> 23546</ul> 23547<p><strong>easyconfigs</strong></p> 23548<ul> 23549<li>added easyconfigs for new Fujitsu toolchain: FCC/4.5.0 23550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12999">#12999</a>, 23551 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12995">#12995</a>, 23552 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13007">#13007</a>), 23553 ffmpi/4.5.0 23554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13000">#13000</a>) 23555 and Fujitsu/21.05 23556 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13001">#13001</a>, 23557 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13007">#13007</a>)</li> 23558<li>add easyconfigs for updates of common toolchains: foss/2021a 23559 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12867">#12867</a>, 23560 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12975">#12975</a>), 23561 intel/2021a 23562 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12885">#12885</a>, 23563 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12975">#12975</a>)<ul> 23564<li>see also 23565 <a href="https://easybuild.readthedocs.io/en/latest/Common-toolchains.html">https://easybuild.readthedocs.io/en/latest/Common-toolchains.html</a></li> 23566</ul> 23567</li> 23568<li>added easyconfig for gomkl/2021a toolchain 23569 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12987">#12987</a>)</li> 23570<li>added example easyconfig files for 58 new software packages:<ul> 23571<li>Archive-Zip 23572 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12651">#12651</a>), 23573 BirdNET 23574 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12737">#12737</a>, 23575 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12712">#12712</a>, 23576 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12737">#12737</a>), 23577 cell2location 23578 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12448">#12448</a>), 23579 cryoDRGN 23580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12704">#12704</a>), 23581 dm-reverb 23582 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12824">#12824</a>), 23583 DROP 23584 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12559">#12559</a>, 23585 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12801">#12801</a>, 23586 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12950">#12950</a>), 23587 fastahack 23588 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12841">#12841</a>), 23589 fermi-lite 23590 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12856">#12856</a>), 23591 filevercmp 23592 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12841">#12841</a>), 23593 FlexiBLAS 23594 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12476">#12476</a>), 23595 freetype-py 23596 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12918">#12918</a>), 23597 fsom 23598 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12841">#12841</a>), 23599 garnett 23600 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12529">#12529</a>), 23601 gawk 23602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12716">#12716</a>), 23603 gemmi 23604 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12855">#12855</a>), 23605 georges 23606 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12570">#12570</a>), 23607 hifiasm 23608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12897">#12897</a>), 23609 intervaltree 23610 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12838">#12838</a>), 23611 LDC 23612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12671">#12671</a>), 23613 libidn2 23614 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12670">#12670</a>), 23615 librosa 23616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10477">#10477</a>), 23617 librsb 23618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12780">#12780</a>), 23619 line_profiler 23620 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12556">#12556</a>), 23621 loompy 23622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12804">
23622#12804</a>), 23623 mmtf-cpp 23624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12580">#12580</a>), 23625 mongolite 23626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12632">#12632</a>), 23627 msgpack-c 23628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12580">#12580</a>), 23629 multichoose 23630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12839">#12839</a>), 23631 networkTools 23632 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12810">#12810</a>), 23633 NewHybrids 23634 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12528">#12528</a>), 23635 Octopus-vcf 23636 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12598">#12598</a>), 23637 onedrive 23638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12671">#12671</a>), 23639 p4-phylogenetics 23640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12549">#12549</a>), 23641 pagmo 23642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12678">#12678</a>), 23643 pyfaidx 23644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12872">#12872</a>), 23645 pyfasta 23646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12952">#12952</a>), 23647 pygmo 23648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12678">#12678</a>), 23649 pysheds 23650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12791">#12791</a>), 23651 R-INLA 23652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12955">#12955</a>, 23653 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12927">#12927</a>, 23654 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12955">#12955</a>), 23655 RegTools 23656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12874">#12874</a>), 23657 request 23658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12448">#12448</a>), 23659 rMATS-turbo 23660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12982">#12982</a>), 23661 scanpy 23662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12731">#12731</a>), 23663 SeqLib 23664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12856">#12856</a>), 23665 SeuratData 23666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12993">#12993</a>), 23667 SeuratWrappers 23668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12994">#12994</a>), 23669 smithwaterman 23670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12841">#12841</a>), 23671 snp-sites 23672 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12900">#12900</a>), 23673 SSW 23674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12856">#12856</a>), 23675 tabixpp 23676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12837">#12837</a>), 23677 TagDust 23678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11599">#11599</a>), 23679 TALON 23680 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12963">#12963</a>), 23681 tMAE 23682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12559">#12559</a>), 23683 TranscriptClean 23684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12952">#12952</a>), 23685 umap-learn 23686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12448">#12448</a>), 23687 vcflib 23688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12841">#12841</a>), 23689 xESMF 23690 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12799">#12799</a>), 23691 XlsxWriter 23692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12820">#12820</a>)</li> 23693</ul> 23694</li> 23695<li>added additional easyconfigs for various supported software 23696 packages, including:<ul> 23697<li>ABINIT 9.4.1, apex 20210420, astropy 4.2.1, binutils 2.36.1, 23698 BLIS 0.8.1, Bonito 0.3.8, BUSCO 5.1.2, canu 2.1.1, carputils 23699 20210513, CastXML 0.4.3, ccache 4.2.1, CDO 1.9.10, CIRCexplorer2 23700 2.3.8, CLHEP 2.4.4.0, CMake 3.20.1, CNVkit 0.9.8, CUDA(core) 23701 11.3.0, CuPy 8.5.0, cURL 7.76.0, DFA 2.1.2, Doxygen 1.9.1, Eigen 23702 3.3.9, FastANI 1.33, FFTW 3.3.9, GATK 4.2.0.0, GCC 10.3.0 + 23703 11.1.0, GDB 10.2, gdc-client 1.6.0, GDRCopy 2.2, Geant4 10.7.
237031, 23704 Geant4-data 20210510, GeneMark-ET 4.65, glew 2.2.0, GLib 2.68.2, 23705 GLPK 5.0, GMP 6.2.1, Go 1.16.3, Graphviz 2.47.0, GROMACS 2021.2, 23706 GStreamer 1.18.4, GTDB-Tk 1.5.0, Gurobi 9.1.2, HMMER 3.3.2, 23707 Horovod 0.21.3, hwloc 2.4.1, hypothesis 6.13.1, IGV 2.9.4, impi 23708 2021.2.0, imkl 2021.2.0, intel-compilers 2021.2.0, JasPer 23709 2.0.28, Julia 1.6.1, Kraken2 2.1.1, KronaTools 2.8, libarchive 23710 3.5.1, libdeflate 1.7, libdrm 2.4.106, libfabric 1.12.1, 23711 libreadline 8.1, libRmath 4.0.0, libsndfile 1.0.31, LIBSVM 3.24, 23712 LibTIFF 4.2.0, libunwind 1.5.0, libwebp 1.2.0, LLVM 11.1.0, LMDB 23713 0.9.28, LUMPY 0.3.1, lz4 1.9.3, Mako 1.1.4, MATLAB 2021a, Mesa 23714 21.1.1, meshalyzer 2.2, Meson 0.58.0, MetaBAT 2.15, metaWRAP 23715 1.3, minimap2 2.18, Molden 6.8, MotionCor2 1.4.2, ncview 2.1.8, 23716 NetPIPE 5.1.4, nettle 3.7.2, NiBabel 3.2.1, Nilearn 0.7.1, Nim 23717 1.4.6, Ninja 1.10.2, NLopt 2.7.0, NSS 3.65, numactl 2.0.14, 23718 NWChem 7.0.2, OpenBLAS 0.3.15, openCARP 6.0, OpenEXR 3.0.1, 23719 OpenMM 7.5.0, OpenMPI 4.1.1, OpenSSL 1.1 (wrapper), 23720 OSU-Micro-Benchmarks 5.7.1, Pandoc 2.13, parallel 20210322, 23721 parasail 2.4.3, PAUP 4.0a168, PCRE2 10.36, Perl 5.32.1, pigz 23722 2.6, PMIx 3.2.3, Primer3 2.5.0, PRSice 2.3.3, py-aiger 6.1.14, 23723 pybind11 2.6.2, PyCharm 2021.1.1, pydot 1.4.2, pyproj 3.0.1, 23724 PySAT 0.1.7.dev1, PyTorch 1.8.1, python-parasail 1.2.4, Pylint 23725 2.7.4, Python 3.9.5, Qt5 5.15.2, R-keras 2.4.0, rasterio 1.2.3, 23726 RAxML-NG 1.0.2, rclone 1.54.1, re2c 2.1.1, ReFrame 3.5.2, Rmath 23727 4.0.4, Rust 1.52.1, Sambamba 0.8.0, samblaster 0.1.26, samclip 23728 0.4.0, scikit-allel 1.3.2, SciPy-bundle 2021.05, SCons 23729 4.1.0.post1, snakemake 6.1.0, SQLite 3.35.4, SRPRISM 3.1.2, Tcl 23730 8.6.11, TCLAP 1.2.4, tmux 3.2, tqdm 4.60.0, UCX 1.10.0, Valgrind 23731 3.17.0, WannierTools 2.5.1, wget 1.21.1, wxWidgets 3.1.4, X11 23732 20210518, x264 20210414, x265 3.5, xorg-macros 1.19.3, YAXT 23733 0.9.0, zarr 2.8.1, zstd 1.4.9</li> 23734</ul> 23735</li> 23736<li>minor enhancements, including:<ul> 23737<li>add additional extensions to R v4.0.3 and v4.0.4: miceadds, 23738 visdat, UpSetR, naniar, stringdist, image.binarization 23739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12735">#12735</a>), 23740 lassosum 23741 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12821">#12821</a>), 23742 lslx, regsem, semPLS 23743 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/13005">#13005</a>)</li> 23744<li>add GenABEL to R-bundle-Bioconductor 23745 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12822">#12822</a>)</li> 23746</ul> 23747</li> 23748<li>various bug fixes, including:<ul> 23749<li>disable automatic acceptance of NVHPC EULA 23750 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12014">#12014</a>)</li> 23751<li>enhance RStudio-Server, add patch to inherit environment 23752 variables, add sanity check commands to verify installation 23753 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12544">#12544</a>)</li> 23754<li>add fix to scipy to handle <code>NaN</code> arguments to <code>vi</code> function 23755 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12551">#12551</a>)</li> 23756<li>copy all binaries + examples & co for PAML v4.9j 23757 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12567">#12567</a>)</li> 23758<li>add patch to fix hardcoded <code>num_cores</code> in DMCfun extension 23759 included with R 4.0.x 23760 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12583">#12583</a>)</li> 23761<li>backport Charm++ patch for NAMD/2.14 on intel/2020a to handle 23762 newer glibc 23763 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12594">#12594</a>)</li> 23764<li>add setuptools_scm and pytest-runner extensions to Pylint 23765 easyconfigs 23766 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12599">#12599</a>)</li> 23767<li>fix typo in Delly easyconfig to actually do parallel build 23768 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12633">#12633</a>)</li> 23769<li>fix potential memory leak in OpenBLAS 0.3.12 23770 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12649">#12649</a>)</li> 23771<li>consistently use pip to install Python packages in recent Python 23772 easyconfigs 23773 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12650">#12650</a>)</li> 23774<li>replace bintray source url for Groovy 23775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12652">#12652</a>)</li> 23776<li>
23776add missing Python & Perl dependencies to AUGUSTUS v3.4.0 with 23777 foss/2020b 23778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12662">#12662</a>)</li> 23779<li>fix wget dependency: use libidn2 rather than libidn 23780 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12670">#12670</a>)</li> 23781<li>fix source URLs for recent ELPA versions 23782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12700">#12700</a>)</li> 23783<li>override host compiler check in CUDAcore 23784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12701">#12701</a>)</li> 23785<li>add Python build dependency to libpsl 0.21.0 easyconfigs 23786 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12715">#12715</a>)</li> 23787<li>fix error in libgpg-error 1.36 with gawk builtin 23788 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12716">#12716</a>)</li> 23789<li>add libtool build dependency to leidenalg 23790 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12741">#12741</a>)</li> 23791<li>fix source URLs for Boost 1.71.0 - 1.74.0 easyconfigs 23792 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12743">#12743</a>) 23793 and Boost.Python 23794 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12744">#12744</a>)</li> 23795<li>add patches for PyTorch 1.7.1 avoiding failures on POWER and 23796 A100 23797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12753">#12753</a>)</li> 23798<li>add patch for OpenPGM 5.2.122 eaysconfigs to fix non-existent 23799 directory in *.pc (pkgconfig) file 23800 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12774">#12774</a>)</li> 23801<li>add missing Perl build dependency to recent wget easyconfigs 23802 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12787">#12787</a>)</li> 23803<li>make sure Python dependency is used in preCICE 2.x easyconfigs 23804 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12793">#12793</a>)</li> 23805<li>don't skip source step in FastTree easyconfigs + fix SHA256 23806 checksum for FastTree 2.1.11 23807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12794">#12794</a>)</li> 23808<li>add patch for rhdf5filters extension in Bioconductor 3.12 bundle 23809 to fix installation on aarch64 23810 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12836">#12836</a>)</li> 23811<li>add IceLake detection to OpenBLAS 0.3.12 and 0.3.15 23812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12865">#12865</a>)</li> 23813<li>fix checksum for MaxBin 2.2.7 23814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12869">#12869</a>)</li> 23815<li>run <code>make clean</code> before building FragGeneScan, to clean up 23816 object files included in source tarball 23817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12870">#12870</a>)</li> 23818<li>clean up install of KronaTools 23819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12871">#12871</a>)</li> 23820<li>add UCX dependency to OneAPI versions of impi 23821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12873">#12873</a>)</li> 23822<li>correct description in libdeflate easyconfig 23823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12886">#12886</a>)</li> 23824<li>override Makefile with hardcoded <code>CC=cc</code> in UnZip easyconfigs 23825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12887">#12887</a>)</li> 23826<li>fix compatibility of FLAIR v1.5.1-20200630 with rpy2 v3.x 23827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12899">#12899</a>)</li> 23828<li>fix test step for libxc 4.3.4 and 5.1.x when using RPATH linking 23829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12912">#12912</a>)</li> 23830<li>fix source URLs in BLAST 2.10.x easyconfigs 23831 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12914">#12914</a>)</li> 23832<li>add missing xproto build dependency to imake easyconfig 23833 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12930">#12930</a>)</li> 23834<li>
23834add patch to fix GCC 10.2.0 rejecting valid code on PPC 23835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12948">#12948</a>)</li> 23836<li>in easyconfig tests, check version of dependencies named Python, 23837 not if dependencies with certain versions are named Python 23838 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12962">#12962</a>)</li> 23839<li>update easyconfigs for binutils 2.35 to use binutils 2.35.2 23840 source tarball instead to pick up bug fixes 23841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12967">#12967</a>, 23842 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12988">#12988</a>)</li> 23843<li>fix download URL for DB 18.1.40 23844 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12974">#12974</a>)</li> 23845<li>fix test failure in TensorFlow 2.4.1 on recent CUDA drivers 23846 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12979">#12979</a>)</li> 23847<li>fix error in <code>configopts</code> for netCDF and HDF5 and add missing 23848 dependencies of ABINIT 9.x 23849 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12981">#12981</a>)</li> 23850<li>add patch to fix buffer overflow in OpenMPI 4.1.x 23851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12983">#12983</a>)</li> 23852</ul> 23853</li> 23854<li>other changes:<ul> 23855<li>update <code>setup.py</code> to indicate compatibility with Python 3.8 and 23856 3.9 23857 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12565">#12565</a>)</li> 23858<li>add <code>-Java</code> versionsuffix for Hadoop easyconfig using 23859 GCCcore/10.2.0 toolchain, since it depends on Java 1.8 23860 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12709">#12709</a>)</li> 23861<li>remove unnecessary workaround for missing version of 23862 OpenDataCube and Spyder for 2020+ toolchains 23863 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12757">#12757</a>)</li> 23864<li>remove <code>unpack_sources = False</code> from recent easyconfigs that use 23865 a *.whl file as source 23866 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12783">#12783</a>)</li> 23867<li>whitelist Seaborn 0.10.1 for NanoComp 1.13.1 and NanoPlot 1.33.0 23868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12790">#12790</a>)</li> 23869<li>add check to make sure that source step is not being skipped 23870 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12807">#12807</a>)</li> 23871<li>use <code>EasyConfig.disable_templating</code> method in test suite 23872 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12848">#12848</a>)</li> 23873<li>disable usNIC by default in libfabric to avoid problems due to 23874 linking to both libnl and libnl-3 23875 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12854">#12854</a>)</li> 23876<li>use OpenSSL wrapper as dependency in easyconfigs using 23877 GCCcore/10.3.0 toolchain 23878 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12922">#12922</a>, 23879 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12944">#12944</a>)</li> 23880<li>dump easyconfig before initializing easyblock in order to 23881 compare it with original easyconfig 23882 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12925">#12925</a>)</li> 23883<li>remove postinstallcmds from imkl 2020.x easyconfigs, easyblock 23884 now installs examples 23885 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12937">#12937</a>)</li> 23886</ul> 23887</li> 23888</ul> 23889<h2 id="release_notes_eb434">EasyBuild v4.3.4 (Apr 9th 2021)<a class="headerlink" href="#release_notes_eb434" title="Permanent link">¶</a></h2> 23890<p>bugfix/update release</p> 23891<p><strong>framework</strong></p> 23892<ul> 23893<li>various enhancements, including:<ul> 23894<li>add support for filtering dependencies by using <code>False</code> as 23895 version 23896 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3506">#3506</a>)</li> 23897<li>add <code>create_unused_dir</code> function to create a directory which 23898 does not yet exist 23899 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3551">#3551</a>)</li> 23900<li>avoid running expensive <code>module use</code> and <code>module unuse</code> commands 23901 when using Lmod as modules tool, update <code>$MODULEPATH</code> directly 23902 instead 23903 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3557">#3557</a>, 23904 <a href="https://github.com/easybuilders/easybuild-framework/pull/3633">#3633</a>)</li> 23905<li>create CUDA cache (for JIT compiled PTX code) in build dir 23906 instead of <code>$HOME</code> 23907 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3569">#3569</a>)</li> 23908<li>
23908add "Citing" section to module files 23909 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3596">#3596</a>)</li> 23910<li>add support for using fallback <code>arch=*</code> key in dependency 23911 version specified as arch->version mapping 23912 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3600">#3600</a>)</li> 23913<li>also check for pending change requests and mergeable_state in 23914 <code>check_pr_eligible_to_merge</code> 23915 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3604">#3604</a>)</li> 23916<li>ignore undismissed <code>changes requested</code> review if there is an 23917 <code>approved</code> review by the same user 23918 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3607">#3607</a>, 23919 <a href="https://github.com/easybuilders/easybuild-framework/pull/3608">#3608</a>)</li> 23920<li>sort output of <code>eb --search</code> in natural order (respecting 23921 numbers) 23922 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3609">#3609</a>)</li> 23923<li>enhance <code>eb</code> command to ensure that <code>easybuild.main</code> can be 23924 imported before settling on python* command to use 23925 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3610">#3610</a>)</li> 23926<li>add <code>--env-for-shebang</code> configuration option to define the <code>env</code> 23927 command to use for shebangs 23928 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3613">#3613</a>)</li> 23929<li>add templates for architecture independent Python wheels 23930 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3618">#3618</a>)</li> 23931<li>mention easyblocks PR in gist when uploading test report for 23932 it + fix <code>clean_gists.py</code> script 23933 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3622">#3622</a>)</li> 23934<li>also accept regular expression value for <code>--accept-eula-for</code> 23935 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3630">#3630</a>)</li> 23936<li>update <code>validate_github_token</code> function to accept GitHub token 23937 in new format 23938 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3632">#3632</a>)</li> 23939</ul> 23940</li> 23941<li>various bug fixes, including:<ul> 23942<li>fix <code>$BLAS_LIB_MT</code> for OpenBLAS, ensure <code>-lpthread</code> is included 23943 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3584">#3584</a>)</li> 23944<li>use <code>--opt=val</code> for passing settings from config file to option 23945 parser to avoid error for values starting with <code>-</code> or <code>--</code> 23946 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3594">#3594</a>)</li> 23947<li>avoid raised exception when getting output from interactive 23948 command in <code>run_cmd_qa</code> 23949 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3599">#3599</a>)</li> 23950<li>add option to write file from file-like object and use in 23951 <code>download_file</code> 23952 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3614">#3614</a>)</li> 23953<li>make sure that path to <code>eb</code> is always found by tests 23954 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3617">#3617</a>)</li> 23955</ul> 23956</li> 23957<li>other changes:<ul> 23958<li>add <code>pick_default_branch</code> function to clean up duplicate code in 23959 <code>tools/github.py</code> 23960 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3592">#3592</a>)</li> 23961<li>refactor the CI configuration to use inclusion instead of 23962 exclusion 23963 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3616">#3616</a>)</li> 23964<li>use develop branch when testing push access in <code>--check-github</code> 23965 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3629">#3629</a>)</li> 23966<li>deprecate <code>--accept-eula</code>, rename to <code>--accept-eula-for</code> 23967 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3630">#3630</a>)</li> 23968</ul> 23969</li> 23970</ul> 23971<p><strong>easyblocks</strong></p> 23972<ul> 23973<li>minor enhancements, including:<ul> 23974<li>make OpenCV easyblock aware of protobuf, libwebp and OpenEXR 23975 dependencies provided via EasyBuild 23976 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2346">#2346</a>)</li> 23977<li>update CP2K easyblock w.r.t. running regtest for CP2K v8.1 23978 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2350">#2350</a>)</li> 23979<li>update GROMACS easyblock for GROMACS/2021 with CUDA 23980 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2353">#2353</a>)</li> 23981<li>adjust call to <code>python-config</code> for Python >= 3.8 in VMD 23982 easyblock 23983 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2355">#2355</a>)</li> 23984<li>enhance cuDNN and CUDA easyblocks to support <code>aarch64</code> 23985 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2356">#2356</a>)</li> 23986<li>pass down compiler flags provided by EasyBuild in g2clib 23987 easyblock 23988 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2357">#2357</a>)</li> 23989<li>update VTune easyblock for version 2020 23990 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2359">#2359</a>)</li> 23991<li>make WRF and WPS easyblocks aware of <code>(pre)configopts</code> 23992 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2361">#2361</a>)</li> 23993<li>
23993add Clang version 12.0.0 for AOCC 3.0.0 to mapping in custom 23994 easyblock for AOCC 23995 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2362">#2362</a>)</li> 23996<li>use <code>PYPI_SOURCE</code> as the default for source_urls of 23997 PythonPackage 23998 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2364">#2364</a>, 23999 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2370">#2370</a>)</li> 24000<li>enhance PythonPackage easyblock to catch faulty version (0.0.0) 24001 for installed Python packages 24002 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2367">#2367</a>, 24003 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2377">#2377</a>)</li> 24004<li>enhance BWA easyblock: pass compiler flags + use <code>filetools</code> 24005 functions 24006 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2368">#2368</a>)</li> 24007</ul> 24008</li> 24009<li>various bug fixes, including:<ul> 24010<li>set <code>$R_LIBS_SITE</code> rather than <code>$R_LIBS</code> when installing R 24011 packages 24012 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2326">#2326</a>)</li> 24013<li>update PETSc easyblock to take into account that ScaLAPACK 24014 installation may not have header files + fix building in 24015 parallel 24016 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2348">#2348</a>)</li> 24017<li>disable CMake user package repository in CMakeMake generic 24018 easyblock 24019 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2351">#2351</a>)</li> 24020<li>update LAPACK easyblock to keep control of compiler options for 24021 versions >= 3.9.0 24022 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2358">#2358</a>)</li> 24023<li>also set <code>$TORCH_CUDA_ARCH_LIST</code> for PyTorch tests 24024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2363">#2363</a>)</li> 24025<li>enhance Hadoop easyblock to avoid copying same native library 24026 twice 24027 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2371">#2371</a>)</li> 24028<li>fix pip extension download pattern for PythonPackage easyblock 24029 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2372">#2372</a>)</li> 24030<li>make the CUDA stub libs take preference over system libs when 24031 linking 24032 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2373">#2373</a>)</li> 24033<li>improve Python package version check and add 24034 <code>unversioned_packages</code> easyconfig parameter 24035 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2377">#2377</a>)</li> 24036</ul> 24037</li> 24038</ul> 24039<p><strong>easyconfigs</strong></p> 24040<ul> 24041<li>added easyconfig for goblf/2020b toolchain 24042 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12381">#12381</a>, 24043 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12535">#12535</a>)</li> 24044<li>added example easyconfig files for 41 new software packages:<ul> 24045<li>amplimap 24046 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12205">#12205</a>), 24047 BEEF 24048 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12104">#12104</a>), 24049 bpp 24050 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12036">#12036</a>), 24051 Brotli 24052 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11651">#11651</a>), 24053 CDAT 24054 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12322">#12322</a>), 24055 cicero 24056 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12252">#12252</a>), 24057 CIF2Cell 24058 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12258">#12258</a>), 24059 CompareM 24060 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9377">#9377</a>), 24061 DL_POLY_4 24062 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12324">#12324</a>), 24063 DMCfun 24064 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12412">#12412</a>), 24065 ESMPy 24066 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12339">#12339</a>), 24067 FLAC 24068 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12300">#12300</a>), 24069 gdbm 24070 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12322">#12322</a>), 24071 GPyOpt 24072 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12524">#12524</a>), 24073 json-c 24074 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12344">#12344</a>), 24075 libcdms 24076 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12322">#12322</a>), 24077 libdrs 24078 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12322">#12322</a>), 24079 libogg 24080 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12285">#12285</a>), 24081 libvorbis 24082 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12300">#12300</a>), 24083 LncLOOM 24084 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12287">#12287</a>), 24085 LPJmL 24086 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12344">#12344</a>), 24087 maze 24088 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12354">#12354</a>), 24089 MetaEuk 24090 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12188">#12188</a>), 24091 mrcfile 24092 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12497">#12497</a>), 24093 Myokit 24094 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12261">#12261</a>), 24095 NCCL-tests 24096 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12415">#12415</a>), 24097 pyABC 24098 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12329">#12329</a>), 24099 PyCifRW 24100 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12258">#12258</a>), 24101 PyOD 24102 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12507">#12507</a>), 24103 pyro-api 24104 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12447">#12447</a>), 24105 pyro-ppl 24106 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12447">#12447</a>), 24107 R-opencv 24108 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12226">#12226</a>), 24109 Ratatosk 24110 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12443">#12443</a>), 24111 RevBayes 24112 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12419">#12419</a>), 24113 sansa 24114 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12354">#12354</a>), 24115 scikit-cuda 24116 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12352">#12352</a>), 24117 Seeder 24118 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9057">#9057</a>), 24119 suave 24120 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12354">#12354</a>), 24121 voltools 24122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12497">#12497</a>), 24123 vorbis-tools 24124 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12300">#12300</a>), 24125 YACS 24126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12309">#12309</a>)</li> 24127</ul> 24128</li> 24129<li>
24129added additional easyconfigs for various supported software 24130 packages, including:<ul> 24131<li>AOCC 3.0.0, Arriba 2.1.0, ArviZ 0.11.1, arpack-ng 3.8.0 BCFtools 24132 1.12, BEDTools 2.30.0, BUSCO 5.0.0, BioPerl 1.7.8, Blosc 1.21.0, 24133 Boost.Python 1.74.0, bitarray 1.2.1, bokeh 2.2.3, CP2K 8.1, 24134 CUDAcore 11.2.2, CellRanger 6.0.0, Clang 11.0.1, DIAMOND 2.0.7, 24135 Delly 0.8.7, dask 2021.2.0, dm-tree 0.1.5, Elk 7.0.12, Extrae 24136 3.8.0, FLUENT 2021R1, FabIO 0.11.0, Fiji 20201104, Flye 2.8.3, 24137 FreeSurfer 7.1.1, GDAL 3.2.1, GEOS 3.9.1, GLFW 3.3.3, GMAP-GSNAP 24138 2020-12-17, GROMACS 2021, GetOrganelle 1.7.4, gmsh 4.7.1, HTSeq 24139 0.11.3, HTSlib 1.12, Hypre 2.20.0, hyperopt 0.2.5, iVar 1.3.1, 24140 igraph 0.9.1, Jansson 2.13.1, Kent_tools 411, LAPACK 3.9.1, LAST 24141 1179, LibSoup 2.72.0, libxc 5.1.3, MAFFT 7.475, MCR R2020a.6 + 24142 R2020b.5 + R2021a.0.eb, MDTraj 1.9.5, MUMPS 5.3.5, MaSuRCA 24143 4.0.1, Mercurial 5.7.1, Monocle3 0.2.3, NGS 2.10.9, NVHPC 21.2, 24144 NetLogo 6.2.0, Nextflow 21.03.0, ncbi-vdb 2.10.9, 24145 OSU-Micro-Benchmarks 5.7, OpenCV 4.5.1, OpenEXR 2.5.5, OptiX 24146 7.2.0, PETSc 3.14.4, PLUMED 2.7.0, PROJ 7.2.1, PyAMG 4.0.0, 24147 PyCUDA 2020.1, PyCairo 1.20.0, PyOpenCL 2021.1.2, 24148 PyTorch-Geometric 1.6.3, p7zip 17.03, pFUnit 4.2.0, picard 24149 2.25.1, pocl 1.6, preCICE 2.2.0, protobuf 2.5.0, pymatgen 24150 2022.0.4, python-igraph 0.9.0, Qtconsole 5.0.2, R 4.0.4, RASPA2 24151 2.0.41, RDFlib 5.0.0, ReFrame 3.5.1, Ruby 2.7.2, rnaQUAST 2.2.0, 24152 SAMtools 1.12, SDL2 2.0.14, SIMPLE 3.0.0, SPAdes 3.15.2, 24153 SUNDIALS 5.7.0, Seurat 4.0.1, Spark 3.1.1, scikit-image 0.18.1, 24154 silx 0.14.0, spglib 1.16.1, sympy 1.7.1, tensorboardX 2.1, 24155 tensorflow-probability 0.12.1, tmux 3.1c, USEARCH 11.0.667, VTK 24156 9.0.1, VTune 2020_update3</li> 24157</ul> 24158</li> 24159<li>minor enhancements, including:<ul> 24160<li>verify checksum of all patch files in easyconfigs test suite 24161 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12221">#12221</a>)</li> 24162<li>add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig 24163 with foss/2020a 24164 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12227">#12227</a>)</li> 24165<li>add sanity check commands for vorbis-tools 24166 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12304">#12304</a>)</li> 24167<li>add extensions to R-bundle-Bioconductor 3.12: motifmatchr 24168 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12390">#12390</a>), 24169 OUTRIDER + FRASER 24170 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12510">#12510</a>)</li> 24171<li>add DMCfun extension for R v4.0.3 + v4.0.4 24172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12409">#12409</a>)</li> 24173</ul> 24174</li> 24175<li>various bug fixes, including:<ul> 24176<li>add missing GNU time dependency to WRF 4.0.2 built with 24177 foss/2018b 24178 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12179">#12179</a>)</li> 24179<li>add archive <code>source_urls</code> for Hadoop and Spark 24180 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12220">#12220</a>)</li> 24181<li>add missing Python build dep for SeqAn 2.4.0 24182 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12222">#12222</a>)</li> 24183<li>add missing pkg-config build dependency to VCFtools 0.1.16 24184 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12245">#12245</a>), 24185 GObject-Introspection-1.64.0 24186 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12298">#12298</a>), 24187 libsndfile 24188 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12303">#12303</a>)</li> 24189<li>set <code>$HTSLIB_DIR</code> in HTSlib for use by EnsEMBLCoreAPI & 24190 Bio-DB-HTS 24191 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12253">#12253</a>)</li> 24192<li>bump JasPer version to latest 2.0.24 for 2020b generation of 24193 easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with 24194 GCCcore/10.2.0 24195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12277">#12277</a>, 24196 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12288">#12288</a>)</li> 24197<li>bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode 24198 error 24199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12293">
24199#12293</a>)</li> 24200<li>skip sanity check test in IPython-7.18.1-GCCcore-10.2.0.eb 24201 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12294">#12294</a>)</li> 24202<li>add missing Perl and Autotools build dependencies in recent WRF 24203 easyconfigs 24204 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12301">#12301</a>)</li> 24205<li>add missing groff build dependency for Perl 5.30.0 and 5.32.0 24206 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12307">#12307</a>)</li> 24207<li>add linkcomm + rnetcarto extensions to R v4.0.3 24208 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12311">#12311</a>)</li> 24209<li>add dependency on Flask in all ASE v3.21.1 easyconfigs 24210 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12312">#12312</a>)</li> 24211<li>remove hard-coded <code>-xHost</code> from MMseqs2-11-e1a1c 24212 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12317">#12317</a>)</li> 24213<li>revised outdated easyconfigs for libcerf + replaced obsolete 24214 homepages and source urls 24215 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12323">#12323</a>)</li> 24216<li>consistently include <code>new_archive</code> source URL in Qt5 24217 easyconfigs + add missing checksums 24218 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12325">#12325</a>, 24219 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12426">#12426</a>)</li> 24220<li>fix source URL and add alternate checksum for Hypre 2.14.0 24221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12337">#12337</a>)</li> 24222<li>add patch for recent netCDF easyconfigs to fix MPI_Info_f2c 24223 issue with OpenMPI 24224 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12340">#12340</a>)</li> 24225<li>add SourceForge fallback source URL for recent freetype 24226 easyconfigs 24227 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12341">#12341</a>)</li> 24228<li>revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0 24229 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12345">#12345</a>)</li> 24230<li>use <code>-D_USE_METIS_5p1</code> in OpenSees v3.2.0 patch to correctly 24231 build on top of METIS v5.1.0 24232 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12403">#12403</a>)</li> 24233<li>make sure that path to <code>eb</code> is always found by tests 24234 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12436">#12436</a>)</li> 24235<li>stop tests changing the EasyBuild easyconfigs 24236 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12454">#12454</a>)</li> 24237<li>use pip to install pkgconfig 1.5.1 24238 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12455">#12455</a>)</li> 24239<li>add CI test checking if the Python default <code>source_urls</code> are 24240 used and fix CI check where <code>use_pip=False</code> was ignored 24241 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12456">#12456</a>, 24242 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12471">#12471</a>)</li> 24243<li>fix source URLs in Arrow 0.x easyconfigs 24244 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12475">#12475</a>)</li> 24245<li>fix numpy tests for recent SciPy-bundle easyconfig on POWER 24246 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12481">#12481</a>)</li> 24247<li>don't download hwloc during FIRESTARTER build 24248 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12482">#12482</a>)</li> 24249<li>avoid 0.0.0 install version for various Python apps 24250 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12519">#12519</a>, 24251 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12522">#12522</a>)</li> 24252<li>enable USER_SDPD package and disable building docs in LAMMPS 24253 3Mar2020 24254 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12527">#12527</a>)</li> 24255<li>update <code>$R_LIBS_SITE</code> rather than <code>$R_LIBS</code> in easyconfigs 24256 installing R packages 24257 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12534">#12534</a>)</li> 24258<li>
24258add Python 3 build dep for HMMER 3.3.x test step 24259 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12536">#12536</a>)</li> 24260</ul> 24261</li> 24262<li>other changes:<ul> 24263<li>rename opencv_contrib and update to OpenCV v3.4.1 with contrib 24264 <code>versionsuffix</code> 24265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12229">#12229</a>)</li> 24266<li>fix minor style issues in POV-Ray v3.7.0.8 easyconfigs 24267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12342">#12342</a>)</li> 24268<li>enable <code>-fPIC</code> for g2clib 24269 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12349">#12349</a>)</li> 24270<li>consistently include Keras-Applications and Keras-Preprocessing 24271 extensions in Keras 2.3.1 easyconfigs 24272 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12375">#12375</a>)</li> 24273<li>remove <code>PYPI_SOURCE</code> source URL from easyconfigs using 24274 PythonPackage or PythonBundle 24275 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12541">#12541</a>, 24276 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12452">#12452</a>, 24277 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12453">#12453</a>)</li> 24278<li>require <code>sanity_pip_check</code> for all Python package/bundles 24279 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12464">#12464</a>)</li> 24280</ul> 24281</li> 24282</ul> 24283<h2 id="release_notes_eb433">EasyBuild v4.3.3 (Feb 23rd 2021)<a class="headerlink" href="#release_notes_eb433" title="Permanent link">¶</a></h2> 24284<p>bugfix/update release</p> 24285<p><strong>framework</strong></p> 24286<ul> 24287<li>various enhancements, including:<ul> 24288<li>advise PR labels in <code>--review-pr</code> and add support for 24289 <code>--add-pr-labels</code> 24290 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3177">#3177</a>)</li> 24291<li>add support for using customized HTTP headers in <code>download_file</code> 24292 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3472">#3472</a>, 24293 <a href="https://github.com/easybuilders/easybuild-framework/pull/3583">#3583</a>)</li> 24294<li>also take toolchain dependencies into account when defining 24295 template values 24296 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3541">#3541</a>, 24297 <a href="https://github.com/easybuilders/easybuild-framework/pull/3560">#3560</a>)</li> 24298<li>add support for <code>--accept-eula</code> configuration option + 24299 <code>accept_eula</code> easyconfig parameter 24300 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3535">#3535</a>, 24301 <a href="https://github.com/easybuilders/easybuild-framework/pull/3536">#3536</a>, 24302 <a href="https://github.com/easybuilders/easybuild-framework/pull/3546">#3546</a>)</li> 24303<li>detect <code>SYSTEM</code> toolchain as special case in easystack files 24304 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3543">#3543</a>)</li> 24305<li>enhance <code>extract_cmd</code> function to use <code>cp -a</code> for shell scripts 24306 (.sh) 24307 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3545">#3545</a>)</li> 24308<li>allow use of alternate envvar(s) to <code>$HOME</code> for user modules 24309 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3558">#3558</a>)</li> 24310<li>use <a href="https://sources.easybuild.io">https://sources.easybuild.io</a> as fallback source URL 24311 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3572">#3572</a>, 24312 <a href="https://github.com/easybuilders/easybuild-framework/pull/3576">#3576</a>)</li> 24313<li>add toolchain definition for <code>iibff</code> toolchain 24314 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3574">#3574</a>)</li> 24315<li>add <code>%(cuda_cc_space_sep)s</code> and <code>%(cuda_cc_semicolon_sep)s</code> 24316 templates 24317 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3578">#3578</a>)</li> 24318<li>add support for intel-compiler toolchain (>= 2021.x versions, 24319 oneAPI) 24320 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3581">#3581</a>, 24321 <a href="https://github.com/easybuilders/easybuild-framework/pull/3582">#3582</a>)</li> 24322</ul> 24323</li> 24324<li>various bug fixes, including:<ul> 24325<li>add <code>--init</code> and <code>--recursive</code> options to <code>git submodule update</code> 24326 command that is used when creating source tarball for specific 24327 commit 24328 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3537">#3537</a>)</li> 24329<li>filter out duplicate paths in RPATH wrapper script 24330 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3538">#3538</a>)</li> 24331<li>don't clean up imported modules after verifying imports of 24332 included Python modules 24333 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3544">#3544</a>)</li> 24334<li>avoid no-op changes to <code>$LD_*</code> environment variables in 24335 ModulesTool 24336 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3553">#3553</a>)</li> 24337<li>fix UTF-8 encoding errors when running EasyBuild with Python 24338 3.0.x-3.6.x 24339 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3565">#3565</a>)</li> 24340<li>create <code>lib64</code> symlink as a relative symlink 24341 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3566">#3566</a>)</li> 24342<li>don't reuse variable name in the loop to fix adding extra 24343 compiler flags via toolchainopts 24344 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3571">#3571</a>)</li> 24345<li>symlink <code>lib</code> to <code>lib64</code> if it doesn't exist 24346 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3580">#3580</a>)</li> 24347<li>include <code>%(mpi_cmd_prefix)s</code> and <code>%(cuda_*)s</code> templates in 24348 output of <code>--avail-easyconfig-templates</code> 24349 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3586">#3586</a>)</li> 24350</ul> 24351</li> 24352<li>other changes:<ul> 24353<li>rename <code>EasyBlock._skip_step</code> to <code>EasyBlock.skip_step</code>, to make 24354 it part of the public API 24355 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3561">#3561</a>)</li> 24356<li>make symlinking of <code>posix_c.so</code> to <code>posix.so</code> in test suite 24357 configuration conditional 24358 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3570">#3570</a>)</li> 24359</ul> 24360</li> 24361</ul> 24362<p><strong>easyblocks</strong></p> 24363<ul> 24364<li>2 new software-specific easyblocks:<ul> 24365<li>AOCC 24366 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2295">#2295</a>), 24367 Intel compilers (v2021.x, oneAPI) 24368 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2305">#2305</a>)</li> 24369</ul> 24370</li> 24371<li>minor enhancements, including:<ul> 24372<li>run motorBike tutorial case as sanity check for recent 24373 (community) OpenFOAM versions 24374 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2201">#2201</a>)</li> 24375<li>
24375add foamMonitor to sanity checks of OpenFOAM 24376 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2256">#2256</a>)</li> 24377<li>create versioned symlinks for CMake commands + create symlink 24378 for <code>cmake3</code> in PyTorch easyblock if <code>cmake3</code> command is not 24379 found 24380 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2259">#2259</a>)</li> 24381<li>improve Bazel easyblock: add support for running tests, enable 24382 static linking, use build dir rather than <code>tmpdir</code>, verbose 24383 output 24384 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2285">#2285</a>)</li> 24385<li>add support for skipping steps in Python packages installed as 24386 extension + print progress on individual steps for installing 24387 Python packages as extensions 24388 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2290">#2290</a>)</li> 24389<li>update BerkeleyGW easyblock to support GCC 10 and fftlib 24390 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2297">#2297</a>)</li> 24391<li>update QuantumESPRESSO easyblock to support GCC 10 24392 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2298">#2298</a>)</li> 24393<li>update Clang easyblock to add support for building extra tools + 24394 leveraging hwloc and Z3 as optional dependencies 24395 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2310">#2310</a>)</li> 24396<li>add support for running TensorFlow CPU and GPU tests 24397 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2263">#2263</a>, 24398 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2292">#2292</a>, 24399 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2312">#2312</a>)</li> 24400<li>update impi easyblock for impi 2021.x (oneAPI) 24401 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2313">#2313</a>)</li> 24402<li>update QuantumESPRESSO easyblock to handle v6.7 24403 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2319">#2319</a>)</li> 24404<li>update OpenFOAM easyblock for changes in v2012 24405 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2321">#2321</a>)</li> 24406<li>add sanity check commands to GCC (including LTO support) 24407 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2322">#2322</a>)</li> 24408<li>update FLUENT sanity check for v2021R1 24409 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2334">#2334</a>)</li> 24410</ul> 24411</li> 24412<li>various bug fixes, including:<ul> 24413<li>filter out user packages in LAMMPS easyblock if corresponding 24414 dependency isn't included + only set <code>-DUSER-INTEL</code> on x86_64 24415 systems 24416 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2254">#2254</a>)</li> 24417<li>unify handling of <code>pylibdirs</code> and don't add duplicated 24418 <code>$PYTHONPATH</code> in PythonBundle 24419 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2281">#2281</a>)</li> 24420<li>enhance Amber easyblock to fix running of <code>update_amber</code> script 24421 when <code>python</code> command is not available in OS 24422 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2282">#2282</a>)</li> 24423<li>guard <code>module unload</code> statements in modules for Cray* 24424 toolchains 24425 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2286">#2286</a>)</li> 24426<li>set <code>$PYTHONNOUSERSITE</code> in <code>PythonBundle.extensions_step</code> to 24427 avoid picking up on Python packages installed in $HOME 24428 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2289">#2289</a>)</li> 24429<li>create less temporary directories for TensorFlow by (only) using 24430 <code>--output_user_root</code> 24431 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2293">#2293</a>)</li> 24432<li>fix logic w.r.t. enabling Python support in PETSc 24433 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2299">#2299</a>)</li> 24434<li>make <code>builddeps</code> a list of names in SLEPc easyblock 24435 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2300">#2300</a>)</li> 24436<li>make <code>builddeps</code> a list of names in Trilinos easyblock 24437 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2301">#2301</a>)</li> 24438<li>make sure the installation of <code>libiberty.a</code> in the binutils 24439 easyblock goes into a populated directory 24440 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2308">#2308</a>)</li> 24441<li>fix for building GCC with <code>--sysroot</code> on ppc64le 24442 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2315">#2315</a>)</li> 24443<li>fix OpenFOAM sanity check on POWER 24444 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2320">#2320</a>)</li> 24445<li>use library search paths of compiler for RPATH when building 24446 binutils with system compiler + enhance sanity check by running 24447 <code>--version</code> for binutils commands 24448 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2323">#2323</a>, 24449 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2327">#2327</a>)</li> 24450<li>pass <code>$CXXFLAGS</code> to PDT's configure script via <code>-useropt</code> 24451 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2324">#2324</a>)</li> 24452<li>pass down compilation flags from build environment for ESMF 24453 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2325">#2325</a>)</li> 24454<li>update URLs for test data for WRF to <code>https</code> 24455 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2335">#2335</a>)</li> 24456<li>read MATLAB configuration file in binary mode to avoid UTF-8 24457 encoding errors when using Python 3.6 24458 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2340">#2340</a>)</li> 24459<li>fix Boost sanity check on POWER 24460 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2291">#2291</a>) 24461 and aarch64 24462 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2341">#2341</a>)</li> 24463</ul> 24464</li> 24465<li>other changes, including:<ul> 24466<li>rework module-only tests to use unique software name (rather 24467 than 'foo') 24468 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2287">#2287</a>)</li> 24469<li>prefer default value for extra options in easyblock tests 24470 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2280">#2280</a>, 24471 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2302">
24471#2302</a>)</li> 24472<li>add check for accepted EULA in custom easyblock for NVHPC 24473 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2311">#2311</a>)</li> 24474<li>update optional feature support of TensorFlow 24475 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2314">#2314</a>)</li> 24476<li>make symlinking of <code>posix_c.so</code> to <code>posix.so</code> in test suite 24477 configuration conditional 24478 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2330">#2330</a>)</li> 24479</ul> 24480</li> 24481</ul> 24482<p><strong>easyconfigs</strong></p> 24483<ul> 24484<li>add easyconfig for new iibff toolchain: iibff/2020b 24485 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12185">#12185</a>)</li> 24486<li>added easyconfigs for 6 new toolchains:<ul> 24487<li>gobff/2020b 24488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12098">#12098</a>), 24489 goblf/2018b 24490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6615">#6615</a>), 24491 gomkl/2020b 24492 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12198">#12198</a>), 24493 iimkl/2018a 24494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6092">#6092</a>), 24495 iomkl/2019b 24496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11981">#11981</a>), 24497 iomkl/2020b 24498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12009">#12009</a>)</li> 24499</ul> 24500</li> 24501<li>added example easyconfig files for 72 new software packages:<ul> 24502<li>AOCC 24503 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11868">#11868</a>), 24504 CHERAB 24505 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7141">#7141</a>), 24506 CaDiCaL 24507 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11966">#11966</a>), 24508 CellRanger-ARC 24509 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12114">#12114</a>), 24510 CuPy 24511 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11749">#11749</a>), 24512 DFA 24513 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11979">#11979</a>), 24514 FIGARO 24515 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11924">#11924</a>), 24516 FIRESTARTER 24517 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12160">#12160</a>), 24518 FIt-SNE 24519 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8630">#8630</a>), 24520 GPyTorch 24521 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12010">#12010</a>), 24522 GSEA 24523 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10395">#10395</a>), 24524 GetOrganelle 24525 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11948">#11948</a>), 24526 Glucose 24527 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11965">#11965</a>), 24528 GraPhlAn 24529 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10707">#10707</a>), 24530 ITSx 24531 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10558">#10558</a>), 24532 Kaleido 24533 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11998">#11998</a>), 24534 LAPACK 24535 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6615">#6615</a>), 24536 LSD2 24537 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11903">#11903</a>), 24538 Lingeling 24539 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11964">#11964</a>), 24540 MPB 24541 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7026">#7026</a>), 24542 MiniCARD 24543 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11963">#11963</a>), 24544 MiniSat 24545 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11962">#11962</a>), 24546 NGSpeciesID 24547 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11918">#11918</a>), 24548 NanopolishComp 24549 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11823">#11823</a>), 24550 Nsight-Compute 24551 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12043">
24551#12043</a>), 24552 Nsight-Systems 24553 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12042">#12042</a>), 24554 PHANOTATE 24555 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8667">#8667</a>), 24556 PIPITS 24557 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10558">#10558</a>), 24558 PyClone 24559 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11940">#11940</a>), 24560 PySAT 24561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12000">#12000</a>), 24562 RNAmmer 24563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7262">#7262</a>), 24564 Raysect 24565 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7141">#7141</a>), 24566 SICER2 24567 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12200">#12200</a>), 24568 SOCI 24569 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12045">#12045</a>), 24570 SeisSol 24571 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7194">#7194</a>), 24572 SignalP 24573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11862">#11862</a>), 24574 Stack 24575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11310">#11310</a>), 24576 SuperLU_DIST 24577 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11693">#11693</a>), 24578 Teneto 24579 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12056">#12056</a>), 24580 Transformers 24581 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12032">#12032</a>), 24582 YANK 24583 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11742">#11742</a>), 24584 Z3 24585 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12013">#12013</a>), 24586 bgen 24587 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7456">#7456</a>, 24588 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11867">#11867</a>), 24589 bgen-reader 24590 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7456">#7456</a>, 24591 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11867">#11867</a>), 24592 bpytop 24593 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12040">#12040</a>), 24594 byobu 24595 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11932">#11932</a>), 24596 chi2comb 24597 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11867">#11867</a>), 24598 cuTENSOR 24599 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11914">#11914</a>), 24600 dd 24601 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11978">#11978</a>), 24602 decona 24603 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11891">#11891</a>), 24604 dicom2nifti 24605 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11955">#11955</a>), 24606 eccodes-python 24607 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12083">#12083</a>), 24608 fftlib 24609 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11944">#11944</a>), 24610 flatbuffers-python 24611 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12148">#12148</a>), 24612 fpocket 24613 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11980">#11980</a>), 24614 gh 24615 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11851">#11851</a>), 24616 intel-compilers (oneAPI) 24617 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11982">#11982</a>), 24618 libGDSII 24619 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7026">#7026</a>), 24620 libpci 24621 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11871">#11871</a>), 24622 liknorm 24623 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7456">#7456</a>, 24624 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11867">#11867</a>), 24625 limix 24626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7456">#7456</a>, 24627 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11867">#11867</a>), 24628 logaddexp 24629 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11867">#11867</a>), 24630 neptune-client 24631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11985">#11985</a>), 24632 plinkQC 24633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12068">#12068</a>), 24634 preCICE 24635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11886">#11886</a>), 24636 py-aiger 24637 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11999">#11999</a>), 24638 py-aiger-bdd 24639 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11999">#11999</a>), 24640 pytest-xdist 24641 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11883">#11883</a>, 24642 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11893">#11893</a>), 24643 samblaster 24644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7378">#7378</a>), 24645 terastructure 24646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12197">#12197</a>), 24647 typing-extensions 24648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11636">#11636</a>), 24649 webin-cli 24650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8674">#8674</a>)</li> 24651</ul> 24652</li> 24653<li>
24653added additional easyconfigs for various supported software 24654 packages, including:<ul> 24655<li>ack 3.4.0, AmberTools 20, AMD-LibM 3.6.0-4, AMD-RNG 2.2, 24656 AMD-SecureRNG 2.2, annovar 20191024, ASE 3.21.1, AUGUSTUS 3.4.0, 24657 Bazel 3.7.2, bcgTree 1.1.0, BLAST+ 2.11.0, Bonito 0.3.5, Bowtie2 24658 2.4.2, causalml 0.8.0-20200909, CGAL 5.2, ConnectomeWorkbench 24659 1.4.2, CUDAcore 11.2.1, cuDNN 8.0.5.39, dcm2niix 1.0.20201102, 24660 DendroPy 4.5.2, DIAMOND 0.9.36 + 2.0.6, ecCodes 2.20.0, ELPA 24661 2020.11.001, Emacs 27.1, FusionCatcher 1.30, gensim 3.8.3, GHC 24662 8.6.5, gnuplot 5.4.1, GPAW 21.1.0, Graphviz 2.44.1, GROMACS 24663 2020.5, Gurobi 9.1.0, HH-suite 3.3.0, HMMER 3.3.2, HTSlib 1.11, 24664 Horovod 0.21.1, imbalanced-learn 0.7.0, impi 2021.1.1, inferCNV 24665 1.3.3, ITK 5.1.2, IQ-TREE 2.1.2, JasPer 2.0.24, JUBE 2.4.1, 24666 libgit2 1.1.0, libzip 1.7.3, likwid 5.1.0, MariaDB 10.5.8, 24667 medaka 1.2.0, Meep 1.6.0, mkl-service 2.3.0, MPICH 3.3.2, 24668 muParser 2.3.2, NanoComp 1.13.1, NanoPlot 1.33.0, networkx 2.5, 24669 NLTK 3.5, numba 0.52.0, NVHPC 20.11, nvtop 1.1.0, OpenCoarrays 24670 2.9.2, OpenFOAM v2012, OpenJPEG 2.4.0, OpenMPI 4.1.0, parasail 24671 2.4.2, PLUMED 2.6.2, PostgreSQL 13.2, pydicom 2.1.2, PyMC3 24672 3.11.0, python-parasail 1.2.2, PyTorch 1.7.1, QIIME2 2020.11, 24673 QuantumESPRESSO 6.7, QuickFF 2.2.7, R 4.0.3, 24674 R-bundle-Bioconductor 3.12, ReFrame 3.4.1, RMBlast 2.10.0, RSEM 24675 1.3.3, Salmon 1.4.0, scikit-build 0.11.1, SciPy-bundle 2020.03 24676 w/ Python 2.7.18, Seaborn 0.11.1, SEPP 4.4.0, SHAPEIT4 4.2.0, 24677 SpaceRanger 1.2.2, Stacks 2.54, STAR 2.7.7.a, statsmodels 24678 0.12.1, SuiteSparse 5.8.1, tbb 2020.3, TensorFlow 1.15.5 + 24679 2.4.1, Theano 1.1.2, torchvision 0.8.2, V8 3.4.0, Wannier90 24680 3.1.0</li> 24681</ul> 24682</li> 24683<li>minor enhancements, including:<ul> 24684<li>enable building of QtWebEngine in Qt5 easyconfig using 24685 foss/2017b or intel/2017b 24686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7302">#7302</a>)</li> 24687<li>enable NVPTX offload in GCCcore 9.3.0 easyconfig 24688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11839">#11839</a>)</li> 24689<li>also build shared library in recent HDF easyconfigs 24690 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11847">#11847</a>)</li> 24691<li>add support for HDF4 to GDAL v3.0.2 and v3.0.4 24692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11855">#11855</a>)</li> 24693<li>add patch for magma 2.5.4 with fosscuda/2019b to allow any 24694 <code>sm_*</code> value to be passed via <code>GPU_TARGET</code> 24695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11861">#11861</a>)</li> 24696<li>add missing M4 build dependency to recent SuiteSparse versions 24697 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11869">#11869</a>)</li> 24698<li>enable tests for most recent Bazel versions (3.x) 24699 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11894">#11894</a>)</li> 24700<li>enable gipaw in QuantumESPRESSO 6.6 easyconfig 24701 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11905">#11905</a>)</li> 24702<li>add RCAL + sensemakr extensions to R 4.0.0 24703 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11921">#11921</a>)</li> 24704<li>add additional extensions to R v4.0.3 easyconfig 24705 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11922">#11922</a>, 24706 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12057">#12057</a>)</li> 24707<li>improve sanity_check_paths for AMD-LibM 24708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11933">#11933</a>)</li> 24709<li>symlink <code>include</code>/<code>lib</code> subdirs + enhance <code>sanity_check_paths</code> 24710 for AMD-RNG v2.2-4 24711 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11934">#11934</a>)</li> 24712<li>improve <code>sanity_check_paths</code> for AMD-SecureRNG 24713 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11935">#11935</a>)</li> 24714<li>update Clang 10+ dependencies & build extra tools 24715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12013">#12013</a>)</li> 24716<li>
24716add Inline extension to recent Perl easyconfigs (5.30+) 24717 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12029">#12029</a>)</li> 24718<li>add EnsDb.Hsapiens.v86 to Bioconductor 3.11 24719 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12078">#12078</a>)</li> 24720<li>add sanity check command for bam-readcount v0.8.0 to check 24721 <code>--version</code> output 24722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12092">#12092</a>)</li> 24723<li>add EnsDb.Hsapiens.v75 + Signac extensions to 24724 R-bundle-Bioconductor 3.12 24725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12174">#12174</a>)</li> 24726<li>add tensorboard profile plugin to recent TensorFlow 2.x 24727 easyconfigs 24728 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12136">#12136</a>, 24729 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12137">#12137</a>)</li> 24730</ul> 24731</li> 24732<li>various bug fixes, including:<ul> 24733<li>added missing space in <code>configopts</code> in ParaView 5.8.0 24734 easyconfigs using 2020a toolchain 24735 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10989">#10989</a>)</li> 24736<li>use bfd linker for glibc 2.30 24737 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11331">#11331</a>)</li> 24738<li>add missing moduleclass in UCLUST easyconfig 24739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11477">#11477</a>)</li> 24740<li>don't disable optarch for Clang 11.0.0 24741 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11814">#11814</a>)</li> 24742<li>add patch to fix miscompilation bug on POWER for GCC 8.x and 9.x 24743 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11837">#11837</a>)</li> 24744<li>fix compilation of TensorFlow 2.3.1 with CUDA and glibc 2.26 on 24745 POWER 24746 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11859">#11859</a>)</li> 24747<li>disable building of manpages for GDCM to fix installation 24748 problem with docbook 24749 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11866">#11866</a>)</li> 24750<li>add patch for LLVM 6.0.0 to fix missing exported symbol 24751 <code>LLVMInitializeInstCombine</code> 24752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11873">#11873</a>)</li> 24753<li>fix name of source file for GDRCopy v2.1 24754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11887">#11887</a>)</li> 24755<li>fix Tombo to work with rpy2 v3 when creating DataFrames 24756 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11892">#11892</a>)</li> 24757<li>fix GCCcore 8.1.0 w.r.t. removed <code>sys/ustat.h</code> in glibc 2.28 24758 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11896">#11896</a>)</li> 24759<li>add git as a dependency to GitPython version 3.x 24760 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11902">#11902</a>)</li> 24761<li>fix undefined <code>__ieee128</code> on ppc64le with glibc 2.26 for magma 24762 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11930">#11930</a>) 24763 and PyTorch 24764 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11936">#11936</a>)</li> 24765<li>update Hypre git location for PETSc 3.11.0 using downloaded 24766 dependencies 24767 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11947">#11947</a>)</li> 24768<li>fix source URL in expat easyconfigs (and consistently add custom 24769 <code>sanity_check_paths</code>) 24770 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11960">#11960</a>)</li> 24771<li>use libpng provided by EasyBuild in VTK to fix build issue on 24772 ppc64le 24773 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11990">#11990</a>)</li> 24774<li>add missing pkg-config build dependency for 24775 GObject-Introspection v1.66.1 24776 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11949">#11949</a>)</li> 24777<li>add missing plotly-orca dependency for NanoPlot 24778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11967">#11967</a>, 24779 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12015">#12015</a>)</li> 24780<li>
24780add patch for Boost 1.74.0 to fix missing include file 24781 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12007">#12007</a>)</li> 24782<li>fix for <code>error: 'runtime_error' is not a member of 'std'</code> in 24783 qtlocation for Qt5 v5.14.2 24784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12012">#12012</a>)</li> 24785<li>fix homepage for gnuplot 5.2.8, use <code>http://</code> since homepage is 24786 not reachable via <code>https://</code> 24787 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12047">#12047</a>)</li> 24788<li>fix OS dependencies for libfabric 24789 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12058">#12058</a>)</li> 24790<li>fix vector <code>mul</code> and <code>div</code> with broadcasts in <code>-masm=intel</code> mode 24791 in GCCcore v9.3.0 24792 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12065">#12065</a>)</li> 24793<li>add missing ESMF dependency in NCO easyconfigs 24794 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12071">#12071</a>, 24795 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12072">#12072</a>)</li> 24796<li>add patch to fix version for bam-readcount 0.8.0 24797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12075">#12075</a>)</li> 24798<li>add missing Perl build dep for (recent) libcerf versions, 24799 required for <code>pod2html</code> command 24800 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12085">#12085</a>)</li> 24801<li>add missing bzip2 dependency to recent ncbi-vdb easyconfigs 24802 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12120">#12120</a>)</li> 24803<li>add missing Perl build dependency for BLIS 0.8.0 24804 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12146">#12146</a>)</li> 24805<li>use <code>https://sources.easybuild.io</code> as fallback source URL for 24806 UDUNITS 24807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12049">#12049</a>, 24808 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12156">#12156</a>, 24809 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12182">#12182</a>)</li> 24810<li>correct the GCC version check to allow IBM VSX builds of GROMACS 24811 2020.4 and 2020.5 24812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12159">#12159</a>)</li> 24813<li>add missing mkl-service dependency for Theano built with 24814 intel/2019b + enhance sanity check 24815 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12172">#12172</a>)</li> 24816<li>add patches to fix test problems with p4est 2.2 24817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12028">#12028</a>)</li> 24818<li>fix build of Bison using older system GCC (v4.x) 24819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12203">#12203</a>)</li> 24820<li>fix lack of optimisation for SHAPEIT4 v4.1.3 24821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12206">#12206</a>)</li> 24822<li>add missing gnuplot dependency for OpenFOAM from v2.4.0 to v6 24823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11801">#11801</a>, 24824 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12208">#12208</a>)</li> 24825<li>fix source URL for libspatialite 24826 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12213">#12213</a>)</li> 24827<li>add <code>archive</code> fallback source URL to MAGMA easyconfigs 24828 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12214">#12214</a>)</li> 24829<li>fix checksum for patch in make 4.2.1 easyconfig using 24830 GCC/7.3.0-2.30 24831 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12223">#12223</a>)</li> 24832</ul> 24833</li> 24834<li>other changes:<ul> 24835<li>replace easyconfigs for bpp-core/bpp-phyl/bpp-seq v2.4.1 with a 24836 single easyconfig for BioPP v2.4.1 (using Bundle easyblock) 24837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11609">#11609</a>)</li> 24838<li>add CESM-deps to whitelist in check for custom 24839 <code>sanity_check_paths</code> 24840 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11916">#11916</a>)</li> 24841<li>include '-4' in version for AMD-SecureRNG v2.2-4 24842 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11934">#11934</a>, 24843 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11935">#11935</a>)</li> 24844<li>switch to using python-parasail and tqdm dependencies in Bonito 24845 easyconfigs 24846 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11937">#11937</a>)</li> 24847<li>rename orca to plotly-orca 24848 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12015">#12015</a>)</li> 24849<li>remove duplicate extensions in R 3.5.x easyconfigs, and add test 24850 to detect such issues 24851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12059">#12059</a>)</li> 24852<li>remove Python dependency from ecCodes v2.17.0 since it doesn't 24853 provide Python bindings 24854 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12084">#12084</a>)</li> 24855<li>update Java/1.8 wrapper to Java 1.8.0_281 24856 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11928">#11928</a>, 24857 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12088">#12088</a>)</li> 24858<li>update Bison (build) dependency for flex built with system 24859 compiler to v3.5.3 24860 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12111">#12111</a>)</li> 24861<li>make symlinking of <code>posix.so</code> in test suite configuration 24862 conditional 24863 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12123">#12123</a>)</li> 24864<li>move make 4.3 easyconfigs to GCCcore toolchain 24865 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12166">#12166</a>)</li> 24866<li>move most recent BLIS and libFLAME easyconfigs from GCC to 24867 GCCcore 24868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12168">#12168</a>)</li> 24869<li>rename SNAP to SNAP-HMM and update easyconfig 24870 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/12218">#12218</a>)</li> 24871</ul> 24872</li> 24873</ul> 24874<h2 id="release_notes_eb432">EasyBuild v4.3.2 (December 10th 2020)<a class="headerlink" href="#release_notes_eb432" title="Permanent link">¶</a></h2> 24875<p>bugfix/update release</p> 24876<p><strong>framework</strong></p> 24877<ul> 24878<li>add (experimental) support for specifying easyconfig files via an 24879 "easystack" file 24880 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3479">#3479</a>, 24881 <a href="https://github.com/easybuilders/easybuild-framework/pull/3511">#3511</a>, 24882 <a href="https://github.com/easybuilders/easybuild-framework/pull/3515">#3515</a>, 24883 <a href="https://github.com/easybuilders/easybuild-framework/pull/3517">#3517</a>, 24884 <a href="https://github.com/easybuilders/easybuild-framework/pull/3520">#3520</a>, 24885 <a href="https://github.com/easybuilders/easybuild-framework/pull/3521">#3521</a>)<ul> 24886<li>see also 24887 <a href="https://easybuild.readthedocs.io/en/latest/Easystack-files.html">https://easybuild.readthedocs.io/en/latest/Easystack-files.html</a></li> 24888</ul> 24889</li> 24890<li>
24890add definition for new <code>gobff</code> toolchain using BLIS and LibFLAME 24891 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3505">#3505</a>)</li> 24892<li>various enhancements, including:<ul> 24893<li>add support for toolchain options like <code>extra_cxxflags</code> to 24894 specify extra compiler options 24895 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2193">#2193</a>)</li> 24896<li>fix combination of <code>--copy-ec</code> and <code>--from-pr</code> 24897 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3482">#3482</a>)</li> 24898<li>enhance <code>copy_files</code> function: support single file target, error 24899 on empty input list, support verbose mode 24900 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3483">#3483</a>)</li> 24901<li>cache result of <code>fetch_files_from_pr</code> function (mainly to speed 24902 up framework test suite) 24903 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3484">#3484</a>)</li> 24904<li>add <code>locate_files</code> function to filetools module 24905 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3485">#3485</a>)</li> 24906<li>add support for <code>%(module_name)s</code> template value 24907 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3497">#3497</a>)</li> 24908<li>clarify input format for <code>--cuda-compute-capabilities</code> in 24909 <code>eb --help</code> output 24910 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3509">#3509</a>)</li> 24911<li>add support for skipping unit tests (test step) via 24912 <code>--skip-test-step</code> 24913 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3524">#3524</a>)</li> 24914</ul> 24915</li> 24916<li>various bug fixes, including:<ul> 24917<li>also ignore <code>vsc.*</code> imports coming from from 24918 <code>pkg_resources/__init__.py</code> (setuptools) in fake vsc namespace 24919 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3491">#3491</a>)</li> 24920<li>don't pass username in <code>github_api_get_request</code> when no GitHub 24921 token is available 24922 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3494">#3494</a>)</li> 24923<li>also inject <code>-rpath</code> options for all entries in <code>$LIBRARY_PATH</code> 24924 in <code>RPATH</code> wrappers 24925 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3495">#3495</a>)</li> 24926<li>avoid <code>TypeError</code> being raised by <code>list_toolchains</code> 24927 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3499">#3499</a>)</li> 24928<li>check if PR is already merged in <code>--merge-pr</code> 24929 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3502">#3502</a>)</li> 24930<li>graciously handle wrong PR id in <code>fetch_pr_data</code> 24931 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3503">#3503</a>)</li> 24932<li>fix regression in <code>apply_regex_substitutions</code>: also accept list 24933 of paths to patch 24934 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3507">#3507</a>)</li> 24935<li>update installation procedure for EasyBuild in generated 24936 Singularity container recipes 24937 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3510">#3510</a>)</li> 24938<li>fix GitHub Actions workflow for test suite: run outside of repo 24939 checkout + also test bootstrap script with Python 3.9 24940 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3518">#3518</a>)</li> 24941<li>bump cryptography from 2.9.2 to 3.2 for Python 2 in 24942 <code>requirements.txt</code> 24943 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3519">#3519</a>)</li> 24944<li>fix <code>eb --help=rst</code> when running with Python 3 24945 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3525">#3525</a>)</li> 24946</ul> 24947</li> 24948<li>other changes:<ul> 24949<li>exclude test configurations with Lmod 7 and Python 3, except for 24950 Python 3.6 24951 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3496">#3496</a>)</li> 24952<li>significantly speed up parsing of easyconfig files by only 24953 extracting comments from an easyconfig file when they're 24954 actually needed 24955 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3498">#3498</a>)</li> 24956<li>don't include <code>file</code>/<code>ldd</code>/<code>readelf</code> commands run during RPATH 24957 sanity check in <code>--trace</code> output 24958 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3508">#3508</a>)</li> 24959</ul> 24960</li> 24961</ul> 24962<p><strong>easyblocks</strong></p> 24963<ul> 24964<li>2 new software-specific easyblocks:<ul> 24965<li>code-server 24966 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2255">#2255</a>), 24967 Metagenome-Atlas 24968 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2219">#2219</a>)</li> 24969</ul> 24970</li> 24971<li>minor enhancements, including:<ul> 24972<li>add <code>-fallow-argument-mismatch</code> option when building CP2K 7.1 or 24973 older with GCC 10.x 24974 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2223">#2223</a>)</li> 24975<li>update TensorFlow easyblock for upcoming TensorFlow 2.4 24976 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2225">#2225</a>)</li> 24977<li>
24977add support for building Clang with OpenMP offload support 24978 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2229">#2229</a>)</li> 24979<li>enhance OpenMPI easyblock to catch any <code>--with-ucx*</code> configure 24980 options 24981 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2230">#2230</a>)</li> 24982<li>take into account <code>preinstallopts</code> and <code>installopts</code> in custom 24983 easyblock for NCL 24984 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2234">#2234</a>)</li> 24985<li>add support for <code>withnvptx</code> easyconfig parameter, to enable GPU 24986 offloading, in GCC easyblock 24987 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2235">#2235</a>)</li> 24988<li>take into account versions like <code>4.x</code> in OpenFOAM easyblock 24989 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2239">#2239</a>)</li> 24990<li>also add <code>bin</code> subdir to <code>$PATH</code> when installing a Python 24991 package 24992 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2244">#2244</a>)</li> 24993</ul> 24994</li> 24995<li>various bug fixes, including:<ul> 24996<li>fix two bugs in GROMACS easyblock when using GCC & MKL for FFT 24997 and BLAS/LAPACK 24998 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2212">#2212</a>)</li> 24999<li>fix version check in Qt5 easyblock w.r.t. disabling features on 25000 old Linux kernel versions 25001 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2220">#2220</a>)</li> 25002<li>always define <code>$FCCPP</code> in QuantumESPRESSO easyblock (not just 25003 when using Intel compilers) 25004 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2221">#2221</a>)</li> 25005<li>allow wxPython to be installed as an extension 25006 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2227">#2227</a>, 25007 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2275">#2275</a>)</li> 25008<li>only configure Python with <code>--enable-optimizations</code> when 25009 compiling Python with (recent) GCC compiler 25010 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2228">#2228</a>)</li> 25011<li>fix sanity check for Boost MT libraries 25012 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2231">#2231</a>)</li> 25013<li>fix hardcoded path in NVHPC easyblock to support multiple 25014 architectures 25015 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2233">#2233</a>)</li> 25016<li>fix <code>CPASSERT</code> test faults on RHEL8 in CP2K easyblock 25017 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2236">#2236</a>)</li> 25018<li>stop silently ignoring failing numpy tests, but include support 25019 for ignoring (failing) numpy tests 25020 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2238">#2238</a>, 25021 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2271">#2271</a>)</li> 25022<li>append to module guesses in easyblocks for Chapel, icc, imkl and 25023 impi (rather than overwriting guesses from parent easyblock) 25024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2242">#2242</a>)</li> 25025<li>weed out duplicates when determining paths to <code>include-fixed</code> 25026 subdirectory in GCC easyblock 25027 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2245">#2245</a>)</li> 25028<li>prepend all hardcoded <code>/usr/*</code> paths with sysroot in Python's 25029 setup.py installation script 25030 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2246">#2246</a>)</li> 25031<li>don't try to patch newer versions of Bazel where the patches 25032 won't apply 25033 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2249">#2249</a>)</li> 25034<li>fix setting of <code>$RUNPARALLEL</code> in HDF5 easyblock 25035 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2250">#2250</a>)</li> 25036<li>move <code>--build</code> and <code>--host</code> logic to <code>run_configure_cmd</code> in GCC 25037 easyblock 25038 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2252">#2252</a>)</li> 25039<li>set <code>$UCX_TLS</code> in module for impi installation on top of UCX,
25040 and allow it to be overwritten in impi easyconfig file 25041 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2253">#2253</a>, 25042 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2258">#2258</a>)</li> 25043<li>enhance PyTorch easyblock to ensure it finds MKL (via 25044 <code>$MKLROOT</code>) 25045 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2257">#2257</a>)</li> 25046<li>use integer division to determine number MPI ranks to use in WRF 25047 test step 25048 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2266">#2266</a>)</li> 25049<li>also specify <code>locincpth</code> and <code>glibpth</code> configure options for 25050 Perl based on <code>--sysroot</code> 25051 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2268">#2268</a>)</li> 25052</ul> 25053</li> 25054<li>other changes, including:<ul> 25055<li>add link to GCC mailing list thread confirming that binutils 25056 should not be configured with 25057 <code>--with-sysroot=$EASYBUILD_SYSROOT</code> when GCC is being configured 25058 like that 25059 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2215">#2215</a>)</li> 25060<li>pass paths to patch one by one to <code>apply_regex_substitutions</code> in 25061 GCC easyblock when <code>--sysroot</code> is set 25062 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2217">#2217</a>)<ul> 25063<li>workaround for regression in <code>apply_regex_substitutions</code> 25064 introduced in EasyBuild v4.3.1 (which was fixed for v4.3.2)</li> 25065</ul> 25066</li> 25067</ul> 25068</li> 25069</ul> 25070<p><strong>easyconfigs</strong></p> 25071<ul> 25072<li>add easyconfigs for new <em>gobff</em> toolchain: 25073 <em>gobff/2020.11</em> + <em>gobff/2020.06-amd</em> 25074 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11761">#11761</a>)</li> 25075<li>add easyconfigs for updates of common toolchains: 25076 <em>foss/2020b</em>, <em>fosscuda/2020b</em>, 25077 <em>intel/2020b</em>, <em>intelcuda/2020b</em><ul> 25078<li>see also 25079 <a href="https://easybuild.readthedocs.io/en/latest/Common-toolchains.html">https://easybuild.readthedocs.io/en/latest/Common-toolchains.html</a></li> 25080</ul> 25081</li> 25082<li>added example easyconfig files for 41 new software packages:<ul> 25083<li>alsa-lib 25084 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11658">#11658</a>), 25085 assimp 25086 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11759">#11759</a>), 25087 BioServices 25088 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11602">#11602</a>), 25089 carputils 25090 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11270">#11270</a>), 25091 cctools 25092 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11799">#11799</a>), 25093 code-server 25094 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11778">#11778</a>), 25095 CRISPResso2 25096 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11775">#11775</a>), 25097 elfutils 25098 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11783">#11783</a>), 25099 EMU 25100 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11641">#11641</a>), 25101 fgbio 25102 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11519">#11519</a>), 25103 Flink 25104 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11747">#11747</a>), 25105 FreeSASA 25106 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11699">#11699</a>), 25107 Geant4-data 25108 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11610">#11610</a>), 25109 geocube 25110 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11714">#11714</a>), 25111 IPM 25112 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11768">#11768</a>, 25113 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11772">#11772</a>), 25114 libmicrohttpd 25115 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11783">#11783</a>), 25116 libStatGen 25117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7982">#7982</a>), 25118 libzeep 25119 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11687">#11687</a>), 25120 LLDB 25121 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11822">#11822</a>), 25122 meshalyzer 25123 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11270">#11270</a>), 25124 meshtool 25125 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11270">#11270</a>), 25126 Metagenome-Atlas 25127 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11620">#11620</a>), 25128 MLxtend 25129 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11601">#11601</a>), 25130 MRChem 25131 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11604">#11604</a>), 25132 MRCPP 25133 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11579">#11579</a>), 25134 mxml 25135 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11769">#11769</a>), 25136 mxmlplus 25137 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11771">#11771</a>), 25138 nanocompore 25139 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11690">#11690</a>), 25140 neon 25141 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11797">#11797</a>), 25142 Open-Data-Cube-Core 25143 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11713">#11713</a>), 25144 OpenSees 25145 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11613">#11613</a>), 25146 PEST++ 25147 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11565">#11565</a>), 25148 pyFAI 25149 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11849">
25149#11849</a>), 25150 pymca 25151 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11848">#11848</a>), 25152 RE2 25153 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11718">#11718</a>), 25154 scikit-bio 25155 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11660">#11660</a>), 25156 SpaceRanger 25157 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11776">#11776</a>), 25158 SplAdder 25159 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11607">#11607</a>), 25160 SWAT+ 25161 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11615">#11615</a>), 25162 velocyto 25163 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11744">#11744</a>), 25164 WCT 25165 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11779">#11779</a>)</li> 25166</ul> 25167</li> 25168<li>added additional easyconfigs for various supported software 25169 packages, including:<ul> 25170<li>BBMap 38.87, Boost 1.74.0, CUDA 11.1.1, CellRanger 5.0.0.eb, 25171 CheckM 1.1.3, Clang 11.0.0, cuDNN 8.0.4.30, DMTCP 2.6.0, FDS 25172 6.7.5, FFmpeg 4.3.1, GROMACS 2020.4, Geant4 10.6.2, Ghostscript 25173 9.53.3, GitPython 3.1.9, GlobalArrays 5.8, HDF5 1.10.7, h5py 25174 3.1.0, hypothesis 5.41.5, JasPer 2.0.16, LittleCMS 2.11, libedit 25175 20191231, libyaml 0.2.5, MPFR 4.1.0, magma 2.5.4, matplotlib 25176 3.3.3, NCCL 2.8.3, NLopt 2.6.2, Nextflow 20.10.0, netCDF-Fortran 25177 4.5.3, OpenBLAS 0.3.12, OpenMolcas 20.10, Pillow 8.0.1, PnetCDF 25178 1.12.1, PyYAML 5.3.1, packmol 20.2.2, protobuf 3.14.0, psycopg2 25179 2.8.6, pybind11 2.6.0, pycocotools 2.0.2, Qt5 5.14.2, RAxML-NG 25180 1.0.1, RSeQC 4.0.0, rioxarray 0.1.1, SCOTCH 6.1.0, SciPy-bundle 25181 2020.11, SentencePiece 0.1.94, StringTie 2.1.4, SuperLU 5.2.2, 25182 scikit-learn 0.23.2, snakemake 5.26.1, tqdm 4.51.0, vsc-mympirun 25183 5.2.5, x264 20201026</li> 25184</ul> 25185</li> 25186<li>minor enhancements, including:<ul> 25187<li>add extension to R-bundle-Bioconductor 3.11: snpStats 25188 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11586">#11586</a>), 25189 SCANVIS 25190 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11638">#11638</a>)</li> 25191<li>add extensions to R 4.0.0: coloc, Exact, lmom, gld, DescTools 25192 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11587">#11587</a>); 25193 nlsem 25194 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11733">#11733</a>); 25195 mitools, survey, tableone, jstable 25196 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11841">#11841</a>)</li> 25197<li>add gxmapi extension (Python bindings) to GROMACS 2020.4 25198 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11640">#11640</a>)</li> 25199<li>add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 25200 easyconfigs 25201 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11654">#11654</a>)</li> 25202<li>enable NVPTX offload support in GCCcore 10.2.0 easyconfig 25203 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11720">#11720</a>)</li> 25204</ul> 25205</li> 25206<li>various bug fixes, including:<ul> 25207<li>prevent Minimac4 easyconfig from downloading libStatGen from 25208 GitHub 25209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7982">#7982</a>)</li> 25210<li>limit build parallelism for RAxML-NG to avoid build failure 25211 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10363">#10363</a>)</li> 25212<li>fix <code>source_urls</code> in Geant4 easyconfigs 25213 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11596">#11596</a>)</li> 25214<li>add alternate checksum for extensions in R easyconfigs: 25215 KernSmooth 25216 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11600">#11600</a>), 25217 codetools 25218 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11616">#11616</a>, 25219 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11736">#11736</a>)</li> 25220<li>fix BBMap version check in FusionCatcher v1.20 25221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11608">#11608</a>)</li> 25222<li>
25222add patch for TensorFlow 2.3.1 to fix installation on Arm64 25223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11614">#11614</a>)</li> 25224<li>add patch for GCCcore 10.2 to fix <code>__has_include</code> regression 25225 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11627">#11627</a>)</li> 25226<li>change default <code>bitmaptype</code> for IRkernel to cairo 25227 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11645">#11645</a>)</li> 25228<li>set <code>$JUPYTER_PATH</code> to make Jupyter find the ipywidgets 25229 extension in recent IPython easyconfigs 25230 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11649">#11649</a>)</li> 25231<li>add missing dependencies + fix moduleclass in CheckM easyconfigs 25232 (should be bio) 25233 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11662">#11662</a>)</li> 25234<li>use Python 2 build dep for nodejs 12.19.0 25235 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11679">#11679</a>)</li> 25236<li>use correct OS deps in UCX 25237 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11702">#11702</a>)</li> 25238<li>in-place update to magma 2.5.4 for PyTorch 1.2.0 25239 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11723">#11723</a>)</li> 25240<li>in-place update to magma 2.5.4 for PyTorch easyconfigs using 25241 fosscuda/2019b toolchain 25242 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11726">#11726</a>)</li> 25243<li>add missing Java dep to Prokka 25244 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11732">#11732</a>)</li> 25245<li>add patch to fix possible memory leak in OpenBLAS 0.3.3+ 25246 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11745">#11745</a>)</li> 25247<li>do not treat warnings as errors in Java v1.8_191-b26-OpenJDK 25248 (POWER) 25249 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11755">#11755</a>)</li> 25250<li>add missing PEAR dependency in easyconfig for GBprocesS v2.3 + 25251 enhance sanity check 25252 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11767">#11767</a>)</li> 25253<li>add missing gnuplot dependency in OpenFOAM easyconfigs 25254 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11770">#11770</a>, 25255 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11800">#11800</a>)</li> 25256<li>consistently add Java as a dep for prokka 1.14.5 25257 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11782">#11782</a>)</li> 25258<li>stick to http download URL in fetchMG easyconfig (https doesn't 25259 work) 25260 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11788">#11788</a>)</li> 25261</ul> 25262</li> 25263<li>other changes:<ul> 25264<li>rename XCfun to XCFun 25265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11603">#11603</a>)</li> 25266<li>rename ambiguous Ray easyconfigs to Ray-assembler and 25267 Ray-project 25268 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11727">#11727</a>)</li> 25269<li>change 'rstudio' name to 'RStudio-Server' to agree with 25270 official name and better reflect what it provides 25271 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11764">#11764</a>)</li> 25272<li>rename Sumo to SUMO for consistency 25273 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11791">#11791</a>)</li> 25274</ul> 25275</li> 25276</ul> 25277<h2 id="release_notes_eb431">EasyBuild v4.3.1 (October 29th 2020)<a class="headerlink" href="#release_notes_eb431" title="Permanent link">¶</a></h2> 25278<p>bugfix/update release</p> 25279<p><strong>framework</strong></p> 25280<ul> 25281<li>various enhancements, including:<ul> 25282<li>further GCC toolchain fixes for aarch64 25283 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3433">#3433</a>)</li> 25284<li>take into account <code>--include-easyblocks-from-pr</code> when uploading 25285 test reports 25286 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3446">#3446</a>)</li> 25287<li>add path to pkg-config files in sysroot to <code>$PKG_CONFIG_PATH</code> 25288 when <code>--sysroot</code> is specified 25289 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3451">#3451</a>)</li> 25290<li>
25290add support for NVHPC compiler + toolchain (based on PGI) 25291 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3454">#3454</a>)</li> 25292<li>check for _VERSION and _PREFIX Cray environment variables with 25293 both software and module name 25294 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3460">#3460</a>)</li> 25295<li>allow including easyblocks from multiple PRs 25296 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3480">#3480</a>, 25297 <a href="https://github.com/easybuilders/easybuild-framework/pull/3481">#3481</a>)</li> 25298</ul> 25299</li> 25300<li>various bug fixes, including:<ul> 25301<li>avoid <code>UnicodeDecodeError</code> in <code>apply_regex_substitutions</code> when 25302 patching files that include non-UTF-8 characters 25303 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3450">#3450</a>)</li> 25304<li>avoid appending lib stubs pattern to RPATH filter over and over 25305 again 25306 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3452">#3452</a>)</li> 25307<li>fix missing string template on error for incorrect extension 25308 <code>sources</code> value 25309 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3461">#3461</a>)</li> 25310<li>fix compatibility with Python 3.9 by renaming fancy root logger 25311 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3465">#3465</a>)</li> 25312<li>also remove empty checksums list specified in easyconfig file 25313 when using <code>--inject-checksums</code> 25314 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3466">#3466</a>)</li> 25315<li>avoid confusing error log message when determining impi version 25316 while trying to define value for <code>%(mpi_cmd_prefix)s</code> template 25317 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3474">#3474</a>)</li> 25318<li>unset <code>$LD_LIBRARY_PATH</code> when checking for OS dependencies with 25319 <code>rpm</code> & co 25320 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3477">#3477</a>)</li> 25321<li>don't change directory in <code>download_repo</code> function in 25322 <code>tools.github</code> 25323 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3486">#3486</a>)</li> 25324<li>take <code>source_urls</code>, <code>checksums</code>, <code>patches</code> into account when 25325 extension source is specified via <code>sources</code> 25326 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3487">#3487</a>)</li> 25327</ul> 25328</li> 25329<li>other changes:<ul> 25330<li>consider <code>$EB_INSTALLPYTHON</code> in <code>eb</code> command to specify <code>python</code> 25331 command to use for running EasyBuild 25332 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3428">#3428</a>)</li> 25333<li>use only the sub folder name for <code>createSubmoduleDeps</code> script 25334 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3464">#3464</a>)</li> 25335</ul> 25336</li> 25337</ul> 25338<p><strong>easyblocks</strong></p> 25339<ul> 25340<li>2 new software-specific easyblocks:<ul> 25341<li>CFDEMcoupling 25342 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1439">#1439</a>), 25343 NVHPC 25344 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2190">#2190</a>)</li> 25345</ul> 25346</li> 25347<li>minor enhancements, including:<ul> 25348<li>support having PyQt5 installed as part of Qt5 in QScintilla 25349 easyblock 25350 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2040">#2040</a>)</li> 25351<li>update TensorFlow easyblock to put Bazel build files in build 25352 directory + avoid unnecessary runtime patching 25353 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2166">#2166</a>)</li> 25354<li>update CBLAS easyblock for toolchains that include imkl 25355 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2175">#2175</a>)</li> 25356<li>add workaround for duplicate prefix path in Eigen CMake config 25357 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2176">#2176</a>)</li> 25358<li>enable <code>CTEST_OUTPUT_ON_FAILURE</code> for CMakeMake test step 25359 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2181">#2181</a>)</li> 25360<li>
25360add XLA build support to TensorFlow easyblock 25361 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2182">#2182</a>)</li> 25362<li>also consider libfabric dep (<code>--with-ofi</code>) when setting default 25363 OpenMPI configure options 25364 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2184">#2184</a>)</li> 25365<li>make easyblock for installing CMake aware of <code>--sysroot</code> 25366 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2187">#2187</a>)</li> 25367<li>make OpenBLAS respect the parallelism set by easybuild 25368 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2191">#2191</a>)</li> 25369<li>handle option of building Michigan State University CCT3 & 25370 CCSD3A methods in GAMESS_US easyblock 25371 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2194">#2194</a>)</li> 25372<li>add support to RubyGem easyblock for installing zipped gems 25373 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2203">#2203</a>)</li> 25374<li>update ScaLAPACK easyblock to support installation with CMake 25375 for recent versions (>= v2.1.0) 25376 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2205">#2205</a>)</li> 25377<li>update Score-P easyblock to add support for NVHPC toolchain 25378 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2206">#2206</a>)</li> 25379</ul> 25380</li> 25381<li>various bug fixes, including:<ul> 25382<li>add <code>torch/lib</code> subdirectory in Python lib dir to 25383 <code>$LD_LIBRARY_PATH</code> for PyTorch installations 25384 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2183">#2183</a>)</li> 25385<li>update MUMmer easyblock to use <code>apply_regex_substitutions</code> and 25386 <code>copy_file</code> functions 25387 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2185">#2185</a>)</li> 25388<li>configure OpenMPI 4.x with <code>--without-verbs</code> when using UCX 25389 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2188">#2188</a>)</li> 25390<li>take into account that zlib may be listed in <code>--filter-deps</code> in 25391 custom easyblock for XML R package 25392 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2189">#2189</a>)</li> 25393<li>add sanity check commands to Clang easyblock and print warning 25394 for missing ncurses 25395 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2193">#2193</a>)</li> 25396<li>enhance OpenFOAM easyblock to add symlinks for libraries to 25397 ensure <code>mpi</code> versions have preference over <code>dummy</code> versions 25398 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2196">#2196</a>)</li> 25399<li>leverage installed OpenSSL/BoringSSL when cURL is used as a 25400 dependency for TensorFlow 25401 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2197">#2197</a>)</li> 25402<li>add <code>-ffree-line-length-none</code> to gfortran flags in Siesta 25403 easyblock 25404 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2204">#2204</a>)</li> 25405<li>respect <code>--disable-mpi-tests</code> in Siesta easyblock 25406 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2207">#2207</a>)</li> 25407</ul> 25408</li> 25409<li>other changes, including:<ul> 25410<li>set <code>$EB_INSTALLPYTHON</code> in module generated for EasyBuild rather 25411 than setting <code>$EB_PYTHON</code>, to allow overriding Python command to 25412 be used for running EasyBuild with <code>$EB_PYTHON</code> 25413 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2109">#2109</a>)</li> 25414<li>remove unused custom easyblock for DIRAC 25415 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2192">#2192</a>, 25416 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2198">#2198</a>)</li> 25417</ul> 25418</li> 25419</ul> 25420<p><strong>easyconfigs</strong></p> 25421<ul> 25422<li>added easyconfigs for 2 new toolchains:<ul> 25423<li>fosscuda/2020a 25424 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11424">#11424</a>) 25425 and intelcuda/2020a 25426 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11425">#11425</a>)</li> 25427</ul> 25428</li> 25429<li>
25429added example easyconfig files for 75 new software packages:<ul> 25430<li>Bsoft 25431 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6551">#6551</a>, 25432 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11537">#11537</a>), 25433 causallift 25434 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11436">#11436</a>), 25435 CAVIAR 25436 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11158">#11158</a>), 25437 CCfits 25438 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11505">#11505</a>), 25439 Cereal 25440 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11506">#11506</a>), 25441 CFDEMcoupling 25442 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6465">#6465</a>), 25443 Check 25444 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11295">#11295</a>), 25445 chewBBACA 25446 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11418">#11418</a>), 25447 COMSOL 25448 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11513">#11513</a>), 25449 CUDAcore 25450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11295">#11295</a>), 25451 Dalton 25452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5808">#5808</a>), 25453 DIRAC 25454 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11414">#11414</a>), 25455 ESMValTool 25456 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6329">#6329</a>), 25457 eSpeak-NG 25458 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11236">#11236</a>), 25459 ExifTool 25460 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11521">#11521</a>), 25461 FabIO 25462 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11517">#11517</a>), 25463 festival 25464 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11236">#11236</a>), 25465 fetchMG 25466 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11283">#11283</a>), 25467 FHI-aims 25468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11198">#11198</a>), 25469 Flexbar 25470 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11305">#11305</a>), 25471 FRUIT 25472 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6613">#6613</a>), 25473 FRUIT_processor 25474 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6631">#6631</a>), 25475 Gaussian 25476 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4247">#4247</a>), 25477 GBprocesS 25478 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11512">#11512</a>), 25479 GDRCopy 25480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11295">#11295</a>), 25481 Genome_Profiler 25482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6066">#6066</a>), 25483 groff 25484 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11200">#11200</a>), 25485 ILAMB 25486 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11309">#11309</a>), 25487 kedro 25488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11436">#11436</a>), 25489 leidenalg 25490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11407">#11407</a>), 25491 libav 25492 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6194">#6194</a>), 25493 libmo_unpack 25494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6329">#6329</a>), 25495 libobjcryst 25496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11321">#11321</a>), 25497 makeinfo 25498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11368">#11368</a>), 25499 mauveAligner 25500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11395">#11395</a>), 25501 MBROLA 25502 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11236">#11236</a>), 25503 MDSplus-Java 25504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10705">#10705</a>), 25505 MDSplus-Python 25506 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10705">#10705</a>), 25507 MyCC 25508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11283">#11283</a>), 25509 nanomax-analysis-utils 25510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11517">#11517</a>), 25511 Nek5000 25512 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6408">#6408</a>), 25513 NVHPC 25514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11391">#11391</a>), 25515 OPERA-MS 25516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11410">#11410</a>), 25517 ORFfinder 25518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7031">#7031</a>), 25519 phonemizer 25520 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11236">#11236</a>), 25521 Pingouin 25522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11280">#11280</a>), 25523 Pint 25524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11151">#11151</a>), 25525 pydantic 25526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11151">#11151</a>), 25527 pyobjcryst 25528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11321">#11321</a>), 25529 PyOpenCL 25530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11517">#11517</a>), 25531 pyspoa 25532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11438">#11438</a>), 25533 QtPy 25534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11517">#11517</a>), 25535 Qtconsole 25536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11517">#11517</a>), 25537 rasterio 25538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11468">#11468</a>), 25539 rasterstats 25540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11468">#11468</a>), 25541 ReMatCh 25542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6067">#6067</a>), 25543 Ruby-Tk 25544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6613">#6613</a>), 25545 SBCL 25546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11413">#11413</a>), 25547 scikit-uplift 25548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11432">#11432</a>), 25549 SDL 25550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6202">#6202</a>), 25551 SDL2 25552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6203">#6203</a>), 25553 SDL2_image 25554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6203">#6203</a>), 25555 SDL_image 25556 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6202">#6202</a>), 25557 SeqKit 25558 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11538">#11538</a>), 25559 silx 25560 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11517">#11517</a>), 25561 SiNVICT 25562 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11404">#11404</a>), 25563 sonic 25564 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11236">#11236</a>), 25565 speech_tools 25566 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11236">#11236</a>), 25567 Statistics-R 25568 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11274">#11274</a>), 25569 SUMO 25570 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11435">#11435</a>), 25571 tidybayes 25572 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11335">#11335</a>), 25573 treatSens 25574 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11431">#11431</a>), 25575 tsne 25576 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11283">#11283</a>), 25577 wandb 25578 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11450">#11450</a>), 25579 WisecondorX 25580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11399">#11399</a>)</li> 25581</ul> 25582</li> 25583<li>
25583added additional easyconfigs for various supported software 25584 packages, including:<ul> 25585<li>ABINIT 9.2.1, ASE 3.20.1, Autotools 20200321, Bazel 3.6.0, 25586 Biopython 1.78, CCL 1.12, CMake 3.18.4, CUDA 11.0.2, cURL 25587 7.72.0, deepdiff 5.0.2, fmt 7.0.3, GATK 4.1.8.1, GLib 2.66.1, 25588 GROMACS 2020.3, GTK+ 3.24.23, git 2.28.0, HMMER 3.3.1, Horovod 25589 0.20.3, ICU 67.1, IPython 7.18.1, ichorCNA 0.3.2, JupyterHub 25590 1.1.0, JupyterLab 2.2.8, LLVM 11.0.0, libarchive 3.4.3, 25591 libcircle 0.3, libevent 2.1.12, libfabric 1.11.0, libglvnd 25592 1.3.2, libunwind 1.4.0, libxcb 1.13, MAFFT 7.471, MDSplus 25593 7.96.12, MEGAHIT 1.2.9, MMseqs2 11-e1a1c, Mako 1.1.3, Mesa 25594 20.2.1, Meson 0.55.3, medaka 1.1.3, mpifileutils 0.10.1, NASM 25595 2.15.05, NSPR 4.29, NSS 3.57, Ninja 1.10.1, nettle 3.6, nglview 25596 2.7.7, nodejs 12.19.0, OpenImageIO 2.1.12.0, OpenRefine 3.4.1, 25597 OpenSSL 1.1.1h, PCRE2 10.35, PSI4 1.3.2, Pango 1.47.0, PyGEOS 25598 0.8, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 25599 2.5.0, Python 3.8.6, pandas 1.1.2, phonopy 2.7.1, picard 2.22.1, 25600 pixman 0.40.0, protobuf 3.13.0, pyEGA3 3.4.0, pytest 6.0.1, 25601 ReFrame 3.2. re2c 2.0.3, SAMtools 1.11, SCons 4.0.1, SQLite 25602 3.33.0, Spyder 4.1.5, Subversion 1.14.0, sbt 1.3.13, 25603 spglib-python 1.16.0, spoa 4.0.0, TINKER 8.8.1, TRIQS 3.0.0, 25604 Taiyaki 5.1.0, TensorFlow 2.3.1, Tkinter 2.7.18 + 3.8.6, 25605 torchvision 0.7.0, UCX 1.9.0, V8 3.2.0, VirtualGL 2.6.2, vsc 25606 mympirun 5.2.0 X11 20201008, XGBoost 1.2.0, XZ 5.2.5, Xerces-C++ 25607 3.2.3, xarray 0.16.1, ZeroMQ 4.3.3, zstd 1.4.5</li> 25608</ul> 25609</li> 25610<li>minor enhancements, including:<ul> 25611<li>use more EasyBuild installed dependencies for TensorFlow 2.2.0 25612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11224">#11224</a>)</li> 25613<li>add additional extensions to R 4.0.0 easyconfig 25614 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11340">#11340</a>, 25615 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11430">#11430</a>, 25616 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11487">#11487</a>)</li> 25617<li>add additional extensions to Bioconductor 3.11 bundle 25618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11341">#11341</a>, 25619 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11488">#11488</a>)</li> 25620<li>make libtirpc easier to use as replacement of rpc in glibc (for 25621 RHEL8) 25622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11355">#11355</a>)</li> 25623<li>add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 25624 (for foss/2020a & iomkl/2020a) 25625 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11387">#11387</a>, 25626 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11568">#11568</a>)</li> 25627<li>build LibTIFF with <code>-fPIC</code> 25628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11527">#11527</a>)</li> 25629<li>update Java/1.8 wrapper to also support aarch64 25630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11545">#11545</a>)</li> 25631</ul> 25632</li> 25633<li>various bug fixes, including:<ul> 25634<li>add Python 3 as build dep for Xvfb 1.20.8 easyconfigs 25635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10745">#10745</a>)</li> 25636<li>patch out bug in collective primitive in TensorFlow 2.2.0 25637 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11175">#11175</a>)</li> 25638<li>add missing groff build dependency for Perl (provides nroff tool 25639 requires to install man pages) 25640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11200">#11200</a>)</li> 25641<li>add pocl dependency to GDAL easyconfig using fosscuda/2019b 25642 toolchain to make sure it builds on POWER 25643 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11273">#11273</a>)</li> 25644<li>add libtirpc as a build dep for HDF to fix installation on RHEL8 25645 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11279">#11279</a>)</li> 25646<li>fix build problems with make 4.2.1 on RHEL8 25647 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11282">#11282</a>, 25648 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11371">#11371</a>)</li> 25649<li>change <code>$LIBS</code> in Ghostscript 9.27 easyconfig to include 25650 location of zlib library to link with 25651 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11291">#11291</a>)</li> 25652<li>remove <code>--no-dist-info</code> configuration option for SIP in recent 25653 PyQt5 easyconfigs 25654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11307">#11307</a>)</li> 25655<li>make sure correct zlib is used in recent Ghostscript easyconfigs 25656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11319">#11319</a>)</li> 25657<li>remove GLog and GFlags from PyTorch 1.2.0 25658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11327">#11327</a>), 25659 1.3.1 25660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11325">#11325</a>), 25661 1.4.0 25662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11322">#11322</a>) 25663 and 1.6.0 25664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11323">#11323</a>)</li> 25665<li>use PyTorch easyblock for PyTorch 1.3.1 25666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11325">#11325</a>)</li> 25667<li>
25667add missing git build dependency for OpenImageIO 2.0.12 25668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11328">#11328</a>)</li> 25669<li>fix HDF 4.2.14 easyconfigs for RHEL8 25670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11330">#11330</a>)</li> 25671<li>add patch to fix installation of LAMMPS 7Aug2019 on AMD Epyc 25672 systems 25673 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11334">#11334</a>)</li> 25674<li>fix dependency on Bowtie of v0.x in seq2HLA easyconfigs 25675 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11339">#11339</a>)</li> 25676<li>fix installation of Hadoop v2.10.0 on RHEL8 25677 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11358">#11358</a>)</li> 25678<li>add patch to fix installation of Sailfish v0.10.1 on RHEL8 25679 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11364">#11364</a>)</li> 25680<li>add patch to fix installation of FuSeq v1.1.2 on RHEL8 25681 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11365">#11365</a>)</li> 25682<li>fix installation of Qt5 5.14.1 on top of zlib provided by 25683 Gentoo + stick to Python 2 as build dep 25684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11385">#11385</a>, 25685 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11386">#11386</a>)</li> 25686<li>add patch for LAME configure script to make it check for correct 25687 ncurses symbol 25688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11388">#11388</a>)</li> 25689<li>add protobuf-python as a dependency and corresponding sanity 25690 check to PyTorch 1.6 25691 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11390">#11390</a>)</li> 25692<li>fix Multiwfn 3.6 installation on RHEL8 25693 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11402">#11402</a>)</li> 25694<li>fix OpenFOAM 2.3.1 installation with intel/2019b on RHEL8 25695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11409">#11409</a>)</li> 25696<li>fix broken worker easyconfigs 25697 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11412">#11412</a>)</li> 25698<li>add ncurses runtime dependency to Clang easyconfigs 25699 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11415">#11415</a>, 25700 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11416">#11416</a>, 25701 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11419">#11419</a>, 25702 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11472">#11472</a>)</li> 25703<li>fix installation of Bioconductor 3.11 bundle on aarch64 25704 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11417">#11417</a>)</li> 25705<li>add patch to libunwind fixing a failure on POWER 25706 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11421">#11421</a>)</li> 25707<li>fix infinite loop build bug on ppc64le for R 4.0.0 25708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11428">#11428</a>)</li> 25709<li>fix compilation of Qt5 v5.12.3 and v5.13.1 on Ubuntu 20.04 25710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11434">#11434</a>)</li> 25711<li>fix PyVCF easyconfig, only supports Python 2 25712 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11437">#11437</a>)</li> 25713<li>add patches to fix miscomputation (on POWER) and performance 25714 issues for OpenBLAS 25715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11443">#11443</a>, 25716 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11444">#11444</a>, 25717 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11445">#11445</a>)</li> 25718<li>add missing DB dependency (required for DB_File) to easyconfigs 25719 for Perl 25720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11451">#11451</a>, 25721 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11452">#11452</a>)</li> 25722<li>fix dbarts extension in R v4.0.0 easyconfigs for non-x86_64 25723 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11453">#11453</a>)</li> 25724<li>use Homebrew source mirror to auto-download sources for DB 25725 v18.1.25 and v18.1.32 25726 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11454">#11454</a>)</li> 25727<li>
25727add missing UnZip dependency for Python 3.8.2 25728 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11458">#11458</a>)</li> 25729<li>add support for building OpenBLAS on ARM TSV110 with GCC 8.3 25730 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11464">#11464</a>)</li> 25731<li>allow Kent_tools to build when MySQL installed at the OS level 25732 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11471">#11471</a>)</li> 25733<li>add missing <code>moduleclass</code> to easyconfigs for:<ul> 25734<li>Arlequin 3.5.2.2 25735 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11473">#11473</a>), 25736 MEGAHIT 1.2.8 25737 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11474">#11474</a>) 25738 and 1.2.9 25739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11475">#11475</a>), 25740 PyCUDA 2019.1.2 25741 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11476">#11476</a>)</li> 25742</ul> 25743</li> 25744<li>fix source for SQLite 3.31.1 25745 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11483">#11483</a>)</li> 25746<li>fix installation of worker 1.6.11 with intel/2019b on RHEL 8.2 25747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11498">#11498</a>)</li> 25748<li>fix checksum in NAMD 2.12 easyconfigs + add source URL 25749 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11515">#11515</a>)</li> 25750<li>add BLAS/LAPACK check to GPAW patch adding EasyBuild 25751 configuration files 25752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11523">#11523</a>)</li> 25753<li>backport fixes for Score-P v6.0 25754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11540">#11540</a>)</li> 25755<li>add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 25756 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11561">#11561</a>)</li> 25757<li>add patch for OpenMPI 3.1.4 adding device parameters for 25758 ConnectX-6 25759 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11575">#11575</a>)</li> 25760</ul> 25761</li> 25762<li>other changes:<ul> 25763<li>update README on constructing source file for MATLAB 25764 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6341">#6341</a>)</li> 25765<li>remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, 25766 since latest version still requires PyTorch 1.2.0 25767 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11301">#11301</a>)</li> 25768<li>make CI error messages less confusing ("is" -> "should be") 25769 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11314">#11314</a>)</li> 25770<li>remove extensions from R-bundle-Bioconductor 3.11 easyconfigs 25771 that are also included in R 4.0.0 25772 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11429">#11429</a>)</li> 25773<li>cache M4 source tarball to avoid test failures because of 25774 download problems 25775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11469">#11469</a>)</li> 25776<li>rename jupyterhub to JupyterHub 25777 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11571">#11571</a>)</li> 25778</ul> 25779</li> 25780</ul> 25781<h2 id="release_notes_eb430">EasyBuild v4.3.0 (September 13th 2020)<a class="headerlink" href="#release_notes_eb430" title="Permanent link">¶</a></h2> 25782<p>feature release</p> 25783<p><strong>framework</strong></p> 25784<ul> 25785<li>various enhancements, including:<ul> 25786<li>add script to create <code>sources</code> entries for git submodules 25787 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3369">#3369</a>, 25788 <a href="https://github.com/easybuilders/easybuild-framework/pull/3436">#3436</a>)</li> 25789<li>add templates for CUDA compute capabilities 25790 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3382">#3382</a>)<ul> 25791<li><code>%(cuda_compute_capabilities)s</code>, <code>%(cuda_sm_comma_sep)s</code>, 25792 <code>%(cuda_sm_space_sep)s</code></li> 25793</ul> 25794</li> 25795<li>add EasyBuild configuration option <code>--generate-devel-module</code> 25796 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3388">#3388</a>)<ul> 25797<li>to allow disabling generating of "devel" modules via 25798 <code>--disable-generate-devel-module</code></li> 25799</ul> 25800</li> 25801<li>set up a minimal build environment when using system compiler 25802 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3399">#3399</a>)<ul> 25803<li>by default, <code>$CC</code> is set to <code>gcc</code> and <code>$CXX</code> is set to <code>g++</code> 25804 when using <code>system</code> toolchain</li> 25805<li>minimal build environment can be customized via 25806 <code>--minimal-build-env</code> configuration option</li> 25807</ul> 25808</li> 25809<li>
25809add <code>--sysroot</code> configuration option to specify alternative 25810 location of system root 25811 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3419">#3419</a>)<ul> 25812<li>this is useful when installing software in a Gentoo Prefix 25813 environment (for example)</li> 25814</ul> 25815</li> 25816</ul> 25817</li> 25818<li>various bug fixes, including:<ul> 25819<li>allow including easyblocks from multiple locations, by combining 25820 <code>--include-easyblocks</code> and <code>--include-easyblocks-from-pr</code> 25821 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3311">#3311</a>)</li> 25822<li>also escape backslashes in <code>quote_py_str()</code> 25823 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3386">#3386</a>)</li> 25824<li>use one argument <code>module swap</code> statements in Tcl modulefiles 25825 (required by Modules 4.2.3+) 25826 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3397">#3397</a>)</li> 25827<li>fix copying of (non-existing) file with <code>apply_patch</code> 25828 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3400">#3400</a>)</li> 25829<li>create symlink from <code>lib64</code> to <code>lib</code> subdir in installation 25830 directories to avoid that GCC prefers <code>/lib64</code> system 25831 directories 25832 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3401">#3401</a>)</li> 25833<li>fix default value for <code>lib64_fallback_sanity_check</code> build option 25834 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3402">#3402</a>)</li> 25835<li>correctly determine commit status in <code>--merge-pr</code> 25836 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3406">#3406</a>)</li> 25837<li>stop installing ccache wrapper for Fortran compiler 25838 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3409">#3409</a>)</li> 25839<li>fix issues with applying PR patch in <code>--from-pr</code> 25840 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3414">#3414</a>)</li> 25841<li>make <code>RPATH</code> wrapper script more robust by using 25842 <code>python -E -s -S</code> to run <code>rpath_args.py</code> 25843 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3422">#3422</a>)</li> 25844<li>don't inject <code>-Wl,-rpath</code> options when <code>-x c++-header</code> compiler 25845 option is used 25846 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3424">#3424</a>)</li> 25847<li>fix lack of <code>-mno-recip</code> on aarch64 by tweaking GCC options used 25848 when <code>precise</code> toolchain option is enabled 25849 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3425">#3425</a>)</li> 25850<li>make sure <code>self.start_dir</code> is set in <code>ExtensionEasyBlock</code> 25851 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3426">#3426</a>, 25852 <a href="https://github.com/easybuilders/easybuild-framework/pull/3435">#3435</a>)</li> 25853<li>exclude local variables from typo check in easyconfig files 25854 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3427">#3427</a>)</li> 25855</ul> 25856</li> 25857<li>other changes:<ul> 25858<li>stick to cryptography 2.9.2 when using Python 2.7 to avoid 25859 broken test suite in CI 25860 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3392">#3392</a>)</li> 25861<li>automatically enable <code>--ignore-locks</code> with <code>--fetch</code> 25862 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3404">#3404</a>)</li> 25863<li>switch to status badge based on tests run in GitHub Actions CI 25864 in README 25865 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3415">#3415</a>)</li> 25866<li>make <code>flake8</code> code style checks pass 25867 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3416">#3416</a>, 25868 <a href="https://github.com/easybuilders/easybuild-framework/pull/3417">#3417</a>)</li> 25869<li>limit Travis to only test with Python 2.6 + Lmod 7 25870 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3418">#3418</a>)</li> 25871<li>ignore deprecation warning raised for cryptography when using 25872 Python 3.5 produced by output of test suite 25873 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3423">#3423</a>)</li> 25874</ul> 25875</li> 25876</ul> 25877<p><strong>easyblocks</strong></p> 25878<ul> 25879<li>2 new software-specific easyblocks:<ul> 25880<li>pybind11 25881 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2115">#2115</a>), 25882 PyTorch 25883 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2104">#2104</a>)</li> 25884</ul> 25885</li> 25886<li>minor enhancements, including:<ul> 25887<li>update MATLAB easyblock to use new binary installer for versions 25888 >= 2020a 25889 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2058">#2058</a>)</li> 25890<li>
25890add <code>use_pip_requirement</code> custom easyconfig parameter to 25891 PythonPackage easyblock to allow providing a requirements file 25892 to the <code>pip</code> command, as a source 25893 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2064">#2064</a>)</li> 25894<li>update CP2K easyblock for recent versions (>= 7.0) 25895 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2069">#2069</a>)</li> 25896<li>add <code>multi_deps</code> support into custom easyblock for QScintilla 25897 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2077">#2077</a>)</li> 25898<li>update Mothur easyblock for v1.44.0 and higher 25899 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2084">#2084</a>)</li> 25900<li>update MotionCor2 easyblock to add support for v1.3.2 25901 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2100">#2100</a>)</li> 25902<li>update Tinker easyblock to handle skipping of tests depending on 25903 version and link with <code>fftw_omp</code> 25904 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2102">#2102</a>)</li> 25905<li>launch test & sanity check commands through <code>mpirun</code> for 25906 netcdf4-python if MPI support is enabled 25907 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2106">#2106</a>)</li> 25908<li>check for installation of pip & setuptools in Python 3.4+ 25909 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2108">#2108</a>)</li> 25910<li>update QuantumESPRESSO easyblock to support version 6.6 25911 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2112">#2112</a>)</li> 25912<li>allow NAMD to be built on POWER, and also use the CUDA arch info 25913 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2113">#2113</a>, 25914 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2123">#2123</a>)</li> 25915<li>update Libint easyblock for versions >= 2.6.0 + add custom 25916 easyconfig parameter to enable Fortran support 25917 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2116">#2116</a>)</li> 25918<li>update TensorFlow easyblock to use system/EasyBuild installed 25919 libraries 25920 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2117">#2117</a>, 25921 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2165">#2165</a>, 25922 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2163">#2163</a>, 25923 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2172">#2172</a>)</li> 25924<li>add support in NAMD easyblock to pass additional C++ compiler 25925 options for building Charm++ component with + wrap them in 25926 single quotes 25927 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2118">#2118</a>)</li> 25928<li>automatically add required <code>-G Ninja</code> option when using 25929 CMakeNinja easyblock + add <code>generator</code> custom easyconfig 25930 parameter for CMakeMake 25931 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2120">#2120</a>)</li> 25932<li>make several easyblocks aware of <code>--sysroot</code> EasyBuild 25933 configuration option: binutils 25934 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2147">#2147</a>, 25935 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2159">#2159</a>), 25936 CMakeMake 25937 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2152">#2152</a>), 25938 GCC 25939 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2143">#2143</a>), 25940 Perl 25941 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2142">#2142</a>), 25942 Python 25943 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2143">#2148</a>, 25944 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2149">#2149</a>)</li> 25945<li>make Mesa easyblock aware of aarch64 25946 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2153">#2153</a>)</li> 25947<li>enhance sanity check in custom Doxygen easyblock to catch broken 25948 installation 25949 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2171">#2171</a>)</li> 25950</ul> 25951</li> 25952<li>various bug fixes, including:<ul> 25953<li>make TensorFlow easyblock ignore the <code>PKG_REVISION</code> identifier 25954 if NCCL version if it exists 25955 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2085">#2085</a>)</li> 25956<li>remove version check against the <code>version.txt</code> file in CUDA 25957 easyblock 25958 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2097">#2097</a>)</li> 25959<li>
25959add <code>lib</code> symlink in tbb installation directory when building 25960 from source 25961 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2103">#2103</a>)</li> 25962<li>handle GNUInstallDirs special cases in CMakeMake easyblock 25963 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2105">#2105</a>, 25964 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2124">#2124</a>)</li> 25965<li>patch ELPA's <code>manual_cpp</code> script to fix hardcoded 25966 <code>/usr/bin/python</code> 25967 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2107">#2107</a>)</li> 25968<li>make TensorFlow easyblock also set <code>$GCC_HOST_COMPILER_PREFIX</code> 25969 to specify binutils location 25970 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2110">#2110</a>)</li> 25971<li>ensure stand-alone Python package being installed is in view 25972 when running <code>pip check</code> by loading fake module first 25973 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2114">#2114</a>)</li> 25974<li>be more patient when running interactive configure script for 25975 WRF 25976 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2119">#2119</a>)</li> 25977<li>make sure <code>self.start_dir</code> is set to a full path before 25978 constructing installation command in RPackage easyblock 25979 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2125">#2125</a>)</li> 25980<li>correctly check whether <code>modinc</code> easyconfig parameter is set to 25981 <code>True</code> in CP2K easyblock 25982 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2138">#2138</a>)</li> 25983<li>update PSI easyblock to correctly find Python and enable 25984 PCMSolver/CheMPS2 25985 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2141">#2141</a>)</li> 25986<li>fix running GROMACS tests when using <code>eb --rpath</code> 25987 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2144">#2144</a>, 25988 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2154">#2154</a>)</li> 25989<li>remove existing Python installation directory if both 25990 <code>eb --rpath</code> and <code>--enable-optimizations</code> configuration option 25991 are used 25992 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2146">#2146</a>)</li> 25993<li>ensure <code>libQt5Core.so</code> is compatible with older Linux kernels by 25994 disabling <code>renameat2</code> and <code>getentropy</code> features 25995 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2151">#2151</a>)</li> 25996<li>solve issue where pybind11 picks up on the system Python instead 25997 of one provided by a module 25998 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2158">#2158</a>)</li> 25999<li>fix Qt5 easyblock to support installation on Arm/aarch64 26000 (requires platform to be <code>linux-g++</code>) 26001 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2160">#2160</a>)</li> 26002<li>fix OpenFOAM easyblock to support installation on Arm/aarch64 26003 systems 26004 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2162">#2162</a>)</li> 26005<li>explicitly enable/disable CUDA options in PyTorch easyblock + 26006 fix download check in sanity check + fix for disabling of 26007 *NNPACK on POWER systems 26008 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2164">#2164</a>)</li> 26009<li>fix sanity check in Mathematica easyblock for 11.x versions 26010 older than 11.3 26011 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2168">#2168</a>)</li> 26012<li>unset <code>$COLUMNS</code> if it is set to <code>0</code> before running Perl's 26013 configure script 26014 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2169">#2169</a>)</li> 26015</ul> 26016</li> 26017<li>other changes:<ul> 26018<li>filter out Python in SLEPc configure 26019 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2101">#2101</a>)</li> 26020<li>switch to status badge based on tests run in GitHub Actions CI 26021 in README 26022 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2126">#2126</a>)</li> 26023<li>fix code style issues to make <code>flake8</code> checks pass 26024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2128">#2128</a> - 26025 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2137">#2137</a>, 26026 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2140">#2140</a>, 26027 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2145">#2145</a>, 26028 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2155">#2155</a>)</li> 26029<li>limit test configurations in Travis CI to only Python 2.6 26030 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2139">#2139</a>)</li> 26031</ul> 26032</li> 26033</ul> 26034<p><strong>easyconfigs</strong></p> 26035<ul> 26036<li>added easyconfigs for 2 new toolchains:<ul> 26037<li>gomkl/2020a and iomkl/2020a 26038 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11036">#11036</a>)</li> 26039</ul> 26040</li> 26041<li>
26041added example easyconfig files for 49 new software packages:<ul> 26042<li>almosthere 26043 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11152">#11152</a>), 26044 arcasHLA 26045 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10867">#10867</a>), 26046 BioPP 26047 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11113">#11113</a>), 26048 Bracken 26049 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10829">#10829</a>), 26050 BUFRLIB 26051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11140">#11140</a>), 26052 Calib 26053 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11111">#11111</a>), 26054 CellRanger-ATAC 26055 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11186">#11186</a>), 26056 edlib 26057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10470">#10470</a>, 26058 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11246">#11246</a>), 26059 flatbuffers 26060 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11109">#11109</a>), 26061 gengetopt 26062 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11117">#11117</a>), 26063 graphite2 26064 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11168">#11168</a>), 26065 HeFFTe 26066 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10990">#10990</a>), 26067 hierfstat 26068 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11249">#11249</a>), 26069 immunedeconv 26070 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11136">#11136</a>), 26071 ioapi 26072 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10959">#10959</a>), 26073 itpp 26074 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10958">#10958</a>), 26075 LiBis 26076 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11059">#11059</a>), 26077 libosmium 26078 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11024">#11024</a>), 26079 limix-bgen 26080 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11152">#11152</a>), 26081 minibar 26082 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10470">#10470</a>, 26083 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11246">#11246</a>), 26084 misha 26085 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11127">#11127</a>), 26086 MOABS 26087 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10747">#10747</a>), 26088 moonjit 26089 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11163">#11163</a>), 26090 NGLess 26091 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11128">#11128</a>), 26092 nsync 26093 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11109">#11109</a>), 26094 openCARP 26095 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11117">#11117</a>), 26096 OpenForceField 26097 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11048">#11048</a>), 26098 OpenMMTools 26099 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11046">#11046</a>), 26100 OpenMS 26101 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10994">#10994</a>), 26102 PennCNV 26103 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10986">#10986</a>), 26104 plantcv 26105 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10968">#10968</a>), 26106 PlasmaPy 26107 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10732">#10732</a>), 26108 Portcullis 26109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11038">#11038</a>), 26110 PycURL 26111 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11169">#11169</a>), 26112 PyGEOS 26113 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11110">#11110</a>), 26114 pySCENIC 26115 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11115">#11115</a>), 26116 Reapr 26117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9296">#9296</a>), 26118 RnBeads 26119 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11142">#11142</a>), 26120 sf 26121 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11248">#11248</a>), 26122 SLiM 26123 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11172">#11172</a>), 26124 stars 26125 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11215">#11215</a>, 26126 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11248">#11248</a>), 26127 Sumo 26128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11071">#11071</a>), 26129 Telescope 26130 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10943">
