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181    <h1 class="entry-title">About this site</h1>
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187        <p><a href="https://travis-ci.org/ICIQ/iciq.github.io"><img src="https://travis-ci.org/ICIQ/iciq.github.io.svg?branch=dev" alt="Build Status" /></a> <a href="https://validator.w3.org/feed/check.cgi?url=https%3A//iciq.github.io/atom.xml"><img src="https://iciq.github.io/assets/img/valid-rss-rogers.png" alt="Validate my RSS feed" /></a></p>
188<h1 id="the-website-for-the-iciq-community">The website for the ICIQ community</h1>
189<p>This site is mostly static HTML, generated by <a href="https://github.com/mojombo/jekyll">Jekyll</a> from <a href="https://github.com/iciq/iciq.github.io">source on Github</a>. You are free to fork and modify it for your own needs. It was modified from <a href="https://i2000s.github.io">Xiaodong Qi’s Noteblog site</a> and was originally based on Carl Boettiger’s <a href="http://carlboettiger.info">labnotebook site</a> and David Ketcheson’s <a href="http://davidketcheson.info">customization</a>. Xiaodong Qi and others published the source for their sites on Github and releases it all under <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons</a> and <a href="http://opensource.org/licenses/MIT">MIT</a> licenses, so setting this site up was as easy as following <a href="http://i2000s.github.io/README.html">these instructions</a>, filling in some account information, replacing the _posts directory, and making a few CSS customizations.</p>
190<p>To run the site on a local computer, you need to install Jekyll and dependencies, run <code>bundle install</code> then <code>bundle exec jekyll serve</code> (see detailed instruction below).</p>
191<p>Please report any errors or other feedback in the <a href="https://github.com/iciq/iciq.github.io/issues">Issue Tracker</a>.</p>
192<h1 id="additional-site-features-credits">Additional Site Features &amp; Credits</h1>
193<ul>
194<li>
194CSS generated with <a href="https://github.com/twbs/bootstrap">bootstrap</a></li>
195<li><a href="https://github.com/cboettig/jekyll-labnotebook-plugins">Carl Boettiger’s plugins</a> for Mendeley, Github, Twitter and others</li>
196<li>Integrated with IPython/IJulia/Jupyter notebooks and <a href="https://www.mathjax.org">MathJax</a></li>
197<li>Source code hosting on <a href="https://github.com/ketch/labnotebook">Github</a> with automatic deployment using <a href="http://travis-ci.org">Travis-CI</a> and Rake</li>
198<li>Improved “related posts” plugin from <a href="https://github.com/kemayo/davidlynch.org/blob/master/_plugins/related_posts.rb">David Lynch</a></li>
199<li>Improved publication and citation support from <a href="https://github.com/inukshuk/jekyll-scholar">Jekyll-scholar</a> with some customizations</li>
200<li>Allow pulling BibTeX database of bibliography from an external repository using <a href="https://git-scm.com/docs/git-submodule">submodule</a> for centralized bibliography management</li>
201</ul>
202<h1 id="instruction-on-hosting-the-site-locally">Instruction on hosting the site locally</h1>
203<p>I use Ubuntu 16.04 LTS OS to generate the static website from source code. Instructions on other operating systems should be similar. The first thing to do is to clone the remote repository files to your local computer by</p>
204<pre><code>git clone --recursive https://github.com/iciq/iciq.github.io.git</code></pre>
205<p>where the <code>--recursive</code> option is to make sure submodules (if any) are pulled down completely.</p>
206<p>If you run Jekyll sites for the first time, you may need to install Ruby v2.3.* (tested on v2.3.0 and v2.3.1) and the <code>gem</code> development envirenment. I was basically following <a href="http://tecadmin.net/install-ruby-on-rails-on-ubuntu/">this instruction</a> on my Ubuntu, except for the step of sourcing RVM which I used the following command line instead</p>
207<pre><code>source ~/.rvm/scripts/rvm</code></pre>
208<p>But you may find the source command works for you. An improvement on the source command line following the instruction in the link is to use</p>
209<pre><code>echo &quot;source /etc/profile.d/rvm.sh&quot; &gt;&gt; ~/.bash_profile</code></pre>
