Redirect links

.github/CONTRIBUTING.md

@@ -9,8 +9,8 @@ How to contribute
 
 :bulb: **Check out the [MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools) - and contribute the smart way!**
 
-- Please follow the [Style Guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/STYLEGUIDE.md).
-- More information on writing a **test** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/TESTGUIDE.md) and a template is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/testTemplate.m).
-- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/ISSUEGUIDE.md).
+- Please follow the [Style Guide](https://opencobra.github.io/cobratoolbox/docs/styleGuide.html).
+- More information on writing a **test** is [here](https://opencobra.github.io/cobratoolbox/docs/testGuide.html) and a template is [here](https://opencobra.github.io/cobratoolbox/docs/testTemplate.html).
+- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://opencobra.github.io/cobratoolbox/docs/issueGuide.html).
 
 If you want to use `git` via the command line interface and need help, these [training slides](https://uni-lu.github.io/slides/) will get you started. This [guide](https://www.digitalocean.com/community/tutorials/how-to-create-a-pull-request-on-github) or the official [GitHub guide](https://help.github.com/articles/creating-a-pull-request/) also come in handy.

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,8 +3,8 @@
 
 **I hereby confirm that I have:**
 
-- [ ] Selected `develop` as a target branch (top left drop-down menu)
 - [ ] Tested my code on my own machine
-- [ ] Followed the guidelines in the [Contributing Guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/CONTRIBUTING.md)
+- [ ] Followed the guidelines in the [Contributing Guide](https://opencobra.github.io/cobratoolbox/docs/contributing.html)
+- [ ] Selected `develop` as a target branch (top left drop-down menu)
 
 *(Note: You may replace [ ] with [X] to check the box)*

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img class="readme_logo" src="https://raw.githubusercontent.com/opencobra/cobratoolbox/master/docs/source/_static/logo.png" height="160px"/>
+  <img class="readme_logo" src="https://raw.githubusercontent.com/opencobra/cobratoolbox/master/docs/source/_static/images/logos/logo.png" height="160px"/>
 </p>
 
 The COBRA Toolbox <br> COnstraint-Based Reconstruction and Analysis Toolbox
@@ -32,12 +32,12 @@ The COBRA Toolbox <br> COnstraint-Based Reconstruction and Analysis Toolbox
 System Requirements
 -------------------
 
-<img src="https://prince.lcsb.uni.lu/jenkins/userContent/warning.png" height="20px" alt="warning"> Please follow [this guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md) in order to configure your system properly.
+<img src="https://prince.lcsb.uni.lu/jenkins/userContent/warning.png" height="20px" alt="warning"> Please follow [this guide](https://opencobra.github.io/cobratoolbox/docs/requirements.html) in order to configure your system properly.
 
 Solver Installation
 -------------------
 
-The default solver is `glpk` (for `LP` and `MILP`). You can install `TOMLAB`, `IBM ILOG CPLEX`, `GUROBI`, or `MOSEK` by following these **[detailed instructions](https://github.com/opencobra/cobratoolbox/blob/master/.github/SOLVERS.md)**.
+The default solver is `glpk` (for `LP` and `MILP`). You can install `TOMLAB`, `IBM ILOG CPLEX`, `GUROBI`, or `MOSEK` by following these **[detailed instructions](https://opencobra.github.io/cobratoolbox/docs/solvers.html)**.
 
 Installation
 ------------
@@ -68,7 +68,7 @@ Support and Documentation
 
 - The documentation is available [here](http://opencobra.github.io/cobratoolbox). This version is in development, but the legacy version of the documentation is  [here](http://opencobra.github.io/cobratoolbox/deprecated/docs/index.html).
 
-- Answers to Frequently Asked Questions (**FAQ**) are [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/FAQ.md).
+- Answers to Frequently Asked Questions (**FAQ**) are [here](https://opencobra.github.io/cobratoolbox/docs/FAQ.html).
 
 - If you need support, please feel free to post your question in our <a href="https://groups.google.com/forum/#!forum/cobra-toolbox"><img src="https://img.shields.io/badge/COBRA-forum-blue.svg"></a>.
 