26130#10943</a>), 26131 tensorflow-probability 26132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10312">#10312</a>), 26133 texlive 26134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11168">#11168</a>), 26135 tidymodels 26136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11010">#11010</a>), 26137 Trycycler 26138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11207">#11207</a>), 26139 umi4cPackage 26140 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11127">#11127</a>), 26141 variant_tools 26142 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11169">#11169</a>)</li> 26143</ul> 26144</li> 26145<li>added additional easyconfigs for various supported software 26146 packages, including:<ul> 26147<li>Bazel 3.4.1, Bonito 0.2.2, binutils 2.35, CP2K 7.1, Clang 26148 10.0.1, ccache 3.7.11, ctffind 4.1.14, datamash 1.5, ELPA 26149 2020.05.001, Emacs 26.3, Flye 2.8.1, GCC(core) 10.2.0, 26150 googletest 1.10.0, HDF 4.2.15, Horovod 0.19.5, imageio 2.9.0, 26151 JUBE 2.4.0, Julia 1.5.1, Kent_tools 401, Libint 2.6.0, libxsmm 26152 1.16.1, MDSplus 7.96.8, MDTraj 1.9.4, MariaDB 10.4.13, Meson 26153 0.55.1, MotionCor2 1.3.2, NAMD 2.14, NCO 4.9.3, OpenFOAM 8, 26154 OpenMPI 4.0.5, OptiX 6.5.0, Pandoc 2.10, Perl 5.32.0, PostgreSQL 26155 12.4, PyCUDA 2019.1.2, PyFR 1.9.0, PyTorch 1.6.0, PyZMQ 18.1.1, 26156 patchelf 0.12, pocl 1.5, pycocotools 2.0.1, pyproj 2.6.1.post1, 26157 QuantumESPRESSO 6.6, RDKit 2020.03.3, rgdal 1.5, Salmon 1.3.0, 26158 Spark 3.0.0, scikit-image 0.17.1, scipy 1.4.1, snpEff 5.0, sympy 26159 1.6.2, TINKER 8.7.2, tqdm 4.47.0, Unicycler 0.4.8, VMD 1.9.4a43</li> 26160</ul> 26161</li> 26162<li>minor enhancements, including:<ul> 26163<li>also build Python libraries for ParaView 5.8.0 26164 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10927">#10927</a>)</li> 26165<li>add extensions to recent Bioconductor easyconfigs: 26166 FlowSorted.Blood.EPIC 26167 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11021">#11021</a>), 26168 DRIMSeq + stageR 26169 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11053">#11053</a>)</li> 26170<li>add extensions to recent R easyconfigs: AICcmodavg + biomod2 26171 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11030">#11030</a>), 26172 qqman 26173 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11052">#11052</a>), 26174 poLCA 26175 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11081">#11081</a>), 26176 coxed 26177 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11094">#11094</a>), 26178 testit + data.tree 26179 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11135">#11135</a>), 26180 celestial + fasterize 26181 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11206">#11206</a>)</li> 26182<li>add Config::Simple extension to Perl 5.30.x easyconfigs 26183 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11051">#11051</a>)</li> 26184<li>update TensorFlow v2.1.0 26185 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11109">#11109</a>) 26186 and v2.0.0 26187 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11233">#11233</a>) 26188 easyconfigs to provide more dependencies via EasyBuild</li> 26189<li>add CUDA compute capabilities to torchvision-0.5.0 26190 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11241">#11241</a>)</li> 26191</ul> 26192</li> 26193<li>various bug fixes, including:<ul> 26194<li>patch to fix exporting images with PyQtGraph v0.10.0 26195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10848">#10848</a>)</li> 26196<li>add missing Python dependency to PETSc 3.11.1 26197 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10907">#10907</a>) 26198 and PETSc 3.12.x 26199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10908">#10908</a>) 26200 easyconfigs</li> 26201<li>use CMakeMake easyblock for installing magma to avoid C++11 26202 related failures on POWER 26203 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10929">#10929</a>)</li> 26204<li>fix source URL for Graphviz v2.40.1 26205 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10944">#10944</a>)</li> 26206<li>fix <code>lapack.h</code> for use with C++ in OpenBLAS 0.3.9 easyconfigs 26207 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10960">#10960</a>)</li> 26208<li>
26208add missing build dep on M4 for 2019b versions of netCDF-Fortran 26209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10972">#10972</a>)</li> 26210<li>update easyconfig for PyTorch 1.4 to use custom easyblock and 26211 run on POWER 26212 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11000">#11000</a>)</li> 26213<li>create symlinks to incorrectly named directories in 26214 OpenBabel-3.1.1 so <code>$BABEL_LIBDIR</code> and <code>$BABEL_DATADIR</code> work 26215 properly 26216 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11004">#11004</a>)</li> 26217<li>add missing Python build dep to recent ELPA easyconfigs 26218 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11011">#11011</a>)</li> 26219<li>use <code>is_generic_easyblock</code> from filetools in easyconfigs test 26220 suite 26221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11020">#11020</a>)</li> 26222<li>fix sources in Portcullis v1.2.2 easyconfigs 26223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11038">#11038</a>)</li> 26224<li>add patch for FFTW 3.3.8 to avoid use of <code>-no-gcc</code> when building 26225 with Intel compilers, to fix installation on CentOS 8 (cfr. 26226 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10932">#10932</a>) 26227 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11050">#11050</a>)</li> 26228<li>add missing Python build dep for BEDTools 2.29.x 26229 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11054">#11054</a>)</li> 26230<li>add missing SciPy-bundle and Kent_tools (for bedPartition 26231 command) dependencies to FLAIR 26232 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11057">#11057</a>)</li> 26233<li>add patch to fix bug in LiBiS v20200428 easyconfig 26234 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11059">#11059</a>)</li> 26235<li>use FFTW provided via EasyBuild for ScaFaCoS 26236 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11060">#11060</a>)</li> 26237<li>fix undefined reference to <code>qfloat16::mantissatable</code> in Qt5.14.1 26238 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11063">#11063</a>)</li> 26239<li>add alternative checksum for rstantools 2.0.0 extension 26240 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11081">#11081</a>)</li> 26241<li>update checksums for R 3.6.0 packages and add patch for ppc 26242 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11088">#11088</a>)</li> 26243<li>install scikit-learn 0.23.1 as a bundle and include required 26244 threadpoolctl extension 26245 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11089">#11089</a>)</li> 26246<li>update pybind11 easyconfigs to use custom easyblock to install 26247 with pip 26248 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11091">#11091</a>)</li> 26249<li>add recent six as extension to archspec installed on top of 26250 Python 3.7.4 26251 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11092">#11092</a>)</li> 26252<li>add missing Seaborn dependency to LiBis easyconfig 26253 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11095">#11095</a>)</li> 26254<li>add missing dependencies for OpenPIV + switch to PythonBundle 26255 easyblock and include progressbar2 as extension 26256 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11096">#11096</a>)</li> 26257<li>add missing argparse dep to TEtranscripts easyconfig 26258 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11097">#11097</a>)</li> 26259<li>add missing pkg-config build dep in Octave 5.1.0 easyconfigs 26260 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11100">#11100</a>)</li> 26261<li>don't statically link MUSCLE, to avoid requiring that 26262 glibc-static is installed in OS 26263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11102">#11102</a>)</li> 26264<li>add missing pkg-config build dependency in recent 26265 R-bundle-Bioconductor easyconfigs 26266 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11104">#11104</a>)</li> 26267<li>
26267add patch to h5py 2.8.0 26268 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11119">#11119</a>) 26269 and 2.9.0 26270 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11118">#11118</a>) 26271 easyconfigs to avoid MPI_Init on <code>import h5py</code></li> 26272<li>add patch to support libbfd 2.34 API change in Score-P 6.0 26273 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11123">#11123</a>)</li> 26274<li>use pip to install protobuf-python in 2019b toolchain (requires 26275 re-downloading source tarball!) 26276 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11143">#11143</a>, 26277 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11260">#11260</a>)</li> 26278<li>add missing Keras-Applications extension to TensorFlow 2.2.0 26279 easyconfigs with <code>foss*/2019b</code> toolchain 26280 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11156">#11156</a>)</li> 26281<li>add missing pocl dependency in R 3.6.0 26282 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11157">#11157</a>)</li> 26283<li>update Meson build dep to 0.55.1 for GLib, X11, Mesa & co to fix 26284 aggressive RPATH stripping 26285 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11178">#11178</a>)</li> 26286<li>disable generating of man pages in recent libdrm easyconfigs to 26287 avoid installation failure if docbook-xsl is not installed 26288 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11182">#11182</a>)</li> 26289<li>add fontconfig and bzip2 as direct dependencies for Qt5 to fix 26290 installation with <code>--rpath</code> 26291 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11183">#11183</a>)</li> 26292<li>fix failing <code>make check</code> for MPFR 4.x 26293 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11187">#11187</a>) 26294 and GMP 26295 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11188">#11188</a>) 26296 when installing with <code>eb --rpath</code></li> 26297<li>add pkg-config as a build dependency for libglvnd 26298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11189">#11189</a>)</li> 26299<li>add missing libiconv dep in recent Doxygen easyconfigs 26300 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11191">#11191</a>, 26301 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11257">#11257</a>)</li> 26302<li>enhance Java/11 wrapper to also support for aarch64/Arm 26303 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11192">#11192</a>)</li> 26304<li>add pkg-config as a build dependency to Ghostscript 9.52, needed 26305 on aarch64/arm 26306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11194">#11194</a>)</li> 26307<li>add patch for pycrypto extension in recent Python easyconfigs to 26308 remove hardcoded <code>/usr/include</code> which causes problems when 26309 <code>eb --sysroot</code> is used 26310 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11202">#11202</a>)</li> 26311<li>fix installation of R v3.6.3 and v4.0.0 with foss/2020a on Arm 26312 (aarch64) 26313 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11213">#11213</a>)</li> 26314<li>update PyTorch 1.4 easyconfigs to use custom easyblock (and do 26315 less downloading during installations) 26316 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11219">#11219</a>)</li> 26317</ul> 26318</li> 26319<li>other changes:<ul> 26320<li>don't require custom <code>sanity_check_paths</code> for CUDA bundle 26321 easyconfigs 26322 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10936">#10936</a>)</li> 26323<li>move intervaltree and sortedcontainers to main Python 26324 easyconfigs 26325 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10969">#10969</a>, 26326 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10970">#10970</a>)</li> 26327<li>disable qtwayland in Qt5 v5.14.1 26328 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11107">#11107</a>)</li> 26329<li>remove mklml (small MKL) from PyTorch 1.3.1 and 1.4.0 26330 easyconfigs 26331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11019">#11019</a>)</li> 26332<li>
26332use pip to install h5py 2.10.0 26333 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11044">#11044</a>)</li> 26334<li>stop testing easyconfig PRs with Travis, only use GitHub Actions 26335 from now on 26336 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11008">#11008</a>, 26337 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11055">#11055</a>)</li> 26338<li>switch to Kent_tools built from source as dep for FusionCatcher 26339 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11057">#11057</a>)</li> 26340<li>fall back to using PR target branch when determining "merge 26341 base" between PR branch & target branch fails in test suite 26342 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11069">#11069</a>)</li> 26343<li>rename gtest to googletest 26344 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11082">#11082</a>)</li> 26345<li>rename sdsl-lite to SDSL (to use one single name) 26346 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11084">#11084</a>)</li> 26347<li>stop using <code>remove_usr_bin</code> patch in TensorFlow easyconfig, no 26348 longer required with updated TensorFlow easyblock 26349 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11087">#11087</a>)</li> 26350<li>extend timeout for libxc-4.3.4 to avoid failing tests 26351 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11126">#11126</a>)</li> 26352<li>move GitHub Actions status badge to top of README 26353 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11138">#11138</a>)</li> 26354<li>fix code style issues in test 26355 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11146">#11146</a>)</li> 26356<li>enable <code>flake8</code> on CI and fix issues 26357 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11147">#11147</a>)</li> 26358<li>prefer gc GitHub site for source downloads 26359 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11208">#11208</a>)</li> 26360<li>prefer <code>https</code> over <code>ftp</code> in <code>source_urls</code> of IgBLAST easyconfig 26361 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/11244">#11244</a>)</li> 26362</ul> 26363</li> 26364</ul> 26365<h2 id="release_notes_eb422">EasyBuild v4.2.2 (July 8th 2020)<a class="headerlink" href="#release_notes_eb422" title="Permanent link">¶</a></h2> 26366<p>bugfix/update release</p> 26367<p><strong>framework</strong></p> 26368<ul> 26369<li>various enhancements, including:<ul> 26370<li>add support for using <code>sources</code> and <code>git_config</code> for extensions 26371 in <code>exts_list</code> 26372 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3294">#3294</a>)</li> 26373<li>add support for software minver template (like <code>%(pyminver)s</code>, 26374 etc.) 26375 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3344">#3344</a>, 26376 <a href="https://github.com/easybuilders/easybuild-framework/pull/3345">#3345</a>)</li> 26377<li>add support for updating dictionary or tuple easyconfig 26378 parameters with <code>self.cfg.update</code> 26379 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3356">#3356</a>)</li> 26380</ul> 26381</li> 26382<li>various bug fixes, including:<ul> 26383<li>fix crash in <code>--avail-easyconfig-constants</code> when using 26384 <code>--output-format=rst</code> + ensure sorted output 26385 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3341">#3341</a>)</li> 26386<li>always take into account <code>builddependencies</code> when generating 26387 template values, also when we're not iterating over 26388 <code>builddependencies</code> 26389 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3346">#3346</a>)</li> 26390<li>fix running command as <code>easybuild</code> user in generated Singularity 26391 definition file 26392 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3347">#3347</a>)</li> 26393<li>allow ignoring <code>versionsuffix</code> in <code>--try-update-deps</code> 26394 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3350">#3350</a>, 26395 <a href="https://github.com/easybuilders/easybuild-framework/pull/3353">#3353</a>)</li> 26396<li>retain order of paths when generating <code>prepend_path</code> statements 26397 for module file (don't sort them alphabetically) 26398 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3367">#3367</a>)</li> 26399<li>also put easyblocks used by extensions in <code>reprod</code> directory 26400 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3375">#3375</a>)</li> 26401<li>also copy template values in <code>EasyConfig.copy</code> method to ensure 26402 they are defined when installing extensions 26403 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3377">#3377</a>)</li> 26404<li>skip lines that start with <code>module-version</code> when determining 26405 whether a module exists in <code>ModulesTool.exist</code> 26406 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3379">#3379</a>)</li> 26407</ul> 26408</li> 26409</ul> 26410<p><strong>easyblocks</strong></p> 26411<ul> 26412<li>3 new software-specific easyblocks:<ul> 26413<li>LLVM 26414 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2065">#2065</a>), 26415 Scipion 26416 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1847">#1847</a>), 26417 XALT 26418 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1942">#1942</a>)</li> 26419</ul> 26420</li> 26421<li>minor enhancements, including:<ul> 26422<li>use <code>wclean -platform</code> instead of <code>wcleanPlatform</code> for OpenFOAM 26423 v2006 & newer 26424 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2088">#2088</a>)</li> 26425</ul> 26426</li> 26427<li>various bug fixes, including:<ul> 26428<li>only build OpenCV with IPP support on x86_64 systems 26429 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2056">#2056</a>)</li> 26430<li>make sure <code>CFLAGS</code> and <code>MYCFLAGS</code> are used in Lua easyblock 26431 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2062">#2062</a>)</li> 26432<li>also accept <code>exist_lic</code> as valid value for <code>license_file</code> in 26433 IntelBase easyblock 26434 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2067">#2067</a>)</li> 26435<li>fix minor bug in shared libs handling and correctly setup 26436 SuiteSparse variables in Trilinos easyblock 26437 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2071">#2071</a>)</li> 26438<li>make sure <code>PythonBundle</code> uses correct <code>python</code> command in 26439 extensions filter + also add <code>lib64/python*/site-packages</code> to 26440 <code>$PYTHONPATH</code> (if it exists) 26441 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2075">#2075</a>, 26442 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2081">#2081</a>)</li> 26443<li>fix build environment for WRF by patching shebang in compile 26444 script 26445 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2079">#2079</a>)</li> 26446<li>fix order of <code>intel64/lib</code> paths in generated module for impi 26447 (and drop <code>intel64/lib/release_mt</code>) 26448 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2080">#2080</a>)</li> 26449<li>set <code>$XDG_CACHE_HOME</code> to avoid abuse of <code>$HOME/.cache/pip</code> when 26450 installing DOLFIN 26451 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2082">#2082</a>)</li> 26452<li>make VMD easyblock Python 3 compatible 26453 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2083">#2083</a>)</li> 26454<li>rename include-fixed subdirectory in GCC installation to avoid 26455 problems after OS upgrade 26456 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2087">#2087</a>, 26457 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2093">#2093</a>, 26458 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2094">#2094</a>)</li> 26459<li>use glob pattern to determine name of Mathematica installation 26460 script 26461 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2089">#2089</a>)</li> 26462<li>use <code>mpirun</code> for sanity check commands in LAMMPS easyblock 26463 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2096">#2096</a>)</li> 26464</ul> 26465</li> 26466</ul> 26467<p><strong>easyconfigs</strong></p> 26468<ul> 26469<li>added easyconfigs for 2 new toolchains:<ul> 26470<li>golf/2020a 26471 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10672">
26471#10672</a>)</li> 26472<li>intel/2020.06, based on intel/2020a but with impi 2018 update 5 26473 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10864">#10864</a>)</li> 26474</ul> 26475</li> 26476<li>added example easyconfig files for 36 new software packages:<ul> 26477<li>AmrPlusPlus 26478 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9919">#9919</a>), 26479 arrow 26480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10882">#10882</a>), 26481 attrdict 26482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10827">#10827</a>), 26483 Cartopy 26484 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10685">#10685</a>), 26485 dm-tree 26486 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10775">#10775</a>), 26487 dotNET-SDK 26488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10661">#10661</a>), 26489 FLAIR 26490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10860">#10860</a>), 26491 fastqsplitter 26492 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10706">#10706</a>), 26493 GLFW 26494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10709">#10709</a>), 26495 git-extras 26496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10440">#10440</a>), 26497 hl7apy 26498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10728">#10728</a>), 26499 hyperopt 26500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10735">#10735</a>), 26501 IgBLAST 26502 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10889">#10889</a>), 26503 IntelDAAL 26504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9848">#9848</a>), 26505 ichorCNA 26506 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10595">#10595</a>), 26507 MARS 26508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10691">#10691</a>), 26509 MITObim 26510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10897">#10897</a>), 26511 MUST 26512 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10849">#10849</a>), 26513 mhcnuggets 26514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9743">#9743</a>), 26515 PAUP 26516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10830">#10830</a>), 26517 Percolator 26518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10665">#10665</a>), 26519 PyBerny 26520 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10885">#10885</a>), 26521 poetry 26522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10884">#10884</a>), 26523 pycocotools 26524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10806">#10806</a>), 26525 python-hl7 26526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10673">#10673</a>), 26527 SHAPEIT4 26528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10814">#10814</a>), 26529 SYMPHONY 26530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10058">#10058</a>), 26531 SunPy 26532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10676">#10676</a>), 26533 sdsl-lite 26534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10691">#10691</a>), 26535 TEtranscripts 26536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10909">#10909</a>, 26537 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10921">#10921</a>), 26538 Tombo 26539 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10646">#10646</a>), 26540 tensorboardX 26541 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10774">#10774</a>), 26542 Unidecode 26543 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10828">#10828</a>), 26544 WHAM 26545 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10736">#10736</a>), 26546 XALT 26547 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9792">#9792</a>), 26548 Xvfb 26549 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10512">#10512</a>)</li> 26550</ul> 26551</li> 26552<li>
26552added additional easyconfigs for various supported software 26553 packages, including:<ul> 26554<li>Armadillo 9.900.1, astropy 4.0.1, BLAST+ 2.10.1, BioPerl 1.7.7, 26555 Blitz++ 1.0.2, Bonito 0.2.0, bokeh 2.0.2, CFITSIO 3.48, CGAL 26556 4.14.3, CLHEP 2.4.1.3, cutadapt 2.10, dask 2.18.1, Elk 6.3.2, 26557 GATE 9.0, GLM 0.9.9.8, GRASS 7.8.3, Geant4 10.6, geopandas 26558 0.8.0, giflib 5.2.1, HDF5 1.12.0, HISAT2 2.2.0, Hadoop 2.10.0, 26559 IPython 7.15.0, inferCNV 1.2.1, Julia 1.4.2, LibSoup 2.70.0, 26560 MATIO 1.5.17, MRtrix 3.0.0, Mathematica 12.1.1 MultiQC 1.9, NGS 26561 2.10.5, NiBabel 3.1.0, Nipype 1.4.2, ncbi-vdb 20.10.7, numba 26562 0.50.0, OpenBabel 3.1.1, OpenFOAM v2006, PDT 3.25.1, PRSice 26563 2.3.1, ParaView 5.8.0, ParmEd 3.2.0, PyQt5 5.13.2, Pysam 26564 0.16.0.1, parallel 20200522, plotly.py 4.8.1, pybedtools 0.8.1, 26565 ROOT 6.20.04, ReFrame 3.0, Roary 3.13.0, rjags 4-10, rstudio 26566 1.3.959, SPAdes 3.14.1, SRA-Toolkit 2.10.8, Saxon-HE 9.9.1.7, 26567 Seaborn 0.10.1, Seurat 3.1.5, SimPEG 0.14.1, Spark 2.4.5, 26568 StringTie 2.1.3, scikit-allel 1.2.1, scikit-learn 0.23.1, snpEff 26569 4.3t, Valgrind 3.16.1, VarScan 2.4.4, vsc-mympirun 5.1.0, 26570 WebKitGTK+ 2.27.4, wxPython 4.0.7.post2, zarr 2.4.0</li> 26571</ul> 26572</li> 26573<li>minor enhancements, including:<ul> 26574<li>add extensions to R 4.0.0 easyconfig: drgee + stdReg 26575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10833">#10833</a>), 26576 copCAR 26577 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10911">#10911</a>), 26578 ngspatial 26579 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10913">#10913</a>), 26580 drugCombo 26581 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10914">#10914</a>)</li> 26582<li>add extensions to R-bundle-Bioconductor 3.11 easyconfig: 26583 BSgenome.Cfamiliaris.UCSC.canFam3 26584 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10840">#10840</a>), 26585 SingleR 26586 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10904">#10904</a>)</li> 26587<li>include extra extension and support for MPI in MAFFT v7.453 and 26588 v7.470 26589 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10853">#10853</a>)</li> 26590<li>add Array::Transpose to Perl 26591 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10878">#10878</a>)</li> 26592</ul> 26593</li> 26594<li>various bug fixes, including:<ul> 26595<li>fix dependencies and configuration of CoinUtils ecosystem 26596 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10450">#10450</a>)</li> 26597<li>fix Togl configure patch so that it completely ignores 26598 <code>TCL_SRC_DIR</code> and <code>TK_SRC_DIR</code> 26599 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10662">#10662</a>)</li> 26600<li>change Xerces-C++ to official CMakeMake build (fixes missing 26601 links to curl) 26602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10664">#10664</a>)</li> 26603<li>add <code>-fPIC</code> to <code>toolchainopts</code> in easyconfig for Lua 5.3.5 with 26604 system toolchain 26605 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10671">#10671</a>)</li> 26606<li>remove hardcoded X86 target in LLVM easyconfigs 26607 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10677">#10677</a>)</li> 26608<li>switch to https <code>homepage</code> and <code>source_urls</code> in libGLU 26609 easyconfigs 26610 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10686">#10686</a>)</li> 26611<li>add patch for h5py 2.10.0 to avoid triggering <code>MPI_Init</code> at 26612 import 26613 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10687">#10687</a>)</li> 26614<li>add alternative checksum for pkgmaker, doRNG, cobs extension in 26615 R 3.6.0 easyconfigs 26616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10692">#10692</a>)</li> 26617<li>update UDUNITS <code>source_urls</code> to https sources 26618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10693">#10693</a>)</li> 26619<li>add missing M4 to netCDF-Fortran easyconfigs using 2020a 26620 toolchain 26621 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10695">#10695</a>, 26622 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10697">#10697</a>)</li> 26623<li>
26623add Rgraphviz patch to R-bundle-Bioconductor easyconfigs 26624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10710">#10710</a>)</li> 26625<li>add M4 builddependency to SuiteSparse 2019b easyconfigs 26626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10720">#10720</a>)</li> 26627<li>make sure WHAM is built with correct compiler 26628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10736">#10736</a>)</li> 26629<li>define <code>MAX_JOBS</code> in easyconfigs of PyTorch from v1.1.0 to 26630 v1.4.0 26631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10772">#10772</a>)</li> 26632<li>add dm-tree and lz4 as dependencies to Ray v0.8.4 26633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10775">#10775</a>)</li> 26634<li>fix source URL in recent ant easyconfigs 26635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10790">#10790</a>)</li> 26636<li>bump versions of GO.gb/org.Hs.eg.db/PFAM.db extensions in 26637 Bioconductor 3.11 bundle, since sources for old versions have 26638 disappeared 26639 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10791">#10791</a>)</li> 26640<li>add patch to Armadillo easyconfigs using the foss toolchain to 26641 prevent it from picking up MKL if installed system-wide 26642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10812">#10812</a>)</li> 26643<li>add missing kerneltree extension in FLAIR easyconfig 26644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10860">#10860</a>)</li> 26645<li>fix source URLs in Eigen 3.2.<em> 26646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10872">#10872</a>) 26647 and 3.3.</em> 26648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10869">#10869</a>) 26649 easyconfigs</li> 26650<li>refer to issue in GitHub repo in configparser patch, since 26651 Bitbucket repo is disappearing 26652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10873">#10873</a>)</li> 26653<li>switch to github.com source URL for MetaPhlAn 26654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10874">#10874</a>)</li> 26655<li>switch to GitHub sources for ScientificPython 2.9.4 26656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10875">#10875</a>)</li> 26657<li>switch to GitHub source URL for HPDBSCAN 26658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10876">#10876</a>)</li> 26659<li>download x265 3.2/3.3 sources from 26660 <code>bitbucket.org/multicoreware/x265_git</code> 26661 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10905">#10905</a>)</li> 26662<li>fix download URL for libatomic in gc 7.6.12 easyconfigs 26663 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10915">#10915</a>)</li> 26664<li>fix <code>sanity_check_paths</code> in CFITSIO-3.48-GCCcore-9.3.0.eb 26665 easyconfig 26666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10917">#10917</a>)</li> 26667<li>add missing dependencies for geopandas 0.7.0 26668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10923">#10923</a>)</li> 26669</ul> 26670</li> 26671<li>other changes:<ul> 26672<li>rename OpenPyXL 2.6.4 easyconfig to openpyxl 26673 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10916">#10916</a>)</li> 26674</ul> 26675</li> 26676</ul> 26677<h2 id="release_notes_eb421">EasyBuild v4.2.1 (May 20th 2020)<a class="headerlink" href="#release_notes_eb421" title="Permanent link">¶</a></h2> 26678<p>bugfix/update release</p> 26679<p><strong>framework</strong></p> 26680<ul> 26681<li>various enhancements, including:<ul> 26682<li>also mention CPU architecture (x86_64, POWER) in comment for 26683 test reports 26684 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3281">#3281</a>)</li> 26685<li>add support for enhancing existing sanity check in easyconfigs, 26686 as opposed to overwriting paths/commands 26687 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3288">#3288</a>)</li> 26688<li>clean up locks when EasyBuild session is cancelled with a signal 26689 like <code>SIGTERM</code> 26690 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3291">#3291</a>, 26691 <a href="https://github.com/easybuilders/easybuild-framework/pull/3321">#3321</a>)</li> 26692<li>
26692add <code>find_glob_pattern</code> function to <code>filetools</code> module 26693 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3297">#3297</a>)</li> 26694<li>add constants for common OS dependencies (<code>OS_PKG_IBVERBS_DEV</code>, 26695 <code>OS_PKG_OPENSSL_DEV</code>, ...) 26696 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3309">#3309</a>, 26697 <a href="https://github.com/easybuilders/easybuild-framework/pull/3334">#3334</a>)</li> 26698<li>flesh out <code>get_mpi_cmd_template</code> function from <code>Mpi.mpi_cmd_for</code> 26699 method 26700 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3312">#3312</a>)</li> 26701<li>add variable <code>moddependpaths</code> to specify extra <code>$MODULEPATH</code> 26702 entry to consider for loading dependency modules 26703 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3324">#3324</a>)</li> 26704<li>allow copying of tweaked easyconfigs when using <code>--try-*</code> with 26705 <code>--copy-ec</code> 26706 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3332">#3332</a>)</li> 26707</ul> 26708</li> 26709<li>various bug fixes, including:<ul> 26710<li>make <code>ModulesTool.exist</code> more robust w.r.t. module wrappers, 26711 aliases, defaults, etc. 26712 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3216">#3216</a>, 26713 <a href="https://github.com/easybuilders/easybuild-framework/pull/3337">#3337</a>)</li> 26714<li>clean up rst output of <code>--list-toolchains</code> 26715 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3246">#3246</a>)</li> 26716<li>cast CPU arch name provided by archspec to a regular string 26717 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3286">#3286</a>)</li> 26718<li>get <code>pr_title</code> and <code>pr_descr</code> build_options in 26719 <code>new_pr_from_branch</code> instead of <code>new_pr</code> (and commit_msg in 26720 both) 26721 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3298">#3298</a>)</li> 26722<li>make <code>pypi_source_urls</code> more robust by using <code>HTMLParser</code> rather 26723 than <code>xml.etree.ElementTree</code> 26724 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3303">#3303</a>, 26725 <a href="https://github.com/easybuilders/easybuild-framework/pull/3329">#3329</a>)</li> 26726<li>fix broken test for <code>--include-easyblocks-from-pr</code> 26727 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3304">#3304</a>)</li> 26728<li>don't use <code>distutils.dir_util</code> in <code>copy_dir</code> 26729 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3310">#3310</a>)</li> 26730<li>print trace message for sanity check command before running it 26731 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3316">#3316</a>)</li> 26732<li>fix problems with processing of easyconfigs using a Cray* 26733 toolchain when there are no actual external modules 26734 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3319">#3319</a>)</li> 26735<li>make <code>test_find_eb_script</code> more robust in case <code>$EB_SCRIPT_PATH</code> 26736 is already set 26737 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3320">#3320</a>)</li> 26738<li>fix several small problems with <code>--try-update-deps</code> 26739 (experimental feature) 26740 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3325">#3325</a>, 26741 <a href="https://github.com/easybuilders/easybuild-framework/pull/3326">#3326</a>, 26742 <a href="https://github.com/easybuilders/easybuild-framework/pull/3330">#3330</a>)</li> 26743<li>add <code>--disable-job</code> in <code>eb</code> command used in jobs, to prevent 26744 infinite job cycle 26745 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3328">#3328</a>)</li> 26746<li>avoid empty entries in <code>$LD_LIBRARY_PATH</code> and other path-like 26747 environment variables 26748 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3333">#3333</a>)</li> 26749</ul> 26750</li> 26751<li>other changes:<ul> 26752<li>fix code style issues in <code>easybuild.tools</code> + add <code>flake8</code> 26753 linting test 26754 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3282">#3282</a>)</li> 26755<li>introduce <code>contextmanager</code> for disabling templating and reduce 26756 resolving errors 26757 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3287">#3287</a>)</li> 26758<li>
26758add <code>change_into_dir</code> named argument to <code>extract_file</code> + print 26759 deprecation warning if it's not specified 26760 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3292">#3292</a>)</li> 26761<li>improve <code>install_eb_dep.sh</code> script to install EasyBuild 26762 dependencies in CI environment 26763 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3314">#3314</a>)</li> 26764</ul> 26765</li> 26766</ul> 26767<p><strong>easyblocks</strong></p> 26768<ul> 26769<li>add generic easyblock for installing Go packages: <code>GoPackage</code> 26770 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2042">#2042</a>)</li> 26771<li>minor enhancements, including:<ul> 26772<li>update <code>config.guess</code> for all R packages, required installing 26773 R + extensions on Linux/POWER systems 26774 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1949">#1949</a>)</li> 26775<li>add support for <code>preinstallopts</code> and install in subdirectory to 26776 <code>Tarball</code> generic easyblock 26777 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1989">#1989</a>, 26778 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2049">#2049</a>)</li> 26779<li>rewrite <code>GROMACS</code> easyblock to install all four variations 26780 (single/double precision, with/without MPI) in the same 26781 directory 26782 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1991">#1991</a>)</li> 26783<li>add custom <code>subdir_version</code> easyconfig parameter for FLUENT 26784 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2021">#2021</a>)</li> 26785<li>use updated <code>config.guess</code> in <code>GCC</code> easyblock 26786 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2033">#2033</a>, 26787 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2059">#2059</a>)</li> 26788<li>add extra question pattern to support installing CPLEX 12.10 26789 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2038">#2038</a>)</li> 26790<li>add support for building NWChem on top of external 26791 GlobalArrays + also define <code>$LAPACK_LIB</code> (required for NWChem 26792 7.x) 26793 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2043">#2043</a>)</li> 26794<li>execute minimal test in sanity check commands in <code>impi</code> 26795 easyblock 26796 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2045">#2045</a>)</li> 26797<li>update for <code>MotionCor2</code> easyblock for v1.3.1 26798 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2046">#2046</a>)</li> 26799<li>fixes + enhancements for <code>PETSc</code> easyblock 26800 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2048">#2048</a>)</li> 26801</ul> 26802</li> 26803<li>various bug fixes, including:<ul> 26804<li>use correct version in <code>ELPA</code> preprocessor flag used for 26805 QuantumESPRESSO v6.x 26806 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2027">#2027</a>)</li> 26807<li>generically find the arch folder and add top-level bin/lib 26808 symlinks in <code>PDT</code> & <code>TAU</code> easyblocks 26809 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2029">#2029</a>)</li> 26810<li>fix typo in <code>LAMMPS</code> easyblock preventing disabling the 26811 <code>USER-INTEL</code> package via <code>configopts</code> 26812 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2031">#2031</a>)</li> 26813<li>let <code>CMakeMake</code> remove <code>easybuild_obj</code> build directory if it 26814 already exists 26815 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2032">#2032</a>)</li> 26816<li>include own lib dir in <code>RPATH</code> before system lib dirs in 26817 <code>binutils</code> easyblock 26818 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2044">#2044</a>)</li> 26819<li>clean <code>$CPATH</code> before building ROOT to avoid clash between 26820 external LLVM loaded as a dependency and internal LLVM used by 26821 ROOT 26822 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2047">#2047</a>)</li> 26823<li>
26823don't let <code>extract_file</code> change directory in various easyblocks 26824 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2051">#2051</a>)</li> 26825<li>make <code>postinstallcmds</code> available to Mathematica easyconfigs + 26826 add bin/Executables to <code>$PATH</code> 26827 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2052">#2052</a>)</li> 26828<li>fix the extra dirs added to PATH in <code>FreeSurfer</code> easyblock 26829 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2053">#2053</a>)</li> 26830<li>correct download url for test data in <code>WPS</code> easyblock 26831 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2055">#2055</a>)</li> 26832<li>fix typo in warning in <code>TensorFlow</code> easyblock 26833 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2057">#2057</a>)</li> 26834<li>fix failing sanity check under <code>--module-only</code> in <code>GCC</code> 26835 easyblock 26836 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2059">#2059</a>)</li> 26837</ul> 26838</li> 26839<li>other changes:<ul> 26840<li>add configure options for CubeLib/CubeWriter dependencies in 26841 <code>Score-P</code> easyblock 26842 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2030">#2030</a>)</li> 26843<li>remove local <code>find_glob_pattern</code> in <code>Blender</code> & <code>ROOT</code> 26844 easyblocks, use function provided by <code>filetools</code> instead 26845 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2037">#2037</a>)</li> 26846</ul> 26847</li> 26848</ul> 26849<p><strong>easyconfigs</strong></p> 26850<ul> 26851<li>added easyconfigs for new common toolchains: foss/2020a 26852 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10483">#10483</a>, 26853 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10492">#10492</a>), 26854 intel/2020a 26855 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10494">#10494</a>)</li> 26856<li>added example easyconfig files for 66 new software packages:<ul> 26857<li>Alpha 26858 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9994">#9994</a>), 26859 antiSMASH 26860 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10589">#10589</a>), 26861 Arlequin 26862 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10620">#10620</a>), 26863 artic-ncov2019 26864 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10459">#10459</a>), 26865 augur 26866 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10405">#10405</a>), 26867 AutoMap 26868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10419">#10419</a>), 26869 Bio-EUtilities 26870 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10037">#10037</a>), 26871 CaSpER 26872 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10593">#10593</a>), 26873 cdbfasta 26874 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10547">#10547</a>), 26875 cddlib 26876 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10429">#10429</a>), 26877 CoCoALib 26878 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10429">#10429</a>) 26879 dftd3-lib 26880 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10351">#10351</a>), 26881 DoubletFinder 26882 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10603">#10603</a>), 26883 E-ANTIC 26884 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10429">#10429</a>), 26885 FastViromeExplorer 26886 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10571">#10571</a>), 26887 FIX 26888 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8870">#8870</a>), 26889 FusionCatcher 26890 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10134">#10134</a>), 26891 geopandas 26892 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10322">#10322</a>), 26893 goalign 26894 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10469">#10469</a>), 26895 gotree 26896 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10459">#10459</a>), 26897 gretl 26898 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10413">#10413</a>), 26899 harmony 26900 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10604">#10604</a>), 26901 HDF-EOS 26902 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10534">
26902#10534</a>), 26903 HDF-EOS5 26904 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10536">#10536</a>), 26905 HMMER2 26906 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10588">#10588</a>), 26907 HyPo 26908 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10642">#10642</a>), 26909 king 26910 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10365">#10365</a>), 26911 libdeflate 26912 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10459">#10459</a>), 26913 libfabric 26914 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10616">#10616</a>), 26915 libgit2 26916 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10453">#10453</a>), 26917 libuv 26918 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10444">#10444</a>), 26919 mbuffer 26920 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10524">#10524</a>), 26921 MDAnalysis 26922 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10545">#10545</a>), 26923 MEM 26924 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10605">#10605</a>), 26925 MESS 26926 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10597">#10597</a>), 26927 metaerg 26928 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10037">#10037</a>), 26929 MinCED 26930 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10037">#10037</a>), 26931 MitoZ 26932 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7735">#7735</a>), 26933 nauty 26934 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10429">#10429</a>), 26935 nifti2dicom 26936 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10598">#10598</a>), 26937 NLMpy 26938 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10029">#10029</a>), 26939 ntCard 26940 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10502">#10502</a>), 26941 NTL 26942 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10431">#10431</a>), 26943 pIRS 26944 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10508">#10508</a>), 26945 popscle 26946 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10550">#10550</a>), 26947 ProtHint 26948 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10549">#10549</a>), 26949 protozero 26950 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10495">#10495</a>), 26951 pysndfx 26952 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10452">#10452</a>), 26953 PyVCF 26954 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10564">#10564</a>), 26955 PyWavelets 26956 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10501">#10501</a>), 26957 rampart 26958 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10459">#10459</a>), 26959 rickflow 26960 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10641">#10641</a>), 26961 RNA-Bloom 26962 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10502">#10502</a>), 26963 root_numpy 26964 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10424">#10424</a>), 26965 rstudio 26966 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10619">#10619</a>), 26967 ScaFaCoS 26968 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10537">#10537</a>), 26969 Scythe 26970 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10524">#10524</a>), 26971 SDSL 26972 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10642">#10642</a>), 26973 SHAP 26974 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10379">#10379</a>), 26975 SNPomatic 26976 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10524">#10524</a>), 26977 SoX 26978 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10452">#10452</a>), 26979 swissknife 26980 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10037">#10037</a>),) 26981 Taiyaki 26982 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10573">#10573</a>), 26983 TCLAP 26984 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10598">#10598</a>), 26985 torchaudio 26986 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10516">#10516</a>), 26987 wtdbg2 26988 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10524">#10524</a>)</li> 26989</ul> 26990</li> 26991<li>
26991added additional easyconfigs for various supported software 26992 packages, including:<ul> 26993<li>ADF 2019.303, BRAKER 2.1.5, Bazel 2.0.0, Bonito 0.1.4, 26994 Boost.Python 1.72.0, Bowtie2 2.4.1, CMake 3.16.4, CPLEX 12.10, 26995 CVXOPT 1.2.4, Coreutils 8.32, cURL 7.69.1, DFTB+ 19.1, ecCodes 26996 2.17.0, expat 2.2.9, FFmpeg 4.2.2, FriBidi 1.0.9, GATK 4.1.5.0, 26997 GCC(core) 10.1.0, GDAL 3.0.4, GEOS 3.8.1, GLib 2.64.1, GMP 26998 6.2.0, GROMACS 2020.1, GTK+ 3.24.17, GenomeThreader 1.7.3, 26999 GffCompare 0.11.6, Ghostscript 9.52, GlimmerHMM 3.0.4c, 27000 GlobalArrays 5.7.2, gmpy2 2.1.0b4, gmsh 4.5.6, gpustat 0.6.0, 27001 gradunwarp 1.2.0, HDF5 1.10.6, hwloc 2.2.0, hypothesis 5.6.0, 27002 ICU 66.1, IPython 7.13.0, ImageMagick 7.0.10, Julia 1.4.1, KMC 27003 3.1.2rc1, Kraken2 2.0.9, LMfit 1.0.0, Longshot 0.4.1, libarchive 27004 3.4.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libjpeg-turbo 27005 2.0.4, librsvg 2.48.4, libsigsegv 2.12, lrslib 7.0a, MEME 5.1.1, 27006 MPC 1.1.0, Mako 1.1.2, Mesa 20.0.2, Meson 0.53.2, MotionCor2 27007 1.3.1, MultiQC 1.8, matplotlib 3.2.1, NGS-Python-2.10.4, NGS 27008 2.10.4, NSPR 4.25, NSS 3.51, NWChem 7.0.0, Nextflow 20.04.1, 27009 Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, ncbi-vdb 2.10.4 27010 netCDF 4.7.4, OpenBLAS 0.3.9, OpenEXR 2.4.1, OpenMPI 4.0.3, 27011 OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 27012 10.34, PLUMED 2.6.0, PMIx 3.1.5, PROJ 7.0.0, Perl 5.30.2, Pillow 27013 7.0.0, PyYAML 5.3, Python 2.7.18 + 3.8.2, parallel 20200422, Qt5 27014 5.14.1, R-bundle-Bioconductor 3.11, R 3.6.3 + 4.0.0, RMBlast 27015 2.9.0, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, re2c 1.3, rioxarray 27016 0.0.24, rootpy 1.0.1, rstudio 1.2.5042, SCons 3.1.2, SDL2 27017 2.0.10, SIONlib 1.7.6, SQLite 3.31.1, SRA-Toolkit 2.10.4, Salmon 27018 1.2.0, ScaLAPACK 2.1.0, SciPy-bundle 2020.03, Stacks 2.53, 27019 StringTie 2.1.1, SuiteSparse 5.7.1, snappy 1.1.8, spaln 2.4.03, 27020 sympy 1.5.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 27021 3.8.2, tbl2asn 20200302, torchvision 0.5.0, UCX 1.8.0, UMI-tools 27022 1.0.1, utf8proc 2.5.0, util-linux 2.35, worker 1.6.12, wxWidgets 27023 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, zsh 5.8, 27024 zstd 1.4.4</li> 27025</ul> 27026</li> 27027<li>minor enhancements, including:<ul> 27028<li>add additional extensions for recent versions of R 27029 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10359">#10359</a>, 27030 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10585">#10585</a>, 27031 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10586">#10586</a>, 27032 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10621">#10621</a>) 27033 and R-bundle-Bioconductor 27034 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10585">#10585</a>, 27035 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10596">#10596</a>, 27036 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10621">#10621</a>)</li> 27037<li>add additional extensions for recent versions of Perl 27038 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10412">#10412</a>, 27039 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10546">#10546</a>, 27040 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10623">#10623</a>)</li> 27041<li>include LLVM linker in Clang 7.0.1 on GCC 27042 7.3.0-2.30(<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10458">#10458</a>)</li> 27043<li>include static lib and header in nimimap2 easyconfigs for 27044 foss-2018b and GCC-8.2.0* 27045 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10464">#10464</a>)</li> 27046<li>add alternate checksum for EMBOSS 27047 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10607">#10607</a>)</li> 27048</ul> 27049</li> 27050<li>various bug fixes, including:<ul> 27051<li>fix incorrect checksums for Amber patches 27052 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8870">#8870</a>)</li> 27053<li>add patches to fix installation of R 3.6.2 on POWER 27054 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9830">#9830</a>)</li> 27055<li>
27055add missing build dep. pkg-config in GObject-Introspection 27056 1.63.1 w/ Python 3.7.4 easyconfig 27057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10380">#10380</a>)</li> 27058<li>add Perl as a build dependency for recent Autoconf/Automake 27059 easyconfigs 27060 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10408">#10408</a>, 27061 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10426">#10426</a>)</li> 27062<li>fix source_urls in ICU easyconfigs 27063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10417">#10417</a>)</li> 27064<li>disable <code>USER-INTEL</code> package in LAMMPS easyconfigs using 27065 intel/2019b, since it results in an installation that produces 27066 incorrect results 27067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10418">#10418</a>)</li> 27068<li>fix undefined reference to <code>qfloat16::mantissatable</code> in 27069 Qt5-5.13.1-GCCcore-8.3.0 27070 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10425">#10425</a>)</li> 27071<li>get rid of double '-' in versionsuffix of torchtext easyconfig 27072 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10472">#10472</a>)</li> 27073<li>fix broken Mako easyconfigs 27074 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10480">#10480</a>, 27075 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10627">#10627</a>)</li> 27076<li>move builddependencies to dependencies in OTF2 and Score-P 27077 easyconfigs 27078 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10496">#10496</a>)</li> 27079<li>add missing cURL dep for LAMMPS 27080 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10527">#10527</a>)</li> 27081<li>add Python 2 build dependency for OpenPGM 27082 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10539">#10539</a>)</li> 27083<li>use <code>OS_PKG_IBVERBS_DEV</code> constant for OS dependency in PyTorch 27084 1.4.0 easyconfigs 27085 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10540">#10540</a>)</li> 27086<li>add missing Bison build dep in Graphviz easyconfigs 27087 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10541">#10541</a>)</li> 27088<li>use https in homepage for Mathematica 12.0.0 + clean up sanity 27089 check commands (now done by easyblock) 27090 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10559">#10559</a>)</li> 27091<li>add missing PyVCF dependency for BAMSurgeon 27092 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10564">#10564</a>)</li> 27093<li>remove FFTW dependencies from LAMMPS easyconfigs, no longer 27094 needed (MKL can be used too now) 27095 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10565">#10565</a>)</li> 27096<li>fix ITK v5.0.1 easyconfig w.r.t. locale and location of 27097 libjpeg-turbo library 27098 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10592">#10592</a>)</li> 27099<li>add patch to fix missing <code>const</code> qualifiers for ncurses 27100 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10606">#10606</a>)</li> 27101<li>fix OS dependency for rstudio for Debian-based systems 27102 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10608">#10608</a>)</li> 27103<li>fix Rmath paths in easyconfig for FastQTL v2.184 27104 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10612">#10612</a>)</li> 27105<li>add symlink for Arlequin commands + fix sanity check commands 27106 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10620">#10620</a>)</li> 27107<li>fix recent binutils easyconfigs using system toolchain for 27108 Fedora 32 / GCC 10 27109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10633">#10633</a>)</li> 27110<li>replace '/path/to' with actual installation prefix in FuSeq 27111 scripts 27112 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10640">#10640</a>)</li> 27113</ul> 27114</li> 27115<li>other changes:<ul> 27116<li>check sdist with different Python versions in CI 27117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10388">#10388</a>)</li> 27118<li>use Bison 3.3.2 as build dep for flex 2.6.4 27119 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10403">#10403</a>)</li> 27120<li>mention <code>http://</code> Pfam website rather than <code>ftp://</code> in load 27121 message of BiG-SCAPE easyconfig 27122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10439">#10439</a>)</li> 27123<li>archive old Singularity configs 27124 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10591">#10591</a>)<ul> 27125<li>Singularity is not well suited to install via EasyBuild 27126 because it requires admin privileges to enable setuid</li> 27127</ul> 27128</li> 27129<li>stop using old hpcugent URL for cloning framework/easyblocks 27130 repos in CI 27131 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10635">#10635</a>)</li> 27132<li>use <code>SYSTEM</code> constant for toolchain in easyconfigs already use 27133 <code>system</code> toolchain 27134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10638">#10638</a>)</li> 27135</ul> 27136</li> 27137</ul> 27138<h2 id="release_notes_eb420">EasyBuild v4.2.0 (April 14th 2020)<a class="headerlink" href="#release_notes_eb420" title="Permanent link">¶</a></h2> 27139<p>feature release</p> 27140<p><strong>framework</strong></p> 27141<ul> 27142<li>add support for <code>--try-update-deps</code>
27142 (experimental feature), to 27143 upgrade dependencies based on available easyconfigs 27144 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2599">#2599</a>)</li> 27145<li>adding locking to prevent two parallel builds of the same 27146 installation directory 27147 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3009">#3009</a>)<ul> 27148<li>for more information, see 27149 <a href="https://easybuild.readthedocs.io/en/latest/Locks.html">https://easybuild.readthedocs.io/en/latest/Locks.html</a></li> 27150</ul> 27151</li> 27152<li>significantly speed up <code>-D/--dry-run</code> by avoiding useless 27153 '<code>module show</code>' 27154 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3203">#3203</a>)</li> 27155<li>add support for creating an index & using it when searching for 27156 easyconfigs 27157 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3210">#3210</a>)<ul> 27158<li>for more information, see 27159 <a href="https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html">https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html</a></li> 27160</ul> 27161</li> 27162<li>additional GitHub integration features:<ul> 27163<li>add support for targeting easyblocks and framework repositories 27164 in <code>--new-pr</code> 27165 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1876">#1876</a>, 27166 <a href="https://github.com/easybuilders/easybuild-framework/pull/3189">#3189</a>)</li> 27167<li>add support for <code>--include-easyblocks-from-pr</code> 27168 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3206">#3206</a>)</li> 27169<li>for more information, 27170 <a href="https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html">https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html</a></li> 27171</ul> 27172</li> 27173<li>various other enhancements, including:<ul> 27174<li>add a contrib/hooks dir with some examples of hooks used 27175 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2777">#2777</a>)</li> 27176<li>also mention working directory + input passed via stdin (if any) 27177 in trace output of <code>run_cmd</code> 27178 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3168">#3168</a>)</li> 27179<li>probe external modules for missing metadata that is not provided 27180 via external module metadata file 27181 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3174">#3174</a>)</li> 27182<li>also update <code>$CMAKE_PREFIX_PATH</code> and <code>$CMAKE_LIBRARY_PATH</code> in 27183 generated module file 27184 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3176">#3176</a>)</li> 27185<li>optionally call <code>log.warning</code> in <code>print_warning</code> 27186 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3195">#3195</a>)</li> 27187<li>add an option to <code>git_config</code> to retain the <code>.git</code> directory 27188 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3197">#3197</a>)</li> 27189<li>allow use of <code>SYSTEM</code> as <code>--try-toolchain</code> option 27190 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3213">#3213</a>)</li> 27191<li>mention CPU arch name in comment for uploaded test report, if 27192 it's known by <code>archspec</code> 27193 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3227">#3227</a>)</li> 27194<li>make <code>--merge-pr</code> take into account <code>--pr-target-branch</code> 27195 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3236">#3236</a>)</li> 27196<li>make <code>--check-contrib</code> print a warning when <code>None</code> is used for 27197 checksums 27198 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3244">#3244</a>)</li> 27199<li>update <code>install-EasyBuild-develop.sh</code> script and create script 27200 for 2020a merge sprint 27201 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3245">#3245</a>)</li> 27202<li>add template for <code>mpi_cmd_prefix</code> 27203 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3264">#3264</a>)</li> 27204<li>update <code>copy_dir</code> to include option to merge directories 27205 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3270">#3270</a>)</li> 27206<li>support template name for CUDA version 27207 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3274">#3274</a>)</li> 27208</ul> 27209</li> 27210<li>various bug fixes, including:<ul> 27211<li>use correct module for <code>errors_found_in_log</code> 27212 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3119">#3119</a>)</li> 27213<li>fix <code>EasyConfig.update</code> code to handle both strings and lists as 27214 input 27215 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3170">#3170</a>)</li> 27216<li>fix removing temporary branch on <code>--check-github</code> 27217 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3182">#3182</a>)</li> 27218<li>fix shebang even if first line doesn't start with '<code>#!</code>' 27219 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3183">#3183</a>)</li> 27220<li>make bootstrap script work with Python 3 27221 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3186">#3186</a>)</li> 27222<li>read patch files as bytestring to avoid <code>UnicodeDecodeError</code> for 27223 patches that include funky characters 27224 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3191">#3191</a>)</li> 27225<li>fix online check in <code>--check-github</code>: try repeatedly and with 27226 different URLs to cater for HTTP issues 27227 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3194">#3194</a>)</li> 27228<li>don't crash when GitPython is not installed when using Python 3 27229 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3198">#3198</a>)</li> 27230<li>fix <code>os_name_map</code> for RHEL8 27231 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3201">#3201</a>)</li> 27232<li>don't add shebang to binary files 27233 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3208">#3208</a>)</li> 27234<li>use <code>checkout@v2</code> in GitHub Actions to fix broken re-triggered 27235 tests 27236 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3219">#3219</a>)</li> 27237<li>don't filter out <code>None</code> values in to_checksums, leave them in 27238 place 27239 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3225">#3225</a>)</li> 27240<li>fix defining of <code>$MPI_INC_*</code> and <code>$MPI_LIB_*</code> environment 27241 variables for impi version 2019 and later 27242 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3229">#3229</a>)</li> 27243<li>use correct target account/repo when creating test report & 27244 posting comment in PR 27245 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3234">#3234</a>)</li> 27246<li>reorganize <code>EasyBlock.extensions_step</code> to ensure correct 27247 filtering of extensions 27248 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3235">#3235</a>)</li> 27249<li>also support <code>%(installdir)s</code> and <code>%(builddir)s</code> templates for 27250 extensions 27251 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3237">#3237</a>)</li> 27252<li>unset <code>$GITHUB_TOKEN</code> in Travis after installing token, to avoid 27253 failing <code>test_from_pr_token_log</code> 27254 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3252">#3252</a>)</li> 27255<li>fix reporting when skipping extensions 27256 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3254">#3254</a>)</li> 27257<li>avoid API rate limit errors on online check in <code>--check-github</code> 27258 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3257">#3257</a>)</li> 27259<li>show easyconfig filenames for parallel build 27260 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3258">#3258</a>)</li> 27261<li>make <code>EasyConfig.dump</code> aware of toolchain hierarchy, to avoid 27262 hardcoded subtoolchains in dependencies easyconfig parameters 27263 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3261">#3261</a>)</li> 27264<li>fix use of <code>--copy-ec</code> with a single argument, assume copy to 27265 current working directory 27266 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3262">#3262</a>)</li> 27267<li>fix posting of comment in PR with <code>--upload-test-report</code> 27268 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3272">#3272</a>)</li> 27269<li>take into account dependencies marked as external modules when 27270 composing template values like <code>%(pyver)s</code> 27271 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3273">#3273</a>)</li> 27272</ul> 27273</li> 27274<li>other changes:<ul> 27275<li>increase timeout & use <code>api.github.com</code> for connectivity check 27276 in <code>check_github</code> 27277 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3192">#3192</a>)</li> 27278<li>restore <code>flake8</code> default ignores 27279 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3193">#3193</a>)</li> 27280<li>enable tracking of test suite coverage using coveralls 27281 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3204">#3204</a>)</li> 27282<li>make tests use <code>easybuilders/testrepository</code> rather than 27283 <code>hpcugent/testrepository</code> after it was moved 27284 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3238">#3238</a>)</li> 27285<li>improve raised error in <code>remove_dir</code> and deprecate <code>rmtree2</code> 27286 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3228">#3228</a>)</li> 27287</ul> 27288</li> 27289</ul> 27290<p><strong>easyblocks</strong></p> 27291<ul> 27292<li>7 new software-specific easyblocks:<ul> 27293<li>BerkeleyGW 27294 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1951">#1951</a>), 27295 CMake 27296 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1936">
27296#1936</a>), 27297 ELSI 27298 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1883">#1883</a>), 27299 LAMMPS 27300 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1964">#1964</a>, 27301 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1975">#1975</a>, 27302 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1978">#1978</a>, 27303 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1982">#1982</a>, 27304 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1997">#1997</a>), 27305 libdrm 27306 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1983">#1983</a>), 27307 Mesa 27308 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1892">#1892</a>, 27309 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2006">#2006</a>), 27310 SEPP 27311 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1998">#1998</a>)</li> 27312</ul> 27313</li> 27314<li>minor enhancements, including:<ul> 27315<li>make ParMETIS easyblock compatible with custom <code>configopts</code> 27316 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1774">#1774</a>)</li> 27317<li>update Trinity easyblock for v2.9.0 27318 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1906">#1906</a>)</li> 27319<li>disable ROCM and Android workspace explicitly in TensorFlow 27320 easyblock 27321 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1944">#1944</a>)</li> 27322<li>update QuantumESPRESSO easyblock for version 6.5 27323 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1947">#1947</a>)</li> 27324<li>update Siesta easyblock to support MaX-1.0 release 27325 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1954">#1954</a>)</li> 27326<li>update Ferret easyblock for versions >= 7.5.0 27327 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1956">#1956</a>)</li> 27328<li>update XCrySDen easyblock to support Togl dependency 27329 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1959">#1959</a>)</li> 27330<li>pass value for <code>TARGET</code> specified in <code>buildopts</code> to <code>testopts</code> 27331 and <code>installopts</code> in OpenBLAS easyblock 27332 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1960">#1960</a>)</li> 27333<li>fix netCDF(-Fortran) support in Siesta easyblock 27334 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1967">#1967</a>, 27335 1971)</li> 27336<li>add <code>NCDF_PARALLEL</code> and METIS support to Siesta easyblock 27337 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1973">#1973</a>)</li> 27338<li>add support for <code>use_pip_extras</code> custom easyconfig parameter in 27339 <code>PythonPackage</code> easyblock 27340 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1980">#1980</a>)</li> 27341<li>update Open Babel easyblock for version 3.0.0 27342 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1992">#1992</a>)</li> 27343<li>allow differing names for TensorFlow wheel 27344 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1995">#1995</a>)</li> 27345<li>make MATLAB runtime available from MATLAB 27346 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2008">#2008</a>)</li> 27347</ul> 27348</li> 27349<li>various bug fixes, including:<ul> 27350<li>fix linking of Hypre to external BLAS/LAPACK + support building 27351 (only) static/shared library 27352 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1885">#1885</a>)</li> 27353<li>fix MPI-CXX dependency of PETSc 27354 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1917">#1917</a>)</li> 27355<li>limit amount of parallelism in TensorFlow easyblock 27356 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1934">#1934</a>)</li> 27357<li>support GCCcore and gcc4.8 (if that dir exists) in function 27358 <code>get_tbb_gccprefix</code> in tbb easyblock 27359 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1943">#1943</a>)</li> 27360<li>restore default <code>flake8</code> warnings 27361 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1950">#1950</a>)</li> 27362<li>remove tests from <code>build_step</code> and raise error on failed tests 27363 in OpenBLAS easyblock 27364 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1952">
27364#1952</a>, 27365 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1955">#1955</a>, 27366 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1962">#1962</a>)</li> 27367<li>add optional <code>runtest</code> to the catch for <code>FATAL ERRORS</code> to 27368 OpenBLAS easyblock 27369 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1958">#1958</a>)</li> 27370<li>ensure right '<code>python</code>' command is used to determine Python 27371 lib dir when system Python is used with PythonBundle easyblock 27372 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1961">#1961</a>)</li> 27373<li>make sure <code>lib/python*/lib-dynload</code> exists in Python 27374 installation 27375 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1966">#1966</a>)</li> 27376<li>in version 6.0 of TensorRT, <code>libnvinfer.a</code> is renamed 27377 <code>libnvinfer_static.a</code> 27378 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1970">#1970</a>)</li> 27379<li>handle <code>configopts</code> without configure args in CMake easyblock 27380 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1974">#1974</a>)</li> 27381<li>use <code>checkout@v2</code> in GitHub Actions to fix broken re-triggered 27382 tests 27383 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1976">#1976</a>)</li> 27384<li>don't insist that pylibdir always exists in OpenCV easyblock 27385 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1977">#1977</a>)</li> 27386<li>also set <code>$TRINITY_HOME</code> environment variable in Trinity 27387 easyblock 27388 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1979">#1979</a>)</li> 27389<li>fix sanity check for OpenFOAM-Extend >= 4.1 27390 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1981">#1981</a>)</li> 27391<li>fix pattern matching in regex subst for <code>I_MPI_ROOT</code> in impi 27392 easyblock 27393 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1986">#1986</a>)</li> 27394<li>use <code>remove_dir</code> instead of deprecated <code>rmtree2</code> in various 27395 easyblocks 27396 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1993">#1993</a>)</li> 27397<li>fix "<code>AttributeError: module 'git' has no attribute 'Git'</code>" 27398 that may occur when using Python 3 27399 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1994">#1994</a>)</li> 27400<li>don't sanity check for <code>QtWebEngine</code> in Qt easyblock when 27401 building for POWER 27402 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2000">#2000</a>)</li> 27403<li>fix installation of TensorFlow in some environments, by setting 27404 <code>$PYTHONNOUSERSITE</code> (& more) 27405 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2002">#2002</a>, 27406 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2020">#2020</a>)</li> 27407<li>make sure libxml2 is built with XZ provided as dependency 27408 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2005">#2005</a>)</li> 27409<li>look for Python version directories with suffixes in ROOT 27410 easyblock 27411 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2010">#2010</a>)</li> 27412<li>enable TK, FLTK and OPENGL configure options in VMD easyblock 27413 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2013">#2013</a>)</li> 27414<li>update the contributing docs 27415 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2014">#2014</a>)</li> 27416<li>fix numexpr easyblock to allow (correctly) installing it as 27417 extension 27418 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2022">#2022</a>)</li> 27419</ul> 27420</li> 27421<li>other changes:<ul> 27422<li>simplify various CMakeMake-based easyblocks by enhancing 27423 <code>CMakeMake</code> (w.r.t. <code>CMAKE_BUILD_TYPE</code>, shared vs static libs, 27424 <code>-fPIC</code>) 27425 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1929">#1929</a>)</li> 27426<li>enable out of tree build by default in <code>CMakeMake</code> easyblock 27427 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1933">#1933</a>)</li> 27428<li>force building Clang without CUDA when it is not found as a 27429 proper dependency 27430 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1968">
27430#1968</a>)</li> 27431</ul> 27432</li> 27433</ul> 27434<p><strong>easyconfigs</strong></p> 27435<ul> 27436<li>added example easyconfig files for 114 new software packages:<ul> 27437<li>ABRA2 27438 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10272">#10272</a>), 27439 ABRicate 27440 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10310">#10310</a>), 27441 ADIOS 27442 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10036">#10036</a>), 27443 aNCI 27444 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9929">#9929</a>), 27445 any2fasta 27446 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10310">#10310</a>), 27447 apex 27448 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10269">#10269</a>), 27449 archspec 27450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9898">#9898</a>), 27451 ArviZ 27452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10366">#10366</a>), 27453 autopep8 27454 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9626">#9626</a>), 27455 BAMSurgeon 27456 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10330">#10330</a>), 27457 BatMeth2 27458 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10323">#10323</a>), 27459 BiG-SCAPE 27460 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10352">#10352</a>), 27461 BinSanity 27462 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10001">#10001</a>), 27463 Bonito 27464 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10269">#10269</a>), 27465 BSMAPz 27466 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10283">#10283</a>), 27467 BSseeker2 27468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10039">#10039</a>), 27469 BUStools 27470 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9838">#9838</a>), 27471 Cbc 27472 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10052">#10052</a>), 27473 Cgl 27474 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10048">#10048</a>), 27475 CGmapTools 27476 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10288">#10288</a>), 27477 Clp 27478 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10033">#10033</a>), 27479 CoinUtils 27480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9937">#9937</a>), 27481 dtcwt 27482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9695">#9695</a>), 27483 ELSI 27484 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9857">#9857</a>), 27485 EnsEMBLCoreAPI 27486 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8734">#8734</a>), 27487 fastq-pair 27488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9894">#9894</a>), 27489 FigureGen 27490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10076">#10076</a>), 27491 Fiona 27492 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10321">#10321</a>), 27493 FuSeq 27494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10004">#10004</a>), 27495 GenomeTools 27496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9797">#9797</a>), 27497 GraphMap2 27498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10299">#10299</a>), 27499 GRASP 27500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9896">#9896</a>), 27501 Groovy 27502 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9809">#9809</a>), 27503 gsport 27504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9821">#9821</a>), 27505 gubbins 27506 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9689">#9689</a>), 27507 igv-reports 27508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9977">#9977</a>), 27509 inferCNV 27510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9686">#9686</a>), 27511 iVar 27512 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10291">#10291</a>), 27513 joypy 27514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10212">#10212</a>), 27515 JupyterLab 27516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9752">
27516#9752</a>), 27517 kma 27518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10259">#10259</a>), 27519 LAMMPS 27520 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10371">#10371</a>), 27521 lancet 27522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10271">#10271</a>), 27523 libBigWig 27524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10006">#10006</a>), 27525 libGridXC 27526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9858">#9858</a>), 27527 libPSML 27528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5859">#5859</a>), 27529 LtrDetector 27530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10343">#10343</a>), 27531 manta 27532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5104">#5104</a>), 27533 medImgProc 27534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10228">#10228</a>), 27535 MedPy 27536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9748">#9748</a>), 27537 Mini-XML 27538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10036">#10036</a>), 27539 mkl_fft 27540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9887">#9887</a>), 27541 Monocle3 27542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9825">#9825</a>), 27543 MoreRONN 27544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10255">#10255</a>), 27545 motionSegmentation 27546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10228">#10228</a>), 27547 NanoComp 27548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10212">#10212</a>), 27549 NanoFilt 27550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10212">#10212</a>), 27551 nanoget 27552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10212">#10212</a>), 27553 nanomath 27554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10212">#10212</a>), 27555 NanoPlot 27556 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10212">#10212</a>), 27557 ngspice 27558 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9922">#9922</a>), 27559 ntEdit 27560 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9836">#9836</a>), 27561 ntHits 27562 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9833">#9833</a>), 27563 occt 27564 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9939">#9939</a>), 27565 OCNet 27566 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9955">#9955</a>), 27567 OpenAI-Gym 27568 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10347">#10347</a>), 27569 OpenPIV 27570 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9959">#9959</a>), 27571 OpenPyXL 27572 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10115">#10115</a>), 27573 orca 27574 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9518">#9518</a>), 27575 Osi 27576 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10361">#10361</a>), 27577 PartitionFinder 27578 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9983">#9983</a>), 27579 pauvre 27580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10212">#10212</a>), 27581 polymake 27582 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9904">#9904</a>), 27583 pretty-yaml 27584 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10041">#10041</a>)), 27585 PRSice 27586 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9988">#9988</a>), 27587 pycodestyle 27588 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9626">#9626</a>), 27589 pydot 27590 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9899">#9899</a>), 27591 pygraphviz 27592 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9969">#9969</a>), 27593 pylift 27594 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10051">#10051</a>), 27595 PyMC3 27596 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10279">#10279</a>), 27597 pyparsing 27598 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9983">#9983</a>), 27599 PyRe 27600 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10095">#10095</a>), 27601 python-weka-wrapper3 27602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9704">#9704</a>), 27603 PyTorch-Geometric 27604 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9995">#9995</a>), 27605 qcat 27606 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10244">#10244</a>), 27607 RAxML-NG 27608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9990">#9990</a>), 27609 Ray 27610 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10302">#10302</a>), 27611 rclone 27612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7934">#7934</a>), 27613 Red 27614 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9856">#9856</a>), 27615 rstanarm 27616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9964">#9964</a>), 27617 scikit-build 27618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9762">#9762</a>), 27619 scVelo 27620 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9805">#9805</a>), 27621 SECAPR 27622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9721">#9721</a>), 27623 segmentation-models 27624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10211">#10211</a>), 27625 SentencePiece 27626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10192">#10192</a>), 27627 SEPP 27628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10047">#10047</a>), 27629 Shapely 27630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10309">#10309</a>), 27631 Singular 27632 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10030">#10030</a>), 27633 SLATEC 27634 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7529">#7529</a>), 27635 spatialreg 27636 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9767">#9767</a>), 27637 split-seq 27638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9749">#9749</a>), 27639 spoa 27640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9705">#9705</a>), 27641 SSN 27642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9955">#9955</a>), 27643 STEAK 27644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10337">#10337</a>), 27645 stpipeline 27646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9736">#9736</a>), 27647 SVG 27648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9905">#9905</a>), 27649 Togl 27650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9868">#9868</a>), 27651 torchtext 27652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10193">#10193</a>), 27653 units 27654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9682">#9682</a>), 27655 UQTk 27656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10279">#10279</a>), 27657 WildMagic 27658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10044">#10044</a>), 27659 Winnowmap 27660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10005">#10005</a>), 27661 xtb 27662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9993">#9993</a>), 27663 Zip 27664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9972">#9972</a>)</li> 27665</ul> 27666</li> 27667<li>
27667added additional easyconfigs for various supported software 27668 packages, including:<ul> 27669<li>ABySS 2.1.5, Arrow 0.16.0, BCFtools 1.10.2, BEDTools 2.29.2, 27670 BUSCO 4.0.5, BerkeleyGW 2.1.0, binutils 2.34, CVXPY 1.0.28, 27671 CharLS 2.1.0, CheckM 1.1.2, Clang 10.0.0, CppUnit 1.15.1, canu 27672 1.9, cutadapt 2.8, DIAMOND 0.9.30, davix 0.7.5, ELPA 27673 2019.11.001, FastANI 1.3, FastQC 0.11.9, Ferret 7.5.0, GATK 27674 4.1.4.1, GCCcore 9.3.0, GDB 9.1, GMAP-GSNAP-2019-09-12, 27675 GObject-Introspection 1.63.1, GPAW 20.1.0, GROMACS 2020, GTDB-Tk 27676 1.0.2, GTK+ 3.24.13, Go 1.14.1, Gradle 6.1.1, GraphicsMagick 27677 1.3.34, Graphviz 2.42.2, Gurobi 9.0.1, gSOAP 2.8.100, gnuplot 27678 5.2.8, gtest 1.10.0, HDDM 0.7.5, HTSlib 1.10.2, HarfBuzz 2.6.4, 27679 Horovod 0.19.1, Hypre 2.18.2, IGV 2.8.0, IQ-TREE 1.6.12, 27680 IRkernel 1.1, iccifort 2020.0.166, igraph 0.8.0, impi 27681 2019.6.166, ispc 1.12.0, Java 13(.0.2), Julia 1.4.0, Keras 27682 2.3.1, Kraken2 2.0.8-beta, kim-api 2.1.3, LAST 1045, LASTZ 27683 1.04.03, LLVM 9.0.1 + 10.0.0, LMfit 0.9.14, LS-PrePost 4.7.8, 27684 likwid 5.0.1, MAFFT 7.453, MATLAB 2019b, MMseqs2 10, Maven 27685 3.6.3, Meson 0.53.1, MethylDackel 0.5.0, Mono 6.8.0.105, medaka 27686 0.12.0, Nextflow 20.01.0, ncdf4 1.17, netcdf4-python 1.5.3, 27687 nodejs 12.16.1, numba 0.47.0, numexpr 2.7.1, Octave 5.1.0, 27688 OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 27689 4.1-20191120, OrthoFinder 2.3.11, PETSc 3.12.4, PGI 19.10, PMIx 27690 2.2.1, Pango 1.44.7, PyTables 3.6.1, PyTorch 1.4.0, parasail 27691 2.4.1, pydicom 1.4.2, pyproj 2.4.2, Qhull 2019.1, 27692 QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, RDKit 2019.09.3 27693 Racon 1.4.10, ReFrame 2.21, Ruby 2.7.1, rjags 4-9, rpy2 3.2.6, 27694 SLEPc 3.12.2, SPAdes 3.14.0, SPAdes 3.14.0, STAR-Fusion 1.8.1, 27695 STAR 2.7.3a, Seaborn 0.10.0, SeqAn 1.4.2, Seurat 3.1.2, 27696 SimpleElastix 1.1.0, SimpleITK 1.2.4, Stacks 2.5, Stata 16, 27697 StringTie 2.1.0, scikit-optimize 0.7.4, statsmodels 0.11.0, 27698 TensorFlow 1.15.2 + 2.0.1, Tkinter 2.7.16, Trim_Galore 0.6.5, 27699 Trimmomatic 0.39, Trinity 2.10.0, tbb 2020.2, tqdm 4.41.1, 27700 XCrySDen 1.6.2, XGBoost 0.90, xarray 0.15.1, xmlf90 1.5.4</li> 27701</ul> 27702</li> 27703<li>minor enhancements, including:<ul> 27704<li>add easyconfig for Java 11.0.6 on <code>ppc64le</code> and alter the Java 27705 11 wrapper to support both x86_64 and ppc64le 27706 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9371">#9371</a>)</li> 27707<li>add additional extensions for R: <code>HiddenMarkov</code> 27708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9685">#9685</a>), 27709 <code>lmerTest</code> 27710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9853">#9853</a>), 27711 <code>VSURF</code> + <code>Rborist</code> 27712 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10355">#10355</a>)</li> 27713<li>change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock 27714 for Mesa 27715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9764">#9764</a>)</li> 27716<li>build shared libs and install header files for Ghostscript 27717 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9785">#9785</a>)</li> 27718<li>add MUMPS as dependency in PETSc 3.12.4 easyconfigs 27719 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9880">#9880</a>, 27720 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9891">#9891</a>)</li> 27721<li>add Perl extensions: <code>Term::ReadLine::Gnu</code> 27722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9901">#9901</a>), 27723 <code>URI::Escape</code> and <code>Set::IntervalTree</code> 27724 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10049">#10049</a>)</li> 27725<li>add dat directory to aNCI 27726 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9929">#9929</a>)</li> 27727<li>add patch to create a symlink from <code>libsvm.so.$(SHVER)</code> to 27728 <code>libsvm.so</code> in LIBSVM easyconfigs 27729 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10045">#10045</a>)</li> 27730<li>build SUNDIALS with '<code>pic</code>' 27731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10278">#10278</a>)</li> 27732<li>
27732add <code>BSgenome.Hsapiens.UCSC.hg38</code> + <code>MEDIPS</code> extensions to 27733 R-bundle-Bioconductor v3.10 27734 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10298">#10298</a>)</li> 27735<li>fix checksums for <code>mkl-dnn</code> and <code>tbb</code> extensions (moved to 27736 oneAPI repo) in PyTorch easyconfigs 27737 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10367">#10367</a>)</li> 27738<li>update <code>Java/1.8</code> wrapper to <code>Java/1.8.0_241.eb</code> 27739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10305">#10305</a>)</li> 27740</ul> 27741</li> 27742<li>various bug fixes, including:<ul> 27743<li>use CMake for building double-conversion 27744 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9659">#9659</a>)</li> 27745<li>update recent libdrm easyconfigs to use custom easyblock & avoid 27746 hardcoded x86-specific sanity check 27747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9694">#9694</a>)</li> 27748<li>add alternate checksum for OpenMolcas 18.09 27749 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9701">#9701</a>)</li> 27750<li>use Github to download releases for MariaDB-connector-c 27751 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9702">#9702</a>)</li> 27752<li>add <code>-DOMPI_SKIP_MPICXX</code> in <code>configopts</code> for MathGL, to avoid 27753 using mpicxx during build 27754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9703">#9703</a>)</li> 27755<li>make installing independent of build folder in pybind11 27756 easyconfig 27757 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9738">#9738</a>)</li> 27758<li>add Lua as a dependency to gnuplot 27759 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9773">#9773</a>)</li> 27760<li>stick to <code>http://</code> source URLS for ISL in GCCcore easyconfigs, 27761 since <code>https://</code> doesn't work 27762 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9784">#9784</a>)</li> 27763<li>add alternative checksums for 27764 <code>farver</code>/<code>fracdiff</code>/<code>pkgmaker</code>/<code>rngtools</code>/<code>doRNG</code>/<code>cobs</code> 27765 extensions in R 3.6.2 easyconfigs 27766 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9789">#9789</a>)</li> 27767<li>add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken 27768 tests 27769 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9865">#9865</a>)</li> 27770<li>revert removal of AVX512 vmovd with 64-bit operands in binutils 27771 2.32 easyconfigs 27772 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9866">#9866</a>)</li> 27773<li>fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 27774 0.3.8 27775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9867">#9867</a>)</li> 27776<li>add missing <code>sanity_check_commands</code> to cutadapt v1.18 and v2.7 27777 easyconfigs 27778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9869">#9869</a>)</li> 27779<li>don't overwrite <code>configopts</code> in BLAST+ easyconfigs, append to 27780 it 27781 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9875">#9875</a>)</li> 27782<li>add alternate checksum for <code>LaplacesDemon</code> in R 3.6.x 27783 easyconfigs 27784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9879">#9879</a>, 27785 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10382">#10382</a>)</li> 27786<li>fix redefining of preconfigopts in OpenCV easyconfigs 27787 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9895">#9895</a>)</li> 27788<li>use symlinks for terminfo files instead of hard links in ncurses 27789 6.1 easyconfigs 27790 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9912">#9912</a>)</li> 27791<li>fix NCIPLOT build flags 27792 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9915">#9915</a>)</li> 27793<li>add missing patch to iccifort libxc easyconfigs 27794 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9918">#9918</a>)</li> 27795<li>use <code>checkout@v2</code> in GitHub Actions to fix broken re-triggered 27796 tests 27797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9925">#9925</a>)</li> 27798<li>re-enable building utils in Siesta 4.1-MaX-1.0 release 27799 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9936">#9936</a>)</li> 27800<li>fix homepage and source URLs in SLEPc easyconfigs by using https 27801 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9943">#9943</a>)</li> 27802<li>fix source URLs for rgeos after source tarball was moved to CRAN 27803 archive 27804 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9954">#9954</a>)</li> 27805<li>
27805add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 27806 easyconfig 27807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9957">#9957</a>)</li> 27808<li>patch GCC <code>lisanitizer</code> for glibc 2.31 27809 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9966">#9966</a>)</li> 27810<li>add Zip as build dependency for recent Bazel versions 27811 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9972">#9972</a>)</li> 27812<li>fix checksums in Jellyfish v2.3.0 easyconfigs 27813 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9997">#9997</a>)</li> 27814<li>fix source URLs for ParMGridGen easyconfigs 27815 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10019">#10019</a>)</li> 27816<li>disable unintended Octave support in all libsndfile easyconfigs 27817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10027">#10027</a>)</li> 27818<li>fix sources for LS-PrePost 4.6 27819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10236">#10236</a>)</li> 27820<li>security update for vsc-mympirun 4.1.9 27821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10185">#10185</a>)</li> 27822<li>configure libwebp to also install <code>libwebpmux</code> 27823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10274">#10274</a>)</li> 27824<li>ensure that CVS easyconfigs are included in source tarball 27825 produced by '<code>python setup.py sdist</code>' 27826 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10326">#10326</a>)</li> 27827<li>fix undefined reference error due to libxc 4.3.4 built with 27828 CMake 27829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10356">#10356</a>)</li> 27830<li>fix source_urls for tbb: use (new) official '<code>oneapi-src</code>' 27831 GitHub repository 27832 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10361">#10361</a>)</li> 27833<li>update checksums and homepage in tbb easyconfigs 27834 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10285">#10285</a>)</li> 27835</ul> 27836</li> 27837<li>other changes:<ul> 27838<li>use new custom easyblock in recent CMake easyconfigs 27839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9871">#9871</a>, 27840 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9923">#9923</a>)</li> 27841<li>add check for redefined easyconfig parameters in easyconfig 27842 tests 27843 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9876">#9876</a>)</li> 27844<li>use M4-1.4.18.eb for test installation in easyconfigs test suite 27845 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9926">#9926</a>)</li> 27846<li>use <code>https://</code> in <code>homepage</code>/<code>source_urls</code> of <code>zlib-1.2.11.eb</code> 27847 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10018">#10018</a>)</li> 27848<li>add <code>-GCCcore-9.2.0</code> versionsuffix for <code>intel/2020.00</code> 27849 components 27850 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10083">#10083</a>)</li> 27851<li>add checksum of new tbb 2019_U9 source tarball, next to original 27852 one + update homepage 27853 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10237">#10237</a>)</li> 27854<li>add comment informing about manually setting Gallium drivers in 27855 easyconfigs for Mesa v19.1.7 and v19.2.1 27856 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/10276">#10276</a>)</li> 27857</ul> 27858</li> 27859</ul> 27860<h2 id="release_notes_eb412">EasyBuild v4.1.2 (March 16th 2020)<a class="headerlink" href="#release_notes_eb412" title="Permanent link">¶</a></h2> 27861<p>bugfix release</p> 27862<div class="admonition note"> 27863<p class="admonition-title">Note</p> 27864<p>This release includes a bug fix for the leaking of your GitHub token 27865in the EasyBuild (debug) log file.</p> 27866<p><strong>We strongly encourage that you revoke the GitHub tokens you are 27867using currently, via</strong> <a href="https://github.com/settings/tokens">https://github.com/settings/tokens</a>, <strong>and to 27868replace them using a new token (using</strong> <code>eb --install-github-token --force</code> <strong>).</strong></p> 27869<p>More information in 27870<a href="https://github.com/easybuilders/easybuild-framework/pull/3248">https://github.com/easybuilders/easybuild-framework/pull/3248</a>.</p> 27871</div> 27872<p><strong>framework</strong></p> 27873<ul> 27874<li>
27874fix gitdb dependency on Python 2.6 in test configuration 27875 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3212">#3212</a>)</li> 27876<li>fix broken test for --review-pr by using different PR to test with 27877 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3226">#3226</a>)</li> 27878<li>censor authorization part of headers before logging ReST API request 27879 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3248">#3248</a>)</li> 27880</ul> 27881<p><strong>easyblocks</strong></p> 27882<p><em>(no changes)</em></p> 27883<p><strong>easyconfigs</strong></p> 27884<p><em>(no changes)</em></p> 27885<h2 id="release_notes_eb411">EasyBuild v4.1.1 (January 16th 2020)<a class="headerlink" href="#release_notes_eb411" title="Permanent link">¶</a></h2> 27886<p>bugfix/update release</p> 27887<p><strong>framework</strong></p> 27888<ul> 27889<li>various enhancements, including:<ul> 27890<li>add <code>check_log_for_errors</code> function (in <code>easybuild.tools.run</code>) 27891 to detect and handle multiple errors 27892 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3118">#3118</a>)</li> 27893<li>implement support for <code>eb --show-ec</code> to show contents of 27894 specified easyconfig file 27895 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3132">#3132</a>)</li> 27896<li>also update <code>$XDG_DATA_DIR</code> (share/) and <code>$GI_TYPELIB_PATH</code> 27897 environment variables (lib<em>/girepository-</em>) in generated 27898 module files 27899 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3133">#3133</a>)</li> 27900<li>add support for <code>--copy-ec</code> to copy easyconfig file to specified 27901 location 27902 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3142">#3142</a>)</li> 27903<li>mention <code>--disable-*</code> option in <code>--help</code> output for boolean 27904 options enabled by default 27905 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3151">#3151</a>)</li> 27906<li>add <code>--cuda-compute-capabilities</code> configuration option 27907 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3161">#3161</a>)</li> 27908</ul> 27909</li> 27910<li>various bug fixes, including:<ul> 27911<li>ignore imports from <code>vsc</code> namespace made from pkgutil.py 27912 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3120">#3120</a>)</li> 27913<li>only actually change permissions using <code>os.chmod</code> in 27914 <code>adjust_permissions</code> if the current permissions are not correct 27915 already 27916 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3125">#3125</a>)</li> 27917<li>use <code>shutil.copyfile</code> to just copy file contents if target path 27918 exists and is owned by someone else 27919 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3127">#3127</a>)</li> 27920<li>fix or avoid warnings that commonly arise in build log 27921 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3129">#3129</a>)</li> 27922<li>disable buffering in <code>asyncprocess.Popen</code> using <code>bufsize=0</code>, to 27923 fix <code>run_cmd_qa</code> missing output 27924 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3130">#3130</a>)</li> 27925<li>update pip & install wheel package in generated Singularity 27926 container recipes 27927 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3136">#3136</a>)</li> 27928<li>avoid crash in <code>modify_env</code> & unset <code>unset_env_vars</code> when using 27929 (older versions) of Python 3.5 & 3.6 by using <code>list(...)</code> 27930 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3140">#3140</a>)</li> 27931<li>take into account that lib64 could be a symlink to lib (or vice 27932 versa) in <code>get_software_libdir</code> function 27933 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3141">#3141</a>)</li> 27934<li>only parse docstring if it exists in 27935 <code>gen_easyblock_doc_section_rst</code> function 27936 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3144">#3144</a>)</li> 27937<li>only add useful entries for <code>$CPATH</code>, <code>$(LD_)LIBRARY_PATH</code> and 27938 <code>$PATH</code> (non-empty directories) 27939 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3145">#3145</a>, 27940 <a href="https://github.com/easybuilders/easybuild-framework/pull/3152">#3152</a>)</li> 27941<li>fix <code>--list-software=detailed</code> when using Python 3 by leveraging 27942 <code>
27942sort_looseversions</code> function from <code>py2vs3</code> module 27943 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3146">#3146</a>)</li> 27944<li>ensure subdirectories in software install directory have correct 27945 search (exec) permission 27946 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3147">#3147</a>)</li> 27947<li>take into account that a checksum value may be a tuple of valid 27948 checksum in <code>EasyBlock.check_checksums</code> 27949 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3153">#3153</a>)</li> 27950</ul> 27951</li> 27952<li>other changes:<ul> 27953<li>bump to Lmod 8.2.9 in GitHub CI config 27954 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3115">#3115</a>)</li> 27955<li>update copyright statements for 2020 27956 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3149">#3149</a>)</li> 27957<li>make Hound CI code style checker ignore "Black would make 27958 changes" produced by flake8-black 27959 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3162">#3162</a>)</li> 27960</ul> 27961</li> 27962</ul> 27963<p><strong>easyblocks</strong></p> 27964<ul> 27965<li>new software-specific easyblock for cryptography (to fix missing 27966 <code>-pthread</code> for all versions) 27967 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1874">#1874</a>)</li> 27968<li>minor enhancements, including:<ul> 27969<li>update WPS easyblock for v3.6 & newer 27970 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1315">#1315</a>)</li> 27971<li>update FSL easyblock to support FSL v6.0.2 & newer 27972 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1860">#1860</a>)</li> 27973<li>add <code>setup_cmake_env</code> function in CMakeMake easyblock which can 27974 be leveraged in other easyblocks, and use it for OpenFOAM 27975 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1869">#1869</a>)</li> 27976<li>remove obsolete configure options for Python + build with 27977 optimizations/LTO enabled for recent Python versions 27978 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1876">#1876</a>)</li> 27979<li>update WPS easyblock for recent versions: set <code>$WRF_DIR</code> to 27980 point to location of WRF installation 27981 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1886">#1886</a>)</li> 27982<li>make sure <code>$LIBLAPACK_MT</code> is set before using it in ESMF 27983 easyblock 27984 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1887">#1887</a>)</li> 27985<li>remove useless <code>PATH</code> entries + add <code>PKG_CONFIG_PATH</code> in imkl 27986 easyblock 27987 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1900">#1900</a>)</li> 27988<li>enhance tbb easyblock to support building on POWER 27989 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1912">#1912</a>)</li> 27990<li>enhance TensorFlow easyblock to pick up on 27991 <code>--cuda-compute-capabilities</code>, and issue a warning if no CUDA 27992 compute capabilities are specified 27993 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1913">#1913</a>)</li> 27994<li>add custom easyconfig parameter <code>build_type</code> to generic 27995 CMakeMake easyblock 27996 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1915">#1915</a>, 27997 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1922">#1922</a>)</li> 27998</ul> 27999</li> 28000<li>various bug fixes, including:<ul> 28001<li>fix for conda packages that rely on particular versions of 28002 Python 28003 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1836">#1836</a>)</li> 28004<li>fix path for intel and netCDF lib directories in NCL easyblock 28005 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1862">#1862</a>)</li> 28006<li>fix CUDA 10.1 installation on POWER 28007 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1871">#1871</a>)</li> 28008<li>change Bazel easyblock to prefer using Java dependency rather 28009 than included JDK (fix for POWER9) 28010 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1875">#1875</a>)</li> 28011<li>remove optarch warning in GROMACS for Cray toolchains 28012 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1879">#1879</a>)</li> 28013<li>also fix <code>$WM_COMPILE_OPTION</code> in OpenFOAM rc scripts to make 28014 debug builds work correctly 28015 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1880">#1880</a>)</li> 28016<li>limit MPI ranks used for running WRF test cases to max. 4 + 28017 include contents of rsl.error.0000 output file in case test 28018 failed 28019 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1884">#1884</a>)</li> 28020<li>update <code>$PYTHONPATH</code> + add <code>python -c 'import mrtrix3'</code> as 28021 sanity check command for recent MRtrix versions 28022 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1889">#1889</a>)</li> 28023<li>update sanity check in SAMtools easyblock for version 1.10 28024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1890">#1890</a>)</li> 28025<li>make sure <code>$PYTHONNOUSERSITE</code> it set when performing sanity 28026 check for (bundles of) Python package(s) 28027 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1891">#1891</a>)</li> 28028<li>fix install dir subdir for WPS v4.0+ that is considered for 28029 <code>$PATH</code> and <code>$LD_LIBRARY_PATH</code> 28030 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1895">#1895</a>)</li> 28031<li>impi: don't rebuild libfabric if the source code is not present 28032 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1896">#1896</a>)</li> 28033<li>also copy component patches to self.cfg in Bundle generic 28034 easyblock 28035 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1897">#1897</a>)</li> 28036<li>skip patch step in Bundle generic easyblock (per-component 28037 patches are still applied) 28038 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1898">#1898</a>)</li> 28039<li>derive easyblock for iccifort only from icc easyblock (not 28040 ifort), to avoid adding include subdir to <code>$CPATH</code> 28041 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1899">#1899</a>)</li> 28042<li>
28042add <code>export LANG=C</code> to preinstallopts instead of install_script 28043 path in CUDA easyblock 28044 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1902">#1902</a>)</li> 28045<li>stop setting updating <code>$CPATH</code> and <code>$LIBRARY_PATH</code> for GCC and 28046 GCCcore, not required 28047 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1903">#1903</a>)</li> 28048<li>remove <code>$LIBRARY_PATH</code> entries in iccifort easyblock, already 28049 known to icc et al 28050 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1904">#1904</a>)</li> 28051<li>use major/minor version of Python command being used if 28052 <code>req_py_majver</code>/<code>req_py_minver</code> are not specified 28053 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1907">#1907</a>)</li> 28054<li>define <code>$EB_PYTHON</code> in module for EasyBuild installation, to 28055 make sure correct Python version is used at runtime 28056 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1908">#1908</a>)</li> 28057<li>fix Python easyblock to allow configuring build of Python v3.8 28058 (<code>Setup.dist</code> script was renamed to <code>Setup</code>) 28059 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1909">#1909</a>)</li> 28060<li>fix netCDF easyblock for version 4.4.0 28061 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1911">#1911</a>)</li> 28062<li>correct comment about when we set <code>RUNPARALLEL</code> in HDF5 28063 easyblock 28064 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1914">#1914</a>)</li> 28065<li>do not sanity check on MATLAB compiler, since it requires a 28066 separate license 28067 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1916">#1916</a>)</li> 28068<li>build HDF5 without MPI C++ extension to avoid breaking linkage 28069 for C software that requires HDF5 28070 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1918">#1918</a>, 28071 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1919">#1919</a>)</li> 28072<li>override <code>set_pylibdirs</code> method in 28073 <code>VersionIndependentPythonPackage</code> to hard set <code>self.pylibdir</code> to 28074 'lib' 28075 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1924">#1924</a>)</li> 28076</ul> 28077</li> 28078<li>other changes:<ul> 28079<li>increase timeout for interactive installation command in CUDA 28080 easyblock to 1000 sec. 28081 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1878">#1878</a>)</li> 28082<li>disable running of <code>sudo apt-get update</code> in GitHub CI config, 28083 since it's failing (and we don't really need it) 28084 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1882">#1882</a>)</li> 28085<li>stop requiring Python dep for SWIG, just configure with 28086 <code>--without-python</code> if Python is not a dependency 28087 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1894">#1894</a>)</li> 28088<li>update copyright statements for 2020 28089 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1905">#1905</a>)</li> 28090<li>make Hound CI code style checker ignore "Black would make 28091 changes" produced by flake8-black 28092 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1923">#1923</a>)</li> 28093</ul> 28094</li> 28095</ul> 28096<p><strong>easyconfigs</strong></p> 28097<ul> 28098<li>added example easyconfig files for 27 new software packages:<ul> 28099<li>Autoconf-archive 28100 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9658">#9658</a>), 28101 breseq 28102 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9603">#9603</a>), 28103 CrossMap 28104 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9483">#9483</a>), 28105 CSBDeep 28106 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9560">#9560</a>), 28107 CNT-ILP 28108 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9323">#9323</a>), 28109 cytoolz 28110 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9453">#9453</a>), 28111 Faber 28112 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9553">#9553</a>), 28113 Fiji 28114 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8748">#8748</a>), 28115 GARLI 28116 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9404">#9404</a>), 28117 Globus-CLI 28118 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9565">#9565</a>), 28119 GtkSourceView 28120 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9526">#9526</a>), 28121 gradunwarp 28122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9648">#9648</a>), 28123 gsettings-desktop-schemas 28124 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9529">#9529</a>), 28125 HyPhy 28126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9405">#9405</a>), 28127 horton 28128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7449">#7449</a>), 28129 IGMPlot 28130 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9438">#9438</a>), 28131 LEMON 28132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9323">#9323</a>), 28133 Meld 28134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9530">#9530</a>), 28135 mhcflurry 28136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9554">#9554</a>), 28137 NCIPLOT 28138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9419">#9419</a>), 28139 ncl 28140 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9632">#9632</a>), 28141 OpenSlide 28142 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9499">#9499</a>), 28143 openslide-python 28144 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9499">#9499</a>), 28145 pythran 28146 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9488">#9488</a>, 28147 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9594">#9594</a>), 28148 Qualimap 28149 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9411">#9411</a>), 28150 TinyDB 28151 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9555">#9555</a>), 28152 TreeShrink 28153 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9381">#9381</a>)</li> 28154</ul> 28155</li> 28156<li>
28156added additional easyconfigs for various supported software 28157 packages, including:<ul> 28158<li>Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 28159 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2, GEOS 3.8.0, 28160 GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 28161 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10, lxml 4.4.2, Mothur 1.43.0, 28162 mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 28163 4.5.2, numactl 2.0.13, OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, 28164 OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1, pocl 28165 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, 28166 ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0, SWIG 4.0.1, Salmon 28167 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ 28168 fosscuda/2019b, torchvision 0.4.2, WPS 4.1, WRF 4.1.3</li> 28169</ul> 28170</li> 28171<li>added easyconfigs for <code>intel/2020.00</code> toolchain 28172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9575">#9575</a>)</li> 28173<li>minor enhancements, including:<ul> 28174<li>add POWER9 support to CUDA 10.1 easyconfigs 28175 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9442">#9442</a>)</li> 28176<li>build CMake in parallel 28177 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9543">#9543</a>)</li> 28178<li>use NCCL for GPU ops in Horovod 0.18.2 easyconfig 28179 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9562">#9562</a>)</li> 28180<li>update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) 28181 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9585">#9585</a>)</li> 28182</ul> 28183</li> 28184<li>various bug fixes, including:<ul> 28185<li>fix remote launch of broker and workers for SCOOP 28186 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9366">#9366</a>)</li> 28187<li>fix failing RPATH sanity check for NCL 6.6.2 due to missing 28188 dependencies (+ add easyconfig using <code>foss/2018b</code>) 28189 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9388">#9388</a>)</li> 28190<li>add missing 'wheel' extensions to Spark 2.4.0 easyconfig using 28191 <code>intel/2018b</code> toolchain 28192 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9424">#9424</a>)</li> 28193<li>add missing OS dependencies in Java 1.8 easyconfig used on POWER 28194 systems 28195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9454">#9454</a>)</li> 28196<li>fix build of recent Bazel versions on Power9 + stick to Java/1.8 28197 as dependency 28198 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9455">#9455</a>)</li> 28199<li>fix CMake 3.15.3 build on Power (+ enable building in parallel) 28200 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9469">#9469</a>)</li> 28201<li>fix source URLs in xorg-macros easyconfigs 28202 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9477">#9477</a>, 28203 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9578">#9578</a>)</li> 28204<li>add missing wcwidth extension to Python 2.7.15 + 2.7.16 28205 easyconfigs & enable 'pip check' in sanity check 28206 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9479">#9479</a>)</li> 28207<li>remove (wrong) <code>GI_TYPELIB_PATH</code> and <code>XDG_DATA_DIRS</code> in various 28208 easyconfigs 28209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9528">#9528</a>, 28210 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9577">#9577</a>, 28211 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9615">#9615</a>)</li> 28212<li>use xorg-macros as dependency in X11 easyconfigs (rather than 28213 installing it as a bundle component) 28214 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9546">#9546</a>)</li> 28215<li>fix lpsymphony extension for R-bundle-Bioconductor 28216 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9548">#9548</a>)</li> 28217<li>add correct 'old-versions' source URL to all Mesa easyconfigs 28218 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9569">#9569</a>)</li> 28219<li>add missing SHA256 checksums for Armadillo 28220 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9572">#9572</a>)</li> 28221<li>also define <code>$AUGUSTUS_BIN_PATH</code> and <code>$AUGUSTUS_SCRIPTS_PATH</code> in 28222 generated module file for AUGUSTUS 28223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9579">#9579</a>)</li> 28224<li>
28224add SSL OS dependencies for GDAL 3.0.0 28225 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9586">#9586</a>)</li> 28226<li>add missing jupyter_contrib_core extension for IPython 7.7.0+ + 28227 consistently include jupyter_nbextensions_configurator extension 28228 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9587">#9587</a>)</li> 28229<li>patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long 28230 double in GCC 28231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9590">#9590</a>)</li> 28232<li>patch for GCCcore 8.2.0 to fix '__float128 is not supported 28233 on this target' on ppc64le 28234 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9591">#9591</a>)</li> 28235<li>fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 28236 'monotonic' extension 28237 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9601">#9601</a>)</li> 28238<li>use absolute path for extraction to allow relocating the build 28239 dir for g2log-1.0 28240 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9604">#9604</a>)</li> 28241<li>add alternate SHA256 checksum for kallisto-0.43.1 after 28242 re-release under same version without code changes 28243 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9611">#9611</a>)</li> 28244<li>add additional valid checksum for MASS 7.3-51.4 extension in R 28245 3.6.0 easyconfigs 28246 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9621">#9621</a>)</li> 28247<li>update ctffind website 28248 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9622">#9622</a>)</li> 28249<li>make sure we use easybuild Clang in pocl easyconfigs 28250 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9624">#9624</a>)</li> 28251<li>make <code>postinstallcmds</code> independent of current working directory 28252 in OpenCV 3.1.0 easyconfigs 28253 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9628">#9628</a>)</li> 28254<li>update <code>source_urls</code> to include old releases folder in libsodium 28255 easyconfigs 28256 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9632">#9632</a>)</li> 28257<li>fix source URLs for ant v1.10.5 - v1.10.7 28258 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9633">#9633</a>)</li> 28259<li>update URLs to new location of libxc 28260 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9635">#9635</a>)</li> 28261<li>add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 28262 3.6.0 28263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9644">#9644</a>)</li> 28264<li>update source URLs in QCA 2.1.0 easyconfigs 28265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9647">#9647</a>)</li> 28266<li>fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer 28267 available on PyPI 28268 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9649">#9649</a>)</li> 28269<li>
28269fix tesseract 4.1.0 dependencies 28270 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9650">#9650</a>)</li> 28271<li>make ICU 64.2 depend on Python3 instead of Python 2, to avoid 28272 picking up system Python 3.x 28273 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9652">#9652</a>)</li> 28274<li>use <code>True</code> (boolean value) rather than <code>'True'</code> (string value) 28275 for boolean easyconfig parameters 28276 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9657">#9657</a>)</li> 28277<li>fix pyfits easyconfig by adding missing d2to1 extension 28278 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9687">#9687</a>)</li> 28279</ul> 28280</li> 28281<li>other changes:<ul> 28282<li>disable running of <code>sudo apt-get update</code> in GitHub CI config, 28283 since it's failing (and we don't really need it) 28284 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9492">#9492</a>)</li> 28285<li>require that <code>sanity_pip_check</code> is enabled in new/changed 28286 easyconfigs 28287 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9516">#9516</a>, 28288 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9576">#9576</a>)</li> 28289<li>update copyright statements for 2020 28290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9598">#9598</a>)</li> 28291<li>allow missing '-Python-*' versionsuffix for existing 28292 easyconfig files changed in PRs 28293 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9634">#9634</a>)</li> 28294</ul> 28295</li> 28296</ul> 28297<h2 id="release_notes_eb410">EasyBuild v4.1.0 (December 4th 2019)<a class="headerlink" href="#release_notes_eb410" title="Permanent link">¶</a></h2> 28298<p>bugfix/update release</p> 28299<p><strong>framework</strong></p> 28300<ul> 28301<li>various enhancements, including:<ul> 28302<li>performance improvements:<ul> 28303<li>skip validation when copying EasyConfig object for extension 28304 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3071">#3071</a>)</li> 28305<li>correctly specify that ActiveMNS & co are singleton classes 28306 when using Python 3 28307 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3073">#3073</a>)</li> 28308<li>don't call out to prohibitively expensive 28309 <code>getRootLoggerName</code> in <code>getLogger</code>, just use 'root' 28310 instead 28311 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3074">#3074</a>)</li> 28312<li>fix inconsistent module path usage that leads to repeated 28313 reloading in HMNS 28314 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3099">#3099</a>)</li> 28315</ul> 28316</li> 28317<li>add support for specifying different dependency version based on 28318 processor architecture 28319 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3047">#3047</a>)</li> 28320<li>support use of glob patterns for paths to files with external 28321 modules metadata 28322 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3075">#3075</a>)</li> 28323<li>take into account that external modules may not be visible 28324 directly (due to module hierarchy) 28325 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3083">#3083</a>)</li> 28326<li>add support for including 'extensions' statement in Lua 28327 modules with Lmod 8.2.8+ 28328 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3085">#3085</a>, 28329 <a href="https://github.com/easybuilders/easybuild-framework/pull/3107">#3107</a>, 28330 <a href="https://github.com/easybuilders/easybuild-framework/pull/3110">#3110</a>)</li> 28331<li>add support for <code>--sync-pr-with-develop</code> 28332 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3087">#3087</a>)</li> 28333<li>add support for <code>--new-branch-github</code>, <code>--new-pr-from-branch</code>, 28334 <code>--sync-branch-with-develop</code>, <code>--update-branch-github</code> 28335 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3103">#3103</a>)</li> 28336<li>fix typo in docstring for <code>new_branch_github</code> 28337 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3106">#3106</a>)</li> 28338</ul> 28339</li> 28340<li>various bug fixes, including:<ul> 28341<li>correctly handle <code>iccifortcuda</code> toolchain with standalone 28342 <code>iccifort</code> in <code>det_toolchain_compilers</code> 28343 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3055">#3055</a>)</li> 28344<li>init git repo with <code>git.repo.clone()</code> instead of <code>copy_dir()</code> 28345 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3062">#3062</a>)</li> 28346<li>
28346fix regular expression so depends-on statements are recognized 28347 correctly in Tcl module files 28348 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3065">#3065</a>)</li> 28349<li>update GitPython to latest version that supports Python 2.6 in 28350 requirements.txt to fix broken <code>test_new_update_pr</code> 28351 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3066">#3066</a>)</li> 28352<li>imply <code>--disable-pre-create-installdir</code> with 28353 <code>--inject-checksums</code> 28354 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3069">#3069</a>)</li> 28355<li>handle patches in extensions more like normal patches 28356 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3067">#3067</a>)</li> 28357<li>take into account that <code>platform.linux_distribution</code> and 28358 <code>platform.dist</code> was removed in Python 3.8 28359 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3078">#3078</a>)</li> 28360<li>always include mandatory easyconfig parameters in dumped 28361 easyconfig 28362 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3081">#3081</a>)</li> 28363<li>hide backup module file when using Lmod 6.x (fixes 28364 <a href="https://github.com/easybuilders/easybuild-easyconfigs/issues/9302">#9302</a>) 28365 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3089">#3089</a>)</li> 28366<li>add better error message when mandatory key is missing from a 28367 dictionary easyconfig parameter 28368 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3092">#3092</a>)</li> 28369<li>also create symlinks for default modules in class module folders 28370 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3093">#3093</a>)</li> 28371<li>fix semantics of <code>--set-default-module</code>: only set default for 28372 specified easyconfigs, not for the ones that are installed as 28373 dependencies via <code>--robot</code> 28374 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3094">#3094</a>)</li> 28375<li>fix various issues in extracting comments from original 28376 easyconfig file and including them again in dumped easyconfig 28377 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3095">#3095</a>)</li> 28378<li>don't use <code>%(version)s</code> template in <code>exts_default_options</code> in 28379 dumped easyconfig 28380 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3096">#3096</a>)</li> 28381<li>fix generated module statements in case only a single version is 28382 listed in <code>multi_deps</code> 28383 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3097">#3097</a>)</li> 28384<li>fix broken <code>test_show_system_info</code> on macOS due to 'Python' 28385 binary 28386 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3105">#3105</a>)</li> 28387<li>take into account that dependency version could be a dict rather 28388 than a string value in template_constant_dict 28389 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3111">#3111</a>)</li> 28390</ul> 28391</li> 28392<li>other changes:<ul> 28393<li>deprecate running EasyBuild with Python 2.6 via new 28394 <code>check_python_version()</code> function 28395 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3076">#3076</a>)</li> 28396<li>deprecate support for using Lmod 6.x 28397 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3077">#3077</a>)</li> 28398<li>trim set of test configurations in Travis CI 28399 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3086">#3086</a>)</li> 28400<li>flesh out <code>env_vars_external_module</code> from 28401 <code>
28401Toolchain._simulated_load_dependency_module</code> 28402 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3088">#3088</a>)</li> 28403</ul> 28404</li> 28405</ul> 28406<p><strong>easyblocks</strong></p> 28407<ul> 28408<li>new software-specific easyblock for cuDNN, to allow setting 28409 <code>cudnnarch</code> 28410 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1855">#1855</a>)</li> 28411<li>refactored software-specific easyblock for Xmipp, based on Scons 28412 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1837">#1837</a>)</li> 28413<li>minor enhancements, including:<ul> 28414<li>add <code>prebuildopts</code> to Bazel build command 28415 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1838">#1838</a>)</li> 28416<li>add support to Toolchain generic easyblock for defining $EB* 28417 environment variables for toolchain components that use an 28418 external module 28419 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1849">#1849</a>)</li> 28420<li>add support for running 'pip check' during sanity check in 28421 generic PythonPackage easyblock 28422 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1853">#1853</a>)</li> 28423</ul> 28424</li> 28425<li>various bug fixes, including:<ul> 28426<li>clean up <code>/tmp/cuda-installer.log</code> in CUDA easyblock, to avoid 28427 segfault in cuda-installer 28428 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1835">#1835</a>)</li> 28429<li>minor fix to name of Gctf binary 28430 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1840">#1840</a>)</li> 28431<li>move BLAS toolchain existence check earlier in SuperLU easyblock 28432 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1842">#1842</a>)</li> 28433<li>fixes for TensorFlow easyblocks w.r.t. Bazel build options & 28434 <code>__init__</code> in top-level google-protobuf package dir 28435 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1843">#1843</a>)</li> 28436<li>fix support for sequential version in MUMPS easyblock 28437 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1845">#1845</a>)</li> 28438<li>change default value of <code>files_to_copy</code> to None in MakeCp 28439 generic easyblock + code cleanup & use <code>change_dir</code>, <code>copy_dir</code>, 28440 <code>copy_file</code> and <code>mkdir</code> function from <code>filetools</code> 28441 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1848">#1848</a>)</li> 28442<li>prepend <code>-L$EBROOTZLIB/lib</code> to <code>LDFLAGS</code> in SCOTCH easyblock 28443 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1850">#1850</a>)</li> 28444<li>
28444improve configuration in netCDF and netcdf4_python easyblocks 28445 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1852">#1852</a>)</li> 28446<li>fix CUDA header paths for TensorFlow versions < 1.14 28447 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1854">#1854</a>)</li> 28448<li>handle incorrect regex better in generic CmdCp easyblock 28449 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1861">#1861</a>)</li> 28450<li>add missing docstrings in cmakeninja easyblock 28451 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1867">#1867</a>)</li> 28452</ul> 28453</li> 28454<li>other changes:<ul> 28455<li>add GitHub Actions workflow to run easybuild-easyblocks test 28456 suite 28457 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1844">#1844</a>)</li> 28458</ul> 28459</li> 28460</ul> 28461<p><strong>easyconfigs</strong></p> 28462<ul> 28463<li>added example easyconfig files for 46 new software packages:<ul> 28464<li>Amara 28465 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9340">#9340</a>), 28466 anvio 28467 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9387">#9387</a>), 28468 Arriba 28469 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9226">#9226</a>, 28470 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9244">#9244</a>), 28471 attr 28472 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7824">#7824</a>), 28473 bibtexparser 28474 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9284">#9284</a>), 28475 bwa-meth 28476 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9217">#9217</a>), 28477 CITE-seq-Count 28478 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9237">#9237</a>), 28479 CoordgenLibs 28480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9374">#9374</a>), 28481 dtcmp 28482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9052">#9052</a>), 28483 fatslim 28484 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9193">#9193</a>), 28485 GromacsWrapper 28486 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9177">#9177</a>), 28487 GULP 28488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9243">#9243</a>), 28489 hdf5storage 28490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9195">#9195</a>), 28491 ITSTool 28492 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7260">#7260</a>), 28493 kim-api 28494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8786">#8786</a>), 28495 kwant 28496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9238">#9238</a>), 28497 libarchive 28498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9052">#9052</a>), 28499 libcircle 28500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9052">#9052</a>), 28501 libxml2-python 28502 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7260">#7260</a>), 28503 lifelines 28504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9215">#9215</a>), 28505 lwgrp 28506 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9052">#9052</a>), 28507 maeparser 28508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9374">#9374</a>), 28509 MaxQuant 28510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9281">#9281</a>), 28511 MethylDackel 28512 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9216">#9216</a>), 28513 MoviePy 28514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9205">#9205</a>), 28515 mpifileutils 28516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9052">#9052</a>), 28517 mpiP 28518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9059">#9059</a>), 28519 nanofilt 28520 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8502">#8502</a>), 28521 NOVOPlasty 28522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9326">#9326</a>), 28523 openkim-models 28524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8786">#8786</a>), 28525 parallel-fastq-dump 28526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9218">#9218</a>), 28527 pasta 28528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9348">#9348</a>), 28529 pyqstem 28530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9277">#9277</a>), 28531 python-Levenshtein 28532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9237">#9237</a>), 28533 RapidJSON 28534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9373">#9373</a>), 28535 RDFlib 28536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9346">#9346</a>), 28537 RQGIS3 28538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9125">#9125</a>),
28539 Short-Pair 28540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9376">#9376</a>), 28541 SpliceMap 28542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9375">#9375</a>), 28543 TRIQS-cthyb 28544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9230">#9230</a>), 28545 TRIQS-dft_tools 28546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9230">#9230</a>), 28547 TRIQS-tprf 28548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9230">#9230</a>), 28549 UMI-tools 28550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9237">#9237</a>), 28551 VarDict 28552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7283">#7283</a>), 28553 Xmipp 28554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9257">#9257</a>), 28555 XSD 28556 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9347">#9347</a>)</li> 28557</ul> 28558</li> 28559<li>added additional easyconfigs for various supported software 28560 packages, including:<ul> 28561<li>awscli 1.16.290, BLIS 0.6.0, Bazel 1.1.0, Biopython 1.75, 28562 Blender 2.81, bokeh 1.4.0, CONCOCT 1.1.0, CUDA 10.2.89, Catch2 28563 2.11.0, CellRanger 3.1.0, CheckM 1.0.18, dask 2.8.0, deepTools 28564 3.3.1, FastANI 1.2, Flye 2.6, GDCM 3.0.4, GTDB-Tk 0.3.2, Glade 28565 3.8.6, Hadoop 2.9.2, h5py 2.10.0, hypothesis 4.44.2, IPython 28566 7.9.0, Kaiju 1.7.2, Kraken 1.1.1, libsodium 1.0.18, MEGAHIT 28567 1.2.8, Mesa 19.2.1, MetaBAT 2.14, matplotlib 3.1.1, metaWRAP 28568 1.2.2,cNCCL 2.4.8, NGS 2.10.0, NiBabel 2.5.1, netCDF 4.7.1, 28569 networkx 2.4, numba 0.46.0, OpenCV 3.4.7, OpenCoarrays 2.8.0, 28570 OpenEXR 2.4.0, OpenFOAM v1906, OpenImageIO 2.0.12, ParaView 28571 5.6.2, Pillow 6.2.1, PyTorch 1.3.1, PyYAML 5.1.2, Pysam 0.15.3, 28572 picard 2.21.1, prokka 1.14.5, protobuf 3.10.0, R-keras 2.2.5.0, 28573 Racon 1.4.7, SCOTCH 6.0.9, SRPRISM 3.1.1, Salmon 0.14.2, 28574 SciPy-bundle 2019.10, Subread 2.0.0, scikit-image 0.16.2, 28575 scikit-learn 0.21.3, TRIQS 2.2.1, TensorFlow 1.15.0, TensorFlow 28576 2.0.0 w/ fosscuda/2019b, Tkinter 3.7.4, ToFu 1.4.1, tbb 2019_U9, 28577 Xerces-C++ 3.2.2, Xmipp 3.19.04, yaff 1.6.0</li> 28578</ul> 28579</li> 28580<li>added easyconfigs for <code>intelcuda/2019a</code> toolchain 28581 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9271">#9271</a>)</li> 28582<li>minor enhancements, including:<ul> 28583<li>tweak Java 1.8 wrapper to use different Java version on POWER 28584 systems 28585 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9081">#9081</a>)</li> 28586<li>add jupyter_nbextensions_configurator extension to IPython 7.7.0 28587 easyconfigs 28588 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9133">#9133</a>)</li> 28589<li>add additional extensions to R 3.6.0 easyconfigs 28590 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9184">#9184</a>, 28591 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9275">#9275</a>)</li> 28592<li>add additional extensions to R-bundle-Bioconductor 3.9 28593 easyconfig 28594 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9185">#9185</a>, 28595 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9349">#9349</a>, 28596 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9410">#9410</a>)</li> 28597<li>enhance sanity check in cutadapt 1.18 easyconfigs + consistently 28598 use PythonBundle & <code>use_pip</code> 28599 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9219">#9219</a>)</li> 28600<li>update cuDNN 7.6.4.38 easyconfigs to support both x86_64 and 28601 ppc64le 28602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9331">#9331</a>)</li> 28603<li>
28603tweak NCCL 2.4.8 easyconfig to support x86_64 and ppc64le 28604 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9336">#9336</a>)</li> 28605<li>define <code>$SPARK_HOME</code> in generated module file for Spark 2.4.0 28606 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9408">#9408</a>)</li> 28607<li>add sanity check command for matplotlib 3.x with Python 3 to 28608 check import from mpl_toolkits 28609 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9413">#9413</a>, 28610 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9414">#9414</a>)</li> 28611</ul> 28612</li> 28613<li>various bug fixes, including:<ul> 28614<li>explicitly set <code>SYSCONFDIR</code> configure option in TurboVNC 28615 easyconfig 28616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9317">#9137</a>)</li> 28617<li>patch pigz Makefile so zlib provided by EasyBuild is picked up 28618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9138">#9138</a>)</li> 28619<li>add libjpeg-turbo as dependency to recent LibTIFF easyconfigs, 28620 to avoid picking up LibTIFF installed in system 28621 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9146">#9146</a>)</li> 28622<li>add freetype as dependency to OpenImageIO, to avoid picking up 28623 freetyype installed in system 28624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9147">#9147</a>, 28625 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9152">#9152</a>)</li> 28626<li>fix definition of <code>fosscuda/2019b</code> to make sure it works with 28627 hierarchical MNS 28628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9178">#9178</a>)</li> 28629<li>add missing setuptools_scm extension required to build dateutil 28630 extension in Python 3.7.0 easyconfigs 28631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9209">#9209</a>)</li> 28632<li>add Python as build dependency for recent Bazel versions 28633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9223">#9223</a>, 28634 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9299">#9299</a>, 28635 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9342">#9342</a>)</li> 28636<li>fix homepage & description in Bioconductor easyconfigs 28637 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9225">#9225</a>)</li> 28638<li>fix checksum in Stacks 2.41 easyconfig after sneaky re-release 28639 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9232">#9232</a>)</li> 28640<li>apply fixes to ImageJ 1.51k easyconfig 28641 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9245">#9245</a>)</li> 28642<li>consistently use patch for OpenCV 3.4.7 28643 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9279">#9279</a>)</li> 28644<li>use protobuf 3.10.0 as build dep for TensorFlow 2.0.0 w/ 28645 fosscuda/2019b + use nodocs variant of git as build dep 28646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9298">#9298</a>)</li> 28647<li>add Jasper dependency to Qt5 v.5.13.1 28648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9313">#9313</a>)</li> 28649<li>fix Python 3.7.2 required OpenSSL version for old OS to the one 28650 provided on the same toolchain 28651 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9324">#9324</a>)</li> 28652<li>add missing extensions required by Sphinx & pytest to 28653 easyconfigs for Python 3.7.2 and 3.7.4 28654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9329">#9329</a>)</li> 28655<li>update TensorFlow v1.14.0 + v2.0.0 CUDA patch to handle compiler 28656 wrappers like ccache 28657 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9333">#9333</a>)</li> 28658<li>patch binutils 2.31.1 and 2.32 to fix compatibility with RHEL8 28659 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9335">#9335</a>)</li> 28660<li>add missing extensions in TensorFlow 2.0.0 easyconfigs (+ update 28661 to tensorboard/tensorflow-estimator 2.0.1) 28662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9338">#9338</a>)</li> 28663<li>fix logic to determine location of scripts dir + ensure right 28664 compiler flags are used in KAT easyconfigs 28665 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9360">#9360</a>)</li> 28666<li>