210<p>which will add the rvm path to the bash profile perminantly. If the source is setup correctly, <code>type rvm | head -n 1</code> should give <code>rvm is a function</code> as the output according to <a href="https://rvm.io/rvm/install">this</a>. If you encounter any problem before the sourcing step, you should make sure whether the security key has been updated from the official <a href="https://rvm.io/rvm/install">Ruby site</a>. Or, if you find the problem is due to the certificate, you may want to check out <a href="http://stackoverflow.com/questions/3160909/how-do-i-deal-with-certificates-using-curl-while-trying-to-access-an-https-url/30154802#30154802">this solution</a>. Otherwise, you can also install rvm from a third-party repo following <a href="https://github.com/rvm/ubuntu_rvm">this instruction</a> on Ubuntu OS and follow the outputed command line instruction on sourcing the profile.</p>
211<p>On Ubuntu 16.04, you can follow <a href="https://gorails.com/setup/ubuntu/16.04">this instruction</a> for updated information. I would recommend you to use rvm on Rails to configure a compatible Ruby version, which is employed on travis.CI. In the process of installing Ruby through rvm, if you encounter the <strong><em>permission denied</em></strong> error, you can try</p>
212<pre><code>rvmsudo rvm install 2.3.1</code></pre>
213<p>as an example. Similarly, if <code>gem install rails</code> or other gem install command lines fail, you can also try</p>
214<pre><code>rvmsudo gem install rails</code></pre>
215<p>or similar to help solve some gem/Ruby package installation errors by promoting permissions in rvm.</p>
216<p>For other systems, <a href="https://www.ruby-lang.org/en/documentation/installation/">here</a> is the official guide for Ruby installation.</p>
217<p>Besides, the library of <code>gsl</code> and the <code>pandoc</code> package are recommended to install for better support to the <code>clarifier-reborn</code> and other plugins/scripts used in this site. On Ubuntu, I use the following lines</p>
218<pre><code>sudo add-apt-repository -y ppa:marutter/c2d4u
219sudo apt-get update
220sudo apt-get install pandoc
221sudo apt-get install gsl-bin libgsl0-dev</code></pre>
222<p>On Windows OS, you may be able to follow <a href="https://davidburela.wordpress.com/2015/11/28/easily-install-jekyll-on-windows-with-3-command-prompt-entries-and-chocolatey/">this instruction</a> to install Jekyll. If you find some error related to Ruby Development Kit when you run <code>bundle exec jekyll serve</code> or <code>gem install ***</code>, you may find <a href="http://flatshaded.com/2013/05/installing-jekyll-on-windows/">this experience</a> helpful. <code>gsl</code> should be preinstalled in order to gem install <code>rb-gsl</code>, where the step in the <code>.travis.yml</code> configuration file about installing <code>gsl-bin</code> step does not apply to Windows systems.</p>
223<p>The <code>Gemfile</code> and the configuration files <code>_conf.yml</code> and <code>.travis.yml</code> should include sufficient information on installing correct dependences. Then for a rout
223inely rendering, you only need to run the following command lines:</p>
224<pre><code>bundle install
225bundle exec jekyll serve</code></pre>
226<p>Notice that, I have locked the Jekyll version to <code>~&gt;3.1.6</code>. If you want to use Jekyll version 2.5 or earlier, you may need to tweak the code a little bit.</p>
227<p>If you encounter the missing credentials error for the <code>twitter_feed</code> plugin, you may need to export environmental variables <code>TWIT_KEY</code>, <code>TWIT_SECRET</code>, <code>TWIT_TOK</code> and <code>TWIT_TOK_SECRET</code> before running the jekyll server. All the credentials of the Twitter plugin should be accessible from the TWitter account used for the site.</p>
228<p>By default, the local build should be accessible at <code>http://127.0.0.1:4000</code> on your internet browser.</p>
229<h1 id="how-to-adapt-this-source-code-to-generate-your-own-jekyll-website">How to adapt this source code to generate your own Jekyll website</h1>
230<p>Since Jekyll uses a very efficient way to control common information in fewer places, you can easily modify the source code of this website to generate your own website on GitHub and deploy to elsewhere. In fact, when the site was initially designed and modified especially to my end, it has always been a common goal to make it easy for the community to migrate this source code to other web hosts and adapt to various purposes. I encourage you to post an issue or make a pull request on this repo or the original <a href="http://carlboettiger.info">labnotebook repo</a> if you find a way to improve the general design. Only in this way, the network of people who have adapted this design to their sites can benefit most from the continuous improvement by the community who are following this body of code for open science and beyond. Below are the minimum changes you need to make to serve your own purpose of using the source code.</p>