@@ -83,14 +83,14 @@ How to contribute
 
 <img src="https://prince.lcsb.uni.lu/jenkins/userContent/bulb.png" height="20px" alt="bulb"> **Check out the [MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools) - and contribute the smart way!**
 
-- Please follow the [Style Guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/STYLEGUIDE.md).
-- More information on writing a **test** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/TESTGUIDE.md) and a template is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/testTemplate.m).
-- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/ISSUEGUIDE.md).
+- Please follow the [Style Guide](https://opencobra.github.io/cobratoolbox/docs/styleGuide.html).
+- More information on writing a **test** is [here](https://opencobra.github.io/cobratoolbox/docs/testGuide.html) and a template is [here](https://opencobra.github.io/cobratoolbox/docs/testTemplate.html).
+- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://opencobra.github.io/cobratoolbox/docs/issueGuide.html).
 
 If you want to use `git` via the command line interface and need help, these [training slides](https://uni-lu.github.io/slides/) will get you started. This [guide](https://www.digitalocean.com/community/tutorials/how-to-create-a-pull-request-on-github) or the official [GitHub guide](https://help.github.com/articles/creating-a-pull-request/) also come in handy.
 
 How to cite `The COBRA Toolbox`
----------------
+-------------------------------
 
 When citing `The COBRA Toolbox`, it is important to cite the original paper where an algorithm was first reported, as well as its implementation in `The COBRA Toolbox`. This is important, because the objective of `The COBRA Toolbox` is to amalgamate and integrate the functionality of a wide range of COBRA algorithms and this will be undermined if contributors of new algorithms do not get their fair share of citations. The following is one example how to approach this within the methods section of a paper (**not** the supplemental material please):
 
@@ -110,7 +110,7 @@ For convenience, we provide the [`SBMLToolbox 4.1.0`](http://sbml.org/Software/S
 [Binaries](https://github.com/opencobra/COBRA.binary) for these libraries are provided in a submodule for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 10.0 (64-bit), and Microsoft Windows 7 (64-bit).
 For unsupported OS, please refer to their respective building instructions ([`glpk_mex`](https://github.com/blegat/glpkmex#instructions-for-compiling-from-source), [`libSBML`](http://sbml.org/Software/libSBML/5.13.0/docs//cpp-api/libsbml-installation.html)).
 
-Read more on the compatibility with SBML-FBCv2 [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/NOTES.md).
+Read more on the compatibility with SBML-FBCv2 [here](https://opencobra.github.io/cobratoolbox/docs/notes.html).
 
 Disclaimer
 ----------

docs/source/_templates/README.html

@@ -2,7 +2,7 @@ <h1 align="center"> Documentation <br> COnstraint-Based Reconstruction <br>and A
 <br>
 <br>
 <div class="alert alert-info" align="center">
-    View The COBRA Toolbox <strong>source code</strong> on <a href="https://github.com/opencobra/cobratoolbox/"><img src="_static/github.png" height="40px"></a>.
+    View The COBRA Toolbox <strong>source code</strong> on <a href="https://github.com/opencobra/cobratoolbox/"><img src="_static/images/logos/github.png" height="40px"></a>.
 </div>
 <br>
 <br>

docs/source/conf.py

@@ -188,7 +188,7 @@ def linkcode_resolve(domain, info):
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 #
-html_logo = '_static/logo.png'
+html_logo = '_static/images/logos/logo.png'
 
 # The name of an image file (relative to this directory) to use as a favicon of
 # the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