28666add missing GCCcore-6.3.0_fix-sanitizer_linux.patch in GCCcore 28667 6.4.0 easyconfig 28668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9362">#9362</a>)</li> 28669<li>fix linker errors when linking with libhts.a for MetaBAT 2.12.1 28670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9379">#9379</a>)</li> 28671<li>add egg-info file via patch in VTK v8.2.0, for Python 2.7.15, 28672 3.7.2, 3.7.4 28673 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9386">#9386</a>)</li> 28674<li>promote binutils to a runtime dependency for Python in GCCcore 28675 based builds 28676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9402">#9402</a>)</li> 28677<li>fix archive URL typo for ncdf4 28678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9407">#9407</a>)</li> 28679<li>fix problems with mpl_toolkits namespace for matplotlib 28680 easyconfigs using Python 2 28681 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9415">#9415</a>, 28682 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9416">#9416</a>, 28683 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9417">#9417</a>)</li> 28684</ul> 28685</li> 28686<li>other changes:<ul> 28687<li>ignore commented out lines in easyconfig files when checking for 28688 <a href="http://">http://</a> URLs 28689 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9224">#9224</a>)</li> 28690<li>add GitHub Actions workflow to run easybuild-easyconfigs test 28691 suite 28692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9231">#9231</a>, 28693 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9255">#9255</a>)</li> 28694<li>archive old patches for Xmipp 3.1 28695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9256">#9256</a>)</li> 28696<li>speed up easyconfigs test suite by avoiding re-parsing and 28697 re-ordering of easyconfigs 28698 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9236">#9236</a>)</li> 28699<li>only run easyconfigs test suite with Python 2.7 & 3.6 + Lmod 7 28700 in Travis CI 28701 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9297">#9297</a>)</li> 28702<li>archive ACML easyconfigs 28703 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9365">#9367</a>)</li> 28704<li>update CMake build in Eigen 3.3.7 to use more recent toolchain 28705 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9398">#9398</a>)</li> 28706</ul> 28707</li> 28708</ul> 28709<h2 id="release_notes_eb401">EasyBuild v4.0.1 (October 15th 2019)<a class="headerlink" href="#release_notes_eb401" title="Permanent link">¶</a></h2> 28710<p>bugfix/update release</p> 28711<p><strong>framework</strong></p> 28712<ul> 28713<li>various enhancements, including:<ul> 28714<li>add '<code>parallel</code>' to list of config templates 28715 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3036">#3036</a>)</li> 28716<li>add GitHub Actions workflow to run easybuild-framework test 28717 suite 28718 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3039">#3039</a>)</li> 28719<li>add '<code>retest</code>' as a reason to <code>--close-pr</code>, to close/re-open 28720 PRs to trigger re-test in Travis 28721 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3040">#3040</a>)</li> 28722<li>define <code>$EB_SCRIPT_PATH</code> in '<code>eb</code>' wrapper script, and 28723 consider it before location of '<code>eb</code>' determined via <code>$PATH</code> 28724 in <code>get_paths_for</code> function 28725 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3046">#3046</a>)</li> 28726<li>add support for <code>--remove-ghost-install-dirs</code> configuration 28727 option, and warn about (potential) ghost install dirs by default 28728 when <code>--force</code>/<code>--rebuild</code> is used 28729 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3050">#3050</a>)</li> 28730</ul> 28731</li> 28732<li>various bug fixes, including:<ul> 28733<li>update bootstrap script to support installing EasyBuild v4.0 28734 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3017">#3017</a>)</li> 28735<li>fix broken <code>test_download_repo</code> due to archiving of easyconfigs 28736 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3019">#3019</a>, 28737 <a href="https://github.com/easybuilders/easybuild-framework/pull/3023">#3023</a>)</li> 28738<li>avoid that <code>--inject-checksums</code> introduces list of patches for 28739 extensions as a single long line 28740 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3025">#3025</a>, 28741 <a href="https://github.com/easybuilders/easybuild-framework/pull/3034">#3034</a>)</li> 28742<li>enhance regex in <code>fix_shebang</code> method to fix more Python/Perl 28743 shebangs + avoid patching binary files 28744 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3029">#3029</a>)</li> 28745<li>delete test gist that is created by <code>--check-github</code> 28746 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3031">#3031</a>)</li> 28747<li>disable templates when defining easyconfig parameters in 28748 <code>EasyConfig.set_keys()</code> 28749 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3037">#3037</a>)</li> 28750<li>avoid setting GC3Pie's max_in_flight to <code>None</code> if 28751 <code>--job-max-jobs</code> is not specified 28752 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3038">#3038</a>)</li> 28753<li>fix use of <code>obtain_file</code> method for extensions 28754 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3042">#3042</a>)</li> 28755<li>error out if some GC3Pie job failed 28756 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3044">#3044</a>)</li> 28757</ul> 28758</li> 28759</ul> 28760<p><strong>easyblocks</strong></p> 28761<ul> 28762<li>one new generic easyblock: <code>CMakeNinja</code> 28763 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1829">#1829</a>)</li> 28764<li>new software-specific easyblock for Gctf 28765 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1827">#1827</a>), 28766 MotionCor2 28767 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1819">#1819</a>)</li> 28768<li>minor enhancements, including:<ul> 28769<li>update OpenFOAM easyblock for changes in version 1906 w.r.t. 28770 wamke rules 28771 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1772">#1772</a>)</li> 28772<li>
28772add <code>%(cudaarch)s</code> template variable so that it can be used in 28773 sources 28774 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1797">#1797</a>)</li> 28775<li>update Boost easyblock for versions >=1.71.0 28776 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1814">#1814</a>)</li> 28777<li>update RepeatMasker easyblock for version 4.0.9 28778 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1815">#1815</a>)</li> 28779<li>add <code>--verbose</code> flag to '<code>pip install</code>' when running EB in 28780 debug mode 28781 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1822">#1822</a>)</li> 28782<li>update TensorFlow easyblock to support TensorFlow 2.0 28783 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1823">#1823</a>)</li> 28784<li>add support in TensorFlow easyblock to run a custom test script 28785 as smoke test 28786 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1824">#1824</a>)</li> 28787<li>add support for installing QScintilla on top of PyQt5 28788 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1825">#1825</a>)</li> 28789<li>update VEP easyblock to make installation compatible with 28790 <code>Bio::EnsEMBL::XS</code> 28791 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1828">#1828</a>)</li> 28792</ul> 28793</li> 28794<li>various bug fixes, including:<ul> 28795<li>enhance TensorFlow easyblock to support installing TF 1.14.0 28796 with CUDA and MPI support 28797 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1811">#1811</a>, 28798 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1816">#1816</a>)</li> 28799<li>avoid <code>UnicodeDecodeError</code> when reading '<code>configure</code>' script 28800 and checking for '<code>Generated by GNU Autoconf</code>' in 28801 <code>ConfigureMake</code> 28802 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1817">#1817</a>, 28803 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1821">#1821</a>)</li> 28804<li>don't require '<code>python</code>' command to install libxml2 without 28805 Python bindings 28806 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1818">#1818</a>)</li> 28807<li>make sure "<code>generic=True</code>" actually turns on generic build in 28808 GCC easyblock 28809 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1826">#1826</a>)</li> 28810<li>fix compatibility of Trilinos easyblock with Python 3 28811 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1831">#1831</a>)</li> 28812</ul> 28813</li> 28814</ul> 28815<p><strong>easyconfigs</strong></p> 28816<ul> 28817<li>added example easyconfig files for 58 new software packages:<ul> 28818<li>ADOL-C 28819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9098">#9098</a>), 28820 ALFA 28821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9106">#9106</a>), 28822 ASTRID 28823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9088">#9088</a>), 28824 Annif 28825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8536">#8536</a>), 28826 bnpy 28827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8989">#8989</a>), 28828 bpp-core 28829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9064">#9064</a>), 28830 bpp-phyl 28831 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9064">#9064</a>), 28832 bpp-seq 28833 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9064">#9064</a>), 28834 Clang-Python-bindings 28835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9084">#9084</a>), 28836 CPB 28837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5869">#5869</a>), 28838 Centrifuge 28839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8714">#8714</a>), 28840 Chromaprint 28841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9047">#9047</a>), 28842 Con3F 28843 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8755">#8755</a>), 28844 DeepSurv 28845 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8096">#8096</a>), 28846 Essentia 28847 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9054">#9054</a>), 28848 FastRFS 28849 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9088">#9088</a>), 28850 GAT 28851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5871">#5871</a>), 28852 Gaia 28853 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9049">#9049</a>), 28854 Gctf 28855 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9097">#9097</a>), 28856 GenomeMapper 28857 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5872">#5872</a>), 28858 Infomap 28859 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9091">#9091</a>), 28860 kpcalg 28861 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8740">#8740</a>), 28862 libglvnd 28863 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9111">#9111</a>, 28864 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9130">#9130</a>), 28865 libsamplerate 28866 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9046">#9046</a>), 28867 libssh 28868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8865">#8865</a>), 28869 libzip 28870 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9073">#9073</a>), 28871 MetaboAnalystR 28872 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8773">#8773</a>), 28873 Metaxa2 28874 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8939">#8939</a>), 28875 MotionCor2 28876 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8942">#8942</a>), 28877 NFFT 28878 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9085">#9085</a>), 28879 PhyML 28880 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9103">#9103</a>), 28881 PlaScope 28882 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8714">#8714</a>), 28883 PyCharm 28884 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9100">#9100</a>), 28885 pbcopper 28886 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8928">#8928</a>), 28887 pbmm2 28888 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8929">#8929</a>), 28889 phylokit 28890 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9088">#9088</a>), 28891 phylonaut 28892 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9088">#9088</a>), 28893 phyx 28894 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9090">#9090</a>), 28895 pycma 28896 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8834">#8834</a>), 28897 Q6 28898 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9069">#9069</a>), 28899 Qt5Webkit 28900 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9120">
28900#9120</a>), 28901 ROME 28902 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9050">#9050</a>, 28903 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9062">#9062</a>), 28904 rioxarray 28905 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9007">#9007</a>), 28906 SVDquest 28907 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9088">#9088</a>), 28908 savvy 28909 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9124">#9124</a>), 28910 sciClone 28911 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7806">#7806</a>), 28912 shapAAR 28913 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8983">#8983</a>), 28914 shrinkwrap 28915 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9124">#9124</a>), 28916 Structure 28917 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5866">#5866</a>), 28918 trimAl 28919 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9063">#9063</a>), 28920 thurstonianIRT 28921 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9080">#9080</a>), 28922 TurboVNC 28923 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9110">#9110</a>, 28924 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9111">#9111</a>, 28925 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9128">#9128</a>), 28926 Tracer 28927 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8970">#8970</a>), 28928 TagLib 28929 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9048">#9048</a>), 28930 TRIQS 28931 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8835">#8835</a>), 28932 THetA 28933 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8875">#8875</a>), 28934 vcfnp 28935 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5862">#5862</a>), 28936 WebSocket++ 28937 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8842">#8842</a>)</li> 28938</ul> 28939</li> 28940<li>added additional easyconfigs for various supported software 28941 packages, including:<ul> 28942<li>Armadillo 9.700.2, arpack-ng 3.7.0, BLASR 5.3.3, Bazel 0.26.1 + 28943 Bazel 0.29.1, Cufflinks 20190706, DL_POLY_Classic 1.10, FFmpeg 28944 4.2.1, Go 1.13.1, Horovod 0.18.1, IOR 3.2.1, Julia 1.2.0, LLVM 28945 9.0.0, Mesa 19.1.7, Molden 6.1, Mono 6.4.0.198, NCO 4.8.1, , 28946 Net-core 3.0.0, Nim 1.0.0, OpenFOAM 2.2.x, PGI 19.7, PLUMED 28947 2.5.2, PMIx 3.1.4, PostgreSQL 11.3, psycopg2 2.8.3, QGIS 3.4.12, 28948 QScintilla 2.11.2, Qt5 5.13.1, ReFrame 2.19, Rust 1.37.0, Spack 28949 0.12.1, TAMkin 1.2.6, TensorFlow 1.14.0 w/ fosscuda/2019a, 28950 TensorFlow 2.0.0 w/ foss/2019a, UCX 1.6.1, VEP 96.0, xarray 28951 0.13.0</li> 28952</ul> 28953</li> 28954<li>added easyconfigs for <code>fosscuda/2019a</code> toolchain 28955 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9066">#9066</a>)</li> 28956<li>minor enhancements, including:<ul> 28957<li>add EBImage extension to easyconfig for R-bundle-Bioconductor 28958 3.9 28959 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8982">#8982</a>)</li> 28960<li>add check for <code>http://</code> URLs in easyconfig files added/changed 28961 in PRs 28962 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9012">#9012</a>)</li> 28963<li>add bbmle/emdbook/SOAR/rasterVis/tictoc extensions to R 3.6.0 28964 easyconfigs 28965 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9037">#9037</a>)</li> 28966<li>updated PyQt5 5.12.1 easyconfig to also build sip files + minor 28967 readability changes 28968 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9071">#9071</a>)</li> 28969<li>enabled <code>SQLITE_ENABLE_COLUMN_METADATA</code>, which is needed for 28970 GDAL (and QGIS) 28971 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9118">#9118</a>)</li> 28972<li>also install include/GL/internal/ for recent Mesa installations 28973 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9129">#9129</a>)</li> 28974</ul> 28975</li> 28976<li>various bug fixes, including:<ul> 28977<li>add ncurses as dependency to lftp 28978 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8646">#8646</a>)</li> 28979<li>
28979add patch for gettext 0.19.8* to avoid picking up global git 28980 config that could break the installation 28981 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8957">#8957</a>)</li> 28982<li>fix source URLs in GlimmerHMM easyconfigs 28983 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8980">#8980</a>)</li> 28984<li>add patch for PyTorch 1.2.0 to use version of torchvision that 28985 is compatible with PyTorch 1.2.0 28986 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8986">#8986</a>)</li> 28987<li>clarify the comment regarding the optarch setting in ITK-5.0.1 28988 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8991">#8991</a>)</li> 28989<li>fix homepage & description in easyconfig file for YAPS 28990 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8993">#8993</a>)</li> 28991<li>add patch for PyTorch 1.2.0 to fix failing softmax test on Intel 28992 Sandy Bridge 28993 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9010">#9010</a>)</li> 28994<li>fix permissions for TRF 28995 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9034">#9034</a>)</li> 28996<li>ICU needs Python 2.7+ to build, so add that as builddependency 28997 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9053">#9053</a>)</li> 28998<li>fix urls for Anaconda and Miniconda 28999 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9087">#9087</a>)</li> 29000<li>use a cuDNN version that has support for the CUDA version in 29001 <code>fosscuda/2019a</code> (CUDA 10.1) in PyTorch, TensorFlow and Theano 29002 easyconfigs 29003 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9112">#9112</a>)</li> 29004</ul> 29005</li> 29006<li>other changes:<ul> 29007<li>make sources in CUDA 10.1.105 use <code>%(cudaarch)s</code> template value 29008 (to use different source on POWER systems) 29009 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8136">#8136</a>)</li> 29010<li>update <code>Java/1.8</code> wrapper to <code>Java/1.8.0_221</code> 29011 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9038">#9038</a>)</li> 29012<li>allow divergent Java dep version as long as it's indicated by 29013 versionsuffix 29014 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/9041">#9041</a>)</li> 29015</ul> 29016</li> 29017</ul> 29018<h2 id="release_notes_eb400">EasyBuild v4.0.0 (September 20th 2019)<a class="headerlink" href="#release_notes_eb400" title="Permanent link">¶</a></h2> 29019<p>feature release (incl. backwards-incompatible changes)</p> 29020<p><strong>framework</strong></p> 29021<ul> 29022<li><strong>fixed compatibility with Python 3.5+</strong> 29023 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2708">#2708</a>, 29024 <a href="https://github.com/easybuilders/easybuild-framework/pull/2713">#2713</a>, 29025 <a href="https://github.com/easybuilders/easybuild-framework/pull/2714">#2714</a>, 29026 <a href="https://github.com/easybuilders/easybuild-framework/pull/2719">#2719</a>, 29027 <a href="https://github.com/easybuilders/easybuild-framework/pull/2721">#2721</a>, 29028 <a href="https://github.com/easybuilders/easybuild-framework/pull/2723">#2723</a>, 29029 <a href="https://github.com/easybuilders/easybuild-framework/pull/2729">#2729</a>, 29030 <a href="https://github.com/easybuilders/easybuild-framework/pull/2743">#2743</a>, 29031 <a href="https://github.com/easybuilders/easybuild-framework/pull/2744">#2744</a>, 29032 <a href="https://github.com/easybuilders/easybuild-framework/pull/2751">#2751</a>, 29033 <a href="https://github.com/easybuilders/easybuild-framework/pull/2756">#2756</a>, 29034 <a href="https://github.com/easybuilders/easybuild-framework/pull/2759">#2759</a>, 29035 <a href="https://github.com/easybuilders/easybuild-framework/pull/2761">#2761</a>, 29036 <a href="https://github.com/easybuilders/easybuild-framework/pull/2762">#2762</a>, 29037 <a href="https://github.com/easybuilders/easybuild-framework/pull/2765">#2765</a>, 29038 <a href="https://github.com/easybuilders/easybuild-framework/pull/2766">#2766</a>, 29039 <a href="https://github.com/easybuilders/easybuild-framework/pull/2767">#2767</a>, 29040 <a href="https://github.com/easybuilders/easybuild-framework/pull/2768">#2768</a>, 29041 <a href="https://github.com/easybuilders/easybuild-framework/pull/2774">#2774</a>, 29042 <a href="https://github.com/easybuilders/easybuild-framework/pull/2775">#2775</a>, 29043 <a href="https://github.com/easybuilders/easybuild-framework/pull/2778">#2778</a>, 29044 <a href="https://github.com/easybuilders/easybuild-framework/pull/2780">#2780</a>, 29045 <a href="https://github.com/easybuilders/easybuild-framework/pull/2785">#2785</a>, 29046 <a href="https://github.com/easybuilders/easybuild-framework/pull/2787">#2787</a>, 29047 <a href="https://github.com/easybuilders/easybuild-framework/pull/2789">#2789</a>, 29048 <a href="https://github.com/easybuilders/easybuild-framework/pull/2791">#2791</a>, 29049 <a href="https://github.com/easybuilders/easybuild-framework/pull/2792">#2792</a>, 29050 <a href="https://github.com/easybuilders/easybuild-framework/pull/2794">#2794</a>, 29051 <a href="https://github.com/easybuilders/easybuild-framework/pull/2800">#2800</a>, 29052 <a href="https://github.com/easybuilders/easybuild-framework/pull/2801">#2801</a>, 29053 <a href="https://github.com/easybuilders/easybuild-framework/pull/2805">#2805</a>, 29054 <a href="https://github.com/easybuilders/easybuild-framework/pull/2806">#2806</a>, 29055 <a href="https://github.com/easybuilders/easybuild-framework/pull/2895">#2895</a>, 29056 <a href="https://github.com/easybuilders/easybuild-framework/pull/2932">
29056#2932</a>, 29057 <a href="https://github.com/easybuilders/easybuild-framework/pull/2982">#2982</a>, 29058 <a href="https://github.com/easybuilders/easybuild-framework/pull/2992">#2992</a>, 29059 <a href="https://github.com/easybuilders/easybuild-framework/pull/3007">#3007</a>, 29060 <a href="https://github.com/easybuilders/easybuild-framework/pull/3011">#3011</a>)<ul> 29061<li>supported Python versions: 2.6, 2.7, 3.5, 3.6, 3.7</li> 29062<li>some functionality from the Python standard library should be 29063 imported from the new <code>easybuild.tools.py2vs3</code> package</li> 29064<li>see <a class="autorefs autorefs-internal" title="Compatibility with Python 3" href="../python-2-3-compatibility/#py2_py3_compatibility">Compatibility with Python 2 and Python 3</a> & 29065 <a class="autorefs autorefs-internal" href="../easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_functions_classes_constants">Overview of relocated functions, classes and constants in EasyBuild v4.0</a></li> 29066</ul> 29067</li> 29068<li><strong>ingested relevant code from</strong> <code>vsc-base</code> & <code>vsc-install</code> 29069 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2708">#2708</a>, 29070 <a href="https://github.com/easybuilders/easybuild-framework/pull/2713">#2713</a>, 29071 <a href="https://github.com/easybuilders/easybuild-framework/pull/2714">#2714</a>, 29072 <a href="https://github.com/easybuilders/easybuild-framework/pull/2763">#2763</a>, 29073 <a href="https://github.com/easybuilders/easybuild-framework/pull/2790">#2790</a>, 29074 <a href="https://github.com/easybuilders/easybuild-framework/pull/2993">#2993</a>)<ul> 29075<li><code>vsc-base</code> & <code>vsc-install</code> are no longer required as 29076 dependencies</li> 29077<li>the functionality that was provided by these packages is now 29078 (mostly) available from the <code>easybuild.base</code> package</li> 29079<li>any import statements from the '<code>vsc</code>' namespace will result 29080 in an error</li> 29081<li>see also <a class="autorefs autorefs-internal" href="../easybuild-v4/overview-of-changes/#eb4_changes_ingested_vsc_base">Ingested functionality from <code>vsc-base</code> and <code>vsc-install</code></a> and 29082 <a class="autorefs autorefs-internal" href="../easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_functions_classes_constants">Overview of relocated functions, classes and constants in EasyBuild v4.0</a></li> 29083</ul> 29084</li> 29085<li><code>setuptools</code> <strong>is longer required</strong> (neither for installing or using 29086 EasyBuild) 29087 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2836">#2836</a>, 29088 <a href="https://github.com/easybuilders/easybuild-framework/pull/2837">#2837</a>, 29089 <a href="https://github.com/easybuilders/easybuild-framework/pull/2984">#2984</a>, 29090 <a href="https://github.com/easybuilders/easybuild-framework/pull/2986">#2986</a>, 29091 <a href="https://github.com/easybuilders/easybuild-framework/pull/2988">#2988</a>)<ul> 29092<li>see also <a class="autorefs autorefs-internal" href="../easybuild-v4/overview-of-changes/#eb4_no_required_deps">No more required Python packages</a></li> 29093<li>this required moving some classes and constants, see 29094 <a class="autorefs autorefs-internal" href="../easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_functions_classes_constants">Overview of relocated functions, classes and constants in EasyBuild v4.0</a></li> 29095</ul> 29096</li> 29097<li><strong>the</strong> '<code>dummy</code>' <strong>toolchain is deprecated and replaced by the</strong> 29098 '<code>system</code>' <strong>toolchain</strong> 29099 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2877">#2877</a>, 29100 <a href="https://github.com/easybuilders/easybuild-framework/pull/3001">#3001</a>)<ul> 29101<li>if '<code>dummy</code>' is still used as a toolchain in easyconfig files, 29102 a warning will be printed</li> 29103<li>use "<code>toolchain = SYSTEM</code>" instead</li> 29104<li>for more information, see <a class="autorefs autorefs-internal" href="../system-toolchain/#system_toolchain">System toolchain</a></li> 29105</ul> 29106</li> 29107<li><strong>a warning is printed when local variables in easyconfig file 29108 don't follow the recommended naming scheme</strong> 29109 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2938">#2938</a>, 29110 <a href="https://github.com/easybuilders/easybuild-framework/pull/2968">#2968</a>)<ul> 29111<li>see also <a class="autorefs autorefs-internal" href="../easyconfig-files-local-variables/#easyconfig_files_local_variables">Local variables in easyconfig files</a></li> 29112</ul> 29113</li> 29114<li><strong>names of software installation directories are independent of 29115 module naming scheme by enabling</strong> 29116 <code>--fixed-installdir-naming-scheme</code> <strong>by default</strong> 29117 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2999">#2999</a>)<ul> 29118<li>see 29119 <a class="autorefs autorefs-internal" href="../easybuild-v4/overview-of-changes/#eb4_changes_fixed_installdir_naming_scheme"><code>--fixed-installdir-naming-scheme</code> enabled by default</a> for more information</li> 29120</ul> 29121</li> 29122<li>various other small enhancements, including:<ul> 29123<li>use requests instead of urllib2 for 403 errors 29124 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2695">#2695</a>)</li> 29125<li>
29125use pip requirements file in Travis 29126 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2874">#2874</a>)</li> 29127<li>add support for <code>--fix-deprecated-easyconfigs</code> 29128 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2881">#2881</a>, 29129 2898, 29130 <a href="https://github.com/easybuilders/easybuild-framework/pull/2938">#2938</a>)</li> 29131<li>add <code>-L$EBROOTIMKL/lib/intel64</code> to <code>$LDFLAGS</code> for MKL 29132 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2930">#2930</a>)</li> 29133<li>handle dict-type checksums in check_checksums_for 29134 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2974">#2974</a>)</li> 29135<li>allow that <code>icc</code> & <code>ifort</code> are not actual dependencies in 29136 <code>iccifort</code> toolchain module 29137 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2995">#2995</a>)</li> 29138<li>define mapping for <code>iccifort</code>-><code>intel</code> for <code>iccifort</code> 29139 compiler-only toolchain for HMNS 29140 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2996">#2996</a>)</li> 29141<li>also consider concatenation of compiler module names to 29142 determine details of toolchain compiler component 29143 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2997">#2997</a>)</li> 29144<li>update metadata for Cray-provided external modules 29145 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3013">#3013</a>)</li> 29146</ul> 29147</li> 29148<li>various bug fixes, including:<ul> 29149<li>update the PyPI trove classifiers in setup.py 29150 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2875">#2875</a>)</li> 29151<li>reverse lists for <code>$LDFLAGS</code> and <code>$CPPFLAGS</code> 29152 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2931">#2931</a>)</li> 29153<li>enhance/fix to_template_str function to do a better job at using 29154 template values in dumped easyconfigs 29155 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2948">#2948</a>)</li> 29156<li>also take into account <code>--filter-deps</code> when finalizing parsed 29157 dependencies to fix problem with dependency filters using 29158 version ranges 29159 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2983">#2983</a>)</li> 29160<li>fix broken <code>--from-pr</code> tests due to archiving of easyconfigs 29161 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2985">#2985</a>)</li> 29162<li>fixes required to avoid breaking Cray support 29163 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3008">#3008</a>)</li> 29164<li>fixes for <code>--read-only-installdir</code>: avoid crash with <code>ModuleRC</code> 29165 easyblock + also make log file in installdir read-only 29166 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3012">#3012</a>)</li> 29167</ul> 29168</li> 29169<li>other changes:<ul> 29170<li>add check to ensure that <code>--robot</code> argument specifies an 29171 existing directory 29172 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2086">#2086</a>)</li> 29173<li>remove old scripts that are no longer useful (+ minor fixes to 29174 others) 29175 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2897">#2897</a>)</li> 29176<li>use '<code>command -v</code>' to avoid requiring '<code>which</code>' in '<code>eb</code>' 29177 command 29178 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2979">#2979</a>)</li> 29179<li>add <code>modluafooter</code> & <code>modtclfooter</code> at the end of the generated 29180 module file 29181 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3003">#3003</a>)</li> 29182<li>print warning when '<code>eb</code>' command is not found in <code>$PATH</code> and 29183 for empty robot search path 29184 (<a href="https://github.com/easybuilders/easybuild-framework/pull/3006">#3006</a>)</li> 29185</ul> 29186</li> 29187</ul> 29188<p><strong>easyblocks</strong></p> 29189<ul> 29190<li>fixes due to backwards-incompatible changes in easybuild-framework 29191 v4.0.0<ul> 29192<li>use <code>is_system_toolchain()</code> rather than checking toolchain name 29193 against DUMMY_TOOLCHAIN_NAME constant 29194 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1690">#1690</a>, 29195 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1728">#1728</a>)</li> 29196</ul> 29197</li> 29198<li>fix compatibility of various easyblocks with Python 3 29199 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1640">#1640</a>, 29200 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1644">#1644</a>, 29201 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1648">
29201#1648</a>, 29202 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1721">#1721</a>, 29203 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1794">#1794</a>, 29204 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1808">#1808</a>, 29205 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1795">#1795</a>, 29206 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1796">#1796</a>, 29207 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1807">#1807</a>, 29208 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1809">#1809</a>)</li> 29209<li>new software-specific easyblocks for <code>OpenMPI</code> 29210 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1789">#1789</a>, 29211 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1801">#1801</a>), 29212 <code>iccifort</code> 29213 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1799">#1799</a>) 29214 and <code>numexpr</code> 29215 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1803">#1803</a>, 29216 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1804">#1804</a>)</li> 29217<li>various other enhancements, including:<ul> 29218<li>removed checks for Boussinesq and sonic solvers for OpenFOAM 7, 29219 since those have been deprecated 29220 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1733">#1733</a>)</li> 29221<li>update Paraver easyblock to support recent versions 29222 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1790">#1790</a>)</li> 29223</ul> 29224</li> 29225<li>various bug fixes, including:<ul> 29226<li>update the PyPI trove classifiers 29227 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1723">#1723</a>)</li> 29228<li>make the plugins build use the correct Tcl library version in 29229 VMD easyblock 29230 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1786">#1786</a>)</li> 29231<li>use <code>*_MT libs</code> for BLAS/LAPACK only if <code>openmp</code> is enabled in 29232 Trilinos easyblock 29233 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1791">#1791</a>)</li> 29234<li>filter out empty entries in <code>$CPATH</code> or <code>$C_INCLUDE_PATH</code> when 29235 building Perl, since that breaks the build 29236 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1800">#1800</a>)</li> 29237<li>set <code>$XDG_CACHE_HOME</code> in TensorFlow easyblock to avoid that 29238 <code>pip</code> (ab)uses <code>$HOME/.cache</code> 29239 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1802">#1802</a>)</li> 29240<li>don't load modules for dependencies in 29241 <code>CrayToolchain.prepare_step</code> 29242 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1805">#1805</a>)</li> 29243</ul> 29244</li> 29245<li>other changes:<ul> 29246<li>drop requirement for setuptools as runtime dependency 29247 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1689">#1689</a>)</li> 29248<li>enable '<code>check_ldshared</code>' in generic PythonPackage easyblock 29249 by default for recent Python versions 29250 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1788">#1788</a>)</li> 29251<li>stop trying to use <code>setuptools.setup</code> in <code>setup.py</code>, always use 29252 <code>distutils.core.setup</code> instead 29253 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1793">#1793</a>)</li> 29254</ul> 29255</li> 29256</ul> 29257<p><strong>easyconfigs</strong></p> 29258<ul> 29259<li>fixes due to changes in easybuild-framework v4.0.0<ul> 29260<li>use <code>SYSTEM</code> toolchain rather than deprecated <code>dummy</code> toolchain 29261 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8369">#8369</a>, 29262 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8711">#8711</a>, 29263 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8822">#8822</a>)</li> 29264<li>fix names of local variables 29265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8682">#8682</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8688">#8688</a>, 29266 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8690">#8690</a>, 29267 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8695">#8695</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8702">#8702</a>, 29268 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8709">#8709</a>, 29269 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8710">#8710</a>, 29270 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8715">#8715</a>, 29271 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8717">#8717</a>, 29272 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8718">#8718</a>, 29273 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8720">#8720</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8732">#8732</a>, 29274 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8822">#8822</a>)</li> 29275<li>enable <code>--local-var-naming-check=error</code> for easyconfigs tests 29276 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8784">#8784</a>)</li> 29277<li>stick to '<code>dummy</code>' toolchain for now in easyconfig for latest 29278 EasyBuild 3.x 29279 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8829">#8829</a>)</li> 29280</ul> 29281</li> 29282<li>fix compatibility with Python 3: also run easyconfigs tests with 29283 Python 3.5, 3.6 and 3.7 29284 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7778">#7778</a>, 29285 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7836">#7836</a>, 29286 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8293">#8293</a>)</li> 29287<li>
29287added easyconfigs for new common toolchains: <code>foss/2019b</code> 29288 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8567">#8567</a>), 29289 <code>intel/2019b</code> 29290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8681">#8681</a>)<ul> 29291<li><code>iccifort</code> is now installed as a single entity (no more separate 29292 <code>icc</code>/<code>ifort</code> installations from <code>intel/2019b</code> onwards) (see 29293 also 29294 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8879">#8879</a>)</li> 29295<li><code>versionsuffix</code> has been stripped down for toolchain components 29296 (GCC/binutils/OpenBLAS versions are no longer included)</li> 29297<li>see also 29298 <a href="https://easybuild.readthedocs.io/en/latest/Common-toolchains.html">https://easybuild.readthedocs.io/en/latest/Common-toolchains.html</a></li> 29299</ul> 29300</li> 29301<li>added example easyconfig files for 28 new software packages:<ul> 29302<li>AGFusion 29303 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8840">#8840</a>), 29304 Bonmin 29305 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8855">#8855</a>), 29306 causalml 29307 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8871">#8871</a>), 29308 ClonalFrameML 29309 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6082">#6082</a>), 29310 Control-FREEC 29311 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8794">#8794</a>), 29312 corner 29313 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8886">#8886</a>), 29314 CVXPY 29315 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8662">#8662</a>), 29316 cytosim 29317 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8368">#8368</a>), 29318 dill 29319 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8885">#8885</a>), 29320 Dsuite 29321 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8713">#8713</a>), 29322 GDCHART 29323 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8679">#8679</a>), 29324 gifsicle 29325 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8664">#8664</a>), 29326 guenomu 29327 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8677">#8677</a>), 29328 JsonCpp 29329 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8841">#8841</a>), 29330 libxml++ 29331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8896">#8896</a>), 29332 LOHHLA 29333 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7227">#7227</a>), 29334 Longshot 29335 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8830">#8830</a>), 29336 MDBM 29337 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8850">#8850</a>), 29338 nglview 29339 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8860">#8860</a>), 29340 ownCloud 29341 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6804">#6804</a>), 29342 ptemcee 29343 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8884">#8884</a>), 29344 pubtcrs 29345 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7500">#7500</a>), 29346 pyiron 29347 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8860">#8860</a>), 29348 qpth 29349 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8665">#8665</a>), 29350 QtKeychain 29351 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6804">#6804</a>), 29352 rgdal 29353 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8826">#8826</a>), 29354 smallgenomeutilities 29355 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8507">#8507</a>), 29356 umis 29357 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8812">#8812</a>)</li> 29358</ul> 29359</li> 29360<li>added additional easyconfigs for various supported software 29361 packages, including:<ul> 29362<li>Blosc 1.17.0, bokeh 1.3.4, cURL 7.66.0, csvkit 1.0.4, dask 29363 2.3.0, Extrae 3.7.1, FSL 6.0.1, GLibmm 2.49.7, git 2.23.0, 29364 IPython 7.7.0, numexpr 2.7.0, OSU-Micro-Benchmarks 5.6.2, 29365 OpenBLAS 0.3.7, OpenSSL 1.1.1d, ParaView 5.5.2, Paraver 4.8.1, 29366 Perl 5.30.0, PnetCDF 1.10.0, Porechop 0.2.4, PyTables 3.5.2, 29367 PyTorch 1.2.0, Python 2.7.16 + 3.7.4, parallel 20190622, phonopy 29368 2.2.0, QIIME2 2019.7, Qiskit 0.12.0, REMORA 1.8.3, scikit-image 29369 0.15.0, spglib-python 1.14.1.post0, torchvision 0.3.0, X11 29370 20190717</li> 29371</ul> 29372</li> 29373<li>various additional minor enhancements, including:<ul> 29374<li>add several extensions to R 3.6.0 easyconfigs 29375 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8843">#8843</a>, 29376 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8881">#8881</a>)</li> 29377<li>
29377add pRoloc to R-bundle-Bioconductor v3.9 29378 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8882">#8882</a>)</li> 29379<li>clean up OpenMPI 3.1.* and 4.* easyconfigs to use custom 29380 OpenMPI easyblock 29381 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8889">#8889</a>, 29382 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8890">#8890</a>)</li> 29383<li>update numexpr easyconfigs to use custom easyblock for numexpr 29384 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8901">#8901</a>)</li> 29385<li>switch to <code>PythonBundle</code> & enable use_pip in old dask easyconfig 29386 files 29387 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8922">#8922</a>)</li> 29388<li>update <code>CrayCCE</code>, <code>CrayGNU</code>, <code>CrayIntel</code> and <code>CrayPGI</code> 29389 toolchains to 19.06 29390 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8944">#8944</a>)</li> 29391</ul> 29392</li> 29393<li>various bug fixes, including:<ul> 29394<li>make TensorFlow 1.7.0 work for AMD CPUs 29395 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6256">#6256</a>)</li> 29396<li>make sure that right Python wrapper is used in VTK8 29397 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7296">#7296</a>)</li> 29398<li>update the PyPI trove classifiers 29399 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8298">#8298</a>)</li> 29400<li>add missing checksum for matplotlib v3.0.3 29401 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8643">#8643</a>)</li> 29402<li>add patch to <code>plugins/Make-arch</code> to use the correct Tcl library 29403 version in VMD 29404 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8820">#8820</a>)</li> 29405<li>fix issue where '<code>print_qiime_config.py -t</code>' sanity check 29406 command fails for QIIME 1.9.1 because of missing subdir in 29407 <code>$PYTHONPATH</code> 29408 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8838">#8838</a>)</li> 29409<li>update homepage info in likwid 29410 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8846">#8846</a>)</li> 29411<li>disable threading in <code>preprocessCore</code> extension included with 29412 Bioconductor 3.9 to work around conflict with OpenBLAS's 29413 threading 29414 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8847">#8847</a>)</li> 29415<li>add <code>-lrt</code> patch to PyTorch 1.1.0 easyconfig 29416 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8852">#8852</a>)</li> 29417<li>fix incorrect escaping in SIP configure options in PyQt5 29418 easyconfigs 29419 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8856">#8856</a>)</li> 29420<li>add missing Autotools build dep for fastq-tools 29421 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8858">#8858</a>)</li> 29422<li>add missing deps for zlib, bzip2, and XZ for angsd 29423 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8867">#8867</a>)</li> 29424<li>apply patch to R package uroot in R 3.6.0 29425 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8872">#8872</a>)</li> 29426<li>consider archive source URL for all extensions in R-tesseract 29427 easyconfig 29428 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8897">#8897</a>)</li> 29429<li>add pkg-config build dep for tesseract v4.0.0 29430 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8898">#8898</a>)</li> 29431<li>fix <code>source_urls</code> in byacc easyconfig files 29432 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8899">#8899</a>, 29433 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8908">#8908</a>)</li> 29434<li>add missing cairo dependency to PRINSEQ easyconfig file 29435 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8902">#8902</a>)</li> 29436<li>configure OpenMPI 1.10.x with <code>--without-ucx</code> to avoid problems 29437 when <code>ucx-devel</code> is installed in the OS 29438 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8903">#8903</a>)</li> 29439<li>
29439add GDAL 3.0.0 for Python 2.7.15 and fix the Python 3.7.2 29440 version 29441 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8912">#8912</a>)</li> 29442<li>fix homepage & description in scikit-image easyconfigs 29443 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8916">#8916</a>)</li> 29444<li>add faulthandler patches to Python 3.7.0 easyconfigs 29445 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8832">#8832</a>)</li> 29446</ul> 29447</li> 29448<li>other changes:<ul> 29449<li>archive ancient CUDA 5.0.35 easyconfigs with creative way of 29450 determining sources 29451 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7796">#7796</a>)</li> 29452<li>remove ancient easyconfigs from archive 29453 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8542">#8542</a>)</li> 29454<li>archive easyconfigs using deprecated toolchains 29455 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8557">#8557</a>, 29456 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8558">#8558</a>, 29457 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8585">#8585</a>)</li> 29458<li>archive ancient versions of GC3Pie/GCC/OpenMPI/ORCA 29459 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8586">#8586</a>) 29460 & CPLEX 29461 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8765">#8765</a>)</li> 29462<li>
29462rename SALMON to SALMON-TDDFT to fix name clash with Salmon 29463 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8613">#8613</a>)</li> 29464<li>bump AnnotationDb version in bundle for Bioconductor 3.9 29465 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8854">#8854</a>)</li> 29466<li>stop trying to use <code>setuptools.setup</code> in <code>setup.py</code>, always use 29467 <code>distutils.core.setup</code> instead 29468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8866">#8866</a>, 29469 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8892">#8892</a>, 29470 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8894">#8894</a>)</li> 29471<li>archive easyconfigs using ancient <code>Cray*</code> toolchains 29472 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8945">#8945</a>)</li> 29473</ul> 29474</li> 29475</ul> 29476<h2 id="release_notes_eb394">EasyBuild v3.9.4 (August 23rd 2019)<a class="headerlink" href="#release_notes_eb394" title="Permanent link">¶</a></h2> 29477<p>bugfix/update release</p> 29478<p><strong>framework</strong></p> 29479<ul> 29480<li>various enhancements, including:<ul> 29481<li>add support for specifying checksum via dict providing a 29482 filename-to-checksum mapping 29483 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2946">#2946</a>)</li> 29484<li>enhance 'completed' message with how much time was needed for 29485 the installation 29486 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2956">#2956</a>)</li> 29487<li>add support for specifying tuple of alternative checksums 29488 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2958">#2958</a>)</li> 29489<li>support using '<code>system</code>' as alias for '<code>dummy</code>' toolchain + 29490 <code>SYSTEM</code> constant 29491 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2960">#2960</a>)</li> 29492<li>ensure '<code>docurls</code>' easyconfig parameter value is a list of 29493 string values, not a single string value 29494 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2963">#2963</a>)</li> 29495<li>automatically enable <code>--ignore-osdeps</code> when using 29496 <code>--check-contrib</code> or <code>--check-style</code> 29497 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2965">#2965</a>)</li> 29498</ul> 29499</li> 29500<li>various bug fixes, including:<ul> 29501<li>escape '<code>+</code>' in search queries + handle invalid search queries 29502 better 29503 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2967">#2967</a>)</li> 29504<li>also consider extension patches when determining for which 29505 easyconfig a given patch file is intended in 29506 <code>--new-pr</code>/<code>--update-pr</code> 29507 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2969">#2969</a>)</li> 29508<li>unset <code>$CDPATH</code> early on if it is defined 29509 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2970">#2970</a>)</li> 29510<li>create specified temporary log directory if it doesn't exist 29511 yet in <code>init_logging</code> 29512 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2972">#2972</a>)</li> 29513<li>don't indicate first multi_deps version as default in module 29514 help text when <code>multi_deps_load_default=False</code> 29515 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2973">#2973</a>)</li> 29516</ul> 29517</li> 29518<li>other changes:<ul> 29519<li>deprecate toolchains older than <code>gompi/2016a</code> and <code>foss/2016a</code> 29520 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2951">#2951</a>)</li> 29521</ul> 29522</li> 29523</ul> 29524<p><strong>easyblocks</strong></p> 29525<ul> 29526<li>new software-specific easyblock for MSM 29527 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1770">#1770</a>, 29528 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1775">#1775</a>, 29529 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1776">#1776</a>)</li> 29530<li>minor enhancements, including:<ul> 29531<li>allow specifying the license file directly in MATLAB easyblock 29532 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1712">#1712</a>)</li> 29533<li>
29533enhance CPLEX easyblock to also build Python bindings 29534 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1738">#1738</a>)</li> 29535<li>workaround for XCrySDen for Tcl 8.6 29536 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1749">#1749</a>)</li> 29537<li>update WIEN2k easyblock to support version 19.1 29538 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1758">#1758</a>)</li> 29539<li>resolve custom <code>%(cudaarch)s</code> template value for CUDA sources 29540 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1766">#1766</a>)</li> 29541<li>enhance sanity check for Blender to make sure that Cycles render 29542 engine is available 29543 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1779">#1779</a>)</li> 29544</ul> 29545</li> 29546<li>various bug fixes, including:<ul> 29547<li>only check for qtwebengine in custom easyblock for Qt(5) if 29548 glibc is sufficiently recent 29549 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1771">#1771</a>)</li> 29550<li>correctly define <code>comp.src</code> in Bundle easyblock, to fix 29551 compatibility with easyblocks that leverage <code>self.src</code> 29552 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1777">#1777</a>)</li> 29553<li>fix <code>Bundle.check_checksums</code> to checksums for extensions are 29554 also checked 29555 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1778">#1778</a>)</li> 29556</ul> 29557</li> 29558</ul> 29559<p><strong>easyconfigs</strong></p> 29560<ul> 29561<li>added example easyconfig files for 36 new software packages:<ul> 29562<li>ArrayFire 29563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8461">#8461</a>), 29564 BRAKER 29565 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8437">#8437</a>), 29566 bwidget 29567 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8477">#8477</a>), 29568 Catch2 29569 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8703">#8703</a>), 29570 core-counter 29571 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8749">#8749</a>), 29572 CubeGUI 29573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6328">#6328</a>), 29574 CubeLib 29575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6328">#6328</a>), 29576 CubeWriter 29577 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6328">#6328</a>), 29578 dagitty 29579 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8606">#8606</a>), 29580 enaBrowserTool 29581 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8795">#8795</a>), 29582 GEMMA 29583 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8270">#8270</a>), 29584 GeneMark-ET 29585 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8437">#8437</a>), 29586 GenomeThreader 29587 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8437">#8437</a>), 29588 ieeg-cli 29589 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8793">#8793</a>, 29590 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8811">#8811</a>), 29591 Judy 29592 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8543">#8543</a>), 29593 Julia 29594 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8578">#8578</a>), 29595 libaio 29596 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8543">#8543</a>), 29597 libtirpc 29598 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8792">#8792</a>), 29599 magick 29600 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8545">#8545</a>), 29601 MSM 29602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8556">#8556</a>), 29603 MSPC 29604 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8531">#8531</a>), 29605 mygene 29606 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8809">#8809</a>), 29607 OpenMolcas 29608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7699">#7699</a>), 29609 PhiPack 29610 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8750">#8750</a>), 29611 plc 29612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8796">#8796</a>), 29613 plotly.py 29614 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8756">#8756</a>), 29615 pymemcache 29616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8663">#8663</a>), 29617 PySCF 29618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8736">#8736</a>), 29619 qcint 29620 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8736">#8736</a>), 29621 Qiskit 29622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7592">#7592</a>), 29623 QuaZIP 29624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8672">#8672</a>), 29625 re2c 29626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8543">#8543</a>), 29627 SeqAn3 29628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8651">#8651</a>), 29629 snippy 29630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8635">#8635</a>), 29631 spaln 29632 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8437">#8437</a>), 29633 V8 29634 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8676">#8676</a>)</li> 29635</ul> 29636</li> 29637<li>
29637added additional easyconfigs for various supported software 29638 packages, including:<ul> 29639<li>ASE 3.18.0, BEDTools 2.28.0, Bowtie 1.2.3, bzip2 1.0.8, CPLEX 29640 12.9, CUDA 10.1 update 2, cyvcf2 0.11.5, EIGENSOFT 7.2.1, GC3Pie 29641 2.5.2, GCC(core) 9.2.0, GPAW 19.8.1, GlobalArrays 5.7, IMB 29642 2019.3, imageio 2.5.0, jemalloc 5.2.0, nodejs 10.15.3, PyTorch 29643 1.1.0, pybedtools 0.8.0, Quandl 3.4.8, R 3.6.0 w/ intel/2019a, 29644 R-bundle-Bioconductor 3.9, Salmon 0.14.1, Scalasca 2.5, Score-P 29645 6.0, Stacks 2.41, TensorFlow 1.14.0, ToFu 1.4.0, WIEN2k 19.1, 29646 Wannier90 3.0.0, XCrySDen 1.5.60</li> 29647</ul> 29648</li> 29649<li>minor enhancements, including:<ul> 29650<li>add patch and dependencies to easyconfig for Qt5 5.12.3 to fix 29651 Xlib support & enhance the installation 29652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8544">#8544</a>)</li> 29653<li>update nodejs to version 10.15.3 and build libnode and libv8 29654 shared libs 29655 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8546">#8546</a>)</li> 29656<li>add extensions to R 3.6.0 easyconfig: <code>MIIVsem</code> 29657 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8565">#8565</a>), 29658 <code>medflex</code> 29659 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8680">#8680</a>), 29660 <code>Rserve</code>/<code>spls</code> 29661 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8758">#8758</a>), 29662 <code>Boruta</code>/<code>CovSel</code>/<code>ctmle</code>/<code>BayesPen</code> 29663 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8805">#8805</a>)</li> 29664<li>include PyQtWebEngine bindings in easyconfig for PyQt5 5.12.1 29665 using Python 3.7.2 29666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8572">#8572</a>)</li> 29667<li>switch GLX backend to Gallium in Mesa-19.0.1 29668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8594">#8594</a>)</li> 29669</ul> 29670</li> 29671<li>various bug fixes, including:<ul> 29672<li>fix typo in description in GroopM easyconfig file 29673 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8346">#8346</a>)</li> 29674<li>add missing bugfix patch to easyconfig for OpenMPI 3.1.4 29675 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8566">#8566</a>)</li> 29676<li>downgrade AtomPAW to last supported version in ABINIT 8.10.3 29677 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8571">#8571</a>)</li> 29678<li>switch easyconfig for glew 2.1.0 to <code>ConfigureMake</code> easyblock 29679 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8595">#8595</a>)</li> 29680<li>fix checksum for source tarball in <code>foss/2018b</code> easyconfig of 29681 NAMD v2.13 29682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8602">#8602</a>)</li> 29683<li>update URL for bzip2 easyconfigs 29684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8614">
29684#8614</a>)</li> 29685<li>add patch for M4 1.4.17 to fix installation on top of glibc 2.28 29686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8666">#8666</a>)</li> 29687<li>add patch for Bison 3.0.4 to fix installation on top of glibc 29688 2.28 29689 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8675">#8675</a>)</li> 29690<li>avoid needless requirement for matplotlib < 3.0.0 in MultiQC 29691 easyconfigs 29692 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/8691">#8691</a>)</li> 29693<li>fix checksum in OpenMPI 1.8.8 easyconfigs 29694 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8692">#8692</a>)</li> 29695<li>add alternative checksums for <code>nlme</code>/<code>mgcv</code>/<code>foreign</code>/<code>boot</code> 29696 extensions in R 3.5.1 and 3.6.0 easyconfigs 29697 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8564">#8564</a>, 29698 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8762">#8762</a>)</li> 29699<li>add missing core-counter dependency for worker 1.6.8 29700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8749">#8749</a>)</li> 29701<li>add missing pkg-config build dependency in various easyconfigs 29702 for 29703 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8763">#8763</a>, 29704 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8775">#8775</a>, 29705 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8777">#8777</a>, 29706 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8776">#8776</a>, 29707 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8764">#8764</a>, 29708 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8787">#8787</a>, 29709 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8816">#8816</a>)</li> 29710<li>add patch to Python 3.7.2 easyconfig to fix faulthandler 29711 segfault 29712 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8781">#8781</a>)</li> 29713<li>set <code>$CPLUS_INCLUDE_PATH</code> in easyconfigs for older matplotlib 29714 versions 29715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8785">#8785</a>)</li> 29716<li>patch out removed glibc 2.28 header from GCC libsanitizer 29717 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8789">#8789</a>)</li> 29718<li>include <code>sysmacros.h</code> directly to work around removal from glibc 29719 header in numactl easyconfig 29720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8790">#8790</a>)</li> 29721<li>adapt gzip's bundled gnulib for glibc 2.28 29722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8791">#8791</a>)</li> 29723<li>add libtirpc and depend on it in easyconfig for libdap 3.20.3 29724 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8792">#8792</a>)</li> 29725<li>add missing YAML extension to Perl 5.28.0 easyconfig (required 29726 by BioPerl scripts) 29727 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8806">#8806</a>)</li> 29728</ul> 29729</li> 29730<li>other changes:<ul> 29731<li>remove broken easyconfigs for ciftify due to non-trivial missing 29732 dependencies 29733 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8560">#8560</a>)</li> 29734</ul> 29735</li> 29736</ul> 29737<h2 id="release_notes_eb393">EasyBuild v3.9.3 (July 8th 2019)<a class="headerlink" href="#release_notes_eb393" title="Permanent link">¶</a></h2> 29738<p>bugfix/update release</p> 29739<p><strong>framework</strong></p> 29740<ul> 29741<li>various enhancements, including:<ul> 29742<li>add a URL whatis line to generated module files 29743 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2933">#2933</a>)</li> 29744</ul> 29745</li> 29746<li>various bug fixes, including:<ul> 29747<li>stick to Ubuntu Trusty when testing with Python 2.6 in Travis 29748 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2928">#2928</a>)</li> 29749<li>honor <code>--tmp-logdir</code> when determining location of temporary log 29750 file 29751 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2937">#2937</a>)</li> 29752</ul> 29753</li> 29754</ul> 29755<p><strong>easyblocks</strong></p> 29756<ul> 29757<li>minor enhancements, including:<ul> 29758<li>also install docs and demos in Rosetta easyblock 29759 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1745">#1745</a>)</li> 29760<li>update HEALPix easyblock to work with latest version of 29761 HEALPix' <code>configure.sh</code> 29762 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1752">#1752</a>)</li> 29763<li>make HPCG log pattern more generic, it changed in 3.1 29764 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1753">#1753</a>)</li> 29765<li>allow bootstrapping GCC with profile-guided optimizations 29766 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1756">#1756</a>)</li> 29767<li>only require vsc-base for EasyBuild 2.x and 3.x in EasyBuildMeta 29768 easyblock 29769 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1757">#1757</a>)</li> 29770<li>extend question patterns with '<code>https</code>' URL entry in Modeller 29771 easyblock for recent versions 29772 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1762">#1762</a>)</li> 29773<li><code>modextrapaths</code> implemented on easyblock level, 29774 <code>sanity_check_step</code>, <code>gcc_target</code> added in HEALPix easyblock 29775 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1763">#1763</a>)</li> 29776<li>update OpenBLAS easyblock to be aware of POWER9 support in 29777 OpenBLAS 0.3.6 29778 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1765">#1765</a>)</li> 29779</ul> 29780</li> 29781<li>various bug fixes, including:<ul> 29782<li>stick to Ubuntu Trusty when testing with Python 2.6 in Travis 29783 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1751">#1751</a>)</li> 29784<li>fix scripts installation path in SNPhylo easyblock 29785 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1759">#1759</a>)</li> 29786<li>be more patient when running interactive <code>
29786Allwmake.firstInstall</code> 29787 command for recent OpenFOAM-Extend versions 29788 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1761">#1761</a>)</li> 29789<li>also add <code>--without-go</code> configure option for SWIG as we 29790 "disable everything by default" 29791 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1754">#1754</a>)</li> 29792<li>don't assume cmake arguments when configure_cmd is set in 29793 CMakeMake easyblock 29794 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1750">#1750</a>)</li> 29795</ul> 29796</li> 29797</ul> 29798<p><strong>easyconfigs</strong></p> 29799<ul> 29800<li>added example easyconfig files for 25 new software packages:<ul> 29801<li>Arb 29802 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8137">#8137</a>), 29803 AtomPAW 29804 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8506">#8506</a>), 29805 ciftify 29806 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8457">#8457</a>), 29807 cysignals 29808 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8459">#8459</a>), 29809 deal.II 29810 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8440">#8440</a>), 29811 FastQTL 29812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8449">#8449</a>), 29813 FLINT 29814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8137">#8137</a>), 29815 gdbgui 29816 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8488">#8488</a>), 29817 gearshifft 29818 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8482">#8482</a>), 29819 jbigkit 29820 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8442">#8442</a>), 29821 lavaan 29822 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8539">#8539</a>), 29823 libRmath 29824 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8449">#8449</a>), 29825 OR-Tools 29826 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8364">#8364</a>, 29827 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8523">#8523</a>), 29828 p4est 29829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8440">#8440</a>), 29830 ppl 29831 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8459">#8459</a>), 29832 pplpy 29833 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8459">#8459</a>), 29834 PRISMS-PF 29835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8440">#8440</a>), 29836 PyAPS3 29837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8398">#8398</a>), 29838 pyEGA3 29839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8418">#8418</a>), 29840 ReFrame 29841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8481">#8481</a>), 29842 S4 29843 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8487">#8487</a>), 29844 SALMON 29845 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8478">#8478</a>), 29846 TM-align 29847 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8510">#8510</a>), 29848 UnZip 29849 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8474">#8474</a>), 29850 XTandem 29851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8517">#8517</a>)</li> 29852</ul> 29853</li> 29854<li>added additional easyconfigs for various supported software 29855 packages, including:<ul> 29856<li>ABINIT 8.10.3, CFITSIO 3.47, GDB 8.3, GROMACS 2019.3, HEALPix 29857 3.50, HPCG 3.1, Nilearn 0.5.2, OpenBLAS 0.3.6, Xerces-C++ 3.2.0</li> 29858</ul> 29859</li> 29860<li>minor enhancements, including:<ul> 29861<li>update easyconfig for CFITSIO 3.45 with https and sanity check 29862 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8472">#8472</a>)</li> 29863<li>add AtomPAW and Wannier90 support to ABINIT 8.10.2 easyconfig 29864 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8506">#8506</a>)</li> 29865<li>add '<code>resample</code>' extension to R 3.5.1 + 3.6.0 easyconfigs 29866 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8538">#8538</a>)</li> 29867</ul> 29868</li> 29869<li>various bug fixes, including:<ul> 29870<li>fix source URLs for Mesa 17.{2,3} with fosscuda toolchain 29871 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8446">#8446</a>)</li> 29872<li>
29872add in Boost dependency to canu-1.8 easyconfigs using <code>foss</code> 29873 toolchain 29874 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8470">#8470</a>)</li> 29875<li>stick to Ubuntu Trusty when testing with Python 2.6 in Travis 29876 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8483">#8483</a>)</li> 29877<li>fix incorrect order of extensions for Python-2.7.14 easyconfigs 29878 (<code>pycparser</code> and <code>cffi</code> must come before <code>cryptography</code>) 29879 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8495">#8495</a>)</li> 29880<li>suppress installation of <code>libbfd</code> and <code>libopcode</code> for GDB 29881 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8496">#8496</a>)</li> 29882<li>fix KronaTools easyconfigs to make sure symlinks in bin are not 29883 broken 29884 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8508">#8508</a>)</li> 29885<li>make additional configopts in PETSc easyconfigs work after 29886 uncommenting 29887 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8522">#8522</a>)</li> 29888<li>add <code>pkg-config</code> build dep to easyconfig for pocl 1.2 29889 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8528">#8528</a>)</li> 29890<li>download correct source tarball for Net-core 2.1.8 29891 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8530">#8530</a>)</li> 29892<li>fix '<code>Permission denied</code>' error when running '<code>cp -a</code>' for 29893 ANTs 2.3.1 installation by first removing the <code>.git</code> 29894 subdirectories causing them 29895 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8535">#8535</a>)</li> 29896<li>fix checksum for boot 1.3-22 extension in R 3.6.0 easyconfig 29897 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8537">#8537</a>)</li> 29898</ul> 29899</li> 29900</ul> 29901<h2 id="release_notes_eb392">EasyBuild v3.9.2 (June 9th 2019)<a class="headerlink" href="#release_notes_eb392" title="Permanent link">¶</a></h2> 29902<p>bugfix/update release</p> 29903<p><strong>framework</strong></p> 29904<ul> 29905<li>various enhancements, including:<ul> 29906<li>enhance (experimental) support for generating Singularity 29907 container recipes/images 29908 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2884">#2884</a>, 29909 <a href="https://github.com/easybuilders/easybuild-framework/pull/2900">#2900</a>, 29910 <a href="https://github.com/easybuilders/easybuild-framework/pull/2902">#2902</a>, 29911 <a href="https://github.com/easybuilders/easybuild-framework/pull/2903">#2903</a>, 29912 <a href="https://github.com/easybuilders/easybuild-framework/pull/2907">#2907</a>, 29913 <a href="https://github.com/easybuilders/easybuild-framework/pull/2909">#2909</a>, 29914 <a href="https://github.com/easybuilders/easybuild-framework/pull/2910">#2910</a>, 29915 <a href="https://github.com/easybuilders/easybuild-framework/pull/2913">
29915#2913</a>, 29916 <a href="https://github.com/easybuilders/easybuild-framework/pull/2915">#2915</a>)<ul> 29917<li>add support for specifying container configuration via 29918 <code>--container-config</code> (<code>--container-base</code> option has been 29919 removed)</li> 29920<li>add support for providing custom template for container 29921 recipe via <code>--container-template-recipe</code></li> 29922<li>add support for '<code>sif</code>' Singularity 3.x container image 29923 format</li> 29924<li>add support for specifying non-image based Singularity 29925 bootstrap agents</li> 29926<li>install default set of OS packages in container recipes 29927 starting from scratch</li> 29928<li>configure Lmod and update Lmod spider cache in generated 29929 Singularity container recipes</li> 29930<li>configure EasyBuild via environment variables (to allow 29931 overriding configuration settings via options to '<code>eb</code>' 29932 command)</li> 29933<li>also consider <code>/tmp/easybuild/sources</code> in source path (to 29934 allow seeding in sources in container build environment)</li> 29935<li>updated documentation is available at 29936 <a href="https://easybuild.readthedocs.io/en/latest/Containers.html">https://easybuild.readthedocs.io/en/latest/Containers.html</a></li> 29937</ul> 29938</li> 29939</ul> 29940</li> 29941<li>various bug fixes, including:<ul> 29942<li>make sure that easyconfig file for EasyBuild version being 29943 bootstrapped is found in robot search path 29944 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2899">#2899</a>)</li> 29945<li>remove interpreter options when fixing script shebang 29946 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2905">#2905</a>, 29947 <a href="https://github.com/easybuilders/easybuild-framework/pull/2906">#2906</a>)</li> 29948<li>fix crash on iterated installation when using Cray toolchains 29949 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2914">#2914</a>)</li> 29950<li>disable checking of read/exec permissions when checking for 29951 availability of '<code>sudo</code>' command 29952 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2918">#2918</a>)</li> 29953</ul> 29954</li> 29955<li>other changes:<ul> 29956<li>stick to vsc-base < 2.9.0 in bootstrap script to avoid 29957 requiring '<code>future</code>' dependency 29958 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2892">#2892</a>)</li> 29959</ul> 29960</li> 29961</ul> 29962<p><strong>easyblocks</strong></p> 29963<ul> 29964<li>new software-specific easyblock for ELPA 29965 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1621">#1621</a>)</li> 29966<li>minor enhancements, including:<ul> 29967<li>allow Boost to build both Python 2 and Python 3 libraries 29968 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1718">#1718</a>)</li> 29969<li>update CPLEX sanity check: convert tool was removed in CPLEX 29970 12.8 29971 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1737">#1737</a>)</li> 29972<li>don't try to patch <code>CROSSTOOL</code> script for recent Bazel versions 29973 (since it's no longer there) 29974 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1741">#1741</a>)</li> 29975</ul> 29976</li> 29977<li>various bug fixes, including:<ul> 29978<li>fix version check on using '<code>-log</code>' option to '<code>Allwmake</code>' 29979 in OpenFOAM easyblock 29980 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1739">#1739</a>)</li> 29981<li>fix GROMACS easyblock for list-type <code>configopts</code> 29982 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1740">#1740</a>)</li> 29983<li>fix configure step for GROMACS version < 4.6 29984 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1742">#1742</a>)</li> 29985</ul> 29986</li> 29987</ul> 29988<p><strong>easyconfigs</strong></p> 29989<ul> 29990<li>added example easyconfig files for 17 new software packages:<ul> 29991<li>adjustText 29992 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8354">#8354</a>), 29993 cowsay 29994 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8380">#8380</a>), 29995 fxtract 29996 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8426">#8426</a>), 29997 google-java-format 29998 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8373">#8373</a>), 29999 libtar 30000 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8379">#8379</a>), 30001 mkl-service 30002 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8390">#8390</a>), 30003 msprime 30004 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8371">#8371</a>), 30005 pygrib 30006 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8395">#8395</a>), 30007 pyhdf 30008 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8394">#8394</a>), 30009 pyproj 30010 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8395">#8395</a>), 30011 PyStan 30012 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8410">#8410</a>), 30013 Racon 30014 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8358">#8358</a>), 30015 rapidtide 30016 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8256">#8256</a>), 30017 SingleM 30018 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8428">
30018#8428</a>), 30019 smafa 30020 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8420">#8420</a>), 30021 SVDetect 30022 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8399">#8399</a>), 30023 Unicycler 30024 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8376">#8376</a>)</li> 30025</ul> 30026</li> 30027<li>added additional easyconfigs for various supported software 30028 packages, including:<ul> 30029<li>BLAST+ 2.9.0, Boost.Python 1.70.0, DIAMOND 0.9.24, EMAN2 2.3, 30030 ecCodes 2.12.5, GDAL 3.0.0, ImageMagick 7.0.8-46, Libint 2.5.0, 30031 matplotlib 2.2.4, NLopt 2.6.1, OrfM 0.7.1, PGI 19.4, PostgreSQL 30032 11.3, R 3.6.0, R-bundle-Bioconductor 3.8, Rust 1.35.0, STAR 30033 2.7.1a</li> 30034</ul> 30035</li> 30036<li>minor enhancements, including:<ul> 30037<li>use CMake rather than configure script for libxc 4.3.4 30038 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8361">#8361</a>, 30039 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8453">#8453</a>)</li> 30040<li>add '<code>cobs</code>' extension to R 3.5.1 easyconfigs 30041 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8389">#8389</a>)</li> 30042<li>add sanity check command to PSI4 1.2.1 easyconfigs to ensure 30043 that '<code>import psi4</code>' works 30044 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8393">#8393</a>)</li> 30045<li>include the provided backports patch in QuantumESPRESSO-6.4.1 30046 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8405">#8405</a>)</li> 30047<li>add <code>Logger::Simple</code>, <code>Scalar::Util::Numeric</code>, <code>YAML</code>, 30048 <code>Object::InsideOut</code> extensions to Perl 5.28.1 easyconfig 30049 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8432">#8432</a>)</li> 30050<li>update Java 1.8 to 1.8.0_212 30051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8443">#8443</a>)</li> 30052</ul> 30053</li> 30054<li>various bug fixes, including:<ul> 30055<li>add missing build dependency on gettext to ATK/2.28.1 for 30056 fosscuda/2018b 30057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8402">#8402</a>)</li> 30058<li>add patch to fix OpenBLAS v0.3.1 matrices multiplication issue 30059 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8396">#8396</a>)</li> 30060<li>make Eigen a build dependency for nanopolish 30061 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8448">#8448</a>)</li> 30062</ul> 30063</li> 30064<li>other changes:<ul> 30065<li>clean up ELPA 2018.11.001 easyconfig to use custom easyblock for 30066 ELPA 30067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8360">#8360</a>)</li> 30068<li>remove unused checksum for <code>ballgown</code> extension in Bioconductor 30069 3.7 easyconfigs 30070 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8363">#8363</a>)</li> 30071</ul> 30072</li> 30073</ul> 30074<h2 id="release_notes_eb391">EasyBuild v3.9.1 (May 20th 2019)<a class="headerlink" href="#release_notes_eb391" title="Permanent link">¶</a></h2> 30075<p>bugfix/update release</p> 30076<p><strong>framework</strong></p> 30077<ul> 30078<li>various enhancements, including:<ul> 30079<li>add function to determine whether specified easyblock is generic 30080 or not 30081 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2838">#2838</a>)</li> 30082<li>add support to <code>apply_regex_substitutions</code> function to skip 30083 creation of backup 30084 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2844">#2844</a>)</li> 30085<li>add support for <code>%(pymajver)s</code> (& co) 30086 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2850">#2850</a>)</li> 30087<li>add support for '<code>fix_python_shebang_for</code>' and 30088 '<code>fix_perl_shebang_for</code>' easyconfig parameters 30089 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2878">#2878</a>)</li> 30090<li>add <code>multi_deps</code> information to generated module, help and 30091 whatis sections 30092 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2882">#2882</a>)</li> 30093<li>add support for '<code>eb --missing</code>' ('<code>eb -M</code>') 30094 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2883">#2883</a>)<ul> 30095<li>see also 30096 <a href="https://easybuild.readthedocs.io/en/latest/Using_the_EasyBuild_command_line.html#getting-an-overview-of-missing-installations-missing-m">https://easybuild.readthedocs.io/en/latest/Using_the_EasyBuild_command_line.html#getting-an-overview-of-missing-installations-missing-m</a></li> 30097</ul> 30098</li> 30099</ul> 30100</li> 30101<li>various bug fixes, including:<ul> 30102<li>only call '<code>scontrol release</code>' when there's at least one job 30103 submitted 30104 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2834">#2834</a>)</li> 30105<li>fix small bug in <code>find_eb_script</code> + various minor issues with 30106 tests (related to environment in which tests are run) 30107 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2835">#2835</a>)</li> 30108<li>list build dependencies <em>before</em> runtime dependencies, so 30109 dependencies listed via <code>multi_deps</code> are loaded first in 30110 toolchain environment 30111 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2839">#2839</a>)</li> 30112<li>allow setting parallel to <code>0</code> or <code>False</code> to disable adding the 30113 <code>-j</code> argument 30114 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2842">#2842</a>)</li> 30115<li>be more careful when using single quotes for Tcl syntax 30116 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2847">#2847</a>)</li> 30117<li>append to existing <code>.modulerc</code> file rather than overwriting it 30118 (if <code>--force</code> is used) 30119 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2848">#2848</a>)</li> 30120<li>correctly resolve template values used for extensions 30121 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2852">#2852</a>)</li> 30122<li>update template values after updating iterative easyconfig 30123 parameters 30124 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2854">#2854</a>)</li> 30125<li>
30125add top-level directories of hierarchical module naming scheme 30126 to <code>$MODULEPATH</code> before loading dependencies 30127 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2857">#2857</a>)</li> 30128<li>inject dependencies specified via <code>multi_deps</code> before normal 30129 build dependencies 30130 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2861">#2861</a>)</li> 30131<li>include Python version(s) in PR titles auto-generated by 30132 <code>--new-pr</code> 30133 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2863">#2863</a>, 30134 <a href="https://github.com/easybuilders/easybuild-framework/pull/2880">#2880</a>)</li> 30135<li>update <code>HierarchicalMNS</code> for GCCcore toolchain 30136 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2870">#2870</a>)</li> 30137<li>bump iteration index counter at the correct time 30138 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2886">#2886</a>)</li> 30139<li>don't specify <code>--ntasks-per-node</code> when submitting Slurm jobs 30140 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2887">#2887</a>)</li> 30141<li>fix order of easyconfig parameters in output generated by 30142 '<code>eb --avail-easyconfig-params --output-format rst</code>' 30143 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2888">#2888</a>)</li> 30144</ul> 30145</li> 30146<li>other changes:<ul> 30147<li>lower required version in Slurm job backend to 16.05 30148 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2833">#2833</a>)</li> 30149<li>add Lmod 8 to test suite 30150 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2849">#2849</a>)</li> 30151<li>deprecate useless 'skip_lower' named argument in 30152 template_constant_dict, always define <code>*lower</code> templates 30153 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2856">#2856</a>)</li> 30154<li>fix Python classifiers in <code>setup.py</code>, should be (only) Python 30155 2.6 & 2.7 30156 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2876">#2876</a>)</li> 30157</ul> 30158</li> 30159</ul> 30160<p><strong>easyblocks</strong></p> 30161<ul> 30162<li>one new generic easyblock: <code>CMakeMakeCp</code> 30163 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1725">#1725</a>)</li> 30164<li>new software-specific easyblock for Blender 30165 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1595">#1595</a>), 30166 Lua 30167 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1396">#1396</a>), 30168 OpenBLAS 30169 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1693">#1693</a>, 30170 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1697">#1697</a>)<ul> 30171<li>OpenBLAS easyblock also supports installation on POWER systems</li> 30172</ul> 30173</li> 30174<li>minor enhancements, including:<ul> 30175<li>enhance VMD easyblock to also build Surf & Stride + pick up 30176 netCDF for VMD >= 1.9.3 30177 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1314">#1314</a>)</li> 30178<li>update CGAL easyblock to support CGAL 4.12 & newer 30179 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1679">#1679</a>)</li> 30180<li>update QuantumESPRESSO easyblock for v6.4.1 30181 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1692">#1692</a>)</li> 30182<li>enhance Advisor & VTune easyblocks, since no license is required 30183 starting with version 2019 update 3 30184 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1694">#1694</a>, 30185 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1695">#1695</a>)</li> 30186<li>handle new multi-deps Python setup with <code>$EBPYTHONPREFIXES</code> for 30187 Tensorflow 30188 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1702">#1702</a>)</li> 30189<li>make CHARMM easyblock pick up on <code>prebuildopts</code> and <code>runtest</code> 30190 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1707">#1707</a>)</li> 30191<li>change default value for <code>'use_pip</code>' to None, so we can 30192 discriminate from '<code>
30192use_pip</code>' being set to False explicitly 30193 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1709">#1709</a>)</li> 30194<li>make PythonPackage aware of <code>(pre)testopts</code> 30195 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1715">#1715</a>)</li> 30196<li>enable GPU offloading in Clang if CUDA is included as a dep 30197 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1716">#1716</a>)</li> 30198<li>add support to Clang easyblock for also building libc++ and RTTI 30199 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1717">#1717</a>)</li> 30200<li>rebuild internal libfabric for impi 2019.x & more recent 30201 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1730">#1730</a>)</li> 30202<li>update Q&A patterns in SAS easyblock for version 9.4 + add 30203 support for custom license file path 30204 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1731">#1731</a>)</li> 30205</ul> 30206</li> 30207<li>various bug fixes, including:<ul> 30208<li>only install mkl-dnn by default with TensorFlow on x86-64 30209 systems 30210 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1666">#1666</a>)</li> 30211<li>make sure <code>ldconfig</code> can be found before using it in CUDA 30212 easyblock 30213 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1684">#1684</a>)</li> 30214<li>use temporary directory for pip cache (rather than 30215 <code>$HOME/.cache/pip</code>) in <code>PythonPackage</code> easyblock 30216 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1687">#1687</a>)</li> 30217<li>allow oversubscription when testing FFTW on top of OpenMPI >= 30218 3.0 30219 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1688">#1688</a>)</li> 30220<li>make sure <code>$HOME/.cache/pip</code> isn't used while installing 30221 Tkinter 30222 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1691">#1691</a>)</li> 30223<li>set default <code>exts_filter</code> in <code>PythonBundle</code>, so already 30224 installed extensions in a bundle can be skipped 30225 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1701">#1701</a>)</li> 30226<li>instruct Bazel to not use <code>$HOME/.cache/bazel</code> in TensorFlow 30227 easyblock 30228 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1704">#1704</a>)</li> 30229<li>also set <code>$XDG_CACHE_HOME</code> during installation of Python, to 30230 ensure that '<code>pip</code>' that comes along with it doesn't touch 30231 <code>$HOME/.cache/pip</code> 30232 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1705">#1705</a>)</li> 30233<li>use <code>-fp-model precise</code> if FMA instructions are missing in 30234 GROMACS easyblock 30235 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1706">#1706</a>)</li> 30236<li>make sure Perl install dir follows a standard format 30237 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1708">#1708</a>)</li> 30238<li>attach <code>source_urls</code> directly to sources for components in 30239 generic <code>Bundle</code> easyblock 30240 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1711">#1711</a>)</li> 30241<li>avoid that <code>--no-build-isolation</code> option is specified multiple 30242 times in <code>PythonPackage</code> easyblock 30243 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1713">#1713</a>)</li> 30244<li>fix prefix in impi compiler wrappers 30245 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1727">#1727</a>)</li> 30246<li>only embed zlib in binutils if it is listed a build dependency 30247 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1732">#1732</a>)</li> 30248</ul> 30249</li> 30250<li>other changes:<ul> 30251<li>fix Python classifiers in <code>setup.py</code>, should be (only) Python 30252 2.6 & 2.7 30253 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1724">#1724</a>)</li> 30254</ul> 30255</li> 30256</ul> 30257<p><strong>easyconfigs</strong></p> 30258<ul> 30259<li>added easyconfigs for new toolchains:<ul> 30260<li><code>fosscuda/2019a</code> 30261 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8063">#8063</a>), 30262 <code>gimkl/2018b</code> 30263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8287">#8287</a>), 30264 <code>gomkl/2018b</code> 30265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8216">#8216</a>), 30266 <code>gomkl/2019a</code> 30267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8218">#8218</a>), 30268 intelcuda/2019a 30269 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8069">#8069</a>)</li> 30270</ul> 30271</li> 30272<li>
30272added example easyconfig files for 52 new software packages:<ul> 30273<li>ADDA 30274 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8207">#8207</a>), 30275 AMD-LibM 30276 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7164">#7164</a>), 30277 AMD-RNG 30278 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7165">#7165</a>), 30279 AMD-SecureRNG 30280 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7165">#7165</a>), 30281 ARGoS 30282 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8039">#8039</a>, 30283 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8104">#8104</a>), 30284 ARWEN 30285 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8213">#8213</a>), 30286 Canvas 30287 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7716">#7716</a>), 30288 cdsapi 30289 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7970">#7970</a>), 30290 charmm 30291 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8202">#8202</a>), 30292 emcee 30293 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7989">#7989</a>), 30294 FlexiDot 30295 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8228">#8228</a>, 30296 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8275">#8275</a>), 30297 FreeImage 30298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8039">#8039</a>), 30299 Hello 30300 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7704">#7704</a>), 30301 HLAminer (8094), hypothesis 30302 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8307">#8307</a>), 30303 imgaug 30304 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8229">#8229</a>), 30305 INTEGRATE 30306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8193">#8193</a>, 30307 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8304">#8304</a>), 30308 INTEGRATE-Neo 30309 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8094">#8094</a>), 30310 IRkernel 30311 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8050">#8050</a>, 30312 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8099">#8099</a>), 30313 JiTCODE 30314 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7148">#7148</a>, 30315 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8327">#8327</a>), 30316 libFLAME 30317 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7163">#7163</a>), 30318 libpsml 30319 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5859">#5859</a>), 30320 LibSoup 30321 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8116">#8116</a>), 30322 libutempter 30323 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6426">#6426</a>), 30324 LS-PrePost 30325 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8070">#8070</a>), 30326 LUSCUS 30327 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7191">#7191</a>, 30328 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8105">#8105</a>, 30329 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8285">#8285</a>), 30330 memory-profiler 30331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8255">#8255</a>), 30332 metaWRAP 30333 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7896">#7896</a>), 30334 Net-core 30335 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7716">#7716</a>), 30336 netMHC 30337 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8094">#8094</a>), 30338 Nextflow 30339 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8195">#8195</a>), 30340 nvtop 30341 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8024">#8024</a>), 30342 openpyxl 30343 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8121">#8121</a>), 30344 py-cpuinfo 30345 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8245">#8245</a>), 30346 pyFFTW 30347 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8198">#8198</a>), 30348 PyQtGraph 30349 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7525">#7525</a>, 30350 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8253">#8253</a>), 30351 R-tesseract 30352 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7933">#7933</a>), 30353 RBFOpt 30354 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8178">#8178</a>), 30355 rnaQUAST 30356 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8040">#8040</a>), 30357 RStan 30358 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7996">#7996</a>), 30359 scikit-multilearn 30360 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8142">
30360#8142</a>), 30361 simpy 30362 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8177">#8177</a>, 30363 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8250">#8250</a>), 30364 SMARTdenovo 30365 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7630">#7630</a>), 30366 socat 30367 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8305">#8305</a>), 30368 SymEngine 30369 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7148">#7148</a>, 30370 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8327">#8327</a>), 30371 unixODBC 30372 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8074">#8074</a>), 30373 VAtools 30374 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7938">#7938</a>), 30375 VirtualGL 30376 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8008">#8008</a>), 30377 WebKitGTK+ 30378 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8118">#8118</a>, 30379 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8241">#8241</a>), 30380 xmlf90 30381 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5858">#5858</a>), 30382 YAPS 30383 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7976">#7976</a>), 30384 zingeR 30385 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7264">#7264</a>)</li> 30386</ul> 30387</li> 30388<li>added additional easyconfigs for various supported software 30389 packages, including:<ul> 30390<li>Boost 1.70.0, cairo 1.16.0, CGAL 4.14, Clang 8.0, cutadapt 2.1, 30391 dask 1.1.4, ELPA 2018.11.001, FFmpeg 4.1.3, GCC 9.1.0, GEOS 30392 3.7.2, GLib 2.60.1, gmsh 4.2.2, GROMACS 2019.2, GTK+ 3.24.8, 30393 h5py 2.9.0, hwloc 1.11.12, Hypre 2.15.1, Mathematica 12.0.0, 30394 matplotlib 3.0.3, Mesa 19.0.1, NBO 7.0, NCL 6.6.2, NCO 4.7.9, 30395 NiBabel 2.4.0, numba 0.43.1, OpenMPI 3.1.4, OrthoFinder 2.3.3, 30396 PCMSolver 1.2.3, PETSc 3.11.1, PROJ 6.0.0, PyQt5 5.12.1, PyTorch 30397 1.0.1, PyYAML 5.1, Qt5 5.12.3, QuantumESPRESSO 6.4.1, R 3.5.1 30398 (w/ intel/2018b), RNAIndel 1.0.0, Ruby 2.6.3, scikit-learn 30399 0.20.3, SLEPc 3.11.0, sympy 1.4, Tkinter 3.7.2, Vim 8.1.1209, 30400 VTK 8.2.0, wrf-python 1.3.1, wxPython 4.0.4, wxWidgets 3.0.4, 30401 xarray 0.12.1, zstd 1.4.0</li> 30402</ul> 30403</li> 30404<li>minor enhancements, including:<ul> 30405<li>enable auto-download of VMD 1.9.3 + add patches for Surf and 30406 Stride 30407 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7305">#7305</a>)</li> 30408<li>add mlegp extension in R 3.5.1 easyconfigs 30409 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7814">#7814</a>)</li> 30410<li>add pkg-config file to bzip2 easyconfigs 30411 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8200">#8200</a>)</li> 30412<li>allow use of '<code>use_pip = False</code>' in easyconfigs if pip 30413 doesn't work 30414 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8220">#8220</a>)</li> 30415</ul> 30416</li> 30417<li>various bug fixes, including:<ul> 30418<li>fix checksums for nlme extensions in R easyconfigs 30419 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7814">#7814</a>, 30420 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8054">#8054</a>)</li> 30421<li>add missing XZ dependency for Pysam > 0.12 30422 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7971">#7971</a>)</li> 30423<li>define <code>$GRACE_HOME</code> in Grace easyconfigs, so that font dir can 30424 be located 30425 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8048">#8048</a>)</li> 30426<li><code>$XDG_DATA_DIRS</code> must be set for GTK+ 30427 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8089">#8089</a>)</li> 30428<li>add missing FriBidi dependency for Pango 1.43.0 30429 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8103">#8103</a>)</li> 30430<li>add (back) custom <code>sanity_check_paths</code> in recent Pango 30431 easyconfigs 30432 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8106">#8106</a>)</li> 30433<li>fix missing extensions in cutadapt 1.16 easyconfigs 30434 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8130">#8130</a>)</li> 30435<li>
30435add missing cURL dependency for recent SAMtools versions 30436 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8131">#8131</a>)</li> 30437<li>add singledispatch extension to Python 2.7.15 easyconfig using 30438 <code>GCCcore/8.2.0</code> toolchain 30439 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8164">#8164</a>)</li> 30440<li>add missing X11 dependency for Gdk-Pixbuf 2.38.1 30441 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8222">#8222</a>)</li> 30442<li>make sure <code>hdf5r</code> picks up HDF5 dependency in R 3.5.1 30443 easyconfigs 30444 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8223">#8223</a>)</li> 30445<li>enable zstd compression in GRASS 7.6.0 easyconfig 30446 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8224">#8224</a>)</li> 30447<li>add missing ICU dependency on ICU for Harfbuzz 2.4.0 30448 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8226">#8226</a>)</li> 30449<li>disable AVX512 DGEMM kernels in OpenBLAS 0.3.5 30450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8227">#8227</a>)</li> 30451<li>fix homepage/description in OrthoFinder easyconfig 30452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8234">#8234</a>)</li> 30453<li>add <code>Parallel::ForkManager</code> extension to Perl 5.28.x easyconfigs 30454 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8247">#8247</a>)</li> 30455<li>replace LibUUID dependencies with util-linux 30456 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8258">#8258</a>)</li> 30457<li>add jemalloc & pkg-config as build deps for Salmon 0.12.0 30458 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8264">#8264</a>)</li> 30459<li>fix MAJIQ easyconfig by fixing order of extensions + avoid numpy 30460 test hang 30461 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8272">#8272</a>)</li> 30462<li>fix shebang in GLib Python script + clarify runtime dependency 30463 on Python 30464 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8277">#8277</a>)</li> 30465<li>add pkg-config and expat as (build) dependency for DBus 30466 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8283">#8283</a>)</li> 30467<li>define <code>$GI_TYPELIB_PATH</code> in GTK+ and Pango easyconfigs 30468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8246">#8246</a>, 30469 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8286">#8286</a>)</li> 30470<li>add pkg-config build dep to PROJ 6.0.0 easyconfig 30471 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8309">#8309</a>)</li> 30472<li>fix source URLS in recent libcerf easyconfigs 30473 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8332">#8332</a>, 30474 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8243">#8243</a>)</li> 30475<li>make zlib a real dependency rather than a build dep in recent 30476 binutils easyconfigs (>= 2.28) 30477 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8340">#8340</a>)</li> 30478<li>add fix-ib-query patch to OpenMPI 2.1.x and 3.0.x easyconfigs 30479 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8341">#8341</a>)</li> 30480<li>set <code>$XDG_CACHE_HOME</code> to $TMPDIR before '<code>pip install</code>' in 30481 Arrow 0.12.0 easyconfigs 30482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8347">#8347</a>)</li> 30483</ul> 30484</li> 30485<li>other changes:<ul> 30486<li>remove xbitmaps dependency from motif 30487 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7530">#7530</a>)</li> 30488<li>require custom <code>sanity_check_paths</code> in easyconfigs touched in 30489 PRs when generic easyblock is used 30490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8101">#8101</a>, 30491 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8123">#8123</a>)</li> 30492<li>use CMake built with GCCcore toolchain when installing Eigen 30493 3.3.4+ 30494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8261">#8261</a>)</li> 30495<li>fix Python classifiers in <code>setup.py</code>, should be (only) Python 30496 2.6 & 2.7 30497 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8299">#8299</a>)</li> 30498<li>use custom easyblock for OpenBLAS in OpenBLAS 0.3.x easyconfigs 30499 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8345">#8345</a>, 30500 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8339">#8339</a>)</li> 30501</ul> 30502</li> 30503</ul> 30504<h2 id="release_notes_eb390">EasyBuild v3.9.0 (April 12th 2019)<a class="headerlink" href="#release_notes_eb390" title="Permanent link">¶</a></h2> 30505<p>feature release</p> 30506<p><strong>framework</strong></p> 30507<ul> 30508<li>various enhancements, including:<ul> 30509<li>add <code>(pre)testopts</code> easyconfig parameters 30510 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2793">#2793</a>)</li> 30511<li>
30511add support for <code>multi_deps</code> easyconfig parameter 30512 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2741">#2741</a>, 30513 <a href="https://github.com/easybuilders/easybuild-framework/pull/2810">#2810</a>, 30514 <a href="https://github.com/easybuilders/easybuild-framework/pull/2811">#2811</a>, 30515 <a href="https://github.com/easybuilders/easybuild-framework/pull/2812">#2812</a>, 30516 <a href="https://github.com/easybuilders/easybuild-framework/pull/2813">#2813</a>, 30517 <a href="https://github.com/easybuilders/easybuild-framework/pull/2825">#2825</a>, 30518 <a href="https://github.com/easybuilders/easybuild-framework/pull/2826">#2826</a>, 30519 <a href="https://github.com/easybuilders/easybuild-framework/pull/2827">#2827</a>, 30520 <a href="https://github.com/easybuilders/easybuild-framework/pull/2828">#2828</a>)</li> 30521</ul> 30522</li> 30523<li>various bug fixes, including:<ul> 30524<li>fix argument name in <code>close_pr</code> 30525 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2752">#2752</a>)</li> 30526<li>fix undefined variable '<code>prefix</code>' in 30527 <code>Compiler._set_compiler_vars</code> 30528 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2757">#2757</a>)</li> 30529<li>fix test account for GitHub-related tests 30530 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2760">#2760</a>)</li> 30531<li>make sure read permissions are always set in <code>permissions_step</code> 30532 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2770">#2770</a>)</li> 30533<li>make test for <code>dep_graph</code> function robust against changing order 30534 of lines in resulting dot file 30535 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2772">#2772</a>)</li> 30536<li>fix problem with <code>import_available_modules</code> when running from 30537 easybuild-framework directory 30538 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2786">#2786</a>)</li> 30539<li>prepend location of test easyblocks to <code>$PYTHONPATH</code> to 30540 <code>test_generate_software_list</code>, rather than append 30541 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2788">#2788</a>)</li> 30542<li>use pid in backup name candidate to reduce risk of two processes 30543 colliding 30544 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2796">#2796</a>)</li> 30545<li>automatically enable <code>--ignore-osdeps</code> when using <code>--preview-pr</code> 30546 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2799">#2799</a>)</li> 30547<li>use temporary checkout of repository as robot path for 30548 <code>--new-pr</code> and <code>--update-pr</code> to determine locations for patch 30549 files 30550 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2803">#2803</a>)</li> 30551<li>avoid relying on order in which keys are processed in 30552 <code>to_dependency</code> 30553 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2804">#2804</a>)</li> 30554<li>fix yeb format to work with PyYAML 5 30555 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2809">#2809</a>)</li> 30556<li>fix typo in error message for use of unknown easyconfig 30557 parameter 30558 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2817">#2817</a>)</li> 30559<li>enhance <code>log_file_format</code> to fix problem when <code>%(name)s</code> 30560 template value is used for log directory 30561 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2818">#2818</a>)</li> 30562<li>iterate over subdirectories in order in <code>find_egg_dir_for</code> of 30563 bootstrap script, to ensure oldest vsc-install is picked 30564 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2819">#2819</a>)</li> 30565<li>replace <code>-Wl,--enable-new-dtags</code> compiler option with 30566 <code>-Wl,--disable-new-dtags</code> in RPATH wrapper script 30567 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2821">#2821</a>)</li> 30568<li>updated <code>COMPILER_F77</code> for PGI >= 19.1 30569 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2823">#2823</a>)</li> 30570<li>
30570added <code>FFTW_STATIC_LIBS_MT</code> to <code>FFTW_MAP_CLASS</code>, otherwise 30571 <code>FFTW_STATIC_LIBS_MT</code> are incorrectly defined 30572 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2822">#2822</a>)</li> 30573<li>sort available version list when selecting/generating easyconfig 30574 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2732">#2732</a>)</li> 30575</ul> 30576</li> 30577<li>other changes:<ul> 30578<li>use <code>assertEqual</code> rather than <code>assertEquals</code> (which is 30579 deprecated) 30580 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2746">#2746</a>)</li> 30581<li>test with Tmod 4.1.4 (packaged in RHEL8) in Travis CI 30582 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2747">#2747</a>)</li> 30583<li>replace deps by hidden deps instead of removing them from the 30584 lists 30585 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2748">#2748</a>)</li> 30586<li>ensure non-zero exit code for all test subsuites (+ fix trivial 30587 style issues) 30588 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2773">#2773</a>)</li> 30589<li>silence printed deprecation warnings for easyconfigs/toolchains 30590 while running (easyconfigs) test suite 30591 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2781">#2781</a>)</li> 30592<li>avoid printing of messages/warnings in framework test suite 30593 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2782">#2782</a>)</li> 30594<li>enable silent mode for <code>--new-pr</code> and <code>--update-pr</code> 30595 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2802">#2802</a>)</li> 30596<li>update Travis config to reflect that PyYAML 5.x is no longer 30597 compatible with Python 2.6 30598 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2807">#2807</a>)</li> 30599</ul> 30600</li> 30601</ul> 30602<p><strong>easyblocks</strong></p> 30603<ul> 30604<li>new software-specific easyblock for TensorRT 30605 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1627">#1627</a>)</li> 30606<li>minor enhancements, including:<ul> 30607<li>make sure CMake doesn't pick up on system Boost in CMakeMake 30608 generic easyblock 30609 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1618">#1618</a>)</li> 30610<li>modified <code>ConfigureMake</code> and <code>CMakeMake</code> generic easyblocks to 30611 allow changing <code>configure_cmd</code>, <code>build_cmd</code> and <code>install_cmd</code> to 30612 fit various needs 30613 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1628">#1628</a>, 30614 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1658">#1658</a>)</li> 30615<li>update ANSYS easyblock to deal with changed versioning scheme 30616 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1631">#1631</a>)</li> 30617<li>add extra path to builddir for SNPhylo >= 20160204 30618 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1632">#1632</a>)</li> 30619<li>add better support for TensorRT to TensorFlow 30620 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1634">#1634</a>)</li> 30621<li>add support for newer versions of wxPython to wxPython easyblock 30622 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1635">#1635</a>)</li> 30623<li>update OCaml easyblock to support OPAM 2.x 30624 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1638">#1638</a>)</li> 30625<li>update sanity check in TensorFlow easyblock for TensorFlow 30626 1.13.x 30627 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1642">#1642</a>)</li> 30628<li>make <code>ConfigureMake</code>, <code>MesonNinja</code> and <code>SCons</code> generic 30629 easyblocks aware of pretestopts 30630 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1645">#1645</a>)</li> 30631<li>add support for installing Python packages with '<code>pip</code>' 30632 without using <code>--ignore-installed</code> 30633 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1647">#1647</a>)</li> 30634<li>add support to <code>CMakeMake</code> easyblock to specify compilers using 30635 absolute file path 30636 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1652">
30636#1652</a>, 30637 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1655">#1655</a>)</li> 30638<li>stop checking for deprecated <code>pgf77</code> in sanity check of PGI 30639 easyblock 30640 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1653">#1653</a>)</li> 30641<li>accommodate version 10.1 in CUDA easyblock 30642 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1654">#1654</a>)</li> 30643<li>install <code>sitecustomize.py</code> with Python to support Python package 30644 installations for multiple Python versions in a single directory 30645 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1657">#1657</a>)</li> 30646<li>enhance SAMtools easyblock to also install <code>libhts.a</code> and 30647 include/htslib (when applicable) 30648 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1661">#1661</a>)</li> 30649<li>tweak <code>PythonPackage</code> & <code>PythonBundle</code> to update 30650 <code>$EBPYTHONPREFIXES</code> rather than <code>$PYTHONPATH</code> for multi-Python 30651 installations + make <code>sanity_check_step</code> aware of multi_deps 30652 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1664">#1664</a>, 30653 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1678">#1678</a>)</li> 30654<li>replace <code>-openmp</code> with <code>-fopenmp</code> when building TINKER with 30655 Intel compilers (+ modernize easyblock) 30656 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1668">#1668</a>)</li> 30657<li>make sure Meson is configured with <code>-Dlibdir=lib</code> so it doesn't 30658 install libraries in <code>lib/x86_64-linux-gnu</code> on Debian/Ubuntu 30659 multiarch systems 30660 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1673">#1673</a>)</li> 30661<li>allow for external libfabric via <code>ofi_libfabric</code> parameter in 30662 impi easyblock 30663 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1676">#1676</a>)</li> 30664<li>pass down compiler names and options to Qt5 5.8 & more recent 30665 via corresponding <code>QMAKE_*</code> configuration options 30666 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1677">#1677</a>)</li> 30667</ul> 30668</li> 30669<li>various bug fixes, including:<ul> 30670<li>create symlinks to <code>.modulerc</code> in symlinked module directories 30671 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1636">#1636</a>)</li> 30672<li>add missing import in FFTW easyblock 30673 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1641">#1641</a>)</li> 30674<li>fix finding of Python 3 include subdir + <code>libpython*.so</code> in 30675 OpenBabel easyblock 30676 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1633">#1633</a>)</li> 30677<li>add <code>no_qa</code> pattern for interactive installation command for 30678 ABAQUS 30679 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1637">#1637</a>)</li> 30680<li>make serial, smpar and dm+sm builds of WRF work and pass tests 30681 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1646">#1646</a>)</li> 30682<li>configure CP2K with correct <code>DATA_DIR</code> value rather than relying 30683 on <code>$CP2K_DATA_DIR</code> environment variable 30684 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1650">#1650</a>)</li> 30685<li>CP2K fixes: only call configure_LAPACK/ScaLAPACK when imkl is 30686 not used, prefer using 2^2 MPI processes for tests 30687 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1651">#1651</a>)</li> 30688<li>also take into account custom easyconfig parameters from 30689 <code>CMakeMake</code> in BamTools easyblock 30690 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1656">#1656</a>)</li> 30691<li>make sure Perl scripts are installed in the right location 30692 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1660">#1660</a>)</li> 30693<li>make sure setenv is used for CUDA_PATH etc. 30694 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1663">#1663</a>)</li> 30695<li>cleanup <code>sanity_check_paths</code> in numpy & scipy easyblocks 30696 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1665">#1665</a>, 30697 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1667">#1667</a>)</li> 30698<li>always set <code>self.pylibdir</code> in <code>PythonPackage.set_pylibdirs()</code>, 30699 which is important when installing Python packages for multiple
30700 Python versions via <code>multi_deps</code> 30701 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1671">#1671</a>)</li> 30702<li>fix custom definition of <code>load_module</code> method in LAPACK module 30703 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1675">#1675</a>)</li> 30704</ul> 30705</li> 30706<li>other changes:<ul> 30707<li>replace '<code>except OSError, err:</code>' pattern with 30708 '<code>except OSError as err:</code>' (for compatibility with Python 3.x) 30709 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1639">#1639</a>)</li> 30710<li>clean up Java easyblock to use <code>filetools</code> functionality 30711 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1649">#1649</a>)</li> 30712</ul> 30713</li> 30714</ul> 30715<p><strong>easyconfigs</strong></p> 30716<ul> 30717<li>added easyconfigs for new toolchains: <code>intel/2019.02</code> 30718 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7598">#7598</a>), 30719 <code>intel/2019.03</code> 30720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7846">#7846</a>)</li> 30721<li>added example easyconfig files for 68 new software packages:<ul> 30722<li>ACT 30723 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7928">#7928</a>), 30724 aiohttp 30725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7728">#7728</a>), 30726 at-spi2-atk and at-spi2-core 30727 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7658">#7658</a>), 30728 Bader 30729 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7804">#7804</a>), 30730 barrnap 30731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7738">#7738</a>), 30732 BCEL 30733 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7937">#7937</a>), 30734 biscuit 30735 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5868">#5868</a>), 30736 bitarray 30737 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7772">#7772</a>), 30738 BlobTools 30739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7565">#7565</a>, 30740 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7583">#7583</a>), 30741 bmtagger 30742 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7890">#7890</a>), 30743 bsddb3 30744 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7642">#7642</a>), 30745 CheckM 30746 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7712">#7712</a>), 30747 Cheetah 30748 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7952">#7952</a>), 30749 CONCOCT 30750 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7891">#7891</a>), 30751 cyvcf2 30752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8031">#8031</a>), 30753 DAS_Tool 30754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7741">#7741</a>), 30755 ExaBayes 30756 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7801">#7801</a>), 30757 FastANI 30758 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7992">#7992</a>), 30759 fastp 30760 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7693">#7693</a>), 30761 Flask 30762 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7734">#7734</a>), 30763 giflib 30764 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7663">#7663</a>), 30765 Giza 30766 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7843">#7843</a>), 30767 glew 30768 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7685">#7685</a>), 30769 gpustat 30770 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8025">#8025</a>), 30771 GRASS 30772 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7489">#7489</a>), 30773 GTDB-Tk 30774 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7995">#7995</a>), 30775 HPCX 30776 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7725">#7725</a>), 30777 IntelPython 30778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7920">#7920</a>), 30779 KNIME 30780 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7554">#7554</a>), 30781 KronaTools 30782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7721">#7721</a>), 30783 KyotoCabinet 30784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/795
307845">#7955</a>), 30785 Leptonica 30786 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7932">#7932</a>), 30787 libepoxy 30788 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7655">#7655</a>), 30789 libpsl 30790 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7666">#7666</a>), 30791 MAGMA 30792 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7829">#7829</a>), 30793 MATLAB-Engine 30794 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7758">#7758</a>), 30795 MaxBin 30796 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7767">#7767</a>), 30797 MetaBAT 30798 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7746">#7746</a>, 30799 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7931">#7931</a>), 30800 MinPath 30801 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7763">#7763</a>), 30802 ncdu 30803 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7505">#7505</a>), 30804 NGSadmix 30805 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7524">#7524</a>), 30806 NIMBLE 30807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7564">#7564</a>), 30808 PCAngsd 30809 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7727">#7727</a>), 30810 pizzly 30811 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7724">#7724</a>), 30812 Ploticus 30813 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7545">#7545</a>), 30814 pocl 30815 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7681">#7681</a>), 30816 POT 30817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8011">#8011</a>), 30818 ProjectQ 30819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7576">#7576</a>), 30820 pullseq 30821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7740">#7740</a>), 30822 pyBigWig 30823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7600">#7600</a>), 30824 Pyke3 30825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8034">#8034</a>), 30826 PyRETIS 30827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8041">#8041</a>), 30828 RDKit 30829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7973">#7973</a>), 30830 RNAIndel 30831 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8009">#8009</a>), 30832 scikit-optimize 30833 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7613">#7613</a>), 30834 SciPy-bundle 30835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7922">#7922</a>), 30836 sep 30837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8032">#8032</a>), 30838 slidingwindow 30839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7909">#7909</a>), 30840 SPLASH 30841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7843">#7843</a>), 30842 SqueezeMeta 30843 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7771">#7771</a>), 30844 SRPRISM 30845 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7890">#7890</a>), 30846 taxator-tk 30847 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7894">#7894</a>), 30848 TensorRT 30849 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7584">#7584</a>), 30850 tesseract 30851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7932">#7932</a>), 30852 Transrate 30853 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5108">#5108</a>), 30854 VCF-kit 30855 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7786">#7786</a>, 30856 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7882">#7882</a>), 30857 VV 30858 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7297">#7297</a>)</li> 30859</ul> 30860</li> 30861<li>added additional easyconfigs for various supported software 30862 packages, including:<ul> 30863<li>AFNI 19.0.01, Arrow 0.7.1, BLAST+ 2.8.1, CUDA 10.1.105,
30864 GCC(core) 8.3.0, GTK+ 3.22.30, Java (OpenJDK) 11(.0.2), Meson 30865 0.50.0, MultiQC 1.7, Nim 0.19.2, Ninja 1.9.0, netCDF 4.6.2, 30866 netCDF-Fortran 4.4.5, PCRE 8.43, Perl 5.28.1, PGI 19.1, Python 30867 3.7.2, RELION 3.0.4, Ruby 2.6.1, SCons 3.0.4, SQLite 3.27.2, 30868 SuiteSparse 5.4.0, TINKER 8.6.1, TensorFlow 1.13.1, X11 20190311</li> 30869</ul> 30870</li> 30871<li>minor enhancements, including:<ul> 30872<li>add various extensions to R 3.5.1 easyconfigs: <code>asnipe</code> 30873 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7572">#7572</a>), 30874 <code>liquidSVM</code> 30875 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7597">#7597</a>), 30876 <code>oddsratio</code>/<code>mltools</code>/<code>h2o</code> 30877 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7744">#7744</a>), 30878 <code>mlegp</code> 30879 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7814">#7814</a>), 30880 <code>bartMachine</code>/<code>lqa</code> 30881 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7865">#7865</a>), 30882 <code>PresenceAbsence</code>/<code>GUTS</code>/<code>GenSA</code> 30883 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7905">#7905</a>), 30884 <code>parsedate</code> 30885 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7935">#7935</a>), 30886 <code>circular</code> 30887 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7975">#7975</a>)</li> 30888<li>add <code>ujson</code> extension in recent Python easyconfigs 30889 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7517">#7517</a>)</li> 30890<li>run various checks on easyconfigs that are touched in pull 30891 requests and involve Python packages 30892 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7754">#7754</a>)</li> 30893<li>add <code>cpanminus</code> extension to recent Perl easyconfigs 30894 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7866">#7866</a>)</li> 30895<li>also install ANTs scripts (and set <code>$ANTSPATH</code> as required by 30896 those scripts) 30897 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7940">#7940</a>)</li> 30898<li>add missing <code>configopts</code> in GATE 8.1 easyconfig to enable Davis 30899 feature 30900 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8000">#8000</a>)</li> 30901</ul> 30902</li> 30903<li>various bug fixes, including:<ul> 30904<li>add patch for Mesa 18.1.1 to detect MIT-SHM 30905 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7536">#7536</a>)</li> 30906<li>add proper description to MINC-2.4.03 30907 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7551">#7551</a>)</li> 30908<li>add libunwind dependency to recent Mesa easyconfig when building 30909 with foss/GCC 30910 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7629">#7629</a>)</li> 30911<li>add/reorder missing/misplaced extensions in Python 2.7.15 and 30912 3.6.6 easyconfigs 30913 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7696">#7696</a>)</li> 30914<li>fix Jellyfish dependency in easyconfig for Kraken 1.0 (Jellyfish 30915 1.x is required) 30916 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7743">#7743</a>)</li> 30917<li>use <code>https://</code> in most recent XZ easyconfigs 30918 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7782">#7782</a>)</li> 30919<li>add patch for OpenMPI 3.1.x to fix ib-query 30920 '<code>Invalid argument</code>' error 30921 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7789">#7789</a>)</li> 30922<li>build OpenBLAS with <code>-fno-tree-vectorize</code> (asm constraint bugs 30923 for <0.3.6) + cleanup & SHA256 checksums 30924 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7790">#7790</a>, 30925 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7793">#7793</a>)</li> 30926<li>extra patch for TensorFlow 1.12.0 to remove <code>-B/usr/bin</code> from 30927 <code>linker_bin_path_flag</code> in <code>cuda_configure.bzl</code> 30928 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7800">#7800</a>)</li> 30929<li>fix easyconfig for STAR-Fusion 1.5.0 30930 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7802">#7802</a>)</li> 30931<li>fix checksums for boot/nlme extensions in R easyconfigs 30932 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7814">#7814</a>, 30933 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8054">#8054</a>)</li> 30934<li>
30934add patch for OpenMPI 3.x to fix UCX memory leak 30935 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7535">#7535</a>, 30936 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7824">#7824</a>)</li> 30937<li>replace <code>ncurses-devel</code> OS dependency in CMake easyconfigs using 30938 <code>dummy</code> toolchain with proper ncurses dependency 30939 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7834">#7834</a>)</li> 30940<li>use <code>PythonBundle</code> for 30941 <code>snakemake-5.2.4-foss-2018b-Python-3.6.6.eb</code> (+ fix moduleclass) 30942 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7842">#7842</a>)</li> 30943<li>use correct <code>buildopts</code> + add missing zlib dependency in 30944 StringTie 1.3.5 easyconfig 30945 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7845">#7845</a>)</li> 30946<li>update GStreamer to not enable dw and fix some missing 30947 dependencies 30948 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7889">#7889</a>)</li> 30949<li>add missing XZ dependency to most recent Pysam easyconfigs 30950 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7897">#7897</a>)</li> 30951<li>expat: add configure option <code>--without-docbook</code> to avoid 30952 docbook2X dependency 30953 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7930">#7930</a>)</li> 30954<li>fix source URLs for mawk 30955 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7960">#7960</a>)</li> 30956<li>fix LWM2, OTF2, OPARI2, and Score-P download URLs 30957 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7994">#7994</a>)</li> 30958<li>use <code>https://</code> in homepage & source_urls for OpenMPI and hwloc 30959 easyconfigs 30960 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8013">#8013</a>, 30961 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8014">#8014</a>, 30962 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8015">#8015</a> 30963 and 30964 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8016">#8016</a>)</li> 30965<li>add missing bokeh dependency for dask 1.0.0 (+ add 30966 dask-jobqueue) 30967 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8029">#8029</a>)</li> 30968<li>fix checking of binutils build dep in easyconfig tests 30969 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8038">#8038</a>)</li> 30970</ul> 30971</li> 30972<li>other changes:<ul> 30973<li>avoid use of <code>.items()</code> in R (bundle) easyconfigs, to fix 30974 compatibility with EasyBuild running on top of Python 3 30975 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7791">#7791</a>)</li> 30976<li>trim down test configuration: only test with Lmod 6.x with 30977 Tcl/Lua on Python 2.6/2.7 30978 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7795">#7795</a>, 30979 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7798">#7798</a>)</li> 30980<li>use <code>%(pyshortver)s</code> template in (old) SIP easyconfigs 30981 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7797">#7797</a>)</li> 30982<li>add PyTorch to whitelist for not having '<code>use_pip</code>' enabled 30983 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7844">#7844</a>)</li> 30984<li>don't use local variable '<code>pylibdir</code>' in list comprehension 30985 in PyQt easyconfig, since that doesn't work in Python 3 30986 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7848">#7848</a>)</li> 30987<li>use pip instead of setup.py with h5py/2.7.1 and 2017b toolchains 30988 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7864">#7864</a>)</li> 30989<li>prefer <code>https://</code> over <code>ftp://</code> for source_urls in recent 30990 GROMACS easyconfigs 30991 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7948">#7948</a>)</li> 30992<li>rename arrow to Arrow for old easyconfig 30993 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/8007">#8007</a>)</li> 30994</ul> 30995</li> 30996</ul> 30997<h2 id="release_notes_eb381">EasyBuild v3.8.1 (January 29th 2019)<a class="headerlink" href="#release_notes_eb381" title="Permanent link">¶</a></h2> 30998<p>bugfix/update release</p> 30999<p><strong>framework</strong></p> 31000<ul> 31001<li>various minor enhancements, including:<ul> 31002<li>
31002speed up checking of OS dependencies 31003 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2703">#2703</a>)</li> 31004<li>add support for '<code>eb --show-system-info</code>' 31005 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2722">#2722</a>)</li> 31006<li>add support for '<code>%(arch)s</code>' template value in easyconfig 31007 files (x86-64, aarch64, ppc64le, ...) 31008 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2728">#2728</a>)</li> 31009</ul> 31010</li> 31011<li>various bug fixes, including:<ul> 31012<li>add timestamp to reprod dir while in tmp space 31013 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2705">#2705</a>)</li> 31014<li>avoid '<code>+</code>' in directory name for <code>g++</code> rpath wrapper 31015 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2710">#2710</a>)</li> 31016<li>pre-install vsc-install < 0.11.4 in bootstrap script to avoid 31017 requiring '<code>mock</code>' Python package 31018 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2717">#2717</a>)</li> 31019<li>fix check in <code>--merge-pr</code> whether PR is eligible for merging in 31020 to only consider the status of the last test report 31021 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2720">#2720</a>)</li> 31022<li>don't recreate build directory when '<code>buildininstalldir</code>' is 31023 enabled for iterative installations 31024 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2724">#2724</a>)</li> 31025<li>filter (CUDA) <code>lib*/stubs</code> paths in RPATH wrapper script 31026 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2725">#2725</a>)</li> 31027</ul> 31028</li> 31029<li>other changes:<ul> 31030<li>replace '<code>except IOError, err:</code>' pattern with 31031 '<code>except IOError as err:</code>' for compatibility with Python 3.x 31032 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2711">#2711</a>)</li> 31033<li>make all <code>print</code> statements compatible with Python 3 31034 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2715">#2715</a>)</li> 31035<li>avoid use of <code>sys.maxint</code> in dependencies_for 31036 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2716">#2716</a>)</li> 31037</ul> 31038</li> 31039</ul> 31040<p><strong>easyblocks</strong></p> 31041<ul> 31042<li>minor enhancements, including:<ul> 31043<li>update Ferret easyblock to handle Ferret 7.3 31044 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1349">#1349</a>)</li> 31045<li>add support for defining <code>$LDSHARED</code> when installing Python 31046 packages if Python's value doesn't use toolchain compiler 31047 ($CC) 31048 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1455">#1455</a>)</li> 31049<li>update CP2K easyblock to add support for CP2K 6.1, and fix 31050 incorrect LibInt references 31051 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1545">#1545</a>)</li> 31052<li>make OpenFOAM easyblock handle debug build 31053 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1609">#1609</a>)</li> 31054<li>handle multiple installation keys for MATLAB 31055 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1610">#1610</a>)</li> 31056<li>run '<code>make check</code>' in parallel for GROMACS since it involves 31057 more compilation 31058 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1611">#1611</a>)</li> 31059<li>update OpenCV easyblock for recent versions (3.4.x >= 3.4.4 + 31060 4.0.x) 31061 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1616">#1616</a>)</li> 31062</ul> 31063</li> 31064<li>various bug fixes, including:<ul> 31065<li>check current <code>start_dir</code> value before appending '<code>src</code>' 31066 subdirectory in MrBayes easyblock 31067 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1582">#1582</a>)</li> 31068<li>avoid that (system) Intel compilers are always considered when 31069 building SuiteSparse 31070 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1612">#1612</a>)</li> 31071<li>fix missing import statement in ROOT easyblock 31072 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1614">#1614</a>)</li> 31073<li>answer SELinux question with '<code>no</code>' in Mathematica easyblock 31074 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1617">#1617</a>)</li> 31075<li>disable "build isolation" feature in pip > 10.x in 31076 PythonPackage generic easyblock 31077 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1623">#1623</a>)</li> 31078</ul> 31079</li> 31080<li>other changes<ul> 31081<li>cleanup in Perl and PerlModule easyblocks 31082 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1603">#1603</a>)</li> 31083</ul> 31084</li> 31085</ul> 31086<p><strong>easyconfigs</strong></p> 31087<ul> 31088<li>added easyconfigs for new toolchains <code>foss/2019a</code> 31089 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7371">#7371</a>), 31090 <code>intel/2019a</code> 31091 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7372">#7372</a>) 31092 and <code>iomkl/2019.01</code> 31093 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7375">#7375</a>)<ul> 31094<li>see also 31095 <a href="https://easybuild.readthedocs.io/en/latest/Common-toolchains.html">https://easybuild.readthedocs.io/en/latest/Common-toolchains.html</a></li> 31096</ul> 31097</li> 31098<li>
31098added example easyconfig files for 43 new software packages:<ul> 31099<li>Assimulo 31100 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6740">#6740</a>), 31101 C3D 31102 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7059">#7059</a>), 31103 CellMix 31104 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>), 31105 CESM-deps 31106 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6654">#6654</a>, 31107 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6675">#6675</a>, 31108 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6823">#6823</a>), 31109 DSA 31110 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>), 31111 DeMixT 31112 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>), 31113 deconf 31114 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>), 31115 DeconICA 31116 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>), 31117 double-conversion 31118 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7307">#7307</a>), 31119 dxpy 31120 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7079">#7079</a>), 31121 EPIC 31122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>), 31123 expect 31124 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7387">#7387</a>), 31125 Flye 31126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7430">#7430</a>), 31127 FMILibrary 31128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6740">#6740</a>), 31129 FMRIprep 31130 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7059">#7059</a>), 31131 FUSE 31132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7078">#7078</a>), 31133 GDCM 31134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7310">#7310</a>), 31135 HDDM 31136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7396">#7396</a>), 31137 ICA-AROMA 31138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7059">#7059</a>), 31139 IntaRNA 31140 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7334">#7334</a>), 31141 imageio 31142 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6738">#6738</a>), 31143 KWIML 31144 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7308">#7308</a>), 31145 kWIP 31146 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7444">#7444</a>), 31147 MagresPython 31148 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7395">#7395</a>), 31149 medaka 31150 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7426">#7426</a>), 31151 MINC 31152 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7311">#7311</a>), 31153 MuSiC 31154 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>), 31155 netMHCIIpan 31156 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7377">#7377</a>), 31157 NIfTI 31158 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7311">#7311</a>), 31159 OPERA 31160 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7408">#7408</a>), 31161 psrecord 31162 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7331">#7331</a>), 31163 pyfits 31164 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7273">#7273</a>), 31165 PyFMI 31166 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6740">#6740</a>), 31167 PyGWAS 31168 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5852">#5852</a>), 31169 Pylint 31170 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6675">#6675</a>), 31171 QDD 31172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7284">#7284</a>), 31173 RERconverge 31174 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7289">#7289</a>), 31175 samclip 31176 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7226">#7226</a>), 31177 SCIPhI 31178 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7419">#7419</a>), 31179 swarm 31180 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7453">#7453</a>), 31181 VXL 31182 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7309">#7309</a>), 31183 wrf-python 31184 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6736">#6736</a>), 31185 xCell 31186 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7422">#7422</a>)</li> 31187</ul> 31188</li> 31189<li>
31189added additional easyconfigs for various supported software 31190 packages, including:<ul> 31191<li>Amber 18, Arrow 0.12.0, Biopython 1.73, Boost 1.69.0, CP2K 6.1, 31192 canu 1.8, Ferret 7.3, GATE 8.1.p01, GROMACS 2019, Geant4 10.5, 31193 HPL 2.3, libxsmm 1.10, matplotlib 3.0.2, NEURON 7.6.5, Octave 31194 4.4.1, OpenBLAS 0.3.5, OpenCV 3.4.5 + 4.0.1, OpenFOAM v1812, PGI 31195 18.10, PLUMED 2.5.0, ROOT 6.14.06, Theano 1.0.3, TopHat 2.1.2, 31196 Yade 2018.02b</li> 31197</ul> 31198</li> 31199<li>minor enhancements, including:<ul> 31200<li>add additional extensions to R 3.5.1 easyconfigs:<ul> 31201<li>statnet 31202 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7370">#7370</a>), 31203 NMF, ComICS, dtangle, MCMCpack, shinythemes 31204 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7420">#7420</a>), 31205 csSAM 31206 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7423">#7423</a>), 31207 bridgedist 31208 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7477">#7477</a>)</li> 31209</ul> 31210</li> 31211<li>add DeconRNASeq and GSVA extensions to R-bundle-Bioconductor 3.7 31212 easyconfigs 31213 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7421">#7421</a>)</li> 31214<li>also install header files and CMake module for SeqAn 2.4.0 built 31215 with <code>foss/2018b</code> 31216 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7434">#7434</a>)</li> 31217<li>add download URL for <code>intel/2018a</code> components 31218 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7436">#7436</a>)</li> 31219<li>add missing checksums for protobuf easyconfigs using dummy 31220 toolchain 31221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7492">#7492</a>)</li> 31222</ul> 31223</li> 31224<li>various bug fixes, including:<ul> 31225<li>fix source URL in Doxygen easyconfigs 31226 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7324">#7324</a>)</li> 31227<li>add fallback source URL for recent pigz versions 31228 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7346">#7346</a>)</li> 31229<li>promote FriBiDi to runtime dep of Pango rather than only build 31230 dep 31231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7369">#7369</a>)</li> 31232<li>add <code>--without-systemdsystemunitdir</code> configure option to recent 31233 DBus easyconfigs 31234 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7373">#7373</a>)</li> 31235<li>fix issue of building M4 1.4.18 with glibc 2.28 31236 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7384">#7384</a>)</li> 31237<li>fix broken source URLs in MariaDB easyconfigs 31238 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7413">#7413</a>)</li> 31239<li>bump up build dependency of flex 2.6.4 from Bison 3.0.4 to 3.0.5 31240 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7414">#7414</a>)</li> 31241<li>disable building of OpenColorIO Python bindings since Python is 31242 not included as a dependency 31243 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7416">#7416</a>)</li> 31244<li>add missing build dependencies in old Harfbuzz/Pango easyconfigs 31245 (2016a generation) 31246 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7433">#7433</a>)</li> 31247<li>fix XML-LibXML linking with Intel compiler and GCCcore Perl 31248 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7440">#7440</a>)</li> 31249<li>prevent non-critical error from stopping Guile v1.8.8 build 31250 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7446">#7446</a>)</li> 31251<li>use <code>%(arch)s</code> template rather than hardcoding '<code>x86_64</code>' in 31252 XML-Parser easyconfigs 31253 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7450">#7450</a>)</li> 31254<li>use uniform configopts for Guile 1.8.8 31255 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7452">#7452</a>)</li> 31256<li>fix configopts in PyQt5 easyconfig files to avoid installation 31257 of files in Python/Qt5 installation directories 31258 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7470">#7470</a>)</li> 31259</ul> 31260</li> 31261<li>other changes:<ul> 31262<li>fix homepage in easyconfigs for <code>foss</code> toolchains 31263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7482">#7482</a>) 31264 and <code>intel</code> toolchains 31265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7483">#7483</a>)</li> 31266</ul> 31267</li> 31268</ul> 31269<h2 id="release_notes_eb380">EasyBuild v3.8.0 (December 18th 2018)<a class="headerlink" href="#release_notes_eb380" title="Permanent link">¶</a></h2> 31270<p>feature release</p> 31271<p><strong>framework</strong></p> 31272<ul> 31273<li>various enhancements, including:<ul> 31274<li>support use of version ranges in <code>--filter-deps</code> 31275 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2357">#2357</a>)</li> 31276<li>