231<ol type="1">
232<li><p>Fork this repo under your GitHub account, and then clone the repo to your local folder by <code>git clone --recursive YOURGITREPOREMOTE</code>.</p></li>
233<li><p>Change information defined in the <code>_config.yml</code> file for your case. There you will find definitions for your site, Github account and repo information, as well as your personal contact information. I will explain more advanced setting information below.</p></li>
234<li><p>Add encrypted information in the <code>.travis.yml</code> file. There you will find the <code>env/global</code> section where global variables are defined to automatically generate twitter timeline, github comment history and <a href="http://awestruct.org/auto-deploy-to-github-pages/">deploy the site as gh-pages on the Travis-CI server</a>. You should remove all the original code starting with <code>secure</code> and replace with your own encrypted codes line by line in the <code>.travis.yml</code> file or on the Travis-CI setting page. The recommended minimum global variables to be encrypted are: <a href="https://help.github.com/articles/creating-an-access-token-for-command-line-use/">Github Token</a> (variable name <code>GH_TOKEN</code>), git commit author name (<code>GIT_NAME</code>), git commit author email (<code>GIT_EMAIL</code>); if you want to generate a Twitter message line on your site using the <code>twitter_feed.rb</code> plugin, you will also need to encrypt Twitter key (<code>TWIT_KEY</code>), secret (<code>TWIT_SECRET</code>), token (<code>TWIT_TOK</code>), token secret (<code>TWIT_TOK_SECRET</code>). Before you commit this step, make sure you have <a href="https://travis-ci.org/getting_started">ativated the Travis-CI module for your Github repo</a>. You can then generate the encrypted variables by installing travis while on your local repo directory with command <code>gem install travis</code> and using the following command line format <code>travis encrypt GIT_NAME=&quot;Xiaodong Qi&quot;</code>. You should replace the variable name and value with the real cases as bash commands one after one. Notice that when the variable value has a space inside, you need to use a pair of quotation marks as the example I gave–otherwise no need to use quotation marks in most cases; if you have special characters that bash command doesn’t like, you need to <a href="http://wiki.bash-hackers.org/syntax/quoting">escape those characters</a>. The last command line should generate a long string of random characters which you should be able to add to the <code>env/global</code> section of the <code>.travis.yml</code> file in the format of <code>- secure Your_Encrypt_Random_bits</code>. You can certainly add more encrypt variables or define some non-sensitive variables as explicit/non-encrypted variables in a similar way, but the Github token has to be encrypted to pass the security check of Github.</p></li>
235<li><p>If you have different amount of social accounts or plugin items defined in the <code>_config.yml</code> file, you need to double modify the scripts appeared in the header and footer template under the <code>_include</code> directory. Notice that, by using different set of social account info in the configure file, the default social media icons will link to the front page of those empty social network websites. To avoid these unwanted icons, you may want to delete/comment out those icon blocks in the footer templates and the index.html pages. Similarly, if you want to add new social media icons, you can modify the configure file and corresponding footers with a compatible icon image. On the top of this README file, there is an icon showing the compilation status of Travis-CI, you might want to modify the icon address to your case–pay attention to the username/organization name which is capital sensitive to Travis-CI.</p></li>
236<li><p>Check the <code>metadata.html</code> template defined under the <code>_include</code> directory to make sure necessary information are shown correctly for you. This metadata is just for different search engines and robots to recognize your website in particular formats. I have used fields like <code>OtherName</code> to identify the author’s local language name, as well as both Google analytics and Baidu analytics IDs for page visitor statistics. You can delete this field in the <code>config.yml</code> and the <code>metadata.html</code> files. The <code>analytics.html</code> template in the <code>_include</code> directory has the website visiting analytics scripts for Google and Baidu which you may 