31276add support for <code>--list-prs</code> 31277 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2400">#2400</a>, 31278 <a href="https://github.com/easybuilders/easybuild-framework/pull/2668">#2668</a>)</li> 31279<li>add support for <code>--close-pr</code> 31280 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2401">#2401</a>)</li> 31281<li>allow setting <code>optarch</code> compiler flags in the easyconfig via 31282 <code>toolchainopts</code> easyconfig parameter 31283 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2595">#2595</a>)</li> 31284<li>add option to skip pre-creation of install directory: 31285 <code>--disable-pre-create-installdir</code> 31286 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2629">#2629</a>, 31287 <a href="https://github.com/easybuilders/easybuild-framework/pull/2637">#2637</a>)</li> 31288<li>flesh out setting up of configuration into dedicated 31289 '<code>set_up_configuration</code>' function 31290 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2638">#2638</a>)</li> 31291<li>clean error when '<code>eb</code>' is cancelled by user 31292 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2641">#2641</a>)</li> 31293<li>add support for using Slurm as backend for <code>--job</code>, via 31294 <code>--job-backend=Slurm</code> 31295 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2642">#2642</a>, 31296 <a href="https://github.com/easybuilders/easybuild-framework/pull/2666">#2666</a>)</li> 31297<li>save easyblocks along with easyconfig in '<code>reprod</code>' 31298 subdirectory of install directory 31299 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2653">#2653</a>)</li> 31300<li>add support for deprecating easyconfig files & toolchains 31301 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2656">#2656</a>)</li> 31302<li>changed <code>EasyConfig.update</code> to be able to specify not to allow 31303 duplicate values 31304 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2657">#2657</a>)</li> 31305<li>move adding of dependencies to prepare step instead of check 31306 readiness step 31307 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2674">#2674</a>)</li> 31308<li>add support for disabling mapping of (sub)toolchains when 31309 <code>--try-toolchain</code> is used, via <code>--disable-map-toolchains</code> 31310 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2682">#2682</a>)</li> 31311<li>add '<code>astro</code>' and '<code>quantum</code>' module classes 31312 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2693">#2693</a>)</li> 31313</ul> 31314</li> 31315<li>various bug fixes, including:<ul> 31316<li>make <code>--from-pr</code> always try to apply PR patch on top of PR 31317 target branch 31318 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2631">#2631</a>)</li> 31319<li>fix bug that could cause to silently overwrite an existing 31320 easyconfig when using <code>--try-*</code> 31321 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2635">#2635</a>)</li> 31322<li>don't pass down specific environment variables into submitted 31323 jobs 31324 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2643">#2643</a>)</li> 31325<li>update template constants for source URLs to use https 31326 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2648">#2648</a>)</li> 31327<li>fix lib64 fallback for '<code>lib</code>'/'<code>lib64</code>' dirs entry in 31328 <code>sanity_check_paths</code> 31329 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2649">#2649</a>)</li> 31330<li>change PGI F90 Fortran compiler to pgf90 31331 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2650">#2650</a>)</li> 31332<li>use <code>--set-upstream-to</code> in <code>install-EasyBuild-develop.sh</code> script 31333 to deal with deprecated/no longer supported <code>--set-upstream</code> 31334 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2651">#2651</a>)</li> 31335<li>fix order of keys in '<code>toolchain</code>' value for dumped easyconfig 31336 file (name, version) + run style check on dumped easyconfigs in 31337 dump tests 31338 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2660">#2660</a>)</li> 31339<li>ensure checksums beside sources in dumped easyconfigs 31340 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2661">#2661</a>)</li> 31341<li>fix problems with easyconfig file saved in '<code>reprod</code>' 31342 directory by copying it before running any installation steps 31343 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2664">#2664</a>)</li> 31344<li>make print functions more robust w.r.t. arguments being passed 31345 to format the message to be printed 31346 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2670">#2670</a>)</li> 31347<li>use '<code>git am</code>' to apply patch for PRs in 31348 <code>fetch_easyconfigs_from_pr</code> 31349 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2680">#2680</a>)</li> 31350<li>correctly define <code>$LIBFFT_MT</code> for Intel MKL 31351 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2688">#2688</a>)</li> 31352<li>don't always require easyconfig files to resolve dependencies 31353 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2690">#2690</a>, 31354 <a href="https://github.com/easybuilders/easybuild-framework/pull/2692">#2692</a>, 31355 <a href="https://github.com/easybuilders/easybuild-framework/pull/2697">#2697</a>, 31356 <a href="https://github.com/easybuilders/easybuild-framework/pull/2698">#2698</a>, 31357 <a href="https://github.com/easybuilders/easybuild-framework/pull/2699">#2699</a>)</li> 31358</ul> 31359</li> 31360<li>fixes for Travis CI config:<ul> 31361<li>stop testing with Lmod 6.6.3, testing with Lmod 6.5.1 is 31362 sufficient 31363 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2627">#2627</a>)</li> 31364<li>Python 2.6 requires python-daemon 1.x as dep for GC3Pie 31365 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2673">#2673</a>)</li> 31366<li>
31366stick to idna<2.8 with Python 2.6 in Travis + distable broken 31367 test for HgRepository 31368 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2678">#2678</a>)</li> 31369</ul> 31370</li> 31371<li>other changes:<ul> 31372<li>always skip symlinks in <code>adjust_permissions</code> 31373 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2644">#2644</a>)</li> 31374<li>flesh out '<code>avail_easyblocks</code>' function from support for 31375 <code>--list-easyblocks</code> 31376 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2663">#2663</a>)</li> 31377<li>deprecate the <code>ictce</code> toolchain 31378 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2667">#2667</a>)</li> 31379<li>deprecate <code>goolf</code> and <code>goolfc</code> toolchains 31380 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2676">#2676</a>)</li> 31381<li>deprecate <code>intel</code> toolchains older than <code>intel/2016a</code> (+ 31382 <code>iccifort</code> & <code>iimpi</code> subtoolchains) 31383 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2677">#2677</a>)</li> 31384<li>deprecate ancient <code>gompi</code> toolchain versions 31385 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2684">#2684</a>)</li> 31386<li>use '<code>tar xzf</code>' (gzip) rather than '<code>tar xZf</code>' (ancient 31387 <code>compress</code>) to unpack <code>*.tar.Z</code> source files 31388 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2686">#2686</a>)</li> 31389<li>flesh out '<code>set_parallel</code>' method to it can be called 31390 separately 31391 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2687">#2687</a>)</li> 31392</ul> 31393</li> 31394</ul> 31395<p><strong>easyblocks</strong></p> 31396<ul> 31397<li>new generic easyblocks:<ul> 31398<li><code>PythonBundle</code> for installing a bundle of Python packages 31399 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1553">#1553</a>)</li> 31400<li><code>MesonNinja</code> for installing using Meson & Ninja 31401 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1561">#1561</a>)</li> 31402</ul> 31403</li> 31404<li>new software specific easyblock for <code>RepeatMasker</code> 31405 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1600">#1600</a>)</li> 31406<li>minor enhancements, including:<ul> 31407<li>add <code>-fno-delete-null-pointer-checks</code> compiler flag for OpenFOAM 31408 versions older than v3.0 31409 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1311">#1311</a>)</li> 31410<li>add support for building Tau with OTF included as dependency 31411 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1313">#1313</a>)</li> 31412<li>add support for Intel MPI version 2019 31413 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1546">#1546</a>)</li> 31414<li>also populate the include dir for CP2K 31415 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1554">#1554</a>)</li> 31416<li>add custom easyconfig parameter in GCC easyblock to control use 31417 of gold linker: <code>use_gold_linker</code> 31418 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1555">#1555</a>)</li> 31419<li>replace '<code>-</code>' with '<code>_</code>' in default '<code>import</code>' check for 31420 Python packages 31421 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1560">#1560</a>)</li> 31422<li>update WRF and WPS to support version 4 31423 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1563">#1563</a>)</li> 31424<li>adapt PSI easyblock for PSI4 > 1.2 31425 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1568">#1568</a>)</li> 31426<li>update Siesta easyblock to 4.1-b4 and add custom test_step 31427 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1573">#1573</a>)</li> 31428<li>enhance Mothur easyblock to support use of Boost and HDF5 as 31429 dependencies 31430 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1576">#1576</a>)</li> 31431<li>enhance sanity check for icc & ifort: also check for 31432 <code>compilers_and_libraries_*/linux</code> subdirectory 31433 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1577">#1577</a>)</li> 31434<li>update Trinity easyblock for latest version 2.8 31435 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1579">#1579</a>)</li> 31436<li>
31436add version check in sanity check step of SCOTCH easyblock (+ 31437 code cleanup) 31438 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1580">#1580</a>)</li> 31439<li>add support in Clang easyblock to skip running of all tests 31440 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1584">#1584</a>)</li> 31441<li>update WRF easyblock to allow serial HDF5 + pick up on parallel 31442 netCDF 31443 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1592">#1592</a>)</li> 31444<li>avoid hardcoding '<code>PREFIX=<installdir></code>' in build/install 31445 options when using <code>SCons</code> easyblock 31446 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1594">#1594</a>)</li> 31447<li>enable TensorFlow to detect any MPI runtime 31448 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1597">#1597</a>)</li> 31449<li>enhance <code>Bundle</code> easyblock to allow installation of bundle 31450 components with additional easyblocks + build components in 31451 parallel 31452 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1598">#1598</a>)</li> 31453<li>enhance Trilinos easyblock to support building against MKL 31454 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1601">#1601</a>)</li> 31455</ul> 31456</li> 31457<li>various bug fixes, including:<ul> 31458<li>make FDTD_Solutions easyblock do the install by copying files 31459 instead of '<code>rpm rebuild</code>' 31460 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1307">#1307</a>)</li> 31461<li>re-add missing <code>VT_(S)LIB_DIR</code> env variable to itac module 31462 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1309">#1309</a>)</li> 31463<li>fix in QuantumESPRESSO easyblock: ifort compiler needs 31464 <code>-assume byterecl</code> 31465 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1556">#1556</a>)</li> 31466<li>extract targets from buildopts in Quantumespresso easyblock 31467 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1558">#1558</a>)</li> 31468<li>fixes for TensorFlow easyblock 31469 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1559">#1559</a>)<ul> 31470<li>pass <code>$PYTHONPATH</code> while building TensorFlow</li> 31471<li>disable cross-compilation mode if optarch is set</li> 31472<li>fix sanity check for installing TensorFlow as extension</li> 31473</ul> 31474</li> 31475<li>added a test to disable compiling FFTW with MPI if the toolchain 31476 does not support MPI 31477 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1562">#1562</a>)</li> 31478<li>fix permissions problem with CUDA nvvp tar files + correctly 31479 handle numactl symlink in LLVM subdir in PGI easyblock 31480 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1569">#1569</a>)</li> 31481<li>fix TensorFlow test tempdir problem 31482 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1572">#1572</a>)</li> 31483<li>tweak VMD easyblock so that <code>configopts</code> don't contain 31484 duplicate values (otherwise it fails to rebuild) 31485 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1575">#1575</a>)</li> 31486<li>fix running netcdf4-python tests to also support installation as 31487 extension 31488 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1578">#1578</a>)</li> 31489<li>added the openmp flags in the linker flags in MUMPS easyblock 31490 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1585">#1585</a>)</li> 31491<li>avoid hardcoding <code>--with-rdma</code> configure option in MVAPICH2 31492 easyblock 31493 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1586">#1586</a>)</li> 31494<li>fix location of path-to-source argument in configure command of 31495 <code>CMakeMake</code> 31496 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1591">#1591</a>)</li> 31497<li>fix GROMACS use of MKL for non-Intel compilers (e.g. gomkl 31498 toolchain) 31499 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1596">#1596</a>)</li> 31500</ul> 31501</li> 31502<li>other changes<ul> 31503<li>inform Hound CI about Python 2 builtins 31504 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1604">#1604</a>)</li> 31505</ul> 31506</li> 31507</ul> 31508<p><strong>easyconfigs</strong></p> 31509<ul> 31510<li>added easyconfigs for new toolchains: <code>intel/2018.04</code> 31511 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7171">#7171</a>), 31512 <code>intel/2019.00</code> 31513 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/72
3151318">#7218</a>), 31514 <code>intel/2019.01</code> 31515 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7219">#7219</a>)</li> 31516<li>added example easyconfig files for 36 new software packages:<ul> 31517<li>4ti2 31518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7040">#7040</a>), 31519 ARPACK++ 31520 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6750">#6750</a>), 31521 CellRanger 31522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7242">#7242</a>), 31523 CharLS 31524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6762">#6762</a>) 31525 cscope 31526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7057">#7057</a>), 31527 ctags 31528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7057">#7057</a>), 31529 datamash 31530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6693">#6693</a>), 31531 dcm2niix 31532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6762">#6762</a>), 31533 DCMTK 31534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6761">#6761</a>), 31535 deepdiff 31536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7109">#7109</a>), 31537 Drake 31538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7182">#7182</a>), 31539 fast5 31540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7250">#7250</a>), 31541 gap 31542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7040">#7040</a>), 31543 Gerris 31544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7211">#7211</a>), 31545 GPAW-setups 31546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6984">#6984</a>), 31547 iCount 31548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7080">#7080</a>), 31549 ipyparallel 31550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6797">#6797</a>), 31551 Kratos 31552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7149">#7149</a>), 31553 LCov 31554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7160">#7160</a>), 31555 libvdwxc 31556 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6984">#6984</a>), 31557 libwebp 31558 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7065">#7065</a>), 31559 lrslib 31560 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7040">#7040</a>), 31561 MuPeXI 31562 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6991">#6991</a>), 31563 netMHCpan 31564 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6991">#6991</a>), 31565 Normaliz 31566 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7040">#7040</a>), 31567 OpenColorIO 31568 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7146">#7146</a>), 31569 OpenJPEG 31570 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7216">#7216</a>), 31571 PHLAT 31572 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7036">#7036</a>), 31573 poppler 31574 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7069">#7069</a>), 31575 RECON 31576 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7042">#7042</a>), 31577 RepeatMasker 31578 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7281">#7281</a>), 31579 TreeMix 31580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7133">#7133</a>), 31581 unrar 31582 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7117">#7117</a>), 31583 utf8proc 31584 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7083">#7083</a>), 31585 VSEARCH 31586 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7153">#7153</a>), 31587 XMDS2 31588 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7121">#7121</a>)</li> 31589</ul> 31590</li> 31591<li>added additional easyconfigs for various supported software 31592 packages, including:<ul> 31593<li>CheMPS2 1.8.8, Clang 6.0.1 + 7.0.0, dask 1.0.0, FFmpeg 4.1,
31594 GCC(core) 6.5.0 + 7.4.0, GPAW 1.4.0, HMMER 3.2.1, IPython 7.2.0, 31595 ITK 4.13.1, Keras 2.2.4, LLVM 7.0.0, Mothur 1.41.0, MultiQC 1.6, 31596 NAMD 2.13, OpenBLAS 0.3.4, OpenMPI 3.1.3 + 4.0.0, PSI4 1.2.1, 31597 Qt5 5.11.2, QuantumESPRESSO 6.3, Rust 1.30.1, Spark 2.4.0, 31598 Spyder 3.3.1, TensorFlow 1.11.0 + 1.12.0</li> 31599</ul> 31600</li> 31601<li>minor enhancements, including:<ul> 31602<li>install misc tools for angsd 31603 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6995">#6995</a>)</li> 31604<li>add libXp component to X11 bundle for GCCcore 6.4.0 31605 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7062">#7062</a>)</li> 31606<li>also install shared libraries for LZO 31607 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7073">#7073</a>)</li> 31608<li>add extensions to R 3.5.1 easyconfigs: <code>gllvm</code> 31609 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7123">#7123</a>), 31610 <code>grpreg</code> 31611 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7140">#7140</a>), 31612 <code>gamlss</code> + <code>gamlss.tr</code> 31613 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7263">#7263</a>)</li> 31614<li>install Tk private headers 31615 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7155">#7155</a>)</li> 31616<li>add <code>File::Next</code> extension to Perl 5.28.0 easyconfig 31617 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7276">#7276</a>)</li> 31618</ul> 31619</li> 31620<li>various bug fixes, including:<ul> 31621<li>fix installation of scikit-image 0.13.x by including missing 31622 required <code>PyWavelets</code> extension 31623 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7061">#7061</a>)</li> 31624<li>add missing dependencies to easyconfig for GC3Pie 2.5.0 31625 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7066">#7066</a>)</li> 31626<li>stop setting ignored '<code>full_sanity_check</code>' easyconfig 31627 parameter in easyconfigs 31628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7094">#7094</a>)</li> 31629<li>add missing checksums in X11/2016* easyconfigs 31630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7095">#7095</a>)</li> 31631<li>add missing checksums in X11/2017* easyconfigs 31632 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7096">#7096</a>)</li> 31633<li>add missing <code>cffi</code> & <code>pycparser</code> extensions to recent Python 31634 easyconfigs 31635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7105">#7105</a>, 31636 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7118">#7118</a>)</li> 31637<li>fix homepage in QuantumESPRESSO easyconfigs 31638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7114">#7114</a>)</li> 31639<li>use empty toolchain version in picard easyconfigs to ensure Java 31640 dependency is loaded during installation 31641 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7116">#7116</a>)</li> 31642<li>fix checksum for <code>mgcv</code> extension in R 3.5.* easyconfigs 31643 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7122">#7122</a>)</li> 31644<li>add missing 'patsy' extension in ARCH easyconfig + switch to 31645 using <code>PythonBundle</code> easyblock 31646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7124">#7124</a>)</li> 31647<li>add missing (dummy) sklearn extension in NeuroKit easyconfig 31648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7126">#7126</a>)</li> 31649<li>fix order of extensions in recent IPython easyconfigs to make 31650 '<code>pip check</code>' pass 31651 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7131">#7131</a>)</li> 31652<li>fix missing required Python packages in ASE 3.16.2 easyconfigs 31653 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7139">#7139</a>)</li> 31654<li>fix <code>source_urls</code> in CP2K easyconfigs (for official releases) 31655 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7240">#7240</a>)</li> 31656<li>update SCOTCH 6.0.5 easyconfigs in-place to 6.0.6 to fix wrong 31657 download URL 31658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7159">#7159</a>)</li> 31659<li>
31659add Autotools build dep in patchelf easyconfig 31660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7175">#7175</a>)</li> 31661<li>STREAM fixes: use https + versioned source 31662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7193">#7193</a>)</li> 31663<li>fix checksum in Molden easyconfig 31664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7251">#7251</a>)</li> 31665<li>fix source URL for ADMIXTURE 31666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7258">#7258</a>)</li> 31667<li>fix source URLs & versions + build procedure for SKESA 31668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7275">#7275</a>)</li> 31669<li>fix checksum for TRF 4.09 31670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7278">#7278</a>)</li> 31671<li>add missing zlib dependency for NSS 31672 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7293">#7293</a>)</li> 31673<li>add required build deps for QtWebEngine in recent Qt5 31674 easyconfigs 31675 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7300">#7300</a>)</li> 31676<li>fix ImageMagick source URLs: use <code>launchpad.net</code> for old 31677 versions, switch to GitHub for 7.0.8-* onwards 31678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7301">#7301</a>)</li> 31679</ul> 31680</li> 31681<li>other changes:<ul> 31682<li>update <code>Java/1.8</code> wrapper to Java 1.8.0_192 31683 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7097">#7097</a>)</li> 31684<li>don't enable <code>optarch</code> toolchain option in VCFtools 31685 easyconfigs, since it's enabled by default 31686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7106">#7106</a>)</li> 31687<li>stop using lowopt in libxc 4.2.3 easyconfigs 31688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7115">#7115</a>)</li> 31689<li>deprecate easyconfigs for <code>ictce</code> toolchains + <code>intel</code> 31690 toolchains older than <code>intel/2016a</code> 31691 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7231">#7231</a>)</li> 31692<li>deprecate easyconfigs for <code>goolf(c)</code> + corresponding <code>gompi(c)</code> 31693 subtoolchains 31694 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7243">#7243</a>)</li> 31695</ul> 31696</li> 31697</ul> 31698<h2 id="release_notes_eb371">EasyBuild v3.7.1 (October 18th 2018)<a class="headerlink" href="#release_notes_eb371" title="Permanent link">¶</a></h2> 31699<p>bugfix/update release</p> 31700<p><strong>framework</strong></p> 31701<ul> 31702<li>various enhancements, including:<ul> 31703<li>generate <code>.modulerc.lua</code> when Lua syntax and Lmod >= 7.8 is 31704 used 31705 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2597">#2597</a>)</li> 31706<li>allow <code>--force</code> to use regex if <code>--try-toolchain</code> can not map 31707 intelligently 31708 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2605">#2605</a>)</li> 31709<li>add support for disabling modules tool version check 31710 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2610">#2610</a>)</li> 31711<li>add support to <code>ModuleGenerator.modulerc</code> method to also write 31712 <code>.modulerc</code> file 31713 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2611">#2611</a>)</li> 31714<li>check whether module file being wrapped exists in same directory 31715 as module wrapper when using Lmod 6.x 31716 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2611">#2611</a>)</li> 31717</ul> 31718</li> 31719<li>various bug fixes, including:<ul> 31720<li>stop relying on '<code>easy_install</code>' in bootstrap script, use 31721 '<code>python -m easy_install</code>' instead 31722 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2590">#2590</a>)</li> 31723<li>fix templating of values in <code>list_software</code> function 31724 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2591">#2591</a>)</li> 31725<li>fix composing of <code>lib64</code> fallback paths in sanity check 31726 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2602">#2602</a>)</li> 31727<li>determine <code>file_info</code> for all easyconfigs before any actual 31728 copying in <code>copy_easyconfigs</code> function 31729 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2604">#2604</a>)</li> 31730<li>also check for module wrappers in <code>ModulesTool.exist</code> method 31731 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2606">#2606</a>)</li> 31732<li>
31732add trailing newline to module load message if it's not there 31733 yet 31734 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2613">#2613</a>)</li> 31735<li>retain all dependencies when determining dependency tree of a 31736 toolchain 31737 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2617">#2617</a>)</li> 31738<li>protect <code>exts_lists</code> from templating in <code>dump</code> method 31739 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2619">#2619</a>)</li> 31740<li>making CUDA capability detection more robust 31741 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2621">#2621</a>)</li> 31742</ul> 31743</li> 31744<li>other changes:<ul> 31745<li>lower required Lmod version to 6.5.1 31746 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2593">#2593</a>)</li> 31747</ul> 31748</li> 31749</ul> 31750<p><strong>easyblocks</strong></p> 31751<ul> 31752<li>new software specific easyblocks for fastStructure 31753 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1529">#1529</a>)</li> 31754<li>minor enhancements, including:<ul> 31755<li>support bypassing use of system type obtained with recent 31756 <code>config.guess</code> in <code>ConfigureMake</code> 31757 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1531">#1531</a>)</li> 31758<li>enhance generated module file for FreeSurfer 31759 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1543">#1543</a>)</li> 31760<li>add option in Qt easyblock to check for QtWebEngine component in 31761 sanity check 31762 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1544">#1544</a>)</li> 31763<li>also install CP2K as a library + code cleanup in CP2K easyblock 31764 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1547">#1547</a>)</li> 31765</ul> 31766</li> 31767<li>various bug fixes, including:<ul> 31768<li>fix checking for downloaded dependencies for stand-alone 31769 installations in <code>PythonPackage</code> generic easyblock 31770 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1530">#1530</a>)</li> 31771<li>also specify <code>--host</code> option to configure script based on 31772 config.guess result in <code>ConfigureMake</code> easyblock 31773 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1532">#1532</a>)</li> 31774<li>use short module name when creating module wrapper in <code>ModuleRC</code> 31775 generic easyblock 31776 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1535">#1535</a>)</li> 31777<li>use <code>DOT_MODULERC</code> constant in <code>ModuleRC</code> easyblock rather than 31778 hardcoding '<code>.modulerc</code>' 31779 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1533">#1533</a>)</li> 31780<li>use <code>--no-deps</code> when installing .whl in TensorFlow easyblock if 31781 extension are being installed, move test run to sanity check 31782 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1537">#1537</a>)</li> 31783<li>use <code>os.getcwd()</code> rather than <code>self.startdir</code> in TensorFlow 31784 easyblock to fix installation of TensorFlow as extension in a 31785 bundle 31786 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1540">#1540</a>)</li> 31787<li>add symlink to wrapped module file when creating <code>.modulerc</code> in 31788 temporary location 31789 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1539">#1539</a>)</li> 31790<li>properly handle Python dependency in Qscintilla easyblock 31791 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1499">#1499</a>)</li> 31792</ul> 31793</li> 31794<li>other changes:<ul> 31795<li>cleanup Tarball easyblock by using <code>copy_dir</code> function 31796 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1541">#1541</a>)</li> 31797</ul> 31798</li> 31799</ul> 31800<p><strong>easyconfigs</strong></p> 31801<ul> 31802<li>added easyconfigs for new toolchain <code>foss/2018.08</code> with GCC/8.2.0 31803 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6992">#6992</a>)</li> 31804<li>added example easyconfig files for 26 new software packages:<ul> 31805<li>ARCH 31806 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6939">#6939</a>), 31807 fbm 31808 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6948">#6948</a>), 31809 GenomeTester4 31810 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6970">#6970</a>), 31811 GlobusConnectPersonal 31812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6974">#6974</a>), 31813 MMseqs2 31814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6964">#6964</a>), 31815 NAG 31816 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5772">#5772</a>), 31817 NAGfor 31818 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5772">#5772</a>), 31819 NSPR 31820 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7005">#7005</a>), 31821 NSS 31822 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7005">#7005</a>), 31823 NeuroKit 31824 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6947">#6947</a>), 31825 novoalign 31826 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6944">#6944</a>), 31827 OptiType 31828 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6924">#6924</a>), 31829 OrthoFinder 31830 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6964">#6964</a>), 31831 pandas-datareader 31832 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6938">#6938</a>), 31833 pFUnit 31834 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6949">#6949</a>), 31835 PMIx 31836 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/693
318360">#6930</a>), 31837 PSolver 31838 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6888">#6888</a>), 31839 PyDatastream 31840 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6951">#6951</a>), 31841 PyFR 31842 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6846">#6846</a>), 31843 Pyomo 31844 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6910">#6910</a>), 31845 Quandl 31846 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6950">#6950</a>), 31847 RTG-Tools 31848 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6862">#6862</a>), 31849 seq2HLA 31850 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6969">#6969</a>), 31851 suds 31852 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6951">#6951</a>), 31853 UCX 31854 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6931">#6931</a>), 31855 XMLSec 31856 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6929">#6929</a>)</li> 31857</ul> 31858</li> 31859<li>added additional easyconfigs for various supported software 31860 packages, including:<ul> 31861<li>binutils 2.31.1, dask 0.19.4, GCC(core) 8.2.0, OpenBLAS 0.3.3, 31862 OpenMPI 3.1.2, Pillow 5.3.0, PyCUDA 2018.1</li> 31863</ul> 31864</li> 31865<li>minor enhancements, including:<ul> 31866<li>add clustree + plotly extensions (+ deps) for R 3.5.1 31867 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6901">#6901</a>)</li> 31868<li>add tclsh symlink to recent Tcl easyconfigs 31869 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6915">#6915</a>)</li> 31870<li>update GROMACS 2016.3 with NVML patches 31871 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6936">#6936</a>)</li> 31872<li>use <code>make=make</code> in build options for ParMGridGen easyconfigs 31873 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6952">#6952</a>)</li> 31874<li>add <code>Data::Dump</code> as extension to Perl (dependency for GIMIC) 31875 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7004">#7004</a>)</li> 31876</ul> 31877</li> 31878<li>various bug fixes, including:<ul> 31879<li>inhibit <code>-Werror</code> in binutils 2.26 as new system GCC has case 31880 fallthrough warnings 31881 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5793">#5793</a>)</li> 31882<li>change fastStructure easyconfig to use custom easyblock 31883 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6893">#6893</a>)</li> 31884<li>fix toolchain for tbb dependency in 31885 <code>Bowtie2-2.3.4.2-foss-2018b.eb</code> 31886 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6927">#6927</a>)</li> 31887<li>fix uroot installation in R-3.5.1-foss-2018b 31888 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6934">#6934</a>)</li> 31889<li>add missing Python packages in TensorFlow 1.10.x easyconfigs 31890 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6940">#6940</a>)</li> 31891<li>add missing dep for Szip in 2017b builds of netCDF 31892 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6942">#6942</a>)</li> 31893<li>fix missing comment from 31894 <code>OpenBabel-2.4.1-fix-link-path-tests.patch</code> 31895 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6943">#6943</a>)</li> 31896<li>add patch to Python 3.6.1 - 3.6.3 that removes comment in 31897 comment 31898 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6946">#6946</a>)</li> 31899<li>add missing <code>ulimit_unlimited=True</code> (see issue 31900 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6484">#6484</a>) 31901 in the newest Python builds 31902 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6959">#6959</a>)</li> 31903<li>solve '<code>version UUID_1.0 not found</code>' problem in LibUUID 31904 easyconfigs 31905 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6962">#6962</a>)</li> 31906<li>eliminate dependency on ancient problematic LibUUID library, 31907 replace with util-linux 31908 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6963">#6963</a>)</li> 31909<li>force building of <code>ccmake</code>
31909 for CMake 3.12.1 + fix deps 31910 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6967">#6967</a>)</li> 31911<li>fix broken installation for Python 3.6.2 & 3.6.3 with PyNaCl as 31912 dep for paramiko extension by explicitly including previous 31913 PyNaCl version as extension 31914 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6971">#6971</a>)</li> 31915<li>fix source URL for ADMIXTURE (no https) + add SHA256 checksum 31916 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6982">#6982</a>)</li> 31917<li>add missing NSS/DBus dependencies to Qt 5.10.1 easyconfigs built 31918 with foss toolchain to ensure that QtWebEngine component gets 31919 installed 31920 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7005">#7005</a>)</li> 31921<li>add '<code>openssl</code>' OS deps in Perl 5.28.0 easyconfig for 31922 <code>Net::ssleay</code> 31923 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7008">#7008</a>)</li> 31924<li>add missing checksum for ipaddress extension in Python 31925 easyconfigs 31926 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7021">#7021</a> 31927 and 31928 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7033">#7033</a>)</li> 31929<li>add missing extensions to Python 2.7.14 31930 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7022">#7022</a> 31931 and 31932 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7023">#7023</a>), 31933 3.6.2 31934 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7025">#7025</a>), 31935 3.6.3 31936 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7027">#7027</a>) 31937 and 3.6.4 31938 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7029">#7029</a> 31939 and 31940 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7030">#7030</a>)</li> 31941<li>add missing OS dependencies for git 31942 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7028">#7028</a>)</li> 31943<li>create default configuration for RTG-Tools 31944 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7032">#7032</a>)</li> 31945<li>also run checks on changed files when target branch for PR is 31946 something different than 'develop' 31947 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/7034">#7034</a>)</li> 31948</ul> 31949</li> 31950<li>other changes:<ul> 31951<li>removed dead 'bzip.org' source URL for bzip2 source tarball 31952 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6983">#6983</a>)</li> 31953</ul> 31954</li> 31955</ul> 31956<h2 id="release_notes_eb370">EasyBuild v3.7.0 (September 25th 2018)<a class="headerlink" href="#release_notes_eb370" title="Permanent link">¶</a></h2> 31957<p>feature release</p> 31958<p><strong>framework</strong></p> 31959<ul> 31960<li>minimal Lmod version requirement bumped to 6.6.3 31961 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2575">#2575</a>)</li> 31962<li>various enhancements, including:<ul> 31963<li>add support to bootstrap script to force install specific 31964 EasyBuild version 31965 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2382">#2382</a>, 31966 <a href="https://github.com/easybuilders/easybuild-framework/pull/2580">#2580</a>)</li> 31967<li>consider potential of multiple subtoolchains when resolving 31968 dependencies 31969 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2464">#2464</a>, 31970 <a href="https://github.com/easybuilders/easybuild-framework/pull/2465">#2465</a>, 31971 <a href="https://github.com/easybuilders/easybuild-framework/pull/2466">#2466</a>, 31972 <a href="https://github.com/easybuilders/easybuild-framework/pull/2585">#2585</a>)</li> 31973<li>fall back to downloading using the <code>requests</code> Python package (if 31974 installed) when <code>urllib2</code> fails due to SSL error 31975 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2538">#2538</a>)</li> 31976<li>make <code>--try-toolchain</code> more aware of subtoolchains 31977 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2539">#2539</a>)<ul> 31978<li>subtoolchain of original toolchains are now mapped to 31979 subtoolchains of target toolchain</li> 31980</ul> 31981</li> 31982<li>
31982add support for BLIS and goblf toolchain that uses BLIS for BLAS 31983 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2540">#2540</a>)</li> 31984<li>allow skipping of sanity check step via '<code>skipsteps</code>' 31985 easyconfig parameter 31986 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2549">#2549</a>)</li> 31987<li>add support for <code>--check-contrib</code> 31988 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2551">#2551</a>)<ul> 31989<li>equivalent with <code>--check-style</code>, but also verifies presence 31990 of SHA256 checksums (+ more checks in the future)</li> 31991</ul> 31992</li> 31993<li>added support to 'download' sources from git 31994 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2555">#2555</a>)<ul> 31995<li>see 31996 <a href="https://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#downloading-from-a-git-repository">https://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#downloading-from-a-git-repository</a></li> 31997</ul> 31998</li> 31999<li>add '<code>parse</code>' hook to add support for applying site-specific 32000 customisations to the 'raw' easyconfig 32001 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2562">#2562</a>, 32002 <a href="https://github.com/easybuilders/easybuild-framework/pull/2566">#2566</a>)<ul> 32003<li>see <a href="https://easybuild.readthedocs.io/en/develop/Hooks.html">https://easybuild.readthedocs.io/en/develop/Hooks.html</a></li> 32004</ul> 32005</li> 32006<li>lift invalidating of module caches into helper method that can 32007 be used by easyblocks 32008 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2571">#2571</a>)</li> 32009<li>always dump a fully parsed easyconfig to the '<code>reprod</code>' subdir 32010 of the installation directory 32011 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2574">#2574</a>)</li> 32012<li>add '<code>modulerc</code>' method to <code>ModuleGenerator</code> class 32013 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2575">#2575</a>)</li> 32014</ul> 32015</li> 32016<li>various bug fixes, including:<ul> 32017<li>make GC3Pie stop build process if a dependency failed 32018 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2474">#2474</a>)</li> 32019<li>filter out patched files in test/ in <code>fetch_easyconfigs_from_pr</code> 32020 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2547">#2547</a>)</li> 32021<li>check GC3pie version using the <code>pkg_resources</code> API rather than 32022 using <code>__version__</code> (which was removed in GC3Pie 2.5.0) 32023 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2554">#2554</a>)</li> 32024<li>fix enforcing of checksums for extensions 32025 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2561">#2561</a>, 32026 <a href="https://github.com/easybuilders/easybuild-framework/pull/2570">#2570</a>, 32027 <a href="https://github.com/easybuilders/easybuild-framework/pull/2579">#2579</a>)</li> 32028<li>skip running of configuration checks while only a single 32029 configuration level is taken into account during <code>--show-config</code> 32030 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2567">#2567</a>)</li> 32031<li>fix error statements in modules tool version checks 32032 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2576">#2576</a>)</li> 32033<li>fix finding of software subdirectory for specified patch file in 32034 <code>--new-pr</code>/<code>--update-pr</code> 32035 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2577">#2577</a>)</li> 32036<li>take into account dependency 'wrappers' in check_conflicts 32037 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2583">#2583</a>)</li> 32038<li>stick to pycparser < 2.19 with Python 2.6 in Travis config 32039 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2584">#2584</a>)</li> 32040</ul> 32041</li> 32042<li>other changes:<ul> 32043<li>use <code>namelower</code> as default for '<code>github_account</code>' easyconfig 32044 parameter 32045 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2528">#2528</a>)</li> 32046<li>use <code>.counts()</code> rather than deprecated <code>.stats()</code> for GC3Pie 32047 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2573">#2573</a>)</li> 32048</ul> 32049</li> 32050</ul> 32051<p><strong>easyblocks</strong></p> 32052<ul> 32053<li>new generic easyblock: <code>ModuleRC</code> 32054 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1503">#1503</a>, 32055 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1518">#1518</a>)</li> 32056<li>new software specific easyblocks for BWISE 32057 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1497">#1497</a>) 32058 and VEP 32059 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1512">#1512</a>)</li> 32060<li>minor enhancements, including:<ul> 32061<li>update QuantumESPRESSO easyblock: stop building in installation 32062 dir, do not use external FoX dependency, support for recent 32063 versions 32064 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1312">#1312</a>)</li> 32065<li>updates to TensorFlow easyblock:<ul> 32066<li>require cuDNN if CUDA support is enabled, enable mkl-dnn by 32067 default, fix problem with internal protobuf problem, add 32068 awareness for TensorRT & NCCL 32069 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1453">#1453</a>)</li> 32070<li>
32070add support for IntelMPI 32071 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1507">#1507</a>)</li> 32072</ul> 32073</li> 32074<li>update WIEN2k easyblock for version 18.1 32075 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1460">#1460</a>)</li> 32076<li>add CUDA '<code>stubs</code>' subdirectory to $LIBRARY_PATH 32077 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1464">#1464</a>)</li> 32078<li>add support for building ScaLAPACK on top of BLIS 32079 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1467">#1467</a>)</li> 32080<li>handle X11 better and make '<code>static</code>' a build flag in Amber 32081 easyblock 32082 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1468">#1468</a>)</li> 32083<li>update Boost easyblock for Boost 1.67.0 (name change in Python 32084 3.x library files) 32085 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1472">#1472</a>)</li> 32086<li>add CEI/bin to $PATH for ANSYS 19 & newer 32087 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1476">#1476</a>)</li> 32088<li>enhance SCons easyblock to enable building in parallel 32089 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1477">#1477</a>)</li> 32090<li>add awareness for CCOLAMD and CAMD in Trilinos easyblock 32091 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1480">#1480</a>)</li> 32092<li>add support to apply (binary) patches after main CUDA install 32093 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1481">#1481</a>, 32094 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1483">#1483</a>)</li> 32095<li>add support for only building Python bindings (+ code cleanup) 32096 in Boost easyblock 32097 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1484">#1484</a>, 32098 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1495">#1495</a>)</li> 32099<li>provide control over subdirectory in which R packages are 32100 installed 32101 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1485">#1485</a>)</li> 32102<li>added regex to fix <code>$WM_PROJECT_VERSION</code> correctly in OpenFOAM 32103 easyblock 32104 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1489">#1489</a>)</li> 32105<li>improve PGI siterc so it allows <code>-pthread</code> switch 32106 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1494">#1494</a>)</li> 32107<li>customise <code>check_checksums method</code> in Bundle easyblock to fix 32108 checking of checksums for components 32109 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1496">#1496</a>)</li> 32110<li>include a pkgconfig file '<code>hdf5.pc</code>' to HDF5 installations 32111 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1504">#1504</a>)</li> 32112<li>(download &) use an updated <code>config.guess</code> script in generic 32113 ConfigureMake easyblock 32114 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1506">#1506</a>, 32115 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1522">#1522</a>, 32116 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1523">#1523</a>, 32117 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1524">#1524</a>)</li> 32118<li>make <code>IntelBase</code> generic easyblock aware of <code>(pre)installopts</code> 32119 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1509">#1509</a>)</li> 32120<li>update Siesta easyblock for v3.2 to 4.1-b3 32121 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1510">#1510</a>)</li> 32122<li>take <code>(pre)installopts</code> into account in RPackage generic 32123 easyblock 32124 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1513">#1513</a>)</li> 32125<li>update DOLFIN easyblock for latest version 32126 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/2018">#2018</a>.1) 32127 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1521">#1521</a>)</li> 32128</ul> 32129</li> 32130<li>various bug fixes, including:<ul> 32131<li>drop useless definition of <code>$NLSPATH</code> in <code>IntelBase</code> + fix ipp 32132 library paths 32133 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1442">#1442</a>)</li> 32134<li>fix order of arguments in log message in <code>PythonPackage</code> 32135 easyblock 32136 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1459">#1459</a>)</li> 32137<li>run <code>ldconfig</code> in post-install step of CUDA easyblock to create 32138 missing symlinks in 'stubs' subdirectory 32139 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1473">#1473</a>)</li> 32140<li>
32140take into account that only name/version may be specified for 32141 some components in <code>Bundle</code> easyblock 32142 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1474">#1474</a>)</li> 32143<li>make SuperLU easyblock consider both <code>lib</code> and <code>lib64</code> 32144 subdirectories 32145 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1479">#1479</a>)</li> 32146<li>use short build dir for Trilinos to dance around 32147 "<code>Argument list too long</code>" problem + link with <code>libmetis.a</code> 32148 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1486">#1486</a>)</li> 32149<li>correct check for Red Hat 6 based OS in TensorFlow easyblock 32150 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1487">#1487</a>)</li> 32151<li>improve configuration choice in FSL easyblock 32152 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1498">#1498</a>)</li> 32153<li>don't check for <code>mcc</code> in MATLAB sanity check as it requires a 32154 specific toolbox license 32155 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1514">#1514</a>)</li> 32156<li>make sure Bazel doesn't write files in $HOME/.cache when 32157 building TensorFlow 32158 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1519">#1519</a>)</li> 32159<li>enable VSX on POWER for FFTW >= 3.3.7 32160 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1520">#1520</a>)</li> 32161<li>add <code>librt</code> as dependency when linking Trilinos with SuiteSparse 32162 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1525">#1525</a>)</li> 32163</ul> 32164</li> 32165<li>other changes:<ul> 32166<li>switch to using CMake install procedure for Eigen 3.3.4 & newer 32167 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1482">#1482</a>)</li> 32168<li>bump Lmod version used in Travis config to 6.6.3 (now required 32169 by framework) 32170 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1505">#1505</a>)</li> 32171</ul> 32172</li> 32173</ul> 32174<p><strong>easyconfigs</strong></p> 32175<ul> 32176<li>added easyconfigs for new toolchains: <code>fosscuda/2017b</code> 32177 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6706">#6706</a>), 32178 <code>intelcuda/#2017b</code> 32179 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6709">#6709</a>), 32180 <code>iomkl/2018b</code> 32181 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6661">#6661</a>)</li> 32182<li>added example easyconfig files for 49 new software packages:<ul> 32183<li>alleleCount 32184 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6676">#6676</a>), 32185 BCALM 32186 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6796">#6796</a>), 32187 BDBag 32188 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6672">#6672</a>), 32189 BFC 32190 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6647">#6647</a>), 32191 Bio-DB-HTS 32192 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6854">#6854</a>), 32193 bioawk 32194 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6865">#6865</a>), 32195 biomart-perl 32196 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6745">#6745</a>), 32197 BLIS 32198 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6614">#6614</a>), 32199 Boost.Python 32200 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6763">#6763</a>), 32201 BWISE 32202 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6802">#6802</a>), 32203 CapnProto 32204 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6542">#6542</a>), 32205 CaVEMan 32206 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6708">#6708</a>), 32207 CCL 32208 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5802">#5802</a>), 32209 cDNA_Cupcake 32210 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6787">#6787</a>), 32211 cget 32212 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6780">#6780</a>), 32213 coevol 32214 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6589">#6589</a>, 32215 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6642">#6642</a>), 32216 Delly 32217 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6735">#6735</a>), 32218 earthengine-api 32219 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6556">#6556</a>), 32220 fineRADstructure 32221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6586">#6586</a>), 32222 GIMIC 32223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6575">#6575</a>), 32224 GitPython 32225 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6850">#6850</a>), 32226 HiC-Pro 32227 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5873">#5873</a>), 32228 Inelastica 32229 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6831">#6831</a>), 32230 JAXFrontCE 32231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6837">
32231#6837</a>), 32232 jq 32233 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6632">#6632</a>), 32234 KAT 32235 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6808">#6808</a>), 32236 KMC 32237 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6553">#6553</a>), 32238 Kraken2 32239 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6569">#6569</a>), 32240 Lighter 32241 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6553">#6553</a>), 32242 Mash 32243 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6542">#6542</a>), 32244 MetaPhlAn2 32245 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6600">#6600</a>), 32246 Minimac4 32247 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6781">#6781</a>), 32248 mordecai 32249 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6670">#6670</a>), 32250 NCCL 32251 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5802">#5802</a>), 32252 NxTrim 32253 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6646">#6646</a>), 32254 parasail 32255 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6601">#6601</a>), 32256 PheWAS 32257 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6030">#6030</a>), 32258 Pilon 32259 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6553">#6553</a>), 32260 python-parasail 32261 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6601">#6601</a>), 32262 SearchGUI 32263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6637">#6637</a>), 32264 shovill 32265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6553">#6553</a>), 32266 SKESA 32267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6553">#6553</a>), 32268 snakemake 32269 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6851">#6851</a>), 32270 strelka 32271 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6742">#6742</a>), 32272 SWIPE 32273 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6795">#6795</a>), 32274 ToFu 32275 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6322">#6322</a>), 32276 tqdm 32277 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6721">#6721</a>), 32278 TRUST 32279 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6601">#6601</a>), 32280 VEP 32281 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6854">#6854</a>)</li> 32282</ul> 32283</li> 32284<li>added additional easyconfigs for various supported software 32285 packages, including:<ul> 32286<li>Bazel 0.16.0, Boost 1.67.0 + 1.68.0, CUDA 10.0.1, DOLFIN 32287 (FEniCS) 2018.1, FSL 5.0.11, GC3Pie 2.5.0, GROMACS 2018.3, 32288 HTSlib + SAMtools 1.9, IPython 6.4.0, matplotlib 3.0.0, 32289 OpenCoarrays 2.2.0, OpenFOAM 6 & v1806, PyTorch 0.4.1, Python 32290 3.6.6, R 3.5.1, TensorFlow 1.10.1, Trilinos 12.12.1, WIEN2k 18.1</li> 32291</ul> 32292</li> 32293<li>minor enhancements, including:<ul> 32294<li>add test to enforce SHA256 checksums in touched files in pull 32295 requests to develop 32296 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5005">#5005</a>)</li> 32297<li>add various extensions to recent R easyconfigs 32298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6590">#6590</a>, 32299 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6686">#6686</a>, 32300 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6858">#6858</a>)</li> 32301<li>add <code>mpmath</code> extension to Python 3.6.4 + 3.7.0 easyconfigs 32302 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6607">#6607</a>, 32303 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6713">#6713</a>)</li> 32304<li>add Java 1.8 easyconfig that can be updated in-place to more 32305 recent JDK 1.8.x 32306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6712">#6712</a>)<ul> 32307<li>see also 32308 <a href="https://easybuild.readthedocs.io/en/latest/Wrapping_dependencies.html">https://easybuild.readthedocs.io/en/latest/Wrapping_dependencies.html</a></li> 32309</ul> 32310</li> 32311<li>
32311add <code>iso_c_binding</code> support to arpack-ng 3.6.2 32312 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6718">#6718</a>)</li> 32313<li>add <code>XML::Parser</code>, <code>XML::RegExp</code> & <code>XML::DOM</code> extensions to 32314 Perl(<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6744">#6744</a>)</li> 32315<li>add <code>tabulate</code> extension to all Python > 3.6 easyconfigs 32316 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6809">#6809</a>)</li> 32317<li>enable MPI version of arpack-ng 3.5.0 32318 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6840">#6840</a>)</li> 32319<li>add <code>wish</code> symlink to <code>wish8.6</code> in recent Tk easyconfigs 32320 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6870">#6870</a>)</li> 32321<li>add <code>libXp</code> and <code>printproto</code> to X11 bundle 32322 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6873">#6873</a>)</li> 32323</ul> 32324</li> 32325<li>various bug fixes, including:<ul> 32326<li>define '<code>_GNU_SOURCE</code>' to ensure that '<code>reallocarray</code>' is 32327 defined in flex 2.6.4 easyconfigs, fixes bootstrap crash 32328 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5792">#5792</a>, 32329 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6766">#6766</a>)</li> 32330<li>added tabix dependency in VCFtools 32331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6584">#6584</a>)</li> 32332<li>added zlib dependency to BWA 32333 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6591">#6591</a>), 32334 BEDTools 32335 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6592">#6592</a>), 32336 VCFtools 32337 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6653">#6653</a>)</li> 32338<li>add checksums to googletest easyconfigs 32339 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6611">#6611</a>)</li> 32340<li>fix source URL + add checksum to 32341 wkhtmltopdf-0.12.3-Linux-x86_64.eb 32342 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6628">#6628</a>, 32343 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6641">#6641</a>)</li> 32344<li>don't use external FoX dependency in QuantumESPRESSO 6.2 32345 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6638">#6638</a>)</li> 32346<li>update hwloc easyconfigs with libxml2 and libpciaccess 32347 dependencies 32348 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6639">#6639</a>)</li> 32349<li>fix gettext build dep for Mono-5.10.0.160 32350 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6640">#6640</a>)</li> 32351<li>remove no longer existing config option 32352 <code>--enable-mpi-thread-multiple</code> in OpenMPI 3.x easyconfigs 32353 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6645">#6645</a>)</li> 32354<li>fix homepage in recent HDF5 easyconfigs 32355 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6687">#6687</a>)</li> 32356<li>add expat dependency to Mesa v18.1.1 32357 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6706">#6706</a>)</li> 32358<li>add missing <code>--with-trio-flavor=netcdf</code> flag to ABINIT 8.x 32359 easyconfigs 32360 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6711">#6711</a>)</li> 32361<li>remove useless definition of $TORCH_CUDA_ARCH_LIST in PyTorch 32362 easyconfig that doesn't use CUDA 32363 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6719">#6719</a>)</li> 32364<li>fix building GCCcore 6.3.0 on recent OSs by backporting patches 32365 from 6.4.0 32366 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6727">#6727</a>)</li> 32367<li>fix <code>source_urls</code> in bzip2 easyconfigs 32368 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6728">#6728</a>)</li> 32369<li>specify location of dependencies in configure options for libgd 32370 (to avoid system libraries being used instead) 32371 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6731">#6731</a>)</li> 32372<li>also install docs/man pages in recent git easyconfigs (versions 32373 2.1x.y) 32374 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6751">#6751</a>)</li> 32375<li>
32375add CMake build dep for Eigen 3.3.4 32376 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6756">#6756</a>, 32377 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6784">#6784</a>)</li> 32378<li>add expat dependency to Perl 5.26.0 32379 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6758">#6758</a>)</li> 32380<li>add ncurses OS dependency to CMake for Debian distros 32381 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6783">#6783</a>)</li> 32382<li>fix checksums for pkgmaker, rngtools & RcppProgress extensions 32383 in R 3.4.3 easyconfigs 32384 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6815">#6815</a>)</li> 32385<li>add pkg-config build dependency to GTS 32386 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6819">#6819</a>)</li> 32387<li>do not check if hwloc-dump-hwdata utility was installed, since 32388 it's only built on x86 systems 32389 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6836">#6836</a>)</li> 32390<li>patch libxc 3.x and 4.0.x to compile on POWER 32391 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6868">#6868</a>)</li> 32392<li>consistently add patch for paycheck extension in Python 3.6/3.7 32393 to fix UTF8 issue with README 32394 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6892">#6892</a>)</li> 32395</ul> 32396</li> 32397<li>other changes:<ul> 32398<li>bump Lmod version used in Travis config to 6.6.3 (now required 32399 by framework) 32400 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6834">#6834</a>)</li> 32401</ul> 32402</li> 32403</ul> 32404<h2 id="release_notes_eb362">EasyBuild v3.6.2 (July 11th 2018)<a class="headerlink" href="#release_notes_eb362" title="Permanent link">¶</a></h2> 32405<p>bugfix/update release</p> 32406<p><strong>framework</strong></p> 32407<ul> 32408<li>various enhancements, including:<ul> 32409<li>add support for including environment variable that is resolved 32410 at "module load time" in user module path 32411 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2395">#2395</a>)<ul> 32412<li><code>{RUNTIME_ENV::EXAMPLE}</code> is replaced by value of <code>$EXAMPLE</code> 32413 when module is loaded</li> 32414</ul> 32415</li> 32416<li>also support generating Docker container recipes & image via 32417 <code>--containerize</code> (still experimental) 32418 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2479">#2479</a>)</li> 32419<li>add support for specifying source URLs directly in '<code>sources</code>' 32420 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2520">#2520</a>)</li> 32421<li>perform early 'raw' parse of provided easyconfig file to check 32422 for syntax error or faulty inputs 32423 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2523">#2523</a>)</li> 32424<li>add '<code>bitbucket_account</code>' easyconfig parameter and template, 32425 and let <code>BITBUCKET*</code> templates use it 32426 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2525">#2525</a>)</li> 32427</ul> 32428</li> 32429<li>various bug fixes, including:<ul> 32430<li>take into account <code>--filter-deps</code> when re-loading build 32431 dependencies in <code>extensions_step</code> 32432 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2516">#2516</a>)</li> 32433<li>fix for offline use of bootstrap script: ignore errors when 32434 determining source URLs if source tarballs are provided 32435 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2517">#2517</a>)</li> 32436<li>fix error message that is raised for incorrect type of value in 32437 <code>sanity_check_paths</code> 32438 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2524">#2524</a>)</li> 32439</ul> 32440</li> 32441<li>other changes:<ul> 32442<li>move flake8 config into <code>setup.cfg</code> + fix style issues in 32443 <code>easybuild/tools/options.py</code> 32444 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2511">#2511</a>)</li> 32445<li>make test that verifies that <code>BuildOptions</code> does not support 32446 updating a bit more flexible 32447 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2518">#2518</a>)</li> 32448</ul> 32449</li> 32450</ul> 32451<p><strong>easyblocks</strong></p> 32452<ul> 32453<li>new software-specific easyblock for OpenCV 32454 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1444">#1444</a>)</li> 32455<li>minor enhancements, including:<ul> 32456<li>use <code>$CPATH</code>/<code>$LD_LIBRARY_PATH</code>
32456 for CMake's 32457 <code>find_path</code>/<code>find_library</code> functions in <code>CMakeMake</code> easyblock 32458 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1165">#1165</a>)</li> 32459<li>make cdft lib compilation optional for Intel MKL, by detecting 32460 MPI availability 32461 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1393">#1393</a>)</li> 32462<li>add <code>use_glibcxx11_abi</code> easyconfig parameter in Boost easyblock 32463 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1434">#1434</a>)</li> 32464<li>enable filtering of paths in <code>$CPATH</code> and <code>$LIBRARY_PATH</code> in 32465 TensorFlow easyblock 32466 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1436">#1436</a>)</li> 32467<li>add support for building GROMACS with <code>--optarch=GENERIC</code> 32468 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1440">#1440</a>)</li> 32469<li>check current stack limit and set it to '<code>unlimited</code>' if 32470 possible in Python easyblock 32471 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1441">#1441</a>)</li> 32472<li>trivial update for Q&A in SAS easyblock 32473 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1448">#1448</a>)</li> 32474<li>allow skipping tests when installing Perl extensions, by setting 32475 '<code>runtest</code>' to <code>False</code> 32476 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1451">#1451</a>)</li> 32477<li>add support for installing Intel products using serial numbers 32478 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1452">#1452</a>)</li> 32479<li>update version check to FFTW 3.3.8 for tests to pass on POWER 32480 (ppc64le) 32481 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1454">#1454</a>)</li> 32482</ul> 32483</li> 32484<li>various bug fixes, including:<ul> 32485<li>build MPFR in GCC stage 1 without LTO if (system) GCC used is 32486 too old 32487 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1435">#1435</a>)</li> 32488<li>make sure xmlpatterns always gets built with Qt 32489 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1437">#1437</a>)</li> 32490<li>fix symlink check in NWChem easyblock + use 32491 <code>change_dir</code>/<code>remove_file</code>/<code>symlink</code> functions 32492 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1438">#1438</a>)</li> 32493</ul> 32494</li> 32495<li>other changes:<ul> 32496<li>move flake8 configuration to <code>setup.cfg</code> and make HoundCI aware 32497 of it 32498 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1430">#1430</a>)</li> 32499</ul> 32500</li> 32501</ul> 32502<p><strong>easyconfigs</strong></p> 32503<ul> 32504<li>added easyconfigs for new toolchains: <code>foss/2018b</code> 32505 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6424">#6424</a>), 32506 <code>fosscuda/2018b</code> 32507 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6555">#6555</a>) 32508 and <code>intel/2018b</code> 32509 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6409">#6409</a>)</li> 32510<li>added example easyconfig files for 28 new software packages:<ul> 32511<li>CUnit 32512 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6469">#6469</a>), 32513 eggnog-mapper 32514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6513">#6513</a>), 32515 FANN 32516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6468">#6468</a>), 32517 FTGL 32518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6421">#6421</a>), 32519 FreeFem++ 32520 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5918">#5918</a>), 32521 fastStructure 32522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6448">#6448</a>), 32523 fastq-tools 32524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5396">#5396</a>), 32525 fullrmc 32526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6422">#6422</a>), 32527 GDGraph 32528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6529">#6529</a>), 32529 heaptrack 32530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6450">#6450</a>), 32531 libgpuarray 32532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5429">#5429</a>), 32533 lz4 32534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6449">#6449</a>), 32535 MAJIQ 32536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5983">#5983</a>), 32537 makedepf90 32538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6504">#6504</a>), 32539 nanopolish 32540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6464">#6464</a>), 32541 opencv_contrib 32542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6441">#6441</a>), 32543 PRC 32544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6477">#6477</a>), 32545 Pillow-SIMD 32546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6152">#6152</a>), 32547 Pytorch 32548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6152">#6152</a>), 32549 poretools 32550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6467">#6467</a>), 32551 pystran 32552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6395">#6395</a>), 32553 R-keras 32554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6530">#6530</a>), 32555 Scoary 32556 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6521">#6521</a>), 32557 Scrappie 32558 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6469">#6469</a>), 32559 torchvision 32560 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6152">#6152</a>), 32561 WISExome 32562 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6524">#6524</a>), 32563 WannierTools 32564 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6539">#6539</a>), 32565 zstd 32566 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6449">#6449</a>, 32567 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6452">#6452</a>)</li> 32568</ul> 32569</li> 32570<li>
32570added additional easyconfigs for various supported software 32571 packages, including:<ul> 32572<li>GROMACS 2018.2, HDF5 1.10.2, IPython 6.3.1, Kraken 1.0, Mesa 32573 18.1.1, netCDF 4.6.1, NWChem 6.8, OpenBLAS 0.3.1, OpenMPI 3.1.1, 32574 Perl 5.28.0, Python 2.7.15, R 3.5.0, X11 20180604</li> 32575</ul> 32576</li> 32577<li>minor enhancements, including:<ul> 32578<li>add hint on file name differences between downloaded and 32579 expected in cuDNN easyconfig 32580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6042">#6042</a>)</li> 32581<li>add '<code>gee</code>' extension to R 3.4.4 easyconfigs 32582 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6376">#6376</a>)</li> 32583<li>enable building of MPI libraries in VTK 8.1.0 easyconfigs 32584 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6460">#6460</a>, 32585 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6429">#6429</a>)</li> 32586</ul> 32587</li> 32588<li>minor changes, including:<ul> 32589<li>rename '<code>Canu</code>' to '<code>canu</code>' for v1.7 32590 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6389">#6389</a>)</li> 32591<li>update existing easyconfigs for OpenCV 3.4.1 to use new custom 32592 easyblock for OpenCV 32593 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6509">#6509</a>)</li> 32594<li>fix software name in <code>Bsoft</code> easyconfig 32595 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6557">#6557</a>)</li> 32596</ul> 32597</li> 32598<li>various bug fixes, including:<ul> 32599<li>fix SAMtools dependency for ChimPipe, required SAMtools < 1.0 32600 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5930">#5930</a>)</li> 32601<li>skip installing of documentation in easyconfig for jemalloc 32602 5.0.1 32603 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6428">#6428</a>)</li> 32604<li>stop including GCCcore 6.4.0 as build dep for GCCcore 8.1.0 32605 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6431">#6431</a>)<ul> 32606<li>no longer needed with updated GCC easyblock</li> 32607</ul> 32608</li> 32609<li>add patch for GCCcore 6.4.0 to fix compilation problems on glibc 32610 2.26 systems 32611 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6432">#6432</a>, 32612 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6495">#6495</a>)</li> 32613<li>fix checksums for 32614 <code>pkgmaker</code>/<code>rngtools</code>/<code>RWeka</code>/<code>RcppProgress</code>/<code>mgcv</code> extensions 32615 in R 3.4.4 easyconfigs 32616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6446">#6446</a>, 32617 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6502">#6502</a>)</li> 32618<li>added necessary compiler flag for Guile 1.8.8 32619 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6457">#6457</a>)</li> 32620<li>build hwloc 1.11.10 with <code>-fno-tree-vectorize</code> to avoid 32621 segfaulting lstopo on Intel Skylake 32622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6461">#6461</a>)</li> 32623<li>add patch for binutils 2.30 to fix assertion failure 32624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6463">#6463</a>)</li> 32625<li>sync extensions in <code>Python-3.6.4-iomkl-2018a.eb</code> easyconfig with 32626 other Python 3.6.4 easyconfigs using 2018a toolchain 32627 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6471">#6471</a>)</li> 32628<li>enable checking/setting of unlimited stack limit in Python 3.6.x 32629 easyconfigs using an '<code>intel</code>' toolchain 32630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6485">#6485</a>, 32631 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6492">#6492</a>)</li> 32632<li>add missing <code>libxml2</code> dependency for HDF5 1.10.1 32633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6498">#6498</a>)</li> 32634<li>also copy eggnog-mapper scripts 32635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6522">#6522</a>)</li> 32636<li>fix missing dependencies for Perl modules included as extensions 32637 for Perl 5.26.1 32638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6532">#6532</a>) 32639 and 5.28.0 32640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6533">#6533</a>)</li> 32641<li>fix location of include directory in libffi 3.2.1 easyconfigs 32642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6565">#6565</a>)</li> 32643</ul> 32644</li> 32645<li>other changes<ul> 32646<li>also check for multiple dependency variants in easyconfigs using 32647 GCCcore 7.3.0 & newer 32648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6444">#6444</a>)</li> 32649</ul> 32650</li> 32651</ul> 32652<h2 id="release_notes_eb361">EasyBuild v3.6.1 (May 26th 2018)<a class="headerlink" href="#release_notes_eb361" title="Permanent link">¶</a></h2> 32653<p>bugfix/update release</p> 32654<p><strong>framework</strong></p> 32655<ul> 32656<li>various enhancements, including:<ul> 32657<li>add support for enabling fallback in sanity check to consider 32658 <code>lib64</code> equivalent for seemingly missing libraries 32659 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2477">#2477</a>)</li> 32660<li>
32660add <code>GITHUB_LOWER_SOURCE</code> constant 32661 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2491">#2491</a>)</li> 32662<li>add '<code>exts_download_dep_fail</code>' as known easyconfig parameter 32663 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2493">#2493</a>)</li> 32664<li>add support for passing custom messages on failing sanity check 32665 for extensions 32666 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2494">#2494</a>)</li> 32667<li>add definition for <code>fosscuda</code> toolchain 32668 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2507">#2507</a>)</li> 32669</ul> 32670</li> 32671<li>various bug fixes, including:<ul> 32672<li>make <code>--inject-checksums</code> always re-order 32673 <code>source_urls</code>/<code>sources</code>/<code>patches</code>/<code>checksums</code> 32674 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2487">#2487</a>)</li> 32675<li>fix git remote url in <code>CONTRIBUTING.md</code> 32676 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2490">#2490</a>)</li> 32677<li>make <code>flake8</code> happy in <code>easyblock.py</code> 32678 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2492">#2492</a>)</li> 32679<li>handle missing permissions for adding labels in <code>--new-pr</code> 32680 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2497">#2497</a>)</li> 32681<li>restore tweaked <code>$TMPDIR</code> value after loading module (for sanity 32682 check) 32683 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2498">#2498</a>)</li> 32684<li>enhance <code>get_module_path</code> function to auto-detect generic vs 32685 software-specific easyblock class names 32686 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2502">#2502</a>)</li> 32687<li>don't blindly overwrite an existing easyconfig in <code>tweak_one</code> 32688 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2504">#2504</a>)</li> 32689<li>take account that <code>PlaintextKeyring</code> may be provided via 32690 <code>keyrings.alt</code> 32691 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2505">#2505</a>)</li> 32692<li>prepend location for temporary module file to <code>$MODULEPATH</code> with 32693 high priority + mark it as default in <code>load_fake_module</code> method 32694 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2506">#2506</a>)</li> 32695</ul> 32696</li> 32697</ul> 32698<p><strong>easyblocks</strong></p> 32699<ul> 32700<li>minor enhancements, including:<ul> 32701<li>add support for detecting auto-downloaded dependencies in 32702 <code>PythonPackage</code> easyblock 32703 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1377">#1377</a>)<ul> 32704<li>disabled by default, can be enabled using 32705 "<code>download_dep_fail = True</code>" in easyconfig file</li> 32706</ul> 32707</li> 32708<li>add support to enable integration of pscom in psmpi easyblock 32709 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1397">#1397</a>)</li> 32710<li>set <code>$CMAKE_*_PATH</code> when <code>CMake</code> is loaded in <code>PythonPackage</code> 32711 easyblock 32712 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1398">#1398</a>)</li> 32713<li>update WIEN2k easyblock for v17 32714 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1405">#1405</a>)</li> 32715<li>disable jemalloc support in TensorFlow on CentOS 6 & co (+ minor 32716 cleanups) 32717 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1412">#1412</a>)</li> 32718<li>update Maple easyblock to support recent versions 32719 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1414">#1414</a>)</li> 32720<li>enable <code>nc-config</code> usage for netCDF in ESMF >=7.1 32721 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1419">#1419</a>)</li> 32722<li>enhance PETSc easyblock for version 3.9 32723 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1421">#1421</a>)</li> 32724<li>check output of MATLAB installation command for invalid 32725 installation key error 32726 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1423">#1423</a>)</li> 32727<li>fix suffix for Boost Python library in Boost 1.67.0 & newer 32728 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1424">#1424</a>)</li> 32729<li>support adding specific paths to <code>$PATH</code> for generic Binary 32730 easyblock via '<code>prepend_to_path</code>' custom easyconfig parameter 32731 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1426">#1426</a>)</li> 32732</ul> 32733</li> 32734<li>minor changes, including:<ul> 32735<li>assume PGI Community edition is used when no license file is 32736 specified 32737 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1427">#1427</a>)</li> 32738</ul> 32739</li> 32740<li>various bug fixes, including:<ul> 32741<li>fix imkl sanity check overwriting base libs with interface libs 32742 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1392">#1392</a>)</li> 32743<li>install Chimera in a subdirectory to avoid its dependencies 32744 being added to the environment 32745 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1413">#1413</a>)</li> 32746<li>
32746add conditional so "<code>--with-x</code>" is only added to configopts if 32747 left unspecified in R easyblock 32748 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1415">#1415</a>)</li> 32749<li>make <code>configure</code> and <code>make</code> look for FoX in <code>$EBROOTFOX</code> in 32750 QuantumESPRESSO easyblock 32751 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1420">#1420</a>)</li> 32752<li>fix path for <code>$ICEM_ACN</code> in ANSYS easyblock 32753 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1422">#1422</a>)</li> 32754<li>avoid hardcoding defaults in question patterns in Doris 32755 easyblock 32756 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1428">#1428</a>)</li> 32757</ul> 32758</li> 32759</ul> 32760<p><strong>easyconfigs</strong></p> 32761<ul> 32762<li>added easyconfigs for new toolchains <code>fosscuda/2018a</code> 32763 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6363">#6363</a>) 32764 and <code>giolfc/2017b</code> 32765 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5799">#5799</a>)</li> 32766<li>added example easyconfig files for 24 new software packages:<ul> 32767<li>BAGEL 32768 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6332">#6332</a>), 32769 Bottleneck 32770 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6334">#6334</a>), 32771 cisTEM 32772 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6370">#6370</a>), 32773 cftime 32774 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6337">#6337</a>), 32775 dotNET-Core-Runtime 32776 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6345">#6345</a>), 32777 ecCodes 32778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6235">#6235</a>), 32779 feh 32780 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6300">#6300</a>), 32781 Graphene 32782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5043">#5043</a>), 32783 gffread 32784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6306">#6306</a>), 32785 HOME 32786 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6227">#6227</a>), 32787 HiCExplorer 32788 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6342">#6342</a>), 32789 ICU 32790 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6371">#6371</a>), 32791 Imlib2 32792 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6300">#6300</a>), 32793 KmerGenie 32794 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5929">#5929</a>), 32795 libgeotiff 32796 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6262">#6262</a>), 32797 NetPIPE 32798 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6062">#6062</a>), 32799 Pandoc 32800 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6247">#6247</a>), 32801 Pisces 32802 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6347">#6347</a>), 32803 Proteinortho 32804 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6333">#6333</a>), 32805 pyshp 32806 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6364">#6364</a>), 32807 SIMPLE 32808 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6019">#6019</a>), 32809 STIR 32810 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6349">#6349</a>), 32811 SimpleElastix 32812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6114">#6114</a>), 32813 wxWidgets 32814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6370">#6370</a>)</li> 32815</ul> 32816</li> 32817<li>added additional easyconfigs for various supported software 32818 packages, including:<ul> 32819<li>Boost 1.67.0, ESMF 7.1.0r, GATK 4.0.4.0, GCC 8.1.0, GROMACS 32820 2018, OpenBLAS 0.3.0, PETSc 3.9.1, PGI 18.4, TensorFlow 1.8.0, 32821 WIEN2k 17.1</li> 32822</ul> 32823</li> 32824<li>minor enhancements, including:<ul> 32825<li>add <code>py_expression_eval</code> extension to (recent) Python 2.7.14 & 32826 3.6.4 easyconfigs 32827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6285">#6285</a>)</li> 32828<li>
32828add <code>README</code> for Java with information on downloading source 32829 tarball 32830 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6294">#6294</a>)</li> 32831<li>add several extensions to Perl 5.26.1 easyconfigs, incl 32832 <code>Dist::Zilla</code> & dependencies 32833 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6297">#6297</a>)</li> 32834<li>also include archive URLs for Bioconductor 3.6 32835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6311">#6311</a>)</li> 32836<li>add <code>README.md</code> file for installing icc/ifort 32837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6317">#6317</a>)</li> 32838</ul> 32839</li> 32840<li>various bug fixes, including:<ul> 32841<li>consistently specify '<code>intel-mkl</code>' component in recent Intel 32842 MKL easyconfigs 32843 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6234">#6234</a>)</li> 32844<li>add <code>pkg-config</code> as build dependency to libdrm 32845 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6243">#6243</a>)</li> 32846<li>add <code>pkg-config</code> build dep to most recent libdrm easyconfigs 32847 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6244">#6244</a>)</li> 32848<li>fix checksum for foreign extension in R 3.4.3 and R 3.4.4 32849 easyconfigs 32850 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6245">#6245</a>)</li> 32851<li>fix installation of Libint 2.4.2 by building with <code>-std=c++11</code> 32852 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6251">#6251</a>)</li> 32853<li>fix source spec for networkx 2.1 extension in scikit-image 32854 easyconfig 32855 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6254">#6254</a>)</li> 32856<li>avoid that Nipype downloads dependencies for included extensions 32857 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6261">#6261</a>, 32858 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6263">#6263</a>)</li> 32859<li>consistently include patch for FLTK 1.3.4 32860 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6265">#6265</a>)</li> 32861<li>fix Perl shebang in MCL v14.137 scripts 32862 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6269">#6269</a>)</li> 32863<li>add patch to build particular source file of matrixStats 32864 extension in R 3.4.4 easyconfig with <code>-O1</code> to work around ICE in 32865 Skylake systems 32866 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6278">#6278</a>)</li> 32867<li>add <code>pkg-config</code> build dependency to FFmpeg >= 3.3.1 32868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6291">#6291</a>)</li> 32869<li>change back checksum for libdap 3.19.1 32870 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6305">#6305</a>)</li> 32871<li>add patch for Automake 1.15 to fix issue with recent Perl 32872 versions 32873 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6358">#6358</a>)</li> 32874<li>fix <code>glog</code> causing intel error in Intel compilers on Intel 32875 Skylake 32876 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6360">#6360</a>)</li> 32877<li>include ICU as dependency in recent R easyconfigs (v3.4.3 & 32878 v3.4.4) 32879 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6371">#6371</a>)</li> 32880<li>fix checksum for RSEM 1.3.0 after sneaky re-release 32881 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6379">#6379</a>)</li> 32882</ul> 32883</li> 32884</ul> 32885<h2 id="release_notes_eb360">EasyBuild v3.6.0 (April 26th 2018)<a class="headerlink" href="#release_notes_eb360" title="Permanent link">¶</a></h2> 32886<p>feature release</p> 32887<p><strong>framework</strong></p> 32888<ul> 32889<li>(experimental) support for generating Singularity container recipes 32890 & (optionally) images via '<code>sudo singularity</code>' 32891 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2332">#2332</a>, 32892 <a href="https://github.com/easybuilders/easybuild-framework/pull/2480">#2480</a>, 32893 <a href="https://github.com/easybuilders/easybuild-framework/pull/2481">#2481</a>, 32894 <a href="https://github.com/easybuilders/easybuild-framework/pull/2482">#2482</a>, 32895 <a href="https://github.com/easybuilders/easybuild-framework/pull/2483">#2483</a>)<ul> 32896<li>see documentation at 32897 <a href="http://easybuild.readthedocs.io/en/latest/Containers.html">http://easybuild.readthedocs.io/en/latest/Containers.html</a></li> 32898</ul> 32899</li> 32900<li>include <code>-ftree-vectorize</code> and <code>-fno-math-errno</code> in default compiler 32901 optimisation flags for GCC 32902 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2388">#2388</a>)<ul> 32903<li>this significantly improves performance of generated binaries 32904 when building with a GCC-based toolchain</li> 32905<li>can be disabled if needed via the <code>vectorize</code> toolchain option</li> 32906</ul> 32907</li> 32908<li>several enhancements/fixes to GitHub integration support:<ul> 32909<li>loosen commit message requirements for <code>--new-pr</code> w.r.t. to 32910 patches as long as all easyconfigs are new 32911 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2438">#2438</a>)</li> 32912<li>automatically add '<code>new</code>' and/or '<code>update</code>' labels in 32913 <code>--new-pr</code> 32914 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2384">#2384</a>)</li> 32915<li>
32915add <code>force_in_dry_run=True</code> to <code>copy_file</code> in <code>copy_patch_files</code> 32916 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2442">#2442</a>)</li> 32917<li>test for custom commit message when deleting a file instead of 32918 when adding a patch 32919 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2443">#2443</a>)</li> 32920<li>make <code>diff_stat</code> pattern also match output of older git versions 32921 in tests for <code>--new</code>/<code>update-pr</code> 32922 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2444">#2444</a>)</li> 32923<li>remove duplicates from <code>--new-pr</code> title 32924 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2478">#2478</a>)</li> 32925</ul> 32926</li> 32927<li>add support for "<code>eb --fetch</code>" to only download sources (even 32928 without having a modules tool installed) 32929 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2457">#2457</a>)</li> 32930<li>add definitions for a bunch of new toolchains:<ul> 32931<li><code>golf</code> 32932 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2458">#2458</a>), 32933 <code>gmkl</code> 32934 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2460">#2460</a>), 32935 <code>gomkl</code> 32936 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2455">#2455</a>), 32937 <code>pmkl</code> 32938 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2460">#2460</a>)</li> 32939<li>toolchains including CUDA: <code>gmklc</code>, <code>gomklc</code>, <code>iimklc</code>, 32940 <code>iompic</code>, <code>iomklc</code> 32941 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2461">#2461</a>)</li> 32942</ul> 32943</li> 32944<li>various minor enhancements, including:<ul> 32945<li>avoid that '<code>--inject-checksums</code>' adds lines longer than 120 32946 characters 32947 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2434">#2434</a>)</li> 32948<li>enable caching of <code>$HOME/.cache/pip</code> in Travis config 32949 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2435">#2435</a>)</li> 32950<li>replace raw strings with bytes literal as iterator sentinels in 32951 checksum calculation 32952 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2446">#2446</a>)</li> 32953<li>new command-line option '<code>--job-max-jobs</code>' to cap nr of 32954 submitted build jobs with GC3Pie 32955 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2378">#2378</a>)</li> 32956<li>add configuration for houndci + flake8 32957 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2451">#2451</a>)</li> 32958<li>add <code>Accept</code> header when downloading file 32959 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2437">#2437</a>)</li> 32960<li>include running of '<code>eb --check-github</code>' in Travis config 32961 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2449">#2449</a>, 32962 <a href="https://github.com/easybuilders/easybuild-framework/pull/2454">#2454</a>)</li> 32963<li>flesh out common code blocks in <code>test/framework/options.py</code> 32964 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2452">#2452</a>)</li> 32965<li>support '<code>depends_on</code>' load statements in generated modules 32966 via <code>--module-depends-on</code> and <code>module_depends_on</code> easyconfig 32967 parameter 32968 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2391">#2391</a>)</li> 32969<li>fix compatibility with Modules v4.1.x 32970 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2470">#2470</a>)</li> 32971<li>add support to <code>run_cmd</code> to enable streaming output 32972 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2476">#2476</a>)</li> 32973</ul> 32974</li> 32975<li>various bug fixes, including:<ul> 32976<li>determine whether included easyblocks are generic or not based 32977 on class they define 32978 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2432">#2432</a>)</li> 32979<li>make sure GitHub token is used in test for <code>--preview-pr</code> 32980 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2436">#2436</a>)</li> 32981<li>take into account that toolchain components may be hidden when 32982 determining toolchain composition 32983 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2440">#2440</a>)</li> 32984<li>stick to autopep8 1.3.4 when testing with Python 2.6 32985 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2462">#2462</a>)</li> 32986<li>strip off <code>.lua</code> extension when backing up modules to ensure 32987 Lmod 6.x doesn't pick up on them 32988 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2463">#2463</a>)</li> 32989<li>check for <code>modulecmd.tcl</code> before modulecmd in bootstrap script 32990 to discriminate between Modules 4.1.x vs 3.2.10 32991 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2468">#2468</a>)</li> 32992<li>fix <code>derive_alt_pypi_url</code> after PyPI switching to sha256 in
32993 package URLs + fix broken test for <code>pypi_source_urls</code> + fix 32994 bootstrap script 32995 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2471">#2471</a>)</li> 32996<li>make sure that both '<code>get_git_revision</code>' and 32997 '<code>this_is_easybuild</code>' return regular strings rather than 32998 Unicode strings 32999 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2472">#2472</a>)</li> 33000</ul> 33001</li> 33002</ul> 33003<p><strong>easyblocks</strong></p> 33004<ul> 33005<li>new software-specific easyblock for Nim 33006 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1402">#1402</a>)</li> 33007<li>minor enhancements, including:<ul> 33008<li>enhance <code>RPackage</code> easyblock to support installing from unpacked 33009 sources 33010 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1383">#1383</a>)</li> 33011<li>add support to <code>PythonPackage</code> easyblock to install with 33012 '<code>pip install --editable</code>' 33013 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1384">#1384</a>)</li> 33014<li>add <code>$EBROOTIFORT/include</code> in <code>$CPATH</code> for ifort 33015 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1385">#1385</a>)</li> 33016<li>add houndci + flake8 configuration 33017 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1388">#1388</a>)</li> 33018<li>add additional location to <code>$PATH</code> for FLUENT installations 33019 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1389">#1389</a>)</li> 33020<li>make <code>PythonPackage</code> generic easyblock aware of 33021 '<code>unpack_options</code>' easyconfig parameter 33022 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1391">#1391</a>)</li> 33023<li>minor updates to ABAQUS easyblock to support latest version 33024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1394">#1394</a>)</li> 33025<li>add support for extracting sources in <code>Binary</code> easyblock 33026 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1401">#1401</a>)</li> 33027</ul> 33028</li> 33029<li>various bug fixes, including:<ul> 33030<li>fix linking to FFTW for Doris: should be <code>-lfftw3f</code> 33031 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1387">#1387</a>)</li> 33032<li>fix for installing TensorFlow 1.6.0: use the absolute path for 33033 the C compiler when compiling with GPU support 33034 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1386">#1386</a>)</li> 33035<li>also take <code>lib64</code> into account for binutils libraries 33036 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1399">#1399</a>)</li> 33037<li>make sanity check in MPICH easyblock aware of libraries in 33038 <code>lib64</code> subdir 33039 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1403">#1403</a>)</li> 33040<li>take into account that <code>self.debuggerpath</code> may not be set in icc 33041 easyblock 33042 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1408">#1408</a>)</li> 33043<li>extend noqa in configure step of Qt easyblock 33044 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1409">#1409</a>)</li> 33045</ul> 33046</li> 33047</ul> 33048<p><strong>easyconfig</strong></p> 33049<ul> 33050<li>added easyconfigs for new toolchain golf/2018a 33051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6080">#6080</a>)</li> 33052<li>added example easyconfig files for 39 new software packages:<ul> 33053<li>ARAGORN 33054 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6138">#6138</a>, 33055 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6219">#6219</a>), 33056 amask 33057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6105">#6105</a>), 33058 BamBam 33059 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5490">#5490</a>), 33060 Bandage 33061 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6053">#6053</a>), 33062 bcgTree 33063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6057">#6057</a>), 33064 biobambam2 33065 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6040">#6040</a>), 33066 CODEX2 33067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5972">#5972</a>), 33068 coverage 33069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5964">#5964</a>), 33070 DANPOS2 33071 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5870">#5870</a>), 33072 EasyQC 33073 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6175">#6175</a>), 33074 elastix 33075 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6074">#6074</a>), 33076 FRANz 33077 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6035">#6035</a>), 33078 Filtlong 33079 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6050">#6050</a>), 33080 FriBidi 33081 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6181">#6181</a>), 33082 Gblocks 33083 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6057">#6057</a>), 33084 Grace 33085 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6036">#6036</a>), 33086 LMfit 33087 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6119">#6119</a>), 33088 libmaus2 33089 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6040">#6040</a>), 33090 MathGL 33091 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6033">#6033</a>), 33092 MiGEC 33093 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6047">#6047</a>), 33094 MiXCR 33095 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6045">#6045</a>), 33096 Miniconda3 33097 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6075">#6075</a>), 33098 Multiwfn 33099 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5403">#5403</a>), 33100 mosdepth 33101 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6169">#6169</a>), 33102 Nim 33103 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6167">#6167</a>), 33104 Porechop 33105 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6051">#6051</a>), 33106 propy 33107 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6091">#6091</a>), 33108 Roary 33109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6056">#6056</a>), 33110 Rtree 33111 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6222">#6222</a>), 33112 SALib 33113 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6145">#6145</a>), 33114 SMRT-Link 33115 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6218">#6218</a>), 33116 SimpleITK 33117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6172">#6172</a>), 33118 spectral.methods 33119 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6104">#6104</a>), 33120 supernova 33121 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6193">#6193</a>), 33122 TEToolkit 33123 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5912">#5912</a>), 33124 tbl2asn 33125 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6139">#6139</a>), 33126 udocker 33127 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5770">#5770</a>), 33128 vartools 33129 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6102">#6102</a>), 33130 XCfun 33131 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5975">#5975</a>)</li> 33132</ul> 33133</li> 33134<li>
33134added new easyconfigs for existing toolchains:<ul> 33135<li><code>gmpich/2017.08</code> 33136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6143">#6143</a>), 33137 <code>goolfc/2018a</code> 33138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6129">#6129</a>), 33139 <code>intel/2018.02</code> 33140 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6077">#6077</a>), 33141 <code>iomkl/2018.02</code> 33142 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6088">#6088</a>)</li> 33143</ul> 33144</li> 33145<li>added additional easyconfigs for various supported software 33146 packages, including:<ul> 33147<li>ABINIT 8.6.3, Anaconda2 5.1.0, Anaconda3 5.1.0, binutils 2.30, 33148 dask 0.17.2, FFmpeg 4.0, GCC(core) 7.3.0, GROMACS 2016.5, HTSlib 33149 1.8, LLVM 6.0.0, Mesa 17.3.6, netCDF 4.6.0, Octave 4.2.2, OpenCV 33150 3.4.1, PLUMED 2.4.1, PROJ 5.0.0, PostgreSQL 10.3, Qt5 5.10.1, R 33151 3.4.4, SAMtools 1.8, Spack 0.11.2, TensorFlow 1.7.0, VTK 8.1.0</li> 33152</ul> 33153</li> 33154<li>minor enhancements, including:<ul> 33155<li>add test to ensure there's only one variant for each dependency 33156 in dep graph of easyconfigs using particular toolchains 33157 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5970">#5970</a>, 33158 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6023">#6023</a>)</li> 33159<li>add extensions required by CODEX2 v20180227 to Bioconductor w/ R 33160 3.4.3 33161 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5972">#5972</a>)</li> 33162<li>add config file for <a href="https://pre-commit.com/">https://pre-commit.com/</a> 33163 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5785">#5785</a>)</li> 33164<li>add custom sanity check paths for GraphicsMagick consistently 33165 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5997">#5997</a>)</li> 33166<li>add custom sanity check paths to recent Ghostscript easyconfigs 33167 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5998">#5998</a>)</li> 33168<li>add svd, Rssa, JBTools, RUnit, DistributionUtils and gapfill 33169 extensions for R 3.4.3 33170 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6099">#6099</a>)</li> 33171<li>add additional extensions to Bioconductor 3.6 bundle 33172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6136">#6136</a>)</li> 33173<li>add xlrd extension to recent Python 2.x and 3.x easyconfigs 33174 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6162">#6162</a>)</li> 33175</ul> 33176</li> 33177<li>minor changes, including:<ul> 33178<li>use gettext 0.19.8.1 on top of libxml2 2.9.7 as dep for git 33179 built with <code>foss/2018a</code> 33180 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5993">#5993</a>)</li> 33181<li>bump hwloc dep for OpenMPI 2.1.2 that is part of <code>iomkl/2018a</code> 33182 to v1.11.8 33183 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5994">#5994</a>)</li> 33184<li>use non-interactive plotting backend by default for matplotlib 33185 2.1.2 33186 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6024">#6024</a>)</li> 33187<li>don't use bare Perl as dependency for git with <code>foss/2018a</code>, 33188 use variant with extensions 33189 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6058">#6058</a>)</li> 33190</ul> 33191</li> 33192<li>various bug fixes, including:<ul> 33193<li>fix <code>moduleclass</code> & add custom <code>sanity_check_paths</code> in gettext 33194 easyconfigs 33195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5991">#5991</a>)</li> 33196<li>drop use of <code>--disable-dlopen</code> in (recent) OpenMPI easyconfigs 33197 due to negative performance impact 33198 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6060">#6060</a>)</li> 33199<li>add missing XZ dep in Python 3.6.4 easyconfigs built with 33200 <code>*/2018a</code> toolchain 33201 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6065">#6065</a>)</li> 33202<li>add 10 packages that were previously downloaded in Python 3.6.4 33203 easyconfigs 33204 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6081">#6081</a>)</li> 33205<li>
33205add patch for Tensorflow 1.6 & 1.7 to include missing -lrt link 33206 flag (needed in CentOS6) 33207 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6089">#6089</a>)</li> 33208<li>fix checksums for R extensions that were updated in place in 33209 easyconfigs for R versions 3.4.3 & 3.4.4 33210 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6118">#6118</a>)</li> 33211<li>include pkg-config as build dep in recent R easyconfigs 33212 (required for at least nloptr) 33213 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6122">#6122</a>)</li> 33214<li>remove Intel-specific workaround for 33215 '<code>undefined symbol: __stack_chk_guard</code>' issue from Python 33216 3.6.4 foss/2018a easyconfig 33217 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6130">#6130</a>)</li> 33218<li>add configopt <code>--without-matlab</code>/<code>octave</code> to all NLopt 33219 easyconfigs 33220 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6132">#6132</a>)</li> 33221<li>also consider <code>lib64</code> in <code>sanity_check_paths</code> for Bison 3.0.4 33222 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6170">#6170</a>)</li> 33223<li>don't use libyaml built with dummy as dep for PyYAML 33224 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6208">#6208</a>)</li> 33225<li>add missing pkg-config build dep in recent 33226 GObject-Introspection, GLib & cairo easyconfigs 33227 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6216">#6216</a>)</li> 33228<li>don't include (ancient version of) <code>Time::HiRes</code> as Perl 33229 extension, since it's a core Perl module 33230 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6225">#6225</a>)<ul> 33231<li>this fixes problems with the installation of BioPerl and 33232 proovread</li> 33233</ul> 33234</li> 33235<li>add missing XML-LibXML dependency in recent BioPerl easyconfigs 33236 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6226">#6226</a>)</li> 33237<li>add <code>--without-ada</code> configure option in recent ncurses 33238 easyconfigs 33239 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6228">#6228</a>)</li> 33240<li>add patch for snaphu to fix segmentation fault due to use of 33241 short integer 33242 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/6230">#6230</a>)</li> 33243</ul> 33244</li> 33245</ul> 33246<h2 id="release_notes_eb353">EasyBuild v3.5.3 (March 7th 2018)<a class="headerlink" href="#release_notes_eb353" title="Permanent link">¶</a></h2> 33247<p>bugfix/update release</p> 33248<p><strong>framework</strong></p> 33249<ul> 33250<li>various enhancements, including:<ul> 33251<li>re-enable testing against environment modules, bump Lmod to 33252 7.7.16 33253 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2425">#2425</a>)</li> 33254<li>print which hook is being executed in the command line output 33255 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2427">#2427</a>)</li> 33256</ul> 33257</li> 33258<li>various bug fixes, including:<ul> 33259<li>fix order in result of gen_list_easyblocks and 33260 gen_easyblocks_overview_rst 33261 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2421">#2421</a>)</li> 33262<li>fix target account for branch pushed when using <code>--new-pr</code> 33263 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2426">#2426</a>)</li> 33264</ul> 33265</li> 33266</ul> 33267<p><strong>easyblocks</strong></p> 33268<ul> 33269<li>minor enhancements, including:<ul> 33270<li>make GROMACS easyblock select build type based on value for 33271 '<code>debug</code>' in '<code>toolchainopts</code>' 33272 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1374">#1374</a>)</li> 33273<li>re-enable testing against environment modules, bump Lmod to 33274 7.7.16 33275 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1376">#1376</a>)</li> 33276<li>enhance Gurobi easyblock to support installing Python bindings 33277 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1378">#1378</a>)</li> 33278</ul> 33279</li> 33280</ul> 33281<p><strong>easyconfigs</strong></p> 33282<ul> 33283<li>added example easyconfig files for 2 new software packages:<ul> 33284<li>CNVkit and hmmlearn 33285 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5954">#5954</a>)</li> 33286</ul> 33287</li> 33288<li>
33288added additional easyconfigs for various supported software 33289 packages, including:<ul> 33290<li>matplotlib 2.1.2, TensorFlow 1.6.0</li> 33291</ul> 33292</li> 33293<li>minor enhancements, including:<ul> 33294<li>re-enable testing against environment modules, bump Lmod to 33295 7.7.16 33296 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5944">#5944</a>)</li> 33297<li>add cghFLasso extension to R 3.4.3 easyconfigs 33298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5953">#5953</a>)</li> 33299<li>add '<code>Math::CDF</code>' extension to recent Perl modules 33300 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5957">#5957</a>)</li> 33301</ul> 33302</li> 33303<li>various bug fixes, including:<ul> 33304<li>add missing <code>--enable-ld-version-script</code> configure option for 33305 LibTIFF 4.0.9 built with <code>GCCcore/6.4.0</code> 33306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5945">#5945</a>)</li> 33307<li>hard disable UCX support in recent OpenMPI versions, to dance 33308 around bug in OpenMPI configure script 33309 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5949">#5949</a>)</li> 33310</ul> 33311</li> 33312</ul> 33313<h2 id="release_notes_eb352">EasyBuild v3.5.2 (March 2nd 2018)<a class="headerlink" href="#release_notes_eb352" title="Permanent link">¶</a></h2> 33314<p>bugfix/update release</p> 33315<p><strong>framework</strong></p> 33316<ul> 33317<li>various enhancements, including:<ul> 33318<li>add functionality to skip devel module with naming scheme 33319 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2374">#2374</a>)</li> 33320<li>add pagination support in <code>clean_gists.py</code> 33321 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2379">#2379</a>)</li> 33322<li>allow basic compiler modulenames to be specified as keys in 33323 <code>--optarch</code> 33324 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2387">#2387</a>)</li> 33325<li>initial set of OHPC module meta data for EasyBuild 33326 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2392">#2392</a>)</li> 33327<li>allow different target account in <code>post_comment_in_issue</code> 33328 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2399">#2399</a>)</li> 33329<li>declare support for RPATH linking stable 33330 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2409">#2409</a>)</li> 33331</ul> 33332</li> 33333<li>various bug fixes, including:<ul> 33334<li>update bootstrap script to be compatible with Modules v4 33335 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2390">#2390</a>)</li> 33336<li>avoid fatal error when determining glibc version on non-glibc 33337 Linux system (e.g. Alphine Linux) 33338 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2398">#2398</a>)</li> 33339<li>exclude location of RPATH wrappers from <code>$PATH</code> to avoid fork 33340 bomb 33341 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2410">#2410</a>)</li> 33342<li>fix target account for <code>--update-pr</code> in case it's different 33343 from GitHub account being used to push branch 33344 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2419">#2419</a>)</li> 33345</ul> 33346</li> 33347</ul> 33348<p><strong>easyblocks</strong></p> 33349<ul> 33350<li>new software-specific easyblocks for COMSOL 33351 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1317">#1317</a>), 33352 Stata 33353 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1241">#1241</a>) 33354 and TensorFlow 33355 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1287">#1287</a>, 33356 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1361">#1361</a>)</li> 33357<li>enhance GCC easyblock to support building generically (via 33358 '<code>generic</code>' easyconfig parameter or <code>--optarch=GENERIC</code>) 33359 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1336">#1336</a>)</li> 33360<li>minor enhancements, including:<ul> 33361<li>make GROMACS easyblock aware of building for KNL via 33362 <code>--optarch=MIC-AVX512</code> 33363 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1360">#1360</a>)</li> 33364<li>unset <code>$PERL_MM_OPT</code> and <code>$PERL_MB_OPT</code> when installing Perl 33365 modules to avoid problems 33366 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1362">#1362</a>)</li> 33367<li>
33367add custom '<code>use_pip_for_deps</code>' easyconfig parameter to 33368 <code>PythonPackage</code> easyblock 33369 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1366">#1366</a>)</li> 33370<li>add support for '<code>default_component_specs</code>' easyconfig 33371 parameter in <code>Bundle</code> easyblock 33372 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1369">#1369</a>)</li> 33373</ul> 33374</li> 33375<li>various bug fixes, including:<ul> 33376<li>fix logic in icc easyblock w.r.t. location of debugger libraries 33377 (libipt library for gdb) 33378 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1224">#1224</a>)</li> 33379<li>fix Tkinter easyblock to install Tkinter 3.x 33380 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1347">#1347</a>)</li> 33381<li>let impi modules also update <code>$MANPATH</code> 33382 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1354">#1354</a>)</li> 33383<li>enhance Octave extension filter to avoid false positives 33384 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1355">#1355</a>)</li> 33385<li>make CUDA easyblock aware of '<code>preinstallopts</code>' easyconfig 33386 parameter 33387 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1367">#1367</a>)</li> 33388<li>fix handling of per-component (checksums for) patches in 33389 <code>Bundle</code> easyblock 33390 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1369">#1369</a>)</li> 33391</ul> 33392</li> 33393</ul> 33394<p><strong>easyconfigs</strong></p> 33395<ul> 33396<li>added example easyconfig files for 24 new software packages:<ul> 33397<li>AMPL-MP 33398 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5800">#5800</a>), 33399 AmberTools 33400 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5632">#5632</a>), 33401 bcolz 33402 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5864">#5864</a>), 33403 detonate 33404 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5709">#5709</a>), 33405 dropEst 33406 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5734">#5734</a>), 33407 EvidentialGene 33408 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5627">#5627</a>), 33409 faceswap 33410 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5825">#5825</a>), 33411 fineSTRUCTURE 33412 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5663">#5663</a>), 33413 Gradle 33414 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5828">#5828</a>), 33415 gbs2ploidy 33416 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5877">#5877</a>), 33417 HIPS 33418 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5725">#5725</a>), 33419 Ipopt 33420 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5800">#5800</a>), 33421 libMemcached 33422 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5804">#5804</a>), 33423 MEGAHIT 33424 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5748">#5748</a>), 33425 Mmg 33426 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5807">#5807</a>), 33427 methylpy 33428 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5874">#5874</a>), 33429 pstoedit 33430 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5884">#5884</a>), 33431 python-igraph 33432 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5905">#5905</a>), 33433 RNAcode 33434 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5854">#5854</a>), 33435 Seq-Gen 33436 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5695">#5695</a>), 33437 Stata 33438 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5102">#5102</a>), 33439 scikit-allel 33440 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5864">#5864</a>), 33441 TetGen 33442 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5681">#5681</a>), 33443 zarr 33444 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5864">#5864</a>)</li> 33445</ul> 33446</li> 33447<li>
33447added new easyconfigs for existing toolchains: giolf/2018a 33448 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5777">#5777</a>), 33449 goolfc/2017b 33450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5768">#5768</a>), 33451 iomkl/2018a 33452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5878">#5878</a>)</li> 33453<li>added additional easyconfigs for various supported software 33454 packages, including:<ul> 33455<li>CP2K 5.1, IPython 6.2.1, OpenFOAM v1712, Perl 5.26.1, Python 33456 3.6.4, TensorFlow 1.5.0, X11 20180131</li> 33457</ul> 33458</li> 33459<li>minor enhancements, including:<ul> 33460<li>add <code>feather</code> and <code>tidyverse</code> as extensions for R 3.4.3 33461 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5693">#5693</a>)</li> 33462<li>build recent PLUMED versions with all modules enabled 33463 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5696">#5696</a>)</li> 33464<li>add MAST/splatter/scDD to Bioconductor 3.6 bundle 33465 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5704">#5704</a>)</li> 33466<li>add <code>dummies</code> as extension for R 3.4.3 + <code>monocle</code>/<code>scde</code>/<code>ROTS</code> 33467 (+ deps) to Bioconductor 3.6 bundle 33468 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5724">#5724</a>)</li> 33469<li>include <code>io</code> and <code>statistics</code> extensions to Octave 4.2.1 33470 easyconfigs 33471 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5798">#5798</a>)</li> 33472<li>switch to using TensorFlow as backend for recent versions of 33473 Keras 33474 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5821">#5821</a>)</li> 33475</ul> 33476</li> 33477<li>various bug fixes, including:<ul> 33478<li>using the correct binutils in jemalloc 5.0.1 easyconfig using 33479 <code>GCCcore/6.4.0</code> 33480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5659">#5659</a>)</li> 33481<li>fix source URLs for MPC 33482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5662">#5662</a>)</li> 33483<li>add Tkinter as dependency for ASE & matplotlib using Python 33484 3.6.3 33485 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5658">#5658</a>)</li> 33486<li>fix versions for updated extensions in Bioconductor 3.6 bundle 33487 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5704">#5704</a>, 33488 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5724">#5724</a>, 33489 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5880">#5880</a>)</li> 33490<li>fix missing M4 build dependency in nettle easyconfigs 33491 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5722">#5722</a>)</li> 33492<li>fix homepage for OpenFOAM 4.x & 5.x, should be <code>openfoam.org</code> 33493 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5422">#5422</a>, 33494 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5780">#5780</a>)</li> 33495<li>add matplotlib, cairo & PyCairo dependencies for graph-tool 33496 2.26 + enhance sanity check 33497 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5787">#5787</a>)</li> 33498<li>fix hardcoded version in scikit-image easyconfigs 33499 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5822">#5822</a>)</li> 33500<li>fix pkgconfig moduleclass, '<code>data</code>' doesn't make much sense 33501 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5817">#5817</a>)</li> 33502<li>add sanity check in recent matplotlib easyconfigs to ensure that 33503 Tkinter is available 33504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5689">#5689</a>, 33505 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5896">#5896</a>)</li> 33506<li>correct MPI path when building ABINIT with '<code>foss</code>' toolchain 33507 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5760">#5760</a>)</li> 33508<li>patch Hyperopt to make it work with networkx 2.0 33509 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5642">#5642</a>)</li> 33510<li>
33510add Tkinter sanity check to ASE easyconfigs 33511 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5691">#5691</a>, 33512 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5909">#5909</a>)</li> 33513<li>include autotools as build dep in git easyconfigs 33514 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5718">#5718</a>)</li> 33515<li>fix sanity check paths for Debian OS in JasPer easyconfigs 33516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5897">#5897</a>)</li> 33517<li>fix source_urls for recent versions of ABINIT 33518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5908">#5908</a>)</li> 33519<li>add patch for recent GDAL easyconfigs using <code>intel</code> toolchain to 33520 fix icc get stuck on compiling <code>ceos.c</code> 33521 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5915">#5915</a>)</li> 33522<li>add explicit zlib dependency in Tkinter 2.x and 3.x 33523 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5797">#5797</a>, 33524 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5926">#5926</a>)</li> 33525<li>fix source URLs & homepage in Singularity easyconfigs 33526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5927">#5927</a>)</li> 33527<li>fix installation of TensorFlow 1.3 via binary wheel after 33528 introducing TensorFlow easyblock 33529 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5938">#5938</a>)</li> 33530</ul> 33531</li> 33532</ul> 33533<h2 id="release_notes_eb351">EasyBuild v3.5.1 (January 16th 2018)<a class="headerlink" href="#release_notes_eb351" title="Permanent link">¶</a></h2> 33534<p>bugfix/update release</p> 33535<p><strong>framework</strong></p> 33536<ul> 33537<li>various enhancements, including:<ul> 33538<li>add definition of <code>giolfc</code> toolchain 33539 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2359">#2359</a>)</li> 33540<li>add support for Environment Modules 4 33541 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2365">#2365</a>)</li> 33542</ul> 33543</li> 33544<li>various bug fixes, including:<ul> 33545<li>install SQLAlchemy < 1.2.0 with Python 2.6 in Travis config 33546 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2367">#2367</a>)</li> 33547<li>make code in <code>easybuild/tools/job/gc3pie.py</code> forward-compatible 33548 with GC3Pie 2.5 33549 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2373">#2373</a>)</li> 33550</ul> 33551</li> 33552</ul> 33553<p><strong>easyblocks</strong></p> 33554<ul> 33555<li>minor enhancements, including:<ul> 33556<li>auto-detect default build target for Clang 33557 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1115">#1115</a>)</li> 33558<li>build GROMACS for target architecture based on <code>--optarch</code> 33559 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1163">#1163</a>)</li> 33560<li>ensure correct $PYTHONPATH for recent OpenBabel versions 33561 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1219">#1219</a>)</li> 33562<li>enhance Amber easyblock with support for OpenBLAS and better 33563 Intel MPI support 33564 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1305">#1305</a>)</li> 33565<li>also support only installing AmberTools through Amber easyblock 33566 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1305">#1305</a>)</li> 33567<li>also pick locations for CUPTI headers & libraries in CUDA 33568 easyblock 33569 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1306">#1306</a>)</li> 33570<li>update patching out of sanitizer tests for recent Clang versions 33571 (>=5.0) 33572 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1327">#1327</a>)</li> 33573<li>update known questions for Qt5 to support installing recent 33574 versions 33575 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1328">#1328</a>)</li> 33576<li>update BamTools easyblock for v2.5.0 33577 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1332">#1332</a>, 33578 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1337">#1337</a>)</li> 33579<li>disable <code>libfox</code> target if external module found in 33580 QuantumESPRESSO easyblock 33581 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1333">#1333</a>)</li> 33582<li>
33582add support for linking Octave with multi-threaded BLAS/LAPACK 33583 library 33584 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1340">#1340</a>)</li> 33585<li>support <code>install_target</code> in PythonPackage + deprecate 33586 <code>use_easy_install</code> & <code>use_setup_py_develop</code> 33587 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1341">#1341</a>, 33588 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1342">#1342</a>)</li> 33589</ul> 33590</li> 33591<li>various bug fixes, including:<ul> 33592<li>make RubyGem easyblock use <code>$GEM_*</code> environment variables except 33593 if as extension of Ruby itself 33594 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1247">#1247</a>)</li> 33595<li>move initialisation in <code>SystemCompiler</code> & <code>SystemMPI</code> easyblocks 33596 to the prepare step 33597 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1282">#1282</a>)</li> 33598<li>enable skipping sanitizer tests by default in Clang easyblock, 33599 they can't be relied on 33600 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1329">#1329</a>)</li> 33601<li>fix quotes when using <code>$ORIGIN</code> in <code>RPATH</code> locations for DOLFIN 33602 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1338">#1338</a>)</li> 33603<li>fix sanity check for shared libraries in Trilinos easyblock 33604 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1339">#1339</a>)</li> 33605</ul> 33606</li> 33607</ul> 33608<p><strong>easyconfigs</strong></p> 33609<ul> 33610<li>added easyconfigs for <code>foss/2018a</code> and <code>intel/2018a</code> common 33611 toolchains 33612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5577">#5577</a>), 33613 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5578">#5578</a>)</li> 33614<li>added example easyconfig files for 26 new software packages:<ul> 33615<li>BeautifulSoup 33616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5601">#5601</a>), 33617 Calendrical 33618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5588">#5588</a>), 33619 ChimPipe 33620 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5560">#5560</a>), 33621 crb-blast 33622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5124">#5124</a>)), 33623 dammit 33624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5125">#5125</a>), 33625 deepTools 33626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5536">#5536</a>), 33627 FastQ_Screen 33628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5404">#5404</a>), 33629 FoX 33630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5496">#5496</a>), 33631 GffCompare 33632 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5581">#5581</a>), 33633 GlimmerHMM 33634 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5559">#5559</a>), 33635 LocARNA 33636 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5548">#5548</a>), 33637 MapSplice 33638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5566">#5566</a>), 33639 MariaDB-connector-c 33640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5557">#5557</a>), 33641 NextGenMap 33642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5430">#5430</a>), 33643 nd2reader 33644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5545">#5545</a>), 33645 PIMS 33646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5545">#5545</a>), 33647 Pysolar 33648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5585">#5585</a>), 33649 phono3py 33650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5551">#5551</a>), 33651 preseq 33652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5569">#5569</a>), 33653 proovread 33654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5513">#5513</a>), 33655 QUAST 33656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5610">#5610</a>), 33657 RNA-SeQC 33658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5589">#5589</a>), 33659 RNAclust 33660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5607">#5607</a>), 33661 Ragout 33662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5608">#5608</a>), 33663 SOAPfuse 33664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5417">#5417</a>), 33665 TransDecoder 33666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5125">#5125</a>)</li> 33667</ul> 33668</li> 33669<li>
33669added additional easyconfigs for various supported software 33670 packages, including:<ul> 33671<li>BLAST+ 2.7.1, BamTools 2.5.0, Boost 1.66.0, Clang 5.0.0, dask 33672 0.16.0, FFmpeg 3.4.1, GROMACS 2016.4, HDF5 1.8.20, matplotlib 33673 2.1.1, PLUMED 2.4.0, Pillow 5.0.0, Qt5 5.9.3, QuantumESPRESSO 33674 6.2, Ruby 2.5.0, Rust 1.22.1</li> 33675</ul> 33676</li> 33677<li>minor enhancements, including:<ul> 33678<li>include <code>gomms</code> in list of extensions for R 3.4.3 33679 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5547">#5547</a>)</li> 33680<li>clean up BamTools easyconfigs to rely on updated easyblock + add 33681 SHA256 checksums 33682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5575">#5575</a>)</li> 33683<li>add <code>Time::HiRes</code> to recent Perl versions 33684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5616">#5616</a>)</li> 33685<li>add <code>DNAcopy</code> & <code>dupRadar</code> extensions to bundle for Bioconductor 33686 3.6 33687 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5587">#5587</a>, 33688 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5618">#5618</a>)</li> 33689<li>switch to using <code>install_target</code> rather than now deprecated 33690 <code>use_easy_install</code> and <code>use_setup_py_develop</code> 33691 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5625">#5625</a>)</li> 33692</ul> 33693</li> 33694<li>various bug fixes, including:<ul> 33695<li>avoid auto-downloading of parcel in gdc-client 1.3.0 easyconfig 33696 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5523">#5523</a>)</li> 33697<li>fix permissions on <code>make_raw_alos.pl</code> script in ROI_PAC 33698 installation 33699 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5546">#5546</a>)</li> 33700<li>remove erroneous patch for Intel compiler support in Perl 5.26.0 33701 easyconfig built with <code>GCCcore/6.4.0</code> 33702 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5561">#5561</a>)</li> 33703<li>include <code>HWxtest</code> as extension to fix issue with <code>diveRsity</code> in 33704 R 3.4.3 easyconfig file 33705 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5570">#5570</a>)</li> 33706<li>add pkg-config as build dependency for fontconfig, harfbuzz, 33707 gnuplot, pango 33708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5580">#5580</a>)</li> 33709<li>fix versions of updated extensions in BioConductor bundle 33710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5587">#5587</a>, 33711 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5618">#5618</a>)</li> 33712<li>add missing libpng dependency in ROOT 6.10.08 easyconfigs 33713 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5595">#5595</a>)</li> 33714<li>fix option passed to configure in M4 33715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5606">#5606</a>)</li> 33716<li>rename SIBELia to Sibelia 33717 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5603">#5603</a>)</li> 33718<li>add patch for binutils 2.26 to fix compatibility with GCC 6.x 33719 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5611">#5611</a>)</li> 33720<li>fix for dependencies was set twice in OpenMPI 3.0.0 easyconfig 33721 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5619">#5619</a>)</li> 33722<li>fix download URL in comment of Kent tools easyconfigs 33723 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5633">#5633</a>)</li> 33724<li>add SHA256 checksums to various easyconfigs 33725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5635">#5635</a>, 33726 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5636">#5636</a>, 33727 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5639">#5639</a>)</li> 33728<li>add <code>rdma-core-devel</code> to OS dependencies for OpenMPI 3.0.0 33729 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5648">#5648</a>)</li> 33730</ul> 33731</li> 33732</ul> 33733<h2 id="release_notes_eb350">EasyBuild v3.5.0 (December 15th 2017)<a class="headerlink" href="#release_notes_eb350" title="Permanent link">¶</a></h2> 33734<p>feature release</p> 33735<p><strong>framework</strong></p> 33736<ul> 33737<li>add support for implementing pre- and post-step hooks 33738 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2343">#2343</a>)<ul> 33739<li>documentation available at
33740 <a href="http://easybuild.readthedocs.io/en/latest/Hooks.html">http://easybuild.readthedocs.io/en/latest/Hooks.html</a></li> 33741</ul> 33742</li> 33743<li>various enhancements, including:<ul> 33744<li>add support for foss-like toolchain with Spectrum MPI: <code>gsolf</code> 33745 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2329">#2329</a>)</li> 33746<li>add support for <code>--preview-pr</code> 33747 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2331">#2331</a>, 33748 <a href="https://github.com/easybuilders/easybuild-framework/pull/2337">#2337</a>, 33749 <a href="https://github.com/easybuilders/easybuild-framework/pull/2348">#2348</a>)<ul> 33750<li>see also 33751 <a href="http://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html#previewing-easyconfig-pull-requests-preview-pr">http://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html#previewing-easyconfig-pull-requests-preview-pr</a></li> 33752</ul> 33753</li> 33754<li>flesh out <code>find_extension</code> function, hoist dict with extract 33755 commands into a constant 33756 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2336">#2336</a>)</li> 33757<li>add support for using <code>self.start_dir</code> rather than using 33758 <code>self.cfg['start_dir']</code> 33759 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2339">#2339</a>)</li> 33760<li>add support for '<code>exts_default_options</code>' easyconfig parameter 33761 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2345">#2345</a>, 33762 <a href="https://github.com/easybuilders/easybuild-framework/pull/2346">#2346</a>)</li> 33763<li>allow use of '<code>start_dir</code>' easyconfig parameter in extensions 33764 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2353">#2353</a>)</li> 33765</ul> 33766</li> 33767<li>various bug fixes, including:<ul> 33768<li>fix typo in '<code>giolf</code>' toolchain definition 33769 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2327">#2327</a>)</li> 33770<li>fix minor issues with <code>--inject-checksums</code> 33771 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2333">#2333</a>)</li> 33772<li>fix error message when '<code>gv</code>' Python package is not available 33773 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2340">#2340</a>)</li> 33774<li>install paramiko version < 2.4.0 for Python 2.6 in Travis 33775 config 33776 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2344">#2344</a>)</li> 33777<li>disable broken log rotation, avoid duplicate logging of output 33778 of executed commands under '<code>--debug</code>' 33779 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2347">#2347</a>)</li> 33780<li>also include $ORIGIN and absolute paths to '<code>lib</code>' and 33781 '<code>lib64</code>' subdirectories in RPATH locations 33782 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2358">#2358</a>)</li> 33783<li>fix repo references in <code>install-EasyBuild-develop.sh</code> script 33784 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2360">#2360</a>)</li> 33785</ul> 33786</li> 33787</ul> 33788<p><strong>easyblocks</strong></p> 33789<ul> 33790<li>new software-specific easyblock for Bazel 33791 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1286">#1286</a>) 33792 and Octave 33793 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1304">#1304</a>)</li> 33794<li>new generic easyblock for installing Octave packages as extensions 33795 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1304">#1304</a>, 33796 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1318">#1318</a>)</li> 33797<li>minor enhancements, including:<ul> 33798<li>remove <code>foamExec</code> & <code>wdot</code> from sanity checks, add <code>blockMesh</code> & 33799 <code>checkMesh</code> + enable logging for recent OpenFOAM versions 33800 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1205">#1205</a>, 33801 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1272">#1272</a>)</li> 33802<li>add exceptions for FFTW/3.3.6 on POWER with GCC 5/6/7 33803 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1274">#1274</a>)</li> 33804<li>
33804add support for Spectrum MPI to the <code>SystemMPI</code> easyblock 33805 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1275">#1275</a>)</li> 33806<li>allow skipping of steps for <code>Bundle</code> components + fix issues 33807 with templates & formatting of error message 33808 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1278">#1278</a>)</li> 33809<li>update HPCG easyblock for v3.0 by changing configure syntax 33810 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1284">#1284</a>)</li> 33811<li>correctly configure for BLAS/LAPACK in R easyblock & check 33812 configure output 33813 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1292">#1292</a>, 33814 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1300">#1300</a>)</li> 33815<li>make R easyblock set configure options for dependencies 33816 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1297">#1297</a>, 33817 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1303">#1303</a>)</li> 33818<li>allow tuning of build command in <code>PythonPackage</code> via custom 33819 '<code>buildcmd</code>' easyconfig parameter 33820 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1299">#1299</a>)</li> 33821<li>set default Java encoding to <code>UTF8</code> when installing Trinity 33822 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1302">#1302</a>)</li> 33823<li>also define <code>$CUDA_ROOT</code> in generated module for CUDA 33824 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1234">#1234</a>)</li> 33825<li>make the ScaLAPACK easyblock capable of building in parallel 33826 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1288">#1288</a>, 33827 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1321">#1321</a>, 33828 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1324">#1324</a>)</li> 33829</ul> 33830</li> 33831<li>various bug fixes, including:<ul> 33832<li>avoid changing <code>$CPATH</code>, <code>$LD_LIBRARY_PATH</code> an <code>$LIBRARY_PATH</code> 33833 in generated modules for Intel Advisor, Inspector, and VTune 33834 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1229">#1229</a>)</li> 33835<li>fix check for Intel MKL in PSI easyblock 33836 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1273">#1273</a>)</li> 33837<li>fix missing space in fftw easyblock 33838 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1277">#1277</a>)</li> 33839<li>fix use of FFTW on top of Intel MKL in CP2K easyblock 33840 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1281">#1281</a>)</li> 33841<li>fix wrong sanity check for Boost when using Python 3.x 33842 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1283">#1283</a>)</li> 33843<li>pick up per-component checksums in <code>Bundle</code> generic easyblock 33844 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1285">#1285</a>)</li> 33845<li>correctly pass down optimization flags in CP2K easyblock 33846 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1293">#1293</a>)</li> 33847</ul> 33848</li> 33849</ul> 33850<p><strong>easyconfigs</strong></p> 33851<ul> 33852<li>added example easyconfig files for 39 new software packages:<ul> 33853<li>AmberMini 33854 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5476">#5476</a>), 33855 arrow 33856 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5416">#5416</a>), 33857 bat 33858 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5416">#5416</a>), 33859 CIRCexplorer 33860 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5356">#5356</a>), 33861 CIRCexplorer2 33862 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5470">#5470</a>), 33863 CIRI 33864 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5358">#5358</a>), 33865 FALCON 33866 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5265">#5265</a>), 33867 FastaIndex 33868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5465">#5465</a>), 33869 find_circ 33870 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5348">#5348</a>), 33871 future 33872 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5236">#5236</a>), 33873 GapCloser 33874 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5465">#5465</a>),
33875 glibc 33876 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5428">#5428</a>), 33877 GRNBoost 33878 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5373">#5373</a>), 33879 HDFView 33880 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5391">#5391</a>), 33881 Horovod 33882 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5239">#5239</a>), 33883 HPDBSCAN 33884 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5371">#5371</a>), 33885 Hyperopt 33886 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5455">#5455</a>), 33887 IntelClusterChecker 33888 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4970">#4970</a>), 33889 ITK 33890 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5434">#5434</a>), 33891 LAST 33892 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5465">#5465</a>), 33893 MDTraj 33894 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5317">#5317</a>), 33895 Meson 33896 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5228">#5228</a>), 33897 mkl-dnn 33898 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5319">#5319</a>, 33899 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5362">#5362</a>), 33900 Ninja 33901 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5228">#5228</a>), 33902 OpenKIM-API 33903 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5479">#5479</a>), 33904 ParmEd 33905 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5476">#5476</a>), 33906 PCRaster 33907 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5386">#5386</a>), 33908 piSvM 33909 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5308">#5308</a>), 33910 piSvM-JSC 33911 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5316">#5316</a>), 33912 PTESFinder 33913 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5359">#5359</a>), 33914 pybedtools 33915 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5347">#5347</a>), 33916 pymbar 33917 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5476">#5476</a>), 33918 pyScaf 33919 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5465">#5465</a>), 33920 QIIME2 33921 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5355">#5355</a>), 33922 QTLtools 33923 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5361">#5361</a>), 33924 Redundans 33925 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5465">#5465</a>), 33926 Rmath 33927 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5361">#5361</a>), 33928 sbt 33929 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5373">#5373</a>), 33930 SNAP 33931 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5465">#5465</a>)</li> 33932</ul> 33933</li> 33934<li>added new easyconfigs for existing toolchains: <code>intel/2017.09</code> 33935 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5303">#5303</a>), 33936 <code>intel/2018.00</code> 33937 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5129">#5129</a>), 33938 <code>intel/2018.01</code> 33939 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5345">#5345</a>)</li> 33940<li>added additional easyconfigs for various supported software 33941 packages, including:<ul> 33942<li>CGAL 4.11, CMake 3.10.0, Caffe 1.0, FFTW 3.3.7, GATE 8.0, 33943 gnuplot 5.2.2, HPCG 3.0, HTSlib 1.6, Keras 2.1.2, LLVM 5.0.0, 33944 Mesa 17.2.5, mpi4py 3.0.0, netCDF 4.5.0, OpenFOAM 5.0, ParaView 33945 5.4.1, R 3.4.3, Ruby 2.4.2, Rust 1.21.0, SCons 3.0.1, Szip 33946 2.1.1, Theano 1.0.0, VTK 8.0.1, X11 20171023</li> 33947</ul> 33948</li> 33949<li>minor enhancements, including:<ul> 33950<li>add SHA256 checksums to Autoconf 33951 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5304">#5304</a>), 33952 Automake 33953 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5305">#5305</a>), 33954 libtool 33955 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5306">#5306</a>) 33956 and M4 33957 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5307">#5307</a>) 33958 easyconfigs</li> 33959<li>
33959avoid hardcoding extension versions in worker easyconfig, 33960 include '<code>perl</code>' as OS dep 33961 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5324">#5324</a>)</li> 33962<li>enable building ScaLAPACK in parallel with enhanced ScaLAPACK 33963 easyblock 33964 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5331">#5331</a>)</li> 33965<li>include <code>RInside</code> extension in R 3.4.0 easyconfig 33966 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5354">#5354</a>)</li> 33967<li>clean up configure options that are now handled by R easyblock 33968 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5478">#5478</a>, 33969 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5485">#5485</a>)</li> 33970<li>update Octave easyconfigs to use Octave easyblock, add 33971 extensions for latest Octave versions 33972 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5484">#5484</a>, 33973 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5503">#5503</a>, 33974 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5507">#5507</a>)</li> 33975<li>add <code>Log4perl</code> extension to Perl 5.26.0 easyconfigs 33976 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5511">#5511</a>)</li> 33977</ul> 33978</li> 33979<li>various bug fixes, including:<ul> 33980<li>add missing extensions required by MultiQC & stick to networkx 33981 1.11 33982 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5240">#5240</a>)</li> 33983<li>disable <code>optarch</code> when using Intel compilers and enable tests in 33984 all libxc easyconfigs 33985 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5256">#5256</a>, 33986 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5257">#5257</a>)</li> 33987<li>avoid downloads when installing matplotlib 2.1.0 w/ Python 33988 2.7.14 33989 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5267">#5267</a>)</li> 33990<li>fix <code>$CPATH</code> in recent libffi easyconfigs + enhance sanity check 33991 & add checksum 33992 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5271">#5271</a>)</li> 33993<li>use Github source URL, run <code>autogen.sh</code> + include Autotools 33994 build dep for numactl 33995 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5286">#5286</a>, 33996 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5296">#5296</a>, 33997 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5297">#5297</a>, 33998 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5299">#5299</a>, 33999 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5302">#5302</a>)</li> 34000<li>add hwloc to GROMACS dependencies 34001 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5295">#5295</a>)</li> 34002<li>fix <code>source_urls</code> (& <code>sources</code> spec) for GATE 34003 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5367">#5367</a>)</li> 34004<li>consistently add Autotools build dep in recent netCDF 34005 easyconfigs 34006 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5394">#5394</a>)</li> 34007<li>fix check in test suite for binutils build dep when <code>GCCcore</code> 34008 used as toolchain 34009 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5436">#5436</a>)</li> 34010<li>libdap 3.19.1 checksum changed 34011 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5473">#5473</a>)</li> 34012<li>disable new rfkill feature in easyconfig for util-linux 2.31 34013 since it requires a recent kernel 34014 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5480">#5480</a>)</li> 34015<li>add missing PROJ dependency in recent GDAL easyconfigs 34016 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5481">#5481</a>)</li> 34017<li>fix name in TensorFlow easyconfigs (was 'TensorFlow') 34018 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5495">#5495</a>)</li> 34019<li>fix checksum for Szip 2.1.1 34020 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5517">#5517</a>)</li> 34021<li>fix order of extensions for FSLeyes, add missing MarkupSafe (dep 34022 for Jinja2) 34023 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5520">#5520</a>)</li> 34024</ul> 34025</li> 34026</ul> 34027<h2 id="release_notes_eb341">EasyBuild v3.4.1 (October 17th 2017)<a class="headerlink" href="#release_notes_eb341" title="Permanent link">¶</a></h2> 34028<p>bugfix/update release</p> 34029<p><strong>framework</strong></p> 34030<ul> 34031<li>various enhancements, including:<ul> 34032<li>improve trace output for executed commands + drop requirement 34033 for <code>--experimental</code> for <code>--trace</code> 34034 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2306">#2306</a>)</li> 34035<li>
34035add <code>giolf</code> toolchain definition: GCC, IntelMPI, OpenBLAS, 34036 (Sca)LAPACK and FFTW 34037 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2310">#2310</a>)</li> 34038<li>add support for <code>--force-download</code> and <code>--ignore-checksums</code> 34039 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2313">#2313</a>, 34040 <a href="https://github.com/easybuilders/easybuild-framework/pull/2314">#2314</a>)</li> 34041<li>flesh out <code>pypi_source_urls</code> from <code>derive_alt_pypi_url</code> 34042 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2319">#2319</a>)</li> 34043</ul> 34044</li> 34045<li>various bug fixes, including:<ul> 34046<li>also check for use of <code>--rebuild</code> next to <code>--force</code> to skip 34047 sanity check with <code>--module-only</code> 34048 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2307">#2307</a>)</li> 34049<li>ensure <code>$TMPDIR</code> is set to a short path for OpenMPI v2.x 34050 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2311">#2311</a>)</li> 34051<li>guard '<code>module load</code>' commands in generated modules under 34052 <code>--recursive-unload</code> to avoid load storms 34053 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2316">#2316</a>)</li> 34054<li>correctly deal with use of special characters in description & 34055 co 34056 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2320">#2320</a>)</li> 34057<li>fix incorrect <code>FFT_INC_DIR</code> for Intel MKL 34058 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2323">#2323</a>)</li> 34059</ul> 34060</li> 34061</ul> 34062<p><strong>easyblocks</strong></p> 34063<ul> 34064<li>add generic '<code>SystemMPI</code>' easyblock 34065 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1106">#1106</a>, 34066 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1261">#1261</a>, 34067 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1262">#1262</a>)</li> 34068<li>add software-specific easyblock for SAS 34069 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1263">#1263</a>)</li> 34070<li>minor enhancements, including:<ul> 34071<li>run '<code>wcleanAll</code>' or '<code>wcleanPlatform -all</code>' before building 34072 OpenFOAM 34073 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/780">#780</a>, 34074 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1258">#1258</a>)</li> 34075<li>enhance generic '<code>SystemCompiler</code>' easyblock 34076 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1106">#1106</a>)</li> 34077<li>clean up <code>--trace</code> output for Python & Python packages 34078 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1248">#1248</a>)</li> 34079<li>update Intel MPI easyblock to support 2018.* versions 34080 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1253">#1253</a>)</li> 34081<li>add support for Intel MPI and Intel MKL to ScaLAPACK easyblock 34082 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1255">#1255</a>)</li> 34083<li>enhance GCC easyblock to also put symlinks in place for 34084 <code>cc</code>/<code>c++</code>/<code>f77</code>/<code>f95</code> commands 34085 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1256">#1256</a>)</li> 34086</ul> 34087</li> 34088<li>various bug fixes, including:<ul> 34089<li>allow that '<code>gcc -print-multiarch</code>' fails in icc easyblock 34090 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1249">#1249</a>)</li> 34091<li>fix prefix subdirectory for older versions of icc (in particular 34092 2011.3.174) 34093 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1250">#1250</a>)</li> 34094<li>use <code>remove_file</code> rather than <code>os.remove</code> in generic <code>IntelBase</code> 34095 easyblock to correctly deal with broken symlinks 34096 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1251">#1251</a>)</li> 34097<li>fix sanity check for MXNet easyblock + correctly detect unpacked 34098 source directory 34099 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1257">#1257</a>)</li> 34100<li>avoid building CP2K twice due to incorrect attempt at running 34101 '<code>make clean</code>' first 34102 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1266">#1266</a>)</li> 34103</ul> 34104</li> 34105</ul> 34106<p><strong>easyconfigs</strong></p> 34107<ul> 34108<li>added easyconfigs for new toolchain <code>giolf/2017b</code> 34109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5140">#5140</a>)</li> 34110<li>
34110added example easyconfig files for 13 new software packages:<ul> 34111<li>ASAP3 34112 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5200">#5200</a>), 34113 Albacore 34114 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5153">#5153</a>), 34115 CatMAP 34116 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5225">#5225</a>), 34117 DLCpar 34118 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5209">#5209</a>), 34119 FSLeyes 34120 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5192">#5192</a>), 34121 IQ-TREE 34122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3695">#3695</a>), 34123 NEST 34124 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5515">#5515</a>), 34125 nanonet 34126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5149">#5149</a>), 34127 OMA 34128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5211">#5211</a>), 34129 , oxford_asl 34130 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5193">#5193</a>), 34131 QEMU 34132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5220">#5220</a>), 34133 REMORA 34134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5159">#5159</a>), 34135 SAS 34136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5208">#5208</a>), 34137 supermagic 34138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5187">#5187</a>)</li> 34139</ul> 34140</li> 34141<li>added additional easyconfigs for various supported software 34142 packages, including:<ul> 34143<li>Anaconda2/3 4.4.0, Blender 2.79, Boost 1.65.1, CMake 3.9.4, 34144 FFmpeg 3.3.4, GCC 5.5.0, h5py 2.7.1, Keras 2.0.8, matplotlib 34145 2.1.0, mympingpong 0.8.0, OpenCV 3.3.0, OpenFOAM-Extend 4.0, 34146 OpenMPI 2.1.2 + 3.0.0, Pillow 4.3.0, Python 2.7.14 + 3.6.3, 34147 SAMtools 1.6, scikit-image 0.13.0, scikit-learn 0.19.0, 34148 Tensorflow 1.3.0, vsc-mympirun 4.0.2</li> 34149</ul> 34150</li> 34151<li>minor enhancements, including:<ul> 34152<li>add <code>xkeyboard-config</code> component in X11 bundle 34153 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5066">#5066</a>)</li> 34154<li>clean up use of <code>wcleanAll</code> in OpenFOAM-Extend easyconfigs, now 34155 handled by OpenFOAM easyblock 34156 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5131">#5131</a>)</li> 34157<li>also install <code>run_rcorrector.pl</code> with Rcorrector 34158 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5135">#5135</a>)</li> 34159<li>add SHA256 checksum to PyCUDA easyconfig 34160 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5154">#5154</a>)</li> 34161<li>fix/improve description in HDF5 easyconfigs 34162 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5182">#5182</a>)</li> 34163<li>include heatmap3 extension for R 3.4.0 34164 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5185">#5185</a>)</li> 34165<li>add ComplexHeatmap to Bioconductor 3.5 bundle + dep pkgs in R 34166 3.4.0 easyconfig 34167 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5195">#5195</a>)</li> 34168</ul> 34169</li> 34170<li>various bug fixes, including:<ul> 34171<li>fix source URLs for AUGUSTUS 3.2.3 34172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5119">#5119</a>)</li> 34173<li>fix building Bison 2.5 on systems with recent glibc 34174 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5130">#5130</a>)</li> 34175<li>also consider <code>rdma-core-devel</code> as alternative to 34176 <code>libibverbs-devel</code> OS dependency 34177 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5132">#5132</a>)</li> 34178<li>consistently use empty toolchain version in icc & ifort 34179 easyconfigs to ensure that GCC(core) dep is loaded during 34180 installation 34181 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5133">#5133</a>, 34182 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5134">#5134</a>)</li> 34183<li>add patches for Boost 1.64.0 to fix known issues 34184 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5148">#5148</a>)</li> 34185<li>remove PyCUDA easyconfig for <code>intel/2017a</code>, doesn't work due to 34186 incompatibility between GCC 6.3.0 & CUDA 8 34187 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5156">#5156</a>)</li> 34188<li>
34188add missing Perl extensions in easyconfig for Worker 1.6.7 34189 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5157">#5157</a>)</li> 34190<li>fix checksums for packages that download from 34191 <code>github.com/x/y/archive</code> 34192 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5162">#5162</a>)</li> 34193<li>add missing libpng dependency to g2lib-1.4.0 easyconfig using 34194 intel-2017a 34195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5196">#5196</a>)</li> 34196<li>fix source_urls for Szip 2.1 & include SHA256 checksum 34197 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5206">#5206</a>)</li> 34198<li>remove unneeded <code>--with-fft-incs</code> configure option for ABINIT 34199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5207">#5207</a>)</li> 34200<li>disable optarch for libjpeg-turbo 1.5.1 built with <code>intel/2017a</code> 34201 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5214">#5214</a>)</li> 34202<li>update <code>$R_LIBS</code> in plotly easyconfig 34203 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5215">#5215</a>)</li> 34204<li>include NLopt as a dependency in R easyconfigs that include 34205 <code>nloptr</code> as extension 34206 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5217">#5217</a>)</li> 34207</ul> 34208</li> 34209</ul> 34210<h2 id="release_notes_eb340">EasyBuild v3.4.0 (September 10th 2017)<a class="headerlink" href="#release_notes_eb340" title="Permanent link">¶</a></h2> 34211<p>feature release</p> 34212<p><strong>framework</strong></p> 34213<ul> 34214<li>various enhancements, including:<ul> 34215<li>add support for backing up modules via <code>--backup-modules</code> 34216 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2134">#2134</a>)<ul> 34217<li>enabled automatically with <code>--module-only</code> and <code>--skip</code></li> 34218<li>see also 34219 <a href="http://easybuild.readthedocs.io/en/latest/Backup_modules.html">http://easybuild.readthedocs.io/en/latest/Backup_modules.html</a></li> 34220</ul> 34221</li> 34222<li>add support for <code>--search-paths</code> to extend list of locations 34223 considered by <code>--search</code>/<code>-S</code> 34224 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2255">#2255</a>)</li> 34225<li>include <code>userInGroup</code> check in Lua modules when installation is 34226 group-restricted 34227 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2274">#2274</a>)</li> 34228<li>add experimental support for '<code>eb --trace</code>' 34229 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2285">#2285</a>)<ul> 34230<li>see also 34231 <a href="http://easybuild.readthedocs.io/en/latest/Tracing_progress.html">http://easybuild.readthedocs.io/en/latest/Tracing_progress.html</a></li> 34232</ul> 34233</li> 34234<li>add support for '<code>eb --inject-checksums</code>' 34235 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2286">#2286</a>, 34236 <a href="https://github.com/easybuilders/easybuild-framework/pull/2292">#2292</a>, 34237 <a href="https://github.com/easybuilders/easybuild-framework/pull/2293">#2293</a>)<ul> 34238<li>see also 34239 <a href="http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#adding-or-replacing-checksums-using-inject-checksums">http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#adding-or-replacing-checksums-using-inject-checksums</a></li> 34240</ul> 34241</li> 34242<li>add support for <code>append_paths</code> in module generator 34243 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2294">#2294</a>)</li> 34244</ul> 34245</li> 34246<li>various bug fixes, including:<ul> 34247<li>strip provided GitHub token of spaces in 34248 <code>--install-github-token</code> 34249 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2270">#2270</a>)</li> 34250<li>remove '<code>provides</code>' line from <code>setup.py</code> 34251 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2275">#2275</a>)</li> 34252<li>pass down stdin in '<code>import</code>' check for extensions during 34253 sanity check 34254 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2276">#2276</a>)</li> 34255<li>make sure location to 'eb' installed during stage 1 is 34256 included in <code>$PATH</code> during stage 2 of bootstrap procedure 34257 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2281">#2281</a>)</li> 34258<li>make resolve_path robust against <code>None</code> path being provided 34259 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2282">#2282</a>)</li> 34260<li>ensure clean error message on easyconfig file parse failure 34261 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2290">#2290</a>)</li> 34262<li>fix regex to avoid sucking up additional lines prior to module 34263 file path in <code>modulefile_path</code> 34264 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2291">#2291</a>)</li> 34265<li>fix error message when <code>--use-ccache</code> is used but <code>ccache</code> is 34266 not available in <code>$PATH</code> 34267 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2295">#2295</a>)</li> 34268</ul> 34269</li> 34270</ul> 34271<p><strong>easyblocks</strong></p> 34272<ul> 34273<li>minor enhancements, including:<ul> 34274<li>update Siesta easyblock for versions 4.0.1 and 4.1-b3 34275 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1218">#1218</a>)</li> 34276<li>updates GAMESS-US easyblock for version 20170420R1 + move 34277 <code>ddikick.x</code> when <code>ddi_comm</code> is set to '<code>sockets</code>' 34278 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1221">#1221</a>)</li> 34279<li>update MRtrix easyblock for 3.0 & beyond + use <code>copy</code> function 34280 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1230">#1230</a>)</li> 34281<li>update ROOT easyblock to support recent versions that require 34282 using CMake, add sanity check, clean up/enhance <code>make_module*</code> 34283 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1236">#1236</a>)</li> 34284<li>enhance icc easyblock to include multipath include dir in 34285 <code>$CPATH</code> 34286 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1237">#1237</a>, 34287 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1242">#1242</a>)</li> 34288</ul> 34289</li> 34290<li>various bug fixes, including:<ul> 34291<li>use <code>plumed-patch</code> command rather than '<code>plumed patch</code>' in 34292 GROMACS easyblock 34293 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1212">#1212</a>)</li> 34294<li>remove '<code>provides</code>' line from <code>setup.py</code> 34295 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1217">#1217</a>)</li> 34296<li>fixed wrong use of <code>build_type</code> in <code>self.cfg</code> in WRF easyblock 34297 that resulted in an raised exception 34298 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1220">#1220</a>)</li> 34299<li>
34299added a call to super <code>post_install_step</code> in CUDA easyblock 34300 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1226">#1226</a>)</li> 34301<li>fix <code>$MCRROOT</code> definition in generated module file under 34302 <code>--module-only</code> in MCR easyblock 34303 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1228">#1228</a>)</li> 34304<li>fix permissions for directories in SuiteSparse 34305 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1238">#1238</a>)</li> 34306<li>fix function signature for <code>fetch_extension_sources</code> in OCaml 34307 easyblock 34308 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1240">#1240</a>)</li> 34309</ul> 34310</li> 34311</ul> 34312<p><strong>easyconfigs</strong></p> 34313<ul> 34314<li>added easyconfigs for <code>foss/2017b</code> and <code>intel/2017b</code> common 34315 toolchains 34316 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4768">#4768</a>), 34317 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4618">#4618</a>)</li> 34318<li>added new easyconfigs for existing toolchains:<ul> 34319<li><code>iomkl/2017b</code> 34320 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5097">#5097</a>)</li> 34321</ul> 34322</li> 34323<li>added example easyconfig files for 31 new software packages:<ul> 34324<li>BAMM 34325 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4650">#4650</a>), 34326 BamM 34327 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4650">#4650</a>), 34328 bcl2fastq2 34329 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4902">#4902</a>), 34330 CGNS 34331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5078">#5078</a>), 34332 CLAPACK 34333 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5096">#5096</a>), 34334 CLISP 34335 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4926">#4926</a>, 34336 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4986">#4986</a>), 34337 cadaver 34338 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4873">#4873</a>), 34339 destiny 34340 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5009">#5009</a>), 34341 GroopM 34342 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4650">#4650</a>), 34343 Lucene-Geo-Gazetteer 34344 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5064">#5064</a>), 34345 libffcall 34346 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4850">#4850</a>), 34347 libsigsegv 34348 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4840">#4840</a>), 34349 MERCKX 34350 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5056">#5056</a>), 34351 minimap2 34352 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4991">#4991</a>), 34353 ncompress 34354 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4852">#4852</a>), 34355 OpenNLP 34356 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5059">#5059</a>, 34357 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5061">#5061</a>), 34358 OpenRefine 34359 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5058">#5058</a>), 34360 PHAST 34361 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5096">#5096</a>), 34362 PYTHIA 34363 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5083">#5083</a>), 34364 ParallelIO 34365 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5071">#5071</a>), 34366 PnetCDF 34367 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5071">#5071</a>), 34368 plotly 34369 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5010">#5010</a>), 34370 QML 34371 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5101">#5101</a>), 34372 Quorum 34373 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5095">#5095</a>), 34374 Rcorrector 34375 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5095">#5095</a>), 34376 SCnorm 34377 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5008">#5008</a>), 34378 SOAPdenovo-Trans 34379 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5095">#5095</a>), 34380 Shannon 34381 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5095">#5095</a>), 34382 Tika 34383 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5063">#5063</a>), 34384 UNAFold 34385 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4997">#4997</a>), 34386 VERSE 34387 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4843">#4843</a>)</li> 34388</ul> 34389</li> 34390<li>
34390added additional easyconfigs for various supported software 34391 packages, including:<ul> 34392<li>Boost 1.65.0, binutils 2.29, GAMESS-US 20170420-R1, GCC(core) 34393 7.2.0, gzip 1.8, HDF5 1.8.19, LLVM 4.0.1, MRtrix 3.0_RC2, Perl 34394 5.26.0, ROOT 6.10.04, Spark 2.2.0</li> 34395</ul> 34396</li> 34397<li>minor enhancements, including:<ul> 34398<li>add checksums to Perl 5.24.1 easyconfigs 34399 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4973">#4973</a>, 34400 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4992">#4992</a>)</li> 34401<li>add additional extensions for R 3.4.0 and Bioconductor 3.5 34402 bundle 34403 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5007">#5007</a>, 34404 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5028">#5028</a>, 34405 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5029">#5029</a>, 34406 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5062">#5062</a>, 34407 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5079">#5079</a>)</li> 34408<li>also define <code>$INCLUDEPATH</code> and <code>$LIBRARY_PATH</code> in 34409 Tesla-Deployment-Kit easyconfig 34410 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5018">#5018</a>)</li> 34411<li>add check to see whether binutils is included as build dep when 34412 GCCcore toolchain is used 34413 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5084">#5084</a>)</li> 34414</ul> 34415</li> 34416<li>various bug fixes, including:<ul> 34417<li>added Rmpi patch file for R built with intel toolchains incl. 34418 impi 5.x 34419 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4623">#4623</a>)</li> 34420<li>use single-line description in <code>setup.py</code> 34421 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4881">#4881</a>)</li> 34422<li>fix version and source for Seurat + add extensions required by 34423 Seurat in R 3.4.0 easyconfig 34424 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4889">#4889</a>)</li> 34425<li>add zlib as dependency to util-linux easyconfigs 34426 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4900">#4900</a>, 34427 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4998">#4998</a>)</li> 34428<li>use <code>modextrapaths</code> instead of <code>modextravars</code> in OpenMM 34429 easyconfig 34430 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4903">#4903</a>)</li> 34431<li>update deprecated PLINK urls 34432 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4920">#4920</a>, 34433 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5006">#5006</a>)</li> 34434<li>fix <code>moduleclass</code> for Cookiecutter 34435 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4947">#4947</a>)</li> 34436<li>fix order of OpenMPI dependency in <code>iomkl/2016.09*</code> easyconfigs, 34437 must come after icc/ifort 34438 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5024">#5024</a>)</li> 34439<li>fix typo in comment in util-linux easyconfigs & add SHA256 34440 checksums 34441 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5052">#5052</a>)</li> 34442<li>remove superfluous <code>$CPATH</code> update in GLib 2.44.0 easyconfig 34443 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5053">#5053</a>)</li> 34444<li>update ncurses to not build a separate libtinfo but provide a 34445 soft link instead + force linking to ncurses in libreadline 34446 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5067">#5067</a>, 34447 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5074">#5074</a>)</li> 34448<li>include Autotools as build dep for netCDF 34449 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5077">#5077</a>)</li> 34450<li>add missing binutils build dep for texinfo 34451 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/5099">#5099</a>)</li> 34452</ul> 34453</li> 34454</ul> 34455<h2 id="release_notes_eb331">EasyBuild v3.3.1 (July 12th 2017)<a class="headerlink" href="#release_notes_eb331" title="Permanent link">¶</a></h2> 34456<p>bugfix/update release</p> 34457<p><strong>framework</strong></p> 34458<ul> 34459<li>various enhancements, including:<ul> 34460<li>add support for '<code>
34460allow_prepend_abs_path</code>' easyconfig 34461 parameter 34462 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2254">#2254</a>)</li> 34463<li>support for <code>--merge-pr</code> 34464 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2266">#2266</a>)</li> 34465</ul> 34466</li> 34467<li>various bug fixes, including:<ul> 34468<li>resolve symlinks to location of '<code>eb</code>' in <code>get_paths_for</code> 34469 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2248">#2248</a>)</li> 34470<li>fall back to checking location relative to '<code>eb</code>' location in 34471 <code>find_eb_script</code> 34472 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2249">#2249</a>)</li> 34473<li>respect <code>--suffix-modules-path</code> value for user-specific module 34474 path extensions 34475 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2250">#2250</a>)</li> 34476<li>update EasyBuild bootstrap script to download <code>distribute</code> 34477 tarball from <a href="http://easybuilders.github.io/easybuild/files">http://easybuilders.github.io/easybuild/files</a> 34478 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2256">#2256</a>)</li> 34479<li>fix default target GitHub account/organisation for <code>--new-pr</code> & 34480 co + fix tests that got broken by migration to 34481 github.com/easybuilders 34482 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2258">#2258</a>)</li> 34483<li>fix checking for new easyconfigs in <code>copy_easyconfigs</code>, pick up 34484 specified commit message as PR title if none was provided 34485 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2259">#2259</a>)</li> 34486<li>get rid of references to <code>hpcugent</code> after move to 34487 github.com/easybuilders 34488 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2261">#2261</a>)</li> 34489<li>automatically enable <code>--ignore-osdeps</code> under <code>--new-pr</code> and 34490 <code>--update-pr</code> 34491 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2262">#2262</a>)</li> 34492</ul> 34493</li> 34494</ul> 34495<p><strong>easyblocks</strong></p> 34496<ul> 34497<li>minor enhancements, including:<ul> 34498<li>enhance HDF5 easyblock: define <code>$HDF5_DIR</code> & include 34499 <code>-DMPICH_IGNORE_CXX_SEEK</code> in <code>$CXXFLAGS</code> 34500 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1200">#1200</a>)</li> 34501<li>consistently pass down (named) arguments in <code>prepare_step</code>, and 34502 check for it in the tests 34503 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1202">#1202</a>)</li> 34504<li>remove no longer supported <code>VersionIndependentPythonPackage</code> 34505 generic easyblock 34506 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1202">#1202</a>)</li> 34507<li>update ABAQUS easyblock for recent versions, incl. support for 34508 installing hotfixes 34509 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1203">#1203</a>)</li> 34510<li>get rid of references to '<code>hpcugent</code>' organisation after move 34511 to github.com/easybuilders 34512 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1206">#1206</a>)</li> 34513<li>make Boost easyblock fully aware of <code>(pre)configopts</code>, 34514 <code>(pre)buildopts</code> and <code>(pre)installopts</code> 34515 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1207">#1207</a>)</li> 34516<li>drop check for '<code>ipython</code>' in sanity check of Anaconda 34517 easyblock, to also support Miniconda 34518 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1210">#1210</a>)</li> 34519</ul> 34520</li> 34521</ul> 34522<p><strong>easyconfigs</strong></p> 34523<ul> 34524<li>added example easyconfig files for 6 new software packages:<ul> 34525<li>FastME 34526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4811">#4811</a>), 34527 geopy 34528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4821">#4821</a>), 34529 Miniconda2 34530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4841">#4841</a>), 34531 ngmlr 34532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4818">#4818</a>), 34533 OpenCoarrays 34534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4799">#4799</a>), 34535 Seurat 34536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4832">#4832</a>)</li> 34537</ul> 34538</li> 34539<li>
34539added additional easyconfigs for various supported software 34540 packages, including:<ul> 34541<li>ABAQUS 2017, GCC(core) 6.4.0, Keras 2.0.5, NCBI-Toolkit 18.0.0, 34542 numpy 1.13.0, Tensorflow 1.2.0</li> 34543</ul> 34544</li> 34545<li>minor enhancements, including:<ul> 34546<li>add <code>SVG</code> and <code>Statistics::Basic</code> to recent Perl versions 34547 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4796">#4796</a>)</li> 34548<li>remove <code>buildopts</code> from HDF5 easyconfigs, taken care of by 34549 updated HDF5 easyblock now 34550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4779">#4779</a>)</li> 34551<li>include <code>joblib</code> as extension in recent Python easyconfigs 34552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4805">#4805</a>)</li> 34553<li>changed moduleclass in mpi4py to better reflect what it is and 34554 to not confuse HMNS 34555 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4807">#4807</a>)</li> 34556<li>get rid of references to '<code>hpcugent</code>' organisation after move 34557 to github.com/easybuilders 34558 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4815">#4815</a>, 34559 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4837">#4837</a>)</li> 34560<li>add <code>Rtsne</code> as extension to R 3.4.0 34561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4831">#4831</a>)</li> 34562</ul> 34563</li> 34564<li>various bug fixes, including:<ul> 34565<li>use <code>PYPI_SOURCE</code> as source URL in Tensorflow easyconfigs 34566 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4786">#4786</a>)</li> 34567<li>fix <code>homepage</code> for skewer 34568 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4791">#4791</a>)</li> 34569<li>sync/fix <code>source_urls</code> & <code>homepage</code> in HDF5 easyconfigs 34570 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4800">#4800</a>)</li> 34571<li>fix <code>ubsan</code> error blocking build of GCCcore 6.1.0, 6.2.0, 6.3.0 34572 with system GCC 7.1 34573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4813">#4813</a>)</li> 34574</ul> 34575</li> 34576</ul> 34577<h2 id="release_notes_eb330">EasyBuild v3.3.0 (June 26th 2017)<a class="headerlink" href="#release_notes_eb330" title="Permanent link">¶</a></h2> 34578<p>feature release</p> 34579<p><strong>framework</strong></p> 34580<ul> 34581<li>various enhancements, including:<ul> 34582<li>clean up easyconfigs that are copied for inclusion in pull 34583 request 34584 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2197">#2197</a>, 34585 <a href="https://github.com/easybuilders/easybuild-framework/pull/2227">#2227</a>)</li> 34586<li>use devel logging where relevant in <code>easybuild.tools.toolchain</code> 34587 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2198">#2198</a>)</li> 34588<li>check exit code for executed <code>module</code> commands 34589 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2200">#2200</a>)</li> 34590<li>also copy patches to installation directory & easyconfigs 34591 archive along with easyconfig file 34592 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2202">#2202</a>, 34593 <a href="https://github.com/easybuilders/easybuild-framework/pull/2241">#2241</a>)</li> 34594<li>add support for SHA256 checksums 34595 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2215">#2215</a>)<ul> 34596<li>also auto-detect whether provided checksum is MD5 or SHA256 34597 based on length (if not checksum type is specified)</li> 34598<li>add support for <code>--enforce-checksums</code>, to require 34599 availability of checksums for sources/patches</li> 34600<li>see 34601 <a href="http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#source-files-patches-and-checksums">http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#source-files-patches-and-checksums</a></li> 34602</ul> 34603</li> 34604<li>add support for renaming sources on download 34605 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2223">#2223</a>)<ul> 34606<li>also involves deprecating use of 2-tuple elements in list of 34607 sources, see 34608 <a href="http://easybuild.readthedocs.io/en/latest/Deprecated-functionality.html#depr-sources-2-element-tuple">http://easybuild.readthedocs.io/en/latest/Deprecated-functionality.html#depr-sources-2-element-tuple</a></li> 34609</ul> 34610</li> 34611<li>
34611add support for <code>--detect-loaded-modules</code> 34612 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2228">#2228</a>)</li> 34613<li>give extensions access to <code>module_generator</code> of parent 34614 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2229">#2229</a>)</li> 34615<li>pass down additional arguments to <code>copy_dir</code> down to 34616 <code>shutil.copytree</code> 34617 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2230">#2230</a>)</li> 34618<li>avoid reloading already loaded modules that extend <code>$MODULEPATH</code> 34619 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2232">#2232</a>)</li> 34620</ul> 34621</li> 34622<li>various bug fixes, including:<ul> 34623<li>make sure test account & accompanying token is used in tests for 34624 <code>github.py</code> 34625 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2220">#2220</a>, 34626 <a href="https://github.com/easybuilders/easybuild-framework/pull/2224">#2224</a>)</li> 34627<li>only use MPD for old versions of Intel MPI (<4.1) in 34628 <code>mpi_cmd_for</code> 34629 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2221">#2221</a>)</li> 34630<li>escape dots in package filename to ensure correct match in 34631 <code>derive_alt_pypi_url</code> 34632 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2225">#2225</a>)</li> 34633<li>fix <code>GNU_SOURCE</code> template by adding missing <code>/gnu/</code> 34634 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2235">#2235</a>)</li> 34635<li>catch exception <code>shutil.Error</code> in <code>copy_file</code> 34636 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2239">#2239</a>)</li> 34637<li>report full error and traceback on unhandled exception in test 34638 report 34639 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2240">#2240</a>)</li> 34640<li>fix <code>--set-default-module</code> flag 34641 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2243">#2243</a>)</li> 34642</ul> 34643</li> 34644</ul> 34645<p><strong>easyblocks</strong></p> 34646<ul> 34647<li>added easyblocks for MXNet 34648 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1135">#1135</a>), 34649 Tkinter(<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1184">#1184</a>)</li> 34650<li>minor enhancements, including:<ul> 34651<li>enhance sanity check for NCL 34652 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1169">#1169</a>, 34653 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1179">#1179</a>)</li> 34654<li>enable building of shared FFTW libraries 34655 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1180">#1180</a>)</li> 34656<li>include update statements for <code>$CPATH</code> and <code>$*LIBRARY_PATH</code> in 34657 generated module in numpy easyblock 34658 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1183">#1183</a>)</li> 34659<li>stop using deprecated '<code>copytree</code>' function from 34660 <code>easybuild.tools.filetools</code> 34661 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1185">#1185</a>)</li> 34662<li>update SAMtools easyblock for v0.1.17 34663 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1189">#1189</a>)</li> 34664<li>update MATLAB easyblock for 2016b & 2017a versions (adjust 34665 permissions and change dir) 34666 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1182">#1182</a>, 34667 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1197">#1197</a>)</li> 34668<li>consider <code>$EB_*_LICENSE_SERVER(_PORT)</code> in MATLAB and ANSYS 34669 easyblocks 34670 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1195">#1195</a>)</li> 34671<li>add <code>omp_num_threads</code> custom parameter in CP2K easyblock to 34672 allow defining <code>$OMP_NUM_THREADS</code> during testing 34673 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1196">#1196</a>)</li> 34674</ul> 34675</li> 34676<li>various bug fixes, including:<ul> 34677<li>fix Siesta easyblock to enable and verify parallel build 34678 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1186">#1186</a>)</li> 34679<li>fix bug in alias definition in impi easyblock for <code>mpigxx</code>, 34680 <code>mpiicpc</code> and <code>mpiifort</code> 34681 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1192">#1192</a>)</li> 34682</ul> 34683</li> 34684</ul> 34685<p><strong>easyconfigs</strong></p> 34686<ul> 34687<li>enable automatic style checks in easyconfig tests 34688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2506">#2506</a>)</li> 34689<li>
34689added example easyconfig files for 28 new software packages:<ul> 34690<li>ada 34691 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4594">#4594</a>), 34692 Aspera-CLI 34693 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4635">#4635</a>), 34694 AUGUSTUS 34695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4624">#4624</a>), 34696 ada 34697 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4594">#4594</a>), 34698 Bio-SamTools 34699 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4637">#4637</a>), 34700 Bpipe 34701 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4590">#4590</a>), 34702 BUSCO 34703 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4624">#4624</a>), 34704 CNVnator 34705 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4649">#4649</a>), 34706 davix 34707 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4755">#4755</a>), 34708 EricScript 34709 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4594">#4594</a>), 34710 FUNWAVE-TVD 34711 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4743">#4743</a>), 34712 gmpy2 34713 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4609">#4609</a>), 34714 gSOAP 34715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4755">#4755</a>), 34716 libsndfile 34717 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4628">#4628</a>), 34718 lpsolve 34719 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4264">#4264</a>), 34720 LUMPY 34721 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4682">#4682</a>), 34722 MaSuRCA 34723 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4706">#4706</a>), 34724 modred 34725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4729">#4729</a>), 34726 MXNet 34727 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4765">#4765</a>), 34728 NRGLjubljana 34729 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4651">#4651</a>), 34730 OrfM 34731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4703">#4703</a>), 34732 Perl4-CoreLibs 34733 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4670">#4670</a>), 34734 prodigal 34735 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4468">#4468</a>), 34736 pydlpoly 34737 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4756">#4756</a>), 34738 SeqAn 34739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4603">#4603</a>), 34740 sharutils 34741 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4745">#4745</a>), 34742 Spyder 34743 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4627">#4627</a>), 34744 Tkinter 34745 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4620">#4620</a>), 34746 VariantMetaCaller 34747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4632">#4632</a>)</li> 34748</ul> 34749</li> 34750<li>added new easyconfigs for existing toolchains:<ul> 34751<li><code>gimkl/2017a</code> 34752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4646">#4646</a>)</li> 34753</ul> 34754</li> 34755<li>added additional easyconfigs for various supported software 34756 packages, including:<ul> 34757<li>ABINIT 8.2.2, BLAST+ 2.6.0, Bowtie2 2.3.2, FFmpeg 3.3.1, NCL 34758 6.4.0, Rust 1.18.0, SAMtools 1.5, VTK 7.1.1</li> 34759</ul> 34760</li> 34761<li>minor enhancements, including:<ul> 34762<li>use '<code>git diff --name-only</code>' and <code>$TRAVIS_COMMIT_RANGE</code> in 34763 Travis config to get list of changed files 34764 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4606">#4606</a>, 34765 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4619">#4619</a>)</li> 34766<li>add tuneR, seewave, soundecology, vcfR extensions for R 3.4.0 (+ 34767 libsndfile as dep) 34768 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4628">#4628</a>, 34769 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4680">#4680</a>, 34770 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4747">#4747</a>)</li> 34771<li>also copy <code>README</code> for GapFiller 34772 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4631">#4631</a>)</li> 34773<li>enable inclusion of version symbol by using 34774 <code>--enable-ld-version-script</code> configure option for LibTIFF 34775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4639">#4639</a>)</li> 34776<li>
34776add SHA256 checksums for libpciaccess to discriminate from old 34777 tarballs that required running <code>autogen.sh</code> 34778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4688">#4688</a>)</li> 34779<li>fix <code>NE_GLOBAL_DIR</code> path for ne by also specifying <code>PREFIX</code> in 34780 <code>buildopts</code> 34781 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4698">#4698</a>)</li> 34782<li>more (trivial) style fixes 34783 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4761">#4761</a>)</li> 34784<li>avoid use of <code>import</code> in ANSYS & MATLAB easyconfigs 34785 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4762">#4762</a>)</li> 34786<li>set <code>$OMP_NUM_THREADS</code> during CP2K test step via dedicated 34787 easyconfig parameter 34788 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4763">#4763</a>)</li> 34789<li>avoid use of '<code>import</code>' in BFAST easyconfigs, just strip of 34790 '<code>a</code>' from version 34791 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4764">#4764</a>)</li> 34792<li>add the docopt module to all Python 2017a easyconfigs 34793 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4770">#4770</a>)</li> 34794<li>stop using deprecated 2-element tuple format in sources, use 34795 equivalent dict format instead 34796 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4774">#4774</a>)</li> 34797</ul> 34798</li> 34799<li>various bug fixes, including:<ul> 34800<li>fix typo in statsmodels source url (<code>/sources/</code> -> <code>/source/</code>) 34801 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4612">#4612</a>)</li> 34802<li>add location to <code>DotLib.pm</code> to <code>$PERL5LIB</code> for SSPACE_Basic 34803 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4638">#4638</a>)</li> 34804<li>add missing <code>/gnu/</code> in ftpmirror.gnu.org <code>source_urls</code>, or use 34805 <code>GNU_SOURCE</code> where possible 34806 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4653">#4653</a>)</li> 34807<li>consistently use <code>--with-harfbuzz=no</code> configure option in 34808 freetype easyconfigs 34809 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4668">#4668</a>)</li> 34810<li>use <code>--with-x=yes</code> in R easyconfigs that include X11 as a 34811 dependency 34812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4701">#4701</a>)</li> 34813<li>remove '<code>4.0</code>' in tbb description 34814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4707">#4707</a>)</li> 34815<li>add lib sanity check paths for Debian compatibility in nettle 34816 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4722">#4722</a>)</li> 34817<li>fix source URLs for HDF5 34818 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4749">#4749</a>)</li> 34819</ul> 34820</li> 34821</ul> 34822<h2 id="release_notes_eb321">EasyBuild v3.2.1 (May 12th 2017)<a class="headerlink" href="#release_notes_eb321" title="Permanent link">¶</a></h2> 34823<p>bugfix/update release</p> 34824<p><strong>framework</strong></p> 34825<ul> 34826<li>various enhancements, including:<ul> 34827<li>make hardcoded max ratio for failures in <code>adjust_permissions</code> 34828 configurable 34829 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2213">#2213</a>)</li> 34830<li>allow <code>https://</code> on direct download in sources 34831 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2214">#2214</a>)</li> 34832</ul> 34833</li> 34834<li>various bug fixes, including:<ul> 34835<li>bump version bootstrap script to sync with latest update 34836 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2208">#2208</a>)</li> 34837<li>fix crash during module generation when '<code>%</code>' character is 34838 used in description 34839 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2209">#2209</a>)</li> 34840</ul> 34841</li> 34842</ul> 34843<p><strong>easyblocks</strong></p> 34844<ul> 34845<li>added easyblock for Siesta 34846 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1105">#1105</a>)</li> 34847<li>minor enhancements, including:<ul> 34848<li>enhance GROMACS easyblock to build with PLUMED support 34849 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1121">#1121</a>)</li> 34850<li>enhance NAMD easyblock: add OpenMP support, update for recent 34851 NAMD versions (2.12), fix compatibility with Tcl versions other 34852 than 8.5 34853 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1173">#1173</a>)</li> 34854</ul> 34855</li> 34856</ul> 34857<p><strong>easyconfigs</strong></p> 34858<ul> 34859<li>added example easyconfig files for 12 new software packages:<ul> 34860<li>AdapterRemoval 34861 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4509">#4509</a>), 34862 blasr_libcpp 34863 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4566">#4566</a>), 34864 canu 34865 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4473">#4473</a>), 34866 enchant 34867 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4567">#4567</a>), 34868 hunspell 34869 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4567">#4567</a>), 34870 memkind 34871 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4544">#4544</a>), 34872 NLTK 34873 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4565">#4565</a>), 34874 pbbam 34875 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4566">#4566</a>), 34876 pbdagcon 34877 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4566">#4566</a>), 34878 pyenchant 34879 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4567">#4567</a>), 34880 Siesta 34881 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4562">#4562</a>), 34882 xarray 34883 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4556">#4556</a>)</li> 34884</ul> 34885</li> 34886<li>
34886added new easyconfigs for existing toolchains:<ul> 34887<li>goolfc 2017.01 34888 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4577">#4577</a>)</li> 34889</ul> 34890</li> 34891<li>added additional easyconfigs for various supported software 34892 packages, including:<ul> 34893<li>HDF5 1.10.1, NAMD 2.12, OpenFOAM 4.1, pandas 0.20.1, ParaView 34894 5.2.0, R 3.4.0, R-bundle-Bioconductor 3.5, Tensorflow 1.1.0</li> 34895</ul> 34896</li> 34897<li>minor enhancements, including:<ul> 34898<li>update source URLs in libpciaccess easyconfigs 34899 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3960">#3960</a>)</li> 34900<li>enable use of double precision floating point in METIS 5.1.0 34901 <code>foss/2016a</code> easyconfig 34902 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4555">#4555</a>)</li> 34903</ul> 34904</li> 34905</ul> 34906<h2 id="release_notes_eb320">EasyBuild v3.2.0 (May 5th 2017)<a class="headerlink" href="#release_notes_eb320" title="Permanent link">¶</a></h2> 34907<p>feature release</p> 34908<p><strong>framework</strong></p> 34909<ul> 34910<li>various enhancements, including:<ul> 34911<li>add support for marking installed module file as new default 34912 version using <code>--set-default-module</code> 34913 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2110">#2110</a>)</li> 34914<li>additional easyconfig parameters for documentation: <code>docpaths</code>, 34915 <code>examples</code>, <code>site_contacts</code>, <code>upstream_contacts</code>, <code>usage</code> 34916 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2113">#2113</a>)</li> 34917<li>add support for <code>--allow-use-as-root-and-accept-consequences</code> 34918 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2123">#2123</a>)</li> 34919<li>enable extraction of patches from compressed files before 34920 applying them 34921 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2128">#2128</a>)</li> 34922<li>alphabetically sort functions and methods in <code>module_generator</code> 34923 module 34924 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2132">#2132</a>)</li> 34925<li>introduce function <code>ensure_iterable_license_specs</code> 34926 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2157">#2157</a>)</li> 34927<li>bump Travis config to use Lmod 7.4 34928 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2176">#2176</a>)</li> 34929<li>implement <code>copy_dir</code> function in <code>filetools</code> 34930 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2177">#2177</a>)</li> 34931<li>clarify error message when no software-specific easyblock was 34932 found 34933 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2178">#2178</a>)</li> 34934<li>make <code>log.deprecated</code> more verbose by also printing deprecation 34935 warnings to stderr 34936 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2179">#2179</a>)</li> 34937<li>add <code>copy</code> function to <code>filetools</code> for easy copying of lists of 34938 files/directories 34939 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2180">#2180</a>)</li> 34940<li>add support for <code>--verify-easyconfig-filenames</code> 34941 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2185">#2185</a>)</li> 34942<li>add support for <code>--package-tool-options</code> 34943 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2187">#2187</a>)</li> 34944<li>take into account inline trailing comments in 34945 <code>fetch_parameters_from_easyconfig</code> 34946 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2192">#2192</a>)</li> 34947<li>add support for customising easyconfig parameters on a 34948 per-extension basis 34949 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2194">#2194</a>)</li> 34950<li>perform sanity check after stage 2 of EasyBuild bootstrap 34951 script, module file should be in place 34952 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2199">#2199</a>)</li> 34953<li>change order in which module commands are checked, consider Lmod 34954 first 34955 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2201">#2201</a>)</li> 34956</ul> 34957</li> 34958<li>various bug fixes, including:<ul> 34959<li>fix use of compiler-specific <code>--optarch</code> value in combination 34960 with <code>--job</code> 34961 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2183">#2183</a>)</li> 34962<li>call <code>run_all_steps</code> in regtest mode rather than running steps 34963 individually 34964 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2203">#2203</a>)</li> 34965</ul> 34966</li> 34967</ul> 34968<p><strong>easyblocks</strong></p> 34969<ul> 34970<li>added easyblocks for Doris 34971 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1154">#1154</a>, 34972 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1161">#1161</a>), 34973 VMD 34974 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1148">
34974#1148</a>) 34975 and WRF-Fire 34976 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1153">#1153</a>, 34977 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1159">#1159</a>)</li> 34978<li>minor enhancements, including:<ul> 34979<li>update <code>IntelBase</code>, PGI and TotalView easyblocks to allow list 34980 of license files/servers via '<code>license_file</code>' easyconfig 34981 parameter 34982 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1129">#1129</a>)</li> 34983<li>update Bowtie2 easyblock to set correct build options, copy more 34984 files, extend sanity check 34985 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1146">#1146</a>)</li> 34986<li>added the option to build Boost with multi-threading support 34987 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1147">#1147</a>)</li> 34988<li>allow libpng as OS dependency for WPS 34989 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1150">#1150</a>)</li> 34990<li>extend Boost <code>TIME_UTC</code> patch to Boost versions <= 1.49.0 34991 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1152">#1152</a>)</li> 34992<li>enhance Python sanity check to check for Tkinter support if Tk 34993 is included as a dependency 34994 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1156">#1156</a>, 34995 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1158">#1158</a>)</li> 34996<li>add support to install Python extensions without unpacking 34997 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1166">#1166</a>)</li> 34998<li>enhance TBB easyblock to also support building open source 34999 versions 35000 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1168">#1168</a>)</li> 35001</ul> 35002</li> 35003<li>various bug fixes, including:<ul> 35004<li>update FFTW easyblock: <code>--enable-avx-128-fma</code> depends on the 35005 <code>fma4</code> CPU feature (AMD), not <code>fma</code> 35006 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1142">#1142</a>)</li> 35007<li>fix problems when <code>usempi</code> not defined in toolchain in NAMD 35008 easyblock 35009 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1162">#1162</a>)</li> 35010</ul> 35011</li> 35012</ul> 35013<p><strong>easyconfigs</strong></p> 35014<ul> 35015<li>added example easyconfig files for 34 new software packages:<ul> 35016<li>ACTC 35017 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4386">#4386</a>), 35018 atomate 35019 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4484">#4484</a>), 35020 BreakDancer 35021 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4455">#4455</a>), 35022 bx-python 35023 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4486">#4486</a>), 35024 ClusterShell 35025 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4432">#4432</a>), 35026 custodian 35027 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4484">#4484</a>), 35028 DFTB+ 35029 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4398">#4398</a>), 35030 Doris 35031 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4404">#4404</a>), 35032 ED2 35033 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4402">#4402</a>), 35034 FireWorks 35035 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4484">#4484</a>), 35036 GETORB 35037 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4414">#4414</a>), 35038 GapFiller 35039 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4462">#4462</a>), 35040 IPy 35041 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4450">#4450</a>), 35042 imbalanced-learn 35043 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4373">#4373</a>), 35044 ipyrad 35045 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4507">#4507</a>), 35046 libiconv 35047 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4499">#4499</a>), 35048 MultiQC 35049 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3564">#3564</a>), 35050 NLopt 35051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1750">#1750</a>), 35052 Node-RED 35053 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4542">#4542</a>), 35054 PyCUDA 35055 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4523">#4523</a>), 35056 pymatgen-db 35057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4484">#4484</a>), 35058 QuTiP 35059 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4371">#4371</a>), 35060 ROI_PAC 35061 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4414">#4414</a>), 35062 Rascaf 35063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4459">#4459</a>), 35064 RepastHPC 35065 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4395">#4395</a>), 35066 rootpy 35067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4242">#4242</a>), 35068 SSPACE_Basic 35069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4461">#4461</a>), 35070 Sambamba 35071 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4442">#4442</a>), 35072 Spack 35073 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4431">#4431</a>), 35074 SpiceyPy 35075 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4406">#4406</a>), 35076 StaMPS 35077 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4454">#4454</a>), 35078 samblaster 35079 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4435">#4435</a>), 35080 VMD 35081 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4391">#4391</a>), 35082 WRF-Fire 35083 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4403">#4403</a>)</li> 35084</ul> 35085</li> 35086<li>
35086added additional easyconfigs for various supported software 35087 packages, including:<ul> 35088<li>BamTools 2.4.1, Boost 1.64.0, GCC 7.1.0, IPython 5.3.0, LLVM 35089 4.0.0, Mesa 17.0.2, Octave 4.2.1, OpenMPI 2.1.0, PETSc 3.7.5, 35090 PGI 17.3, Perl 5.24.1, Python 2.7.13 + 3.6.1 (incl. numpy 35091 1.12.1, scipy 0.19.0), R 3.3.3, SuiteSparse 4.5.5</li> 35092</ul> 35093</li> 35094<li>various enhancements, including:<ul> 35095<li>sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock 35096 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4380">#4380</a>)</li> 35097<li>use <code>pl2</code> source tarball for FFTW 3.3.6 which already includes 35098 patch for <code>F03</code> interface 35099 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4529">#4529</a>)</li> 35100</ul> 35101</li> 35102<li>various bug fixes, including:<ul> 35103<li>add missing XZ dep in easyconfig for libunwind 1.1 w/ 35104 <code>GCC/4.9.2</code>, sync <code>sanity_check_paths</code> across libunwind 35105 easyconfigs 35106 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4369">#4369</a>)</li> 35107<li>use '<code>use_fma4</code>' rather than deprecated '<code>use_fma</code>' 35108 easyconfig parameter in FFTW easyconfigs using <code>intel</code> toolchain 35109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4384">#4384</a>)</li> 35110<li>fix <code>pkgconfig</code> patch for Qhull 35111 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4451">#4451</a>)</li> 35112<li>also use patch for METIS 5.1.0 to enable use of doubles in 35113 easyconfig for <code>foss/2016b</code> 35114 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4467">#4467</a>)</li> 35115<li>add dependency NLopt for R extension <code>nloptr</code> 35116 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4481">#4481</a>)</li> 35117<li>fix issue with <code>configparser</code> and <code>backports</code> namespace blocking 35118 inclusion of <code>nbconvert</code> with IPython 35119 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4504">#4504</a>)</li> 35120<li>change source_urls of pycrypto to encrypted 35121 <code>https://pypi.python.org/...</code> 35122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4505">#4505</a>)</li> 35123<li>fix sources spec for HMMER 3.1b2 + minor style fixes + better 35124 sanity check 35125 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4531">#4531</a>)</li> 35126<li>also build IMB-IO in IMB 4.1 easyconfig using <code>foss/2016a</code> 35127 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4539">#4539</a>)</li> 35128</ul> 35129</li> 35130</ul> 35131<h2 id="release_notes_eb312">EasyBuild v3.1.2 (March 20th 2017)<a class="headerlink" href="#release_notes_eb312" title="Permanent link">¶</a></h2> 35132<p>bugfix/update release</p> 35133<p><strong>framework</strong></p> 35134<ul> 35135<li>fix broken packaging support by fixing <code>run_cmd</code> bug with 35136 <code>shell=False</code> 35137 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2153">#2153</a>)</li> 35138<li>minor enhancements, including:<ul> 35139<li>implement <code>change_dir</code> function in <code>filetools</code> module 35140 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2155">#2155</a>)</li> 35141<li>use <code>checker_state</code> in trailing whitespace style check + add 35142 dedicated test 35143 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2160">#2160</a>, 35144 <a href="https://github.com/easybuilders/easybuild-framework/pull/2169">#2169</a>)</li> 35145<li>consider both <code>pycodestyle</code> and <code>pep8</code> Python modules in style 35146 checks 35147 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2161">#2161</a>)</li> 35148<li>make bootstrap script aware various modules-related 35149 <code>$EASYBUILD_*</code> environment variables 35150 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2170">#2170</a>)</li> 35151</ul> 35152</li> 35153<li>various bug fixes, including:<ul> 35154<li>interpret statements that extend <code>$MODULEPATH</code> in 35155 <code>modpath_extensions_for</code> method 35156 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2104">#2104</a>)<ul> 35157<li>also fixes inclusion of superfluous load statements in 35158 modules installed in user HMNS module tree (cfr. 35159 <a href="https://github.com/easybuilders/easybuild-framework/pull/2172">#2172</a>)</li> 35160</ul> 35161</li> 35162<li>take into account that <code>$PATH</code> or <code>$PYTHONPATH</code> may be empty 35163 when running tests 35164 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2149">#2149</a>)</li> 35165<li>handle duplicates in <code>--include-*</code> 35166 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2151">#2151</a>)</li> 35167<li>exclude dependencies of dependencies that extend <code>$MODULEPATH</code> 35168 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2152">#2152</a>)</li> 35169<li>
35169add <code>ld.bfd</code> to RPATH wrappers 35170 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2156">#2156</a>)</li> 35171<li>fix <code>test_vsc_location</code>, <code>vsc.__file__</code> may not be available 35172 when <code>vsc</code> is installed as a namespace package 35173 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2159">#2159</a>)</li> 35174<li>fix reported problems with scripts & docs tests 35175 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2164">#2164</a>)</li> 35176<li>fix <code>--try-software-version</code> using non-greedy matching + 35177 lookahead assertion, add test for <code>tweak_one</code> 35178 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2166">#2166</a>)</li> 35179<li>avoid creating empty modulefile directories when using 35180 <code>modaltsoftname</code> 35181 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2168">#2168</a>)</li> 35182<li>fix <code>fftw_libs</code> for MKL without interface libraries 35183 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2171">#2171</a>)</li> 35184</ul> 35185</li> 35186</ul> 35187<p><strong>easyblocks</strong></p> 35188<ul> 35189<li>add easyblock for QScintilla 35190 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1127">#1127</a>)</li> 35191<li>minor enhancements, including:<ul> 35192<li>auto-disable quad precision on POWER and ARM in FFTW 35193 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1102">#1102</a>, 35194 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1138">#1138</a>)</li> 35195<li>allow "download install" for PETSc 35196 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1114">#1114</a>)</li> 35197<li>modify Trinity sanity check for versions 2.3 and above 35198 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1133">#1133</a>)</li> 35199<li>make unpacking Python extensions optional 35200 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1134">#1134</a>)</li> 35201<li>update SAMtools easyblock for version 1.4 35202 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1139">#1139</a>)</li> 35203</ul> 35204</li> 35205<li>various bug fixes, including:<ul> 35206<li>reduce number of environment variables in <code>icc</code> and <code>ifort</code> 35207 modules 35208 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1126">#1126</a>, 35209 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1143">#1143</a>)</li> 35210<li>also run tests with Tcl module syntax, Lua is the default in 35211 EasyBuild v3.x 35212 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1128">#1128</a>)</li> 35213<li>rename member variable to avoid conflict with member of base 35214 class in PGI 35215 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1137">#1137</a>)</li> 35216<li>don't set <code>$FPATH</code> environment variable in multiple easyblocks 35217 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1140">#1140</a>)</li> 35218</ul> 35219</li> 35220</ul> 35221<p><strong>easyconfigs</strong></p> 35222<ul> 35223<li>add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface 35224 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4334">#4334</a>)<ul> 35225<li>note that this warrants rebuilding FFTW that is a part of 35226 <code>foss/2017a</code></li> 35227</ul> 35228</li> 35229<li>added example easyconfig files for 14 new software packages:<ul> 35230<li>DBG2OLC 35231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4281">#4281</a>), 35232 disambiguate 35233 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4125">#4125</a>), 35234 fqtrim 35235 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4280">#4280</a>), 35236 GFOLD 35237 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4293">#4293</a>), 35238 Kaiju 35239 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4349">#4349</a>), 35240 LSMS 35241 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4335">#4335</a>), 35242 L_RNA_scaffolder 35243 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4282">#4282</a>), 35244 PileOMeth 35245 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4289">#4289</a>), 35246 psycopg2 35247 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4319">#4319</a>), 35248 QGIS 35249 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4307">#4307</a>, 35250 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4332">#4332</a>), 35251 QJson 35252 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4305">#4305</a>), 35253 QScintilla 35254 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4306">#4306</a>, 35255 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4313">#4313</a>), 35256 sketchmap 35257 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4360">#4360</a>), 35258 snaphu 35259 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4362">#4362</a>)</li> 35260</ul> 35261</li> 35262<li>
35262added additional easyconfigs for various supported software 35263 packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4</li> 35264<li>various enhancements, including:<ul> 35265<li>fix style in several easyconfigs 35266 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4267">#4267</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4271">#4271</a>, 35267 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4274">#4274</a>, 35268 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4275">#4275</a>, 35269 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4277">#4277</a>, 35270 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4279">#4279</a>, 35271 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4286">#4286</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4288">#4288</a>, 35272 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4318">#4318</a>)</li> 35273</ul> 35274</li> 35275<li>various bug fixes, including:<ul> 35276<li>correctly set <code>$PYTHONPATH</code> in ROOT easyconfigs 35277 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4239">#4239</a>, 35278 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4331">#4331</a>)</li> 35279<li>correct libjpeg turbo references in GDAL 35280 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4276">#4276</a>)</li> 35281<li>make sure that HDF5 provided via EasyBuild is used in BLASR 35282 easyconfigs 35283 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4278">#4278</a>)</li> 35284<li>fix issues with miRDeep2 installation 35285 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4291">#4291</a>, 35286 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4301">#4301</a>, 35287 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4316">#4316</a>)</li> 35288<li>also run tests with Tcl module syntax, Lua is the default in 35289 EasyBuild v3.x 35290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4315">#4315</a>)</li> 35291<li>fix PostgreSQL homepage + minor style fixes 35292 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4318">#4318</a>)</li> 35293<li>detect use of '<code>$root</code>', which is not compatible with module 35294 files in Lua syntax 35295 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4330">#4330</a>)</li> 35296<li>fix <code>homepage</code>/<code>source_urls</code> for ViennaRNA 35297 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4338">#4338</a>)</li> 35298<li>pass down <code>$FFLAGS</code> via <code>FLAGS_OPT</code> in SWASH easyconfigs 35299 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4341">#4341</a>)</li> 35300<li>remove <code>include/GL/wglext.h</code> from Mesa sanity check 35301 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4354">#4354</a>)</li> 35302<li>rename <code>S.A.G.E.</code> to <code>SAGE</code>, can't have directories with 35303 trailing dot in Windows 35304 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4368">#4368</a>)</li> 35305</ul> 35306</li> 35307</ul> 35308<h2 id="release_notes_eb311">EasyBuild v3.1.1 (March 7th 2017)<a class="headerlink" href="#release_notes_eb311" title="Permanent link">¶</a></h2> 35309<p>bugfix/update release</p> 35310<p><strong>framework</strong></p> 35311<ul> 35312<li>minor enhancements, including:<ul> 35313<li>print more useful error message when no compiler-specific 35314 <code>optarch</code> flag is defined 35315 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1950">#1950</a>)</li> 35316<li>add <code>ec</code> parameter to <code>expand_toolchain_load()</code> 35317 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2103">#2103</a>)</li> 35318<li>clarify unstable/closed PR warning message 35319 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2129">#2129</a>)</li> 35320</ul> 35321</li> 35322<li>various bug fixes, including:<ul> 35323<li>ensure that <code>$EBEXTSLIST*</code> is also included in generated module 35324 under <code>--module-only</code> 35325 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2112">#2112</a>)</li> 35326<li>fix formatting issues in generated documentation for 35327 <code>--list-software</code> and <code>--avail-easyconfig-licenses</code> 35328 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2121">#2121</a>)</li> 35329<li>fix problem with backticks in description breaking '<code>fpm</code>' 35330 packaging command 35331 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2124">#2124</a>)</li> 35332<li>replace <code>--enable-new-dtags</code> with <code>--disable-new-dtags</code> instead 35333 of removing it in RPATH wrapper script 35334 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2131">#2131</a>)</li> 35335<li>only perform <code>is_short_modname_for</code> sanity check in 35336 <code>det_short_module_name</code> if <code>modaltsoftname</code> is available 35337 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2138">#2138</a>)</li> 35338<li>fix logic in <code>make_module_dep</code> w.r.t. excluding loads for 35339 toolchain & toolchain components 35340 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2140">#2140</a>)</li> 35341<li>skip <code>test_check_style</code> if <code>pep8</code> is not available 35342 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2142">#2142</a>)</li> 35343</ul> 35344</li> 35345</ul> 35346<p><strong>easyblocks</strong></p> 35347<ul> 35348<li>minor enhancements, including:<ul> 35349<li>change the sanity check for MCR 2016b since the directory 35350 structure has changed 35351 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1096">#1096</a>)</li> 35352<li>update NWChem easyblock for version 6.6.x and to handle 35353 different versions of OpenMPI for older versions 35354 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1104">#1104</a>)</li> 35355<li>allow per-component <code>source_urls</code> with templating in <code>Bundle</code> 35356 easyblock 35357 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1108">#1108</a>)</li> 35358<li>
35358add slib to <code>$LD_LIBRARY_PATH</code> for itac 35359 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1112">#1112</a>)</li> 35360<li>consider both <code>lib</code> and <code>lib64</code> in CGAL sanity check 35361 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1113">#1113</a>)</li> 35362<li>add support for installing Intel tools that do not require 35363 license at installation time 35364 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1117">#1117</a>)<ul> 35365<li>required for Intel MPI and Intel MKL version 2017.2.174</li> 35366</ul> 35367</li> 35368<li>remove <code>prefix_opt</code> as custom easyconfig parameter for Qt 35369 easyblock 35370 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1120">#1120</a>)</li> 35371</ul> 35372</li> 35373<li>various bug fixes, including:<ul> 35374<li>use '<code>-prefix <path></code>' rather than '<code>--prefix=<path></code>' for 35375 <code>configure</code> in Qt 35376 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1109">#1109</a>)</li> 35377<li>fix indentation problem in PETSc easyblock 35378 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1111">#1111</a>)</li> 35379</ul> 35380</li> 35381</ul> 35382<p><strong>easyconfigs</strong></p> 35383<ul> 35384<li>added example easyconfig files for 16 new software packages:<ul> 35385<li>Caffe 35386 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3667">#3667</a>), 35387 DIAMOND 35388 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4107">#4107</a>), 35389 fmt 35390 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4131">#4131</a>), 35391 googletest 35392 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4132">#4132</a>), 35393 igraph 35394 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4172">#4172</a>), 35395 MEGA 35396 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4202">#4202</a>), 35397 meRanTK 35398 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4175">#4175</a>), 35399 meshio 35400 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4178">#4178</a>), 35401 miRDeep2 35402 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4229">#4229</a>, 35403 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4255">#4255</a>), 35404 OOMPA 35405 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4211">#4211</a>), 35406 PBSuite 35407 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4224">#4224</a>, 35408 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4230">#4230</a>), 35409 randfold 35410 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4217">#4217</a>), 35411 skewer 35412 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4246">#4246</a>), 35413 Smoldyn 35414 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4110">#4110</a>), 35415 SpiecEasi 35416 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4215">#4215</a>), 35417 stress 35418 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4180">#4180</a>)</li> 35419</ul> 35420</li> 35421<li>added additional easyconfigs for various supported software 35422 packages, including:<ul> 35423<li>binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 35424 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0, PCRE 8.40, 35425 Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 35426 2017.01a</li> 35427</ul> 35428</li> 35429<li>added new easyconfigs for existing toolchains:<ul> 35430<li><code>iomkl/2017a</code> 35431 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4216">#4216</a>), 35432 <code>intel/2017.02</code> 35433 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4248">#4248</a>)</li> 35434</ul> 35435</li> 35436<li>various enhancements, including:<ul> 35437<li>fix style in several easyconfigs 35438 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4174">#4174</a>, 35439 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4176">#4176</a>, 35440 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4190">#4190</a>, 35441 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4233">#4233</a>)</li> 35442<li>
35442add sanity check command to Yade easyconfig to make sure that 35443 '<code>import yade</code>' works, include bzip2 as dep 35444 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4193">#4193</a>)</li> 35445<li>add <code>PDF::API2</code> extension to Perl 5.24.0 easyconfigs + sync 35446 <code>exts_list</code> 35447 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4221">#4221</a>)</li> 35448</ul> 35449</li> 35450<li>various bug fixes, including:<ul> 35451<li>add Bison and gettext as build deps for X11 35452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4111">#4111</a>)</li> 35453<li>clean up dependencies in libdrm 35454 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4113">#4113</a>)</li> 35455<li>make sure Ghostscript picks up external libraries 35456 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4118">#4118</a>)</li> 35457<li>fix ippicv source download and library install for OpenCV v3.1.0 35458 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4126">#4126</a>)</li> 35459<li>fix software name for OrthoMCL + modernise OrthoMCL easyconfigs 35460 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4134">#4134</a>, 35461 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4135">#4135</a>)</li> 35462<li>get rid of backticks in gettext descriptions, causes problems 35463 when packaging with FPM 35464 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4146">#4146</a>)</li> 35465<li>remove duplicate sources specification in OpenMPI 35466 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4150">#4150</a>)</li> 35467<li>fix definition of <code>buildopts</code>/<code>installopts</code> in Cantera 35468 easyconfig 35469 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4133">#4133</a>, 35470 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4164">#4164</a>, 35471 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4177">#4177</a>)</li> 35472<li>use <code>http://</code> rather than <code>ftp://</code> source URLs in CFITSIO 35473 easyconfigs 35474 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4167">#4167</a>)</li> 35475<li>add patch for XZ 5.2.2 to include <code>5.1.2alpha</code> symbols required 35476 by '<code>rpm</code>' command on CentOS 7.x 35477 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4179">#4179</a>)</li> 35478<li>add patch for Boost v1.61-1.63 to fix problem with 35479 <code>make_array</code>/<code>array_wrapper</code> in Boost serialization library 35480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4192">#4192</a>)</li> 35481<li>set <code>CMAKE_PREFIX_PATH</code> to ncurses install directory in CMake 35482 easyconfigs 35483 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4196">#4196</a>)</li> 35484<li>switch to <code>lowopt=True</code> for libxc v2.2.* and v3.* 35485 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4199">#4199</a>)</li> 35486<li>remove custom <code>sanity_check_paths</code>, since it's identical to 35487 that used by the R easyblock 35488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4200">#4200</a>)</li> 35489<li>fix <code>version</code> (& <code>homepage</code>) in ea-utils easyconfigs 35490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4205">#4205</a>)</li> 35491<li>remove <code>--with-threads</code> configure option in OpenMPI-2.* 35492 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4213">#4213</a>)</li> 35493<li>fix check for Szip library in configure script for netCDF 4.1.3 35494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4226">#4226</a>)</li> 35495</ul> 35496</li> 35497<li>fix <code>source_urls</code> in several easyconfigs, including:<ul> 35498<li>bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, 35499 Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion 35500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4227">#4227</a>)</li> 35501</ul> 35502</li> 35503</ul> 35504<h2 id="release_notes_eb310">EasyBuild v3.1.0 (February 3rd 2017)<a class="headerlink" href="#release_notes_eb310" title="Permanent link">¶</a></h2> 35505<p>feature release</p> 35506<p><strong>framework</strong></p> 35507<ul> 35508<li>various enhancements, including:<ul> 35509<li>ARM: GCC optimal/generic architecture compiler flags 35510 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1974">#1974</a>)</li> 35511<li>
35511add support for <code>--check-style</code> to check style in easyconfig 35512 files 35513 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1618">#1618</a>, 35514 <a href="https://github.com/easybuilders/easybuild-framework/pull/2038">#2038</a>)</li> 35515<li>add <code>HOME</code> and <code>USER</code> from env to available cfg file constants 35516 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2063">#2063</a>)</li> 35517<li><code>--optarch</code> can now be specified on a toolchain basis 35518 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2071">#2071</a>)</li> 35519<li>implement <code>get_cpu_features</code> function in systemtools 35520 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2074">#2074</a>, 35521 <a href="https://github.com/easybuilders/easybuild-framework/pull/2078">#2078</a>)</li> 35522<li>support use of <code>linalg</code> without MPI, add <code>iimkl</code> toolchain 35523 definition 35524 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2082">#2082</a>)</li> 35525<li>spoof HTTP request header with empty agent 35526 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2083">#2083</a>)</li> 35527<li>exclude dependencies of dependencies that extend $MODULEPATH in 35528 make_module_dep 35529 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2091">#2091</a>)</li> 35530</ul> 35531</li> 35532<li>various bug fixes, including:<ul> 35533<li>make <code>fetch_github_token</code> more robust against <code>RuntimeError</code> 35534 from <code>keyring</code> 35535 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2070">#2070</a>)</li> 35536<li>POWER: Fix <code>--optarch=GENERIC</code> for GCC 35537 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2073">#2073</a>)</li> 35538<li>fix docstring in toolchain class 35539 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2075">#2075</a>)</li> 35540<li>skip test cases involving <code>.yeb</code> if <code>PyYAML</code> is not installed, 35541 silence test in options subsuite 35542 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2081">#2081</a>)</li> 35543<li>fix traceback with '<code>eb --check-github</code>' if <code>GitPython</code> is not 35544 installed 35545 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2085">#2085</a>)</li> 35546<li>fix regex for determining list of patched files in GitHub diff 35547 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2088">#2088</a>)</li> 35548<li>modify robot so that it only appends dependencies of tweaked 35549 easyconfigs 35550 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2090">#2090</a>)</li> 35551<li>escape metacharacters in paths passed to <code>re.compile</code> in 35552 <code>dry_run_set_dirs</code> 35553 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2098">#2098</a>)</li> 35554<li>fix broken error message in <code>get_toolchain_hierarchy</code> + 35555 dedicated test case 35556 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2099">#2099</a>)</li> 35557</ul> 35558</li> 35559</ul> 35560<p><strong>easyblocks</strong></p> 35561<ul> 35562<li>new easyblock for FFTW 35563 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1083">#1083</a>)</li> 35564<li>various enhancements, including:<ul> 35565<li>update sanity check for flex 2.6.3, no more <code>libfl_pic.a</code> 35566 library 35567 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1077">#1077</a>)</li> 35568<li>cleanup build before proceeding with full Boost 35569 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1080">#1080</a>)</li> 35570<li>update CP2K easyblock: copy data dir, support version 4.1, 35571 support ELPA, fix psmp build with foss toolchain 35572 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/996">#996</a>, 35573 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1020">#1020</a>, 35574 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1043">#1043</a>, 35575 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1084">#1084</a>)</li> 35576<li>add sanity check support for OpenSSL 1.1 35577 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1087">#1087</a>)</li> 35578<li>support the latest changes in Inspector 2017 35579 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1047">#1047</a>)</li> 35580<li>update NEURON easyblock to support the lack of <code>hoc_ed</code> in 7.4 35581 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/987">#987</a>)</li> 35582<li>
35582add support for WPS 3.8 35583 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1079">#1079</a>)</li> 35584<li>also consider <code>setuptools</code> in <code>EasyBuildMeta</code> easyblock 35585 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1093">#1093</a>)</li> 35586</ul> 35587</li> 35588<li>various bug fixes, including:<ul> 35589<li>(correctly) define <code>$ROSETTA3_DB</code> in Rosetta easyblock 35590 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1092">#1092</a>)</li> 35591</ul> 35592</li> 35593</ul> 35594<p><strong>easyconfigs</strong></p> 35595<ul> 35596<li>added easyconfigs for <code>foss/2017a</code> and <code>intel/2017a</code> common 35597 toolchains 35598 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3968">#3968</a>, 35599 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3969">#3969</a>)</li> 35600<li>added example easyconfig files for 16 new software packages:<ul> 35601<li>ack 35602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3983">#3983</a>), 35603 cclib 35604 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4065">#4065</a>), 35605 ConnectomeWorkbench 35606 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3411">#3411</a>), 35607 GroIMP 35608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3994">#3994</a>), 35609 hyperspy 35610 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3991">#3991</a>), 35611 I-TASSER 35612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1216">#1216</a>), 35613 ImageJ 35614 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4023">#4023</a>, 35615 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4062">#4062</a>), 35616 libconfig 35617 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4051">#4051</a>), 35618 libspatialindex 35619 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4002">#4002</a>), 35620 mahotas 35621 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3990">#3990</a>), 35622 Minia 35623 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3949">#3949</a>), 35624 muParser 35625 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4007">#4007</a>), 35626 NetLogo 35627 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3941">#3941</a>), 35628 QIIME 35629 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3868">#3868</a>), 35630 QwtPolar 35631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4019">#4019</a>), 35632 Tensorflow 35633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4084">#4084</a>, 35634 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4095">#4095</a>)</li> 35635</ul> 35636</li> 35637<li>added additional easyconfigs for various supported software 35638 packages, including:<ul> 35639<li>Boost 1.62.0 + 1.63.0, CP2K 4.1, GSL 2.3, PLUMED 2.3.0, Qt5 35640 5.7.1, WRF 3.8, WPS 3.8, Yade 2016.06a, zlib 1.2.11</li> 35641</ul> 35642</li> 35643<li>various enhancements, including:<ul> 35644<li>update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable 35645 running of tests 35646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3985">#3985</a>)</li> 35647<li>add FME extensions (+ deps) in R 3.3.1 easyconfigs 35648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4063">#4063</a>)</li> 35649</ul> 35650</li> 35651<li>various bug fixes, including:<ul> 35652<li>add libxml2 dependency on HDF5 35653 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3759">#3759</a>)</li> 35654<li>remove unnecessary dependency in libmatheval 35655 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3988">#3988</a>)</li> 35656<li>fix permissions on SWASH binaries 35657 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4003">#4003</a>)</li> 35658<li>add conda-forge channel to perl-app-cpanminus 35659 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4012">#4012</a>)</li> 35660<li>add missing deps (libpthread-stubs, libpciaccess) to libdrm 35661 2.4.70 35662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4032">#4032</a>)</li> 35663<li>modloadmsg style fixes in multiple easyconfigs 35664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4035">#4035</a>)</li> 35665<li>include X11 as dep for Molden 35666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4082">#4082</a>)</li> 35667<li>remove incorrect definition for $ROSETTA3_DB, now (correctly) 35668 defined via Rosetta easyblock 35669 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4083">#4083</a>)</li> 35670</ul> 35671</li> 35672<li>fix source URLs for several easyconfigs, including:<ul> 35673<li>arpack-ng 3.1.3 + 3.1.5 35674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4050">#4050</a>), 35675 ChIP-Seq 1.5-1 35676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4050">#4050</a>), 35677 Ghostscript 9.10, 9.14 + 9.16 35678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4050">#4050</a>), 35679 Git 1.7.12, 1.8.2 + 1.8.3.1 35680 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4050">#4050</a>), 35681 HBase 1.0.2 35682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4043">#4043</a>), 35683 libevent 2.0.22 35684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4037">#4037</a>), 35685 libsodium 1.0.3 35686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4046">#4046</a>), 35687 lynx 2.8.7 35688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4050">#4050</a>), 35689 Maven 3.2.2 and 3.3.3 35690 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4039">#4039</a>), 35691 MEME 4.8.0 35692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4050">#4050</a>), 35693 PCC 20131024 35694 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4044">#4044</a>), 35695 S-Lang 2.3.0 35696 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4045">#4045</a>), 35697 Spark 1.3.0 35698 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4041">#4041</a>), 35699 splitRef 0.0.2 35700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/4040">#4040</a>)</li> 35701</ul> 35702</li> 35703</ul> 35704<h2 id="release_notes_eb302">EasyBuild v3.0.2 (December 22nd 2016)<a class="headerlink" href="#release_notes_eb302" title="Permanent link">¶</a></h2> 35705<p>bugfix release</p> 35706<p><strong>framework</strong></p> 35707<ul> 35708<li>various bug fixes, including:<ul> 35709<li>
35709also skip dependencies of dependencies marked as external module 35710 in get_toolchain_hierarchy 35711 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2042">#2042</a>)</li> 35712<li>disable verbose setvar in modules.py 35713 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2044">#2044</a>)</li> 35714<li>force copying of easyconfigs in --new-pr/--update-pr, even 35715 when combined with -x 35716 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2045">#2045</a>)</li> 35717<li>fix verification of filename for easyconfigs used to resolve 35718 deps 35719 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2051">#2051</a>)</li> 35720<li>skip RPATH sanity check when toolchain did not use RPATH 35721 wrappers 35722 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2052">#2052</a>)</li> 35723<li>check whether file-like paths are readable before reading them 35724 in systemtools module 35725 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2065">#2065</a>)</li> 35726</ul> 35727</li> 35728<li>various small enhancements, including:<ul> 35729<li>add 'rpath' toolchain option to selectively disable use of 35730 RPATH wrappers 35731 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2047">#2047</a>)</li> 35732</ul> 35733</li> 35734</ul> 35735<p><strong>easyblocks</strong></p> 35736<ul> 35737<li>various enhancements, including:<ul> 35738<li>enhance DL_POLY_Classic easyblock to support building with 35739 Plumed support (REVIEW) 35740 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/829">#829</a>)</li> 35741<li>make the Allinea easyblock search for the templates in the 35742 easyconfig paths 35743 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1025">#1025</a>)</li> 35744<li>make FortranPythonPackage aware of (pre)buildopts 35745 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1065">#1065</a>)</li> 35746<li>update sanity check for Mono to support recent versions 35747 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1069">#1069</a>)</li> 35748<li>fix Eigen sanity check for latest version 3.3.1 35749 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1074">#1074</a>)</li> 35750</ul> 35751</li> 35752<li>various bug fixes, including:<ul> 35753<li>skip RPATH sanity check for binary installations 35754 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1056">#1056</a>)</li> 35755<li>pass CXXFLAGS and LDFLAGS to Boost bjam 35756 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1064">#1064</a>)</li> 35757<li>make pip ignore already installed versions of the package being 35758 installed 35759 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1066">#1066</a>)</li> 35760<li>don't pass empty string as custom installopts for numpy in 35761 test_step 35762 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1067">#1067</a>)</li> 35763<li>make the Rosetta EasyBlock work in --module-only mode 35764 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1073">#1073</a>)</li> 35765</ul> 35766</li> 35767</ul> 35768<p><strong>easyconfigs</strong></p> 35769<ul> 35770<li>added example easyconfig files for 13 new software packages:<ul> 35771<li>CryptoMiniSat 35772 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3952">#3952</a>), 35773 MATSim 35774 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3902">#3902</a>), 35775 Molcas 35776 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2084">#2084</a>), 35777 ne 35778 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3376">#3376</a>), 35779 psmc 35780 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3910">#3910</a>), 35781 PyCogent 35782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3897">#3897</a>), 35783 PyNAST 35784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3897">#3897</a>), 35785 RASPA2 35786 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3903">#3903</a>, 35787 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3946">#3946</a>), 35788 SimPEG 35789 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3876">#3876</a>), 35790 SolexaQA++ 35791 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3892">#3892</a>), 35792 taco 35793 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3882">#3882</a>), 35794 UCLUST 35795 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3896">#3896</a>), 35796 USPEX 35797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3767">#3767</a>)</li> 35798</ul> 35799</li> 35800<li>
35800added additional easyconfigs for various supported software 35801 packages, including:<ul> 35802<li>Mono 4.6.2.7, PGI 16.10, ROOT 6.08.02</li> 35803</ul> 35804</li> 35805<li>various enhancements, including:<ul> 35806<li>trivial style fixes 35807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3878">#3878</a>, 35808 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3893">#3893</a>, 35809 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3895">#3895</a>)</li> 35810</ul> 35811</li> 35812<li>various bug fixes, including:<ul> 35813<li>add X11 develop libs to ncview easyconfig 35814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3881">#3881</a>)</li> 35815<li>fix source_urls in pkg-config easyconfigs 35816 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3907">#3907</a>)</li> 35817<li>install numpy/scipy as .egg to ensure shadowing of numpy/scipy 35818 in parent Python installation 35819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3921">#3921</a>)</li> 35820<li>fix broken source URL + homepage for Infernal 35821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3928">#3928</a>)</li> 35822<li>fix test that verifies dumped easyconfig, take into account that 35823 dumped dependencies may include hardcoded dependency 35824 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3932">#3932</a>)</li> 35825<li>include libGLU as dependency in freeglut easyconfigs with recent 35826 Mesa 35827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3936">#3936</a>)</li> 35828<li>add patch for FreeSurfer to fix issue with MATLAB 2013 35829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3954">#3954</a>)</li> 35830</ul> 35831</li> 35832</ul> 35833<h2 id="release_notes_eb301">EasyBuild v3.0.1 (November 30th 2016)<a class="headerlink" href="#release_notes_eb301" title="Permanent link">¶</a></h2> 35834<p>bugfix release</p> 35835<p><strong>framework</strong></p> 35836<ul> 35837<li>important changes<ul> 35838<li>always use Intel-specific MPI compiler wrappers (<code>mpiicc</code>, 35839 <code>mpiicpc</code>, <code>mpiifort</code>) for toolchains using both Intel compilers 35840 and Intel MPI 35841 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2005">#2005</a>)</li> 35842</ul> 35843</li> 35844<li>various small enhancements, including:<ul> 35845<li>use <code>setvar</code> in <code>modules.py</code> to define environment variables 35846 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2011">#2011</a>)</li> 35847<li>include output of <code>sanity_check_commands</code> in the build log 35848 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2020">#2020</a>)</li> 35849</ul> 35850</li> 35851<li>various bug fixes, including:<ul> 35852<li>fix testing of bootstrap script in Travis config 35853 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2003">#2003</a>)</li> 35854<li>use correct module syntax in bootstrap script if Lmod is not 35855 used (i.e. Tcl) 35856 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2007">#2007</a>)</li> 35857<li>fix packaging issue with non-Python scripts in easybuild/scripts 35858 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2015">#2015</a>)<ul> 35859<li>fixes issue where RPATH wrapper template script 35860 (<code>rpath_wrapper_template.sh.in</code>) was not included in the 35861 v3.0.0 release</li> 35862</ul> 35863</li> 35864<li>make tests more robust against running headless 35865 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2016">#2016</a>)</li> 35866<li>avoid rewrapping already wrapped compiler/linker command with 35867 RPATH wrapper script 35868 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2022">#2022</a>)</li> 35869<li>fix <code>log.error</code> traceback due to '<code>raise EasyBuildError</code>' 35870 involving a '<code>%s</code>' in error message 35871 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2024">#2024</a>)</li> 35872<li>make sure '<code>modules_tool</code>' attribute is also defined for 35873 extensions 35874 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2026">#2026</a>)</li> 35875<li>only dump easyconfig with modified deps due to 35876 <code>--minimal-toolchains</code> to 'reprod' subdir of install dir 35877 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2028">#2028</a>)</li> 35878<li>avoid appending '<code>-h'</code> to sanity check commands specified as a 35879 string 35880 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2030">#2030</a>)</li> 35881<li>fix bug in <code>
35881list_software_rst</code>: always include version suffix 35882 regardless of value 35883 (<a href="https://github.com/easybuilders/easybuild-framework/pull/2032">#2032</a>)</li> 35884</ul> 35885</li> 35886</ul> 35887<p><strong>easyblocks</strong></p> 35888<ul> 35889<li>various enhancements, including:<ul> 35890<li>update SAMtools easyblock for recent versions 35891 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1048">#1048</a>)</li> 35892</ul> 35893</li> 35894<li>various bugfixes, including:<ul> 35895<li>fix QuantumESPRESSO easyblock to handle gipaw correctly 35896 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1041">#1041</a>)</li> 35897<li>always specify name of serial Fortran compiler to ALADIN, it 35898 already knows to use MPI wrapper commands 35899 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1050">#1050</a>)</li> 35900</ul> 35901</li> 35902</ul> 35903<p><strong>easyconfigs</strong></p> 35904<ul> 35905<li>added example easyconfig files for 7 new software packages:<ul> 35906<li>Cookiecutter 35907 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3827">#3827</a>), 35908 ETE 35909 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3857">#3857</a>), 35910 findhap 35911 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3860">#3860</a>), 35912 graphviz (Python bindings, 35913 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3826">#3826</a>), 35914 LoFreq 35915 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3856">#3856</a>), 35916 PhyloBayes-MPI 35917 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3859">#3859</a>), 35918 XGBoost 35919 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3849">#3849</a>)</li> 35920</ul> 35921</li> 35922<li>added additional easyconfigs for various supported software packages</li> 35923<li>various enhancements, including:<ul> 35924<li>add <code>ipywidgets</code> and <code>widgetsnbextension</code> extensions to IPython 35925 5.1.0 easyconfigs 35926 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3818">#3818</a>, 35927 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3823">#3823</a>)</li> 35928<li>run dadi test suite as a sanity check command 35929 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3858">#3858</a>)</li> 35930</ul> 35931</li> 35932<li>various bug fixes, including:<ul> 35933<li>fix incorrect descriptions for ifort 35934 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3817">#3817</a>)</li> 35935<li>fix <code>modulename</code> for Jinja2 and Pygments 35936 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3823">#3823</a>)</li> 35937<li>fix download URL in BLAST 2.2.26 easyconfig 35938 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3861">#3861</a>)</li> 35939</ul> 35940</li> 35941</ul> 35942<h2 id="release_notes_eb300">EasyBuild v3.0.0 (November 16th 2016)<a class="headerlink" href="#release_notes_eb300" title="Permanent link">¶</a></h2> 35943<p>feature release</p> 35944<p><strong>framework</strong></p> 35945<ul> 35946<li>backward-incompatible changes:<ul> 35947<li>make robot always consider subtoolchains, even without 35948 <code>--minimal-toolchains</code> (but in reverse order) 35949 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1973">#1973</a>)</li> 35950<li>clean up behaviour that was deprecated for EasyBuild v3.0 35951 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1978">#1978</a>)</li> 35952<li>change <em>default</em> config to use <code>Lmod</code>/<code>Lua</code> for modules 35953 tool/syntax, <code>GC3Pie</code> as job backend 35954 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1985">#1985</a>)</li> 35955<li>the minimal required version of Lmod was bumped to 5.8 35956 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1985">#1985</a>)</li> 35957</ul> 35958</li> 35959<li>major new features:<ul> 35960<li>(experimental) support for RPATH linking via <code>--rpath</code> 35961 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1942">#1942</a>)<ul> 35962<li>see 35963 <a href="http://easybuild.readthedocs.org/en/latest/RPATH-support.html">http://easybuild.readthedocs.org/en/latest/RPATH-support.html</a></li> 35964</ul> 35965</li> 35966<li>
35966add support for <code>--consider-archived-easyconfigs</code> 35967 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1972">#1972</a>)<ul> 35968<li>see 35969 <a href="http://easybuild.readthedocs.org/en/latest/Archived-easyconfigs.html">http://easybuild.readthedocs.org/en/latest/Archived-easyconfigs.html</a></li> 35970</ul> 35971</li> 35972<li>stabilize <code>--new-pr</code> and <code>--update-pr</code> 35973 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1979">#1979</a>)<ul> 35974<li>see 35975 <a href="http://easybuild.readthedocs.org/en/latest/Integration_with_GitHub.html">http://easybuild.readthedocs.org/en/latest/Integration_with_GitHub.html</a></li> 35976</ul> 35977</li> 35978</ul> 35979</li> 35980<li>various other small enhancements, including:<ul> 35981<li>add support for '<code>devel</code>' log level 35982 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1815">#1815</a>)</li> 35983<li>make <code>remove_file</code> aware of <code>--extended-dry-run</code> + add dedicated 35984 unit test 35985 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1932">#1932</a>)</li> 35986<li>add support for filtering out setting/updating particular 35987 environment variables from generated modules 35988 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1943">#1943</a>)<ul> 35989<li>see <code>--filter-env-vars</code></li> 35990</ul> 35991</li> 35992<li>clean up output of EasyBuild bootstrap script & add version 35993 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1944">#1944</a>)</li> 35994<li>improved ARM platform/CPU detection 35995 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1953">#1953</a>)</li> 35996<li>use '<code>0</code>' as letter dir for funky software names that don't 35997 start with a letter, e.g., <code>3to2</code> 35998 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1954">#1954</a>)</li> 35999<li>make bootstrap script aware of <code>vsc-install</code> for offline 36000 installation 36001 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1955">#1955</a>)</li> 36002<li>add support for <code>blas_family()</code> and <code>lapack_family()</code> methods in 36003 <code>Toolchain</code> instances 36004 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1961">#1961</a>)</li> 36005<li>make <code>copy_file</code> dry-run aware 36006 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1963">#1963</a>)</li> 36007<li>reorganise test easyconfigs to match structure in easyconfigs 36008 repo 36009 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1970">#1970</a>)</li> 36010<li>add a toolchain compiler option for enforcing IEEE-754 36011 conformance 36012 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1975">#1975</a>)</li> 36013<li>support for <code>intelcuda</code> compiler toolchain 36014 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1976">#1976</a>)</li> 36015<li>check that each glob pattern matches at least one file 36016 <code>expand_glob_paths</code> (important for <code>--include-*</code>) 36017 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1980">#1980</a>)</li> 36018<li>enhance bootstrap to auto-skip stage 0 in case a suitable 36019 setuptools is already available 36020 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1946">#1946</a>, 36021 <a href="https://github.com/easybuilders/easybuild-framework/pull/1984">#1984</a>)</li> 36022<li>simplify <code>GC3Pie</code> version check 36023 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1987">#1987</a>)</li> 36024<li>include suggestion on how to change configuration w.r.t. modules 36025 tool/syntax 36026 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1989">#1989</a>)</li> 36027</ul> 36028</li> 36029<li>various bug fixes, including:<ul> 36030<li>fix test for <code>find_easybuild_easyconfig</code> 36031 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1931">#1931</a>)</li> 36032<li>remove existing module file under <code>--force</code>/<code>--rebuild</code> 36033 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1933">#1933</a>)</li> 36034<li>fix combining <code>--search</code> and <code>--try-*</code> 36035 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1937">#1937</a>)</li> 36036<li>fix appending to existing <code>buildstats</code> in 36037 <code>FileRepository.add_easyconfig</code> 36038 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1948">#1948</a>)</li> 36039<li>fix handling of iterate easyconfig parameters, restore them 36040 during cleanup 36041 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1949">#1949</a>)</li> 36042<li>fix filtering loads for (hidden) build deps from generated 36043 module 36044 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1959">#1959</a>)</li> 36045<li>handle multi-flag compiler options on all types of options 36046 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1966">#1966</a>)</li> 36047<li>fix <code>--list-software</code> by making <code>letter_dir_for</code> function aware 36048 of '<code>*</code>' wildcard name 36049 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1969">#1969</a>)</li> 36050<li>
36050skip dependencies of toolchain marked as external modules when 36051 determining module hierarchy 36052 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1977">#1977</a>)</li> 36053<li>bump page limit in <code>fetch_latest_commit_sha</code>, spit out more 36054 meaningful error if too many branches were encountered 36055 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1981">#1981</a>)</li> 36056<li>fix CUDA-related issues in <code>HierarchicalMNS</code> 36057 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1986">#1986</a>)</li> 36058</ul> 36059</li> 36060</ul> 36061<p><strong>easyblocks</strong></p> 36062<ul> 36063<li>backwards incompatible changes:<ul> 36064<li>remove deprecated GenomeAnalysisTK/GATK easyblock 36065 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1001">#1001</a>)</li> 36066<li>remove deprecated '<code>get_netcdf_module_set_cmds</code>' function from 36067 netCDF easyblock 36068 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1015">#1015</a>)</li> 36069<li>remove deprecated '<code>get_blas_lib</code>' function from LAPACK 36070 easyblock 36071 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1016">#1016</a>)</li> 36072<li>remove <code>QLogicMPI</code> easyblock 36073 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1023">#1023</a>)</li> 36074</ul> 36075</li> 36076<li>new easyblock for installing Anaconda 36077 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/950">#950</a>)</li> 36078<li>add generic easyblock for Conda installations 36079 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/950">#950</a>)</li> 36080<li>various enhancements, including:<ul> 36081<li>enable use of <code>GCCcore</code> as toolchain for Clang, fail if no GCC 36082 prefix is found 36083 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1002">#1002</a>)</li> 36084<li>also build Boost MPI library in parallel 36085 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1005">#1005</a>, 36086 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1038">#1038</a>)</li> 36087<li>enhance g2clib easyblock to allow to install 1.6.0 or higher 36088 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1006">#1006</a>)</li> 36089<li>update QuantumESPRESSO easyblock to support packaging changes in 36090 6.0 36091 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1007">#1007</a>)</li> 36092<li>add support to <code>Scons</code> generic easyblock to provide argument to 36093 specify installation prefix 36094 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1008">#1008</a>)</li> 36095<li>update <code>IntelBase</code> and imkl easyblocks to handle the 2017 36096 versions of compilers/imkl 36097 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1012">#1012</a>)</li> 36098<li>leverage <code>toolchain.linalg</code> functionality in ScaLAPACK 36099 easyblock, use <code>copy_file</code> 36100 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1014">#1014</a>)</li> 36101<li>allow netCDF-C++4 to be used with ESMF 36102 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1019">#1019</a>)</li> 36103<li>update Advisor easyblock to support latest versions 36104 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1021">#1021</a>)</li> 36105<li>update CBLAS easyblock to build with <code>foss</code> toolchain 36106 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1024">#1024</a>)</li> 36107<li>update Gurobi easyblock to use <code>copy_file</code> 36108 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1028">#1028</a>)</li> 36109<li>add support for giving <code>/lib</code> preference over <code>/lib64</code> & co in 36110 GCC installation 36111 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1030">#1030</a>, 36112 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1035">#1035</a>)</li> 36113<li>enable installation of <code>libiberty</code> by default for binutils 36114 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1030">#1030</a>)</li> 36115<li>avoid CMake fiddling with the RPATHs injected by EasyBuild via 36116 <code>--rpath</code> in CMakeMake and METIS easyblocks 36117 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1031">#1031</a>, 36118 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1034">#1034</a>)</li> 36119<li>simplify scipy sanity check to make it more robust w.r.t. 36120 version updates 36121 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1037">#1037</a>)</li> 36122</ul> 36123</li> 36124<li>various bug fixes, including:<ul> 36125<li>make sure '<code>None</code>
36125' doesn't appear in modules generated with 36126 <code>--module-only</code> 36127 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/998">#998</a>)</li> 36128<li>fix ATLAS easyblock for non-x86 systems 36129 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1003">#1003</a>)</li> 36130<li>fix '<code>usempi</code>' and '<code>with_mpi</code>' usage to allow for a serial 36131 build of Amber 16 36132 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1013">#1013</a>)</li> 36133<li>add both <code>lib/python2.7/site-packages/{,wx-3.0-gtk2}</code> to 36134 <code>$PYTHONPATH</code> for wxPython 36135 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1018">#1018</a>)</li> 36136<li>only hard inject RPATH for <code>/usr/lib*</code> directories when building 36137 binutils with <code>dummy</code> toolchain 36138 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1026">#1026</a>)</li> 36139<li>make HDF5 easyblock handle <code>--filter-deps</code> correctly 36140 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1027">#1027</a>)</li> 36141<li>update Travis config w.r.t. changes framework config defaults 36142 and required Lmod version 36143 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1029">#1029</a>)</li> 36144<li>be more patient when running Mathematica Q&A installer 36145 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1036">#1036</a>)</li> 36146</ul> 36147</li> 36148</ul> 36149<p><strong>easyconfigs</strong></p> 36150<ul> 36151<li>backwards incompatible changes:<ul> 36152<li>archive easyconfigs using old inactive toolchains<ul> 36153<li>see 36154 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3725">#3725</a>, 36155 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3728">#3728</a>, 36156 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3729">#3729</a>, 36157 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3730">#3730</a>, 36158 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3731">#3731</a>, 36159 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3732">#3732</a>, 36160 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3733">#3733</a>, 36161 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3735">#3735</a>, 36162 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3736">#3736</a>, 36163 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3737">#3737</a>, 36164 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3738">#3738</a></li> 36165<li>only taken into account by EasyBuild if 36166 <code>--consider-archived-easyconfigs</code> is enabled</li> 36167<li>no easyconfigs available outside of archive for QLogicMPI + 36168 15 toolchains:<ul> 36169<li><code>ClangGCC</code>, <code>cgmpich</code>, <code>cgmpolf</code>, <code>cgmvapich2</code>, 36170 <code>cgmvolf</code>, <code>cgompi</code>, <code>cgoolf</code>, <code>gmacml</code>, <code>goalf</code>, 36171 <code>gpsmpi</code>, <code>gpsolf</code>, <code>iiqmpi</code>, <code>intel-para</code>, <code>ipsmpi</code>, 36172 <code>iqacml</code></li> 36173</ul> 36174</li> 36175</ul> 36176</li> 36177<li>fix name in PyTables easyconfigs (was 'pyTables') 36178 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3785">#3785</a>)</li> 36179</ul> 36180</li> 36181<li>added example easyconfig files for 32 new software packages:<ul> 36182<li>3to2 36183 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3655">#3655</a>), 36184 Anaconda2 36185 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3337">#3337</a>), 36186 Anaconda3 36187 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3337">#3337</a>), 36188 ART 36189 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3724">#3724</a>), 36190 atools 36191 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3631">#3631</a>), 36192 awscli 36193 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3645">#3645</a>), 36194 behave 36195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3751">#3751</a>), 36196 Blosc 36197 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3785">#3785</a>), 36198 bokeh 36199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3790">#3790</a>), 36200 Cantera 36201 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3655">#3655</a>), 36202 Cargo 36203 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3764">#3764</a>), 36204 dadi v1.7.0, distributed 36205 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3786">#3786</a>), 36206 ea-utils 36207 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3634">
36207#3634</a>), 36208 Elk 36209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3644">#3644</a>), 36210 FGSL 36211 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3638">#3638</a>), 36212 gencore_variant_detection 36213 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3337">#3337</a>), 36214 help2man 36215 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3768">#3768</a>), 36216 lbzip2 36217 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3791">#3791</a>), 36218 Log-Log4perl 36219 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3574">#3574</a>), 36220 Minimac2 36221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3783">#3783</a>), 36222 mypy 36223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3694">#3694</a>), 36224 OBITools 36225 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3573">#3573</a>), 36226 perl-app-cpanminus 36227 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3337">#3337</a>), 36228 PGDSpider 36229 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3625">#3625</a>), 36230 prokka 36231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3755">#3755</a>), 36232 Reads2snp 36233 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3609">#3609</a>), 36234 spglib-python 36235 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3620">#3620</a>), 36236 SUNDIALS 36237 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3654">#3654</a>, 36238 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3655">#3655</a>), 36239 SelEstim 36240 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3626">#3626</a>), 36241 XMLStarlet 36242 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3797">#3797</a>), 36243 x265 36244 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3090">#3090</a>)</li> 36245</ul> 36246</li> 36247<li>added easyconfigs for new '<code>intelcuda</code>' toolchain 36248 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3750">#3750</a>)</li> 36249<li>added new easyconfigs for existing toolchains:<ul> 36250<li><code>goolfc/2016.08</code> 36251 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3796">#3796</a>), 36252 <code>goolfc/2016.10</code> 36253 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3666">#3666</a>, 36254 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3775">#3775</a>), 36255 <code>intel/2017.00</code> 36256 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3543">#3543</a>), 36257 <code>intel/2017.01</code> 36258 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3757">#3757</a>), 36259 <code>iomkl/2016.09-GCC-4.9.3-2.25</code> 36260 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3680">#3680</a>), 36261 <code>iomkl/2016.09-GCC-5.4.0-2.26</code> 36262 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3772">#3772</a>)</li> 36263</ul> 36264</li> 36265<li>added additional easyconfigs for various supported software 36266 packages, including:<ul> 36267<li>Advisor 2017 update 1, Amber 16, ATLAS 3.10.2, GROMACS 2016, 36268 Octave 4.0.3, OpenFOAM 3.0.1, PyTables 3.3.0, QuantumESPRESSO 36269 6.0, Rust v1.12.1</li> 36270</ul> 36271</li> 36272<li>various other enhancements, including:<ul> 36273<li>STREAM builds using ~56GiB and ~111GiB 36274 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3670">#3670</a>)</li> 36275</ul> 36276</li> 36277<li>various bug fixes, including:<ul> 36278<li>fix source spec in VASP easyconfig, ensure static linking with 36279 Intel MKL 36280 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3381">#3381</a>)</li> 36281<li>fix source URL in GCCcore 6.2.0 easyconfig 36282 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3608">#3608</a>)</li> 36283<li>correct STAMP dependency in i-cisTarget, must be 1.3 36284 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3613">#3613</a>)</li> 36285<li>consistently specify to use <code>-fgnu89-inline</code> flag in M4 1.4.17 36286 easyconfigs 36287 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3623">#3623</a>)</li> 36288<li>fix source URLs for Cython 36289 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3636">#3636</a>)</li> 36290<li>
36290add Bison as build dep and M4 as runtime dep for flex 2.6.0 36291 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3656">#3656</a>)</li> 36292<li>enable parallel building of flex 2.6.0 36293 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3630">#3630</a>)</li> 36294<li>add zlib and bzip2 dependencies to X11 bundle 36295 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3662">#3662</a>)</li> 36296<li>use '<code>letter_dir_for</code>' function rather than just grabbing 1st 36297 letter of software name in easyconfigs tests 36298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3664">#3664</a>)</li> 36299<li>add patch to fix typo in GRIT 2.0.5 36300 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3675">#3675</a>)</li> 36301<li>fix typo in patch for WRF 3.8.0 36302 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3702">#3702</a>)</li> 36303<li>use <code>$CC</code>, <code>$CXX</code> rather than <code>$I_MPI_CC</code>, <code>$I_MPI_CXX</code> in patch 36304 for OpenFOAM 4.0 36305 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3703">#3703</a>)</li> 36306<li>patch FLTK to fix '<code>undefined symbol</code>' issue when building 36307 Octave 36308 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3704">#3704</a>)</li> 36309<li>include Pillow as a proper dep for scikit-image rather than as 36310 extension, since it has deps itself 36311 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3723">#3723</a>)</li> 36312<li>update Travis config w.r.t. changes framework config defaults 36313 and required Lmod version 36314 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3773">#3773</a>)</li> 36315<li>don't limit parallellism to 4 in recent GCC easyconfigs 36316 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3776">#3776</a>, 36317 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3777">#3777</a>, 36318 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3778">#3778</a>)</li> 36319<li>include M4 as dependency in flex 2.5.39 easyconfigs + fix 36320 consistency issues 36321 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3782">#3782</a>)</li> 36322<li>consistently apply patch for ncurses 6.0 36323 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3792">#3792</a>)</li> 36324<li>eliminate dependency on <code>mpi-mic-rt</code> in ifort 36325 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3793">#3793</a>)</li> 36326<li>include Autotools as build dependency in all beagle-lib and 36327 MrBayes easyconfigs 36328 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3794">#3794</a>)</li> 36329<li>make OpenBLAS use the LAPACK version specified in the easyconfig 36330 (v0.2.18 & v0.2.19) 36331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3795">#3795</a>)</li> 36332<li>include original download URL for ISL source tarball in GCC 36333 easyconfigs 36334 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3798">#3798</a>)</li> 36335<li>disable installing <code>libiberty</code> for binutils built with intel 36336 toolchain 36337 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3802">#3802</a>)</li> 36338</ul> 36339</li> 36340</ul> 36341<h2 id="release_notes_eb290">EasyBuild v2.9.0 (September 23rd 2016)<a class="headerlink" href="#release_notes_eb290" title="Permanent link">¶</a></h2> 36342<p>feature release</p> 36343<p><strong>framework</strong></p> 36344<ul> 36345<li>note: vsc-base 2.5.4 or more recent is now required</li> 36346<li>various small enhancements, including:<ul> 36347<li>change option <code>--color</code> choices to auto/always/never 36348 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1701">#1701</a>, 36349 <a href="https://github.com/easybuilders/easybuild-framework/pull/1898">#1898</a>, 36350 <a href="https://github.com/easybuilders/easybuild-framework/pull/1911">#1911</a>)</li> 36351<li>add support for '<code>hidden</code>' easyconfig parameter 36352 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1837">#1837</a>)</li> 36353<li>
36353add support for using <code>ccache</code> and <code>f90cache</code> compiler caching 36354 tools 36355 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1844">#1844</a>, 36356 <a href="https://github.com/easybuilders/easybuild-framework/pull/1912">#1912</a>)<ul> 36357<li>see <code>--use-ccache</code> and <code>--use-f90cache</code></li> 36358</ul> 36359</li> 36360<li>update Cray metadata for 16.06 CrayPE release 36361 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1851">#1851</a>)</li> 36362<li>also include patch files in <code>--new-pr</code> and <code>--update-pr</code> 36363 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1852">#1852</a>)</li> 36364<li>handle deleted files in <code>--new-pr</code> 36365 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1853">#1853</a>)</li> 36366<li>add support for <code>--install-latest-eb-release</code> 36367 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1861">#1861</a>)</li> 36368<li>add support for hiding toolchains, see <code>--hide-toolchains</code> and 36369 '<code>hidden</code>' key in '<code>toolchain</code>' spec 36370 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1871">#1871</a>)</li> 36371<li>add template for GitHub source URL 36372 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1872">
36372#1872</a>)</li> 36373<li>add support for combining <code>--new-pr</code>/<code>--update-pr</code> and <code>--robot</code> 36374 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1881">#1881</a>)</li> 36375<li>add support for <code>--list-software</code> and 36376 <code>--list-installed-software</code> 36377 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1883">#1883</a>, 36378 <a href="https://github.com/easybuilders/easybuild-framework/pull/1910">#1910</a>, 36379 <a href="https://github.com/easybuilders/easybuild-framework/pull/1917">#1917</a>)</li> 36380<li>print message on which extension is being installed, incl. 36381 progress counter 36382 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1886">#1886</a>, 36383 <a href="https://github.com/easybuilders/easybuild-framework/pull/1914">#1914</a>)</li> 36384<li>add support for <code>--github-org</code> to specify GitHub organisation 36385 rather than GitHub user 36386 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1894">#1894</a>)</li> 36387<li>add support for running Lmod in debug mode 36388 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1895">#1895</a>)</li> 36389<li>
36389avoid needless use of deepcopy, speed up support for templating 36390 in easyconfigs 36391 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1897">#1897</a>)</li> 36392<li>convert <code>all_dependencies</code> to a property in <code>EasyConfig</code> class 36393 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1909">#1909</a>)</li> 36394<li>add support for <code>--mpi-cmd-template</code> 36395 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1918">#1918</a>)</li> 36396<li>add support for <code>--disable-mpi-tests</code> 36397 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1920">#1920</a>)</li> 36398</ul> 36399</li> 36400<li>various bug fixes, including:<ul> 36401<li>merge with develop when using <code>--from-pr</code> 36402 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1838">#1838</a>, 36403 <a href="https://github.com/easybuilders/easybuild-framework/pull/1867">#1867</a>)</li> 36404<li>ensure <code>--new-pr</code> doesn't open empty pull requests 36405 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1846">#1846</a>)</li> 36406<li>better error handling for outdated <code>GitPython</code> module in 36407 <code>--check-github</code> 36408 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1847">#1847</a>)</li> 36409<li>fix formatting for generated easyblocks documentation 36410 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1860">#1860</a>)</li> 36411<li>make sure the robot ignores filtered dependencies when creating 36412 toolchain cache 36413 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1862">#1862</a>)</li> 36414<li>honor <code>--filter-deps</code> under <code>--minimal-toolchains</code> 36415 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1863">#1863</a>)</li> 36416<li>correct format for '<code>param</code>' and '<code>author</code>' tags in 36417 docstrings 36418 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1866">#1866</a>)</li> 36419<li>ignore failing bootstrap test in Travis config file 36420 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1870">#1870</a>)</li> 36421<li>make sure all output of executed command is included in 36422 generated temporary log file 36423 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1873">#1873</a>, 36424 <a href="https://github.com/easybuilders/easybuild-framework/pull/1874">#1874</a>)</li> 36425<li>ensure <code>--show_hidden</code> is used in the correct location for 36426 '<code>avail</code>' with Lmod 36427 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1875">#1875</a>)</li> 36428<li>make sure <code>self.path</code> is passed down in copy method of 36429 <code>EasyConfig</code> object 36430 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1884">#1884</a>)</li> 36431<li>take into account possible multi-line modloadmsg in 36432 <code>ModuleGeneratorLua</code> 36433 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1885">#1885</a>)</li> 36434<li>fix extracting <code>.bz2</code> source files 36435 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1889">#1889</a>)</li> 36436<li>don't resolve path to Lmod command 36437 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1892">#1892</a>)</li> 36438<li>fix skipping of stage 0 in bootstrap script 36439 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1893">#1893</a>)</li> 36440<li>fix function signature of <code>log.deprecated</code> compared to 36441 <code>fancylogger.deprecated</code> 36442 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1896">#1896</a>, 36443 <a href="https://github.com/easybuilders/easybuild-framework/pull/1899">#1899</a>)</li> 36444<li>apply patch to Tcl/C environment modules tool for Tcl 8.6 36445 support in Travis config 36446 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1901">#1901</a>)</li> 36447<li>fix combining <code>--extended-dry-run</code> with <code>--from-pr</code> 36448 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1902">#1902</a>)</li> 36449<li>also template dict keys 36450 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1904">#1904</a>)</li> 36451<li>don't pass '<code>--try-*</code>' command-line options to EB instance 36452 running within job script 36453 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1908">#1908</a>)</li> 36454<li>
36454add workaround for incorrectly passing command line arguments 36455 with <code>--job</code> 36456 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1915">#1915</a>)</li> 36457<li>fix issues with <code>--module-only</code> 36458 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1919">#1919</a>, 36459 <a href="https://github.com/easybuilders/easybuild-framework/pull/1924">#1924</a>, 36460 <a href="https://github.com/easybuilders/easybuild-framework/pull/1925">#1925</a>)<ul> 36461<li>correctly deal with specified start_dir</li> 36462<li>do not remove installation directory when 36463 build-in-installdir is enabled</li> 36464</ul> 36465</li> 36466<li>make sure '<code>which</code>' function returns path to a file 36467 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1921">#1921</a>)</li> 36468<li>fix <code>:param:</code>, <code>:return:</code> tags in docstrings & add test for it 36469 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1923">#1923</a>)</li> 36470</ul> 36471</li> 36472</ul> 36473<p><strong>easyblocks</strong></p> 36474<ul> 36475<li>new easyblocks for 6 software packages that require customized 36476 support:<ul> 36477<li>cppcheck 36478 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/983">#983</a>), 36479 HEALPix 36480 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/982">#982</a>), 36481 IMOD 36482 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/847">#847</a>), 36483 IronPython 36484 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/321">#321</a>), 36485 Mono 36486 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/321">#321</a>), 36487 MyMediaLite 36488 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/321">#321</a>)</li> 36489</ul> 36490</li> 36491<li>various enhancements, including:<ul> 36492<li>extend OpenFoam-Extend sanity check for decomp libraries 36493 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/784">#784</a>)</li> 36494<li>enhance Java easyblock to support installing Java 6.x 36495 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/940">#940</a>)</li> 36496<li>make QuantumESPRESSO easyblock aware of multithreaded FFT 36497 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/954">#954</a>)</li> 36498<li>extend PSI easyblock to use PCMSolver and CheMPS2 36499 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/967">#967</a>)</li> 36500<li>make Boost easyblock add definition for <code>$BOOST_ROOT</code> to 36501 generated module file 36502 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/976">#976</a>)</li> 36503<li>add support to Bundle easyblock to install list of components 36504 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/980">#980</a>)</li> 36505<li>enhance & clean up libxml2 easyblock to also enable installing 36506 without Python bindings 36507 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/984">#984</a>)</li> 36508<li>update Libint easyblock for Libint 2.1.x 36509 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/985">#985</a>)</li> 36510<li>update sanity check for OpenFOAM to support OpenFOAM 4.x 36511 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/986">#986</a>)</li> 36512<li>make easyblocks that run MPI tests aware of '<code>mpi_tests</code>' 36513 build option 36514 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/993">#993</a>)</li> 36515</ul> 36516</li> 36517<li>various bug fixes, including:<ul> 36518<li>fix compatibility of OpenFOAM easyblock with <code>--module-only</code> 36519 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/784">#784</a>)</li> 36520<li>fix testing of <code>--module-only</code> compatibility for OpenFOAM and 36521 IMOD easyblocks 36522 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/784">#784</a>)</li> 36523<li>add '<code>include/libxml2</code>' to <code>$CPATH</code> in libxml2 easyblock 36524 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/981">#981</a>)</li> 36525<li>fix compatibility of IntelBase generic easyblock with 36526 <code>--module-only</code> 36527 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/994">#994</a>)</li> 36528<li>make sure correct config script is used for Tcl/Tk deps of R 36529 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/995">#995</a>)</li> 36530</ul> 36531</li> 36532</ul> 36533<p><strong>easyconfigs</strong></p> 36534<ul> 36535<li>added example easyconfig files for 88 new software packages:<ul> 36536<li>ADMIXTURE 36537 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3359">#3359</a>), 36538 angsd 36539 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3593">#3593</a>), 36540 ASHS 36541 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3429">#3429</a>), 36542 AutoDock 36543 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3465">#3465</a>), 36544 AutoGrid 36545 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3466">#3466</a>), 36546 BayeScan 36547 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2748">#2748</a>, 36548 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3356">#3356</a>), 36549 BayPass 36550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3451">#3451</a>), 36551 Bazel 36552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3379">#3379</a>), 36553 Blender 36554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3553">#3553</a>, 36555 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3558">#3558</a>), 36556 bwakit 36557 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3567">#3567</a>), 36558 BXH_XCEDE_TOOLS 36559 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3410">#3410</a>), 36560 CastXML 36561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3403">#3403</a>), 36562 CHASE 36563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3304">#3304</a>), 36564 configparser 36565 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3368">#3368</a>, 36566 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3424">#3424</a>), 36567 configurable-http-proxy 36568 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3380">#3380</a>), 36569 cppcheck 36570 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3508">#3508</a>), 36571 CRPropa 36572 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/779">#779</a>), 36573 DicomBrowser 36574 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3432">#3432</a>), 36575 DMTCP 36576 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3422">#3422</a>), 36577 entrypoints 36578 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3368">#3368</a>, 36579 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3424">#3424</a>), 36580 f90cache 36581 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3570">#3570</a>), 36582 fastPHASE 36583 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3343">#3343</a>), 36584 fastQValidator 36585 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3192">#3192</a>), 36586 FFindex 36587 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1135">#1135</a>), 36588 FragGeneScan 36589 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1198">#1198</a>),
36590 gdc-client 36591 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3399">#3399</a>), 36592 gflags 36593 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3417">#3417</a>), 36594 glog 36595 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3417">#3417</a>), 36596 GRIT 36597 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3561">#3561</a>), 36598 H5hut 36599 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3431">#3431</a>), 36600 HAPGEN2 36601 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3344">#3344</a>), 36602 HEALPix 36603 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/779">#779</a>), 36604 IMOD 36605 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1187">#1187</a>, 36606 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3347">#3347</a>), 36607 IronPython 36608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/607">#607</a>), 36609 jhbuild 36610 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3476">#3476</a>), 36611 jupyterhub 36612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3380">#3380</a>), 36613 Keras 36614 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3581">#3581</a>), 36615 khmer 36616 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1158">#1158</a>), 36617 LeadIT 36618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3345">#3345</a>, 36619 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3599">#3599</a>), 36620 LevelDB 36621 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3417">#3417</a>), 36622 libbitmask 36623 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3481">#3481</a>), 36624 libcpuset 36625 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3481">#3481</a>), 36626 LMDB 36627 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3417">#3417</a>), 36628 log4cplus 36629 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1136">#1136</a>), 36630 MACH 36631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3346">#3346</a>), 36632 Mako 36633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3460">#3460</a>), 36634 Maq 36635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3428">#3428</a>), 36636 MetaGeneAnnotator 36637 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3307">#3307</a>), 36638 Metal 36639 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3324">#3324</a>), 36640 Mono 36641 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/607">#607</a>), 36642 MyMediaLite 36643 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/607">#607</a>), 36644 nco 36645 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2575">#2575</a>), 36646 nose-parameterized 36647 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3579">#3579</a>), 36648 OpenEXR 36649 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3553">#3553</a>), 36650 OpenImageIO 36651 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3553">#3553</a>), 36652 path.py 36653 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3368">#3368</a>, 36654 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3424">#3424</a>), 36655 PCRE2 36656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3325">#3325</a>), 36657 pftoolsV3 36658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3317">#3317</a>), 36659 PHASE 36660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3385">#3385</a>), 36661 PLAST 36662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3288">#3288</a>), 36663 PLINKSEQ 36664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3402">#3402</a>), 36665 POV-Ray 36666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3551">#3551</a>), 36667 ProbABEL 36668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3108">#3108</a>), 36669 prompt-toolkit 36670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3368">#3368</a>, 36671 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3424">#3424</a>), 36672 protobuf-python 36673 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3563">#3563</a>), 36674 PSORTb 36675 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3317">#3317</a>), 36676 py 36677 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3403">#3403</a>, 36678 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3482">#3482</a>), 36679 pygccxml 36680 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3403">#3403</a>, 36681 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3482">#3482</a>), 36682 pyGIMLi 36683 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3403">#3403</a>, 36684 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3482">#3482</a>), 36685 pyplusplus 36686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3403">#3403</a>, 36687 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3482">#3482</a>), 36688 PyQt5 36689 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3533">#3533</a>), 36690 Pyro4 36691 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3527">#3527</a>), 36692 pytest 36693 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3403">#3403</a>, 36694 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3482">#3482</a>), 36695 QCA 36696 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3595">#3595</a>), 36697 RDMC 36698 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1137">#1137</a>), 36699 S.A.G.E. 36700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3427">#3427</a>), 36701 SDL2 36702 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3551">#3551</a>), 36703 SHORE 36704 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3531">#3531</a>), 36705 SimVascular 36706 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3555">#3555</a>), 36707 SortMeRNA 36708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3326">#3326</a>), 36709 SUMACLUST 36710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3316">#3316</a>), 36711 SUMATRA 36712 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3316">#3316</a>), 36713 Text-CSV 36714 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3323">#3323</a>), 36715 Triangle 36716 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3403">#3403</a>), 36717 VEGAS 36718 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3457">#3457</a>), 36719 VirSorter 36720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3307">#3307</a>), 36721 wcwidth 36722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3368">#3368</a>, 36723 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3424">#3424</a>), 36724 X11 36725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3340">#3340</a>)</li> 36726</ul> 36727</li> 36728<li>