236need to delete one or add a new one according to your preference. The metadata file also defines the language information and keywords where you should most likely modify for your own version. Other information if you don’t understand, leaving them alone should be fine in most cases.</p>
237<p>The publication and citation databases are defined in the <code>asset</code> directory as bibtex files with suffix <code>.bib</code>, which you may want to replace with your own.<br />The rest is to delete or keep posts and pages to fit into your needs. Notice that you can use <a href="https://git-scm.com/docs/git-submodule">submodule</a> and put references in a folder like <code>assets/bibliography/refs</code> to a centralized bibliography database. The information of the submodule is then recorded in the <code>.gitsubmodules</code> file under the root direction of the repo. To use your own submodule, add the submodule by <code>git submodule add -b YOURBibliographyBRANCH https://YOURBibliographyRemoteAddress.git assets/bibliography/refs</code>. It might be also necessary to run <code>git submodule init</code> or <code>git submodule update</code> to pull your submodule files into the actual folder if it’s empty. After that, you also need to update the bibliography address in the corresponding <code>pandoc</code> bibliography extension configuration item of the <code>_config.yml</code> file. One advantage of using the <a href="https://git-scm.com/docs/git-submodule">submodule</a> feature of Git is that you can commit and push changes from this webpage repo to your bibliography repo on the specific branch and vice verse. Changes of the submodule can be committed in the corresponding submodule folder using Git the same as an independent git repo. When you want to pull changes from the centralized bibliography repo, you can use <code>git submodule update --remote</code> and the webpage repo will have the corresponding SHA reference recorded in the git configuration file. Make sure you always commit the submodule changes before committing to this webpage development repo (also regarded as the <em>superproject</em>).</p></li>
238</ol>
239<p>I suggest to put this source code in a branch other than <code>master</code> or <code>gh-pages</code> in your Github repository, which you need to define in the <code>_config.yml</code> file as the <code>sourcebranch</code>
239. The Travis-CI server will commit the generate website onto the <code>master</code> or <code>gh-pages</code> github branch depending on your case. Once you have all the necessary configurations done, Travis-CI will be happily deploying your site on Github. If you want the site to be deployed on a host other than Github, you may want to modify and run the <code>publish.sh</code> bash script to synchronize your locally generated <code>_site</code> folder or the master/gh-pages branch updated by Travis-CI to your target site host.</p>
240<h1 id="copyrights-and-licenses">Copyrights and Licenses</h1>
241<p><a href="http://opensource.org/licenses/MIT">MIT</a> license for the plugins (in the <code>_plugins</code> directory of this repo) shown initially written by Carl Boettiger or Xiaodong Qi. Creative Commons Attributions 3.0 Unported <a href="http://creativecommons.org/licenses/by/3.0/deed.en_US">CC-BY</a> license for the content originally created by David Ketcheson. Creative Commons Attributions 4.0 <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY</a> license for content other than plugins originally written by Xiaodong Qi and all the other unspecified cases. If a license is clarified at a much specified scope, that specified license should apply to the scope it covers. You can find the full editing history of each file. Credits should be given appropriately to the origination and the initial author at less and all following contributors if situation permits.</p>
242<p>For instance, you can cite or attribute posts/works originally from this site/repository as:</p>
243<p>Xiaodong Qi (“Page publication date”), “Page Title”, Lab Notebook, <a href="http://i2000s.github.io">http://i2000s.github.io</a></p>
244<p>with appropriate page title and publication date as indicated. <a href="http://greycite.knowledgeblog.org/">Greycite</a> is an excellent online tool that can generate the citation information for any particular page given it’s URL.</p>
245<p>This website is also built with HTML KickStart (Joshua Gatcke http://www.99lime.com | HTML KickStart) which is <a href="https://github.com/joshuagatcke/HTML-KickStart#html-kickstart-is-free-and-open-source">released under MIT Open Source license</a>.</p>
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