36728added new easyconfigs for existing toolchains:<ul> 36729<li>CrayGNU + CrayIntel 2016.06 36730 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3377">#3377</a>)</li> 36731<li>foss 2016.07 36732 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3517">#3517</a>) + 36733 2016.09 36734 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3523">#3523</a>)</li> 36735<li>iomkl 2016.07 36736 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3458">#3458</a>)</li> 36737<li>pomkl 2016.09 36738 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3516">#3516</a>)</li> 36739</ul> 36740</li> 36741<li>added additional easyconfigs for various supported software 36742 packages, including:<ul> 36743<li>FFTW 3.3.5, GCC 4.9.4 + 6.2.0, GROMACS 5.1.4, IPython 5.1.0, 36744 LLVM 3.9.0, Mesa 12.0.1, OpenCV 3.1.0, OpenFOAM 4.0, OpenMPI 36745 2.0.1, ParaView 5.1.2, PGI 16.7, QuantumESPRESSO 5.4.0, Qt5 36746 5.7.0, R-bundle-Bioconductor 3.3, VTK 7.0.0, Yade 2016.06a</li> 36747</ul> 36748</li> 36749<li>various enhancements, including:<ul> 36750<li>adjust PSI4 easyconfigs for updated easyblock 36751 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3312">#3312</a>)</li> 36752<li>clean up libxml2 easyconfigs according to updated libxml2 36753 easyblock 36754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3479">#3479</a>, 36755 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3509">#3509</a>)</li> 36756<li>significantly speed up verifying of dumped easyconfig by 36757 resorting to 'shallow' parsing 36758 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3520">#3520</a>)</li> 36759<li>include sanity checks for all MATIO config files 36760 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3528">#3528</a>)</li> 36761<li>remove <code>--with-tcl-config</code>/<code>--with-tk-config</code> from R easyconfig, 36762 already done in R easyblock 36763 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3580">#3580</a>)</li> 36764</ul> 36765</li> 36766<li>various bug fixes, including:<ul> 36767<li>disable testing in all ParaView 4.4.0 easyconfigs, required 36768 download is too much of a PITA 36769 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3178">#3178</a>)</li> 36770<li>add SQLite as dep to GDAL 2.1.0 easyconfigs 36771 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3342">#3342</a>)</li> 36772<li>add zlib/SQLite/LibTIFF as dep to R 3.3.1 easyconfigs 36773 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3342">#3342</a>)</li> 36774<li>add bzip2 as a dependency of freetype 36775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3464">#3464</a>)</li> 36776<li>specify correct MPI target in FDS easyconfigs 36777 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3488">#3488</a>)</li> 36778<li>add tcsh as OS dep in NAMD easyconfigs 36779 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3491">#3491</a>)</li> 36780<li>statically link ncurses/libreadline in Lua easyconfig with 36781 '<code>dummy</code>' toolchain 36782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3545">#3545</a>)</li> 36783<li>add M4 as dep for flex 2.6.x 36784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3542">#3542</a>, 36785 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3550">#3550</a>)</li> 36786<li>add bzip2 and libxcb dependencies to FFmpeg 3.x easyconfigs 36787 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3548">#3548</a>)</li> 36788<li>make sure & check that Graphviz does not install Tcl bindings in 36789 Tcl install prefix 36790 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3556">#3556</a>)</li> 36791<li>add missing patches for extensions in Python 3.x easyconfigs 36792 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3557">#3557</a>)</li> 36793<li>add missing XZ dependency to libxml2 2.9.4 easyconfigs, change 36794 gettext dep of XZ to build-only dep 36795 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3568">#3568</a>)</li> 36796<li>enable running of tests for HPCG 36797 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3578">#3578</a>)</li> 36798<li>fix <code>buildopts</code> in tabix easyconfigs 36799 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3584">#3584</a>)</li> 36800</ul> 36801</li> 36802</ul> 36803<h2 id="release_notes_eb282">EasyBuild v2.8.2 (July 13th 2016)<a class="headerlink" href="#release_notes_eb282" title="Permanent link">¶</a></h2> 36804<p>bugfix release</p> 36805<p><strong>framework</strong></p> 36806<ul> 36807<li>various small enhancements, including:<ul> 36808<li>add support for rst output for <code>--list-*</code> and <code>--avail-*</code> 36809 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1339">#1339</a>)</li> 36810<li>
36810add support for '<code>eb --check-conflicts</code>' 36811 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1747">#1747</a>, 36812 <a href="https://github.com/easybuilders/easybuild-framework/pull/1807">#1807</a>, 36813 <a href="https://github.com/easybuilders/easybuild-framework/pull/1833">#1833</a>)</li> 36814<li>ensure nice error message when non-existing path is passed to 36815 <code>apply_regex_substitutions</code> 36816 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1788">#1788</a>)</li> 36817<li>add check for module output, empty stdout is a sign of trouble 36818 with Lmod 36819 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1793">#1793</a>)</li> 36820<li>add multi-threaded FFT to toolchain 36821 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1802">#1802</a>)</li> 36822<li>avoid special characters like '[', ']' in path to 36823 temporary directory 36824 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1808">#1808</a>)</li> 36825<li>add support for <code>--zip-logs</code> 36826 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1820">#1820</a>)</li> 36827<li>add support for <code>--extra-modules</code> 36828 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1821">#1821</a>)</li> 36829<li>add type conversion for 'checksums' and 'patches' parameter 36830 in .yeb easyconfigs 36831 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1826">#1826</a>, 36832 <a href="https://github.com/easybuilders/easybuild-framework/pull/1840">#1840</a>)</li> 36833<li>add support for filtering tests by name 36834 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1828">#1828</a>)</li> 36835<li>add support for <code>--avail-toolchain-opts</code> 36836 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1830">#1830</a>, 36837 <a href="https://github.com/easybuilders/easybuild-framework/pull/1839">#1839</a>)</li> 36838<li>use absolute path for robot and easyconfig files 36839 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1834">#1834</a>)</li> 36840<li>add backup URL for tarballs hosted on SourceForge in 36841 <code>install_eb_dep.sh</code> script 36842 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1843">#1843</a>)</li> 36843</ul> 36844</li> 36845<li>various bug fixes, including:<ul> 36846<li>fix installation of Lua in <code>install_eb_dep.sh</code> script 36847 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1789">#1789</a>)</li> 36848<li>fix OpenMP flag for Cray compiler wrappers 36849 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1794">#1794</a>)</li> 36850<li>only reset <code>$MODULEPATH</code> before loading a module if environment 36851 was reset 36852 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1795">#1795</a>)</li> 36853<li>include vsc-install as dependency in <code>setup.py</code> 36854 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1805">#1805</a>)</li> 36855<li>cache <code>$PATH</code> & <code>$PYTHONPATH</code> in test setUp, restore them in 36856 tests where '<code>eb</code>' is used 36857 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1806">#1806</a>)</li> 36858<li>don't reset <code>$MODULEPATH</code> in stage 2 of bootstrap script, 36859 support forced installation during stage 2 36860 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1810">#1810</a>)</li> 36861<li>fix issue with templates defined by deps being required while 36862 still parsing deps 36863 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1812">#1812</a>)</li> 36864<li>skip unneeded unuse/use commands on tail of <code>$MODULEPATH</code> in 36865 <code>check_module_path</code> 36866 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1813">#1813</a>)</li> 36867<li>fix auto-convert for all <code>*dependencies</code> params in <code>.yeb</code> 36868 easyconfigs, ensure version is a string 36869 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1818">#1818</a>)</li> 36870<li>fix <code>keyring</code> version in Travis config 36871 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1819">#1819</a>)</li> 36872<li>fix dumping of <code>.yeb</code> easyconfig files in easyconfigs archive 36873 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1822">#1822</a>)</li> 36874<li>fix format of supported easyconfig templates in help output 36875 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1825">#1825</a>)</li> 36876<li>stick to <code>pydot</code> 1.1.0 for Python 2.6 in Travis config 36877 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1827">#1827</a>)</li> 36878</ul> 36879</li> 36880</ul> 36881<p><strong>easyblocks</strong></p> 36882<ul> 36883<li>new easyblocks for 5 software packages that require customized 36884 support:<ul> 36885<li>Amber 36886 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/958">#958</a>), 36887 Extrae 36888 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/955">#955</a>), 36889 Gurobi 36890 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/962">#962</a>), 36891 Paraver 36892 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/956">#956</a>), 36893 Tau 36894 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/887">#887</a>)</li> 36895</ul> 36896</li> 36897<li>various enhancements, including:<ul> 36898<li>add support for building & installing old GROMACS versions 36899 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/569">#569</a>, 36900 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/960">#960</a>)</li> 36901<li>
36901add support for building Boost with Cray toolchain 36902 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/849">#849</a>)</li> 36903<li>libxsmm support for CP2K 36904 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/942">#942</a>)</li> 36905<li>pick up specified components for imkl 36906 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/943">#943</a>)</li> 36907<li>add support for building GROMACS with double precision 36908 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/946">#946</a>, 36909 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/960">#960</a>)</li> 36910<li>add support for building GROMACS with CUDA support and using 36911 dynamic libraries using <code>Cray</code> toolchains 36912 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/951">#951</a>, 36913 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/960">#960</a>)</li> 36914<li>also install vsc-install in <code>EasyBuildMeta</code> easyblock, if 36915 tarball is provided 36916 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/957">#957</a>)</li> 36917<li>enhance PSI easyblock to support PSI4 1.0 36918 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/965">#965</a>)</li> 36919</ul> 36920</li> 36921<li>various bug fixes, including:<ul> 36922<li>also install scripts with MRtrix 0.3.14 36923 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/941">#941</a>)</li> 36924<li>enhance Qt easyblock to support Qt3 36925 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/944">#944</a>)</li> 36926<li>create '<code>release</code>' symlink in MRtrix install dir 36927 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/947">#947</a>)</li> 36928<li>fix <code>make_installdir</code> in Inspector & VTune easyblocks 36929 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/952">#952</a>)</li> 36930<li>make <code>Binary</code> and <code>MakeCp</code> easyblocks aware of 36931 '<code>keepsymlinks</code>' 36932 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/959">#959</a>)</li> 36933<li>correctly define <code>$G4*</code> environment variables in Geant4 36934 easyblock 36935 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/961">#961</a>, 36936 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/970">#970</a>)</li> 36937<li>prepend tmp install path to <code>$PYTHONPATH</code> in numpy test step, 36938 move to build dir when removing '<code>numpy</code>' subdir 36939 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/963">#963</a>)</li> 36940<li>correct full path to ALADIN config file & patch it to use right 36941 Fortran compiler flags 36942 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/964">#964</a>)</li> 36943<li>ensure correct compiler command/flags are used for SAMtools 36944 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/966">#966</a>)</li> 36945</ul> 36946</li> 36947</ul> 36948<p><strong>easyconfigs</strong></p> 36949<ul> 36950<li>added example easyconfig files for 54 new software packages:<ul> 36951<li>Amber 36952 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3200">#3200</a>), 36953 Bullet 36954 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3175">#3175</a>), 36955 CONTRAlign 36956 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/690">#690</a>), 36957 Cluster-Buster 36958 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3191">#3191</a>), 36959 damageproto 36960 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3222">#3222</a>, 36961 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3308">#3308</a>), 36962 DCA++ 36963 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3219">#3219</a>), 36964 EIGENSOFT 36965 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3147">#3147</a>, 36966 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3163">#3163</a>), 36967 Extrae 36968 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/507">#507</a>), 36969 fdstools 36970 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3237">#3237</a>), 36971 ffnet 36972 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3273">#3273</a>), 36973 GP2C 36974 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3257">#3257</a>), 36975 Gurobi 36976 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3239">#3239</a>), 36977 gc 36978 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3202">#3202</a>, 36979 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3261">#3261</a>), 36980 gputools 36981 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/546">#546</a>), 36982 IMa2p 36983 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3300">#3300</a>), 36984 IOzone 36985 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3253">#3253</a>), 36986 i-cisTarget 36987 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3191">#3191</a>, 36988 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3194">#3194</a>), 36989 icmake 36990 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3243">#3243</a>), 36991 io_lib 36992 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3255">#3255</a>), 36993 Kent_tools 36994 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3191">#3191</a>), 36995 libcmaes 36996 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3256">#3256</a>), 36997 libpsortb 36998 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3259">#3259</a>), 36999 libxsmm 37000 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3099">#3099</a>),
37001 MEGACC 37002 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3263">#3263</a>), 37003 MM-align 37004 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1428">#1428</a>), 37005 MOSAIK 37006 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/880">#880</a>), 37007 MView 37008 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1345">#1345</a>), 37009 MySQL-python 37010 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3172">#3172</a>, 37011 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3189">#3189</a>), 37012 magma 37013 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3219">#3219</a>), 37014 mrFAST 37015 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/862">#862</a>), 37016 mrsFAST 37017 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/862">#862</a>), 37018 mysqlclient 37019 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3172">#3172</a>, 37020 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3232">#3232</a>), 37021 NTL 37022 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3183">#3183</a>), 37023 PARI-GP 37024 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3257">#3257</a>), 37025 Paraver 37026 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/508">#508</a>), 37027 psutil 37028 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3171">#3171</a>, 37029 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3231">#3231</a>), 37030 PSI4 37031 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3293">#3293</a>), 37032 Qwt 37033 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3157">#3157</a>), 37034 RMBlast 37035 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3142">#3142</a>), 37036 STAMP 37037 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3191">#3191</a>), 37038 Seqmagick 37039 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3264">#3264</a>), 37040 splitRef 37041 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/946">#946</a>), 37042 TAU 37043 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/509">#509</a>), 37044 TRF 37045 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3141">#3141</a>), 37046 TVB 37047 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3053">#3053</a>, 37048 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3247">#3247</a>, 37049 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3251">#3251</a>), 37050 TVB-deps 37051 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3053">#3053</a>, 37052 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3247">#3247</a>, 37053 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3251">#3251</a>), 37054 tvb-data 37055 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3053">#3053</a>, 37056 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3247">#3247</a>, 37057 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3251">#3251</a>), 37058 tvb-framework 37059 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3053">#3053</a>, 37060 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3247">#3247</a>, 37061 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3251">#3251</a>), 37062 tvb-library 37063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3053">#3053</a>, 37064 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3247">#3247</a>, 37065 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3251">#3251</a>), 37066 VampirTrace 37067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/509">#509</a>), 37068 Voro++ 37069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3174">#3174</a>), 37070 wheel 37071 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3235">#3235</a>), 37072 wxPropertyGrid 37073 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/508">#508</a>), 37074 xonsh 37075 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3159">#3159</a>)</li> 37076</ul> 37077</li> 37078<li>
37078added easyconfigs for update of common toolchains: <code>foss/2016b</code> 37079 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3271">#3271</a>), 37080 <code>intel/2016b</code> 37081 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3270">#3270</a>)</li> 37082<li>added new easyconfigs for existing toolchains: <code>CrayGNU/2016.03</code> & 37083 <code>CrayGNU/2016.04</code> 37084 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3291">#3291</a>), 37085 <code>foss/2016.06</code> 37086 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3184">#3184</a>), 37087 <code>intel/2016.03-GCC-5.4</code> 37088 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3185">#3185</a>)</li> 37089<li>added additional easyconfigs for various supported software 37090 packages, including:<ul> 37091<li>Boost 1.61.0, GCC 5.4.0, GROMACS 3.3.3, HDF5 1.8.17, netCDF 37092 4.4.1, numpy 1.11.0, Perl 5.24.0, PETSc 3.7.2, Python 2.7.12, 37093 Python 3.5.2, Qt 3.3.8, R 3.3.1</li> 37094</ul> 37095</li> 37096<li>various enhancements, including:<ul> 37097<li>use <code>check_conflicts</code> function in easyconfigs tests 37098 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2981">#2981</a>)</li> 37099<li>also include vsc-install in list of sources for recent EasyBuild 37100 easyconfigs, to support offline installation 37101 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3203">#3203</a>)</li> 37102<li>enable building of <code>libmysqld.*</code> in MariaDB easyconfigs 37103 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3230">#3230</a>)</li> 37104<li>add ALDEx2, phyloseq to bundles for Bioconductor 3.2 37105 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3211">#3211</a>, 37106 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3241">#3241</a>)</li> 37107<li>add biom, geepack, lubridate, pim to list of R 3.2.3 extensions 37108 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3186">#3186</a>, 37109 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3211">#3211</a>, 37110 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3275">#3275</a>)</li> 37111</ul> 37112</li> 37113<li>various bug fixes, including:<ul> 37114<li>add patch for Boost 1.60.0 to fix bug resulting in <code>TypeError</code> 37115 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3162">#3162</a>)</li> 37116<li>add fftw dependency to CP2K 2.6.0 easyconfigs using CrayGNU 37117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3176">#3176</a>)</li> 37118<li>fix location of <code>libelf.h</code>, only (also) installed as 37119 <code>include/libelf.h</code> is there's no <code>/usr/include/libelf.h</code> 37120 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3201">#3201</a>)</li> 37121<li>fix software name for Guile & GnuTLS (was 'guile' & 37122 'gnutls') 37123 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3207">#3207</a>)</li> 37124<li>added missing space in Geant4 configopts to specify 37125 <code>-DGEANT4_INSTALL_DATA</code> 37126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3209">#3209</a>)</li> 37127<li>fix Cython download URL in Python 2.7.11 easyconfigs 37128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3212">#3212</a>)</li> 37129<li>add missing build deps for X stack in easyconfigs using 37130 <code>foss/2016a</code> or <code>intel/2016a</code> 37131 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3222">#3222</a>, 37132 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3308">#3308</a>)</li> 37133<li>fix overruling of exts_list in Perl 5.22.2 easyconfig 37134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3224">#3224</a>)</li> 37135<li>add missing dependency on GMP in R 3.2.3 easyconfigs 37136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3226">#3226</a>)</li> 37137<li>don't hard specify toolchain for binutils build dep in likwid 37138 easyconfig, since it matches parent toolchain 37139 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3240">#3240</a>)</li> 37140<li>fix <code>homepage</code> & <code>source_urls</code> in HMMER easyconfigs 37141 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3246">#3246</a>)</li> 37142<li>stick to <code>pydot</code> 1.1.0 for Python 2.6 in Travis config 37143 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3282">#3282</a>)</li> 37144<li>
37144add <code>python-dev(el)</code> to OS deps in GC3Pie easyconfigs 37145 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3310">#3310</a>)</li> 37146</ul> 37147</li> 37148</ul> 37149<h2 id="release_notes_eb281">EasyBuild v2.8.1 (May 30th 2016)<a class="headerlink" href="#release_notes_eb281" title="Permanent link">¶</a></h2> 37150<p>bugfix release</p> 37151<p><strong>framework</strong></p> 37152<ul> 37153<li>various bug fixes, including:<ul> 37154<li>fix error message on missing module command in bootstrap script 37155 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1772">#1772</a>)</li> 37156<li>expand '<code>~</code>' in paths specified to <code>--include-*</code> 37157 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1774">#1774</a>)</li> 37158<li>break after deleting cache entry to avoid attempt to delete 37159 cache entry again 37160 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1776">#1776</a>)</li> 37161<li>avoid changing <code>$MODULEPATH</code> when prepending with symlink of 37162 path already at head of <code>$MODULEPATH</code> 37163 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1777">#1777</a>)</li> 37164<li>filter out duplicates in <code>find_flexlm_license</code> 37165 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1779">#1779</a>)</li> 37166<li>stick with GitPython < 2.0 with Py2.6 in Travis configuration 37167 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1781">#1781</a>)</li> 37168<li>don't use <code>LooseVersion</code> to define 37169 <code>version_major</code>/<code>version_minor</code> 37170 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1783">#1783</a>)</li> 37171</ul> 37172</li> 37173</ul> 37174<p><strong>easyblocks</strong></p> 37175<ul> 37176<li>various enhancements, including:<ul> 37177<li>update MRtrix easyblock for version 0.3.14 37178 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/932">#932</a>)</li> 37179<li>update Inspector easyblock for recent versions 37180 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/934">#934</a>)</li> 37181<li>update VTune easyblock for recent versions 37182 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/935">#935</a>)</li> 37183<li>add debug message to IntelBase easyblock w.r.t. switching to 37184 'exist_lic' 37185 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/936">#936</a>)</li> 37186</ul> 37187</li> 37188</ul> 37189<p><strong>easyconfigs</strong></p> 37190<ul> 37191<li>added example easyconfig files for 13 new software packages:<ul> 37192<li>drFAST 37193 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/906">#906</a>), 37194 git-lfs 37195 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2478">#2478</a>), 37196 grabix 37197 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3127">#3127</a>), 37198 JWM 37199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3007">#3007</a>), 37200 libcroco 37201 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3007">#3007</a>), 37202 librsvg 37203 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3007">#3007</a>), 37204 MaCH 37205 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3136">#3136</a>), 37206 mayavi 37207 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3106">#3106</a>), 37208 OpenMM 37209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2762">#2762</a>), 37210 Pysam 37211 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3080">#3080</a>), 37212 SeqPrep 37213 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3097">#3097</a>), 37214 vt 37215 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3128">#3128</a>), 37216 wkhtmltopdf 37217 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3098">#3098</a>)</li> 37218</ul> 37219</li> 37220<li>added new easyconfigs for existing toolchains: 37221 <code>intel/2016.03-GCC-4.9</code> 37222 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3088">#3088</a>)</li> 37223<li>added additional easyconfigs for various supported software 37224 packages, including:<ul> 37225<li>Boost 1.61.0, ESMF 7.0.0, Inspector 2016 update 3, IPython 4.2,
37226 netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, Perl 5.22.2, VTune 2016 37227 update 3</li> 37228</ul> 37229</li> 37230<li>various bug fixes, including:<ul> 37231<li>apply libreadline patch to fix bug triggering segmentation fault 37232 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3086">#3086</a>)</li> 37233</ul> 37234</li> 37235</ul> 37236<h2 id="release_notes_eb280">EasyBuild v2.8.0 (May 18th 2016)<a class="headerlink" href="#release_notes_eb280" title="Permanent link">¶</a></h2> 37237<p>feature + bugfix release</p> 37238<p><strong>framework</strong></p> 37239<ul> 37240<li>significant speedup improvements of EasyBuild itself, thanks to:<ul> 37241<li>stop creating <code>ModulesTool</code> instances over and over again 37242 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1735">#1735</a>)</li> 37243<li>cache result of '<code>module avail</code>' calls 37244 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1742">#1742</a>)</li> 37245</ul> 37246</li> 37247<li>add support for using PGI as toolchain compiler 37248 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1342">#1342</a>, 37249 <a href="https://github.com/easybuilders/easybuild-framework/pull/1664">#1664</a>, 37250 <a href="https://github.com/easybuilders/easybuild-framework/pull/1759">#1759</a>, 37251 <a href="https://github.com/easybuilders/easybuild-framework/pull/1761">#1761</a>, 37252 <a href="https://github.com/easybuilders/easybuild-framework/pull/1764">#1764</a>)<ul> 37253<li>incl. new toolchain definitions <code>pompi</code> and <code>pomkl</code> 37254 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1724">#1724</a>)</li> 37255</ul> 37256</li> 37257<li>add test configuration for Travis 37258 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1733">#1733</a>, 37259 <a href="https://github.com/easybuilders/easybuild-framework/pull/1737">#1737</a>, 37260 <a href="https://github.com/easybuilders/easybuild-framework/pull/1743">#1743</a>, 37261 <a href="https://github.com/easybuilders/easybuild-framework/pull/1767">#1767</a>)</li> 37262<li>various other enhancements, including:<ul> 37263<li>add <code>get_total_memory()</code> function in <code>systemtools</code> module 37264 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1623">#1623</a>)</li> 37265<li>ignore <code>__init__.py</code> files in <code>--include-*</code> 37266 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1704">#1704</a>)</li> 37267<li>use <code>-fopenmp</code> rather than <code>-openmp</code> for Intel compilers, since 37268 <code>-openmp</code> is deprecated 37269 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1718">#1718</a>)</li> 37270<li>add modules to metadata for Cray modules 37271 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1721">#1721</a>)</li> 37272<li>make sure user write permissions are set after failed removal 37273 attempt of installation directory 37274 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1722">#1722</a>)</li> 37275<li>escape special characters in software name in 37276 <code>find_related_easyconfigs</code> 37277 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1726">#1726</a>)</li> 37278<li>add support for <code>CrayPGI</code> compiler toolchain 37279 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1729">#1729</a>)</li> 37280<li>ensure read permission to all installed files for everybody 37281 (unless other options specify otherwise) 37282 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1731">#1731</a>)</li> 37283<li>also consider <code>$LMOD_CMD</code> in bootstrap script 37284 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1736">#1736</a>)</li> 37285<li>translate PyPI download URL to alternate URL with a hash 37286 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1749">#1749</a>)</li> 37287<li>make <code>get_software_libdir</code> compatible with <code>-x</code> 37288 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1750">#1750</a>)</li> 37289<li>set <code>$LMOD_REDIRECT</code> to '<code>no</code>' when initialising Lmod 37290 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1755">#1755</a>)</li> 37291<li>
37291add test for broken modules tool setup affecting 37292 '<code>module use</code>' 37293 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1758">#1758</a>)</li> 37294</ul> 37295</li> 37296<li>various bug fixes, including:<ul> 37297<li>isolate '<code>options</code>' tests from easyblocks other than the ones 37298 included in the tests 37299 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1699">#1699</a>)</li> 37300<li>don't run '<code>module purge</code>' in tests, since EasyBuild may be 37301 made available through a module 37302 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1702">#1702</a>)</li> 37303<li>avoid rehandling <code>--include-*</code> options over and over again 37304 during <code>--show-config</code> 37305 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1705">#1705</a>)</li> 37306<li>remove useless <code>test_cwd</code> 37307 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1706">#1706</a>)</li> 37308<li>fix bootstrap script: make sure setuptools installed in stage0 37309 is still available at end of stage1 37310 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1727">#1727</a>)</li> 37311<li>forcibly create target branch in <code>--update-pr</code> 37312 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1728">#1728</a>)</li> 37313<li>remove check whether '<code>easybuild</code>' is being imported from dir 37314 that contains <code>easybuild/__init__.py</code> 37315 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1730">#1730</a>)</li> 37316<li>(re)install vsc-base during stage1 using <code>--always-copy</code> in 37317 bootstrap script, if needed 37318 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1732">#1732</a>)</li> 37319<li>use <code>os.path.realpath</code> in <code>test_wrong_modulepath</code> to avoid 37320 symlinked path breaking the test 37321 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1740">#1740</a>)</li> 37322<li>unset <code>$PYTHONPATH</code> in before tested bootstrapped EasyBuild 37323 module 37324 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1743">#1743</a>)</li> 37325<li>take into account that paths in modulepath may be symlinks in 37326 <code>test_module_caches</code> 37327 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1745">#1745</a>)</li> 37328<li>change to install dir rather than buildpath in sanity check of 37329 extension, latter may not exist 37330 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1746">#1746</a>, 37331 <a href="https://github.com/easybuilders/easybuild-framework/pull/1748">#1748</a>)</li> 37332<li>only load modules using short module names 37333 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1754">#1754</a>)</li> 37334<li>(re)load modules for build deps in extensions_step 37335 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1762">#1762</a>)</li> 37336<li>fix <code>modpath_extensions_for method</code>: take into account modules 37337 in Lua syntax 37338 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1766">#1766</a>)</li> 37339<li>fix broken link to VSC website in license headers 37340 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1768">#1768</a>)</li> 37341</ul> 37342</li> 37343</ul> 37344<p><strong>easyblocks</strong></p> 37345<ul> 37346<li>add test configuration for Travis 37347 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/895">#895</a>, 37348 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/897">#897</a>, 37349 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/900">#900</a>, 37350 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/926">#926</a>)</li> 37351<li>new easyblocks for 4 software packages that require customized 37352 support:<ul> 37353<li>binutils 37354 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/907">#907</a>), 37355 libQGLViewer 37356 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/890">#890</a>), 37357 SuperLU 37358 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/860">#860</a>), 37359 wxPython 37360 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/883">#883</a>)</li> 37361</ul> 37362</li> 37363<li>various other enhancements, including:<ul> 37364<li>update SuiteSparse easyblock for version >= 4.5 37365 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/863">#863</a>)</li> 37366<li>enhance imkl easyblock to install on top of PGI 37367 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/866">#866</a>, 37368 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/916">#916</a>)</li> 37369<li>enable runtime logging of install cmd in <code>IntelBase</code> 37370 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/874">#874</a>)</li> 37371<li>enhance Qt easyblock to support installing with <code>dummy</code> 37372 toolchain 37373 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/881">#881</a>)</li> 37374<li>delete libnuma symbolic links in PGI installation directory 37375 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/888">#888</a>)</li> 37376<li>enhance PDT easyblock to support installing with <code>dummy</code> 37377 toolchain 37378 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/894">#894</a>)</li> 37379<li>
37379add support for building Clang with OpenMP support 37380 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/898">#898</a>)</li> 37381<li>update Score-P easyblock for additional compilers, MPI libraries 37382 & dependencies 37383 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/889">#889</a>)</li> 37384<li>drop deprecated '<code>testrb</code>' from sanity check in Ruby easyblock 37385 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/901">#901</a>)</li> 37386<li>enhance WRF easyblock to support versions >= 3.7 37387 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/902">#902</a>)</li> 37388<li>update QuantumESPRESSO easyblock for version 5.3.0 37389 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/904">#904</a>)</li> 37390<li>add support in PythonPackage easyblock to use 37391 '<code>setup.py develop</code>' 37392 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/905">#905</a>)</li> 37393<li>update Qt easyblock for Qt 5.6.0 37394 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/908">#908</a>)</li> 37395<li>extend bzip2 easyblock to also build dynamic libraries 37396 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/910">#910</a>)</li> 37397<li>make threading an explicit option rather than relying on MPI 37398 library in SCOTCH easyblock 37399 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/914">#914</a>)</li> 37400<li>update PGI easyblock to install siterc file so PGI picks up 37401 <code>$LIBRARY_PATH</code> 37402 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/919">#919</a>)</li> 37403<li>enhance sanity check paths for compiler commands in PGI 37404 easyblock 37405 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/919">#919</a>)</li> 37406<li>also filter out <code>-ldl</code> from $LIBBLAS & co for Intel MKL in 37407 numpy easyblock 37408 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/920">#920</a>)</li> 37409<li>define <code>$MIC_LD_LIBRARY_PATH</code> for impi 37410 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/925">#925</a>)</li> 37411</ul> 37412</li> 37413<li>various bug fixes, including:<ul> 37414<li>don't hardcode Python version in 37415 <code>test_make_module_pythonpackage</code> 37416 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/876">#876</a>)</li> 37417<li>make PythonPackage easyblock compatible with <code>--module-only</code> 37418 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/884">#884</a>, 37419 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/906">#906</a>)</li> 37420<li>remove check whether '<code>easybuild</code>' is being imported from dir 37421 that contains <code>easybuild/__init__.py</code> 37422 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/891">#891</a>)</li> 37423<li>fix passing compiler configure option in PDT easyblock 37424 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/894">#894</a>)</li> 37425<li>fix bug in Score-P easyblock w.r.t. <code>--with-libbfd</code> 37426 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/889">#889</a>)</li> 37427<li>fix extension filter for Ruby 37428 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/901">#901</a>)</li> 37429<li>fix <code>ACTIVATION_TYPES</code> list in IntelBase + minor style change 37430 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/913">#913</a>)</li> 37431<li>correctly define <code>$MIC_LD_LIBRARY_PATH</code> in imkl 11.3.x and newer 37432 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/915">#915</a>)</li> 37433<li>fix broken link to VSC website in license headers 37434 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/927">#927</a>)</li> 37435</ul> 37436</li> 37437</ul> 37438<p><strong>easyconfigs</strong></p> 37439<ul> 37440<li>added example easyconfig files for 69 new software packages:<ul> 37441<li>ALPS 37442 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2888">#2888</a>), 37443 annovar 37444 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3010">#3010</a>), 37445 BayeScEnv 37446 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2765">#2765</a>), 37447 BayesAss 37448 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2870">#2870</a>), 37449 BerkeleyGW 37450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2925">#2925</a>), 37451 Blitz++ 37452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2784">#2784</a>, 37453 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3004">#3004</a>), 37454 bam-readcount 37455 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2850">#2850</a>), 37456 Commet 37457 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2938">#2938</a>), 37458 CrossTalkZ 37459 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2939">#2939</a>), 37460 cuDNN 37461 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2882">#2882</a>), 37462 DBus 37463 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37464 DFT-D3 37465 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2107">#2107</a>), 37466 DIAL 37467 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3056">#3056</a>), 37468 dask 37469 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2885">#2885</a>), 37470 dbus-glib 37471 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37472 FFLAS-FFPACK 37473 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2793">#2793</a>), 37474 FLAC 37475 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2824">#2824</a>), 37476 FLANN 37477 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3015">#3015</a>, 37478 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3029">#3029</a>), 37479 FLEUR 37480 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3043">#3043</a>), 37481 GConf 37482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37483 GROMOS++ 37484 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1297">#1297</a>), 37485 GST-plugins-base 37486 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37487 GStreamer 37488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37489 GTOOL 37490 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2805">#2805</a>), 37491 Givaro 37492 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2793">#2793</a>), 37493 gdist 37494 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2935">#2935</a>), 37495 gromosXX 37496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1297">#1297</a>), 37497 HISAT2 37498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2809">#2809</a>), 37499 i-PI 37500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2940">#2940</a>), 37501 Kraken 37502 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3037">#3037</a>, 37503 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3041">#3041</a>), 37504 LAME 37505 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2823">#2823</a>), 37506 LASTZ 37507 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3002">#3002</a>), 37508 LinBox 37509 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2793">#2793</a>), 37510 Loki 37511 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2839">#2839</a>), 37512 libQGLViewer 37513 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2923">#2923</a>, 37514 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3008">#3008</a>), 37515 libXxf86vm 37516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37517 MDSplus 37518 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2787">#2787</a>, 37519 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2838">#2838</a>, 37520 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3027">#3027</a>), 37521 MRIcron 37522 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2831">#2831</a>), 37523 Mawk 37524 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2732">#2732</a>), 37525 minieigen 37526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2839">#2839</a>), 37527 mpmath 37528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3058">#3058</a>), 37529 NBO 37530 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3047">#3047</a>, 37531 3048), NGS 37532 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2803">#2803</a>), 37533 NGS-Python 37534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2810">#2810</a>), 37535 ncbi-vdb 37536 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2808">#2808</a>), 37537 OptiX 37538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2795">#2795</a>), 37539 PCL 37540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3024">#3024</a>), 37541 PEAR 37542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2731">#2731</a>), 37543 PLplot 37544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2990">#2990</a>), 37545 Postgres-XL 37546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2891">#2891</a>), 37547 PyGTS 37548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2969">#2969</a>), 37549 RSeQC 37550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2788">#2788</a>), 37551 Rust 37552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2920">#2920</a>, 37553 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2943">#2943</a>), 37554 rainbow 37555 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2730">#2730</a>), 37556 SHAPEIT 37557 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2806">#2806</a>), 37558 SIONlib 37559 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2908">#2908</a>), 37560 Saxon-HE 37561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2773">#2773</a>), 37562 Singularity 37563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2901">#2901</a>), 37564 SoX 37565 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2825">#2825</a>), 37566 Subread 37567 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2790">#2790</a>), 37568 SuperLU 37569 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2665">#2665</a>), 37570 travis 37571 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2953">#2953</a>), 37572 VASP 37573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2950">#2950</a>), 37574 Wannier90 37575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2906">#2906</a>, 37576 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3042">#3042</a>), 37577 wget 37578 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3041">#3041</a>), 37579 wxPython 37580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37581 xf86vidmodeproto 37582 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2855">#2855</a>), 37583 Yade 37584 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2839">#2839</a>), 37585 Yambo 37586 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2932">
37586#2932</a>)</li> 37587</ul> 37588</li> 37589<li>add test configuration for Travis 37590 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2942">#2942</a>, 37591 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2944">#2944</a>, 37592 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2954">#2954</a>, 37593 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3061">#3061</a>)</li> 37594<li>added easyconfigs for new PGI-based toolchains<ul> 37595<li><code>pomkl/2016.03</code> 37596 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2899">#2899</a>, 37597 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2900">#2900</a>, 37598 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3046">#3046</a>), 37599 <code>pomkl/2016.04</code> 37600 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3044">#3044</a>), 37601 <code>CrayPGI/2016.04</code> 37602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2927">#2927</a>)</li> 37603</ul> 37604</li> 37605<li>added new easyconfigs for existing toolchains:<ul> 37606<li><code>foss/2016.04</code> 37607 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3013">#3013</a>), 37608 <code>intel/2016.02-GCC-5.3</code> 37609 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2523">#2523</a>), 37610 <code>intel/2016.03-GCC-5.3</code> 37611 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3009">#3009</a>)</li> 37612</ul> 37613</li> 37614<li>added additional easyconfigs for various supported software 37615 packages: version updates, different toolchains, ...<ul> 37616<li>incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, 37617 imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181, LLVM 3.8.0, OpenCV 37618 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, 37619 SuiteSparse 4.5.2, WRF 3.8</li> 37620</ul> 37621</li> 37622<li>various other enhancements, including:<ul> 37623<li>enhance ORCA easyconfig for compatibility with SLURM 37624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1819">#1819</a>)</li> 37625<li>enable <code>-fPIC</code> in GraphicsMagick easyconfig, required by Octave 37626 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2764">#2764</a>)</li> 37627<li>clean up binutils easyconfigs to use binutils easyblock 37628 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3006">#3006</a>)</li> 37629<li>add <code>include/GraphicsMagick</code> to <code>$CPATH</code> in GraphicsMagick 37630 easyconfigs 37631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3034">#3034</a>)</li> 37632<li>update SuiteSparse easyconfigs according to updated SuiteSparse 37633 easyblock 37634 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3050">#3050</a>)</li> 37635</ul> 37636</li> 37637<li>various bug fixes, including:<ul> 37638<li>fix Perl extensions download urls 37639 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2738">#2738</a>)</li> 37640<li>add Autoconf as build dep for <code>GCCcore</code> 37641 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2772">#2772</a>)</li> 37642<li>fix versions of extensions in Bioconductor 3.2 bundles 37643 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2769">#2769</a>)</li> 37644<li>fix (build) deps for <code>intel/2016a</code> easyconfigs of cairo, 37645 libXext, libXrender 37646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2785">#2785</a>, 37647 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2874">#2874</a>)</li> 37648<li>use '<code>env</code>' wherever preconfig/build/installopts is used to 37649 set environmental variables 37650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2807">#2807</a>, 37651 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2811">#2811</a>, 37652 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2812">#2812</a>)</li> 37653<li>add zlib as explicit dep in Tk easyconfigs 37654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2815">#2815</a>)</li> 37655<li>consistently specify to use <code>-fgnu89-inline</code> flag in M4 1.4.17 37656 easyconfigs 37657 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2774">#2774</a>, 37658 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2779">#2779</a>, 37659 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2816">#2816</a>)</li> 37660<li>fix homepage and description in Pygments easyconfigs 37661 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2822">#2822</a>)</li> 37662<li>include pkg-config as build dependencies for libXau, libXdmcp, 37663 libxcb 37664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2827">#2827</a>)</li> 37665<li>consistently use <code>XORG_*_SOURCE</code> constants 37666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2829">#2829</a>, 37667 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2830">#2830</a>, 37668 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2848">#2848</a>)</li> 37669<li>update source URLs in ScientificPython easyconfig files 37670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2847">#2847</a>)</li> 37671<li>
37671add checksums in SuiteSparse easyconfigs 37672 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2849">#2849</a>)</li> 37673<li>fix build deps for GObject-Introspection 37674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2852">#2852</a>)</li> 37675<li>correctly specify Perl location in git easyconfig 37676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2866">#2866</a>)</li> 37677<li>fix bitstring 3.1.3 download URL in Python easyconfigs, source 37678 tarball on PyPI disappeared 37679 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2880">#2880</a>)</li> 37680<li>fix Perl dependency in worker easyconfigs, it requires 37681 non-standard Perl modules 37682 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2884">#2884</a>)</li> 37683<li>add XZ as dependency in Python 3.5.1 easyconfigs, required for 37684 lzma 37685 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2887">#2887</a>)</li> 37686<li>fix download URL for packmol 37687 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2902">#2902</a>)</li> 37688<li>drop <code>usempi</code> toolchain in numexpr easyconfigs, not needed 37689 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2937">#2937</a>)</li> 37690<li>fix use of <code>resolve_dependencies</code> in tests according to changes 37691 in framework 37692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2952">#2952</a>)</li> 37693<li>add dependency extensions for MarkupSafe and jsonscheme in 37694 IPython 3.2.3 easyconfigs 37695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2967">#2967</a>)</li> 37696<li>add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being 37697 used 37698 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2971">#2971</a>)</li> 37699<li>add xproto build dependency for makedepend v1.0.5 37700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2982">#2982</a>)</li> 37701<li>disable parallel build for Doxygen 37702 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2986">#2986</a>)</li> 37703<li>fix source URLs for <code>FreezeThaw</code> and <code>Tie::Function</code> extensions 37704 for Perl v5.22.1 37705 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2988">#2988</a>)</li> 37706<li>add <code>sed</code> command in worker easyconfig files to fix module_path 37707 in conf/worker.conf 37708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2997">#2997</a>, 37709 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3000">#3000</a>)</li> 37710<li>drop toolchainopts from Eigen easyconfigs, since it is 37711 headers-only 37712 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3025">#3025</a>)</li> 37713<li>clean up dummy bzip2 easyconfig, define buildopts rather than 37714 defining <code>$CC</code> and <code>$CFLAGS</code> via <code>os.environ</code> 37715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3036">#3036</a>)</li> 37716<li>use <code>%(pyshortver)s</code> template rather than hardcoding 2.7 in VTK 37717 easyconfigs 37718 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3052">#3052</a>)</li> 37719<li>correct install location of OpenCV Python bindings 37720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3054">#3054</a>)</li> 37721<li>include XZ as dependency for libunwind 37722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3055">#3055</a>)</li> 37723<li>add patch to fix broken OpenSSL tests due to expired 37724 certificates 37725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3057">#3057</a>)</li> 37726<li>fix broken link to VSC website in license headers 37727 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/3062">#3062</a>)</li> 37728</ul> 37729</li> 37730</ul> 37731<h2 id="release_notes_eb270">EasyBuild v2.7.0 (March 20th 2016)<a class="headerlink" href="#release_notes_eb270" title="Permanent link">¶</a></h2> 37732<p>feature + bugfix release</p> 37733<p><strong>framework</strong></p> 37734<ul> 37735<li>stabilize Cray support<ul> 37736<li>enable '<code>dynamic</code>' toolchain option by default for <code>Cray*</code> 37737 toolchains 37738 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1581">#1581</a>)</li> 37739<li>remove FFTW from the Cray toolchains definition 37740 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1585">#1585</a>)</li> 37741<li>
37741add external modules metadata for Cray systems 37742 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1638">#1638</a>)</li> 37743<li>fix independency of Cray toolchains w.r.t. toolchain build 37744 environment 37745 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1641">#1641</a>, 37746 <a href="https://github.com/easybuilders/easybuild-framework/pull/1647">#1647</a>)</li> 37747<li>remove requirement to use <code>--experimental</code> for Cray toolchains 37748 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1663">#1663</a>)</li> 37749</ul> 37750</li> 37751<li>enable Python optimization mode in '<code>eb</code>' 37752 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1357">#1357</a>)</li> 37753<li>improved GitHub integration<ul> 37754<li>improve error handling on git commands + better logging for 37755 <code>--new-pr</code>/<code>--update-pr</code> 37756 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1590">#1590</a>)</li> 37757<li>use <code>git</code> rather than <code>https</code> in <code>--new-pr</code>/<code>--update-pr</code> 37758 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1602">#1602</a>)</li> 37759<li>add <code>-u</code> as shorthand for <code>--upload-test-report</code> 37760 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1605">#1605</a>)</li> 37761<li>fix <code>--from-pr</code> for PRs that include renamed/deleted files 37762 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1615">#1615</a>)</li> 37763<li>add support for <code>--install-github-token</code> and <code>--check-github</code> 37764 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1616">#1616</a>)</li> 37765<li>fix <code>fetch_easyconfigs_from_pr</code> w.r.t. duplicate files in PRs 37766 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1628">#1628</a>)</li> 37767</ul> 37768</li> 37769<li>various other enhancements, including:<ul> 37770<li>add support for <code>--search-filename</code> and <code>--terse</code> 37771 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1577">#1577</a>)</li> 37772<li>support complete bash completion 37773 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1580">#1580</a>)</li> 37774<li>add support for <code>%(*ver)s</code> and <code>%(*shortver)s</code> templates 37775 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1595">#1595</a>, 37776 <a href="https://github.com/easybuilders/easybuild-framework/pull/1604">#1604</a>)<ul> 37777<li>incl. <code>%(javaver)s</code>, <code>%(javashortver)s</code>, <code>%(perlver)s</code>, 37778 <code>%(perlshortver)s</code>, <code>%(pyver)s</code>, <code>%(pyshortver)s</code>, 37779 <code>%(rver)s</code>, <code>%(rshortver)s</code></li> 37780</ul> 37781</li> 37782<li>define <code>HOME</code> constant that can be used in easyconfig files 37783 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1607">#1607</a>)</li> 37784<li>implement support for generating '<code>swap</code>' statements in module 37785 files 37786 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1609">#1609</a>)</li> 37787<li>add support for <code>--show-config</code> 37788 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1611">#1611</a>, 37789 <a href="https://github.com/easybuilders/easybuild-framework/pull/1620">#1620</a>)</li> 37790<li>simplified support for <code>--minimal-toolchains</code> 37791 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1614">#1614</a>, 37792 <a href="https://github.com/easybuilders/easybuild-framework/pull/1619">#1619</a>, 37793 <a href="https://github.com/easybuilders/easybuild-framework/pull/1622">#1622</a>, 37794 <a href="https://github.com/easybuilders/easybuild-framework/pull/1625">#1625</a>, 37795 <a href="https://github.com/easybuilders/easybuild-framework/pull/1646">#1646</a>)</li> 37796<li>add support for <code>--dump-env-script</code> 37797 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1624">#1624</a>)</li> 37798<li>enhance ModulesTool.exist to also recognize partial module names 37799 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1630">#1630</a>)</li> 37800<li>improve error message for toolchain definition errors 37801 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1631">#1631</a>)</li> 37802<li>
37802make default is_short_modname_for check less strict to support 37803 versionless external modules as deps 37804 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1632">#1632</a>)</li> 37805<li>mention hostname in comment made by <code>--upload-test-report</code> 37806 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1635">#1635</a>)</li> 37807<li>support providing additional relative path for prefix in 37808 external module metadata 37809 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1637">#1637</a>)</li> 37810<li>add <code>ThematicModuleNamingScheme</code> 37811 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1645">#1645</a>)</li> 37812<li>enhance logging format: remove logger name, mention location 37813 instead 37814 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1649">#1649</a>, 37815 <a href="https://github.com/easybuilders/easybuild-framework/pull/1654">#1654</a>)</li> 37816<li>update kernel versions for SLES12 37817 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1659">#1659</a>)</li> 37818<li>raise <code>EasyBuildError</code> rather than <code>ImportError</code> in 37819 <code>only_if_module_is_available</code> decorator 37820 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1662">#1662</a>)</li> 37821</ul> 37822</li> 37823<li>various bug fixes, including:<ul> 37824<li>fix Lmod spider output in generated modules 37825 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1583">#1583</a>)</li> 37826<li>correctly define '<code>easybuild</code>' namespaces 37827 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1593">#1593</a>, 37828 <a href="https://github.com/easybuilders/easybuild-framework/pull/1666">#1666</a>, 37829 <a href="https://github.com/easybuilders/easybuild-framework/pull/1680">#1680</a>)<ul> 37830<li>this change requires that the <code>setuptools</code> Python package is 37831 available (at runtime)</li> 37832<li>using custom easyblocks by adding them in the Python search 37833 path (<code>$PYTHONPATH</code>) may require adjustments, i.e. also 37834 using <code>pkg_resources.declare_namespace</code> in the <code>__init__.py</code> 37835 files; <em>we highly recommend to use</em> <code>--include-easyblocks</code> 37836 <em>instead</em>, see 37837 <a href="http://easybuild.readthedocs.org/en/latest/Including_additional_Python_modules.html">http://easybuild.readthedocs.org/en/latest/Including_additional_Python_modules.html</a></li> 37838<li>note: this has the side-effect of not being able anymore to 37839 reliably use '<code>eb</code>' in the parent directory of the 37840 easybuild-framework repository 37841 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1667">#1667</a>)</li> 37842</ul> 37843</li> 37844<li>fix template for <code>savannah.gnu.org</code> source URL 37845 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1601">#1601</a>)</li> 37846<li>stop running '<code>module purge</code>', only restore environment 37847 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1608">#1608</a>)</li> 37848<li>fix license headers: Hercules foundation is now FWO 37849 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1629">#1629</a>)</li> 37850<li>avoid that <code>fancylogger</code> tries to import <code>mpi4py</code> to determine 37851 MPI rank 37852 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1648">#1648</a>)</li> 37853<li>fix error in tests when '<code>file</code>' backend is not available in 37854 Python keyring 37855 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1650">#1650</a>)</li> 37856<li>update develop install script 37857 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1651">#1651</a>)</li> 37858<li>handle allowed system deps during <code>prepare_step</code> rather than 37859 during parsing of easyconfig 37860 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1652">#1652</a>)</li> 37861<li>add function to find FlexLM licenses: <code>find_flexlm_license</code> 37862 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1633">#1633</a>, 37863 <a href="https://github.com/easybuilders/easybuild-framework/pull/1653">#1653</a>)</li> 37864<li>fix availability check for external modules with partial module 37865 name 37866 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1634">#1634</a>, 37867 <a href="https://github.com/easybuilders/easybuild-framework/pull/1643">#1643</a>)</li> 37868<li>fix bootstrap script to ensure <code>setuptools</code> is also installed 37869 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1655">#1655</a>)</li> 37870<li>fix issue in bootstrap script with <code>vsc-base</code> being picked up 37871 from the OS 37872 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1656">#1656</a>)</li> 37873<li>fix bootstrap script for environment where '<code>python</code>' is 37874 Python 3.x 37875 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1660">#1660</a>)</li> 37876<li>remove <code>--experimental</code> for tests related to <code>--package</code> 37877 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1665">#1665</a>)</li> 37878<li>ensure path to setuptools is included in <code>$PYTHONPATH</code> being 37879 used to test scripts 37880 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1671">#1671</a>)</li> 37881<li>sanitize environment before initializing easyblocks 37882 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1676">#1676</a>)</li> 37883<li>remove <code>reload</code> statements in <code>include.py</code>, since they are not 37884 required and break <code>--include-toolchains</code> 37885 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1679">#1679</a>)</li> 37886</ul> 37887</li> 37888</ul> 37889<p><strong>easyblocks</strong></p> 37890<ul> 37891<li>new easyblocks for 6 software packages that require customized 37892 support:<ul> 37893<li>ADF 37894 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/826">#826</a>), 37895 MPICH 37896 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/844">#844</a>, 37897 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/852">#852</a>, 37898 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/868">#868</a>), 37899 mutil 37900 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/859">#859</a>), 37901 pplacer 37902 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/835">#835</a>), 37903 psmpi 37904 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/852">#852</a>), 37905 SNPhylo 37906 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/865">#865</a>)</li> 37907</ul> 37908</li> 37909<li>various other enhancements, including:<ul> 37910<li>implement support for '<code>
37910use_pip</code>' in PythonPackage easyblock 37911 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/719">#719</a>, 37912 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/831">#831</a>)</li> 37913<li>add support in CUDA easyblock to install wrappers for host 37914 compilers 37915 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/758">#758</a>)</li> 37916<li>update sanity check for picard version 1.124 and above 37917 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/796">#796</a>)</li> 37918<li>use '<code>module swap</code>' for all components in <code>CrayToolchain</code> 37919 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/823">#823</a>)</li> 37920<li>update PSI4 easyblock to cope with changed name of PSI4 data dir 37921 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/824">#824</a>)</li> 37922<li>use <code>find_flexlm_license</code> function and avoid defining <code>$CPATH</code> 37923 in PGI easyblock 37924 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/837">#837</a>)</li> 37925<li>use <code>find_flexlm_license</code> function in <code>IntelBase</code> generic 37926 easyblock 37927 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/839">#839</a>)</li> 37928<li>add unit test to check module file generated by <code>PythonPackage</code> 37929 easyblock 37930 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/841">#841</a>)</li> 37931<li>rework MVAPICH2 easyblock on top of new MPICH easyblock 37932 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/844">#844</a>)</li> 37933<li>add CUDA support in CP2K easyblock 37934 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/850">#850</a>)</li> 37935<li>also define <code>$LD</code> in <code>buildopts</code> for GATE 37936 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/855">#855</a>)</li> 37937<li>use <code>find_flexlm_license</code> function in TotalView easyblock 37938 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/839">#839</a>)</li> 37939<li>enhance <code>MakeCp</code> easyblock to also support renaming of files 37940 while copying them 37941 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/859">#859</a>)</li> 37942<li>hunt for usable '<code>python</code>' command in <code>PythonPackage</code> 37943 easyblock when system Python is used 37944 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/861">#861</a>)</li> 37945<li>add sanity check in <code>easybuild/__init__.py</code> w.r.t. current 37946 working dir 37947 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/869">#869</a>)</li> 37948<li>change suffix of original file to <code>.easybuild</code> when using 37949 <code>fileinput</code> in impi easyblock 37950 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/870">#870</a>)</li> 37951</ul> 37952</li> 37953<li>various bug fixes, including:<ul> 37954<li>make sure Python unicode settings match that of the system 37955 Python 37956 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/817">#817</a>)</li> 37957<li>remove FFTW related statements in HPL easyblock, since HPL 37958 doesn't require FFTW at all 37959 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/822">#822</a>)</li> 37960<li>use <code>pkg_resources.declare_namespace</code> rather than 37961 <code>pkgutil.extend_path</code> to declare '<code>easybuild</code>' namespaces 37962 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/827">#827</a>)</li> 37963<li>fix license headers: Hercules foundation is now FWO 37964 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/836">#836</a>)</li> 37965<li>fix check for non-empty lib dirs in <code>PythonPackage</code> easyblock 37966 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/840">#840</a>)</li> 37967<li>consider all Python lib dirs in sanity check for libxml2 37968 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/842">#842</a>)</li> 37969<li>correctly handle deprecated configure options 37970 (<code>--with-hwloc</code>/<code>--enable-mpe</code>) in MVAPICH2 easyblock 37971 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/853">#853</a>)</li> 37972<li>use correct configure option for checkpoint/restart in MVAPICH2 37973 easyblock 37974 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/854">#854</a>)</li> 37975<li>ensure list of Python lib dirs always has a '<code>lib/...</code>' entry 37976 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/858">#858</a>)</li> 37977<li>check whether <code>rpm</code>/<code>rpmrebuild</code> commands are available using 37978 '<code>which</code>', rather than checking for OS deps 37979 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/864">#864</a>)</li> 37980<li>fix <code>test_step</code> in UFC easyblock 37981 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/872">#872</a>)</li> 37982</ul> 37983</li> 37984</ul> 37985<p><strong>easyconfigs</strong></p> 37986<ul> 37987<li>added example easyconfig files for 63 new software packages:<ul> 37988<li>ATSAS 37989 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/616">#616</a>, 37990 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2587">#2587</a>), 37991 astropy 37992 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2724">#2724</a>, 37993 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2727">#2727</a>), 37994 attr 37995 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2706">#2706</a>), 37996 BamUtil 37997 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2654">#2654</a>), 37998 BBMap 37999 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2322">#2322</a>), 38000 BH 38001 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2508">#2508</a>), 38002 CheMPS2 38003 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2445">#2445</a>), 38004 CosmoloPy 38005 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2723">#2723</a>, 38006 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2727">#2727</a>), 38007 csvkit 38008 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2639">#2639</a>), 38009 Firefox 38010 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2648">#2648</a>), 38011 FreeXL 38012 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2422">#2422</a>), 38013 GL2PS 38014 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2667">#2667</a>), 38015 Glade 38016 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2631">#2631</a>), 38017 htop 38018 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2538">#2538</a>), 38019 IGV 38020 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2019">#2019</a>), 38021 IGVTools 38022 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2019">#2019</a>), 38023 ImageMagick 38024 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2438">#2438</a>), 38025 jModelTest 38026 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2529">#2529</a>), 38027 KEALib 38028 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2420">#2420</a>), 38029 libcerf 38030 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2656">#2656</a>), 38031 libgcrypt 38032 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2201">#2201</a>), 38033 libglade 38034 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2631">#2631</a>), 38035 libgpg-error 38036 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2201">#2201</a>), 38037 libspatialite 38038 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2431">#2431</a>), 38039 LittleCMS 38040 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2438">#2438</a>), 38041 MAST 38042 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2542">#2542</a>), 38043 MLC 38044 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2577">#2577</a>), 38045 MPJ-Express 38046 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2529">#2529</a>), 38047 mutil 38048 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2201">#2201</a>), 38049 neon 38050 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/758">#758</a>), 38051 NextClip 38052 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2544">#2544</a>), 38053 npstat 38054 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2686">#2686</a>, 38055 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2703">#2703</a>), 38056 Octopus 38057 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2643">#2643</a>), 38058 QuickFF 38059 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2721">#2721</a>), 38060 p4vasp 38061 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2328">#2328</a>), 38062 PCMSolver 38063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2445">#2445</a>), 38064 PFFT 38065 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2643">#2643</a>), 38066 PHYLIP 38067 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2694">#2694</a>), 38068 pkgconfig 38069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2475">#2475</a>, 38070 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2476">#2476</a>), 38071 Platypus 38072 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2618">#2618</a>), 38073 pplacer 38074 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1056">#1056</a>), 38075 PRINSEQ 38076 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2437">#2437</a>, 38077 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2444">#2444</a>, 38078 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2585">#2585</a>), 38079 PyFFmpeg 38080 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2501">#2501</a>, 38081 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2519">#2519</a>), 38082 PyGObject 38083 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2443">#2443</a>), 38084 PyGTK 38085 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2443">#2443</a>), 38086 PyOpenGL 38087 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2628">#2628</a>), 38088 pyringe 38089 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2533">#2533</a>), 38090 qrupdate 38091 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2675">#2675</a>), 38092 rgeos 38093 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2635">#2635</a>), 38094 rpmrebuild 38095 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2402">#2402</a>), 38096 shift 38097 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2201">#2201</a>), 38098 SNAPE-pooled 38099 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2688">#2688</a>), 38100 SNPhylo 38101 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2701">#2701</a>), 38102 sratoolkit 38103 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2715">#2715</a>), 38104 STAR-Fusion 38105 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2463">#2463</a>), 38106 statsmodels 38107 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2719">#2719</a>), 38108 StringTie 38109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2527">#2527</a>), 38110 synchronicity 38111 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2508">#2508</a>), 38112 testpath 38113 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2461">#2461</a>), 38114 USEARCH 38115 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2537">#2537</a>), 38116 VarScan 38117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2464">#2464</a>), 38118 vsc-install 38119 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2165">#2165</a>), 38120 Whoosh 38121 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2725">#2725</a>), 38122 xprop 38123 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2645">#2645</a>)</li> 38124</ul> 38125</li> 38126<li>
38126added new easyconfigs for existing toolchains:<ul> 38127<li><code>intel/2016.02-GCC-4.9</code> 38128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2620">#2620</a>), 38129 <code>gmpolf/2016a</code> & <code>gmvolf/2016a</code> 38130 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2589">#2589</a>)</li> 38131</ul> 38132</li> 38133<li>stable Cray-specific easyconfigs<ul> 38134<li>delete deprecated Cray toolchains and easyconfig files 38135 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2400">#2400</a>)</li> 38136<li>don't hardcode <code>PrgEnv</code> version, remove <code>craype</code> and <code>fftw</code> 38137 components in Cray toolchains 38138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2554">#2554</a>)</li> 38139<li>remove <code>-XC</code> versionsuffix for stable definitions for <code>Cray*</code> 38140 toolchains 38141 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2714">#2714</a>)</li> 38142<li>support for various software packages with <code>CrayGNU</code> and 38143 <code>CrayIntel</code> toolchains: CP2K, GROMACS, WRF</li> 38144</ul> 38145</li> 38146<li>added additional easyconfigs for various supported software 38147 packages: version updates, different toolchains, ...<ul> 38148<li>including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 38149 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1, R 3.2.3, 38150 R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1</li> 38151</ul> 38152</li> 38153<li>various other enhancements, including:<ul> 38154<li>copy <code>contrib</code> dir in Velvet easyconfigs so scripts are also 38155 available 38156 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2456">#2456</a>)</li> 38157<li>redefine matplotlib 1.5.1 easyconfig as a bundle, also include 38158 <code>cycler</code> extension (dep for matplotlib) 38159 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2470">#2470</a>)</li> 38160<li>add bitstring extension to Python 2.7.11 easyconfigs 38161 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2471">#2471</a>)</li> 38162<li>enable building of MetaVelvet in Velvet 1.2.10 easyconfigs 38163 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2473">#2473</a>)</li> 38164<li>add custom sanity check for libjpeg-turbo 38165 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2480">#2480</a>)</li> 38166<li>add Velvet easyconfigs that include BioPerl dependency, so 38167 VelvetOptimizer can use it 38168 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2495">#2495</a>, 38169 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2729">#2729</a>, 38170 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2733">#2733</a>)</li> 38171<li>add source URL in RAxML 7.2.6 easyconfigs 38172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2536">#2536</a>)</li> 38173<li>update MPICH easyconfigs to use new MPICH easyblock 38174 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2589">#2589</a>)</li> 38175<li>free libX11 & co from unneeded Python dependency/versionsuffix 38176 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2549">#2549</a>, 38177 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2563">#2563</a>, 38178 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2605">#2605</a>, 38179 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2664">#2664</a>)</li> 38180<li>add '<code>--enable-utf --enable-unicode-properties</code>' configure 38181 options in PCRE easyconfigs 38182 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2561">#2561</a>)<ul> 38183<li>required for latest R versions</li> 38184</ul> 38185</li> 38186<li>add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles 38187 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2553">#2553</a>, 38188 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2578">#2578</a>)</li> 38189<li>add additional extensions in R 3.2.x easyconfigs that are 38190 required for extra Bioconductor extensions 38191 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2547">#2547</a>, 38192 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2556">#2556</a>)</li> 38193<li>update psmpi easyconfig files to use the new psmpi easyblock 38194 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2619">#2619</a>)</li> 38195<li>
38195add easyconfig for Python 2.7.11 on top of X11-enabled Tk 38196 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2614">#2614</a>, 38197 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2621">#2621</a>)</li> 38198<li>add virtualenv as extension in Python 2.7.11 easyconfigs 38199 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2660">#2660</a>)</li> 38200</ul> 38201</li> 38202<li>various bug fixes, including:<ul> 38203<li>fix software name for GTK+ (was 'gtk+'), PyCairo (was 38204 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') 38205 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2468">#2468</a>)</li> 38206<li>don't hardcode <code>CC</code>/<code>CXX</code> in OpenMPI easyconfigs 38207 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2472">#2472</a>)</li> 38208<li>remove Google Code source URL for mpi4py 38209 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2474">#2474</a>)</li> 38210<li>rename ffmpeg to FFmpeg 38211 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2425">#2425</a>, 38212 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2481">#2481</a>)</li> 38213<li>use available easyblock for flex 38214 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2486">#2486</a>)</li> 38215<li>fix determining list of easyconfigs in unit test suite, don't 38216 assume locations are correct 38217 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2530">#2530</a>)</li> 38218<li>fix specifying DB dependency in DB_File easyconfigs 38219 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2539">#2539</a>)</li> 38220<li>remove hard-coded <code>-xSSE4.2</code> for numpy/scipy with Intel 38221 compilers 38222 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2546">#2546</a>)</li> 38223<li>fix license headers: Hercules foundation is now FWO 38224 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2550">#2550</a>)</li> 38225<li>add <code>--with-zlib</code> configure argument in libxml easyconfigs 38226 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2555">#2555</a>)</li> 38227<li>don't hardcode <code>optarch=True</code> in xextproto/xtrans easyconfigs 38228 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2601">#2601</a>)</li> 38229<li>change toolchain version to '' in easyconfigs that use <code>dummy</code> 38230 toolchain and include dependencies 38231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2612">#2612</a>)</li> 38232<li>GLib doesn't require libxml2 with Python bindings 38233 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2632">#2632</a>)</li> 38234<li>add patch file to imkl 10.2.6.038 32-bit easyconfig to fix 38235 installer not being able to deal with '<code>--</code>' in build path 38236 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2634">#2634</a>)</li> 38237<li>add missing 'pkgconfig' dependency for h5py 38238 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2476">#2476</a>, 38239 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2650">#2650</a>)</li> 38240<li>correct software name in FastQC easyconfigs (was 'fastqc'), 38241 use '<code>dummy</code>' toolchain for all FastQC version 38242 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2657">#2657</a>, 38243 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2666">#2666</a>)</li> 38244<li>add missing libxml2 dependencies in GLib easyconfigs 38245 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2658">#2658</a>)</li> 38246<li>fix Xerces-C++ download location 38247 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2668">#2668</a>)</li> 38248<li>enable <code>XML::Bare</code> extension in all Perl easyconfigs 38249 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2672">#2672</a>)</li> 38250<li>update dead link for SuiteSparse 38251 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2679">#2679</a>)</li> 38252<li>remove custom <code>exts_filter</code> in easyconfigs used <code>PythonPackage</code> 38253 easyblock 38254 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2683">#2683</a>, 38255 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2685">#2685</a>)</li> 38256<li>
38256add M4 as build dep for binutils & flex 38257 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2681">#2681</a>)</li> 38258<li>add missing dependencies in Python 3.5.x easyconfigs: SQLite, 38259 Tk, GMP 38260 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2704">#2704</a>)</li> 38261<li>fix (OS) deps, add checksums, remove parameter definition with 38262 default values in MVAPICH2 easyconfigs 38263 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2707">#2707</a>)</li> 38264</ul> 38265</li> 38266<li>style cleanup in various easyconfigs 38267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2378">#2378</a>, 38268 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2387">#2387</a>, 38269 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2395">#2395</a>, 38270 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2396">#2396</a>, 38271 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2488">#2488</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2493">#2493</a>, 38272 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2496">#2496</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2500">#2500</a>, 38273 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2502">#2502</a>-<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2504">#2504</a>, 38274 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2602">#2602</a>)<ul> 38275<li>working towards automated style review of pull requests</li> 38276</ul> 38277</li> 38278</ul> 38279<h2 id="release_notes_eb260">EasyBuild v2.6.0 (January 26th 2016)<a class="headerlink" href="#release_notes_eb260" title="Permanent link">¶</a></h2> 38280<p>feature + bugfix release</p> 38281<p><strong>framework</strong></p> 38282<ul> 38283<li>add (experimental) support for opening/updating (easyconfigs) pull 38284 requests (<code>--new-pr</code>, <code>--update-pr</code>) 38285 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1528">#1528</a>)</li> 38286<li>sanitize environment before each installation by undefining 38287 <code>$PYTHON*</code> 38288 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1569">#1569</a>, 38289 <a href="https://github.com/easybuilders/easybuild-framework/pull/1572">#1572</a>)</li> 38290<li>various other enhancements, including:<ul> 38291<li>allow user-local modules with hierarchical naming schemes 38292 (<code>--subdir-user-modules</code>) 38293 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1472">#1472</a>)</li> 38294<li>enhance <code>--extended-dry-run</code> output to include paths for 38295 requirements in <code>make_module_req</code> 38296 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1520">#1520</a>)</li> 38297<li>rewrite read_file to use '<code>with</code>' 38298 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1534">#1534</a>)</li> 38299<li>add support for <code>eb --last-log</code> 38300 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1541">#1541</a>)</li> 38301<li>support using fixed install dir scheme 38302 (<code>--fixed-installdir-naming-scheme</code>) 38303 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1546">#1546</a>)</li> 38304<li>add edge attributes for build dependencies in <code>--dep-graph</code> 38305 output 38306 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1548">#1548</a>)</li> 38307<li>check whether dependencies marked as external module are hidden 38308 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1552">#1552</a>)</li> 38309<li>implement support for <code>--modules-header</code> 38310 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1558">#1558</a>)</li> 38311<li>add support to specify '<code>else</code>' body for conditional 38312 statements in modules 38313 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1559">#1559</a>)</li> 38314<li>add extra test for <code>--include-easyblocks</code> for generic easyblocks 38315 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1562">#1562</a>)</li> 38316<li>allow user to define the default compiler optimization level 38317 (<code>--default-opt-level</code>) 38318 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1565">#1565</a>)</li> 38319<li>make <code>toolchain.get_variable</code> more robust w.r.t. dummy toolchain 38320 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1566">#1566</a>)</li> 38321</ul> 38322</li> 38323<li>various bug fixes, including:<ul> 38324<li>fix missing '<code>yaml</code>' module check in tests 38325 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1525">#1525</a>)</li> 38326<li>fix 'develop' install script 38327 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1529">#1529</a>)</li> 38328<li>correctly quote FPM option values in packagin support 38329 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1530">#1530</a>)</li> 38330<li>correctly handle '<code>.</code>' in software name w.r.t. <code>$EB*</code> 38331 environment variables 38332 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1538">#1538</a>)</li> 38333<li>exclude logs and test reports from packages 38334 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1544">#1544</a>)</li> 38335<li>also pass down <code>--job-cores</code> for <code>pbs_python</code> job backend 38336 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1547">#1547</a>)</li> 38337<li>
38337skip dependencies marked as external modules when packaging 38338 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1550">#1550</a>)</li> 38339<li>fix syntax for <code>set_alias</code> statement in Lua syntax 38340 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1554">#1554</a>)</li> 38341<li>handle the case of all 'offline' nodes correctly for <code>--job</code> 38342 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1560">#1560</a>)</li> 38343<li>fix <code>test_modules_tool_stateless</code> unit test for stateless 38344 ModulesTool with Lmod as modules tool 38345 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1570">#1570</a>)</li> 38346</ul> 38347</li> 38348</ul> 38349<p><strong>easyblocks</strong></p> 38350<ul> 38351<li>add generic easyblock for Cray toolchains 38352 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/766">#766</a>)</li> 38353<li>new easyblocks for 2 software packages that require customized 38354 support:<ul> 38355<li>EggLib 38356 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/811">#811</a>), 38357 PGI 38358 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/658">#658</a>)</li> 38359</ul> 38360</li> 38361<li>various other enhancements, including:<ul> 38362<li>update BamTools easyblock for versions 2.3.x and newer: some 38363 shared libraries are now static) 38364 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/785">#785</a>)</li> 38365<li>don't hardcode <code>.so</code>, use <code>get_shared_lib_ext</code> instead 38366 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/789">#789</a>, 38367 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/790">#790</a>, 38368 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/791">#791</a>, 38369 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/793">#793</a>, 38370 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/794">#794</a>, 38371 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/803">#803</a>, 38372 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/815">#815</a>)</li> 38373<li>enhance CPLEX easyblock by adding more subdirs to <code>$PATH</code>, 38374 define <code>$LD_LIBRARY</code> and <code>$CPLEXDIR</code> 38375 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/797">#797</a>)</li> 38376<li>make sanity check for netcdf4-python work with both egg and 38377 non-egg installs 38378 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/799">#799</a>)</li> 38379<li>update sanity check in PETSc/SLEPc easyblocks for v3.6.x 38380 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/800">#800</a>)</li> 38381<li>update Trinity easyblock for 2.x versions 38382 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/802">#802</a>)</li> 38383<li>update DOLFIN easyblock for v1.6.0 38384 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/804">#804</a>)</li> 38385<li>check for <code>libkokkoscore.a</code> rather than <code>libkokkos.a</code> for 38386 Trilinos 12.x 38387 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/805">#805</a>)</li> 38388<li>add an option to skip the sanitizer tests of Clang 38389 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/806">#806</a>)</li> 38390<li>update Molpro easyblock to support binary installs and 2015 38391 version 38392 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/807">#807</a>)</li> 38393<li>make <code>ConfigureMake</code> more robust w.r.t. custom easyconfig 38394 parameters 38395 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/810">#810</a>)</li> 38396</ul> 38397</li> 38398<li>various bug fixes, including:<ul> 38399<li>add back support for Eigen 2.x in Eigen easyblock 38400 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/798">#798</a>)</li> 38401<li>fix for vsc-base being picked up from OS in EasyBuildMeta 38402 easyblock 38403 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/813">#813</a>)</li> 38404<li>remove <code>setuptools.pth</code> if it includes absolute paths after 38405 installing EasyBuild 38406 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/813">#813</a>)</li> 38407</ul> 38408</li> 38409</ul> 38410<p><strong>easyconfigs</strong></p> 38411<ul> 38412<li>add easyconfigs for <code>foss/2016a</code> and <code>intel/2016</code> common toolchains 38413 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2310">#2310</a>, 38414 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2311">#2311</a>, 38415 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2339">#2339</a>, 38416 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2363">#2363</a>)<ul> 38417<li>incl. easyconfigs for Boost, CMake, Python, Perl using these 38418 toolchains</li> 38419</ul> 38420</li> 38421<li>
38421added example easyconfig files for 21 new software packages:<ul> 38422<li>BLASR 38423 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/922">#922</a>), 38424 BioKanga 38425 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2247">#2247</a>), 38426 BoltzTraP 38427 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2365">#2365</a>), 38428 basemap 38429 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2221">#2221</a>), 38430 CppUnit 38431 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2271">#2271</a>), 38432 EggLib 38433 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2335">#2335</a>), 38434 FLASH 38435 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2281">#2281</a>), 38436 GLM 38437 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2288">#2288</a>), 38438 hub 38439 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2249">#2249</a>), 38440 MACS2 38441 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1983">#1983</a>), 38442 MotEvo 38443 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/843">#843</a>), 38444 numba 38445 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2243">#2243</a>), 38446 PGI 38447 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1833">#1833</a>, 38448 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2367">#2367</a>), 38449 PLY 38450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2305">#2305</a>), 38451 PaStiX 38452 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2319">#2319</a>, 38453 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2326">#2326</a>), 38454 patchelf 38455 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2327">#2327</a>), 38456 pip 38457 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2284">#2284</a>), 38458 RSEM 38459 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2316">#2316</a>), 38460 RcppArmadillo 38461 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2289">#2289</a>), 38462 SCDE 38463 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2289">#2289</a>), 38464 slepc4py 38465 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2318">#2318</a>)</li> 38466</ul> 38467</li> 38468<li>added additional easyconfigs for various supported software 38469 packages: version updates, different toolchains, ...<ul> 38470<li>including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, 38471 DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0, LLVM 38472 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, 38473 SLEPc 3.6.2, Trilinos 12.4.2, Trinity 2.1.1, VTK 6.3.0</li> 38474</ul> 38475</li> 38476<li>various other enhancements, including:<ul> 38477<li>added new <code>Cray*</code> toolchain versions with pinned dependency 38478 versions 38479 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2222">#2222</a>)</li> 38480<li>don't hardcode <code>.so</code>, use <code>SHLIB_EXT</code> constant instead 38481 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2245">#2245</a>)</li> 38482<li>add custom sanity check in GEOS easyconfigs 38483 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2285">#2285</a>)</li> 38484</ul> 38485</li> 38486<li>various bug fixes, including:<ul> 38487<li>add Autotools (M4) as a build dependency in GMP v6.x easyconfigs 38488 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2096">#2096</a>)</li> 38489<li>remove argparse from list of extensions in Python 3.2+ 38490 easyconfigs, since it became part of stdlib 38491 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2323">#2323</a>)</li> 38492</ul> 38493</li> 38494<li>various style fixes, including:<ul> 38495<li>get rid of tabs 38496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2302">#2302</a>)</li> 38497<li>remove trailing whitespace 38498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2341">#2341</a>)</li> 38499</ul> 38500</li> 38501</ul> 38502<h2 id="release_notes_eb250">EasyBuild v2.5.0 (December 17th 2015)<a class="headerlink" href="#release_notes_eb250" title="Permanent link">¶</a></h2> 38503<p>feature + bugfix release</p> 38504<p><strong>framework</strong></p> 38505<ul> 38506<li>add support for IBM XL compilers on Power7 and PowerPC (BlueGene) 38507 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1470">#1470</a>)</li> 38508<li>
38508add support for generic compilation using <code>--optarch=GENERIC</code> 38509 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1471">#1471</a>)<ul> 38510<li>see also 38511 <a class="autorefs autorefs-internal" href="../controlling-compiler-optimization-flags/#controlling_compiler_optimization_flags">Controlling compiler optimization flags</a></li> 38512</ul> 38513</li> 38514<li>update experimental support for <code>.yeb</code> easyconfigs 38515 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1515">#1515</a>)<ul> 38516<li>support clean way to specify toolchain + dependencies in <code>.yeb</code> 38517 easyconfigs</li> 38518</ul> 38519</li> 38520<li>various other enhancements, including:<ul> 38521<li>add support for '<code>whatis</code>' easyconfig parameter 38522 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1271">#1271</a>)</li> 38523<li>add support for SLES 12 and kernel 3.12.x 38524 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1412">#1412</a>)</li> 38525<li>add GCCcore toolchain definition 38526 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1451">#1451</a>)</li> 38527<li>use '<code>diff --git</code>' lines to determine patched files in pull 38528 request with <code>--from-pr</code> 38529 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1460">#1460</a>)</li> 38530<li>add proper option parser to bootstrap script 38531 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1468">#1468</a>)</li> 38532<li>add <code>get_gcc_version()</code> function in systemtools module 38533 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1496">#1496</a>)</li> 38534<li>don't load fake module in sanity_check_step during a dry run 38535 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1499">#1499</a>)</li> 38536<li>allow string values to be passed in <code>make_module_req</code> by 38537 hoisting them into a list 38538 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1502">#1502</a>)</li> 38539<li>add support for listing build dependencies as hidden 38540 dependencies 38541 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1503">#1503</a>)</li> 38542<li>also consider <code>lib32/pkgconfig</code> and <code>lib64/pkgconfig</code> for 38543 <code>$PKG_CONFIG_PATH</code> 38544 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1505">#1505</a>)</li> 38545<li>add support to <code>make_module_dep</code> to specify module to unload 38546 before loading a dependency module 38547 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1506">#1506</a>)</li> 38548<li>add support to <code>make_module_extra</code> to specify alternative 38549 root/version for <code>$EBROOT</code>/<code>$EBVERSION</code> 38550 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1508">#1508</a>)</li> 38551<li>packaging support is no longer considered experimental 38552 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1510">#1510</a>)</li> 38553</ul> 38554</li> 38555<li>various bug fixes, including:<ul> 38556<li>also consider <code>lib64</code> in sanity check performed during EasyBuild 38557 bootstrap 38558 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1464">#1464</a>)</li> 38559<li>also add description/homepage to packages created with FPM 38560 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1469">#1469</a>)</li> 38561<li>fix develop setup script to install EasyBuild-develop module in 38562 subdirectory 38563 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1480">#1480</a>)</li> 38564<li>don't create a whole set of temporary '<code>minimal-easyconfigs</code>' 38565 subdirs with <code>--minimal-toolchains</code> 38566 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1484">#1484</a>)</li> 38567<li>only keep polling if exit code is <code>None</code> in <code>run_cmd_qa</code>, to 38568 correctly deal with negative exit codes 38569 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1486">#1486</a>)</li> 38570<li>fix bootstrap script for missing sys_platform by using newer 38571 distribute 0.6.49 in stage 0 38572 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1490">#1490</a>)</li> 38573<li>make sure that extra custom easyconfig parameters are known for 38574 extensions 38575 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1498">#1498</a>)</li> 38576<li>
38576add missing import for <code>EasyBuildError</code> in 38577 <code>easybuild/toolchains/linalg/libsci.py</code> 38578 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1512">#1512</a>)</li> 38579<li>isolate tests from possible system-wide configuration files 38580 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1513">#1513</a>)</li> 38581<li>only use <code>glob</code> in <code>make_module_req</code> on non-empty strings 38582 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1519">#1519</a>)<ul> 38583<li>this fixes the problem where <code>$CUDA_HOME</code> and <code>$CUDA_PATH</code> 38584 are not defined in module files for CUDA</li> 38585</ul> 38586</li> 38587</ul> 38588</li> 38589</ul> 38590<p><strong>easyblocks</strong></p> 38591<ul> 38592<li>update easyblocks for Intel tools to support 2016 versions 38593 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/691">#691</a>, 38594 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/745">#745</a>, 38595 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/756">#756</a>, 38596 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/777">#777</a>)<ul> 38597<li>IntelBase easyblock has been enhanced to support specifying 38598 which components to install</li> 38599</ul> 38600</li> 38601<li>new easyblocks for 3 software packages that require customized 38602 support:<ul> 38603<li>Intel Advisor 38604 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/767">#767</a>), 38605 DIRAC 38606 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/778">#778</a>), 38607 MRtrix 38608 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/772">#772</a>)</li> 38609</ul> 38610</li> 38611<li>various other enhancements, including:<ul> 38612<li>update numpy and SuiteSparse easyblock to use scikit-umfpack 38613 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/718">#718</a>)</li> 38614<li>add an option to allow removal of the <code>-Dusethreads</code> flag in 38615 Perl easyblock 38616 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/724">#724</a>)</li> 38617<li>update Doxygen easyblock for 1.10.x (CMake) 38618 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/734">#734</a>)</li> 38619<li>update sanity check in Qt easyblock for Qt 5.x 38620 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/740">#740</a>)</li> 38621<li>add support for multilib build of GCC on PowerPC 38622 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/741">#741</a>)</li> 38623<li>add support to OpenFOAM and SCOTCH easyblocks to support 64-bit 38624 integers, via 'i8' toolchain option 38625 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/744">#744</a>)</li> 38626<li>fix sanity check to support numpy 1.10 (dropped _dotblas.so) 38627 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/757">#757</a>, 38628 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/761">#761</a>, 38629 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/762">#762</a>)</li> 38630<li>update IPP easyblock for v9.x 38631 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/759">#759</a>)</li> 38632<li>cleaner output for PythonPackage under dry run, make numpy 38633 easyblock dry-run aware 38634 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/760">#760</a>, 38635 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/671">#671</a>)</li> 38636<li>add support for using netCDF-Fortran as dependency in ALADIN 38637 easyblock 38638 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/764">#764</a>)</li> 38639<li>add support for tbb 4.4.x in tbb easyblock 38640 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/769">#769</a>)</li> 38641<li>add support for specifying altroot/altversion in Bundle 38642 easyblock 38643 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/773">#773</a>)</li> 38644<li>update OpenFOAM easyblock for OpenFOAM-Extend 3.2 + use 38645 apply_regex_substitutions 38646 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/770">#770</a>)</li> 38647</ul> 38648</li> 38649<li>various bug fixes, including:<ul> 38650<li>
38650fix module path extension of system compiler in HMNS setup 38651 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/742">#742</a>)</li> 38652<li>only restore <code>$PYTHONPATH</code> if it was defined in EasyBuildMeta 38653 easyblock 38654 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/743">#743</a>)</li> 38655<li>make sure <code>$PYTHONPATH</code> is defined correctly in module file for 38656 Python packages created with <code>--module-only</code> 38657 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/748">#748</a>)</li> 38658<li>fix WRF easyblock to produce correct module under 38659 <code>--module-only --force</code> 38660 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/746">#746</a>, 38661 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/752">#752</a>)</li> 38662<li>don't hardcode '<code>openPBS</code>' in GATE easyblock, use value for 38663 <code>default_platform</code> easyconfig parameter 38664 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/753">#753</a>)</li> 38665<li>avoid adding lib subdirs to <code>$*LIBRARY_PATH</code> if no libraries are 38666 there in <code>PythonPackage</code> easyblock 38667 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/755">#755</a>)</li> 38668<li>fix installing Python bindings for libxml2 to correct 38669 installation prefix 38670 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/765">#765</a>)</li> 38671</ul> 38672</li> 38673</ul> 38674<p><strong>easyconfigs</strong></p> 38675<ul> 38676<li> 38677<p>add GCCcore easyconfig that can be used as base for all compilers 38678 (without getting in the way) 38679 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2214">#2214</a>)</p> 38680<ul> 38681<li>along with easyconfig for <code>GCC/4.9.3-2.25</code>: bundle of GCCcore 38682 4.9.3 and binutils 2.25</li> 38683<li>intended to replace the GNU toolchain</li> 38684</ul> 38685</li> 38686<li> 38687<p>added example easyconfig files for 39 new software packages:</p> 38688<ul> 38689<li>DIRAC 38690 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2212">#2212</a>), 38691 GeoIP 38692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2172">#2172</a>, 38693 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2185">#2185</a>), 38694 GeoIP-C 38695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2172">#2172</a>, 38696 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2185">#2185</a>), 38697 graph-tool 38698 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1591">#1591</a>), 38699 gtkglext 38700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2217">#2217</a>), 38701 Intel Advisor 38702 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2210">#2210</a>), 38703 InterProScan 38704 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2225">#2225</a>, 38705 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2227">#2227</a>, 38706 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2234">#2234</a>), 38707 intltool 38708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38709 kallisto 38710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2173">#2173</a>), 38711 LibUUID 38712 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1930">#1930</a>), 38713 LuaJIT 38714 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2153">#2153</a>), 38715 libXcursor 38716 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38717 libXrandr 38718 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38719 libXtst 38720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2143">#2143</a>), 38721 libdap 38722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1930">#1930</a>), 38723 libtasn1 38724 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2208">#2208</a>), 38725 libxkbcommon 38726 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38727 MRtrix 38728 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2217">#2217</a>, 38729 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2218">#2218</a>), 38730 MultiNest 38731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2166">#2166</a>, 38732 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2168">#2168</a>), 38733 Nipype 38734 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2150">#2150</a>), 38735 PPfold 38736 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2183">#2183</a>, 38737 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2187">#2187</a>), 38738 p11-kit 38739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2208">
38739#2208</a>), 38740 pangox-compat 38741 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2217">#2217</a>), 38742 Qt5 38743 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38744 randrproto 38745 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38746 rhdf5 38747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2175">#2175</a>), 38748 Stampy 38749 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2180">#2180</a>, 38750 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2182">#2182</a>), 38751 scikit-umfpack 38752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2061">#2061</a>), 38753 scp (Python pkg) 38754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2196">#2196</a>), 38755 sleuth 38756 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2175">#2175</a>), 38757 traits 38758 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2150">#2150</a>), 38759 vincent 38760 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2169">#2169</a>, 38761 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2185">#2185</a>), 38762 XKeyboardConfig 38763 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38764 xcb-util 38765 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38766 xcb-util-image 38767 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38768 xcb-util-keysyms 38769 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38770 xcb-util-renderutil 38771 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38772 xcb-util-wm 38773 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2136">#2136</a>), 38774 zlibbioc 38775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2175">#2175</a>)</li> 38776</ul> 38777</li> 38778<li> 38779<p>added new easyconfigs for existing toolchains:</p> 38780<ul> 38781<li><code>intel/2015.08</code> 38782 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2194">#2194</a>), 38783 <code>intel/2016.00</code> 38784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2209">#2209</a>), 38785 <code>intel/2016.01</code> 38786 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2219">#2219</a>), 38787 <code>iomkl/2015.03</code> 38788 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2155">#2155</a>)</li> 38789</ul> 38790</li> 38791<li> 38792<p>added additional easyconfigs for various supported software 38793 packages: version updates, different toolchains, ...</p> 38794<ul> 38795<li>including CMake 3.4.1, HDF5 1.8.16, netCDF 4.3.3.1, 38796 netCDF-Fortran 4.4.2, numpy 1.10.1, Octave 4.0.0, OpenFOAM 38797 3.0.0, OpenFOAM-Extend 3.2, Python 2.7.11</li> 38798</ul> 38799</li> 38800<li> 38801<p>various other enhancements, including:</p> 38802<ul> 38803<li>add tidyr to R 3.2.1 easyconfigs 38804 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2174">#2174</a>)</li> 38805<li>enable C++ support in MIGRATE-N 38806 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2178">#2178</a>)</li> 38807<li>also installed shared libraries for AMD and UMFPACK in 38808 SuiteSparse 38809 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2061">#2061</a>)</li> 38810<li>fix software name for ParaView (was: Paraview) 38811 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2132">#2132</a>)</li> 38812<li>enable building of shared libraries for binutils 38813 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2133">#2133</a>)</li> 38814<li>harden binutils built with dummy toolchain by linking to system 38815 libraries via <code>RPATH</code> 38816 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2228">#2228</a>)</li> 38817<li>enhance easyconfig unit tests to check that each easyconfig file 38818 is in the right subdirectory 38819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2232">#2232</a>)</li> 38820</ul> 38821</li> 38822<li> 38823<p>various bug fixes, including:</p> 38824<ul> 38825<li>fix ALADIN patch file to not use relative paths, and adjust list 38826 of ALADIN sources accordingly 38827 ((<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2207">#2207</a>), 38828 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2213">#2213</a>))</li> 38829<li>
38829rename patch files for OpenFOAM to be in line with other patches 38830 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2226">#2226</a>)</li> 38831<li>fix typo in bzip2 source URLs 38832 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2204">#2204</a>)</li> 38833<li>force linking of ncurses in libreadline 38834 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2206">#2206</a>)</li> 38835<li>enable <code>-fPIC</code> in all zlib 1.2.8 easyconfigs 38836 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2220">#2220</a>)</li> 38837<li>move Net-LibIDN/SRA-Toolkit/bbftpPRO/o2scl easyconfigs to right 38838 location 38839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2232">#2232</a>)</li> 38840<li>restrict parallel build in OpenFOAM-Extend easyconfigs via 38841 '<code>maxparallel</code>', not '<code>parallel</code>' 38842 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2233">#2233</a>)</li> 38843</ul> 38844</li> 38845</ul> 38846<h2 id="release_notes_eb240">EasyBuild v2.4.0 (November 10th 2015)<a class="headerlink" href="#release_notes_eb240" title="Permanent link">¶</a></h2> 38847<p>feature + bugfix release</p> 38848<p><strong>framework</strong></p> 38849<ul> 38850<li>add support for <code>--extended-dry-run</code>/<code>-x</code> 38851 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1388">#1388</a>, 38852 <a href="https://github.com/easybuilders/easybuild-framework/pull/1450">#1450</a>, 38853 <a href="https://github.com/easybuilders/easybuild-framework/pull/1453">#1453</a>, 38854 <a href="https://github.com/easybuilders/easybuild-framework/pull/1455">#1455</a>)<ul> 38855<li>detailed documentation is available at 38856 <a class="autorefs autorefs-internal" href="../extended-dry-run/#extended_dry_run">Extended dry run</a></li> 38857</ul> 38858</li> 38859<li>fix checking of sanity check paths w.r.t. discriminating between 38860 files and directories 38861 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1436">#1436</a>)<ul> 38862<li>this impacts several easyconfig files where <code>sanity_check_paths</code> 38863 was not 100% correct</li> 38864</ul> 38865</li> 38866<li>make '<code>eb</code>' script aware of Python v3.x, fall back to using 38867 <code>python2</code> if required 38868 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1411">#1411</a>)</li> 38869<li>add experimental support for parsing .yeb easyconfig files in YAML 38870 syntax 38871 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1447">#1447</a>, 38872 <a href="https://github.com/easybuilders/easybuild-framework/pull/1448">#1448</a>, 38873 <a href="https://github.com/easybuilders/easybuild-framework/pull/1449">#1449</a>)<ul> 38874<li>see also [Writing easyconfig files in YAML syntax][easyconfig_yeb_format]</li> 38875</ul> 38876</li> 38877<li>add experimental support for resolving dependencies with minimal 38878 toolchains 38879 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1306">#1306</a>)<ul> 38880<li>see also <a class="autorefs autorefs-internal" href="../manipulating-dependencies/#minimal_toolchains">Using minimal toolchains for dependencies</a></li> 38881</ul> 38882</li> 38883<li>various other enhancements, including:<ul> 38884<li>refactor <code>extract_cmd</code> function to get rid of if/elif/else 38885 spaghetti blob 38886 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1382">#1382</a>)</li> 38887<li>add support for <code>--review-pr</code> 38888 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1383">#1383</a>)</li> 38889<li>add <code>apply_regex_substitutions</code> function to perform runtime 38890 patching from easyblocks 38891 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1388">#1388</a>, 38892 <a href="https://github.com/easybuilders/easybuild-framework/pull/1458">#1458</a>)</li> 38893<li>add support for specifying alternate name to be part of 38894 generated module name 38895 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1389">#1389</a>)<ul> 38896<li>via '<code>modaltsoftname</code>' easyconfig parameter</li> 38897</ul> 38898</li> 38899<li>support overriding # used cores via <code>--parallel</code> 38900 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1393">#1393</a>)</li> 38901<li>also define <code>$FC</code> and <code>$FCFLAGS</code> in build environment 38902 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1394">#1394</a>)</li> 38903<li>
38903add support extracting for <code>.tar.Z</code> files 38904 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1396">#1396</a>)</li> 38905<li>include easybuild/scripts in installation 38906 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1397">#1397</a>)</li> 38907<li>ignore hidden directories in find_base_dir 38908 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1413">#1413</a>, 38909 <a href="https://github.com/easybuilders/easybuild-framework/pull/1415">#1415</a>)</li> 38910<li>add <code>only_if_module_is_available</code> decorator function to guard 38911 functionality that uses optional dependencies 38912 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1416">#1416</a>)</li> 38913<li>give easyblocks the possibility to choose <code>maxhits</code> for 38914 <code>run_cmd_qa</code> 38915 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1417">#1417</a>)</li> 38916<li>use class name (string) rather than License instances as values 38917 for software license constants 38918 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1418">#1418</a>)</li> 38919<li>support controlling recursive unloading of dependencies via 38920 '<code>recursive_module_unload</code>' easyconfig parameter 38921 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1425">#1425</a>)</li> 38922<li>implement basic support for type checking of easyconfig 38923 parameters 38924 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1427">#1427</a>)</li> 38925<li>support auto-converting to expected value type for easyconfig 38926 parameters (enabled by default) 38927 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1428">#1428</a>, 38928 <a href="https://github.com/easybuilders/easybuild-framework/pull/1437">#1437</a>)</li> 38929<li>add support for <code>--rebuild</code> command line option, alternative for 38930 <code>--force</code> which doesn't imply <code>--ignore-osdeps</code> 38931 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1435">#1435</a>)</li> 38932<li>add support for Mercurial easyconfig repository 38933 (<a href="https://github.com/easybuilders/easybuild-framework/pull/979">#979</a>, 38934 <a href="https://github.com/easybuilders/easybuild-framework/pull/1446">#1446</a>)</li> 38935<li>add dedicated class for psmpi toolchain MPI component, and use 38936 it in gpsmpi and ipsmpi toolchains 38937 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1454">#1454</a>)</li> 38938</ul> 38939</li> 38940<li>various bug fixes, including:<ul> 38941<li>fix extracting of comments from an easyconfig file that includes 38942 'tail' comments 38943 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1381">#1381</a>)</li> 38944<li>fix dev version to follow PEP-440, as required by recent 38945 setuptools versions 38946 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1403">#1403</a>)<ul> 38947<li>required to avoid that setuptools transforms the version 38948 itself</li> 38949<li>see also 38950 <a href="https://www.python.org/dev/peps/pep-0440/#developmental-releases">https://www.python.org/dev/peps/pep-0440/#developmental-releases</a></li> 38951</ul> 38952</li> 38953<li>allow <code>get_cpu_speed</code> to return <code>None</code> if CPU freq could not be 38954 determined 38955 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1421">#1421</a>)</li> 38956<li>relax <code>sanity_check_paths</code> in EasyBuild bootstrap script to deal 38957 with possible zipped .egg 38958 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1422">#1422</a>)</li> 38959<li>use empty list as default value for src/patches in Extension 38960 class 38961 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1434">#1434</a>)</li> 38962<li>skip symlinked files in <code>adjust_permissions</code> function 38963 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1439">#1439</a>)</li> 38964<li>fix HierarchicalMNS to always use full version number 38965 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1440">#1440</a>)</li> 38966</ul> 38967</li> 38968</ul> 38969<p><strong>easyblocks</strong></p> 38970<ul> 38971<li>3 new generic easyblocks: OCamlPackage 38972 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/467">#467</a>), 38973 SCons 38974 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/689">#689</a>, 38975 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/700">#700</a>), 38976 Waf 38977 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/722">#722</a>)</li> 38978<li>new easyblocks for 2 software packages that require customized 38979 support:<ul> 38980<li>OCaml 38981 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/467">#467</a>), 38982 Samcef 38983 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/678">#678</a>)</li> 38984</ul> 38985</li> 38986<li>various other enhancements, including:<ul> 38987<li>add support for installing OpenFOAM with external METIS, CGAL 38988 and Paraview 38989 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/497">#497</a>)</li> 38990<li>
38990update netCDF easyblock updated for netCDF v4.3.3.1 38991 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/674">#674</a>)</li> 38992<li>update Rosetta easyblock for recent Rosetta versions 38993 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/677">#677</a>)</li> 38994<li>make unpacked source dir detection in easyblock for VSC-tools a 38995 little bit more flexible 38996 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/679">#679</a>)</li> 38997<li>add support for building with Plumed support enabled in CP2K 38998 easyblock 38999 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/681">#681</a>)</li> 39000<li>update Go easyblock for Go v1.5 39001 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/683">#683</a>)</li> 39002<li>use <code>apply_regex_substitutions</code> function in WRF easyblock 39003 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/685">#685</a>)</li> 39004<li>update MUMPS easyblock for 5.x 39005 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/686">#686</a>)</li> 39006<li>implement runtime patching of <code>$WM_*</code> and compiler variables for 39007 OpenFOAM 39008 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/688">#688</a>)</li> 39009<li>specify sequential compiler to use in compiler command that gets 39010 injected in OpenFOAM easyblock 39011 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/692">#692</a>)</li> 39012<li>make <code>PythonPackage</code> and WRF easyblocks dry-run aware 39013 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/696">#696</a>)<ul> 39014<li>see also 39015 <a class="autorefs autorefs-internal" href="../extended-dry-run/#extended_dry_run_guidelines_easyblocks">Guidelines for easyblocks</a></li> 39016</ul> 39017</li> 39018<li>add support in <code>PythonPackage</code> for installing with 39019 <code>easy_install</code> + installing zipped eggs 39020 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/698">#698</a>, 39021 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/711">#711</a>, 39022 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/715">#715</a>)</li> 39023<li>update Bowtie easyblock for recent Bowtie versions 39024 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/707">#707</a>)</li> 39025<li>update CUDA easyblock for CUDA 39026 7.x(<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/708">#708</a>)</li> 39027<li>also consider <code>config/make.sys.in</code> for want in QuantumESRESSO 39028 easyblock 39029 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/714">#714</a>)</li> 39030<li>define <code>$NWCHEM_LONG_PATH</code> if needed in NWChem easyblock 39031 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/720">#720</a>)</li> 39032<li>remove custom post-install step in PDT easyblock 39033 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/723">#723</a>)<ul> 39034<li>no longer needed now that <code>adjust_permissions</code> functions 39035 ignores symlinks</li> 39036</ul> 39037</li> 39038<li>use <code>$LIBS</code> in HPL easyblock 39039 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/727">#727</a>, 39040 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/736">#736</a>)</li> 39041</ul> 39042</li> 39043<li>various bug fixes, including:<ul> 39044<li>also define <code>$MCRROOT</code> for MCR in module 39045 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/687">#687</a>)</li> 39046<li>add missing '<code>super</code>' call in <code>configure_step</code> of easyblock 39047 for python-meep 39048 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/694">#694</a>)</li> 39049<li>only prepend existing non-empty paths to <code>$PYTHONPATH</code> in 39050 <code>PythonPackage</code> easyblock 39051 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/697">#697</a>)</li> 39052<li>fix extra_options definition in <code>CMakePythonPackage</code> easyblock 39053 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/698">#698</a>)</li> 39054<li>fix dev version to follow PEP-440, as required by recent 39055 setuptools versions 39056 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/702">#702</a>, 39057 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/703">#703</a>, 39058 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/704">#704</a>)<ul> 39059<li>required to avoid that setuptools transforms the version 39060 itself</li> 39061<li>see also 39062 <a href="https://www.python.org/dev/peps/pep-0440/#developmental-releases">https://www.python.org/dev/peps/pep-0440/#developmental-releases</a></li> 39063</ul> 39064</li> 39065<li>consider both <code>lib</code> and <code>lib64</code> in sanity check paths for flex 39066 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/705">#705</a>)</li> 39067<li>also copy signature file and don't copy CMake files in Eigen 39068 easyblock 39069 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/709">#709</a>)</li> 39070<li>fix directory names in <code>make_module_req_guess</code> of ANSYS 39071 easyblock 39072 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/713">#713</a>)</li> 39073<li>fix imports for <code>set_tmpdir</code> in easyblock unit tests after 39074 function was moved in EasyBuild framework 39075 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/726">#726</a>)</li> 39076<li>use <code>--with-tcltk*</code> configure options for Python to point to 39077 ensure Tcl/Tk deps are picked up 39078 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/729">#729</a>)</li> 39079<li>fix order of subdirs for QuantumESPRESSO binaries 39080 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/730">#730</a>)</li> 39081<li>correctly handle having both <code>$FC</code>/<code>$FCFLAGS</code> and 39082 <code>$F90</code>/<code>$F90FLAGS</code> defined when building MVAPICH2 39083 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/732">#732</a>)</li> 39084<li>fix OpenSSL sanity check paths: lib/engines is a directory 39085 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/731">#731</a>, 39086 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/733">#733</a>)</li> 39087<li>fix sanity check paths for netcdf-python 39088 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/735">#735</a>)</li> 39089</ul> 39090</li> 39091</ul> 39092<p><strong>easyconfigs</strong></p> 39093<ul> 39094<li>added example easyconfig files for 45 new software packages:<ul> 39095<li>animation 39096 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2007">#2007</a>),
39097 ANSYS CFD 39098 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1969">#1969</a>), 39099 ANTLR 39100 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1191">#1191</a>, 39101 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1980">#1980</a>), 39102 APR 39103 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1970">#1970</a>), 39104 APR-util 39105 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1970">#1970</a>), 39106 Aspera Connect 39107 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2005">#2005</a>), 39108 ChIP-Seq 39109 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2119">#2119</a>), 39110 deap 39111 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2082">#2082</a>), 39112 DISCOVARdenovo 39113 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1932">#1932</a>), 39114 FastQC 39115 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1984">#1984</a>), 39116 fontsproto 39117 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1618">#1618</a>, 39118 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2038">#2038</a>), 39119 GraphicsMagick 39120 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2007">#2007</a>), 39121 HBase 39122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1990">#1990</a>), 39123 ISIS 39124 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1972">#1972</a>), 39125 libedit 39126 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/293">#293</a>), 39127 libfontenc 39128 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1618">#1618</a>, 39129 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2038">#2038</a>), 39130 libGLU 39131 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1627">#1627</a>), 39132 libXdamage 39133 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1618">#1618</a>, 39134 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2038">#2038</a>), 39135 libXfont 39136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1618">#1618</a>, 39137 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2038">#2038</a>), 39138 LLVM 39139 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1620">#1620</a>, 39140 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1989">#1989</a>, 39141 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2031">#2031</a>), 39142 MIGRATE-N 39143 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1944">#1944</a>), 39144 MIRA 39145 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1938">#1938</a>), 39146 mympingpong 39147 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2049">#2049</a>), 39148 MySQLdb 39149 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2011">#2011</a>), 39150 NCO 39151 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1191">#1191</a>, 39152 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1980">#1980</a>), 39153 NIPY 39154 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2064">#2064</a>), 39155 Nilearn 39156 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2064">#2064</a>), 39157 NiBabel 39158 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2064">#2064</a>), 39159 PBZIP2 39160 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1038">#1038</a>), 39161 PIL 39162 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2062">#2062</a>), 39163 PhyloCSF 39164 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2018">#2018</a>), 39165 pycairo 39166 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2085">#2085</a>), 39167 pydicom 39168 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2063">#2063</a>), 39169 Salmon 39170 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2051">#2051</a>), 39171 Samcef 39172 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1941">#1941</a>), 39173 scikit-image 39174 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1974">#1974</a>, 39175 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2006">#2006</a>), 39176 Serf 39177 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1970">#1970</a>), 39178 SSAHA2 39179 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1039">#1039</a>), 39180 Subversion 39181 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1970">#1970</a>), 39182 SWASH 39183 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2059">#2059</a>), 39184 time 39185 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1954">#1954</a>), 39186 Trim_Galore 39187 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1984">#1984</a>), 39188 Trimmomatic 39189 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1987">#1987</a>), 39190 WEKA 39191 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1986">#1986</a>), 39192 x264 39193 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2017">#2017</a>)</li> 39194</ul> 39195</li> 39196<li>
39196added new easyconfigs for existing toolchains: <code>gimkl/2.11.5</code> 39197 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2093">#2093</a>)</li> 39198<li>added additional easyconfigs for various supported software 39199 packages: version updates, different toolchains, ...<ul> 39200<li>including Clang + LLVM 3.7.0, CMake 3.3.2, CUDA 7.5.18, 39201 hanythingondemand v3.0.1, Mesa 11.0.2, mpi4py v2.0.0, ncurses 39202 6.0, OpenFOAM 2.4.0, Paraview 4.4.0, Python 3.5.0, 39203 QuantumESPRESSO v5.2.1</li> 39204</ul> 39205</li> 39206<li>various other enhancements, including:<ul> 39207<li>enable '<code>pic</code>' toolchain option in libxml2 easyconfigs 39208 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1993">#1993</a>)</li> 39209<li>extend list of R libraries included in R v3.2.1 easyconfigs 39210 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2042">#2042</a>, 39211 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2046">#2046</a>, 39212 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2067">#2067</a>, 39213 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2072">#2072</a>)</li> 39214<li>add Rsubread in Bioconductor easyconfigs 39215 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1971">#1971</a>)</li> 39216</ul> 39217</li> 39218<li>various bug fixes, including:<ul> 39219<li>fix software name for <code>BEEF</code> (was '<code>libbeef</code>') 39220 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1679">#1679</a>)</li> 39221<li>add patch to install <code>qhull.pc</code> (pkgconfig) file with Qhull 39222 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1975">#1975</a>)</li> 39223<li>don't enable experimental nouveau API in libdrm easyconfigs 39224 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1994">#1994</a>)</li> 39225<li>fix dev version to follow PEP-440, as required by recent 39226 setuptools versions 39227 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1997">#1997</a>)<ul> 39228<li>required to avoid that setuptools transforms the version 39229 itself</li> 39230<li>see also 39231 <a href="https://www.python.org/dev/peps/pep-0440/#developmental-releases">https://www.python.org/dev/peps/pep-0440/#developmental-releases</a></li> 39232</ul> 39233</li> 39234<li>correct homepage in Cufflinks easyconfigs 39235 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2060">#2060</a>)</li> 39236<li>fix imports for <code>set_tmpdir</code> in easyblock unit tests after 39237 function was moved in EasyBuild framework 39238 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2097">#2097</a>)</li> 39239<li>add patch for Tk 8.6.4 to fix problem with <code>tk.tcl</code> not being 39240 found 39241 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2102">#2102</a>)</li> 39242<li>don't use <code>%(version)s</code> template in toolchain version, causes 39243 problems with HierarchicalMNS 39244 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2104">#2104</a>)</li> 39245<li>fix sanity check paths in several easyconfig 39246 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2109">#2109</a>, 39247 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2120">#2120</a>, 39248 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2121">#2121</a>, 39249 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/2125">#2125</a>)<ul> 39250<li>required because of bug fix in <code>sanity_check_step</code> 39251 implementation</li> 39252<li>CVXOPT, h5py, LIBSVM, libunistring, MDP, monty, PhyloCSF, 39253 Pyke, pandas, pycosat, pyhull, pymatgen, python-dateutils, 39254 Seaborn, Theano, XML-LibXML, XML-Simple</li> 39255</ul> 39256</li> 39257</ul> 39258</li> 39259</ul> 39260<h2 id="release_notes_eb230">EasyBuild v2.3.0 (September 2nd 2015)<a class="headerlink" href="#release_notes_eb230" title="Permanent link">¶</a></h2> 39261<p>feature + bugfix release</p> 39262<p><strong>framework</strong></p> 39263<ul> 39264<li>requires vsc-base v2.2.4 or more recent 39265 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1343">#1343</a>)<ul> 39266<li>required for <code>mk_rst_table</code> function in <code>vsc.utils.docs</code></li> 39267</ul> 39268</li> 39269<li>various other enhancements, including:<ul> 39270<li>add support for generating documentation for (generic) 39271 easyblocks in <code>
39271.rst</code> format 39272 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1317">#1317</a>)</li> 39273<li>preserve comments in easyconfig file in <code>EasyConfig.dump()</code> 39274 method 39275 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1327">#1327</a>)</li> 39276<li>add <code>--cleanup-tmpdir</code> option 39277 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1365">#1365</a>)<ul> 39278<li>enables to preserve the used temporary directory via 39279 <code>--disable-cleanup-tmpdir</code></li> 39280</ul> 39281</li> 39282<li>enhance <code>EasyConfig.dump()</code> to reformat dumped easyconfig 39283 according to style guidelines 39284 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1345">#1345</a>)</li> 39285<li>add support for extracting <code>.iso</code> files using 7z (p7zip) 39286 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1375">#1375</a>)</li> 39287</ul> 39288</li> 39289<li>various bug fixes, including:<ul> 39290<li>correctly deal with special characters in template strings in 39291 <code>EasyConfig.dump()</code> method 39292 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1323">#1323</a>)</li> 39293<li>rework <code>easybuild.tools.module_generator</code> module to avoid 39294 keeping state w.r.t. fake modules 39295 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1348">#1348</a>)</li> 39296<li>fix dumping of hidden deps 39297 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1354">#1354</a>)</li> 39298<li>fix use of <code>--job</code> with hidden dependencies: include <code>--hidden</code> 39299 in submitted job script when needed 39300 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1356">#1356</a>)</li> 39301<li>fix <code>ActiveMNS.det_full_module_name()</code> for external modules 39302 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1360">#1360</a>)</li> 39303<li>fix <code>EasyConfig.all_dependencies</code> definition, fix tracking of 39304 job dependencies 39305 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1359">#1359</a>, 39306 <a href="https://github.com/easybuilders/easybuild-framework/pull/1361">#1361</a>)</li> 39307<li>fix <code>ModulesTool.exist()</code> for hidden Lua module files 39308 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1364">#1364</a>)</li> 39309<li>only call <code>EasyBlock.sanity_check_step</code> for non-extensions 39310 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1366">#1366</a>)<ul> 39311<li>this results in significant speedup when installing 39312 easyconfigs with lots of extensions, but also results in 39313 checking the default sanity check paths if none were defined 39314 for extensions installed as a module</li> 39315</ul> 39316</li> 39317<li>fix using module naming schemes that were included via 39318 <code>--include-module-naming-schemes</code> 39319 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1370">#1370</a>)</li> 39320</ul> 39321</li> 39322</ul> 39323<p><strong>easyblocks</strong></p> 39324<ul> 39325<li>new easyblocks for 2 software packages that require customized 39326 support:<ul> 39327<li>MCR 39328 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/623">#623</a>), 39329 Molpro 39330 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/665">#665</a>)</li> 39331</ul> 39332</li> 39333<li>various other enhancements, including:<ul> 39334<li>enhance BWA easyblock to also install man pages 39335 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/650">#650</a>)</li> 39336<li>enhance tbb easyblock to consider lib dirs in order and also 39337 define <code>$CPATH</code>, <code>$LIBRARY_PATH</code>, <code>$TBBROOT</code> 39338 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/653">#653</a>, 39339 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/654">#654</a>)</li> 39340<li>call <code>PythonPackage.configure_step</code> in 39341 <code>ConfigureMakePythonPackage.configure_step</code> 39342 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/668">#668</a>)</li> 39343<li>add '<code>foldx3b6</code>' as possible binary name in FoldX easyblock 39344 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/671">#671</a>)</li> 39345<li>enhance/cleanup MATLAB easyblock 39346 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/672">#672</a>)</li> 39347<li>move preparing of '<code>intel</code>' subdir in <code>$HOME</code> to 39348 <code>configure_step</code> in <code>IntelBase</code> easyblock 39349 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/673">#673</a>)</li> 39350</ul> 39351</li> 39352<li>various bug fixes, including:<ul> 39353<li>add missing super call in <code>post_install_step</code> of imkl easyblock 39354 (<a href="https://github.com/easybuilders/easybuild-framework/pull/648">#648</a>, 39355 <a href="https://github.com/easybuilders/easybuild-framework/pull/660">#660</a>)</li> 39356<li>fix regex used to correct <code>I_MPI_ROOT</code> in impi <code>mpivars.sh</code> 39357 scripts 39358 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/662">#662</a>)</li> 39359<li>fix regex used to patch <code>.mk</code> file in configure step of 39360 SuiteSparse easyblock 39361 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/666">#666</a>)</li> 39362<li>correctly specify installation prefix via <code>$GEM_HOME</code> in 39363 <code>RubyGem</code> easyblock 39364 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/667">#667</a>)</li> 39365<li>
39365add custom sanity check in scipy easyblock 39366 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/669">#669</a>)</li> 39367<li>specify to always use the bfd linker for OpenFOAM, to stay away 39368 from using <code>ld.gold</code> 39369 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/670">#670</a>)</li> 39370</ul> 39371</li> 39372</ul> 39373<p><strong>easyconfigs</strong></p> 39374<ul> 39375<li>added example easyconfig files for 19 new software packages:<ul> 39376<li>ATK 39377 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39378 Atkmm 39379 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39380 cairomm 39381 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39382 GLibmm 39383 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39384 GlobalArrays 39385 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1868">#1868</a>), 39386 gdk-pixbuf 39387 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39388 gtk+ 39389 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39390 Gtkmm 39391 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39392 libbeef 39393 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1827">#1827</a>), 39394 libsigc++ 39395 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39396 libsodium 39397 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1876">#1876</a>), 39398 MACS 39399 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1869">#1869</a>), 39400 MCR 39401 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1677">#1677</a>), 39402 Molpro 39403 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1880">#1880</a>), 39404 NFFT 39405 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1921">#1921</a>), 39406 p7zip 39407 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1931">#1931</a>), 39408 Pangomm 39409 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1780">#1780</a>), 39410 pygraphviz 39411 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1861">#1861</a>), 39412 pycosat 39413 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1859">#1859</a>)</li> 39414</ul> 39415</li> 39416<li>added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 39417 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1836">#1836</a>), 39418 foss/2015b 39419 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1695">#1695</a>), 39420 intel/2015b 39421 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1696">#1696</a>)<ul> 39422<li>add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 39423 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1, Perl 5.20.2 + 5.22.0 (bare), 39424 Python 2.7.10, R 3.2.1</li> 39425</ul> 39426</li> 39427<li>added additional easyconfigs for various supported software 39428 packages: version updates, different toolchains, ...<ul> 39429<li>including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0</li> 39430</ul> 39431</li> 39432<li>various other enhancements, including:<ul> 39433<li>enhance texinfo easyconfig w.r.t. <code>texmf</code>, only use it as a 39434 build dependency 39435 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1840">#1840</a>)</li> 39436<li>enable building of <code>ld.gold</code> in binutils 2.25 39437 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1885">#1885</a>)</li> 39438</ul> 39439</li> 39440<li>various bug fixes, including:<ul> 39441<li>fix enabling MPI support for h5py 2.5.0 39442 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1825">#1825</a>)</li> 39443<li>fix versions of Bioconductor packages + add a couple extra 39444 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1828">#1828</a>, 39445 <a href="https://github.com/easybuilders/easybuild-framework/pull/1852">#1852</a>, 39446 <a href="https://github.com/easybuilders/easybuild-framework/pull/1895">#1895</a>, 39447 <a href="https://github.com/easybuilders/easybuild-framework/pull/1917">#1917</a>)</li> 39448<li>put dummy values in place for <code>builddir</code>/<code>installdir</code> templates 39449 in easyconfigs unit tests 39450 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1835">#1835</a>)</li> 39451<li>fix easyconfigs unit tests w.r.t. changes made in framework 39452 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1853">#1853</a>, 39453 <a href="https://github.com/easybuilders/easybuild-framework/pull/1870">#1870</a>, 39454 <a href="https://github.com/easybuilders/easybuild-framework/pull/1874">#1874</a>, 39455 <a href="https://github.com/easybuilders/easybuild-framework/pull/1875">#1875</a>)</li> 39456<li>
39456add GMP as missing dep in Python 2.7.10 easyconfigs, required 39457 for pycrypto extension 39458 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1858">#1858</a>)</li> 39459<li>specify installation prefix for SIP 39460 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1888">#1888</a>, 39461 <a href="https://github.com/easybuilders/easybuild-framework/pull/1892">#1892</a>)</li> 39462<li>add custom sanity check paths in various easyconfigs 39463 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1889">#1889</a>, 39464 <a href="https://github.com/easybuilders/easybuild-framework/pull/1894">#1894</a>, 39465 <a href="https://github.com/easybuilders/easybuild-framework/pull/1897">#1897</a> - 39466 <a href="https://github.com/easybuilders/easybuild-framework/pull/1909">#1909</a>)<ul> 39467<li>required because of fix in EasyBuild framework, causing 39468 default sanity check paths to be considered for extensions 39469 that are installed as a module</li> 39470<li>affected easyconfigs include: AnalyzeFMRI, Biggus, 39471 bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql, evmix, 39472 fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, 39473 netifaces, NetLibIDN, networkx, ordereddict, 39474 Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, 39475 rjags, runjags, scikit-learn, SOBAcl, vsc-processcontrol, 39476 vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, 39477 YAML-Syck</li> 39478</ul> 39479</li> 39480<li>don't enable '<code>static</code>' toolchain option in SuiteSparse 4.4.3 39481 easyconfig 39482 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1911">#1911</a>)</li> 39483<li>add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic 39484 symlink causing problems when unpacking 39485 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1925">#1925</a>)</li> 39486</ul> 39487</li> 39488</ul> 39489<h2 id="release_notes_eb220">EasyBuild v2.2.0 (July 15th 2015)<a class="headerlink" href="#release_notes_eb220" title="Permanent link">¶</a></h2> 39490<p>feature + bugfix release</p> 39491<p><strong>framework</strong></p> 39492<ul> 39493<li>add support for using GC3Pie as a backend for <code>--job</code> 39494 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1008">#1008</a>)<ul> 39495<li>see also <a class="autorefs autorefs-internal" href="../submitting-jobs/#submitting_jobs">Submitting jobs using <code>--job</code></a></li> 39496</ul> 39497</li> 39498<li>add support for <code>--include-*</code> configuration options to include 39499 additional easyblocks, toolchains, etc. 39500 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1301">#1301</a>)<ul> 39501<li>see <a class="autorefs autorefs-internal" href="../including-additional-python-modules/#including_additional_python_modules">Including additional Python modules</a></li> 39502</ul> 39503</li> 39504<li>add (experimental) support for packaging installed software using 39505 FPM 39506 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1224">#1224</a>)<ul> 39507<li>see <a class="autorefs autorefs-internal" href="../packaging-support/#packaging_support">Packaging support</a></li> 39508</ul> 39509</li> 39510<li>various other enhancements, including:<ul> 39511<li>use https for PyPI URL templates 39512 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1286">#1286</a>)</li> 39513<li>add GNU toolchain definition 39514 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1287">#1287</a>)</li> 39515<li>make bootstrap script more robust 39516 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1289">#1289</a>, 39517 <a href="https://github.com/easybuilders/easybuild-framework/pull/1325">#1325</a>):<ul> 39518<li>exclude 'easyblocks' pkg from <code>sys.path</code> to avoid that 39519 <code>setup.py</code> for easybuild-easyblocks picks up wrong version</li> 39520<li>undefine <code>$EASYBUILD_BOOTSTRAP*</code> environment variables, 39521 since they do not correspond with known config options</li> 39522</ul> 39523</li> 39524<li>improve error reporting/robustness in 39525 <code>fix_broken_easyconfigs.py</code> script 39526 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1290">#1290</a>)</li> 39527<li>reset keep toolchain component class 'constants' every time 39528 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1294">#1294</a>)</li> 39529<li>make <code>--strict</code> also a build option 39530 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1295">#1295</a>)</li> 39531<li>fix purging of loaded modules in unit tests' setup method 39532 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1297">#1297</a>)</li> 39533<li>promote <code>MigrateFromEBToHMNS</code> to a 'production' MNS 39534 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1302">#1302</a>)</li> 39535<li>
39535add support for <code>--read-only-installdir</code> and 39536 <code>--group-writable-installdir</code> configuration options 39537 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1304">#1304</a>)</li> 39538<li>add support for <em>not</em> expanding relative paths in 39539 <code>prepend_paths</code> 39540 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1310">#1310</a>)</li> 39541<li>enhance <code>EasyConfig.dump()</code> method to use easyconfig templates 39542 where possible 39543 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1314">#1314</a>), 39544 <a href="https://github.com/easybuilders/easybuild-framework/pull/1319">#1319</a>), 39545 <a href="https://github.com/easybuilders/easybuild-framework/pull/1320">#1320</a>), 39546 <a href="https://github.com/easybuilders/easybuild-framework/pull/1321">#1321</a>)</li> 39547</ul> 39548</li> 39549<li>various bug fixes, including:<ul> 39550<li>fix issue with cleaning up (no) logfile if <code>--logtostdout</code>/<code>-l</code> 39551 is used 39552 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1298">#1298</a>)</li> 39553<li>stop making <code>ModulesTool</code> class a singleton since it causes 39554 problems when multilple toolchains are in play 39555 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1299">#1299</a>)</li> 39556<li>don't modify values of 'paths' list passed as argument to 39557 prepend_paths in <code>ModuleGenerator</code> 39558 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1300">#1300</a>)</li> 39559<li>fix issue with <code>EasyConfig.dump()</code> + cleanup 39560 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1308">#1308</a>), 39561 <a href="https://github.com/easybuilders/easybuild-framework/pull/1311">#1311</a>)</li> 39562<li>re-enable (and fix) accidentally disabled test 39563 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1316">#1316</a>)</li> 39564</ul> 39565</li> 39566</ul> 39567<p><strong>easyblocks</strong></p> 39568<ul> 39569<li>modified easybuild.easyblocks package declaration to support giving 39570 preference to custom easyblocks 39571 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/617">#617</a>)</li> 39572<li>2 new generic easyblocks: RubyGem 39573 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/565">#565</a>), 39574 SystemCompiler 39575 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/633">#633</a>)</li> 39576<li>new easyblocks for 5 software packages that require customized 39577 support:<ul> 39578<li>NEMO 39579 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/564">#564</a>), 39580 pbdMPI 39581 (<a href="https://github.com/easybuilders/easybuild-framework/pull/612">#612</a>), 39582 <a href="https://github.com/easybuilders/easybuild-framework/pull/620">#620</a>), 39583 pbdSLAP 39584 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/620">#620</a>), 39585 PDT 39586 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/624">#624</a>), 39587 Ruby 39588 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/565">#565</a>)</li> 39589</ul> 39590</li> 39591<li>various other enhancements, including:<ul> 39592<li>update CUDA easyblock for v6.x 39593 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/476">#476</a>)</li> 39594<li>make METIS easyblock take into account configopts 39595 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/494">#494</a>)</li> 39596<li>enable building of EOMIP and EOMEA for NWChem versions 6.5 and 39597 up 39598 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/508">#508</a>)</li> 39599<li>make out-of-source build with CMake truly out-of-source 39600 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/615">#615</a>)</li> 39601<li>add support in Bundle easyblock to run full sanity check 39602 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/627">#627</a>)</li> 39603<li>also take platform-specific Python lib dirs into account in 39604 PythonPackage easyblock 39605 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/628">#628</a>)</li> 39606<li>fix mpivars scripts in Intel MPI installation for versions where 39607 the installation is moved 39608 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/629">#629</a>)</li> 39609<li>don't restrict <code>det_pylibdir</code> function to only 39610 EasyBuild-provided Python 39611 (<a href="https://github.com/easybuilders/easybuild-framework/pull/631">#631</a>), 39612 <a href="https://github.com/easybuilders/easybuild-framework/pull/641">#641</a>)</li> 39613<li>support snappy and other optional native libs in Hadoop 39614 easyblock 39615 (<a href="https://github.com/easybuilders/easybuild-framework/pull/632">#632</a>), 39616 <a href="https://github.com/easybuilders/easybuild-framework/pull/638">#638</a>), 39617 <a href="https://github.com/easybuilders/easybuild-framework/pull/640">#640</a>), 39618 <a href="https://github.com/easybuilders/easybuild-framework/pull/642">#642</a>)</li> 39619</ul> 39620</li> 39621<li>various bug fixes, including:<ul> 39622<li>fix Xmipp easyblock, use provided <code>install.sh</code> script 39623 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/630">#630</a>)</li> 39624<li>update Clang easyblock to disable tests that may fail when 39625 unlimited stack size is used 39626 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/622">#622</a>)</li> 39627<li>fix setting of <code>$INTEL_LICENSE_FILE</code> for <a href="mailto:port@server">port@server</a> values 39628 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/635">#635</a>)</li> 39629</ul> 39630</li> 39631</ul> 39632<p><strong>easyconfigs</strong></p> 39633<ul> 39634<li>added example easyconfig files for <strong>62</strong> new software packages:<ul> 39635<li>ADF 39636 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/899">#899</a>), 39637 AutoDock_Vina 39638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/808">#808</a>), 39639 bibtexparser 39640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1726">#1726</a>), 39641 Biggus 39642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1770">#1770</a>), 39643 Bismark 39644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/990">#990</a>), 39645 blasr 39646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1662">
39646#1662</a>), 39647 BSMAP 39648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1171">#1171</a>), 39649 Check 39650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/811">#811</a>), 39651 Circuitscape 39652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1222">#1222</a>), 39653 CONTRAfold 39654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/689">#689</a>), 39655 cramtools 39656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1741">#1741</a>), 39657 DBD-Pg 39658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1066">#1066</a>), 39659 DendroPy 39660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/995">#995</a>), 39661 EMAN2 39662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1737">#1737</a>), 39663 ETSF_IO 39664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/727">#727</a>), 39665 eudev 39666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1578">#1578</a>), 39667 fastqc 39668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1636">#1636</a>), 39669 FDS 39670 (<a href="https://github.com/easybuilders/easybuild-framework/pull/814">#814</a>), 39671 <a href="https://github.com/easybuilders/easybuild-framework/pull/1617">#1617</a>), 39672 <a href="https://github.com/easybuilders/easybuild-framework/pull/1625">#1625</a>), 39673 FPM 39674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1440">#1440</a>), 39675 frealign 39676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1619">#1619</a>), 39677 g2log 39678 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1035">#1035</a>), 39679 GC3Pie 39680 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1692">#1692</a>), 39681 <a href="https://github.com/easybuilders/easybuild-framework/pull/1756">#1756</a>), 39682 <a href="https://github.com/easybuilders/easybuild-framework/pull/1768">#1768</a>), 39683 GenotypeHarmonizer 39684 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1672">#1672</a>), 39685 gensim 39686 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1762">#1762</a>), 39687 GraphViz 39688 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1658">#1658</a>), 39689 hisat 39690 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1674">#1674</a>), 39691 IDBA-UD 39692 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1045">#1045</a>), 39693 IMa2 39694 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/828">#828</a>), 39695 IMPUTE2 39696 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/824">#824</a>), 39697 JUBE 39698 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1396">#1396</a>), 39699 LAMARC 39700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/760">#760</a>), 39701 libXScrnSaver 39702 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1653">#1653</a>), 39703 MATIO 39704 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1004">#1004</a>), 39705 MuTect 39706 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1483">#1483</a>), 39707 ncdf 39708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/617">#617</a>), 39709 NEMO 39710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1640">#1640</a>), 39711 ngspice 39712 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1116">#1116</a>), 39713 ordereddict 39714 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1774">#1774</a>), 39715 OSU Micro-Benchmarks 39716 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1777">#1777</a>), 39717 Parallel-ForkManager 39718 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/847">#847</a>), 39719 pBWA 39720 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1009">#1009</a>), 39721 PeakSeq 39722 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1412">#1412</a>), 39723 Pillow 39724 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1702">#1702</a>), 39725 Pindel 39726 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1126">#1126</a>), 39727 PLUMED 39728 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1596">#1596</a>), 39729 <a href="https://github.com/easybuilders/easybuild-framework/pull/1665">#1665</a>), 39730 PostgreSQL 39731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1066">#1066</a>), 39732 PROJ 39733 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1006">#1006</a>), 39734 PyAMG 39735 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1222">#1222</a>), 39736 Pyke 39737 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1776">#1776</a>), 39738 rpy2 39739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1775">#1775</a>), 39740 Sailfish 39741 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1035">#1035</a>), 39742 SCANMS 39743 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1386">#1386</a>), 39744 Seaborn 39745 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1763">#1763</a>), 39746 snpEff 39747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1680">#1680</a>), 39748 SOBAcl 39749 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1658">#1658</a>), 39750 SPIDER 39751 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1624">#1624</a>), 39752 <a href="https://github.com/easybuilders/easybuild-framework/pull/1723">#1723</a>), 39753 STAR 39754 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1043">#1043</a>), 39755 <a href="https://github.com/easybuilders/easybuild-framework/pull/1676">#1676</a>), 39756 system GCC 39757 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1778">#1778</a>), 39758 tabix 39759 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1059">#1059</a>), 39760 tecplot360ex 39761 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1100">#1100</a>), 39762 Vampir 39763 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/512">#512</a>), 39764 VampirServer 39765 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/512">#512</a>), 39766 verifyBamID 39767 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1675">#1675</a>)</li> 39768</ul> 39769</li> 39770<li>
39770added easyconfigs for 4 new software bundles:<ul> 39771<li>R-bundle-Bioconductor 39772 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1573">#1573</a>), 39773 <a href="https://github.com/easybuilders/easybuild-framework/pull/1795">#1795</a>), 39774 R-bundle-devtools 39775 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1621">#1621</a>), 39776 <a href="https://github.com/easybuilders/easybuild-framework/pull/1759">#1759</a>), 39777 R-bundle-extra 39778 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1387">#1387</a>), 39779 <a href="https://github.com/easybuilders/easybuild-framework/pull/1759">#1759</a>), 39780 R-bundle-pbd 39781 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1659">#1659</a>)</li> 39782</ul> 39783</li> 39784<li>added easyconfigs for new GNU toolchain 39785 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1346">#1346</a>), 39786 <a href="https://github.com/easybuilders/easybuild-framework/pull/1669">#1669</a>)</li> 39787<li>added new easyconfigs for existing toolchains: goolf/1.5.16, 39788 intel/2014.06</li> 39789<li>added additional easyconfigs for various supported software 39790 packages: version updates, different toolchains, ...<ul> 39791<li>including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, 39792 GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, Python 2.7.10, R 39793 3.2.0 + 3.2.1, WRF 3.6.1</li> 39794</ul> 39795</li> 39796<li>various other enhancements, including:<ul> 39797<li>update all ncurses easyconfigs to enable ncursesw and use 39798 ConfigureMake easyblock 39799 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1337">#1337</a>)</li> 39800<li>update PDT easyconfigs to use PDT easyblock 39801 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1687">#1687</a>)</li> 39802<li>add custom <code>sanity_check_paths</code> in libxml2 easyconfigs 39803 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1690">#1690</a>)</li> 39804<li>enhance unit tests to also cover EasyConfig.dump() method on all 39805 easyconfigs 39806 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1761">#1761</a>)</li> 39807<li>include snappy as dependency in Hadoop easyconfigs 39808 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1758">#1758</a>), 39809 <a href="https://github.com/easybuilders/easybuild-framework/pull/1773">#1773</a>)</li> 39810<li>enable SSL support in CMake v3.2.3 easyconfigs 39811 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1784">#1784</a>)</li> 39812<li>add additional extensions in R easyconfigs 39813 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1637">#1637</a>)</li> 39814</ul> 39815</li> 39816<li>various bug fixes, including:<ul> 39817<li>add patch file required for correct CUDA-aware OpenMPI v1.7.3 39818 build 39819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/631">#631</a>)</li> 39820<li>fix issue with OpenMPI dependency in ECore easyconfigs 39821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/777">#777</a>)</li> 39822<li>don't run the Bloom tests for Jellyfish, they can randomly fail 39823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1016">#1016</a>)</li> 39824<li>fix source URLs in BioPerl easyconfigs 39825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1075">#1075</a>)</li> 39826<li>patch out svnversion command in Python 2.5.6 to fix build on 39827 recent systems 39828 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1576">#1576</a>)</li> 39829<li>consistently use https for PyPI URLs in homepage/source_urls 39830 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1616">#1616</a>), 39831 <a href="https://github.com/easybuilders/easybuild-framework/pull/1722">#1722</a>)</li> 39832<li>include Tcl and Tk as dependencies in R easyconfig 39833 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1623">#1623</a>)</li> 39834<li>add patch for installing paycheck as Py3 extension 39835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1629">#1629</a>)</li> 39836<li>add Perl dependency in git 2.x easyconfigs 39837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1631">#1631</a>)</li> 39838<li>fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources 39839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1635">#1635</a>)</li> 39840<li>fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs 39841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1652">
39841#1652</a>)</li> 39842<li>include Tk as dependency in Python 2.7.9 easyconfigs 39843 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1654">#1654</a>)</li> 39844<li>include tk-devel is list of OS deps for Python 2.7.9 Cray 39845 easyconfigs, make sure '<code>import Tkinter</code>' works 39846 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1655">#1655</a>)</li> 39847<li>drop gpfs versionsuffix and stop using no longer existing 39848 <code>--enable-gpfs</code> configopt for recent HDF5 versions 39849 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1657">#1657</a>)</li> 39850<li>include missing libxml2 dep in GLib easyconfigs 39851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1666">#1666</a>)</li> 39852<li>fix source URLs in Qt easyconfigs 39853 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1673">#1673</a>)</li> 39854<li>fix source URLs for argparse Python extension 39855 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1697">#1697</a>)</li> 39856<li>fix source URLs for deap Python extension 39857 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1699">#1699</a>)</li> 39858<li>fix easyconfigs unit tests after making ModulesTool a 39859 non-singleton class 39860 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1708">#1708</a>)</li> 39861<li>fix names for Xmipp easyconfigs and patches 39862 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1719">#1719</a>)</li> 39863<li>add patch for Qt 4.8.6 to fix build issue on RHEL6 with 39864 intel/2015a 39865 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1734">#1734</a>)</li> 39866<li>add M4 as build dep for GCC 5.1.0 39867 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1735">#1735</a>)</li> 39868<li>fix Bioconductor extension versions in R 3.1.3 easyconfigs 39869 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1748">#1748</a>)</li> 39870<li>remove custom exts_filter definition from Python 3.4.3 39871 easyconfig 39872 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1765">#1765</a>)</li> 39873<li>fix source_urls in netCDF easyconfigs 39874 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1766">#1766</a>)</li> 39875<li>fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs 39876 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1767">#1767</a>)</li> 39877</ul> 39878</li> 39879</ul> 39880<h2 id="release_notes_eb211">EasyBuild v2.1.1 (May 18th 2015)<a class="headerlink" href="#release_notes_eb211" title="Permanent link">¶</a></h2> 39881<p>bugfix release</p> 39882<p><strong>framework</strong></p> 39883<ul> 39884<li>fix issue with missing load statements when <code>--module-only</code> is used, 39885 don't skip ready/prepare steps 39886 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1276">#1276</a>)</li> 39887<li>enhance <code>--search</code>: only consider actual filename (not entire path), 39888 use regex syntax 39889 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1281">#1281</a>)</li> 39890<li>various other bug fixes, including:<ul> 39891<li>fix <code>generate_software_list.py</code> script w.r.t. dependencies 39892 marked as external modules 39893 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1273">#1273</a>)</li> 39894<li>only use <code>$LMOD_CMD</code> value if <code>lmod</code> binary can't be found in 39895 $PATH 39896 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1275">#1275</a>)</li> 39897<li>fix location of <code>module_only</code> build option w.r.t. default value 39898 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1277">#1277</a>)</li> 39899<li>fix combined use of <code>--hide-deps</code> and <code>hiddendependencies</code> 39900 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1280">#1280</a>)</li> 39901<li>remove log handlers that were added during tests, to ensure 39902 effective cleanup of log files 39903 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1282">#1282</a>)<ul> 39904<li>this makes the unit test suite run ~3x faster!</li> 39905</ul> 39906</li> 39907<li>define <code>$CRAYPE_LINK_TYPE</code> if '<code>dynamic</code>' toolchain option is 39908 enabled for Cray compiler wrappers 39909 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1283">#1283</a>)</li> 39910</ul> 39911</li> 39912</ul> 39913<p><strong>easyblocks</strong></p> 39914<ul> 39915<li>fix compatibility of easyblocks with <code>--module-only</code> + dedicated 39916 unit test module 39917 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/610">#610</a>)</li> 39918<li>minor enhancements, including:<ul> 39919<li>update GROMACS easyblock for version 5 39920 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/513">#513</a>)</li> 39921</ul> 39922</li> 39923<li>various other bug fixes, including:<ul> 39924<li>only check compiler being used if FFTW interfaces are being 39925 built in Intel MKL easyblock 39926 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/606">#606</a>)</li> 39927</ul> 39928</li> 39929</ul> 39930<p><strong>easyconfigs</strong></p> 39931<ul> 39932<li>added example easyconfig files for <strong>3</strong> new software packages:<ul> 39933<li>networkx 39934 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1592">#1592</a>), 39935 Platanus 39936 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1597">#1597</a>), 39937 SaguaroGW 39938 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1600">#1600</a>)</li> 39939</ul> 39940</li> 39941<li>
39941added new easyconfigs for existing toolchains: <code>ictce/7.3.5</code>, 39942 <code>CrayCCE/5.2.40</code>, <code>CrayGNU/5.2.40</code>, <code>CrayIntel/5.2.40</code></li> 39943<li>added easyconfigs using <code>CrayGNU/5.2.25</code> and <code>CrayGNU/5.2.40</code> 39944 toolchains 39945 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1610">#1610</a>, 39946 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1611">#1611</a>)</li> 39947<li>added additional easyconfigs for various supported software 39948 packages: version updates, different toolchains, ...<ul> 39949<li>including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3</li> 39950</ul> 39951</li> 39952<li>various bug fixes, including:<ul> 39953<li>enable usempi in GROMACS easyconfig using CrayGNU toolchain (as 39954 required by GROMACS easyblock) 39955 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1590">#1590</a>)</li> 39956<li>use system-provided tcsh when building WRF on Cray systems, to 39957 avoid hanging build 39958 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1595">#1595</a>)</li> 39959<li>only use '<code>dynamic</code>' toolchain option, not '<code>shared</code>', in 39960 easyconfigs using Cray toolchain 39961 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1609">#1609</a>)</li> 39962</ul> 39963</li> 39964</ul> 39965<h2 id="release_notes_v2.1.0">EasyBuild v2.1.0 (April 30th 2015)<a class="headerlink" href="#release_notes_v2.1.0" title="Permanent link">¶</a></h2> 39966<p>feature + bugfix release</p> 39967<p><strong>framework</strong></p> 39968<ul> 39969<li>requires vsc-base v2.2.0 or more recent<ul> 39970<li>added support for LoggedException 39971 (<a href="https://github.com/hpcugent/vsc-base/pull/160">vsc-base#160</a>, 39972 <a href="https://github.com/hpcugent/vsc-base/pull/163">vsc-base#163</a>, 39973 <a href="https://github.com/hpcugent/vsc-base/pull/165">vsc-base#165</a>, 39974 <a href="https://github.com/hpcugent/vsc-base/pull/167">vsc-base#167</a>)</li> 39975<li>added support for add_flex action in GeneralOption 39976 (<a href="https://github.com/hpcugent/vsc-base/pull/162">vsc-base#162</a>)</li> 39977<li>added support to GeneralOption to act on unknown configuration 39978 environment variables 39979 (<a href="https://github.com/hpcugent/vsc-base/pull/162">vsc-base#162</a>)</li> 39980</ul> 39981</li> 39982<li>add support for only (re)generating module files: <code>--module-only</code> 39983 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1018">#1018</a>)<ul> 39984<li>module naming scheme API is enhanced to include 39985 det_install_subdir method</li> 39986<li>see <a class="autorefs autorefs-internal" href="../partial-installations/#module_only">Only (re)generating (additional) module files using --module-only</a></li> 39987</ul> 39988</li> 39989<li>add support for generating module files in Lua syntax (note: 39990 requires Lmod as modules tool) 39991 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1060">#1060</a>, 39992 <a href="https://github.com/easybuilders/easybuild-framework/pull/1255">#1255</a>, 39993 <a href="https://github.com/easybuilders/easybuild-framework/pull/1256">#1256</a>, 39994 <a href="https://github.com/easybuilders/easybuild-framework/pull/1270">#1270</a>)<ul> 39995<li>see <code>--module-syntax</code> configuration option and 39996 <a class="autorefs autorefs-internal" title="Module files syntax (" href="../configuration/#module_syntax">Module files syntax</a></li> 39997</ul> 39998</li> 39999<li>deprecate <code>log.error</code> method in favor of raising <code>EasyBuildError</code> 40000 exception 40001 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1218">#1218</a>)<ul> 40002<li>see <a class="autorefs autorefs-internal" href="../removed-functionality/#depr_error_reporting"><code>error</code> and <code>exception</code> log methods no longer raise an exception</a></li> 40003</ul> 40004</li> 40005<li>add support for using external modules as dependencies, and to 40006 provide metadata for external modules 40007 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1230">#1230</a>, 40008 <a href="https://github.com/easybuilders/easybuild-framework/pull/1265">#1265</a>, 40009 <a href="https://github.com/easybuilders/easybuild-framework/pull/1267">#1267</a>)<ul> 40010<li>see <a class="autorefs autorefs-internal" href="../using-external-modules/#using_external_modules">Using external modules</a></li> 40011</ul> 40012</li> 40013<li>
40013add experimental support for Cray toolchains on top of PrgEnv 40014 modules: <code>CrayGNU</code>, <code>CrayIntel</code>, <code>CrayCCE</code> 40015 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1234">#1234</a>, 40016 <a href="https://github.com/easybuilders/easybuild-framework/pull/1268">#1268</a>)<ul> 40017<li>see 40018 <a href="https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray">https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray</a></li> 40019</ul> 40020</li> 40021<li>various other enhancements, including:<ul> 40022<li>clear list of checksums when using <code>--try-software-version</code> 40023 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1169">#1169</a>)</li> 40024<li>sort the results of searching for files (e.g., <code>--search</code> 40025 output) 40026 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1214">#1214</a>)</li> 40027<li>enhance test w.r.t. use of templates in cfgfile 40028 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1217">#1217</a>)</li> 40029<li>define '<code>%(DEFAULT_REPOSITORYPATH)s</code>' template for cfgfiles 40030 (see <code>eb --avail-cfgfile-constants</code>) 40031 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1220">#1220</a>)</li> 40032<li>also reset <code>$LD_PRELOAD</code> when running module commands, in case 40033 module defined <code>$LD_PRELOAD</code> 40034 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1222">#1222</a>)</li> 40035<li>move location of '<code>module use</code>' statements in generated module 40036 file (<em>after</em> '<code>module load</code>' statements) 40037 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1232">#1232</a>)</li> 40038<li>add support for <code>--show-default-configfiles</code> 40039 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1240">#1240</a>)<ul> 40040<li>see <a class="autorefs autorefs-internal" href="../configuration/#default_configuration_files">Default configuration files</a></li> 40041</ul> 40042</li> 40043<li>report error on missing configuration files, rather than 40044 ignoring them 40045 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1240">#1240</a>)</li> 40046<li>clean up commit message used in easyconfig git repository 40047 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1248">#1248</a>)</li> 40048<li>add <code>--hide-deps</code> configuration option to specify names of 40049 software that must be installed as hidden modules 40050 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1250">#1250</a>)<ul> 40051<li>see <a class="autorefs autorefs-internal" href="../manipulating-dependencies/#hide_deps">Installing dependencies as hidden modules using <code>--hide-deps</code></a></li> 40052</ul> 40053</li> 40054<li>add support for appending/prepending to <code>--robot-paths</code> to avoid 40055 overwriting default robot search path 40056 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1252">#1252</a>)<ul> 40057<li>see <a class="autorefs autorefs-internal" href="../using-easybuild/#robot_search_path_prepend_append">Prepending/appending to the default robot search path</a></li> 40058</ul> 40059</li> 40060<li>enable detection of use of unknown <code>$EASYBUILD</code>-prefixed 40061 environment variables 40062 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1253">#1253</a>)<ul> 40063<li>see <a class="autorefs autorefs-internal" href="../configuration/#configuration_env_vars">Environment variables</a></li> 40064</ul> 40065</li> 40066<li>add <code>--installpath-modules</code> and <code>--installpath-software</code> 40067 configuration options 40068 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1258">#1258</a>)<ul> 40069<li>see <a class="autorefs autorefs-internal" href="../configuration/#installpath">Software and modules install path</a></li> 40070</ul> 40071</li> 40072<li>use dedicated subdirectory in temporary directory for each test 40073 to ensure better cleanup 40074 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1260">#1260</a>)</li> 40075<li>get rid of <code>$PROFILEREAD</code> hack when running commands, not needed 40076 anymore 40077 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1264">
40077#1264</a>)</li> 40078</ul> 40079</li> 40080<li>various bug fixes, including:<ul> 40081<li>make bootstrap script robust against having <code>vsc-base</code> already 40082 available in Python search path 40083 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1212">#1212</a>, 40084 <a href="https://github.com/easybuilders/easybuild-framework/pull/1215">#1215</a>)</li> 40085<li>set default value for unpack_options easyconfig parameter to 40086 <code>''</code>, so <code>self.cfg.update</code> works on it 40087 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1229">#1229</a>)</li> 40088<li>also copy rotated log files 40089 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1238">#1238</a>)</li> 40090<li>fix parsing of <code>--download-timeout</code> value 40091 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1242">#1242</a>)</li> 40092<li>make <code>test_XDG_CONFIG_env_vars</code> unit test robust against 40093 existing user config file in default location 40094 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1259">#1259</a>)</li> 40095<li>fix minor robustness issues w.r.t. <code>$XDG_CONFIG*</code> and 40096 <code>$PYTHONPATH</code> in unit tests 40097 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1262">#1262</a>)</li> 40098<li>fix issue with handling empty toolchain variables 40099 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1263">#1263</a>)</li> 40100</ul> 40101</li> 40102</ul> 40103<p><strong>easyblocks</strong></p> 40104<ul> 40105<li>replace '<code>log.error</code>' with '<code>raise EasyBuildError</code>' in all 40106 easyblocks 40107 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/588">#588</a>)</li> 40108<li>one new generic easyblock: <code>ConfigureMakePythonPackage</code> 40109 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/540">#540</a>)</li> 40110<li>new easyblocks for 2 software packages that require customized 40111 support:<ul> 40112<li>TINKER 40113 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/578">#578</a>), 40114 Xmipp 40115 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/581">#581</a>)</li> 40116</ul> 40117</li> 40118<li>various other enhancements, including:<ul> 40119<li>enhance WIEN2k easyblock for recent versions + cleanup 40120 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/486">#486</a>)</li> 40121<li>define <code>$PYTHONNOUSERSITE</code> in PythonPackage easyblock so 40122 user-installed packages are not picked up 40123 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/577">#577</a>)</li> 40124<li>add support in CP2K easyblock for building on top of 40125 MPICH/MPICH2 40126 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/579">#579</a>)</li> 40127<li>enhance Hadoop easyblock to support parallel builds 40128 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/580">#580</a>)</li> 40129<li>drop <code>-noroot</code> for recent FLUENT versions, honor <code>installopts</code>, 40130 enable <code>-debug</code> 40131 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/582">#582</a>)</li> 40132<li>include <code>prebuildopts</code> in build command for Python packages 40133 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/585">#585</a>)</li> 40134<li>also install <code>rosetta_tools</code> subdirectory for Rosetta 40135 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/586">#586</a>)</li> 40136<li>update SLEPc easyblock for v3.5 + style cleanup 40137 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/593">#593</a>)</li> 40138<li>minor fix in HPL easyblock w.r.t. checking defined environment 40139 variables 40140 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/595">#595</a>)</li> 40141<li>tweak CP2K easyblock w.r.t. LAPACK/FFTW support 40142 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/596">#596</a>)</li> 40143<li>minor update to GCC easyblock to support GCC v5.x 40144 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/598">#598</a>)</li> 40145<li>update sanity check in R easyblock for version 3.2.0 40146 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/602">#602</a>)</li> 40147</ul> 40148</li> 40149<li>various bug fixes, including:<ul> 40150<li>fix Score-P easyblock for compiler-only toolchains, include Qt 40151 as optional dependency 40152 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/552">
40152#552</a>)</li> 40153<li>fix definition of <code>$MKLROOT</code>, should be set to '<code>mkl</code>' subdir 40154 of install dir 40155 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/576">#576</a>)</li> 40156<li>add <code>-libmpichf90</code> to list of MPI libraries in NWChem easyblock 40157 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/584">#584</a>)</li> 40158<li>stop using '<code>$root</code>' to make easyblocks compatible with module 40159 files in Lua syntax 40160 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/590">#590</a>)</li> 40161<li>also set <code>$PYTHONPATH</code> before installing Python package in 40162 temporary directory in <code>test_step</code> 40163 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/591">#591</a>)</li> 40164<li>unset <code>buildopts</code>/<code>installopts</code> before installing Python 40165 extensions in Python easyblock 40166 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/597">#597</a>)</li> 40167<li>allow not including vsc-base sources when installing EasyBuild 40168 (gets installed with easybuild-framework) 40169 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/600">#600</a>)</li> 40170<li>use <code>self.initial_environ</code> rather than <code>self.orig_environ</code> in 40171 EasyBuildMeta easyblock 40172 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/600">#600</a>)</li> 40173<li>make GCC easyblock compatible with <code>--module-only</code> by setting 40174 default value for <code>self.platform_lib</code> in constructor 40175 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/603">#603</a>)</li> 40176</ul> 40177</li> 40178</ul> 40179<p><strong>easyconfigs</strong></p> 40180<ul> 40181<li>added example easyconfig files for <strong>27</strong> new software packages:<ul> 40182<li>AFNI 40183 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1322">#1322</a>, 40184 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1521">#1521</a>), 40185 BCFtools 40186 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1492">#1492</a>), 40187 getdp 40188 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1518">#1518</a>), 40189 gmsh 40190 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1518">#1518</a>), 40191 gtest 40192 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1244">#1244</a>), 40193 hanythingondemand 40194 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1530">#1530</a>), 40195 mawk 40196 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1369">#1369</a>), 40197 Minimac 40198 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/815">#815</a>), 40199 Minimac3 40200 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1502">#1502</a>), 40201 monty 40202 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1548">#1548</a>), 40203 Octave 40204 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1563">#1563</a>), 40205 pbs_python 40206 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1530">#1530</a>), 40207 pigz 40208 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1036">#1036</a>), 40209 Pygments 40210 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1536">#1536</a>), 40211 pyhull 40212 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1539">#1539</a>), 40213 pymatgen 40214 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1549">#1549</a>), 40215 PyQt 40216 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1322">#1322</a>, 40217 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1521">#1521</a>), 40218 Ray 40219 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1494">#1494</a>), 40220 requests 40221 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1536">#1536</a>), 40222 seqtk 40223 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1524">#1524</a>), 40224 SIP 40225 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1322">#1322</a>, 40226 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1521">#1521</a>), 40227 S-Lang 40228 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1369">#1369</a>), 40229 Spark 40230 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1554">#1554</a>), 40231 spglib 40232 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1549">#1549</a>), 40233 TINKER 40234 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1465">#1465</a>), 40235 tmux 40236 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1369">#1369</a>), 40237 Xmipp 40238 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1489">#1489</a>)</li> 40239</ul> 40240</li> 40241<li>
40241added easyconfigs for new (Cray-specific) toolchains 40242 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1538">#1538</a>): 40243 <code>CrayGNU</code>, <code>CrayIntel</code>, <code>CrayCCE</code><ul> 40244<li>initially supported software (using CrayGNU toolchains): CP2K, 40245 GROMACS, HPL, Python + numpy/scipy, WRF 40246 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1558">#1558</a>)</li> 40247<li>see also 40248 <a href="https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray">https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray</a></li> 40249</ul> 40250</li> 40251<li>added new easyconfigs for existing toolchains: <code>goolf/1.5.16</code>, 40252 <code>intel/2014.06</code></li> 40253<li>added additional easyconfigs for various supported software 40254 packages: version updates, different toolchains, ...<ul> 40255<li>including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, 40256 PETSc/SLEPc v3.5.3, WIEN2k v14.1</li> 40257</ul> 40258</li> 40259<li>various other enhancements, including:<ul> 40260<li>include pbr dependency for lockfile Python extension in Python 40261 v2.7.9 easyconfigs + mock/pytz/pandas 40262 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1462">#1462</a>, 40263 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1540">#1540</a>)</li> 40264<li>include SQLite as dependency in Python v2.7.9 easyconfigs 40265 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1468">#1468</a>)</li> 40266<li>set <code>$LD_PRELOAD</code> for Hoard and jemalloc 40267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1470">#1470</a>)</li> 40268<li>fix homepage in SCOTCH easyconfigs 40269 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1485">#1485</a>)</li> 40270<li>adding missing six/ecdsa dependencies for dateutil/paramiko 40271 Python packages in Python easyconfigs 40272 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1504">#1504</a>, 40273 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1505">#1505</a>, 40274 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1506">#1506</a>, 40275 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1507">#1507</a>, 40276 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1508">#1508</a>, 40277 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1509">#1509</a>, 40278 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1510">#1510</a>)</li> 40279<li>enable <code>pic</code> toolchain option in expat easyconfigs 40280 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1562">#1562</a>)</li> 40281<li>extend list of source URLs for Bioconductor packages in R 40282 easyconfigs to include 'release' source URLs 40283 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1568">#1568</a>)</li> 40284</ul> 40285</li> 40286<li>various bug fixes, including:<ul> 40287<li>adding missing zlib dependency in all Tcl easyconfig files 40288 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1344">#1344</a>)</li> 40289<li>fix homepage in FLUENT easyconfigs 40290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1472">#1472</a>)</li> 40291<li>use <code>--with-verbs</code> rather than deprecated <code>--with-openib</code> in 40292 OpenMPI configure options 40293 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1511">#1511</a>)</li> 40294<li>stop relying on <code>OS_NAME</code> constant to specify OS dependencies in 40295 OpenMPI easyconfigs 40296 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1512">#1512</a>)</li> 40297<li>replace use of '<code>$root</code>' with '<code>%(installdir)s</code>' to ensure 40298 compatibility with module files in Lua syntax 40299 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1532">#1532</a>)</li> 40300<li>stop relying on '<code>$MKLROOT</code>' in ROOT easyconfigs 40301 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1537">#1537</a>)</li> 40302<li>use proper Bundle easyblock for biodeps/PRACE 40303 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1566">#1566</a>)</li> 40304<li>make source_urls in Cube and Scalasca easyconfigs compatible 40305 with --try-software-version 40306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1574">#1574</a>)</li> 40307<li>
40307add patch for Cube to fix configure script w.r.t. Qt dependency, 40308 add --without-java-reader configure option 40309 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1574">#1574</a>)</li> 40310</ul> 40311</li> 40312</ul> 40313<h2 id="release_notes_v2.0.0">EasyBuild v2.0.0 (March 6th 2015)<a class="headerlink" href="#release_notes_v2.0.0" title="Permanent link">¶</a></h2> 40314<p>feature + bugfix release</p> 40315<p><strong>framework</strong></p> 40316<ul> 40317<li>requires vsc-base v2.0.3 or more recent<ul> 40318<li>avoid deprecation warnings w.r.t. use of <code>message</code> attribute 40319 (<a href="https://github.com/hpcugent/vsc-base/pull/155">vsc-base#155</a>)</li> 40320<li>fix typo in log message rendering <code>--ignoreconfigfiles</code> unusable 40321 (<a href="https://github.com/hpcugent/vsc-base/pull/158">vsc-base#158</a>)</li> 40322</ul> 40323</li> 40324<li>removed functionality that was deprecated for EasyBuild version 2.0 40325 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1143">#1143</a>)<ul> 40326<li>see <a class="autorefs autorefs-internal" href="../removed-functionality/#removed_functionality">Removed functionality</a></li> 40327<li>the fix_broken_easyconfigs.py script can be used to update 40328 easyconfig files suffering from this 40329 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1151">#1151</a>, 40330 <a href="https://github.com/easybuilders/easybuild-framework/pull//1206">#1206</a>, 40331 <a href="https://github.com/easybuilders/easybuild-framework/pull//1207">#1207</a>)</li> 40332</ul> 40333</li> 40334<li>stop including a crippled copy of vsc-base, include vsc-base as a 40335 proper dependency instead 40336 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1160">#1160</a>, 40337 <a href="https://github.com/easybuilders/easybuild-framework/pull//1194">#1194</a>)<ul> 40338<li>vsc-base is automatically installed as a dependency for 40339 easybuild-framework, if a Python installation tool is used</li> 40340<li>see <a class="autorefs autorefs-internal" href="../installation/#required_python_packages">Required Python packages</a></li> 40341</ul> 40342</li> 40343<li>various other enhancements, including:<ul> 40344<li>add support for Linux/POWER systems 40345 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1044">#1044</a>)</li> 40346<li>major cleanup in <code>tools/systemtools.py</code> + significantly enhanced 40347 tests 40348 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1044">#1044</a>)</li> 40349<li>add support for '<code>eb -a rst</code>', list available easyconfig 40350 parameters in ReST format 40351 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1131">#1131</a>)</li> 40352<li>add support for specifying one or more easyconfigs in 40353 combination with <code>--from-pr</code> 40354 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1132">#1132</a>)<ul> 40355<li>see <a class="autorefs autorefs-internal" href="../integration-with-github/#github_from_pr_specifying_easyconfigs">Specifying particular easyconfig files</a></li> 40356</ul> 40357</li> 40358<li>define <code>__contains__</code> in EasyConfig class 40359 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1155">#1155</a>)</li> 40360<li>restore support for downloading over a proxy 40361 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1158">#1158</a>)<ul> 40362<li>i.e., use <code>urllib2</code> rather than <code>urllib</code></li> 40363<li>this involved sacrificing the download progress report 40364 (which was only visible in the log file)</li> 40365</ul> 40366</li> 40367<li>let <code>mpi_family</code> return <code>None</code> if MPI is not supported by a 40368 toolchain 40369 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1164">#1164</a>)</li> 40370<li>include support for specifying system-level configuration files 40371 for EasyBuild via <code>$XDG_CONFIG_DIRS</code> 40372 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1166">#1166</a>)<ul> 40373<li>see <a class="autorefs autorefs-internal" href="../configuration/#default_configuration_files">Default configuration files</a></li> 40374</ul> 40375</li> 40376<li>make unit tests more robust 40377 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1167">#1167</a>, 40378 <a href="https://github.com/easybuilders/easybuild-framework/pull//1196">#1196</a>)<ul> 40379<li>see <a class="autorefs autorefs-internal" href="../unit-tests/#unit_tests">Unit tests</a></li> 40380</ul> 40381</li> 40382<li>
40382add hierarchical module naming scheme categorizing modules by 40383 <code>moduleclass</code> 40384 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1176">#1176</a>)</li> 40385<li>enhance bootstrap script to allow bootstrapping using supplied 40386 tarballs 40387 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1184">#1184</a>)</li> 40388<li>disable updating of Lmod user cache by default, add 40389 configuration option <code>--update-modules-tool-cache</code> 40390 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1185">#1185</a>)<ul> 40391<li>for now, only the Lmod user cache can be updated using 40392 <code>--update-modules-tool-cache</code></li> 40393</ul> 40394</li> 40395<li>use available <code>which()</code> function, rather than running 40396 '<code>which</code>' via <code>run_cmd</code> 40397 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1192">#1192</a>)</li> 40398<li>fix <code>install-EasyBuild-develop.sh</code> script w.r.t. vsc-base 40399 dependency 40400 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1193">#1193</a>)</li> 40401<li>also consider robot search path when looking for specified 40402 easyconfigs 40403 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1201">#1201</a>)<ul> 40404<li>see <a class="autorefs autorefs-internal" href="../using-easybuild/#specifying_easyconfigs">Specifying what to install</a></li> 40405</ul> 40406</li> 40407</ul> 40408</li> 40409<li>various bug fixes, including:<ul> 40410<li>stop triggering deprecated/no longer support functionality in 40411 unit tests 40412 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1126">#1126</a>)</li> 40413<li>fix <code>from_pr</code> test by including dummy easyblocks for HPL and 40414 ScaLAPACK 40415 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1133">#1133</a>)</li> 40416<li>escape use of '<code>%</code>' in string with command line options with 40417 <code>--job</code> 40418 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1135">#1135</a>)</li> 40419<li>fix handling specified patch level 0 (+ enhance tests for 40420 fetch_patches method) 40421 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1139">#1139</a>)</li> 40422<li>fix formatting issues in generated easyconfig file obtained via 40423 <code>--try-X</code> 40424 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1144">#1144</a>)</li> 40425<li>use <code>log.error</code> in <code>tools/toolchain/toolchain.py</code> where 40426 applicable 40427 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1145">#1145</a>)</li> 40428<li>stop hardcoding <code>/tmp</code> in <code>mpi_cmd_for</code> function 40429 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1146">#1146</a>, 40430 <a href="https://github.com/easybuilders/easybuild-framework/pull//1200">#1200</a>)</li> 40431<li>correctly determine variable name for <code>$EBEXTLIST</code> when 40432 generating module file 40433 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1156">#1156</a>)</li> 40434<li>do not ignore exit code of failing postinstall commands 40435 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1157">#1157</a>)</li> 40436<li>fix rare case in which used easyconfig and copied easyconfig are 40437 the same 40438 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1159">#1159</a>)</li> 40439<li>always filter hidden deps from list of dependencies 40440 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1161">#1161</a>)</li> 40441<li>fix implementation of <code>path_matches</code> function in 40442 <code>tools/filetools.py</code> 40443 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1163">#1163</a>)</li> 40444<li>make sure plain text keyring is used by unit tests 40445 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1165">#1165</a>)</li> 40446<li>suppress creation of module symlinks for <code>HierarchicalMNS</code> 40447 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1173">#1173</a>)</li> 40448<li>sort all lists obtained via <code>glob.glob</code>, since they are in 40449 arbitrary order 40450 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1187">#1187</a>)</li> 40451<li>stop modifying <code>$MODULEPATH</code> directly in <code>setUp</code>/<code>tearDown</code> of 40452 toolchain tests 40453 (<a href="https://github.com/easybuilders/easybuild-framework/pull//1191">#1191</a>)</li> 40454</ul> 40455</li> 40456</ul> 40457<p><strong>easyblocks</strong></p> 40458<ul> 40459<li>one new generic easyblock for installing a bundle of modules: 40460 <code>Bundle</code> 40461 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/550">#550</a>)<ul> 40462<li>and let the <code>Toolchain</code> generic easyblock derive from <code>Bundle</code></li> 40463</ul> 40464</li> 40465<li>new easyblocks for 2 software packages that require customized 40466 support:<ul> 40467<li>GAMESS-US 40468 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/470">#470</a>, 40469 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/544">#544</a>, 40470 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/558">#558</a>), 40471 Hadoop 40472 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/563">#563</a>)</li> 40473</ul> 40474</li> 40475<li>various other enhancements, including:<ul> 40476<li>move support for <code>staged_install</code> from CPLEX easyblock to 40477 generic <code>Binary</code> easyblock 40478 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/502">#502</a>)</li> 40479<li>fix sanity check in picard easyblock for v1.119 that doesn't 40480 include <code>sam.jar</code> 40481 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/522">#522</a>)</li> 40482<li>log warning message when unlinking jellyfish symlink fails in 40483 Trinity easyblock 40484 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/534">#534</a>)</li> 40485<li>revamp <code>EB_libint2</code> easyblock into <code>EB_Libint</code> that works for 40486 both Libint v1x and v2.x 40487 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/536">#536</a>)</li> 40488<li>update CP2K easyblock for recent versions (no more '<code>fes</code>') 40489 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/537">#537</a>)</li> 40490<li>update SuiteSparse easyblock for recent versions 40491 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/541">#541</a>)</li> 40492<li>fix easyblock unit tests after dropping support for deprecated 40493 behaviour in framework 40494 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/543">#543</a>)</li> 40495<li>rework PSI easyblock to support future releases 40496 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/545">#545</a>)</li> 40497<li>enable always generating a 'verbose' Makefile in the generic 40498 CMakeMake easyblock 40499 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/546">#546</a>)</li> 40500<li>remove functionality in (generic) easyblocks that was deprecated 40501 for EasyBuild v2.0 40502 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/547">#547</a>)</li> 40503<li>enhance generic RPackage easyblock to support installing 40504 extensions in a separate prefix 40505 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/551">#551</a>)</li> 40506<li>deprecate GenomeAnalysisTK easyblock, since it's basically 40507 equivalent to Tarball 40508 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/557">#557</a>)</li> 40509<li>update SAMtools easyblock for v1.2 40510 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/562">#562</a>)</li> 40511<li>take <code>preconfigopts</code> easyconfig parameter into account in ROOT 40512 easyblock 40513 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/566">#566</a>)</li> 40514<li>update easyblock for installing EasyBuild<ul> 40515<li>to support bootstrapping with provided source tarballs 40516 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/559">#559</a>)</li> 40517<li>to also cover vsc-base dependency, and verify 40518 <code>easy-install.pth</code> 40519 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/567">#567</a>)</li> 40520</ul> 40521</li> 40522<li>update disabling sanitizer tests for Clang 3.6 40523 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/570">#570</a>)</li> 40524</ul> 40525</li> 40526<li>various bug fixes, including:<ul> 40527<li>fix handling of LTO in GCC easyblock 40528 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/535">#535</a>)</li> 40529<li>relocate FDTD RPM to fix installation on SL6 40530 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/538">#538</a>)</li> 40531</ul> 40532</li> 40533</ul> 40534<p><strong>easyconfigs</strong></p> 40535<ul> 40536<li>added example easyconfig files for <strong>29</strong> new software packages:<ul> 40537<li>bsoft 40538 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1353">#1353</a>), 40539 Coot 40540 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1400">#1400</a>), 40541 Cuby 40542 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1258">#1258</a>), 40543 DSRC 40544 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1242">#1242</a>), 40545 Exonerate 40546 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/568">#568</a>), 40547 fastqz 40548 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1242">#1242</a>), 40549 FSA 40550 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/568">#568</a>), 40551 fqzcomp 40552 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1242">#1242</a>), 40553 GAMESS-US 40554 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1153">
40554#1153</a>, 40555 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1406">#1406</a>), 40556 Grep 40557 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1308">#1308</a>), 40558 Hadoop 40559 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1418">#1418</a>), 40560 Hoard 40561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1415">#1415</a>), 40562 IMB 40563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1284">#1284</a>), 40564 ISL 40565 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1389">#1389</a>), 40566 jemalloc 40567 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1416">#1416</a>), 40568 libdwarf 40569 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1283">#1283</a>), 40570 libelf 40571 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1283">#1283</a>), 40572 MPC 40573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1310">#1310</a>), 40574 multitail 40575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1327">#1327</a>), 40576 Pmw 40577 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1403">#1403</a>), 40578 Quip 40579 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1242">#1242</a>), 40580 rCUDA 40581 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/720">#720</a>), 40582 SCALCE 40583 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1242">#1242</a>), 40584 SMALT 40585 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/568">#568</a>), 40586 STREAM 40587 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1332">#1332</a>), 40588 worker 40589 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1307">#1307</a>), 40590 Xerces-C++ 40591 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1370">#1370</a>), 40592 XQilla 40593 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1370">#1370</a>), 40594 ZPAQ 40595 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1242">#1242</a>)</li> 40596</ul> 40597</li> 40598<li>added easyconfigs for new (common) toolchains<ul> 40599<li><code>foss/2015a</code> 40600 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1239">#1239</a>), 40601 <code>gompi/1.5.16</code> 40602 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1380">#1380</a>), 40603 <code>gmvolf/1.7.20</code> 40604 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1397">#1397</a>), 40605 <code>goolf/1.7.20</code> 40606 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1294">#1294</a>), 40607 intel/2015a 40608 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1238">#1238</a>), 40609 <code>intel/2015.02</code> 40610 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1393">#1393</a>), 40611 <code>iomkl/2015.01</code> 40612 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1325">#1325</a>), 40613 <code>iomkl/2015.02</code> 40614 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1401">#1401</a>)</li> 40615</ul> 40616</li> 40617<li>added new software bundle: <code>Autotools</code> 40618 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1385">#1385</a>)</li> 40619<li>various other enhancements, including:<ul> 40620<li>don't define <code>$LDSHARED</code> in zlib easyconfigs 40621 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1350">#1350</a>)<ul> 40622<li>this fixes the long-standing 40623 "<code>no version information available</code>" issue with zlib</li> 40624<li>see also 40625 <a href="https://github.com/easybuilders/easybuild-framework/issues/108">framework#108</a></li> 40626</ul> 40627</li> 40628<li>add unit test to check that all <code>extra_options</code> keys are defined 40629 in <code>EasyConfig</code> instance 40630 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1378">#1378</a>)</li> 40631<li>add source MD5 checksums in all GCC easyconfigs 40632 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1391">#1391</a>)</li> 40633<li>speeding up the unit tests by avoiding rereading of same 40634 easyconfig file 40635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1432">#1432</a>)</li> 40636<li>fix conflict detection in unit tests by considering build deps 40637 separately from runtime deps 40638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1447">#1447</a>)</li> 40639<li>fix toolchain for Bison build dep in 40640 <code>MVAPICH2-1.9-iccifort-2011.13.367.eb</code> easyconfig 40641 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1448">#1448</a>)</li> 40642<li>use <code>Bundle</code>
40642 generic easyblock for HPCBIOS bundles and fix 40643 <code>moduleclass</code> 40644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1451">#1451</a>)</li> 40645</ul> 40646</li> 40647<li>various bug fixes, including:<ul> 40648<li>revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 40649 easyconfig 40650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1144">#1144</a>)</li> 40651<li>added Java dependencies to EMBOSS easyconfigs 40652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1167">#1167</a>)</li> 40653<li>don't list '<code>lto</code>' as a language in GCC easyconfigs 40654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1286">#1286</a>)<ul> 40655<li>related to the fixes in the GCC easyblock, see 40656 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/535">easyblocks#535</a></li> 40657</ul> 40658</li> 40659<li>rename libint2 easyconfigs as Libint v2 easyconfigs 40660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1287">#1287</a>)</li> 40661<li>fix mpi4py <code>source_urls</code> in Python easyconfigs 40662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1306">#1306</a>)</li> 40663<li>consistently use CLooG 0.18.0 for GCC 4.8 series 40664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1392">#1392</a>)</li> 40665<li>rename GenomeAnalysisTk easyconfigs to GATK 40666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1399">#1399</a>)</li> 40667<li>include <code>openssl-devel</code> SLES11 OS dependency in 40668 cURL/MySQL/Python easyconfigs 40669 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1422">#1422</a>)</li> 40670<li>add missing Perl dependency in parallel easyconfigs 40671 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1430">#1430</a>)</li> 40672<li>correct name in BLAST+ easyconfigs 40673 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1443">#1443</a>)</li> 40674<li>fix name for sparsehash easyconfigs 40675 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1452">#1452</a>)</li> 40676</ul> 40677</li> 40678</ul> 40679<h2 id="easybuild-v1162-march-6th-2015">EasyBuild v1.16.2 (March 6th 2015)<a class="headerlink" href="#easybuild-v1162-march-6th-2015" title="Permanent link">¶</a></h2> 40680<p>bugfix release</p> 40681<p><strong>framework</strong></p> 40682<p><em>(no changes compared to v1.16.1, simple version bump to stay in sync 40683with easybuild-easyblocks)</em></p> 40684<p><strong>easyblocks</strong></p> 40685<ul> 40686<li>make <code>EB_EasyBuildMeta</code> easyblock aware of vsc-base to make 40687 upgrading to EasyBuild v2.0.0 possible 40688 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/573">#573</a>)</li> 40689</ul> 40690<p><strong>easyconfigs</strong></p> 40691<p><em>(no changes compared to v1.16.1, simple version bump to stay in sync 40692with easybuild-easyblocks)</em></p> 40693<h2 id="easybuild-v1161-december-19th-2014">EasyBuild v1.16.1 (December 19th 2014)<a class="headerlink" href="#easybuild-v1161-december-19th-2014" title="Permanent link">¶</a></h2> 40694<p>bugfix release</p> 40695<p><strong>framework</strong></p> 40696<ul> 40697<li>fix functionality that is broken with <code>--deprecated=2.0</code> or with 40698 <code>$EASYBUILD_DEPRECATED=2.0</code><ul> 40699<li>don't include easyconfig parameters for <code>ConfigureMake</code> in 40700 <code>eb -a</code>, since fallback is deprecated 40701 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1123">#1123</a>)</li> 40702<li>correctly check software_license value type 40703 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1124">#1124</a>)</li> 40704<li>fix <code>generate_software_list.py</code> script w.r.t. deprecated 40705 fallback to <code>ConfigureMake</code> 40706 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1127">#1127</a>)</li> 40707</ul> 40708</li> 40709<li>other bug fixes<ul> 40710<li>fix logging issues in tests, sync with vsc-base v2.0.0 40711 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1120">#1120</a>)</li> 40712</ul> 40713</li> 40714</ul> 40715<p><strong>easyblocks</strong></p> 40716<ul> 40717<li>fix EasyBuild versions for which <code>$EASYBUILD_DEPRECATED=1.0</code> is set 40718 in EasyBuild sanity check 40719 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/531">#531</a>)</li> 40720</ul> 40721<p><strong>easyconfigs</strong></p> 40722<ul> 40723<li>set default easyblock to ConfigureMake in TEMPLATE.eb 40724 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1277">#1277</a>)</li> 40725</ul> 40726<h2 id="easybuild-v1160-december-18th-2014">EasyBuild v1.16.0 (December 18th 2014)<a class="headerlink" href="#easybuild-v1160-december-18th-2014" title="Permanent link">¶</a></h2> 40727<p>feature + bugfix release</p> 40728<p><strong>framework</strong></p> 40729<ul> 40730<li>deprecate automagic fallback to <code>ConfigureMake</code> easyblock 40731 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1113">#1113</a>)<ul> 40732<li>easyconfigs should specify <code>easyblock = 'ConfigureMake'</code> instead 40733 of relying on the fallback mechanism</li> 40734<li><strong>note: automagic fallback to</strong> <code>ConfigureMake</code> <strong>easyblock will 40735 be removed in EasyBuild v2.0</strong></li> 40736<li>see also <a href="http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#configuremake-fallback">Automagic fallback to 40737 ConfigureMake</a></li> 40738</ul> 40739</li> 40740<li>stop triggering deprecated functionality, to enable use of 40741 <code>--deprecated=2.0</code> 40742 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1107">#1107</a>, 40743 <a href="https://github.com/easybuilders/easybuild-framework/pull/1115">#1115</a>, 40744 <a href="https://github.com/easybuilders/easybuild-framework/pull/1119">#1119</a>)<ul> 40745<li>see <a href="http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#configuremake-fallback">Deprecated 40746 functionality</a> 40747 for more information</li> 40748</ul> 40749</li> 40750<li>various other enhancements, including:<ul> 40751<li>add script to clean up gists created via <code>--upload-test-report</code> 40752 (<a href="https://github.com/easybuilders/easybuild-framework/pull/958">#958</a>)</li> 40753<li>also use <code>-xHost</code> when using Intel compilers on AMD systems (as 40754 opposed to <code>-msse3</code>) 40755 (<a href="https://github.com/easybuilders/easybuild-framework/pull/960">#960</a>)</li> 40756<li>
40756add Python version check in <code>eb</code> command 40757 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1046">#1046</a>)</li> 40758<li>take <code>versionprefix</code> into account in <code>HierarchicalMNS</code> module 40759 naming scheme 40760 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1058">#1058</a>)</li> 40761<li>clean up and refactor <code>main.py</code>, move functionality to other 40762 modules 40763 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1059">#1059</a>, 40764 <a href="https://github.com/easybuilders/easybuild-framework/pull/1064">#1064</a>, 40765 <a href="https://github.com/easybuilders/easybuild-framework/pull/1075">#1075</a>, 40766 <a href="https://github.com/easybuilders/easybuild-framework/pull/1087">#1087</a>)</li> 40767<li>add check in <code>download_file</code> function for HTTP return code + 40768 show download progress report 40769 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1066">#1066</a>, 40770 <a href="https://github.com/easybuilders/easybuild-framework/pull/1090">#1090</a>)</li> 40771<li>include info log message with name and location of used 40772 easyblock 40773 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1069">#1069</a>)</li> 40774<li>add toolchains definitions for <code>gpsmpi</code>, <code>gpsolf</code>, <code>impich</code>, 40775 <code>intel-para</code>, <code>ipsmpi</code> toolchains 40776 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1072">#1072</a>, 40777 <a href="https://github.com/easybuilders/easybuild-framework/pull/1073">#1073</a>)<ul> 40778<li>support for Parastation MPI based toolchains</li> 40779</ul> 40780</li> 40781<li>enforce that <code>hiddendependencies</code> is a subset of <code>dependencies</code> 40782 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1078">#1078</a>)<ul> 40783<li>this is done to avoid that site-specific policies w.r.t. 40784 hidden modules slip into contributed easyconfigs</li> 40785</ul> 40786</li> 40787<li>enable use of <code>--show_hidden</code> for <code>avail</code> subcommand with recent 40788 Lmod versions 40789 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1081">#1081</a>)</li> 40790<li>add <code>--robot-paths</code> configure option 40791 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1080">#1080</a>, 40792 <a href="https://github.com/easybuilders/easybuild-framework/pull/1093">#1093</a>, 40793 <a href="https://github.com/easybuilders/easybuild-framework/pull/1095">#1095</a>, 40794 <a href="https://github.com/easybuilders/easybuild-framework/pull/1114">#1114</a>)</li> 40795<li>support use of <code>%(DEFAULT_ROBOT_PATHS)s</code> template in EasyBuild 40796 configuration files 40797 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1100">#1100</a>)<ul> 40798<li>see also <a href="http://easybuild.readthedocs.org/en/latest/Using_the_EasyBuild_command_line.html#controlling-the-robot-search-path">Controlling the robot search 40799 path</a></li> 40800</ul> 40801</li> 40802<li>use <code>-xHost</code> rather than <code>-xHOST</code>, to match Intel documentation 40803 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1084">#1084</a>)</li> 40804<li>update and cleanup <code>README</code> file 40805 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1085">#1085</a>)</li> 40806<li>deprecate <code>self.moduleGenerator</code> in favor of 40807 <code>self.module_generator</code> in <code>EasyBlock</code> 40808 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1088">#1088</a>)</li> 40809<li>also support <code>MPICH</code> MPI family in <code>mpi_cmd_for</code> function 40810 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1098">#1098</a>)</li> 40811<li>update documentation references to point to 40812 <a href="http://easybuild.readthedocs.org">http://easybuild.readthedocs.org</a> 40813 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1102">#1102</a>)</li> 40814<li>check for OS dependencies with <em>both</em> <code>rpm</code> and <code>dpkg</code> (if 40815 available) 40816 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1111">#1111</a>)</li> 40817</ul> 40818</li> 40819<li>various bug fixes, including:<ul> 40820<li>fix picking required software version specified by 40821 <code>--software-version</code> and clean up <code>tweak.py</code> 40822 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1062">
40822#1062</a>, 40823 <a href="https://github.com/easybuilders/easybuild-framework/pull/1063">#1063</a>)</li> 40824<li>escape <code>$</code> characters in module load message specified via 40825 <code>modloadmsg</code> easyconfig parameter) 40826 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1068">#1068</a>)</li> 40827<li>take available hidden modules into account in dependency 40828 resolution 40829 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1065">#1065</a>)</li> 40830<li>fix hard crash when using patch files with an empty list of 40831 sources 40832 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1070">#1070</a>)</li> 40833<li>fix Intel MKL BLACS library being used for MPICH/MPICH2-based 40834 toolchains 40835 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1072">#1072</a>)</li> 40836<li>fix regular expression in <code>fetch_parameter_from_easyconfig_file</code> 40837 function 40838 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1096">#1096</a>)</li> 40839<li>don't hardcode queue names when submitting a job 40840 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1106">#1106</a>)</li> 40841<li>fix affiliation/mail address for Fotis in headers 40842 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1105">#1105</a>)</li> 40843<li>filter out <code>/dev/null</code> entries in patch file in 40844 <code>det_patched_files</code> function 40845 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1108">#1108</a>)</li> 40846<li>fix <code>gmpolf</code> toolchain definition, to have <code>gmpich</code> as MPI 40847 components (instead of <code>gmpich2</code>) 40848 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1101">#1101</a>)<ul> 40849<li>'MPICH' refers to MPICH v3.x, while MPICH2 refers to 40850 MPICH(2) v2.x (MPICH v1.x is ancient/obsolete)</li> 40851<li><strong>note</strong>: this requires to reinstall the <code>gmpolf</code> module, 40852 using the updated easyconfig from 40853 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1217">easybuild-easyconfigs#1217</a></li> 40854</ul> 40855</li> 40856</ul> 40857</li> 40858</ul> 40859<p><strong>easyblocks</strong></p> 40860<ul> 40861<li>new easyblocks for <strong>2</strong> software packages that requires customized 40862 support:<ul> 40863<li>Chimera 40864 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/524">#524</a>), 40865 GATE 40866 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/518">#518</a>)</li> 40867</ul> 40868</li> 40869<li>fix use of deprecated functionality, enhance unit tests to check for 40870 it 40871 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/523">#523</a>)</li> 40872<li>various other enhancements, including:<ul> 40873<li>update PETSc easyblock for recent versions (v3.5) 40874 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/446">#446</a>)</li> 40875<li>only include major/minor version numbers for FLUENT subdir 40876 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/480">#480</a>)</li> 40877<li>factor out 'move after install' code from impi easyblock to 40878 <code>IntelBase</code>, use it for itac 40879 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/487">#487</a>)</li> 40880<li>support custom easyconfig parameters in <code>EB_impi</code> easyblock to 40881 correct behavior of MPI wrapper commands 40882 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/493">#493</a>)</li> 40883<li>consider both <code>lib</code> and <code>lib64</code> in sanity check for GROMACS 40884 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/501">#501</a>)</li> 40885<li>take <code>preinstallopts</code> and <code>installopts</code> into account in <code>Binary</code> 40886 easyblock 40887 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/503">#503</a>)</li> 40888<li>add sanity check command <code>abaqus information=all</code> for ABAQUS 40889 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/504">#504</a>)</li> 40890<li>update and clean up <code>README</code>, refer to 40891 <a href="http://easybuild.readthedocs.org">http://easybuild.readthedocs.org</a> documentation 40892 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/505">#505</a>, 40893 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/516">#516</a>)</li> 40894<li>rename deprecated <code>self.moduleGenerator</code> to 40895 <code>self.module_generator</code> 40896 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/506">#506</a>)<ul> 40897<li>see also 40898 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1088">easybuild-framework#1088</a></li> 40899</ul> 40900</li> 40901<li>check whether specified <code>type</code> value is a known value (<code>psmp</code> or 40902 <code>popt</code>) in CP2K easyblock 40903 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/509">#509</a>)</li> 40904<li>
40904add support to <code>SAMtools</code> easyblock for installing recent 40905 versions (v1.x) 40906 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/512">#512</a>)</li> 40907<li>fix version check + sanity check in Geant4 easyblock + style 40908 fixes 40909 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/517">#517</a>)</li> 40910<li>added <code>$root/modlib</code> to <code>$PYTHONPATH</code> guesses in Modeller 40911 easyblock 40912 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/525">#525</a>)</li> 40913<li>mark <code>license</code> custom easyconfig parameter as deprecated in 40914 <code>IntelBase</code> 40915 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/527">#527</a>)</li> 40916</ul> 40917</li> 40918<li>various bug fixes, including:<ul> 40919<li>fix Libxc version check in CP2K easyblock 40920 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/478">#478</a>)</li> 40921<li>correctly specify <code>mkl_libs</code> when building <em>numpy</em> with GCC and 40922 imkl 40923 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/485">#485</a>)</li> 40924<li>extend noqa for OpenFOAM-Extend in build_step 40925 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/488">#488</a>, 40926 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/520">#520</a>)</li> 40927<li>correctly set <code>$LD_LIBRARY_PATH</code>, <code>$LIBRARY_PATH</code> and 40928 <code>$PKG_CONFIG_PATH</code> for <code>R</code> 40929 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/495">#495</a>)</li> 40930<li>fix default value for <code>files_to_copy</code> in <code>MakeCp</code> easyblock 40931 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/500">#500</a>)</li> 40932<li>treat <code>MPICH</code> MPI family as MPICH v3.x instead of MPICH v1.x 40933 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/519">#519</a>)<ul> 40934<li>see also 40935 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/1112">easybuild-framework#1112</a></li> 40936</ul> 40937</li> 40938<li>fix affiliation/mail address for Fotis in headers 40939 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/521">#521</a>)</li> 40940<li>clean up in <code>extra_options</code> methods, avoid casting return value 40941 to <code>dict</code> or returning via parent 40942 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/528">#528</a>)</li> 40943</ul> 40944</li> 40945</ul> 40946<p><strong>easyconfigs</strong></p> 40947<ul> 40948<li>added example easyconfig files for <strong>39</strong> new software packages:<ul> 40949<li>ANTs 40950 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1232">#1232</a>), 40951 BEOPS 40952 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1264">#1264</a>), 40953 Chhimera 40954 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1255">#1255</a>), 40955 ctffind 40956 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1249">#1249</a>), 40957 DBD-SQLite 40958 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1064">#1064</a>), 40959 DBD-mysql 40960 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1063">#1063</a>), 40961 DIALIGN-TX 40962 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/668">#668</a>), 40963 ffmpeg 40964 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1088">#1088</a>), 40965 GObject-Introspection 40966 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1079">#1079</a>), 40967 GTS 40968 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1079">#1079</a>), 40969 Graphviz 40970 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1079">#1079</a>), 40971 GraphViz2 40972 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1079">#1079</a>), 40973 grace 40974 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1131">#1131</a>), 40975 HarfBuzz 40976 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1079">#1079</a>), 40977 HTSlib 40978 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1161">#1161</a>), 40979 GSSAPI 40980 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1048">
40980#1048</a>), 40981 Kerberos_V5 40982 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1048">#1048</a>), 40983 libevent 40984 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1063">#1063</a>), 40985 libXdmcp 40986 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1129">#1129</a>), 40987 libXft 40988 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1017">#1017</a>), 40989 libXinerama 40990 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1017">#1017</a>), 40991 libXrender 40992 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1017">#1017</a>), 40993 Maven 40994 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1094">#1094</a>), 40995 MySQL 40996 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1063">#1063</a>), 40997 Net-LibIDN 40998 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1060">#1060</a>), 40999 OpenCV 41000 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1088">#1088</a>), 41001 OpenMD 41002 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1105">#1105</a>), 41003 Qhull 41004 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1105">#1105</a>), 41005 Pango 41006 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1079">#1079</a>), 41007 psmpi 41008 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1245">#1245</a>, 41009 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1246">#1246</a>), 41010 RELION 41011 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1017">#1017</a>), 41012 renderproto 41013 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1017">#1017</a>), 41014 rjags 41015 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1125">#1125</a>), 41016 runjags 41017 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1125">#1125</a>), 41018 SPRNG 41019 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1138">#1138</a>, 41020 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1141">#1141</a>), 41021 xineramaproto 41022 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1017">#1017</a>), 41023 XML-Dumper 41024 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1061">#1061</a>), 41025 XML-Parser 41026 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1061">#1061</a>), 41027 XML-Twig 41028 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1061">#1061</a>)</li> 41029</ul> 41030</li> 41031<li>added easyconfigs for new toolchains<ul> 41032<li><code>intel/2014.10</code> & <code>intel/2014.11</code> 41033 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1219">#1219</a>), 41034 <code>intel-para/2014.12</code> 41035 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1246">#1246</a>), 41036 <code>gpsolf/2014.12</code> 41037 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1245">#1245</a>), 41038 <code>iompi/6.6.4</code> 41039 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1215">#1215</a>)</li> 41040</ul> 41041</li> 41042<li>include <code>easyblock = 'ConfigureMake'</code> in relevant easyconfigs to 41043 deal with deprecation of automagic fallback to <code>ConfigureMake</code> 41044 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1248">#1248</a>)<ul> 41045<li>see also 41046 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1113">easybuild-framework#1113</a> 41047 and <a href="http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#configuremake-fallback">Automagic fallback to 41048 ConfigureMake</a></li> 41049</ul> 41050</li> 41051<li>clean up use of deprecated functionality in existing easyconfigs 41052 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1252">#1252</a>, 41053 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1259">#1259</a>)<ul> 41054<li>stop using deprecated <code>makeopts</code>, <code>premakeopts</code> and 41055 <code>shared_lib_ext</code></li> 41056<li>check for use of deprecated functionality in easyconfigs unit 41057 tests</li> 41058<li>see also 41059 <a href="http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#easyconfig-parameters">http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#easyconfig-parameters</a></li> 41060</ul> 41061</li> 41062<li>various other enhancements, including:<ul> 41063<li>also build <code>fftw3_threads</code> libraries, and enhance sanity checks 41064 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1013">#1013</a>)</li> 41065<li>
41065add unit test to verify specified <code>sanity_check_paths</code> 41066 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1119">#1119</a>)</li> 41067<li>update and clean up <code>README</code>, refer to 41068 <a href="http://easybuild.readthedocs.org">http://easybuild.readthedocs.org</a> documentation 41069 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1184">#1184</a>, 41070 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1224">#1224</a>)</li> 41071</ul> 41072</li> 41073<li>various bug fixes, including:<ul> 41074<li>fix unit tests w.r.t. changes in framework 41075 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1146">#1146</a>)</li> 41076<li>remove unnecessary build dependencies for OpenMPI 41077 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1168">#1168</a>)</li> 41078<li>remove duplicate line in OpenMPI easyconfigs 41079 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1207">#1207</a>)</li> 41080<li>fix affiliation/mail address for Fotis in headers 41081 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1237">#1237</a>)</li> 41082<li>fix permissions of easyconfig files for consistency 41083 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1210">#1210</a>)</li> 41084<li>disable symbol lookup feature in cairo to fix build on SL6 41085 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1241">#1241</a>)</li> 41086<li>fix easyconfig <code>gmpolf</code> toolchain w.r.t. MPICH software name 41087 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1217">#1217</a>)<ul> 41088<li>see also 41089 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1112">easybuild-framework#1112</a></li> 41090</ul> 41091</li> 41092<li>fix <code>source_urls</code> for WRF and WPS 41093 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1225">#1225</a>)</li> 41094<li>fix and clean up GATE easyconfigs 41095 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1228">#1228</a>)</li> 41096<li>fix broken CLHEP builds by including <code>-gcc</code> in <code>$CXXFLAGS</code> 41097 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1254">#1254</a>)</li> 41098<li>add patch to fix broken test in Go 41099 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1257">#1257</a>)</li> 41100<li>fix name of GMAP easyconfigs, should be GMAP-GSNAP 41101 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1268">#1268</a>)</li> 41102<li>fix easyconfig filenames, enhance unit test to check easyconfig 41103 filenames 41104 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1271">#1271</a>)</li> 41105</ul> 41106</li> 41107</ul> 41108<h2 id="easybuild-v1152-october-7th-2014">EasyBuild v1.15.2 (October 7th 2014)<a class="headerlink" href="#easybuild-v1152-october-7th-2014" title="Permanent link">¶</a></h2> 41109<p>bugfix release</p> 41110<p><strong>framework</strong></p> 41111<ul> 41112<li>fix <code>$MODULEPATH</code> extensions for Clang/CUDA, to make 41113 <code>goolfc</code>/<code>cgoolf</code> compatible with <code>HierarchicalMNS</code> 41114 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1050">#1050</a>)</li> 41115<li>include <code>versionsuffix</code> in module subdirectory with 41116 <code>HierarchicalMNS</code> 41117 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1050">#1050</a>, 41118 <a href="https://github.com/easybuilders/easybuild-framework/pull/1055">#1055</a>)</li> 41119<li>fix unit tests which were broken with bash patched for ShellShock 41120 bug 41121 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1051">#1051</a>)</li> 41122<li>add definition of gimpi toolchain, required to make gimkl toolchain 41123 compatible with <code>HierarchicalMNS</code> 41124 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1052">#1052</a>)</li> 41125<li>don't override <code>COMPILER_MODULE_NAME</code> obtained from <code>ClangGCC</code> in 41126 Clang-based toolchains 41127 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1053">#1053</a>)</li> 41128<li>fix wrong code in <code>path_to_top_of_module_tree</code> function 41129 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1054">#1054</a>)<ul> 41130<li>because of this, load statements for compilers were potentially 41131 included in higher-level modules under <code>HierarchicalMNS</code></li> 41132</ul> 41133</li> 41134</ul> 41135<p><strong>easyblocks</strong></p> 41136<ul> 41137<li>only disable sanitizer tests for recent Clang versions 41138 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/481">#481</a>, 41139 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/482">#482</a>)</li> 41140<li>
41140pass down installopts to CUDA install command 41141 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/483">#483</a>)</li> 41142</ul> 41143<p><strong>easyconfigs</strong></p> 41144<ul> 41145<li>disable parallel build for slalib 41146 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/968">#968</a>)</li> 41147<li>fix compatibility of goolfc with HierarchicalMNS by using GCC 41148 toolchain for installing CUDA 41149 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1106">#1106</a>, 41150 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1115">#1115</a>)</li> 41151<li>fix zlib OS dependency spec for Debian in Boost easyconfigs 41152 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1109">#1109</a>)</li> 41153<li>fix compatibility of gimkl with HierarchicalMNS by using gimpi 41154 subtoolchain 41155 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1110">#1110</a>)</li> 41156<li>make both GCC and Clang first-class members in Clang-based 41157 toolchains to fix compatibility with HierarchicalMNS 41158 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1113">#1113</a>)</li> 41159</ul> 41160<h2 id="easybuild-v1151-september-23rd-2014">EasyBuild v1.15.1 (September 23rd 2014)<a class="headerlink" href="#easybuild-v1151-september-23rd-2014" title="Permanent link">¶</a></h2> 41161<p>bugfix release</p> 41162<p><strong>framework</strong></p> 41163<ul> 41164<li>take into account that multiple modules may be extending 41165 <code>$MODULEPATH</code> with the same path, when determining path to top of 41166 module tree (see 41167 <a href="https://github.com/easybuilders/easybuild-framework/pull/1047">#1047</a>)<ul> 41168<li>this bug caused a load statement for either <code>icc</code> or <code>ifort</code> to 41169 be included in higher-level modules installed with an 41170 Intel-based compiler toolchain, under the <code>HierarchicalMNS</code> 41171 module naming scheme</li> 41172</ul> 41173</li> 41174<li>make <code>HierarchicalMNS</code> module naming scheme compatible with <code>cgoolf</code> 41175 and <code>goolfc</code> toolchain 41176 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1049">#1049</a>)</li> 41177<li>add definition of <code>iompi</code> (sub)toolchain to make <code>iomkl</code> toolchain 41178 compatible with <code>HierarchicalMNS</code> 41179 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1049">#1049</a>)</li> 41180</ul> 41181<p><strong>easyblocks</strong></p> 41182<p><em>(no changes compared to v1.15.0, simple version bump to stay in sync 41183with easybuild-framework)</em></p> 41184<p><strong>easyconfigs</strong></p> 41185<ul> 41186<li>minor bug fixes, including:<ul> 41187<li>use SHLIB_EXT in GMP/MPFR easyconfigs 41188 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1090">#1090</a>)</li> 41189<li>fix TopHat homepage and source_urls since page moved 41190 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1092">#1092</a>)</li> 41191<li>make iomkl toolchain compatible with HierarchicalMNS 41192 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1099">#1099</a>)</li> 41193</ul> 41194</li> 41195</ul> 41196<h2 id="easybuild-v1150-september-12th-2014">EasyBuild v1.15.0 (September 12th 2014)<a class="headerlink" href="#easybuild-v1150-september-12th-2014" title="Permanent link">¶</a></h2> 41197<p>feature + bugfix release</p> 41198<p><strong>framework</strong></p> 41199<ul> 41200<li>various other enhancements, including:<ul> 41201<li>fetch extension sources in fetch_step to enhance <code>--stop=fetch</code> 41202 (<a href="https://github.com/easybuilders/easybuild-framework/pull/978">#978</a>)</li> 41203<li>add <code>iimpi</code> toolchain definition 41204 (<a href="https://github.com/easybuilders/easybuild-framework/pull/993">#993</a>)</li> 41205<li>prepend robot path with download location of files when 41206 <code>--from-pr</code> is used 41207 (<a href="https://github.com/easybuilders/easybuild-framework/pull/995">#995</a>)</li> 41208<li>add support for excluding module path extensions from generated 41209 modules 41210 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1003">#1003</a>)<ul> 41211<li>see <code>include_modpath_extensions</code> easyconfig parameter</li> 41212</ul> 41213</li> 41214<li>
41214add support for installing hidden modules and using them as 41215 dependencies 41216 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1009">#1009</a>, 41217 <a href="https://github.com/easybuilders/easybuild-framework/pull/1021">#1021</a>, 41218 <a href="https://github.com/easybuilders/easybuild-framework/pull/1023">#1023</a>)<ul> 41219<li>see <code>--hidden</code> and <code>hiddendependencies</code> easyconfig parameter</li> 41220</ul> 41221</li> 41222<li>stop relying on <code>conflict</code> statement in module files to 41223 determine software name of toolchain components 41224 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1017">#1017</a>, 41225 <a href="https://github.com/easybuilders/easybuild-framework/pull/1037">#1037</a>)<ul> 41226<li>instead, the <code>is_short_modname_for</code> method defined by the 41227 module naming scheme implementation is queried</li> 41228</ul> 41229</li> 41230<li>improve error message generated for a missing easyconfig file 41231 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1019">#1019</a>)</li> 41232<li>include path where tweaked easyconfigs are placed in robot path 41233 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1032">#1032</a>)</li> 41234<li>indicate forced builds in <code>--dry-run</code> output 41235 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1034">#1034</a>)</li> 41236<li>fix interaction between <code>--force</code> and <code>--try-toolchain --robot</code> 41237 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1035">#1035</a>)</li> 41238<li>add <code>--software</code> option, disable recursion for 41239 <code>--try-software(-X)</code> 41240 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1036">#1036</a>)</li> 41241</ul> 41242</li> 41243<li>various bug fixes, including:<ul> 41244<li>fix <code>HierarchicalMNS</code> crashing when MPI library is installed 41245 with a dummy toolchain 41246 (<a href="https://github.com/easybuilders/easybuild-framework/pull/986">#986</a>)</li> 41247<li>fix list of FFTW wrapper libraries for Intel MKL 41248 (<a href="https://github.com/easybuilders/easybuild-framework/pull/987">#987</a>)</li> 41249<li>fix stability of unit tests 41250 (<a href="https://github.com/easybuilders/easybuild-framework/pull/988">#988</a>, 41251 <a href="https://github.com/easybuilders/easybuild-framework/pull/1027">#1027</a>, 41252 <a href="https://github.com/easybuilders/easybuild-framework/pull/1033">#1033</a>)</li> 41253<li>make sure <code>$SCALAPACK_INC_DIR</code> (and <code>$SCALAPACK_LIB_DIR</code>) are 41254 defined when using <code>imkl</code> 41255 (<a href="https://github.com/easybuilders/easybuild-framework/pull/990">#990</a>)</li> 41256<li>fix error message on missing FFTW wrapper libs 41257 (<a href="https://github.com/easybuilders/easybuild-framework/pull/992">#992</a>)</li> 41258<li>fix duplicate toolchain elements in <code>--list-toolchains</code> output 41259 (<a href="https://github.com/easybuilders/easybuild-framework/pull/993">#993</a>)</li> 41260<li>filter out load statements that extend the <code>$MODULEPATH</code> to make 41261 the module being installed available 41262 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1016">#1016</a>)</li> 41263<li>fix conflict specification included in module files 41264 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1017">#1017</a>)</li> 41265<li>avoid <code>--from-pr</code> crashing hard unless <code>--robot</code> is used 41266 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1022">#1022</a>)</li> 41267<li>properly quote GCC version string in archived easyconfig 41268 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1028">#1028</a>)</li> 41269<li>fix issue with <code>--repositorypath</code> not honoring <code>--prefix</code> 41270 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1031">#1031</a>)</li> 41271<li>sync with latest vsc-base version to fix log order 41272 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1039">#1039</a>)</li> 41273<li>increase # commits per page for <code>--from-pr</code> 41274 (<a href="https://github.com/easybuilders/easybuild-framework/pull/1040">#1040</a>)</li> 41275</ul> 41276</li> 41277</ul> 41278<p><strong>easyblocks</strong></p> 41279<ul> 41280<li>
41280added support for <strong>2</strong> new software packages that requires 41281 customized support:<ul> 41282<li>Modeller 41283 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/392">#392</a>), 41284 NAMD 41285 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/397">#397</a>)</li> 41286</ul> 41287</li> 41288<li>various enhancements, including:<ul> 41289<li>fix locale used for running Perl unit tests 41290 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/425">#425</a>)</li> 41291<li>fix Rmpi easyblock to correctly configure for Intel MPI 41292 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/435">#435</a>)</li> 41293<li>add support in generic Rpackage easyblock for handling patches 41294 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/435">#435</a>)</li> 41295<li>enhance OpenFOAM easyblock: fix building MPI build of Pstream 41296 and (pt)scotchDecomp + overall cleanup 41297 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/436">#436</a>)</li> 41298<li>enhance NWChem easyblock for version 6.3, clean up running of 41299 test cases 41300 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/441">#441</a>)</li> 41301<li>enhance noqa for interactive configuration of Qt build procedure 41302 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/447">#447</a>)</li> 41303<li>add custom sanity check for R in easyblock 41304 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/449">#449</a>)</li> 41305<li>make perlmodule take into account 41306 <code>(pre){config,build,install}opts</code> 41307 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/450">#450</a>)</li> 41308<li>add support for specifying an activation key after installing 41309 Mathematica 41310 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/452">#452</a>)</li> 41311<li>consider both <code>lib</code> and <code>lib64</code> directories in netCDF sanity 41312 check 41313 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/453">#453</a>)</li> 41314<li>fix sanity check for ANSYS for v15.0.x 41315 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/458">#458</a>)</li> 41316<li>fix Trilinos easyblock for recent version 41317 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/462">#462</a>)</li> 41318<li>enhance impi easyblock to handle install subdir for impi v5.0.1 41319 and future version 41320 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/465">#465</a>, 41321 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/472">#472</a>)</li> 41322<li>include $CFLAGS in linker flags for HPL 41323 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/466">#466</a>)</li> 41324<li>update sanity test checks for GROMACS 5.x 41325 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/471">#471</a>)</li> 41326</ul> 41327</li> 41328<li>various bug fixes:<ul> 41329<li>fix building of FFTW wrappers for Intel MKL v11.1.x + cleanup of 41330 imkl easyblock 41331 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/445">#445</a>)</li> 41332</ul> 41333</li> 41334</ul> 41335<p><strong>easyconfigs</strong></p> 41336<ul> 41337<li>added example easyconfig files for <strong>13</strong> new software packages:<ul> 41338<li>Circos 41339 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/780">#780</a>), 41340 DB_File 41341 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/913">#913</a>), 41342 Emacs 41343 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/970">#970</a>), 41344 evmix 41345 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1077">#1077</a>), 41346 GD 41347 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/780">#780</a>), 41348 gsl 41349 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1077">#1077</a>), 41350 IOR 41351 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/949">#949</a>), 41352 JAGS 41353 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1076">#1076</a>), 41354 libgd 41355 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/780">#780</a>), 41356 MethPipe 41357 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1070">#1070</a>), 41358 Modeller 41359 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/825">#825</a>), 41360 NAMD 41361 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/835">#835</a>),
41362 netCDF-C++4 41363 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1015">#1015</a>)</li> 41364</ul> 41365</li> 41366<li>added easyconfigs for new toolchains 41367 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/986">#986</a>, 41368 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1051">#1051</a>):<ul> 41369<li>gimkl/1.5.9, ictce/7.1.2</li> 41370</ul> 41371</li> 41372<li>added additional easyconfigs for various supported software 41373 packages: version updates, different toolchains, ...<ul> 41374<li>including Python 2.7.8/3.4.1, Perl 5.20.0, R 3.1.1, NWChem 6.3, 41375 OpenFOAM-Extend 3.1, GCC 4.9.1, Clang 3.4.2, ...</li> 41376</ul> 41377</li> 41378<li>various enhancements, including:<ul> 41379<li>make existing ictce/intel toolchains compatible with 41380 HierarchicalMNS 41381 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/1069">#1069</a>)<ul> 41382<li>this involves installing impi with an iccifort toolchain, 41383 and imkl with an iimpi toolchain</li> 41384</ul> 41385</li> 41386</ul> 41387</li> 41388<li>various bug fixes, including:<ul> 41389<li>download link for Perl modules changed to use cpan.metapan.org</li> 41390<li>fix missing MPI-based OpenFOAM libraries (<code>Pstream</code>, 41391 <code>(pt)scotchDecomp</code>), make sure provided SCOTCH is used 41392 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/957">#957</a>)</li> 41393</ul> 41394</li> 41395</ul> 41396<h2 id="easybuild-v1140-july-9th-2014">EasyBuild v1.14.0 (July 9th 2014)<a class="headerlink" href="#easybuild-v1140-july-9th-2014" title="Permanent link">¶</a></h2> 41397<p>feature + bugfix release</p> 41398<p><strong>framework</strong></p> 41399<ul> 41400<li>important changes<ul> 41401<li>required Lmod version bumped to v5.6.3 41402 (<a href="https://github.com/easybuilders/easybuild-framework/pull/944">#944</a>)<ul> 41403<li>required due to enhancements and bug fixes in Lmod, e.g. 41404 making <code>--terse avail</code> significantly faster, and correctly 41405 handling a <code>prepend-path</code> statement that includes multiple 41406 directories at once</li> 41407</ul> 41408</li> 41409<li>required Tcl/C environment modules version set to 3.2.10 (<ul> 41410<li>hard requirement due to fixed <code>modulecmd</code> segmentation fault 41411 bug, that only tends manifests itself when making a large 41412 amount of changes in the environment (e.g. 41413 <code>module load <toolchain></code>)</li> 41414</ul> 41415</li> 41416<li>renamed <code>EasyBuildModuleNamingScheme</code> to <code>EasyBuildMNS</code></li> 41417</ul> 41418</li> 41419<li>enhanced custom module naming schemes functionality to support 41420 hierarchical module naming schemes 41421 (<a href="https://github.com/easybuilders/easybuild-framework/pull/953">#953</a>, 41422 <a href="https://github.com/easybuilders/easybuild-framework/pull/971">#971</a>, 41423 <a href="https://github.com/easybuilders/easybuild-framework/pull/975">#975</a>)<ul> 41424<li>extended API for custom module naming schemes to allow tweaking 41425 different aspects of module naming<ul> 41426<li>see <code>easybuild/tools/module_naming_scheme/mns.py</code> for 41427 abstract <code>ModuleNamingScheme</code> class</li> 41428<li>an example hierarchical module naming scheme is included, 41429 see <code>HierarchicalMNS</code></li> 41430</ul> 41431</li> 41432<li>split up full module names into a module subdirectory part, 41433 which becomes part of <code>$MODULEPATH</code>), and a 'short' module 41434 name (is exposed to end-users)<ul> 41435<li>example: <code>GCC/4.7.2</code> in <code>Core</code> subdir, <code>OpenMPI/1.6.5</code> in 41436 <code>Compiler/GCC/4.7.2</code> subdir</li> 41437</ul> 41438</li> 41439<li>make <code>ModuleNamingScheme</code> class a singleton, move it into 41440 <code>easybuild.tools.module_naming_scheme.mns</code> module</li> 41441<li>implement <code>ActiveMNS</code> wrapper class for querying active module 41442 naming scheme</li> 41443<li>implement toolchain inspection functions that can be used in a 41444 custom module naming scheme<ul> 41445<li><code>det_toolchain_compilers</code>, <code>det_toolchain_mpi</code> in 41446 <code>easybuild.tools.module_naming_scheme.toolchain</code></li> 41447</ul> 41448</li> 41449<li>significant code cleanup & enhanced unit tests</li> 41450</ul> 41451</li> 41452<li>enhance & clean up <code>tools/modules.py</code> 41453 (<a href="https://github.com/easybuilders/easybuild-framework/pull/944">#944</a>, 41454 <a href="https://github.com/easybuilders/easybuild-framework/pull/953">#953</a>, 41455 <a href="https://github.com/easybuilders/easybuild-framework/pull/963">#963</a>, 41456 <a href="https://github.com/easybuilders/easybuild-framework/pull/964">#964</a>, 41457 <a href="https://github.com/easybuilders/easybuild-framework/pull/969">#969</a>)<ul> 41458<li>make <code>ModulesTool</code> a singleton to avoid repeating module 41459 commands over & over again needlessly</li> 41460<li>use <code>module use</code>, <code>module unuse</code> rather than fiddling with 41461 <code>$MODULEPATH</code> directly</li> 41462<li>improve debug logging (include full stdout/stderr output of 41463 module commands)</li> 41464<li>remove deprecated functionality (<code>add_module</code>, <code>remove_module</code>,
41465 indirect module load)</li> 41466</ul> 41467</li> 41468<li>various other enhancements, including:<ul> 41469<li>added toolchain definitions for 'common' toolchains: <code>intel</code> 41470 and <code>foss</code> 41471 (<a href="https://github.com/easybuilders/easybuild-framework/pull/956">#956</a>)</li> 41472<li>implement caching for easyconfig files, parsed easyconfigs and 41473 toolchains 41474 (<a href="https://github.com/easybuilders/easybuild-framework/pull/953">#953</a>)</li> 41475<li>enable <code>--ignore-osdeps</code> implicitly when <code>-D</code>, <code>--dry-run</code> or 41476 <code>--dep-graph</code> are used 41477 (<a href="https://github.com/easybuilders/easybuild-framework/pull/953">#953</a>)</li> 41478<li>flesh out <code>use_group</code> and <code>det_parallelism</code> function, include 41479 them in <code>easybuild.tools.systemtools</code> 41480 (<a href="https://github.com/easybuilders/easybuild-framework/pull/953">#953</a>)</li> 41481<li>make symlinking of module files part of module naming scheme API 41482 (<a href="https://github.com/easybuilders/easybuild-framework/pull/973">#973</a>)<ul> 41483<li>list of symlinks paths can be controlled using 41484 <code>det_module_symlink_paths()</code> method</li> 41485</ul> 41486</li> 41487<li>added support for new configuration options:<ul> 41488<li>tweaking compiler flags triggered by <code>optarch</code> toolchain 41489 options using <code>--optarch</code> 41490 (<a href="https://github.com/easybuilders/easybuild-framework/pull/949">#949</a>)</li> 41491<li>filtering out dependencies from easyconfig files using 41492 <code>--filter-deps</code> 41493 (<a href="https://github.com/easybuilders/easybuild-framework/pull/957">#957</a>)</li> 41494<li>filtering environment included in test reports with 41495 <code>--test-report-env-filter</code> 41496 (<a href="https://github.com/easybuilders/easybuild-framework/pull/959">#959</a>) 41497 e.g. 41498 <code>--test-report-env-filter='^SSH|USER|HOSTNAME|UID|.*COOKIE.*'</code></li> 41499<li>made suffix used for module files install path configurable, 41500 using <code>--suffix-modules-path</code> 41501 (<a href="https://github.com/easybuilders/easybuild-framework/pull/973">#973</a>)</li> 41502</ul> 41503</li> 41504<li>added support for additional easyconfig parameters:<ul> 41505<li>define aliases in module files (<code>modaliases</code>) 41506 (<a href="https://github.com/easybuilders/easybuild-framework/pull/952">#952</a>)</li> 41507<li>add print message on module load (<code>modloadmsg</code>) and Tcl 41508 footer (<code>modtclfooter</code>) in module files 41509 (<a href="https://github.com/easybuilders/easybuild-framework/pull/954">#954</a>, 41510 <a href="https://github.com/easybuilders/easybuild-framework/pull/974">#974</a>)</li> 41511</ul> 41512</li> 41513</ul> 41514</li> 41515<li>various bug fixes, including:<ul> 41516<li>don't try to tweak generated easyconfigs when using <code>--try-X</code> 41517 (<a href="https://github.com/easybuilders/easybuild-framework/pull/942">#942</a>)</li> 41518<li>currently create symlinks to module files modules/all under a 41519 custom module naming scheme 41520 (<a href="https://github.com/easybuilders/easybuild-framework/pull/953">#953</a>)</li> 41521<li>restore traceback error reporting on hard crashes 41522 (<a href="https://github.com/easybuilders/easybuild-framework/pull/965">#965</a>)</li> 41523</ul> 41524</li> 41525</ul> 41526<p><strong>easyblocks</strong></p> 41527<ul> 41528<li>added <strong>one</strong> new <em>generic</em> easyblock: CmdCp 41529 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/395">#395</a>)</li> 41530<li>added support for <strong>2</strong> new software packages that requires 41531 customized support:<ul> 41532<li>ANSYS 41533 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/398">#398</a>), 41534 HPCG 41535 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/408">#408</a>)</li> 41536</ul> 41537</li> 41538<li>various enhancements, including:<ul> 41539<li>updated ABAQUS easyblock so that it works for version 13.2 41540 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/406">#406</a>)</li> 41541<li>enhance BLAT easyblock by using <code>super</code>'s <code>build_step</code> and 41542 <code>prebuildopts</code>/<code>buildopts</code> 41543 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/423">#423</a>)</li> 41544<li>enhance Mothur easyblock to guess correct start dir for recent 41545 versions 41546 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/424">#424</a>)</li> 41547<li>replace use of deprecated (pre)makeopts with (<code>pre</code>)<code>buildopts</code> 41548 in all easyblocks 41549 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/427">#427</a>)</li> 41550<li>fix poor mans version of toolchain compiler detection in imkl 41551 easyblock 41552 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/429">#429</a>)</li> 41553</ul> 41554</li> 41555<li>various bug fixes:<ul> 41556<li>only check for <code>idb</code> for older versions of icc 41557 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/426">#426</a>)</li> 41558<li>fix issues with installing RPMS when <code>rpmrebuild</code> is required 41559 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/433">#433</a>)</li> 41560<li>correctly disable parallel build for ATLAS 41561 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/434">#434</a>)</li> 41562<li>fix sanity check for Intel MPI v5.x (only provides bin64) 41563 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/432">#432</a>)</li> 41564<li>
41564add <code>$MIC_LD_LIBRARY_PATH</code> for MKL v11.x 41565 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/437">#437</a>)</li> 41566</ul> 41567</li> 41568</ul> 41569<p><strong>easyconfigs</strong></p> 41570<ul> 41571<li>added example easyconfig files for <strong>17</strong> new software packages:<ul> 41572<li>ANSYS 41573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/836">#836</a>), 41574 Beast 41575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/912">#912</a>), 41576 ELPH 41577 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/910">#910</a>, 41578 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/911">#911</a>), 41579 FastTree 41580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/900">#900</a>, 41581 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/947">#947</a>), 41582 GEM-library 41583 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/858">#858</a>), 41584 HPCG 41585 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/853">#853</a>), 41586 mdtest 41587 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/925">#925</a>), 41588 ncview 41589 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/648">#648</a>), 41590 PRANK 41591 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/917">#917</a>), 41592 RDP-Classifier 41593 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/903">#903</a>), 41594 SDPA 41595 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/955">#955</a>), 41596 SIBELia 41597 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/886">#886</a>), 41598 SOAPaligner 41599 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/857">#857</a>), 41600 SPAdes 41601 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/884">#884</a>), 41602 stemming 41603 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/891">#891</a>), 41604 WHAM 41605 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/872">#872</a>), 41606 YAXT 41607 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/656">#656</a>)</li> 41608</ul> 41609</li> 41610<li>added easyconfigs for new toolchains 41611 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/935">#935</a>, 41612 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/944">#944</a>, 41613 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/948">#948</a>):<ul> 41614<li>foss/2014b, ictce/6.3.5, intel/2014b</li> 41615</ul> 41616</li> 41617<li>added additional easyconfigs for various supported software 41618 packages: version updates, different toolchains, ...</li> 41619<li>various enhancements, including:<ul> 41620<li>replace use of deprecated <code>(pre)makeopts</code> with <code>(pre)buildopts</code> 41621 in all easyblocks 41622 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/954">#954</a>)</li> 41623<li>disable running embossupdate on installation of EMBOSS 41624 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/963">#963</a>)</li> 41625</ul> 41626</li> 41627<li>various bug fixes, including:<ul> 41628<li>really enable OpenMP support in FastTree easyconfigs 41629 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/947">#947</a>)</li> 41630<li>fix easyconfigs unit tests after changes in framework 41631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/958">#958</a>)</li> 41632</ul> 41633</li> 41634</ul> 41635<h2 id="easybuild-v1130-may-29th-2014">EasyBuild v1.13.0 (May 29th 2014)<a class="headerlink" href="#easybuild-v1130-may-29th-2014" title="Permanent link">¶</a></h2> 41636<p>feature + bugfix release</p> 41637<p><strong>framework</strong></p> 41638<ul> 41639<li>make <code>--try-X</code> command line options work recursively (i.e. 41640 collaborate with <code>--robot</code>) 41641 (<a href="https://github.com/easybuilders/easybuild-framework/pull/922">#922</a>)<ul> 41642<li>EasyBuild will first build a full dependency graph of the 41643 specified easyconfigs, and then apply the <code>--try</code> specifications<ul> 41644<li>the elements of the dependency graph for the used toolchain 41645 and its dependencies are left untouched</li> 41646</ul> 41647</li> 41648<li>this makes 41649 <code>eb foo-1.0-goolf-1.4.10.eb --try-toolchain=ictce,5.5.0 --robot</code> 41650 also work when <code>foo</code> has dependencies</li> 41651<li>caveat: the specified easyconfig files must all use the same 41652 toolchain (version)</li> 41653</ul> 41654</li> 41655<li>
41655add support for testing easyconfig pull requests from EasyBuild 41656 command line 41657 (<a href="https://github.com/easybuilders/easybuild-framework/pull/920">#920</a>, 41658 <a href="https://github.com/easybuilders/easybuild-framework/pull/924">#924</a>, 41659 <a href="https://github.com/easybuilders/easybuild-framework/pull/925">#925</a>, 41660 <a href="https://github.com/easybuilders/easybuild-framework/pull/932">#932</a>, 41661 <a href="https://github.com/easybuilders/easybuild-framework/pull/933">#933</a>, 41662 <a href="https://github.com/easybuilders/easybuild-framework/pull/938">#938</a>)<ul> 41663<li>add <code>--from-pr</code> command line option for downloading easyconfig 41664 files from pull requests</li> 41665<li>add <code>--upload-test-report</code> command line option for uploading a 41666 detailed test report to GitHub as a gist<ul> 41667<li>this requires specifying a GitHub username for which a 41668 GitHub token is available, using <code>--github-user</code></li> 41669<li>with <code>--dump-test-report</code>, the test report can simply be 41670 dumped to file rather than being uploaded to GitHub</li> 41671<li>see also 41672 <a href="https://github.com/easybuilders/easybuild/wiki/Review-process-for-contributions#testing-result">https://github.com/easybuilders/easybuild/wiki/Review-process-for-contributions#testing-result</a></li> 41673</ul> 41674</li> 41675</ul> 41676</li> 41677<li>the <code>makeopts</code> and <code>premakeopts</code> easyconfig parameter are 41678 deprecated, and replaced by <code>buildopts</code> and <code>prebuildopts</code> 41679 (<a href="https://github.com/easybuilders/easybuild-framework/pull/918">#918</a>)<ul> 41680<li>both <code>makeopts</code> and <code>premakeopts</code> will still be honored in 41681 future EasyBuild v1.x versions, but should no longer be used</li> 41682</ul> 41683</li> 41684<li>various other enhancements, including:<ul> 41685<li>add <code>--disable-cleanup-builddir</code> command line option, to keep 41686 the build dir after a (successful) build 41687 (<a href="https://github.com/easybuilders/easybuild-framework/pull/853">#853</a>)<ul> 41688<li>the build dir is still cleaned up by default for successful 41689 builds, i.e. <code>--cleanup-builddir</code> is the default</li> 41690</ul> 41691</li> 41692<li>also consider lib32 in paths checked for <code>$LD_LIBRARY_PATH</code> and 41693 <code>$LIBRARY_PATH</code> 41694 (<a href="https://github.com/easybuilders/easybuild-framework/pull/912">#912</a>)</li> 41695<li>reorganize support for file/git/svn repositories into 41696 <code>repository</code> package, making it extensible 41697 (<a href="https://github.com/easybuilders/easybuild-framework/pull/913">#913</a>)</li> 41698<li>add support for <code>postinstallcmds</code> easyconfig parameter, to 41699 specify commands that need to be run after the install step 41700 (<a href="https://github.com/easybuilders/easybuild-framework/pull/918">#918</a>)</li> 41701<li>make <code>VERSION=</code> part in version of C environment modules tool 41702 optional, which is required for older versions 41703 (<a href="https://github.com/easybuilders/easybuild-framework/pull/930">#930</a>)</li> 41704</ul> 41705</li> 41706<li>various bug fixes, including:<ul> 41707<li>fix small issues in bootstrap script: correctly determine 41708 EasyBuild version and make sure modules path exists 41709 (<a href="https://github.com/easybuilders/easybuild-framework/pull/915">#915</a>)</li> 41710<li>fix github unit tests 41711 (<a href="https://github.com/easybuilders/easybuild-framework/pull/916">#916</a>)</li> 41712<li>disable useless debug logging for unit tests 41713 (<a href="https://github.com/easybuilders/easybuild-framework/pull/919">#919</a>)</li> 41714<li>fix unit test for <code>--skip</code> 41715 (<a href="https://github.com/easybuilders/easybuild-framework/pull/929">#929</a>)</li> 41716<li>make sure <code>start_dir</code> can be set based on location of unpacked 41717 first source file 41718 (<a href="https://github.com/easybuilders/easybuild-framework/pull/931">#931</a>)</li> 41719<li>the <code>vsc</code> package shipped with easybuild-framework is synced 41720 with vsc-base v1.9.1 41721 (<a href="https://github.com/easybuilders/easybuild-framework/pull/935">#935</a>)<ul> 41722<li>fancylogger (used for logging in EasyBuild) is now robust 41723 against strings containing UTF8 characters</li> 41724<li>the <code>deprecated</code> logging function now does a non-strict 41725 version check (rather than an erroneous strict check)</li> 41726<li>the <code>easybuild.tools.agithub</code> module is removed, 41727 <code>vsc.utils.rest</code> now provides the required functionality</li> 41728</ul> 41729</li> 41730<li>fix support for unpacking gzipped source files, don't unpack 41731 <code>.gz</code> files in-place in the source directory 41732 (<a href="https://github.com/easybuilders/easybuild-framework/pull/936">#936</a>)</li> 41733</ul> 41734</li> 41735</ul> 41736<p><strong>easyblocks</strong></p> 41737<ul> 41738<li>
41738added support for <strong>1</strong> new software package that requires 41739 customized support:<ul> 41740<li>Go 41741 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/417">#417</a>)</li> 41742</ul> 41743</li> 41744<li>various enhancements, including:<ul> 41745<li>enhance OpenFOAM easyblock so OpenFOAM-Extend fork can be built 41746 too + style fixes 41747 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/253">#253</a>, 41748 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/416">#416</a>)</li> 41749<li>enhance CPLEX easyblock by adding support for staged 41750 installation 41751 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/372">#372</a>)</li> 41752<li>include support for <code>configure_cmd_prefix</code> easyconfig parameter 41753 in ConfigureMake generic easyblock 41754 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/393">#393</a>)</li> 41755<li>enhance GCC easyblock for building v4.9.0 and versions prior to 41756 v4.5 41757 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/396">#396</a>, 41758 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/400">#400</a>)</li> 41759<li>enhance easyblocks for Intel ipp and itac to support recent 41760 versions 41761 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/399">#399</a>)</li> 41762<li>enhance Clang easyblock: install static analyzer 41763 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/402">#402</a>), 41764 be more robust against changing source dir names 41765 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/413">#413</a>)</li> 41766<li>enhance FoldX easyblock, update list of potential FoldX binaries 41767 to support recent versions 41768 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/407">#407</a>)</li> 41769<li>add runtime patching in Boost easyblock to fix build issue with 41770 old Boost versions and recent glibc (> 2.15) 41771 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/412">#412</a>)</li> 41772<li>enhance <code>MakeCp</code> generic easyblock: use location of 1st unpacked 41773 source as fallback base dir for <code>files_to_copy</code> 41774 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/415">#415</a>)</li> 41775</ul> 41776</li> 41777<li>various bug fixes:<ul> 41778<li>fix installing Mathematica when X forwarding is enabled (make 41779 sure <code>$DISPLAY</code> is unset) 41780 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/391">#391</a>)</li> 41781<li>fix permissions of installed files in SAMtools easyblock, ensure 41782 read/execute for group/other 41783 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/409">#409</a>)</li> 41784<li>fix implementation of <code>det_pylibdir</code> function in PythonPackage 41785 generic easyblock 41786 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/419">#419</a>, 41787 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/420">#420</a>)<ul> 41788<li>determine Python lib dir via <code>distutils</code> Python, which works 41789 cross-OS (as opposed to hardcoding <code>lib</code>)</li> 41790</ul> 41791</li> 41792</ul> 41793</li> 41794</ul> 41795<p><strong>easyconfigs</strong></p> 41796<ul> 41797<li>added example easyconfig files for <strong>32</strong> new software packages:<ul> 41798<li>APBS 41799 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/742">#742</a>), 41800 BayesTraits 41801 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/770">#770</a>), 41802 bc 41803 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/888">#888</a>), 41804 BitSeq 41805 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/791">#791</a>), 41806 CEM 41807 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/789">#789</a>), 41808 CVS 41809 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/888">#888</a>), 41810 eXpress 41811 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/786">#786</a>), 41812 file 41813 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/888">#888</a>), 41814 GEMSTAT 41815 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/861">#861</a>), 41816 GMAP 41817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/594">#594</a>), 41818 Go 41819 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/887">#887</a>), 41820 iscp 41821 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/602">#602</a>), 41822 IsoInfer 41823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/773">#773</a>), 41824 Jellyfish 41825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/868">#868</a>), 41826 less 41827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/888">#888</a>), 41828 libcircle 41829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/883">#883</a>), 41830 mcpp 41831 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/602">#602</a>), 41832 MMSEQ 41833 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/795">#795</a>), 41834 MUSTANG 41835 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/800">#800</a>), 41836 OpenFOAM-Extend 41837 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/437">#437</a>), 41838 popt 41839 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/759">#759</a>), 41840 pscom 41841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/759">#759</a>), 41842 psmpi2 41843 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/759">#759</a>), 41844 QuadProg++ 41845 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/773">#773</a>), 41846 rSeq 41847 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/771">#771</a>), 41848 RSEQtools 41849 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/870">#870</a>), 41850 Ruby 41851 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/873">#873</a>), 41852 segemehl 41853 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/792">#792</a>), 41854 SOAPec 41855 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/879">#879</a>), 41856 SOAPdenovo2 41857 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/874">#874</a>), 41858 SRA-Toolkit 41859 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/793">#793</a>), 41860 texinfo 41861 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/888">#888</a>)</li> 41862</ul> 41863</li> 41864<li>
41864added easyconfig for new toolchain goolfc/1.4.10</li> 41865<li>added additional easyconfigs for various supported software 41866 packages: version updates, different toolchains, ...<ul> 41867<li>e.g., older versions of Boost (1.47.0), GCC (4.1-4.4), & recent 41868 versions of Clang, GCC, Lmod, etc.</li> 41869</ul> 41870</li> 41871<li>various enhancements, including:<ul> 41872<li>add OpenSSL dependency for cURL, to enable HTTPS support 41873 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/881">#881</a>)</li> 41874<li>also install esl-X binaries for HMMER 41875 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/889">#889</a>)</li> 41876</ul> 41877</li> 41878<li>various bug fixes, including:<ul> 41879<li>properly pass down compiler flags for ParMGridGen 41880 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/437">#437</a>)</li> 41881<li>specify proper make options for PLINK, fixing the build on SL6 41882 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/594">#594</a>, 41883 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/772">#772</a>)</li> 41884<li>fix netloc version (0.5 rather than 0.5beta) 41885 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/707">#707</a>)</li> 41886<li>remove Windows-style line ending in netCDF patch file 41887 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/796">#796</a>)</li> 41888<li>bump version of OpenSSL dep for BOINC 41889 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/882">#882</a>)</li> 41890</ul> 41891</li> 41892</ul> 41893<h2 id="easybuild-v1121-april-25th-2014">EasyBuild v1.12.1 (April 25th 2014)<a class="headerlink" href="#easybuild-v1121-april-25th-2014" title="Permanent link">¶</a></h2> 41894<p>bugfix release</p> 41895<p><strong>framework</strong></p> 41896<ul> 41897<li>return to original directory after executing a command in a subdir 41898 (<a href="https://github.com/easybuilders/easybuild-framework/pull/908">#908</a>)</li> 41899<li>fix bootstrap with Lmod, fix issue with module function check and 41900 Lmod 41901 (<a href="https://github.com/easybuilders/easybuild-framework/pull/911">#911</a>)</li> 41902</ul> 41903<p><strong>easyblocks</strong></p> 41904<p><em>(no changes compared to v1.12.0, simple version bump to stay in sync 41905with easybuild-framework)</em></p> 41906<p><strong>easyconfigs</strong></p> 41907<p><em>(no changes compared to v1.12.0, simple version bump to stay in sync 41908with easybuild-framework)</em></p> 41909<h2 id="easybuild-v1120-april-4th-2014">EasyBuild v1.12.0 (April 4th 2014)<a class="headerlink" href="#easybuild-v1120-april-4th-2014" title="Permanent link">¶</a></h2> 41910<p>feature + bugfix release</p> 41911<p><strong>framework</strong></p> 41912<ul> 41913<li>various enhancements, including:<ul> 41914<li>completed support for custom module naming schemes 41915 (<a href="https://github.com/easybuilders/easybuild-framework/pull/879">#879</a>, 41916 <a href="https://github.com/easybuilders/easybuild-framework/pull/904">#904</a>)<ul> 41917<li>a fully parsed easyconfig file is now passed to the 41918 <code>det_full_module_name</code> function</li> 41919<li>this does require that an easyconfig file matching the 41920 dependency specification is available</li> 41921</ul> 41922</li> 41923<li>added more features to better support using a shared install 41924 target with multiple users 41925 (<a href="https://github.com/easybuilders/easybuild-framework/pull/902">#902</a>, 41926 <a href="https://github.com/easybuilders/easybuild-framework/pull/903">#903</a>, 41927 <a href="https://github.com/easybuilders/easybuild-framework/pull/904">#904</a>)</li> 41928<li>further development on support for new easyconfig format (v2.0) 41929 (<a href="https://github.com/easybuilders/easybuild-framework/pull/844">#844</a>, 41930 <a href="https://github.com/easybuilders/easybuild-framework/pull/848">#848</a>)<ul> 41931<li>not considered stable yet, so still requires using 41932 <code>--experimental</code></li> 41933</ul> 41934</li> 41935<li>enhanced bootstrap script to also support Lmod and 41936 <code>modulecmd.tcl</code> module tools 41937 (<a href="https://github.com/easybuilders/easybuild-framework/pull/869">#869</a>)</li> 41938<li>added support to <code>run_cmd_qa</code> function to supply a list of 41939 answers 41940 (<a href="https://github.com/easybuilders/easybuild-framework/pull/887">#887</a>)</li> 41941<li>detect mismatch between definition of <code>module</code> function and 41942 selected modules tool 41943 (<a href="https://github.com/easybuilders/easybuild-framework/pull/871">#871</a>)<ul> 41944<li>allowing mismatch now requires 41945 <code>--allow-modules-tool-mismatch</code>; an empty <code>module</code> function 41946 is simply ignored</li> 41947</ul> 41948</li> 41949<li>provide lib64 fallback option for directories in default sanity 41950 check paths 41951 (<a href="https://github.com/easybuilders/easybuild-framework/pull/896">#896</a>)</li> 41952<li>
41952add support for adding JAR files to <code>$CLASSPATH</code> 41953 (<a href="https://github.com/easybuilders/easybuild-framework/pull/898">#898</a>)</li> 41954<li>enhanced and cleaned up unit tests 41955 (<a href="https://github.com/easybuilders/easybuild-framework/pull/877">#877</a>, 41956 <a href="https://github.com/easybuilders/easybuild-framework/pull/880">#880</a>, 41957 <a href="https://github.com/easybuilders/easybuild-framework/pull/884">#884</a>, 41958 <a href="https://github.com/easybuilders/easybuild-framework/pull/899">#899</a>, 41959 <a href="https://github.com/easybuilders/easybuild-framework/pull/901">#901</a>)</li> 41960<li>code cleanup and refactoring<ul> 41961<li>get rid of global variable for configuration settings in 41962 <code>config.py</code>, use singleton instead 41963 (<a href="https://github.com/easybuilders/easybuild-framework/pull/874">#874</a>, 41964 <a href="https://github.com/easybuilders/easybuild-framework/pull/888">#888</a>, 41965 <a href="https://github.com/easybuilders/easybuild-framework/pull/890">#890</a>, 41966 <a href="https://github.com/easybuilders/easybuild-framework/pull/892">#892</a>)</li> 41967<li>track build options via singleton in <code>config.py</code> rather than 41968 passing them around all over 41969 (<a href="https://github.com/easybuilders/easybuild-framework/pull/886">#886</a>, 41970 <a href="https://github.com/easybuilders/easybuild-framework/pull/889">#889</a>)</li> 41971<li>avoid parsing easyconfig files multiple times by passing a 41972 parsed easyconfig to the easyblock 41973 (<a href="https://github.com/easybuilders/easybuild-framework/pull/891">#891</a>)</li> 41974<li>deprecate list of tuples return type of <code>extra_options</code> 41975 static method 41976 (<a href="https://github.com/easybuilders/easybuild-framework/pull/893">#893</a>, 41977 <a href="https://github.com/easybuilders/easybuild-framework/pull/894">#894</a>)</li> 41978<li>move OS dependency check to <code>systemtools.py</code> module 41979 (<a href="https://github.com/easybuilders/easybuild-framework/pull/895">#895</a>)</li> 41980</ul> 41981</li> 41982</ul> 41983</li> 41984<li>bug fixes, including:<ul> 41985<li>fix linking with <code>-lcudart</code> if CUDA is part of the toolchain, 41986 should also include <code>-lrt</code> 41987 (<a href="https://github.com/easybuilders/easybuild-framework/pull/882">#882</a>)</li> 41988</ul> 41989</li> 41990</ul> 41991<p><strong>easyblocks</strong></p> 41992<ul> 41993<li>various enhancements, including:<ul> 41994<li>also run <code>Perl Build build</code> for Perl modules (usually not 41995 required, but sometimes it is) 41996 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/380">#380</a>)</li> 41997<li>added glob support in generic makecp block 41998 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/367">#367</a>, 41999 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/384">#384</a>)</li> 42000<li>enhance sanity check in GCC easyblock such that it also 42001 passes/works on OpenSuSE 42002 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/365">#365</a>)</li> 42003<li>add multilib support in GCC easyblock 42004 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/379">#379</a>)</li> 42005</ul> 42006</li> 42007<li>various bug fixes:<ul> 42008<li>Clang: disable sanitizer tests when vmem limit is set 42009 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/366">#366</a>)</li> 42010<li>make sure all libraries are installed for recent Intel MKL 42011 versions 42012 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/375">#375</a>)</li> 42013<li>fix appending Intel MPI include directories to <code>$CPATH</code> 42014 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/371">#371</a>)</li> 42015<li>statically link readline/ncurses libraries in Python and NWChem 42016 easyblocks 42017 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/370">#370</a>, 42018 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/383">#383</a>, 42019 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/385">#385</a>)</li> 42020<li>fix easyblock unit tests after changes in framework 42021 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/376">#376</a>, 42022 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/377">#377</a>, 42023 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/378">#378</a>)</li> 42024</ul> 42025</li> 42026</ul> 42027<p><strong>easyconfigs</strong></p> 42028<ul> 42029<li>added example easyconfig files for <strong>6</strong> new software packages:<ul> 42030<li>CLooG 42031 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/653">#653</a>), 42032 ELPA 42033 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/738">#738</a>), 42034 LIBSVM 42035 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/788">#788</a>), 42036 netaddr 42037 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/753">#753</a>), 42038 netifcas 42039 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/753">#753</a>), 42040 slalib-c 42041 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/750">#750</a>)</li> 42042</ul> 42043</li> 42044<li>
42044added easyconfigs for new toolchains:<ul> 42045<li>ClangGCC/1.3.0 42046 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/653">#653</a>), 42047 goolf/1.4.10-no-OFED 42048 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/749">#749</a>), 42049 goolf/1.5.14(-no-OFED) 42050 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/764">#764</a>, 42051 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/767">#767</a>), 42052 ictce/6.2.5 42053 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/726">#726</a>), 42054 iomkl 42055 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/747">#747</a>)</li> 42056</ul> 42057</li> 42058<li>added additional easyconfigs for various supported software 42059 packages: version updates, different toolchains, ...</li> 42060<li>various enhancements, including:<ul> 42061<li>tweak BOINC easyconfig to make use of <code>glob</code> support available 42062 for <code>files_to_copy</code> 42063 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/781">#781</a>)</li> 42064<li>enable <code>-fPIC</code> for libreadline, so it can be linked into shared 42065 libs (e.g. <code>libpython2.x.so</code>) 42066 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/798">#798</a>)</li> 42067</ul> 42068</li> 42069<li>various bug fixes, including:<ul> 42070<li>fix Qt source_urls 42071 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/756">#756</a>)</li> 42072<li>enable <code>-fPIC</code> in ncurses 5.9 ictce/5.2.0 easyconfig, just like 42073 in the others 42074 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/801">#801</a>)</li> 42075<li>fix unit tests after changes to framework 42076 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/763">#763</a>, 42077 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/766">#766</a>, 42078 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/769">#769</a>)</li> 42079</ul> 42080</li> 42081</ul> 42082<h2 id="easybuild-v1111-february-28th-2014">EasyBuild v1.11.1 (February 28th 2014)<a class="headerlink" href="#easybuild-v1111-february-28th-2014" title="Permanent link">¶</a></h2> 42083<p>bugfix release</p> 42084<p><strong>framework</strong></p> 42085<ul> 42086<li>various bug fixes, including:<ul> 42087<li>fix hard crash when <code>$LMOD_CMD</code> specified full path to lmod 42088 binary, but <code>spider</code> binary is not in <code>$PATH</code> 42089 (<a href="https://github.com/easybuilders/easybuild-framework/pull/861">#861</a>, 42090 <a href="https://github.com/easybuilders/easybuild-framework/pull/873">#873</a>)</li> 42091<li>fix bug in initialisation of repositories, causing problems when 42092 a repository subdirectory is specified 42093 (<a href="https://github.com/easybuilders/easybuild-framework/pull/852">#852</a>)</li> 42094<li>avoid long wait when dependency resolution fails if <code>--robot</code> is 42095 not specified 42096 (<a href="https://github.com/easybuilders/easybuild-framework/pull/875">#875</a>)</li> 42097</ul> 42098</li> 42099</ul> 42100<p><strong>easyblocks</strong></p> 42101<p><em>(no changes compared to v1.11.0, simple version bump to stay in sync 42102with easybuild-framework)</em></p> 42103<p><strong>easyconfigs</strong></p> 42104<p><em>(no changes compared to v1.11.0, simple version bump to stay in sync 42105with easybuild-framework)</em></p> 42106<h2 id="easybuild-v1110-february-16th-2014">EasyBuild v1.11.0 (February 16th 2014)<a class="headerlink" href="#easybuild-v1110-february-16th-2014" title="Permanent link">¶</a></h2> 42107<p>feature + bugfix release</p> 42108<p><strong>framework</strong></p> 42109<ul> 42110<li>various enhancements, including:<ul> 42111<li>add checksum support for extensions 42112 (<a href="https://github.com/easybuilders/easybuild-framework/pull/807">#807</a>)</li> 42113<li>make checksum functionality more memory efficient by reading in 42114 blocks 42115 (<a href="https://github.com/easybuilders/easybuild-framework/pull/836">#836</a>)</li> 42116<li>rewrite of dependency solving for speed and better reporting of 42117 missing dependencies 42118 (<a href="https://github.com/easybuilders/easybuild-framework/pull/806">#806</a>, 42119 <a href="https://github.com/easybuilders/easybuild-framework/pull/818">#818</a>)</li> 42120<li>refactoring of <code>main.py</code> 42121 (<a href="https://github.com/easybuilders/easybuild-framework/pull/815">#815</a>, 42122 <a href="https://github.com/easybuilders/easybuild-framework/pull/828">#828</a>)<ul> 42123<li>function/method signatures to pass down build options</li> 42124<li>move functions from main.py into easybuild.framework.X or 42125 easybuild.tools</li> 42126</ul> 42127</li> 42128<li>provide better build statistics 42129 (<a href="https://github.com/easybuilders/easybuild-framework/pull/824">#824</a>)</li> 42130<li>
42130add --experimental, <code>--deprecated</code> and <code>--oldstyleconfig</code> 42131 command line options 42132 (<a href="https://github.com/easybuilders/easybuild-framework/pull/838">#838</a>)<ul> 42133<li>with <code>--experimental</code>, new but incomplete (or partially 42134 broken) features are enabled</li> 42135<li>with <code>--deprecated</code>, removed of deprecated functionality can 42136 be tested (anything deprecated will fail hard)</li> 42137<li>with <code>--disable-oldstyleconfig</code>, support for the old style 42138 configuration is disabled</li> 42139</ul> 42140</li> 42141<li>define <code>$LIBRARY_PATH</code> in generated module files 42142 (<a href="https://github.com/easybuilders/easybuild-framework/pull/832">#832</a>)</li> 42143<li>more constants for source URLs (e.g. for downloads from 42144 bitbucket) 42145 (<a href="https://github.com/easybuilders/easybuild-framework/pull/831">#831</a>)</li> 42146<li>prefer <code>$XDG_CONFIG_HOME</code> and <code>~/.config/easybuild</code> over 42147 <code>~/.easybuild</code> for configuration files 42148 (<a href="https://github.com/easybuilders/easybuild-framework/pull/820">#820</a>)</li> 42149<li>add support for specifying footers to be appended to generated 42150 module files 42151 (<a href="https://github.com/easybuilders/easybuild-framework/pull/808">#808</a>)<ul> 42152<li>see <code>--modules-footer</code> command line option</li> 42153</ul> 42154</li> 42155<li>track version of modules tool + cleanup of <code>modules.py</code> 42156 (<a href="https://github.com/easybuilders/easybuild-framework/pull/839">#839</a>)</li> 42157<li>move actual <code>run_cmd</code> and <code>run_cmd_qa</code> implementations from 42158 <code>tools.filetools</code> into <code>tools.run</code> 42159 (<a href="https://github.com/easybuilders/easybuild-framework/pull/842">#842</a>, 42160 <a href="https://github.com/easybuilders/easybuild-framework/pull/843">#843</a>)</li> 42161<li>add support for generating modules that support recursive 42162 unloading 42163 (<a href="https://github.com/easybuilders/easybuild-framework/pull/830">#830</a>)<ul> 42164<li>see <code>--recursive-module-unload</code> command line option</li> 42165</ul> 42166</li> 42167<li>add flexibility support for specifying OS dependencies 42168 (<a href="https://github.com/easybuilders/easybuild-framework/pull/846">#846</a>)<ul> 42169<li>alternatives can be specified, e.g. (<code>openssl-devel</code>, 42170 <code>libssl-dev</code>)</li> 42171</ul> 42172</li> 42173<li>initial (incomplete) support for easyconfig files in new format 42174 (v2.0) 42175 (<a href="https://github.com/easybuilders/easybuild-framework/pull/810">#810</a>, 42176 <a href="https://github.com/easybuilders/easybuild-framework/pull/826">#826</a>, 42177 <a href="https://github.com/easybuilders/easybuild-framework/pull/827">#827</a>, 42178 <a href="https://github.com/easybuilders/easybuild-framework/pull/841">#841</a>)<ul> 42179<li>requires <code>--experimental</code> to be able to experiment with 42180 format v2 easyconfig files</li> 42181</ul> 42182</li> 42183</ul> 42184</li> 42185<li>various bug fixes, including:<ul> 42186<li>fix problems with use of new-style configuration file 42187 (<a href="https://github.com/easybuilders/easybuild-framework/pull/821">#821</a>)</li> 42188<li>fix removal of old build directories, unless <code>cleanupoldbuild</code> 42189 easyconfig parameter is set 42190 (<a href="https://github.com/easybuilders/easybuild-framework/pull/809">#809</a>)</li> 42191<li>fix support for different types of repository path 42192 specifications 42193 (<a href="https://github.com/easybuilders/easybuild-framework/pull/814">#814</a>)</li> 42194<li>fix unit tests sensitive to <code>$MODULEPATH</code> and available 42195 easyblocks 42196 (<a href="https://github.com/easybuilders/easybuild-framework/pull/845">#845</a>)</li> 42197</ul> 42198</li> 42199</ul> 42200<p><strong>easyblocks</strong></p> 42201<ul> 42202<li>added <strong>one</strong> new <em>generic</em> easyblock: 42203 <code>VSCPythonPackage</code> 42204 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/348">#348</a>)</li> 42205<li>added support for <strong>1</strong> new software package that requires 42206 customized support:<ul> 42207<li>netcdf4-python 42208 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/347">#347</a>)</li> 42209</ul> 42210</li> 42211<li>various enhancements, including:<ul> 42212<li>add support for installing recent tbb versions 42213 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/341">#341</a>)</li> 42214<li>use <code>makeopts</code> in the build step of the generic <code>PythonPackage</code> 42215 easyblock 42216 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/352">#352</a>)</li> 42217<li>define the <code>$CMAKE_INCLUDE_PATH</code> and <code>$CMAKE_LIBRARY_PATH</code> in 42218 the generic <code>CMakeMake</code> easyblock 42219 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/351">#351</a>, 42220 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/360">#360</a>)</li> 42221<li>update Clang easyblock to support v3.4 42222 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/346">#346</a>)</li> 42223<li>
42223make sure Python is built with SSL support, adjust Python 42224 easyblock to pick up OpenSSL dep 42225 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/359">#359</a>)<ul> 42226<li>note: providing OpenSSL via an OS package is still 42227 recommended, such that security updates are picked up</li> 42228</ul> 42229</li> 42230<li>add support for recent netCDF versions 42231 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/347">#347</a>)</li> 42232<li>update SuiteSparse easyblock for new versions, and clean it up a 42233 bit 42234 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/350">#350</a>)</li> 42235</ul> 42236</li> 42237<li>various bug fixes:<ul> 42238<li>fix name of <code>VersionIndependentPythonPackage</code> easyblock, 42239 deprecate <code>VersionIndependendPythonPackage</code> easyblock 42240 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/348">#348</a>)</li> 42241<li>fix detection of machine architecture in FSL easyblock 42242 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/353">#353</a>)</li> 42243<li>fix bug in NWChem easyblock w.r.t. creating local dummy 42244 <code>.nwchem</code> file 42245 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/360">#360</a>)</li> 42246<li>make sure <code>$LIBRARY_PATH</code> is set for Intel compilers and Intel 42247 MPI, fix 64-bit specific paths 42248 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/360">#360</a>)</li> 42249</ul> 42250</li> 42251</ul> 42252<p><strong>easyconfigs</strong></p> 42253<ul> 42254<li>added example easyconfig files for <strong>30</strong> new software packages:<ul> 42255<li>argtable 42256 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/669">#669</a>), 42257 Clustal-Omega 42258 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/669">#669</a>), 42259 Coreutils 42260 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/582">#582</a>), 42261 GMT 42262 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/560">#560</a>), 42263 gperftools 42264 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/596">#596</a>), 42265 grep 42266 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/582">#582</a>), 42267 h4toh5 42268 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/597">#597</a>), 42269 libunwind 42270 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/596">#596</a>), 42271 Lmod 42272 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/600">#600</a>, 42273 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/692">#692</a>), 42274 Lua 42275 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/600">#600</a>, 42276 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/692">#692</a>), 42277 MAFFT 42278 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/654">#654</a>), 42279 Molekel 42280 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/597">#597</a>), 42281 NEdit 42282 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/597">#597</a>), 42283 netcdf4-python 42284 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/660">#660</a>), 42285 nodejs 42286 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/678">#678</a>), 42287 OCaml 42288 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/704">#704</a>), 42289 patch 42290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/582">#582</a>), 42291 PhyML 42292 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/664">#664</a>), 42293 PRACE Common Production Environment 42294 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/599">#599</a>), 42295 protobuf 42296 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/680">#680</a>), 42297 python-dateutil 42298 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/438">#438</a>), 42299 sed 42300 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/582">#582</a>), 42301 sickle 42302 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/651">#651</a>), 42303 Tesla-Deployment-Kit 42304 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/489">#489</a>), 42305 TREE-PUZZLE 42306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/662">#662</a>), 42307 VCFtools 42308 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/626">#626</a>), 42309 Vim 42310 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/665">#665</a>), 42311 vsc-mympirun-scoop 42312 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/661">#661</a>), 42313 vsc-processcontrol 42314 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/661">#661</a>), 42315 XZ 42316 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/582">#582</a>)</li> 42317</ul> 42318</li> 42319<li>
42319added additional easyconfigs for various supported software 42320 packages: version updates, different toolchains, ...<ul> 42321<li>OpenSSL with ictce toolchain 42322 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/703">#703</a>)</li> 42323</ul> 42324</li> 42325<li>various enhancements, including:<ul> 42326<li>using more constants and templates 42327 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/613">#613</a>, 42328 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/615">#615</a>)</li> 42329<li>specify OS dependency for SSL support, with OpenSSL dependency 42330 as fallback 42331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/703">#703</a>)</li> 42332</ul> 42333</li> 42334<li>various bug fixes, including:<ul> 42335<li>fix unit tests after (internal) framework API changes 42336 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/667">#667</a>, 42337 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/672">#672</a>)</li> 42338<li>fix homepage in vsc-mympirun easyconfig file 42339 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/681">#681</a>)</li> 42340<li>align OpenMPI easyconfigs 42341 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/650">#650</a>)</li> 42342<li>add additional source URL in Qt easyconfigs 42343 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/676">#676</a>)</li> 42344<li>specify correct $PATH specification and define <code>$CHPL_HOME</code> for 42345 Chapel 42346 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/683">#683</a>)</li> 42347</ul> 42348</li> 42349</ul> 42350<h2 id="easybuild-v1100-december-24th-2013">EasyBuild v1.10.0 (December 24th 2013)<a class="headerlink" href="#easybuild-v1100-december-24th-2013" title="Permanent link">¶</a></h2> 42351<p>feature + bugfix release</p> 42352<p><strong>framework</strong></p> 42353<ul> 42354<li>various enhancements, including:<ul> 42355<li>set unique default temporary directory, add <code>--tmpdir</code> command 42356 line option 42357 (<a href="https://github.com/easybuilders/easybuild-framework/pull/695">#695</a>)</li> 42358<li>add support for computing and verifying source/patch file 42359 checksums 42360 (<a href="https://github.com/easybuilders/easybuild-framework/pull/774">#774</a>, 42361 <a href="https://github.com/easybuilders/easybuild-framework/pull/777">#777</a>, 42362 <a href="https://github.com/easybuilders/easybuild-framework/pull/779">#779</a>, 42363 <a href="https://github.com/easybuilders/easybuild-framework/pull/801">#801</a>, 42364 <a href="https://github.com/easybuilders/easybuild-framework/pull/802">#802</a>)<ul> 42365<li>cfr. <code>checksums</code> easyconfig parameter</li> 42366</ul> 42367</li> 42368<li>add support for <em>eb --confighelp</em>, which prints out 42369 an example configuration file 42370 (<a href="https://github.com/easybuilders/easybuild-framework/pull/775">#775</a>)</li> 42371<li>add initial support for <code>eb</code> tab completion in bash shells 42372 (<a href="https://github.com/easybuilders/easybuild-framework/pull/775">#775</a>, 42373 <a href="https://github.com/easybuilders/easybuild-framework/pull/797">#797</a>, 42374 <a href="https://github.com/easybuilders/easybuild-framework/pull/798">#798</a>)<ul> 42375<li>see also 42376 <a href="https://github.com/easybuilders/easybuild/wiki/Setting-up-tab-completion-for-bash">https://github.com/easybuilders/easybuild/wiki/Setting-up-tab-completion-for-bash</a></li> 42377<li>note: may be quite slow for now</li> 42378</ul> 42379</li> 42380<li>enhancements for using Lmod as modules tool 42381 (<a href="https://github.com/easybuilders/easybuild-framework/pull/780">#780</a>, 42382 <a href="https://github.com/easybuilders/easybuild-framework/pull/795">#795</a>, 42383 <a href="https://github.com/easybuilders/easybuild-framework/pull/796">#796</a>):<ul> 42384<li>ignore Lmod spider cache by setting <code>$LMOD_IGNORE_CACHE</code> 42385 (requires Lmod 5.2)</li> 42386<li>bump required Lmod version to v5.2</li> 42387<li>get rid of slow workaround for detecting module directories 42388 (only required for older Lmod versions)</li> 42389<li>
42389fix version parsing for Lmod release candidates (rc)</li> 42390<li>improve integration with <em>lmod spider</em> by adding 42391 <code>Description:</code> prefix to <code>module-whatis</code> field of module</li> 42392</ul> 42393</li> 42394<li>add <code>--dry-short-short</code>/<code>-D</code> and <code>--search-short</code>/<code>-S</code> command 42395 line options 42396 (<a href="https://github.com/easybuilders/easybuild-framework/pull/781">#781</a>)</li> 42397<li>add toolchain definition for 'gompic', intended for using with 42398 CUDA-aware OpenMPI 42399 (<a href="https://github.com/easybuilders/easybuild-framework/pull/783">#783</a>)</li> 42400<li>add support for specifying multiple robot paths 42401 (<a href="https://github.com/easybuilders/easybuild-framework/pull/786">#786</a>)</li> 42402<li>add various source URL constants, add support for 42403 <code>%(nameletter)s</code> and <code>%(nameletterlower)s</code> templates 42404 (<a href="https://github.com/easybuilders/easybuild-framework/pull/793">#793</a>)</li> 42405<li>add <code>buildininstalldir</code> easyconfig parameter 42406 (<a href="https://github.com/easybuilders/easybuild-framework/pull/794">#794</a>)</li> 42407<li>add <code>--ignore-osdeps</code> command line option 42408 (<a href="https://github.com/easybuilders/easybuild-framework/pull/799">#799</a>, 42409 <a href="https://github.com/easybuilders/easybuild-framework/pull/802">#802</a>)</li> 42410</ul> 42411</li> 42412<li>various bug fixes, including:<ul> 42413<li>enable <code>-mt_mpi</code> compiler flag if both <code>usempi</code> and <code>openmp</code> 42414 toolchain options are enabled 42415 (<a href="https://github.com/easybuilders/easybuild-framework/pull/771">#771</a>)</li> 42416<li>only use <code>libmkl_solver*</code> libraries for Intel MKL versions prior 42417 to 10.3 42418 (<a href="https://github.com/easybuilders/easybuild-framework/pull/776">#776</a>)</li> 42419<li>fix toolchain support for recent Intel tools 42420 (<a href="https://github.com/easybuilders/easybuild-framework/pull/785">#785</a>)</li> 42421<li>code style fixes in <code>main.py</code> to adhere more to PEP8 42422 (<a href="https://github.com/easybuilders/easybuild-framework/pull/789">#789</a>)</li> 42423<li>make sure <code>easyblock</code> easyconfig parameter is listed in <code>eb -a</code> 42424 (<a href="https://github.com/easybuilders/easybuild-framework/pull/791">#791</a>)</li> 42425<li>fix error that may pop up when using <code>skipsteps=source</code> 42426 (<a href="https://github.com/easybuilders/easybuild-framework/pull/792">#792</a>)</li> 42427</ul> 42428</li> 42429</ul> 42430<p><strong>easyblocks</strong></p> 42431<ul> 42432<li>added <strong>one</strong> new <em>generic</em> easyblock: 42433 <code>VersionIndependendPythonPackage</code> 42434 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/329">#329</a>, 42435 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/334">#334</a>)</li> 42436<li>added support for <strong>2</strong> new software packages that require 42437 customized support:<ul> 42438<li>Charmm 42439 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/318">#318</a>), 42440 GROMACS 42441 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/335">#335</a>, 42442 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/339">#339</a>)</li> 42443</ul> 42444</li> 42445<li>various enhancements, including:<ul> 42446<li>fix support for recent SAMtools version (>= 0.1.19) 42447 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/320">#320</a>)</li> 42448<li>fix support for recent Intel tools (icc, ifort, imkl, impi) 42449 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/325">#325</a>, 42450 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/327">#327</a>, 42451 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/338">#338</a>)</li> 42452<li>enhance generic easyblock for installing RPMs 42453 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/332">#332</a>)</li> 42454<li>pick up <code>preinstallopts</code> in generic <code>PythonPackage</code> easyblock 42455 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/334">#334</a>)</li> 42456<li>enhance CP2K easyblock (libxc support, new versions) + style 42457 cleanup 42458 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/336">#336</a>)</li> 42459</ul> 42460</li> 42461<li>various bug fixes:<ul> 42462<li>use unwanted env var functionality to unset <code>$MKLROOT</code> rather 42463 than failing with an error 42464 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/273">#273</a>)</li> 42465<li>always include <code>-w</code> flag for preprocessor to suppress warnings 42466 that may break QuantumESPRESSO configure 42467 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/317">#317</a>)</li> 42468<li>link with multithreaded LAPACK libs for ESMF 42469 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/319">#319</a>)</li> 42470<li>extend <code>noqanda</code> list of patterns in CUDA easyblock 42471 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/328">#328</a>, 42472 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/337">#337</a>)</li> 42473<li>
42473add <code>import _ctypes</code> to Python sanity check commands to capture 42474 a common build issue 42475 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/329">#329</a>)</li> 42476<li>bug fixes in generic <code>IntelBase</code> easyblock 42477 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/331">#331</a>, 42478 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/333">#333</a>, 42479 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/335">#335</a>)<ul> 42480<li>remove broken symlink <code>$HOME/intel</code> if present</li> 42481<li>fix use of gettempdir to obtain a common (user-specific) tmp 42482 dir to symlink <code>$HOME/intel</code> to</li> 42483</ul> 42484</li> 42485<li>fix build of recent scipy versions with GCC-based toolchain 42486 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/334">#334</a>)</li> 42487<li>fix use of gettempdir to obtain common (user-specific) tmp dir 42488 for <code>$HOME/.nwchemrc</code> symlink 42489 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/340">#340</a>, 42490 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/342">#342</a>)</li> 42491<li>extend <code>noqanda</code> list in Qt easyblock 42492 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/342">#342</a>)</li> 42493</ul> 42494</li> 42495</ul> 42496<p><strong>easyconfigs</strong></p> 42497<ul> 42498<li>added example easyconfig files for <strong>18</strong> new software packages:<ul> 42499<li>BEDTools 42500 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/579">#579</a>, 42501 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/632">#632</a>, 42502 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/635">#635</a>), 42503 CAP3 42504 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/548">#548</a>), 42505 CHARMM 42506 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/584">#584</a>), 42507 cutadapt 42508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/620">#620</a>), 42509 ErlangOTP 42510 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/556">#556</a>, 42511 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/630">#630</a>), 42512 Ghostscript 42513 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/547">#547</a>, 42514 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/632">#632</a>), 42515 HTSeq 42516 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/554">#554</a>, 42517 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/632">#632</a>), 42518 Jansson 42519 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/545">#545</a>), 42520 libjpeg-turbo 42521 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/574">#574</a>), 42522 Molden 42523 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/566">#566</a>), 42524 netloc 42525 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/545">#545</a>), 42526 o2scl 42527 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/633">#633</a>), 42528 packmol 42529 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/566">#566</a>), 42530 PP 42531 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/405">#405</a>), 42532 qtop 42533 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/500">#500</a>), 42534 TAMkin 42535 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/566">#566</a>), 42536 vsc-base 42537 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/621">#621</a>), 42538 vsc-mympirun 42539 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/621">#621</a>)</li> 42540</ul> 42541</li> 42542<li>added easyconfigs for new toolchains 42543 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/545">#545</a>, 42544 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/609">#609</a>, 42545 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/629">#629</a>):<ul> 42546<li>gcccuda/2.6.10, gompic/2.6.10, goolfc/2.6.10, ictce/6.0.5, 42547 ictce/6.1.5</li> 42548</ul> 42549</li> 42550<li>
42550added additional easyconfigs for various supported software 42551 packages: version updates, different toolchains, ...<ul> 42552<li>new versions of icc, ifort, imkl, impi 42553 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/609">#609</a>, 42554 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/629">#629</a>)</li> 42555<li>large collection of ictce/5.3.0 easyconfigs 42556 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/627">#627</a>)</li> 42557</ul> 42558</li> 42559<li>various enhancements, including:<ul> 42560<li>extended list of Python packages as extensions to Python 42561 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/625">#625</a>)</li> 42562<li>add MPI-enabled version of GROMACS + easyconfigs using ictce 42563 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/606">#606</a>, 42564 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/636">#636</a>)</li> 42565<li>clean up templating of <code>source_urls</code> 42566 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/637">#637</a>)</li> 42567</ul> 42568</li> 42569<li>various bug fixes, including:<ul> 42570<li>provide alternative download URL for Mesa 42571 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/532">#532</a>)</li> 42572<li>add Python versionsuffix in OpenBabel filenames 42573 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/566">#566</a>)</li> 42574<li>apply no-gets patch in all M4 v1.4.16 easyconfigs 42575 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/623">#623</a>)</li> 42576<li>fix patching of Python w.r.t. <code>libffi</code>/<code>_ctypes</code> issues 42577 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/625">#625</a>, 42578 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/642">#642</a>)</li> 42579<li>bug fixes in GROMACS easyconfigs 42580 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/606">#606</a>)<ul> 42581<li>change versionsuffix for non-MPI GROMACS easyconfigs to 42582 <code>-mt</code></li> 42583<li>stop using 'CMakeMake' easyblock for GROMACS now that 42584 there's a dedicated GROMACS easyblock, which correctly 42585 specifies building against external BLAS/LAPACK libraries</li> 42586</ul> 42587</li> 42588<li>fix Qt dependency for CGAL 42589 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/642">#642</a>)</li> 42590<li>fix libctl, libmatheval, Meep, PSI build issues caused by full 42591 paths in <code>guile-config</code>/<code>python-config</code> shebang 42592 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/642">#642</a>)</li> 42593<li>make sure HDF easyconfigs specify dedicated <code>include/hdf</code> 42594 include dir 42595 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/642">#642</a>)<ul> 42596<li>this is required to avoid build issues with NCL, because HDF 42597 ships it's own <code>netcdf.h</code></li> 42598<li>this also triggered removal of patch files for NCL that 42599 rewrote <code>include/hdf</code> to <code>include</code></li> 42600</ul> 42601</li> 42602<li>fix WPS v3.5.1 patch file after upstream source tarball was 42603 changed, supply checksum for verification 42604 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/642">#642</a>)</li> 42605</ul> 42606</li> 42607</ul> 42608<h2 id="easybuild-v190-november-17th-2013">EasyBuild v1.9.0 (November 17th 2013)<a class="headerlink" href="#easybuild-v190-november-17th-2013" title="Permanent link">¶</a></h2> 42609<p>feature + bugfix release</p> 42610<p><strong>framework</strong></p> 42611<ul> 42612<li>add support for Tcl environment modules (<code>modulecmd.tcl</code>) 42613 (<a href="https://github.com/easybuilders/easybuild-framework/pull/728">#728</a>, 42614 <a href="https://github.com/easybuilders/easybuild-framework/pull/729">#729</a>, 42615 <a href="https://github.com/easybuilders/easybuild-framework/pull/739">#739</a>)<ul> 42616<li>special care was taken to make sure also the DEISA variant of 42617 <code>modulecmd.tcl</code> can be used</li> 42618</ul> 42619</li> 42620<li>code refactoring to prepare for supporting two formats for 42621 easyconfig files 42622 (<a href="https://github.com/easybuilders/easybuild-framework/pull/693">#693</a>, 42623 <a href="https://github.com/easybuilders/easybuild-framework/pull/750">#750</a>)<ul> 42624<li>this prepares the codebase for supporting easyconfig format v2.0</li> 42625<li>some initial work on adding support for the new easyconfig 42626 format is included, but it's by no means complete yet</li> 42627<li>the current easyconfig format (now dubbed v1.0) is still the 42628 default and only supported format, for now</li> 42629<li>for more details, see 42630 <a href="https://github.com/easybuilders/easybuild/wiki/Easyconfig-format-two">https://github.com/easybuilders/easybuild/wiki/Easyconfig-format-two</a></li> 42631</ul> 42632</li> 42633<li>various other enhancements, including:<ul> 42634<li>include a full version of vsc-base (see the <code>vsc</code> subdirectory) 42635 (<a href="https://github.com/easybuilders/easybuild-framework/pull/740">#740</a>)<ul> 42636<li>this is a first step towards switching to using vsc-base as 42637 a proper dependency</li> 42638</ul> 42639</li> 42640<li>implement get_avail_core_count function in systemtools module 42641 that takes cpusets and co into account 42642 (<a href="https://github.com/easybuilders/easybuild-framework/pull/700">#700</a>)<ul> 42643<li>the <code>get_core_count</code> function is now deprecated</li> 42644</ul> 42645</li> 42646<li>
42646add <code>impmkl</code> toolchain definition 42647 (<a href="https://github.com/easybuilders/easybuild-framework/pull/736">#736</a>)</li> 42648<li>make regtest more robust: put holds on jobs without 42649 dependencies, release holds once all jobs are submitted 42650 (<a href="https://github.com/easybuilders/easybuild-framework/pull/751">#751</a>)</li> 42651<li>add support for specifying multiple alternatives for sanity 42652 check paths 42653 (<a href="https://github.com/easybuilders/easybuild-framework/pull/753">#753</a>)</li> 42654<li>add <code>get_software_libdir</code> function to modules.py (along with 42655 unit tests) 42656 (<a href="https://github.com/easybuilders/easybuild-framework/pull/758">#758</a>)</li> 42657<li>add support for more file extensions and constants w.r.t. 42658 sources 42659 (<a href="https://github.com/easybuilders/easybuild-framework/pull/738">#738</a>, 42660 <a href="https://github.com/easybuilders/easybuild-framework/pull/760">#760</a>, 42661 <a href="https://github.com/easybuilders/easybuild-framework/pull/761">#761</a>)</li> 42662<li>add MPICH2 support in <code>mpi_cmd_for</code> function 42663 (<a href="https://github.com/easybuilders/easybuild-framework/pull/761">#761</a>)</li> 42664</ul> 42665</li> 42666<li>various bug fixes, including:<ul> 42667<li>fix checking of OS dependencies on Debian/Ubuntu that have <code>rpm</code> 42668 command available 42669 (<a href="https://github.com/easybuilders/easybuild-framework/pull/732">#732</a>)</li> 42670<li>make unit tests more robust w.r.t. non-writeable <code>/tmp</code> and 42671 loaded modules prior to starting unit tests 42672 (<a href="https://github.com/easybuilders/easybuild-framework/pull/752">#752</a>, 42673 <a href="https://github.com/easybuilders/easybuild-framework/pull/756">#756</a>)</li> 42674<li>also call <code>EasyBlock</code>'s sanity check in <code>ExtensionEasyblock</code> if 42675 paths/commands are specified in easyconfig 42676 (<a href="https://github.com/easybuilders/easybuild-framework/pull/757">#757</a>)</li> 42677<li>set compiler family for dummy compiler, add definition of 42678 toolchain constant for dummy 42679 (<a href="https://github.com/easybuilders/easybuild-framework/pull/759">#759</a>)</li> 42680</ul> 42681</li> 42682<li>other<ul> 42683<li>add build status badges for master/develop branches to <code>README</code> 42684 (<a href="https://github.com/easybuilders/easybuild-framework/pull/742">#742</a>)</li> 42685<li>add scripts for installing EasyBuild develop version or setting 42686 up git development environment 42687 (<a href="https://github.com/easybuilders/easybuild-framework/pull/730">#730</a>, 42688 <a href="https://github.com/easybuilders/easybuild-framework/pull/755">#755</a>)</li> 42689</ul> 42690</li> 42691</ul> 42692<p><strong>easyblocks</strong></p> 42693<ul> 42694<li>added support for <strong>8</strong> new software packages that require 42695 customized support:<ul> 42696<li>Allinea DDT/MAP 42697 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/279">#279</a>), 42698 ARB 42699 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/291">#291</a>), 42700 GenomeAnalysisTK 42701 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/278">#278</a>), 42702 OpenBabel 42703 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/305">#305</a>, 42704 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/309">#309</a>), 42705 picard 42706 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/278">#278</a>), 42707 PyQuante 42708 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/297">#297</a>), 42709 Scalasca v1.x 42710 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/304">#304</a>), 42711 Score-P 42712 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/304">#304</a>)<ul> 42713<li>the Score-P easyblock is also used for Cube 4.x, LWM2, OTF2, 42714 and Scalasca v2.x</li> 42715</ul> 42716</li> 42717</ul> 42718</li> 42719<li>various enhancements, including:<ul> 42720<li>add support building ScaLAPACK on top of MPICH2, required for 42721 gmpolf toolchain 42722 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/274">#274</a>)</li> 42723<li>add support to ConfigureMake easyblock to customize configure 42724 <code>--prefix</code> option 42725 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/287">#287</a>)</li> 42726<li>
42726add support for specifying install command in Binary easyblock 42727 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/288">#288</a>)</li> 42728<li>enhance CMakeMake easyblock to specify srcdir via easyconfig 42729 parameter, and to perform out-of-source builds 42730 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/303">#303</a>)</li> 42731</ul> 42732</li> 42733<li>various bug fixes:<ul> 42734<li>use correct configure flag for Szip in HDF5 easyblocks, should 42735 be <code>--with-szlib</code> 42736 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/286">#286</a>, 42737 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/301">#301</a>)</li> 42738<li>add support for serial HDF5 builds 42739 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/290">#290</a>, 42740 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/301">#301</a>)</li> 42741<li>enhance robustness of Qt easyblock w.r.t. interactive configure 42742 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/295">#295</a>, 42743 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/302">#302</a>)</li> 42744<li>enhance support for picking up license specification via 42745 environment variables 42746 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/298">#298</a>, 42747 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/307">#307</a>)</li> 42748<li>extend list of values for <code>$CPATH</code> in libint2 easyblock 42749 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/300">#300</a>)</li> 42750<li>fix <code>extra_options</code> <code>super</code> call in Clang easyblock 42751 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/306">#306</a>)</li> 42752<li>add support in Boost easyblock to specify toolset in easyconfig 42753 file 42754 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/308">#308</a>)</li> 42755</ul> 42756</li> 42757<li>other:<ul> 42758<li>add build status badges for master/develop branches to README 42759 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/289">#289</a>)</li> 42760</ul> 42761</li> 42762</ul> 42763<p><strong>easyconfigs</strong></p> 42764<ul> 42765<li>added example easyconfig files for <strong>58</strong> new software packages:<ul> 42766<li>Allinea 42767 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/468">#468</a>), 42768 ARB + dependencies 42769 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/396">#396</a>, 42770 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/493">#493</a>, 42771 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/495">#495</a>), 42772 arpack-ng 42773 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/451">#451</a>, 42774 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/481">#481</a>), 42775 CDO 42776 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/484">#484</a>, 42777 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/521">#521</a>), 42778 Cube 42779 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/505">#505</a>), 42780 ed 42781 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/503">#503</a>), 42782 FLTK 42783 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/503">#503</a>), 42784 GenomeAnalysisTK 42785 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/467">#467</a>), 42786 GIMPS 42787 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/527">#527</a>), 42788 GTI 42789 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/511">#511</a>), 42790 IPython 42791 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/485">#485</a>, 42792 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/519">#519</a>), 42793 LWM2 42794 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/510">#510</a>), 42795 MPICH2 42796 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/460">#460</a>), 42797 MUST 42798 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/511">#511</a>), 42799 ncdf 42800 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/496">#496</a>, 42801 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/522">#522</a>), 42802 OPARI2 42803 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/505">#505</a>), 42804 OpenBabel 42805 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/504">#504</a>, 42806 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/524">#524</a>), 42807 OTF 42808 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/505">#505</a>), 42809 OTF2 42810 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/505">#505</a>), 42811 PandaSEQ 42812 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/475">#475</a>), 42813 ParaView 42814 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/498">#498</a>, 42815 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/514">#514</a>), 42816 ParFlow 42817 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/483">#483</a>, 42818 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/520">#520</a>), 42819 PCC 42820 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/486">#486</a>, 42821 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/528">#528</a>), 42822 PDT 42823 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/505">#505</a>), 42824 picard 42825 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/467">#467</a>), 42826 PnMPI 42827 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/511">#511</a>), 42828 PyQuante 42829 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/499">#499</a>, 42830 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/523">#523</a>), 42831 pysqlite 42832 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/519">#519</a>), 42833 Scalasca 42834 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/505">#505</a>), 42835 Score-P 42836 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/505">#505</a>), 42837 SDCC 42838 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/486">#486</a>, 42839 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/528">#528</a>), 42840 Silo 42841 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/483">#483</a>, 42842 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/520">#520</a>), 42843 Stride 42844 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/503">#503</a>), 42845 SURF 42846 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/503">#503</a>), 42847 TCC 42848 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/486">#486</a>, 42849 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/528">#528</a>)</li> 42850<li>ARB dependencies (23): fixesproto, imake, inputproto, kbproto, 42851 libICE, libSM, libX11, libXau, libXaw, libXext, libXfixes, 42852 libXi, libXmu, libXp, libXpm, libXt, lynx, motif, printproto, 42853 Sablotron, xbitmaps, xextproto, xtrans</li> 42854</ul> 42855</li> 42856<li>
42856added easyconfigs for new gmpich2/1.4.8, gmpolf/1.4.8 and 42857 goolf/1.6.10 toolchains 42858 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/460">#460</a>, 42859 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/525">#525</a>, 42860 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/530">#530</a>)</li> 42861<li>added additional easyconfigs for various software packages (list too 42862 long to include here)<ul> 42863<li>version updates, different toolchains, ...</li> 42864</ul> 42865</li> 42866<li>various bug fixes, including:<ul> 42867<li>enable building of shared libraries for MPICH 42868 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/482">#482</a>)</li> 42869<li>fix HDF configure option for Szip, should be <code>--with-szlib</code> 42870 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/533">#533</a>)<ul> 42871<li>for HDF5, this issue is fixed in the HDF5 easyblock</li> 42872</ul> 42873</li> 42874</ul> 42875</li> 42876<li>other<ul> 42877<li>add build status badges for master/develop branches to README 42878 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/490">#490</a>)</li> 42879</ul> 42880</li> 42881</ul> 42882<h2 id="easybuild-v182-october-18th-2013">EasyBuild v1.8.2 (October 18th 2013)<a class="headerlink" href="#easybuild-v182-october-18th-2013" title="Permanent link">¶</a></h2> 42883<p>bugfix release</p> 42884<p><strong>framework</strong></p> 42885<ul> 42886<li>fix regular expression used for obtaining list of modules from 42887 <code>module avail</code> 42888 (<a href="https://github.com/easybuilders/easybuild-framework/pull/724">#724</a>)<ul> 42889<li>modules marked as default were being hidden from EasyBuild, 42890 causing problems when they are used as dependency</li> 42891</ul> 42892</li> 42893</ul> 42894<p><strong>easyblocks</strong></p> 42895<ul> 42896<li>fix installing of EasyBuild with a loaded EasyBuild module 42897 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/280">#280</a>)<ul> 42898<li>this is important to make upgrading to the latest EasyBuild 42899 version possible with a bootstrapped EasyBuild</li> 42900</ul> 42901</li> 42902</ul> 42903<p><strong>easyconfigs</strong></p> 42904<ul> 42905<li>port thread pool patch to PSI 4.0b4 and include it to avoid hanging 42906 tests 42907 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/471">#471</a>)</li> 42908</ul> 42909<h2 id="easybuild-v181-october-14th-2013">EasyBuild v1.8.1 (October 14th 2013)<a class="headerlink" href="#easybuild-v181-october-14th-2013" title="Permanent link">¶</a></h2> 42910<p>bugfix release</p> 42911<ul> 42912<li>various bug fixes, including:<ul> 42913<li>fix bugs in regtest procedure 42914 (<a href="https://github.com/easybuilders/easybuild-framework/pull/713">#713</a>)<ul> 42915<li>force 2nd and 3rd attempt of build in case 1st attempt 42916 failed</li> 42917</ul> 42918</li> 42919<li>fix copying of install log to install directory 42920 (<a href="https://github.com/easybuilders/easybuild-framework/pull/716">#716</a>)</li> 42921<li>only create first source path if multiple paths are specified 42922 (<a href="https://github.com/easybuilders/easybuild-framework/pull/718">#718</a>)</li> 42923<li>detect failed PBS job submission by checking obtained job ID for 42924 <code>None</code> value 42925 (<a href="https://github.com/easybuilders/easybuild-framework/pull/713">#713</a>, 42926 <a href="https://github.com/easybuilders/easybuild-framework/pull/717">#717</a>, 42927 <a href="https://github.com/easybuilders/easybuild-framework/pull/719">#719</a>, 42928 <a href="https://github.com/easybuilders/easybuild-framework/pull/720">#720</a>)</li> 42929</ul> 42930</li> 42931</ul> 42932<p><strong>easyblocks</strong></p> 42933<ul> 42934<li>various bug fixes:<ul> 42935<li>fix problems in PSI easyblock causing build to fail 42936 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/270">#270</a>)</li> 42937<li>fix issues with running NWChem test cases, fail early in case 42938 broken symlink is present 42939 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/275">#275</a>)</li> 42940</ul> 42941</li> 42942</ul> 42943<p><strong>easyconfigs</strong></p> 42944<ul> 42945<li>added additional easyconfigs for various software packages 42946 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/457">#457</a>):<ul> 42947<li>Boost, bzip2, libreadline, ncurses, PSI, Python, zlib</li> 42948</ul> 42949</li> 42950<li>various bug fixes, including:<ul> 42951<li>fix faulty easyconfig file names for HPCBIOS_Math, MUSCLE, 42952 XML-LibXML and YAML-Syck 42953 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/459">#459</a>, 42954 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/462">#462</a>)</li> 42955<li>stop (re)specifying default maximum ratio for failed tests in 42956 NWChem easyconfig 42957 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/457">#457</a>)</li> 42958</ul> 42959</li> 42960</ul> 42961<h2 id="easybuild-v180-october-4th-2013">EasyBuild v1.8.0 (October 4th 2013)<a class="headerlink" href="#easybuild-v180-october-4th-2013" title="Permanent link">¶</a></h2> 42962<p>feature + bugfix release</p> 42963<p><strong>framework</strong></p> 42964<ul> 42965<li>add support for using alternative module naming schemes 42966 (<a href="https://github.com/easybuilders/easybuild-framework/pull/679">#679</a>, 42967 <a href="https://github.com/easybuilders/easybuild-framework/pull/696">#696</a>, 42968 <a href="https://github.com/easybuilders/easybuild-framework/pull/705">#705</a>, 42969 <a href="https://github.com/easybuilders/easybuild-framework/pull/706">#706</a>, 42970 <a href="https://github.com/easybuilders/easybuild-framework/pull/707">#707</a>)<ul> 42971<li>see 42972 <a href="https://github.com/easybuilders/easybuild/wiki/Using-a-custom-module-naming-scheme">https://github.com/easybuilders/easybuild/wiki/Using-a-custom-module-naming-scheme</a> 42973 for documentation</li> 42974<li>module naming scheme classes that derive from the 'abstract' 42975 <code>ModuleNamingScheme</code> class can be provided to EasyBuild<ul> 42976<li>the Python module providing the class must be available in 42977 the <code>easybuild.tools.module_naming_scheme</code> namespace</li> 42978<li>a function named <code>det_full_module_name</code> must be implemented, 42979 that determines the module name in the form of an string 42980 based on the supplied dictionary(-like) argument</li> 42981</ul> 42982</li> 42983<li>the active module naming scheme is determined by EasyBuild 42984 configuration option <code>--module-naming-scheme</code></li> 42985<li>for now, only the <code>name</code>/<code>version</code>/<code>versionsuffix</code>/<code>toolchain</code> 42986 easyconfig parameters are guaranteed to be provided<ul> 42987<li>consistently providing all easyconfig parameters (i.e., also 42988 for dependencies) requires more work (see 42989 <a href="https://github.com/easybuilders/easybuild-framework/pull/687">#687</a>)</li> 42990</ul> 42991</li> 42992<li>implementing this involved a number of intrusive changes:<ul> 42993<li>the API of the modules.py module needed to be changed, 42994 breaking backward compatibility<ul> 42995<li>the function for which the signatures were modified are 42996 considered to be internal to the framework, so this 42997 should have very minor impact w.r.t. easyblocks not 42998 included with EasyBuild</li> 42999<li>affected functions include: <code>available</code>, <code>exists</code>, 43000 <code>show</code>, <code>modulefile_path</code>, <code>dependencies_for</code></li> 43001</ul> 43002</li> 43003<li>the format for specifying dependencies was extended, to 43004 allow for specifying a custom toolchain<ul> 43005<li>this allows to fix inaccurate dependency specifications, 43006 for example: 43007 <code>('OpenMPI', '1.6.4-GCC-4.7.2')" to "('OpenMPI', '1.6.4', '', ('GCC', '4.7.2'))</code></li> 43008<li>see also 43009 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/431">easyconfigs#431</a></li> 43010</ul> 43011</li> 43012<li>the recommended version for Lmod was bumped to v5.1.5<ul> 43013<li>
43013using earlier 5.x version still works, but may be very 43014 slow when 'available' is used, due to bugs and a 43015 missing feature in Lmod versions prior to v5.1.5 on 43016 which we rely</li> 43017</ul> 43018</li> 43019</ul> 43020</li> 43021</ul> 43022</li> 43023<li>various other enhancements, including:<ul> 43024<li>only (try to) change group id if it is different from what is 43025 wanted 43026 (<a href="https://github.com/easybuilders/easybuild-framework/pull/685">#685</a>)</li> 43027<li>added toy build unit test 43028 (<a href="https://github.com/easybuilders/easybuild-framework/pull/688">#688</a>)</li> 43029<li>support for specifying a list of source paths in EasyBuild 43030 configuration 43031 (<a href="https://github.com/easybuilders/easybuild-framework/pull/690">#690</a>, 43032 <a href="https://github.com/easybuilders/easybuild-framework/pull/702">#702</a>)</li> 43033<li>add function to determine CPU clock speed in <code>systemtools.py</code> 43034 (<a href="https://github.com/easybuilders/easybuild-framework/pull/694">#694</a>, 43035 <a href="https://github.com/easybuilders/easybuild-framework/pull/699">#699</a>)</li> 43036</ul> 43037</li> 43038<li>various bug fixes, including:<ul> 43039<li>avoid importing toolchain modules over and over again to make 43040 toolchain constants available in toolchain module 43041 (<a href="https://github.com/easybuilders/easybuild-framework/pull/679">#679</a>)</li> 43042<li>only change the group id if current gid is different from what 43043 we want in <code>adjust_permissions</code> function 43044 (<a href="https://github.com/easybuilders/easybuild-framework/pull/685">#685</a>)</li> 43045<li>restore original environment after running 'module purge' 43046 (<a href="https://github.com/easybuilders/easybuild-framework/pull/698">#698</a>)<ul> 43047<li>important sidenote: this results in resetting the entire 43048 environment, and has impact on the sanity check step;</li> 43049<li>any environment variables that are set before the 43050 EasyBlock.sanity_check_step method fires, are no longer 43051 there when the sanity check commands are run (cfr. 43052 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/268">easyblocks#268</a>)</li> 43053</ul> 43054</li> 43055</ul> 43056</li> 43057</ul> 43058<p><strong>easyblocks</strong></p> 43059<ul> 43060<li>added <strong>one</strong> new <em>generic</em> easyblock: <code>BinariesTarball</code> 43061 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/255">#255</a>)</li> 43062<li>added support for <strong>5</strong> new software packages that require 43063 customized support:<ul> 43064<li>DB 43065 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/226">#226</a>), 43066 FDTD Solutions 43067 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/239">#239</a>), 43068 FoldX 43069 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/256">#256</a>), 43070 Mathematica 43071 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/240">#240</a>), 43072 MUMPS 43073 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/262">#262</a>)</li> 43074</ul> 43075</li> 43076<li>various enhancements, including:<ul> 43077<li>support optionally running configure in generic <code>MakeCp</code> 43078 easyblock 43079 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/252">#252</a>)</li> 43080<li>enhanced Clang easyblock to support building Clang 3.3 43081 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/248">#248</a>)</li> 43082<li>add support for <code>$INTEL_LICENSE_FILE</code> specifying multiple paths 43083 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/251">#251</a>)</li> 43084<li>enhanced ATLAS easyblock to support building ATLAS 3.10.1 43085 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/258">#258</a>)</li> 43086</ul> 43087</li> 43088<li>various bug fixes:<ul> 43089<li>add zlib lib dir in link path dirs for WPS 43090 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/249">#249</a>)</li> 43091<li>stop using deprecated <code>add_module</code> function in imkl easyblock 43092 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/250">#250</a>)</li> 43093<li>fixed PSI easyblock w.r.t. support for building plugins 43094 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/254">#254</a>, 43095 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/269">#269</a>)</li> 43096<li>move OS check for Clang to <code>check_readiness_step</code>, to allow a 43097 build job to be submitted from SL5 43098 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/263">#263</a>, 43099 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/264">#264</a>)</li> 43100<li>enable verbose build for DOLFIN, to allow for proper debugging
43101 if the build fails 43102 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/265">#265</a>)</li> 43103<li>make sure <code>$LDFLAGS</code> and <code>$INSTANT_*_DIR</code> env vars are set for 43104 DOLFIN sanity check commands 43105 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/268">#268</a>)<ul> 43106<li>this is required after resetting the environment after 43107 running module purge (see framework release notes)</li> 43108</ul> 43109</li> 43110<li>don't try to load module in LAPACK test-only build 43111 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/264">#264</a>, 43112 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/266">#266</a>)</li> 43113</ul> 43114</li> 43115</ul> 43116<p><strong>easyconfigs</strong></p> 43117<ul> 43118<li>added example easyconfig files for <strong>9</strong> new software packages:<ul> 43119<li>BOINC 43120 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/436">#436</a>), 43121 DB 43122 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/343">#343</a>, 43123 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/449">#449</a>), 43124 fastahack 43125 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/374">#374</a>), 43126 FDTD Solutions 43127 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/387">#387</a>), 43128 FoldX 43129 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/440">#440</a>, 43130 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/442">#442</a>), 43131 Mathematica 43132 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/394">#394</a>), 43133 Mesquite 43134 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/447">#447</a>), 43135 MUMPS 43136 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/447">#447</a>), 43137 ParMGridGen 43138 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/447">#447</a>)</li> 43139</ul> 43140</li> 43141<li>added additional easyconfigs for goalf, gompi, ClangGCC, cgmvapich2, 43142 cgmvolf toolchains 43143 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/350">#350</a>, 43144 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/441">#441</a>)</li> 43145<li>added additional easyconfigs for various software packages:<ul> 43146<li>ATLAS, Bison, bzip2, Clang, CMake, cURL, EasyBuild, expat, FFTW, 43147 GDB, gettext, git, HPL, LAPACK, libreadline, M4, METIS, 43148 MVAPICH2, Mercurial, ncurses, OpenBLAS, OpenMPI, ParMETIS, 43149 Python, ScaLAPACK, SCOTCH, Valgrind, zlib</li> 43150</ul> 43151</li> 43152<li>various 'bug' fixes, including:<ul> 43153<li>fix source URL for lockfile in Python easyconfigs 43154 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/428">#428</a>)</li> 43155<li>correct dependency specifications w.r.t. versionsuffix and 43156 toolchain 43157 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/431">#431</a>)<ul> 43158<li>this is required to support building the affected 43159 easyconfigs with a custom module naming scheme</li> 43160</ul> 43161</li> 43162<li>correct PSI patch file to avoid errors w.r.t. memcpy not being 43163 in scope 43164 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/446">#446</a>)</li> 43165<li>fix gettext build with adding <code>--without-emacs</code> configure 43166 options, add gettext as dependency for a2ps 43167 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/448">#448</a>)</li> 43168<li>exclude EMACS support in a2ps because of build failures 43169 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/452">#452</a>)</li> 43170</ul> 43171</li> 43172</ul> 43173<h2 id="easybuild-v170-september-2nd-2013">EasyBuild v1.7.0 (September 2nd 2013)<a class="headerlink" href="#easybuild-v170-september-2nd-2013" title="Permanent link">¶</a></h2> 43174<p>feature + bugfix release</p> 43175<p><strong>framework</strong></p> 43176<ul> 43177<li>various enhancements, including:<ul> 43178<li>also search for patch files in directory where easyconfig file 43179 is located 43180 (<a href="https://github.com/easybuilders/easybuild-framework/pull/667">#667</a>)</li> 43181<li>reduce false positives in reporting of possible errors messages 43182 (<a href="https://github.com/easybuilders/easybuild-framework/pull/669">#669</a>)</li> 43183<li>make module update <code>$ACLOCAL</code> if a share/aclocal subdir is found 43184 (<a href="https://github.com/easybuilders/easybuild-framework/pull/670">#670</a>)</li> 43185<li>
43185add <code>unwanted_env_vars</code> easyconfig parameter to list environment 43186 variables to unset during install procedure 43187 (<a href="https://github.com/easybuilders/easybuild-framework/pull/673">#673</a>)</li> 43188<li>add support for updating list easyconfig values (next to string 43189 values) 43190 (<a href="https://github.com/easybuilders/easybuild-framework/pull/676">#676</a>)</li> 43191<li>add <code>--dry-run</code> command line option which prints installation 43192 overview for specified easyconfig files 43193 (<a href="https://github.com/easybuilders/easybuild-framework/pull/677">#677</a>)</li> 43194</ul> 43195</li> 43196<li>various bug fixes, including:<ul> 43197<li>ensure that all extensions are listed in <code>$EBEXTSLISTX</code> set by 43198 module, also when using <code>--skip</code> 43199 (<a href="https://github.com/easybuilders/easybuild-framework/pull/671">#671</a>)</li> 43200<li>report reason for failed sanity check for extensions 43201 (<a href="https://github.com/easybuilders/easybuild-framework/pull/672">#672</a>, 43202 <a href="https://github.com/easybuilders/easybuild-framework/pull/678">#678</a>)</li> 43203<li>fix <code>--list-toolchains</code> command line option 43204 (<a href="https://github.com/easybuilders/easybuild-framework/pull/675">#675</a>)</li> 43205</ul> 43206</li> 43207</ul> 43208<p><strong>easyblocks</strong></p> 43209<ul> 43210<li>added support for <strong>3</strong> new software packages that require 43211 customized support:<ul> 43212<li>Libint2 43213 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/236">#236</a>), 43214 Qt 43215 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/210">#210</a>), 43216 Rosetta 43217 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/218">#218</a>)</li> 43218</ul> 43219</li> 43220<li>various enhancements, including:<ul> 43221<li>allow building OpenFOAM without 3rd party tools 43222 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/230">#230</a>)</li> 43223<li>also add sitelib path to <code>$PERL5LIB</code>, refactor code to add 43224 generic <code>get_site_suffix</code> function 43225 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/232">#232</a>, 43226 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/233">#233</a>)</li> 43227<li>support building imkl FFT wrappers using MVAPICH2 MPI library 43228 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/234">#234</a>)</li> 43229<li>remove libnpp from CUDA sanity check to support installing CUDA 43230 v5.5 43231 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/238">#238</a>)</li> 43232<li>pick up <code>$INTEL_LICENSE_FILE</code> for Intel tools, if it is set 43233 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/243">#243</a>)<ul> 43234<li>note: gets preference over <code>license_file</code> easyconfig 43235 parameter</li> 43236</ul> 43237</li> 43238</ul> 43239</li> 43240<li>various bug fixes:<ul> 43241<li>call WRF build script with '<code>tcsh <script></code> to ensure that tcsh 43242 available in <code>$PATH</code> is used 43243 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/231">#231</a>)</li> 43244<li>make sure some environment variables that may disrupt the GCC 43245 install procedure are unset 43246 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/237">#237</a>)<ul> 43247<li>e.g., <code>$CPATH</code>, <code>$C_INCLUDE_PATH</code>, <code>$CPLUS_INCLUDE_PATH</code>, 43248 <code>$OBJC_INCLUDE_PATH</code>, <code>$LIBRARY_PATH</code></li> 43249</ul> 43250</li> 43251<li>code cleanup in GEANT4 easyblock: use <code>self.version</code> (instead of 43252 <code>self.get_installversion()</code>) 43253 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/242">#242</a>)</li> 43254<li>enhance list of <code>noqanda</code> patterns for CUDA, to get less failing 43255 installations 43256 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/244">#244</a>)</li> 43257</ul> 43258</li> 43259</ul> 43260<p><strong>easyconfigs</strong></p> 43261<ul> 43262<li>added example easyconfig files for <strong>15</strong> new software packages:<ul> 43263<li>Glib 43264 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/294">#294</a>, 43265 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/400">#400</a>), 43266 GLPK 43267 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/400">#400</a>), 43268 horton 43269 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/413">#413</a>), 43270 libint2 43271 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/413">#413</a>), 43272 molmod 43273 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/413">#413</a>), 43274 Rosetta 43275 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/336">#336</a>), 43276 SCons 43277 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/336">#336</a>), 43278 Stacks 43279 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/367">#367</a>, 43280 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/377">#377</a>), 43281 sympy 43282 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/413">#413</a>), 43283 Qt 43284 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/294">#294</a>), 43285 XML-LibXML 43286 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/397">#397</a>), 43287 XML-Simple 43288 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/397">#397</a>), 43289 yaff 43290 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/413">#413</a>), 43291 YAML-Syck 43292 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/380">#380</a>), 43293 zsh 43294 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/376">#376</a>)</li> 43295</ul> 43296</li> 43297<li>
43297added additional easyconfigs for various software packages:<ul> 43298<li>BLAST, BamTools, BioPerl, Bison, Boost, bzip2, CMake, Cython, 43299 CUDA, FFTW, FIAT, GCC, GMP, gettext, git, h5py, HDF5, libffi, 43300 libreadline, libxc, matplotlib, METIS, ncurses, Oases, Python, 43301 RAxML, ScientificPython, Szip, tcsh, imkl, MVAPICH2, TotalView, 43302 VTune, WRF, zlib</li> 43303</ul> 43304</li> 43305<li>added toolchain easyconfig files for HPCBIOS policies 43306 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/402">#402</a>, 43307 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/407">#407</a>)<ul> 43308<li>HPCBIOS_BioInfo, HPCBIOS_Debuggers, HPCBIOS_LifeSciences, 43309 HPCBIOS_Math, HPCBIOS_Profilers</li> 43310</ul> 43311</li> 43312<li>various enhancements, including:<ul> 43313<li>added more XML Perl modules to non-bare Perl easyconfigs 43314 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/375">#375</a>)</li> 43315</ul> 43316</li> 43317<li>various 'bug' fixes, including:<ul> 43318<li>fix website/description in scipy easyconfigs 43319 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/399">#399</a>)</li> 43320<li>specify OpenMPI libibverbs-dev(el) OS dependency in an 43321 OS-dependent way 43322 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/403">#403</a>)</li> 43323<li>add patch file for M4 to fix building on systems with recent 43324 glibc (>=2.16) 43325 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/406">#406</a>)</li> 43326<li>align moduleclass in R easyconfigs 43327 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/411">#411</a>)</li> 43328<li>fixed filename of Biopython/CD-HIT easyconfig files 43329 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/407">#407</a>)</li> 43330<li>disable parallel building of otcl 43331 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/419">#419</a>)</li> 43332</ul> 43333</li> 43334</ul> 43335<h2 id="easybuild-v160-july-11th-2013">EasyBuild v1.6.0 (July 11th 2013)<a class="headerlink" href="#easybuild-v160-july-11th-2013" title="Permanent link">¶</a></h2> 43336<p>feature + bugfix release</p> 43337<p><strong>framework</strong></p> 43338<ul> 43339<li>added support for using Lmod as module tool 43340 (<a href="https://github.com/easybuilders/easybuild-framework/pull/645">#645</a>)</li> 43341<li>various other enhancements, including:<ul> 43342<li>allow prepending to/appending to/overwriting list easyconfig 43343 parameters using <code>--try-amend-X</code> 43344 (<a href="https://github.com/easybuilders/easybuild-framework/pull/658">#658</a>, 43345 <a href="https://github.com/easybuilders/easybuild-framework/pull/664">#664</a>)</li> 43346</ul> 43347</li> 43348<li>various bug fixes, including:<ul> 43349<li>add salt to temporary log file name 43350 (<a href="https://github.com/easybuilders/easybuild-framework/pull/656">#656</a>, 43351 <a href="https://github.com/easybuilders/easybuild-framework/pull/665">#665</a>)</li> 43352<li>fix determining CPU architecture on Raspberry Pi (ARM) systems 43353 (<a href="https://github.com/easybuilders/easybuild-framework/pull/655">#655</a>, 43354 <a href="https://github.com/easybuilders/easybuild-framework/pull/662">#662</a>)</li> 43355<li>fix support for determining base path of tarballs containing a 43356 single file 43357 (<a href="https://github.com/easybuilders/easybuild-framework/pull/660">#660</a>)</li> 43358</ul> 43359</li> 43360</ul> 43361<p><strong>easyblocks</strong></p> 43362<ul> 43363<li>added support for <strong>2</strong> new software packages that require 43364 customized support:<ul> 43365<li>BamTools 43366 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/224">#224</a>), 43367 BLAT 43368 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/214">#214</a>)</li> 43369</ul> 43370</li> 43371<li>various enhancements, including:<ul> 43372<li>update impi easyblock to allow installing impi v4.1.1, which 43373 features a slight change in build procedure 43374 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/217">#217</a>)</li> 43375<li>enhance <code>PackedBinary</code> easyblock to copy both files and 43376 directories 43377 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/212">#212</a>)</li> 43378<li>
43378added get <code>sitearch_suffix</code> to Perl search path and use it in 43379 <code>PerlModule</code> easyblock 43380 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/209">#209</a>)</li> 43381</ul> 43382</li> 43383<li>various bug fixes:<ul> 43384<li>make sure EasyBuild configuration is initialized when running 43385 unit tests 43386 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/220">#220</a>)</li> 43387<li>make Boost easyblock pick up configopts easyconfig parameter 43388 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/221">#221</a>)</li> 43389<li>add <code>-DMPICH_IGNORE_CXX_SEEK</code> compiler flag for Mothur when MPI 43390 support is enabled 43391 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/222">#222</a>)</li> 43392<li>fix Boost sanity check, only check for <code>libboost_python.so</code> if 43393 Python module is loaded 43394 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/223">#223</a>)</li> 43395<li>enhance Trinity support w.r.t. jellyfish 43396 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/225">#225</a>, 43397 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/227">#227</a>)</li> 43398<li>fix checking for <code>beagle-lib</code> dep (deprecate checking for 43399 BEAGLE) for MrBayes 43400 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/228">#228</a>)</li> 43401</ul> 43402</li> 43403</ul> 43404<p><strong>easyconfigs</strong></p> 43405<ul> 43406<li>added example easyconfig files for <strong>26</strong> new software packages:<ul> 43407<li>ALLPATHS-LG 43408 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/359">#359</a>), 43409 AutoMake 43410 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>), 43411 BamTools 43412 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/319">#319</a>, 43413 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/338">#338</a>), 43414 BLAT 43415 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/340">#340</a>), 43416 Biopython 43417 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/356">#356</a>), 43418 cairo 43419 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>), 43420 CCfits 43421 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/327">#327</a>), 43422 CD-HIT 43423 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/344">#344</a>), 43424 CFITSIO 43425 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/327">#327</a>), 43426 Diffutils 43427 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>), 43428 FASTA 43429 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/358">#358</a>, 43430 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>), 43431 findutils 43432 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>), 43433 fontconfig 43434 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>), 43435 gawk 43436 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>), 43437 gettext 43438 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>), 43439 GLIMMER 43440 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/357">#357</a>, 43441 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>), 43442 libidn 43443 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>), 43444 LibTIFF 43445 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>), 43446 libungif 43447 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>), 43448 make 43449 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/355">#355</a>), 43450 MUSCLE 43451 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/339">#339</a>), 43452 Oases 43453 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/354">#354</a>), 43454 pixman 43455 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>), 43456 PLINK 43457 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/352">#352</a>), 43458 RCS 43459 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>), 43460 SQLite 43461 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>)</li> 43462</ul> 43463</li> 43464<li>
43464added additional easyconfigs for various software packages:<ul> 43465<li>ant, Bash, Bison, bzip2, cURL, expat, GCC, EasyBuild, freetype, 43466 FFTW, GDB, git, HMMER, JUnit, libreadline, libpng, libtool, 43467 libxml2, libxslt, M4, makedepend, Mothur, MVAPICH2, Mercurial, 43468 ncurses, OpenBLAS, Python, ScaLAPACK, Tcl, tcsh, TopHat, 43469 Trinity, Valgrind, Velvet, VTune, zlib (see 43470 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/169">#169</a>, 43471 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/297">#297</a>, 43472 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/298">#298</a>, 43473 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/301">#301</a>, 43474 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/309">#309</a>, 43475 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/323">#323</a>, 43476 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/331">#331</a>, 43477 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/332">#332</a>, 43478 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/341">#341</a>, 43479 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/347">#347</a>, 43480 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/349">#349</a>, 43481 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/351">#351</a>, 43482 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/355">#355</a>, 43483 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>)</li> 43484</ul> 43485</li> 43486<li>various enhancements, including:<ul> 43487<li>added easyconfigs for <code>ictce/5.4.0</code>, <code>ictce/5.5.0</code> and 43488 <code>gmvolf/1.7.12</code> toolchain modules 43489 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/297">#297</a>, 43490 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/332">#332</a>, 43491 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/349">#349</a>)</li> 43492<li>added a template sanity_check_paths as 'MUST' in TEMPLATE.eb 43493 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/329">#329</a>)</li> 43494<li>introduced biodeps 'toolchain' to ease keeping common 43495 dependencies for bio* software in sync 43496 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/309">#309</a>)</li> 43497<li>added collection of easyconfigs for ictce/5.3.0 43498 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/309">#309</a>, 43499 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/323">#323</a>)<ul> 43500<li>bam2fastq, bbFTP, BLAST, Boost, DL_POLY Classic, EMBOSS, 43501 FFTW, libharu, libxml2, libxslt, libyaml, lxml, Mercurial, 43502 Mothur, mpi4py, ncurses, ns, orthomcl, otcl, PAML, Perl, 43503 PyYAML, pandas, problog, scikit-learn, TiCCutils, TiMBL, 43504 TinySVM, TopHat, tclcl, YamCha</li> 43505</ul> 43506</li> 43507<li>added missing dependencies for various software packages 43508 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/323">#323</a>, 43509 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/328">#328</a>, 43510 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/348">#348</a>, 43511 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>)</li> 43512<li>style fixes in various easyconfigs 43513 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/309">#309</a>, 43514 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/323">#323</a>, 43515 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/345">#345</a>, 43516 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/349">#349</a>, 43517 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/355">#355</a>, 43518 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/361">#361</a>)</li> 43519</ul> 43520</li> 43521<li>various 'bug' fixes, including:<ul> 43522<li>added <code>pic</code> toolchain option for Perl goolf easyconfig 43523 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/299">#299</a>)</li> 43524<li>fixed source URLs for R (use correct template 43525 <code>%(version_major)s</code>) 43526 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/302">
43526#302</a>)</li> 43527<li>synced libreadline easyconfigs w.r.t. ncurses dependency 43528 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/303">#303</a>)</li> 43529<li>make sure EasyBuild configuration is initialized when running 43530 unit tests 43531 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/334">#334</a>)</li> 43532<li>specify <code>lowopt</code> (-O1) optimization level for OpenIFS, to avoid 43533 floating-point related issues 43534 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/328">#328</a>)</li> 43535<li>fix naming of 'beagle-lib' (used to be 'BEAGLE'), to avoid 43536 name clashes with other software package(s) 43537 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/346">#346</a>)</li> 43538</ul> 43539</li> 43540</ul> 43541<h2 id="easybuild-v150-june-1st-2013">EasyBuild v1.5.0 (June 1st 2013)<a class="headerlink" href="#easybuild-v150-june-1st-2013" title="Permanent link">¶</a></h2> 43542<p>feature + bugfix release</p> 43543<p><strong>framework</strong></p> 43544<ul> 43545<li>various enhancements, including:<ul> 43546<li>define <code>SHLIB_EXT</code> constant for shared library extension (<code>.so</code>, 43547 <code>.dylib</code>), deprecate <code>shared_lib_ext</code> global var 43548 (<a href="https://github.com/easybuilders/easybuild-framework/pull/630">#630</a>)</li> 43549<li>enhance support for sanity checking extensions 43550 (<a href="https://github.com/easybuilders/easybuild-framework/pull/632">#632</a>, 43551 <a href="https://github.com/easybuilders/easybuild-framework/pull/649">#649</a>)</li> 43552<li>add support for <code>modextrapaths</code> easyconfig parameter 43553 (<a href="https://github.com/easybuilders/easybuild-framework/pull/634">#634</a>, 43554 <a href="https://github.com/easybuilders/easybuild-framework/pull/637">#637</a>)</li> 43555<li>allow <code>source_urls</code> to be templated for extensions 43556 (<a href="https://github.com/easybuilders/easybuild-framework/pull/639">#639</a>, 43557 <a href="https://github.com/easybuilders/easybuild-framework/pull/646">#646</a>, 43558 <a href="https://github.com/easybuilders/easybuild-framework/pull/647">#647</a>)</li> 43559<li>set <code>OMPI_*</code> environment variables for OpenMPI 43560 (<a href="https://github.com/easybuilders/easybuild-framework/pull/640">#640</a>)</li> 43561<li>make BLACS optional as toolchain element, depending on ScaLAPACK 43562 version 43563 (<a href="https://github.com/easybuilders/easybuild-framework/pull/638">#638</a>)</li> 43564</ul> 43565</li> 43566<li>various bug fixes, including:<ul> 43567<li>fixed <code>--list-toolchains</code>, avoid listing toolchains multiple 43568 times 43569 (<a href="https://github.com/easybuilders/easybuild-framework/pull/628">#628</a>)</li> 43570<li>fix templating dictionary after parsing easyconfig file 43571 (<a href="https://github.com/easybuilders/easybuild-framework/pull/633">#633</a>)</li> 43572<li>fix support for ACML as compiler toolchain element 43573 (<a href="https://github.com/easybuilders/easybuild-framework/pull/632">#632</a>)</li> 43574<li>make unit tests clean up after themselves more thoroughly 43575 (<a href="https://github.com/easybuilders/easybuild-framework/pull/641">#641</a>, 43576 <a href="https://github.com/easybuilders/easybuild-framework/pull/642">#642</a>, 43577 <a href="https://github.com/easybuilders/easybuild-framework/pull/643">#643</a>)</li> 43578</ul> 43579</li> 43580</ul> 43581<p><strong>easyblocks</strong></p> 43582<ul> 43583<li>added <strong>one</strong> new <em>generic</em> easyblock: <code>MakeCp</code> 43584 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/208">#208</a>)</li> 43585<li>added support for <strong>5</strong> new software packages that require 43586 customized support:<ul> 43587<li>CBLAS 43588 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/192">#192</a>), 43589 FreeSurfer 43590 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/194">#194</a>), 43591 Mothur 43592 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/206">#206</a>), 43593 OpenIFS 43594 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/200">#200</a>), 43595 PSI 43596 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/191">#191</a>)</li> 43597</ul> 43598</li> 43599<li>various enhancements, including:<ul> 43600<li>add support for building ScaLAPACK 2.x on top of QLogic MPI 43601 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/195">#195</a>)</li> 43602<li>support newer BWA versions 43603 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/199">
43603#199</a>)</li> 43604<li>explicitly list license server type in ABAQUS install options, 43605 required for correct installation of v6.12 43606 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/198">#198</a>)</li> 43607<li>update SCOTCH and OpenFOAM easyblock for recent versions 43608 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/201">#201</a>)</li> 43609</ul> 43610</li> 43611<li>various bug fixes:<ul> 43612<li>fix numpy easyblock to get an optimal build (w.r.t. <code>numpy.dot</code> 43613 performance) 43614 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/192">#192</a>)</li> 43615<li>correct build procedure for MUMmer to yield a complete 43616 installation 43617 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/196">#196</a>, 43618 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/197">#197</a>)</li> 43619<li>make unit tests clean up after themselves more thoroughly 43620 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/203">#203</a>, 43621 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/204">#204</a>)</li> 43622<li>fix getting Perl version for extensions 43623 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/205">#205</a>)</li> 43624</ul> 43625</li> 43626</ul> 43627<p><strong>easyconfigs</strong></p> 43628<ul> 43629<li>added example easyconfig files for <strong>23</strong> new software packages:<ul> 43630<li>bam2fastq 43631 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/287">#287</a>), 43632 CBLAS 43633 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/263">#263</a>), 43634 EMBOSS 43635 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/265">#265</a>, 43636 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/290">#290</a>), 43637 FCM 43638 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/272">#272</a>), 43639 FRC_align 43640 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/273">#273</a>), 43641 freeglut 43642 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/271">#271</a>), 43643 FreeSurfer 43644 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/271">#271</a>), 43645 FSL 43646 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/271">#271</a>), 43647 GATK 43648 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/287">#287</a>), 43649 libharu 43650 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/290">#290</a>), 43651 libxslt 43652 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43653 MariaDB 43654 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/292">#292</a>), 43655 Mothur 43656 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/265">#265</a>) 43657 mpi4py 43658 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/276">#276</a>), 43659 OpenIFS 43660 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/272">#272</a>), 43661 orthomcl 43662 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/265">#265</a>), 43663 PAML 43664 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/287">#287</a>), 43665 pandas 43666 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/262">#262</a>), 43667 phonopy 43668 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43669 problog 43670 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/277">#277</a>), 43671 PSI 43672 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/258">#258</a>), 43673 PyYAML 43674 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43675 RAxML 43676 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/277">#277</a>)</li> 43677</ul> 43678</li> 43679<li>added additional example easyconfig files for:<ul> 43680<li>ABINIT 43681 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43682 ACML 43683 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43684 BLAST 43685 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/275">#275</a>), 43686 Boost 43687 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/273">#273</a>), 43688 BWA 43689 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/270">#270</a>), 43690 bzip2 43691 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/263">#263</a>), 43692 Chapel 43693 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/240">#240</a>), 43694 CMake 43695 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/290">#290</a>), 43696 FFTW2 43697 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/247">#247</a>, 43698 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43699 flex 43700 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43701 freetype 43702 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43703 grib_api 43704 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/272">#272</a>), 43705 gzip 43706 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/265">#265</a>), 43707 Java 43708 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/279">#279</a>), 43709 libpng 43710 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/240">#240</a>, 43711 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/279">#279</a>), 43712 libreadline 43713 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43714 libxml2 43715 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43716 libxml 43717 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43718 matplotlib 43719 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/235">#235</a>), 43720 MCL 43721 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/265">#265</a>), 43722 MUMmer 43723 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/265">#265</a>), 43724 ncurses 43725 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43726 numpy 43727 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43728 OpenFOAM 43729 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43730 Perl 43731 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/265">#265</a>), 43732 Python 43733 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/276">#276</a>, 43734 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/263">#263</a>), 43735 R 43736 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/240">#240</a>, 43737 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/279">#279</a>), 43738 SCOTCH 43739 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43740 ScaLAPACK 43741 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>), 43742 TopHat 43743 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/289">#289</a>), 43744 Valgrind 43745 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/255">#255</a>), 43746 zlib 43747 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/267">#267</a>)</li> 43748</ul> 43749</li> 43750<li>various enhancements, including:<ul> 43751<li>enhance unit test suite, include testing for module conflicts 43752 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/256">#256</a>)
43753 and presence of patch files 43754 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/264">#264</a>)</li> 43755<li>use provided constants and templates in easyconfig files where 43756 appropriate 43757 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/248">#248</a>, 43758 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/266">#266</a>, 43759 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/281">#281</a>)</li> 43760</ul> 43761</li> 43762<li>various 'bug' fixes, including:<ul> 43763<li>get rid of hardcoded license_file paths for VTune, Inspector 43764 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/253">#253</a>)</li> 43765<li>assign proper moduleclass where they were missing 43766 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/278">#278</a>)</li> 43767<li>fix naming for LZO 43768 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/280">#280</a>)</li> 43769<li>make unit tests clean up after themselves more thoroughly 43770 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/283">#283</a>, 43771 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/284">#284</a>, 43772 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/285">#285</a>, 43773 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/286">#286</a>)</li> 43774<li>fix TopHat dependencies 43775 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/289">#289</a>)</li> 43776<li>fix source URLs for XML 43777 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/279">#279</a>)</li> 43778<li>fix versions for all listed R extensions 43779 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/279">#279</a>)</li> 43780<li>fix CUDA easyconfig file for use on Debian Squeeze 43781 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/291">#291</a>)</li> 43782<li>correct easyconfig filename and module name mismatches (bbcp, 43783 DL_POLY Classic, ...) 43784 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/295">#295</a>)</li> 43785</ul> 43786</li> 43787</ul> 43788<h2 id="easybuild-v140-may-2nd-2013">EasyBuild v1.4.0 (May 2nd 2013)<a class="headerlink" href="#easybuild-v140-may-2nd-2013" title="Permanent link">¶</a></h2> 43789<p>feature + bugfix release</p> 43790<p><strong>framework</strong></p> 43791<ul> 43792<li>the unit tests for easybuild-framework were moved to test/framework, 43793 to make things consistent with easybuild-easyblocks and 43794 easybuild-easyconfigs 43795 (<a href="https://github.com/easybuilders/easybuild-framework/pull/611">#611</a>, 43796 <a href="https://github.com/easybuilders/easybuild-framework/pull/613">#613</a>, 43797 <a href="https://github.com/easybuilders/easybuild-framework/pull/624">#624</a>)<ul> 43798<li>running the framework unit tests should now be using 43799 <code>python -m test.framework.suite</code></li> 43800</ul> 43801</li> 43802<li>various other enhancements, including:<ul> 43803<li>extend unit test suite 43804 (<a href="https://github.com/easybuilders/easybuild-framework/pull/593">#593</a>, 43805 <a href="https://github.com/easybuilders/easybuild-framework/pull/599">#599</a>, 43806 <a href="https://github.com/easybuilders/easybuild-framework/pull/603">#603</a>, 43807 <a href="https://github.com/easybuilders/easybuild-framework/pull/618">#618</a>, 43808 <a href="https://github.com/easybuilders/easybuild-framework/pull/620">#620</a>, 43809 <a href="https://github.com/easybuilders/easybuild-framework/pull/622">#622</a>, 43810 <a href="https://github.com/easybuilders/easybuild-framework/pull/624">#624</a>, 43811 ...)</li> 43812<li>extended list of constants and templates that can be used in 43813 easyconfig files 43814 (<a href="https://github.com/easybuilders/easybuild-framework/pull/566">#566</a>)</li> 43815<li>add support for additional compiler toolchains<ul> 43816<li>CUDA-enabled toolchain: <code>goolfc</code> 43817 (<a href="https://github.com/easybuilders/easybuild-framework/pull/603">#603</a>, 43818 <a href="https://github.com/easybuilders/easybuild-framework/pull/624">#624</a>)</li> 43819<li>Clang(+GCC)-based toolchains: <code>cgoolf</code>, <code>cgmpolf</code>, <code>cgmvolf</code> 43820 (<a href="https://github.com/easybuilders/easybuild-framework/pull/593">#593</a>, 43821 <a href="https://github.com/easybuilders/easybuild-framework/pull/598">#598</a>, 43822 <a href="https://github.com/easybuilders/easybuild-framework/pull/600">#600</a>)</li> 43823<li>
43823gmvolf (GCC+MVAPICH2+...) 43824 (<a href="https://github.com/easybuilders/easybuild-framework/pull/585">#585</a>)</li> 43825</ul> 43826</li> 43827<li>properly decode easyblock to module name using <code>decode_*</code> 43828 functions 43829 (<a href="https://github.com/easybuilders/easybuild-framework/pull/618">#618</a>)</li> 43830</ul> 43831</li> 43832<li>various bug fixes, including:<ul> 43833<li>fixed default value for <code>--stop</code> 43834 (<a href="https://github.com/easybuilders/easybuild-framework/pull/601">#601</a>)</li> 43835<li>remove useless <code>sleep()</code> calls in <code>run_cmd</code>, <code>run_cmd_qa</code> 43836 (<a href="https://github.com/easybuilders/easybuild-framework/pull/599">#599</a>)</li> 43837<li>determine module path based on class name, not software name 43838 (<a href="https://github.com/easybuilders/easybuild-framework/pull/606">#606</a>)</li> 43839<li>remove unwanted characters in build dirs 43840 (<a href="https://github.com/easybuilders/easybuild-framework/pull/591">#591</a>, 43841 <a href="https://github.com/easybuilders/easybuild-framework/pull/607">#607</a>)</li> 43842<li>ignore some error codes spit out by modulecmd that are actually 43843 warnings 43844 (<a href="https://github.com/easybuilders/easybuild-framework/pull/609">#609</a>)</li> 43845<li>fix <code>agithub.py</code> w.r.t. changes in GitHub API (user-agent string 43846 is now obligatory for non-authenticated connections) 43847 (<a href="https://github.com/easybuilders/easybuild-framework/pull/617">#617</a>)</li> 43848<li>fix typo breaking the <code>adjust_cmd</code> decorator on SuSE 43849 (<a href="https://github.com/easybuilders/easybuild-framework/pull/615">#615</a>)</li> 43850<li>fix prepending paths with absolute paths in module file 43851 (<a href="https://github.com/easybuilders/easybuild-framework/pull/621">#621</a>)</li> 43852<li>clean up open file handles properly 43853 (<a href="https://github.com/easybuilders/easybuild-framework/pull/620">#620</a>, 43854 <a href="https://github.com/easybuilders/easybuild-framework/pull/624">#624</a>)</li> 43855<li>fix <code>--search</code> help and implementation 43856 (<a href="https://github.com/easybuilders/easybuild-framework/pull/622">#622</a>)</li> 43857</ul> 43858</li> 43859</ul> 43860<p><strong>easyblocks</strong></p> 43861<ul> 43862<li>added a unit test suite for easyblocks 43863 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/175">#175</a>, 43864 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/177">#177</a>, 43865 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/178">#178</a>)<ul> 43866<li>every easyblock is parsed and instantiated as a sanity check</li> 43867</ul> 43868</li> 43869<li>added <strong>one</strong> new <em>generic</em> easyblock: <code>PerlModule</code> 43870 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/183">#183</a>)</li> 43871<li>added support for <strong>8</strong> new software packages that require 43872 customized support:<ul> 43873<li>ABAQUS 43874 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/179">#179</a>), 43875 Bowtie 43876 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/174">#174</a>, 43877 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/185">#185</a>, 43878 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/186">#186</a>), 43879 Clang 43880 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/151">#151</a>), 43881 DL_POLY Classic 43882 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/118">#118</a>), 43883 ESMF 43884 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/171">#171</a>), 43885 Perl 43886 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/183">#183</a>), 43887 Intel VTune and Intel Inspector 43888 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/180">#180</a>)</li> 43889</ul> 43890</li> 43891<li>the <code>CMakeMake.configure_step</code> parameter <code>builddir</code> was renamed to 43892 <code>srcdir</code>, because the name <code>builddir</code> is incorrect 43893 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/151">#151</a>)<ul> 43894<li><code>builddir</code> will remain supported for legacy purposes up until 43895 v2.0</li> 43896</ul> 43897</li> 43898<li>various enhancements, including:<ul> 43899<li>reverted back to hardcoding Python library path, since it's 43900 hardcoded by setuptools too 43901 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/184">#184</a>)</li> 43902<li>
43902added MPICH support in ScaLAPACK easyblock 43903 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/172">#172</a>)</li> 43904<li>enhanced NCL easyblock: add support UDUNITS and ESMF 43905 dependencies 43906 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/171">#171</a>)</li> 43907<li>enhanced MATLAB easyblock: avoid hardcoding Java options, make 43908 sure <code>$DISPLAY</code> is unset, extend list of sanity check paths 43909 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/181">#181</a>)</li> 43910<li>enhanced TotalView easyblock: add support for license file 43911 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/146">#146</a>)</li> 43912</ul> 43913</li> 43914</ul> 43915<p><strong>easyconfigs</strong></p> 43916<ul> 43917<li>added a unit test suite for easyconfigs 43918 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/228">#228</a>, 43919 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/230">#230</a>)</li> 43920<li>added example easyconfig files for <strong>20</strong> new software packages:<ul> 43921<li>ABAQUS 43922 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/231">#231</a>), 43923 BioPerl 43924 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/242">#242</a>), 43925 Bowtie 43926 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/227">#227</a>), 43927 Clang 43928 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/177">#177</a>), 43929 CRF++ 43930 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/131">#131</a>), 43931 DL_POLY Classic 43932 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/132">#132</a>), 43933 ESMF, GROMACS 43934 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/165">#165</a>), 43935 HH-suite 43936 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/219">#219</a>), 43937 Inspector 43938 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/232">#232</a>), 43939 likwid 43940 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/131">#131</a>), 43941 Perl 43942 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/242">#242</a>), 43943 scikit 43944 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/133">#133</a>), 43945 TiCCutils 43946 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/131">#131</a>), 43947 TiMBL 43948 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/131">#131</a>), 43949 TinySVM 43950 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/131">#131</a>), 43951 UDUNITS 43952 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/167">
43952#167</a>), 43953 VTune 43954 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/232">#232</a>), 43955 YamCha 43956 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/131">#131</a>)</li> 43957</ul> 43958</li> 43959<li>add example easyconfigs for new compiler toolchains (use 43960 <code>eb --list-toolchains</code> for a full list of supported toolchains):<ul> 43961<li>the newly added toolchains only differ in compilers/MPI library, 43962 and all feature OpenBLAS, LAPACK, ScaLAPACK and FFTW</li> 43963<li><em>goolfc</em>: GCC, CUDA (co-compiler), OpenMPI 43964 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/191">#191</a>)<ul> 43965<li>a goolfc easyconfig for GROMACS is included as 43966 proof-of-concept 43967 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/165">#165</a>)</li> 43968</ul> 43969</li> 43970<li><em>cgmpolf</em>: Clang (C/C++ compilers), GCC (Fortran compilers), 43971 MPICH 43972 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/213">#213</a>)</li> 43973<li><em>cgmvolf</em>: Clang, GCC, MVAPICH2 43974 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/218">#218</a>)</li> 43975<li><em>cgoolf</em>: Clang, GCC, OpenMPI 43976 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/213">#213</a>)</li> 43977<li><em>gmvolf</em>: GCC, MVAPICH 43978 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/202">#202</a>, 43979 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/222">#222</a>)</li> 43980</ul> 43981</li> 43982<li>ported already available easyconfigs to new compiler toolchains:<ul> 43983<li><em>ictce-5.3.0</em>: 193 easyconfigs 43984 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/229">#229</a>)</li> 43985<li><em>cgmpolf</em>: 11 easyconfigs 43986 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/213">#213</a>)</li> 43987<li><em>cgmvolf</em>: 11 easyconfigs 43988 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/218">#218</a>)</li> 43989<li><em>cgoolf</em>: 12 easyconfigs 43990 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/213">#213</a>)</li> 43991<li><em>gmvolf</em>: 10 easyconfigs 43992 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/215">#215</a>)</li> 43993</ul> 43994</li> 43995<li>added additional example easyconfig files for:<ul> 43996<li>CMake 43997 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/163">#163</a>), 43998 git 43999 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/210">#210</a>), 44000 Java 44001 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/206">#206</a>), 44002 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/221">#221</a>, 44003 Mercurial 44004 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/201">#201</a>, 44005 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/215">#215</a>), 44006 ncurses 44007 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/225">#225</a>), 44008 TotalView 44009 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/160">#160</a>)</li> 44010</ul> 44011</li> 44012<li>various enhancements, including:<ul> 44013<li>added ESMF and UDUNITS dependencies to NCL easyconfigs 44014 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/211">#211</a>)</li> 44015<li>changed value of source_urls in R easyconfigs, to be generic 44016 enough for version 3.0 and possibly beyond 44017 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/251">#251</a>)</li> 44018</ul> 44019</li> 44020<li>various 'bug' fixes, including:<ul> 44021<li>add <code>--enable-mpirun-prefix-by-default</code> configure option for all 44022 OpenMPI easyconfigs 44023 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/205">#205</a>)</li> 44024</ul> 44025</li> 44026</ul> 44027<h2 id="easybuild-v130-april-1st-2013">EasyBuild v1.3.0 (April 1st 2013)<a class="headerlink" href="#easybuild-v130-april-1st-2013" title="Permanent link">¶</a></h2> 44028<p>feature + bugfix release</p> 44029<p><strong>framework</strong></p> 44030<ul> 44031<li>added script to bootstrap EasyBuild with EasyBuild, see
44032 <a href="https://github.com/easybuilders/easybuild/wiki/Bootstrapping-EasyBuild">https://github.com/easybuilders/easybuild/wiki/Bootstrapping-EasyBuild</a> 44033 (<a href="https://github.com/easybuilders/easybuild-framework/pull/531">#531</a>)</li> 44034<li>reorganize framework/easyconfig.py module into framework/easyconfig 44035 package with modules 44036 (<a href="https://github.com/easybuilders/easybuild-framework/pull/574">#574</a>, 44037 <a href="https://github.com/easybuilders/easybuild-framework/pull/580">#580</a>)</li> 44038<li>support EasyBuild configuration via command line, environment 44039 variables and configuration files 44040 (<a href="https://github.com/easybuilders/easybuild-framework/pull/529">#529</a>, 44041 <a href="https://github.com/easybuilders/easybuild-framework/pull/552">#552</a>, 44042 <a href="https://github.com/easybuilders/easybuild-framework/pull/556">#556</a>, 44043 <a href="https://github.com/easybuilders/easybuild-framework/pull/558">#558</a>, 44044 <a href="https://github.com/easybuilders/easybuild-framework/pull/559">#559</a>)</li> 44045<li>various other enhancements, including:<ul> 44046<li>extended set of unit tests for eb command line options and 44047 EasyBuild configuration 44048 (<a href="https://github.com/easybuilders/easybuild-framework/pull/517">#517</a>, 44049 <a href="https://github.com/easybuilders/easybuild-framework/pull/556">#556</a>, 44050 <a href="https://github.com/easybuilders/easybuild-framework/pull/559">#559</a>, 44051 <a href="https://github.com/easybuilders/easybuild-framework/pull/571">#571</a>)</li> 44052<li>made <code>--search</code> also useful when easybuild-easyconfigs package 44053 is not installed 44054 (<a href="https://github.com/easybuilders/easybuild-framework/pull/524">#524</a>)</li> 44055<li>extended set of default module classes 44056 (<a href="https://github.com/easybuilders/easybuild-framework/pull/525">#525</a>)</li> 44057<li>add support for license easyconfig parameter (which will be 44058 mandatory in v2.x) 44059 (<a href="https://github.com/easybuilders/easybuild-framework/pull/526">#526</a>, 44060 <a href="https://github.com/easybuilders/easybuild-framework/pull/569">#569</a>)</li> 44061<li>added <code>setup.cfg</code> for <code>setup.py</code> to allow creating RPMs 44062 (<a href="https://github.com/easybuilders/easybuild-framework/pull/528">#528</a>)</li> 44063<li>added support for obtaining system information, see <code>get_os_*</code> 44064 functions in <code>easybuild/tools/systemtools.py</code> 44065 (<a href="https://github.com/easybuilders/easybuild-framework/pull/543">#543</a>, 44066 <a href="https://github.com/easybuilders/easybuild-framework/pull/546">#546</a>, 44067 <a href="https://github.com/easybuilders/easybuild-framework/pull/547">#547</a>)</li> 44068<li>added support for iterated builds that require cycling over 44069 multiple sets of configure/build/install options, e.g. FFTW 44070 (<a href="https://github.com/easybuilders/easybuild-framework/pull/549">#549</a>)</li> 44071<li>added support for OpenBLAS as toolchain lib for linear algebra 44072 (<a href="https://github.com/easybuilders/easybuild-framework/pull/537">#537</a>, 44073 <a href="https://github.com/easybuilders/easybuild-framework/pull/565">#565</a>)</li> 44074<li>added support for tweaking prefix and separator for library 44075 toolchain variables (<code>LIB*</code>) 44076 (<a href="https://github.com/easybuilders/easybuild-framework/pull/572">#572</a>, 44077 <a href="https://github.com/easybuilders/easybuild-framework/pull/576">#576</a>)</li> 44078<li>skip already built modules in regression testing mode, to ease 44079 regression testing 44080 (<a href="https://github.com/easybuilders/easybuild-framework/pull/582">#582</a>)</li> 44081</ul> 44082</li> 44083<li>various bug fixes, including:<ul> 44084<li>added <code>zip_safe</code> flag to <code>setup.py</code>, to silence multitude of 44085 warnings 44086 (<a href="https://github.com/easybuilders/easybuild-framework/pull/521">#521</a>)</li> 44087<li>only define <code>LIBFFT</code> for Intel MKL if FFTW interface libraries 44088 are available 44089 (<a href="https://github.com/easybuilders/easybuild-framework/pull/518">#518</a>, 44090 <a href="https://github.com/easybuilders/easybuild-framework/pull/567">#567</a>, 44091 <a href="https://github.com/easybuilders/easybuild-framework/pull/579">#579</a>)</li> 44092<li>set POSIX group early in build process, make EasyBuild aware of
44093 consistent chmod/chown failures 44094 (<a href="https://github.com/easybuilders/easybuild-framework/pull/527">#527</a>)</li> 44095<li>properly order the name/version keys for the toolchain 44096 easyconfig parameter when using <code>--try-toolchain</code> 44097 (<a href="https://github.com/easybuilders/easybuild-framework/pull/563">#563</a>)</li> 44098<li>take the <code>skipsteps</code> easyconfig parameter into account in 44099 regression testing mode as well 44100 (<a href="https://github.com/easybuilders/easybuild-framework/pull/583">#583</a>)</li> 44101</ul> 44102</li> 44103</ul> 44104<p><strong>easyblocks</strong></p> 44105<ul> 44106<li>added support for <strong>2</strong> new software packages that require 44107 customized support:<ul> 44108<li>CUDA 44109 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/145">#145</a>), 44110 Ferret 44111 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/160">#160</a>, 44112 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/163">#163</a>)</li> 44113</ul> 44114</li> 44115<li>remove <code>license</code> easyconfig parameter from <code>IntelBase</code>, since it 44116 clashes with generic <code>license</code> parameter 44117 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/153">#153</a>, 44118 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/158">#158</a>)<ul> 44119<li><code>license_file</code> should be used instead (see 44120 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/569/files">framework#569</a>)</li> 44121<li>using <code>license</code> instead of <code>license_file</code> will be supported 44122 until v2.x for legacy purposes</li> 44123</ul> 44124</li> 44125<li>various enhancements, including:<ul> 44126<li>stop hardcoding Python site-packages library dir, obtain it via 44127 <code>distutils.sysconfig</code> instead 44128 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/141">#141</a>, 44129 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/156">#156</a>, 44130 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/159">#159</a>, 44131 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/161">#161</a>)</li> 44132<li>stop hardcoding list of libraries for BLAS libs, ask toolchain 44133 modules or use <code>$LIBBLAS</code> instead 44134 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/150">#150</a>, 44135 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/155">#155</a>)</li> 44136<li>enhanced CP2K easyblock, following Intel guidelines for <code>ictce</code> 44137 builds 44138 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/138">#138</a>)</li> 44139<li>added <code>setup.cfg</code> for <code>setup.py</code> to allow creating RPMs 44140 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/140">#140</a>)</li> 44141<li>clean up specifying BLAS/LAPACK libs for building numpy, check 44142 whether requires patch is being used for IMKL builds 44143 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/155">#155</a>, 44144 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/161">#161</a>)</li> 44145</ul> 44146</li> 44147<li>various bug fixes, including:<ul> 44148<li>added <code>zip_safe</code> flag to <code>setup.py</code>, to silence multitude of 44149 warnings 44150 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/135">#135</a>)</li> 44151<li>install EasyBuild packages in reversed order to avoid funky 44152 setuptools issues 44153 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/139">#139</a>)</li> 44154<li>fixed a typo in the ScaLAPACK easyblock, and set CCFLAGS and 44155 FCFLAGS for v2.x 44156 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/149">#149</a>, 44157 <a href="https://github.com/easybuilders/easybuild-easyblocks/pull/162">#162</a>)</li> 44158<li>fix sanity check for python-meep 44159 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/159">#159</a>)</li> 44160<li>exclude Python tests from DOLFIN sanity check, since they hang 44161 sometimes 44162 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/161">#161</a>)</li> 44163<li>add support in ALADIN easyblock for answering question on 44164 location of <code>libgrib_api.a</code> 44165 (<a href="https://github.com/easybuilders/easybuild-easyblocks/pull/165">#165</a>)</li> 44166</ul> 44167</li> 44168</ul> 44169<p><strong>easyconfigs</strong></p> 44170<ul> 44171<li>added example easyconfig files for <strong>13</strong> new software packages:<ul> 44172<li>Bash, CUDA, ccache, Ferret, gzip, libxc, ns, numactl, OpenBLAS, 44173 otcl, Tar, tclcl, tcsh</li> 44174<li>several of these easyconfig files were contributed by attendees 44175 of the EasyBuild hackathon in Cyprus!</li> 44176</ul> 44177</li> 44178<li>
44178added example easyconfigs for goolf toolchain 44179 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/158">#158</a>)</li> 44180<li>added example easyconfigs for builds with goolf toolchain, i.e. for 44181 all goalf easyconfigs 44182 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/189">#189</a>)<ul> 44183<li>for several software packages, a patch file was needed to get 44184 them to build with GCC 4.7:<ul> 44185<li>AMOS, BEAGLE, Cufflinks, DOLFIN, GATE, ns, Pasha, Trilinos, 44186 Trinity</li> 44187</ul> 44188</li> 44189<li>for PETSc, a patch file was required to make it build with a 44190 toolchain that doesn't include BLACS</li> 44191</ul> 44192</li> 44193<li>added additional example easyconfig files for:<ul> 44194<li>gompi, hwloc, LAPACK, MVAPICH2, OpenMPI, ScaLAPACK</li> 44195</ul> 44196</li> 44197<li>various enhancements, including:<ul> 44198<li>define a proper module class in <em>all</em> easyconfigs, 44199 cfr. default module classes defined in framework 44200 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/150">#150</a>, 44201 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/159">#159</a>, 44202 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/161">#161</a>, 44203 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/162">#162</a>, 44204 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/179">#179</a>, 44205 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/181">#181</a>)</li> 44206<li>extend FFTW easyconfig to 'fat' builds that include single, 44207 double, long double and quad precision libraries in the same 44208 module<ul> 44209<li>quad precision is disabled for Intel compiler based builds 44210 (it requires GCC v4.6+)</li> 44211</ul> 44212</li> 44213<li>the imkl easyconfigs used for the ictce 3.2.2.u3 toolchain now 44214 also enable FFTW interfaces</li> 44215</ul> 44216</li> 44217<li>various 'bug' fixes, including:<ul> 44218<li>fix filename for Mercurial and ROOT easyconfig files</li> 44219<li>fix homepage/description for Hypre</li> 44220<li>fix enabling OpenMP support in OpenMPI: use <code>--enable-openmp</code>, 44221 not <code>--with-openmp</code></li> 44222<li>use correct configure flag for enabling OpenMPI threading 44223 support in v1.6 44224 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/186">#186</a>)<ul> 44225<li><code>--enable-mpi-thread-multiple</code> instead of 44226 <code>--enable-mpi-threads</code></li> 44227</ul> 44228</li> 44229<li>explicitly add <code>--without-openib --without-udapl</code> configure 44230 options in OpenMPI easyconfig using versionsuffix <code>-no-OFED</code> 44231 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/168">#168</a>)<ul> 44232<li>this avoids that OpenMPI auto-detects that it can enable 44233 Infiniband (OpenIB) support, which doesn't fit the -no-OFED 44234 versionsuffix</li> 44235<li>Note: this makes goalf-1.1.0-no-OFED effectively not 44236 suitable to produce software builds that are IB-capable!</li> 44237</ul> 44238</li> 44239<li>remove explicit <code>--with-udapl</code> from OpenMPI easyconfigs, does 44240 more harm than good 44241 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/178">#178</a>)</li> 44242<li>remove libibvers, libibmad, libibumad as explicit dependencies 44243 for OpenMPI/MVAPICH2 44244 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/173">#173</a>, 44245 <a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/182">#182</a>)<ul> 44246<li>leave it up to the OS to provide these, since the required 44247 version is too much tied to the version of IB drivers</li> 44248</ul> 44249</li> 44250<li>use <code>license_file</code> in Intel tools easyconfigs, as opposed to the 44251 new generic <code>license</code> parameter with a different meaning 44252 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/180">#180</a>)</li> 44253<li>modify patch for impi to avoid installation problems due to 44254 hardcoded path in /tmp 44255 (<a href="https://github.com/easybuilders/easybuild-easyconfigs/pull/185">#185</a>)<ul> 44256<li>now uses <code>$USER-$RANDOM</code> subdir to avoid clashes between 44257 different users on the same system</li> 44258</ul> 44259</li> 44260<li>the patch file for numpy was extended to also supporting ATLAS 44261 and other BLAS libraries spread across multiple directories<ul> 44262<li>the extension for ATLAS is required because we now no longer 44263 rely on the automatic numpy mechanism to find the ATLAS libs</li> 44264</ul> 44265</li> 44266<li>fixed dependencies:<ul> 44267<li>libibumad as dependency for libibmad</li> 44268<li>ncurses as dependency for libreadline</li> 44269<li>ncurses and zlib as dependency for SAMtools (+ enhanced 44270 patch)</li> 44271<li>remove explicit FFTW dependency for Meep, ... since 44272 toolchain already provided FFTW</li> 44273</ul> 44274</li> 44275</ul> 44276</li> 44277</ul> 44278<h2 id="easybuild-v120-february-28th-2013">EasyBuild v1.2.0 (February 28th 2013)<a class="headerlink" href="#easybuild-v120-february-28th-2013" title="Permanent link">¶</a></h2> 44279<p>feature + bugfix release</p> 44280<p><strong>framework</strong></p> 44281<ul> 44282<li>new backend module for option parsing: generaloption</li> 44283<li>support for using constants and string templates in easyconfig files<ul> 44284<li>currently disabled for <code>exts_filter</code> and <code>exts_list</code> easyconfig 44285 parameters, for backward compatibility</li> 44286</ul> 44287</li> 44288<li>various other enhancements, including:<ul> 44289<li>support for iqacml and iiqmpi toolchains (Intel compilers + 44290 QLogic MPI based)</li> 44291<li>clearer errors messages when sanity check failed</li> 44292<li>unit tests for (about half of) the <code>eb</code> command line options</li> 44293<li>support for specifying build/install steps to skip in easyconfig 44294 file (<code>skipsteps</code>)</li> 44295<li>support for allowing certain dependencies to be resolved by the 44296 system instead of modules (<code>allow_system_deps</code>)</li> 44297<li>cache ppn value required by regtest, clean up temporary files 44298 let behind by <code>--regtest</code>/<code>--job</code></li> 44299<li>make sure MPD is used as process manager for Intel MPI (required 44300 for impi v4.1 and later)</li> 44301<li>rename template names <code>name</code> and <code>version</code> used in exts_filter 44302 to <code>ext_name</code>, <code>ext_version</code><ul> 44303<li><code>name</code> and <code>version</code> are still supported for legacy reasons</li> 44304</ul> 44305</li> 44306<li>cleaned up module docstrings w.r.t. list of authors</li> 44307</ul> 44308</li> 44309<li>various bug fixes, including:<ul> 44310<li>print correct (lowercase) toolchain names with 44311 <code>--list-toolchains</code></li> 44312<li>correct easyconfig parameter name <code>license_server_port</code></li> 44313<li>fix string quoting in develop modules</li> 44314<li>ensure <code>modulecmd</code> is run with original <code>$LD_LIBRARY_PATH</code> value<ul> 44315<li>to avoid breaking <code>modulecmd</code>, see 44316 <a href="https://bugzilla.redhat.com/show_bug.cgi?id=719785">https://bugzilla.redhat.com/show_bug.cgi?id=719785</a></li> 44317</ul> 44318</li> 44319<li>remove use of hardcoded files/dirs in unit tests</li> 44320<li>fix various inconsistencies w.r.t. paths considered with 44321 <code>--robot</code></li> 44322<li>various cleanup and fixes w.r.t. logging<ul> 44323<li>use correct logger instance in main script</li> 44324<li>stop passing logger instances around</li> 44325<li>make module logging variables private</li> 44326</ul> 44327</li> 44328<li>get rid of <code>ModuleGenerator</code> deconstructor, clean up via 44329 <code>EasyBlock.clean_up_fake_module</code></li> 44330<li>fix disabling of <code>optarch</code> toolchain option (and extend unit 44331 tests to check on this)</li> 44332</ul> 44333</li> 44334</ul> 44335<p><strong>easyblocks</strong></p> 44336<ul> 44337<li>added <strong>one</strong> new <em>generic</em> easyblock: <code>Rpm</code></li> 44338<li>
44338added support for <strong>6</strong> new software packages that require 44339 customized support:<ul> 44340<li>EasyBuild, EPD (Enthought Python Distribution), freetype, 44341 MATLAB, QLogic MPI (RPM), TotalView</li> 44342<li>support for installing EasyBuild with EasyBuild enables 44343 bootstrapping an EasyBuild installation!</li> 44344</ul> 44345</li> 44346<li>various enhancements, including:<ul> 44347<li>corrections in WRF/WPS to also enable building with iqacml 44348 toolchain<ul> 44349<li>use <code>mpi_cmd_for</code> instead of hardcoding test commands, using 44350 correct Fortran compilers (F90)</li> 44351</ul> 44352</li> 44353<li>fix NCL easyblock to also support v6.1.x<ul> 44354<li>use correct Fortran compiler (F90), set correct lib/include 44355 paths for dependencies (netCDF-Fortran, GDAL)</li> 44356</ul> 44357</li> 44358<li>cleanup sweep of license headers and authors list in easyblock 44359 module docstrings</li> 44360<li>use new <code>ext_name</code> template name in <code>exts_filter</code> in Python and 44361 R easyblocks</li> 44362</ul> 44363</li> 44364<li>various bug fixes, including:<ul> 44365<li>general code cleanup<ul> 44366<li>don't set <code>sanityCheckOK</code> in <code>Toolchain</code> easyblock</li> 44367<li>get rid of using <code>os.putenv</code></li> 44368</ul> 44369</li> 44370<li>NEURON easyblock: don't hardcode number of processes used in 44371 test cases</li> 44372<li>make sure <code>easybuild.easyblocks.generic</code> namespace is extendable</li> 44373</ul> 44374</li> 44375</ul> 44376<p><strong>easyconfigs</strong></p> 44377<ul> 44378<li>added example easyconfig files for <strong>41</strong> new software packages:<ul> 44379<li>a2ps, AnalyzeFMRI, aria, bbcp, bbFTP, bbftpPRO, binutils, 44380 Bonnie++, ccache, cflow, cgdb, Corkscrew, EasyBuild, Elinks, 44381 EPD, FLUENT, fmri, GDB, GDAL, gnuplot, gnutls, gperf, Iperf, 44382 lftp, libyaml, lzo, MATLAB, mc, nano, NASM, nettle, numexpr, 44383 parallel, pyTables, QLogic MPI, Stow, TotalView, Valgrind, VTK, 44384 Yasm, zsync</li> 44385</ul> 44386</li> 44387<li>added example easyconfigs for iqacml and iiqmpi toolchains</li> 44388<li>added additional example easyconfig files for:<ul> 44389<li>ABINIT, ABySS, ACML, BFAST, Bison, BLACS, Cython, cURL, Doxygen, 44390 FFTW, flex, g2clib, g2lib, GHC, h5py, HDF, HDF5, HMMER, JasPer, 44391 icc, ictce, ifort, imkl, impi, libpng, libreadline, M4, 44392 matplotlib, MCL, MEME, mpiBLAST, NCL, ncurses, netCDF, 44393 netCDF-Fortran, NWChem, R, ScaLAPACK, Tcl, Tk, WPS, WRF, zlib</li> 44394</ul> 44395</li> 44396<li>various enhancements, including:<ul> 44397<li>fix version of xtable R library in list of extensions for R, to 44398 avoid installation failures</li> 44399</ul> 44400</li> 44401<li>various 'bug' fixes, including:<ul> 44402<li>fix toolchain and file names for ABINIT easyconfigs</li> 44403<li>fix sanity check paths for cURL</li> 44404<li>don't disable <code>optarch</code> for WRF, it's not needed (only disable 44405 heavy optimizations is required)</li> 44406<li>fix homepage/description for ALADIN</li> 44407</ul> 44408</li> 44409</ul> 44410<h2 id="easybuild-v110-january-27th-2013">EasyBuild v1.1.0 (January 27th 2013)<a class="headerlink" href="#easybuild-v110-january-27th-2013" title="Permanent link">¶</a></h2> 44411<p>feature + bugfix release</p> 44412<p><strong>framework</strong></p> 44413<ul> 44414<li>improvements w.r.t. support for software extensions (tested on 44415 Python and R, see easyblocks package)<ul> 44416<li>cleaned up support for building/installing extensions</li> 44417<li>define <code>ExtensionEasyblock</code> class that implements support for 44418 installing extensions as stand-alone module as well</li> 44419<li>return to build dir before building/installing each extension</li> 44420<li>define <code>EBEXTSLIST<NAME></code> environment variable in module if 44421 <code>exts_list</code> was defined</li> 44422<li>make sure sanity check for extensions results in an error if it 44423 fails</li> 44424</ul> 44425</li> 44426<li>various enhancements, including:<ul> 44427<li>log both framework and easyblocks versions</li> 44428<li>add support for <code>gimkl</code>, <code>gmacml</code>, <code>iccifort</code>, <code>iomkl</code> and 44429 <code>ismkl</code> toolchains</li> 44430<li>define <code>*_SEQ compiler</code> variables for sequential compilers</li> 44431<li>add <code>--list-toolchains</code> command line option for listing 44432 supported toolchains</li> 44433<li>add support for customizing software and modules install path 44434 suffixes</li> 44435<li>support both setuptools and distutils installation methods for 44436 finding installed easyconfigs</li> 44437<li>also consider robot path in list of paths searched for patch 44438 files</li> 44439<li>allow skipping of default extension sanity check (by setting 44440 <code>modulename</code> to False in options)</li> 44441</ul> 44442</li> 44443<li>various bug fixes, including:<ul> 44444<li>typos in toolchain Python modules w.r.t. <code>imkl</code> support, 44445 handling of <code>i8</code>/<code>optarch</code>/<code>unroll</code> options</li> 44446<li>purge before loading 'fake' module, unload 'fake' module 44447 before removing it, use original <code>$MODULEPATH</code></li> 44448<li>restore environment after unloading fake module, set variables 44449 that were incorrectly unset, i.e., that were defined before as 44450 well</li> 44451<li>unset <code>$TMPDIR</code> for builds submitted as jobs (required by 44452 <code>IntelBase</code> easyblock)</li> 44453<li>correctly track easyconfig parse error</li> 44454<li>always run all jobs in regtest, also if dependency jobs failed</li> 44455<li>cosmetic adjustments to default EasyBuild configuration file to 44456 avoid confusion between e.g. <code>build_dir</code> and <code>build_path</code> (only 44457 latter matters)</li> 44458<li>fix SuSe hack, only prefix command with sourcing of 44459 <code>/etc/profile.d/modules.sh</code> if it is there</li> 44460<li>leave build directory before it is removed during cleanup step</li> 44461<li>load generated module file before running test cases</li> 44462</ul> 44463</li> 44464</ul> 44465<p><strong>easyblocks</strong></p> 44466<ul> 44467<li>added <strong>3</strong> new <em>generic</em> easyblocks: 44468 <code>CMakePythonPackage</code>, <code>JAR</code>, <code>RPackage</code></li> 44469<li>
44469added support for <strong>23</strong> new software packages that require 44470 customized support:<ul> 44471<li>ACML, ALADIN, ant, Bioconductor (R packages), Chapel, Cufflinks, 44472 ESPResSo, FLUENT, Geant4, GHC, Java, NEURON, NWChem, PyZMQ, 44473 QuantumESPRESSO, R, Rmpi, ROOT, Rserve, SCOOP, Trinity, 44474 VSC-tools, XML</li> 44475</ul> 44476</li> 44477<li>various enhancements, including:<ul> 44478<li>clean up of <code>python.py</code> easyblock:<ul> 44479<li>merge <code>EB_DefaultPythonPackage</code> and <code>PythonPackage</code> 44480 easyblocks into generic <em>easyblock</em> 44481 <code>PythonPackage</code>, which derives from <code>ExtensionEasyblock</code></li> 44482<li>move <code>EB_FortranPythonPackage</code> into dedicated 44483 <em>generic</em> <code>FortranPythonPackage</code> easyblock 44484 module</li> 44485<li>split off support for building/installing <code>nose</code>, <code>numpy</code>, 44486 <code>scipy</code> into dedicated <code>EB_*</code> easyblock modules, which 44487 allows them to be built as stand-alone modules as well</li> 44488</ul> 44489</li> 44490<li>clean up testing of Python packages (<code>PythonPackage</code> easyblock)</li> 44491<li>make sure there is no <code>site.cfg</code> in home dir when building 44492 Python packages, because e.g. <code>scipy</code> will pick it up</li> 44493<li>added support for building Intel MKL wrappers with OpenMPI 44494 toolchain</li> 44495<li>cleaning up of fake module that was loaded for running tests</li> 44496<li>move calls to functions that rely on environment up in the chain 44497 of steps (mostly for cleanup reasons)</li> 44498<li>use better module name for UFC sanity check, minor change to 44499 sanity check paths for UFC</li> 44500</ul> 44501</li> 44502<li>various bug fixes, including:<ul> 44503<li>only call <code>make ptcheck</code> for ATLAS when multi-threading support 44504 is enabled</li> 44505<li>use a symbolic link for $HOME/intel instead of a randomly 44506 suffixed subdirectory in home and patching of Intel install 44507 scripts<ul> 44508<li>latter does not work anymore with recent versions of Intel 44509 tools (2013.x)</li> 44510</ul> 44511</li> 44512</ul> 44513</li> 44514</ul> 44515<p><strong>easyconfigs</strong></p> 44516<ul> 44517<li>added example easyconfig files for <strong>48</strong> new software packages:<ul> 44518<li>ABINIT, ABySS, ACML, ALADIN, ant, BFAST, BLAST, Chapel, CLHEP, 44519 Cufflinks, ESPRresSo, GATE, GHC, Geant4, Greenlet, 44520 google-sparsehash, grib_api, HMMER, Java, JUnit, libibmad, 44521 libibumad, libibverbs, MCL, MDP, MEME, mpiBLAST, NCBI Toolkit, 44522 NEURON, NWChem, numpy, MDP, Oger, OpenPGM, paycheck, PyZMQ, 44523 QuantumESPRESSO, R, ROOT, SCOOP, scipy, Tophat, Trinity, 44524 util-linux, VSC-tools, wiki2beamer, XML, ZeroMQ</li> 44525</ul> 44526</li> 44527<li>added example easyconfigs for gmacml, gmvapich2, iccifort, ictce, 44528 iomkl toolchains</li> 44529<li>added additional example easyconfig files for:<ul> 44530<li>ATLAS, BLACS, Boost, Bowtie2, bzip2, CP2K, Doxygen, FFTW, GCC, 44531 HDF5, hwloc, icc, ifort, imkl, impi, JasPer, Libint, 44532 libreadline, libsmm, libxml, ncurses, netCDF, M4, Meep, 44533 MVAPICH2, OpenMPI, Python, ScaLAPACK, Szip, zlib</li> 44534</ul> 44535</li> 44536<li>various enhancements, including:<ul> 44537<li>major style cleanup of all example easyconfig file (PEP008 44538 compliance)</li> 44539<li>added setuptools to list of Python extensions</li> 44540<li>get rid of <code>parallel</code> versionsuffix for HDF5, as its meaningless 44541 (MPI-enabled build is always parallel)</li> 44542</ul> 44543</li> 44544<li>various 'bug' fixes, i.e. added missing dependencies or replaced 44545 OS dependencies with proper dependencies</li> 44546</ul> 44547<h2 id="easybuild-v102-december-8th-2012">EasyBuild v1.0.2 (December 8th 2012)<a class="headerlink" href="#easybuild-v102-december-8th-2012" title="Permanent link">¶</a></h2> 44548<p>bugfix release</p> 44549<p><strong>framework</strong></p> 44550<ul> 44551<li>properly catch failing sanity check commands</li> 44552<li>fix bug in toolchain support which cause linking environment 44553 variables set by toolchain to include too many libraries<ul> 44554<li>elements in toolchain variables were being passed by reference 44555 instead of by value</li> 44556</ul> 44557</li> 44558<li>fix selecting a compiler toolchain for a specified software package 44559 (<code>--software-name</code>) if only a template is a viable option</li> 44560<li>fix passing command line parameters with <code>--job</code></li> 44561<li>fix list of valid stops (<code>-s</code>/<code>--stop</code>)</li> 44562<li>fix minor issues in help messages (<code>-h</code>/<code>--help</code>)</li> 44563</ul> 44564<p><strong>easyblocks</strong></p> 44565<ul> 44566<li>fix typos in WIEN2k easyblock (missing commas after list elements)</li> 44567</ul> 44568<p><strong>easyconfigs</strong></p> 44569<ul> 44570<li>fixed source URL for ligtextutils (toolchain refactoring error)</li> 44571</ul> 44572<h2 id="easybuild-v101-november-24th-2012">EasyBuild v1.0.1 (November 24th 2012)<a class="headerlink" href="#easybuild-v101-november-24th-2012" title="Permanent link">¶</a></h2> 44573<p>bugfix release</p> 44574<p><strong>framework</strong></p> 44575<ul> 44576<li>fix support for installing with <code>distutils</code> (broken import in 44577 <code>setup.py</code>)</li> 44578<li>fix support for ACML as a toolchain element 44579 (<code>toolchains/linalg/acml.py</code>)</li> 44580<li>
44580add name to aggregated regtest XML so that is parsed correctly by 44581 Jenkins</li> 44582<li>reorder code in <code>main.py</code> so that regtest also works with incomplete 44583 easyconfig paths</li> 44584<li>add bash script for running regression test and sending a trigger to 44585 Jenkins to pull in the XML with results</li> 44586<li>get rid of assumption that loaded modules should have name like 44587 <code>foo/bar</code>, make it more flexible</li> 44588<li>retry failed builds in regtest twice to ignore fluke errors</li> 44589<li>report leaf nodes in dependency graph when regtest is submitted<ul> 44590<li>this is required for setting job dependencies in the regtest 44591 script for the Jenkins trigger job</li> 44592</ul> 44593</li> 44594<li>implement and use rmtree2 as more (NFS) robust replacement for 44595 <code>shutil.rmtree</code></li> 44596<li>bump max hit count for <code>run_cmd_qa</code> from 20 to 50, to make false 44597 positives of unasnwered questions less likely</li> 44598</ul> 44599<p><strong>easyblocks</strong></p> 44600<ul> 44601<li>fix support for installing with <code>distutils</code> (broken import in 44602 <code>setup.py</code>)</li> 44603<li>only build GMP/CLooG/PPL libraries during GCC build in parallel, 44604 don't install in parallel<ul> 44605<li><code>make -j N install</code> doesn't work consistently for GMP</li> 44606</ul> 44607</li> 44608<li>fix GCC build on OS X<ul> 44609<li>location of libraries is slightly different (<code>lib</code> vs <code>lib64</code> 44610 dir)</li> 44611</ul> 44612</li> 44613<li>add support to <code>ConfigureMake</code> easyblock for pre-passing tar options 44614 to configure<ul> 44615<li>see <code>tar_config_opts</code> easyconfig parameter</li> 44616<li>workaround for issue with pax hanging <code>configure</code> with an 44617 interactive prompt</li> 44618</ul> 44619</li> 44620<li>enhance Q&A for WRF and WIEN2k by adding entries to <code>qa</code> dict and 44621 <code>no_qa</code> list</li> 44622<li>use <code>rmtree2</code> from <code>tools/filetools.py</code> as more (NFS) robust 44623 replacement for <code>shutil.rmtree</code></li> 44624</ul> 44625<p><strong>easyconfigs</strong></p> 44626<ul> 44627<li>remove patch file for OpenMPI to resolve issue with pax hanging 44628 configure<ul> 44629<li><code>tar_config_opts</code> should be enabled as needed</li> 44630</ul> 44631</li> 44632<li>disable parallel build for PAPI, seems to be causing problems</li> 44633</ul> 44634<h2 id="easybuild-v10-november-13th-2012">EasyBuild v1.0 (November 13th 2012)<a class="headerlink" href="#easybuild-v10-november-13th-2012" title="Permanent link">¶</a></h2> 44635<ul> 44636<li>split up EasyBuild across three repositories: framework, easyblocks 44637 and easyconfigs</li> 44638<li>packaged EasyBuild, different parts can now be installed easily 44639 using <code>easy_install</code></li> 44640</ul> 44641<p><strong>framework</strong></p> 44642<ul> 44643<li>various changes to both internal and external API:<ul> 44644<li>renamed main script to main.py (from <code>build.py</code>)</li> 44645<li>file and directory organisation</li> 44646<li>module, class, function and function argument renaming and 44647 reorganisation</li> 44648<li>split up <code>Application</code> into <code>EasyBlock</code> and <code>ConfigureMake</code> (see 44649 easybuild-easyblocks for the latter)</li> 44650<li>created <code>EasyConfig</code> class for handling easyconfig files</li> 44651<li>renaming of EasyBuild configuration parameters (non-camelCase)</li> 44652<li>renaming of various easyconfig parameters (non-camelCase)</li> 44653<li>rename <code>SOFTROOT</code> and <code>SOFTVERSION</code> environment variables set in 44654 generated module files to <code>EBROOT</code> and <code>EBVERSION</code></li> 44655<li>use 'extension' as generic terminology for Python packages, R 44656 libraries, Perl modules, ...</li> 44657</ul> 44658</li> 44659<li>added support for building software packages in parallel via PBS 44660 jobs</li> 44661<li>added unit testing framework and initial set of unit tests for basic 44662 functionality<ul> 44663<li>and run them in Jenkins continuous integration service, see 44664 <a href="https://jenkins1.ugent.be/view/EasyBuild/">https://jenkins1.ugent.be/view/EasyBuild/</a></li> 44665</ul> 44666</li> 44667<li>implement single-command regression test (e.g. to test building all 44668 supported software)<ul> 44669<li>eb <code>--regtest</code> --robot</li> 44670</ul> 44671</li> 44672<li>switch to new style Python classes</li> 44673<li>replaced <code>toolkit</code> module with <code>toolchain</code> package (total rewrite), 44674 providing modular support for toolchains</li> 44675<li>adjust default EasyBuild configuration to only use 44676 <code>$HOME/.local/easybuild</code> by default</li> 44677<li>
44677added support for running EasyBuild without supplying an easyconfig 44678 file<ul> 44679<li>make EasyBuild search for a matching easyconfig file</li> 44680<li>support automatic rewriting of an existing partially-matching 44681 easyconfig file (use this with care!)</li> 44682<li>support for automatically generating an easyconfig file 44683 according to given specifications (best effort!)</li> 44684</ul> 44685</li> 44686<li>add support for looking for easyconfig file in Python search path if 44687 it can't be found on specified (relative) path (that way, 44688 easyconfig files available in the easybuild-easyconfigs package can 44689 be used easily)</li> 44690<li>various other enhancements and bug fixes, e.g.:<ul> 44691<li>extended sanity check capabilities</li> 44692<li>cleaned up logging</li> 44693<li>creating of devel module which allows to mimic environment that 44694 was used by EasyBuild to build the software</li> 44695<li>support for creating dependency graphs for a set of easyconfig 44696 files</li> 44697<li>grouped options in help output and categorised available 44698 easyconfig parameters</li> 44699<li>more consistent code style</li> 44700</ul> 44701</li> 44702</ul> 44703<p><strong>easyblocks</strong></p> 44704<ul> 44705<li>implement class name encoding scheme, see wiki 44706 <a href="https://github.com/easybuilders/easybuild/wiki/Encode-class-names">https://github.com/easybuilders/easybuild/wiki/Encode-class-names</a><ul> 44707<li>(non-generic) easyblock class names are now prefixed with <code>EB_</code> 44708 and non-alphanumeric characters are escaped</li> 44709</ul> 44710</li> 44711<li>split off generic easyblocks into separate package 44712 <code>easyblocks.generic</code></li> 44713<li>added custom support for <strong>39</strong> software packages:<ul> 44714<li>Armadillo, BiSearch, Boost, Bowtie2, BWA, bzip2, CGAL, CPLEX, 44715 DOLFIN, Eigen, flex, FSL, Hypre, libxml2, MetaVelvet, METIS, 44716 MTL4, MUMmer, ncurses, OpenFOAM, OpenSSL, ParMETIS, Pasha, 44717 PETSc, Primer3, python-meep, SAMtools, SCOTCH, SHRiMP, SLEPc, 44718 SOAPdenovo, SuiteSparse, SWIG, Tornado, Trilinos, UFC, Velvet, 44719 WIEN2k, XCrySDen</li> 44720</ul> 44721</li> 44722<li>various enhancements and bug fixes to existing easyblocks</li> 44723</ul> 44724<p><strong>easyconfigs</strong></p> 44725<ul> 44726<li>added example easyconfig files for <strong>106</strong> new software packages:<ul> 44727<li>AMOS, Armadillo, ASE, Autoconf, BiSearch, Boost, Bowtie2, BWA, 44728 byacc, bzip2, CGAL, ClustalW2, CMake, CPLEX, cURL, CVXOPT, 44729 Cython, Docutils, DOLFIN, ECore, Eigen, expat, FASTX-Toolkit, 44730 FFC, FIAT, freetype, FSL, GEOS, git, glproto, GMP, gmvapich2, 44731 gompi, GPAW, GSL, guile, h5py, h5utils, Harminv, hwloc, Hypre, 44732 Infernal, Instant, Jinja2, libctl, libdrm, libffi, 44733 libgtextutils, libmatheval, libpciaccess, libpthread-stubs, 44734 libreadline, libtool, libunistring, libxcb, libxml2, makedepend, 44735 matplotlib, Meep, Mercurial, Mesa, MetaVelvet, METIS, MPFR, 44736 MTL4, MUMmer, ncurses, OpenFOAM, OpenSSL, ORCA, PAPI, ParMETIS, 44737 Pasha, PCRE, PETSc, petsc4py, pkg-config, Primer3, python-meep, 44738 RNAz, SAMtools, ScientificPython, SCOTCH, setuptools, Shapely, 44739 SHRiMP, SLEPc, SOAPdenovo, Sphinx, SuiteSparse, SWIG, Tcl, 44740 Theano, Tk, Tornado, Trilinos, UFC, UFL, Velvet, ViennaRNA, 44741 Viper, WIEN2k, xcb-proto, XCrySDen, xorg-macros, xproto</li> 44742</ul> 44743</li> 44744<li>added additional example easyconfig files (versions, builds) for 44745 several software packages<ul> 44746<li>Bison, BLACS, Doxygen, flex, GCC, HDF5, icc, ifort, libpng, M4, 44747 MVAPICH2, OpenMPI, Szip, tbb, zlib</li> 44748</ul> 44749</li> 44750<li>replaced GCC/OpenMPI based easyconfig files with equivalents using 44751 the <em>gompi</em> toolchain<ul> 44752<li>ATLAS, BLACS, FFTW, LAPACK, ScaLAPACK</li> 44753</ul> 44754</li> 44755<li>enhanced Python example easyconfig files (more dependencies required 44756 for features, e.g. libreadline, bzip2, zlib, ...)</li> 44757<li>corrected file name of easyconfig files to adher to standard as 44758 followed by EasyBuild robot dependency resolver</li> 44759<li>style cleanup in existing easyconfig files</li> 44760</ul> 44761<h2 id="easybuild-v08-june-29th-2012">EasyBuild v0.8 (June 29th 2012)<a class="headerlink" href="#easybuild-v08-june-29th-2012" title="Permanent link">¶</a></h2> 44762<ul> 44763<li>
44763added support for building/installing 17 additional software 44764 packages:<ul> 44765<li>BEAGLE, Doxygen, g2clib, g2lib, HDF, HDF5, JasPer, libpng, 44766 Maple, MrBayes, NCL, netCDF, netCDF-Fortran, Szip, WPS, WRF, 44767 zlib</li> 44768</ul> 44769</li> 44770<li>the build procedure for WRF and WPS includes running the tests 44771 available for these packages</li> 44772<li>various bug fixes and enhancements:<ul> 44773<li>made support for interactive installers (<code>run_cmd_qa</code>) more 44774 robust</li> 44775<li>fixed Python git package check</li> 44776<li>implemented toolkit functions for determine compiler family, MPI 44777 type, MPI run command, ...</li> 44778</ul> 44779</li> 44780</ul> 44781<h2 id="easybuild-v07-june-18th-2012">EasyBuild v0.7 (June 18th 2012)<a class="headerlink" href="#easybuild-v07-june-18th-2012" title="Permanent link">¶</a></h2> 44782<ul> 44783<li>fixed BLACS build<ul> 44784<li>diagnostic tools to determine <code>INTERFACE</code> and <code>TRANSCOMM</code> values 44785 are now used</li> 44786</ul> 44787</li> 44788<li>added support for building Bison, CP2K, flex<ul> 44789<li>with regression test enabled for CP2K as part of build process</li> 44790<li>note: BLACS built with EasyBuild prior to v0.7 needs to be 44791 rebuilt for CP2K to work correctly</li> 44792</ul> 44793</li> 44794<li>added <code>--enable-mpi-threads</code> to OpenMPI example easyconfigs<ul> 44795<li>required for correct CP2K psmp build</li> 44796</ul> 44797</li> 44798<li>adjusted libsmm example easyconfig for lower build time<ul> 44799<li>to make the full regression test finish in a reasonable amount 44800 of time</li> 44801</ul> 44802</li> 44803<li>added script to make porting of easyblocks from old to new EasyBuild 44804 codebase easier<ul> 44805<li>takes care of refactoring, checks for PyLint warnings/errors, 44806 ...</li> 44807</ul> 44808</li> 44809<li>fixed several small bugs</li> 44810<li>prefixed EasyBuild messages with <code>==</code></li> 44811<li>full regression test passed (58 easyconfigs tested)</li> 44812</ul> 44813<h2 id="easybuild-v06-may-11th-2012">EasyBuild v0.6 (May 11th 2012)<a class="headerlink" href="#easybuild-v06-may-11th-2012" title="Permanent link">¶</a></h2> 44814<ul> 44815<li>added support for Intel compiler toolkit (ictce)<ul> 44816<li>which included the Intel compilers, Intel Math Kernel Library 44817 (imkl) and Intel MPI library (impi)</li> 44818</ul> 44819</li> 44820<li>added support for building Python with nose/numpy/scipy packages</li> 44821<li>added simple regression test</li> 44822<li>this version is able to build all supplied example easyconfigs</li> 44823</ul> 44824<h2 id="easybuild-v05-april-6th-2012">EasyBuild v0.5 (April 6th 2012)<a class="headerlink" href="#easybuild-v05-april-6th-2012" title="Permanent link">¶</a></h2> 44825<ul> 44826<li>first public release of EasyBuild<ul> 44827<li>after a thorough cleanup of the EasyBuild framework of the 44828 in-house version</li> 44829</ul> 44830</li> 44831<li>supports building HPL with goalf compiler toolkit<ul> 44832<li>the goalf toolkit consists of the GCC compilers, and the 44833 OpenMPI, ATLAS, LAPACK, FFTW and ScaLAPACK libraries</li> 44834</ul> 44835</li> 44836<li>also support build and installation of MVAPICH2</li> 44837</ul> 44838 44839 44840 44841 44842 44843 44844 44845 44846 44847 44848 44849 44850 44851 <aside class="md-source-file"> 44852 44853 44854 <span class="md-source-file__fact"> 44855 <span class="md-icon" title="Last update"> 44856 <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1zM12.5 7v5.2l4 2.4-1 1L11 13V7zM11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2z"/></svg> 44857 </span> 44858 <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date" title="August 9, 2026 18:01:56 UTC">August 9, 2026</span> 44859 </span> 44860 44861 44862 44863 44864 44865 </aside> 44866 44867 44868 44869 44870 44871 44872 44873 44874 </article> 44875 </div> 44876 44877
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