docs/source/contributing.rst

@@ -9,9 +9,9 @@ How to contribute
    </p>
    <p><a href="https://camo.githubusercontent.com/f1f4e83e3a6695a8167251cd8f0b2cb6d9f5b757/68747470733a2f2f7072696e63652e6c6373622e756e692e6c752f6a656e6b696e732f75736572436f6e74656e742f62756c622e706e67" target="_blank"><img src="https://camo.githubusercontent.com/f1f4e83e3a6695a8167251cd8f0b2cb6d9f5b757/68747470733a2f2f7072696e63652e6c6373622e756e692e6c752f6a656e6b696e732f75736572436f6e74656e742f62756c622e706e67" height="20px" alt="bulb" data-canonical-src="https://prince.lcsb.uni.lu/jenkins/userContent/bulb.png" style="max-width:100%;"></a> <strong>Check out the <a href="https://github.com/opencobra/MATLAB.devTools">MATLAB.devTools</a> - and contribute the smart way!</strong></p>
    <ul>
-   <li>Please follow the <a href="https://github.com/opencobra/cobratoolbox/blob/master/.github/STYLEGUIDE.md">Style Guide</a>.</li>
-   <li>More information on writing a <strong>test</strong> is <a href="https://github.com/opencobra/cobratoolbox/blob/master/.github/TESTGUIDE.md">here</a> and a template is <a href="https://github.com/opencobra/cobratoolbox/blob/master/.github/testTemplate.m">here</a>.</li>
-   <li>A guide for reporting an <strong>issue</strong> or submitting a <strong>pull request (PR)</strong> is <a href="https://github.com/opencobra/cobratoolbox/blob/master/.github/ISSUEGUIDE.md">here</a>.</li>
+   <li>Please follow the <a href="https://opencobra.github.io/cobratoolbox/docs/styleGuide.html">Style Guide</a>.</li>
+   <li>More information on writing a <strong>test</strong> is <a href="https://opencobra.github.io/cobratoolbox/docs/testGuide.html">here</a> and a template is <a href="https://opencobra.github.io/cobratoolbox/docs/testTemplate.html">here</a>.</li>
+   <li>A guide for reporting an <strong>issue</strong> or submitting a <strong>pull request (PR)</strong> is <a href="https://opencobra.github.io/cobratoolbox/docs/issueGuide.html">here</a>.</li>
    </ul>
    <p>If you want to use <code>git</code> via the command line interface and need help, these <a href="https://uni-lu.github.io/slides/">training slides</a> will get you started. This <a href="https://www.digitalocean.com/community/tutorials/how-to-create-a-pull-request-on-github">guide</a> or the official <a href="https://help.github.com/articles/creating-a-pull-request/">GitHub guide</a> also come in handy.</p>
    <h2>How to cite <code>The COBRA Toolbox</code></h2>
@@ -23,4 +23,3 @@ How to contribute
    <blockquote>
    <p>[2] = Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. 2011 Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nature Protocols 6:1290-1307.</p>
    </blockquote>
-

docs/source/faq.rst

@@ -1,7 +1,6 @@
 Support
 =======
 
-Answers to Frequently Asked Questions (**FAQ**) are `here <https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/FAQ.md>`_.
+Answers to Frequently Asked Questions (**FAQ**) are `here <https://opencobra.github.io/cobratoolbox/docs/FAQ.html>`_.
 
 If you need support, please feel free to post your question in our `forum <https://groups.google.com/forum/#!forum/cobra-toolbox>`_.
-

docs/source/funding.rst

@@ -29,11 +29,4 @@ Funding
            <div style="align-center;"><a href="https://energy.gov"><img src="_static/images/logos/doe.png" alt="" width="100%"></a></div>
        </li>
    </ul>
-   <br>
-   <br>
-   <br>
-   <p align="center" style="font-size:20px"> <strong> Principal investigators </strong>
-   <br><br>
-   Ronan Fleming &#8213; Ines Thiele &#8213; Thomas Sauter
    </p>
-

docs/source/guides/testGuide.md

@@ -1,6 +1,6 @@
 # Guide for writing a test
 
-Before starting to write a test on your own, it might be instructive to follow common test practices in `/test/verifiedTests`. A style guide on how to write tests is given [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/STYLEGUIDE.md).
+Before starting to write a test on your own, it might be instructive to follow common test practices in `/test/verifiedTests`. A style guide on how to write tests is given [here](https://opencobra.github.io/cobratoolbox/docs/styleGuide.html).
 
 ## Test if an output is correct
 
@@ -55,7 +55,7 @@ Note that this allows the error message to be thrown without failing the test.
 
 ## Test template
 
-A test template is readily available [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/testTemplate.m). The following sections shall be included in a test file:
+A test template is readily available [here](https://opencobra.github.io/cobratoolbox/docs/testTemplate.html). The following sections shall be included in a test file:
 
 #### 1. Header
 ````Matlab

docs/source/installation.rst

@@ -6,12 +6,12 @@ Installation
    <br>
    <div class="alert alert-danger">
      <strong>System Requirements:</strong>
-     Please follow <a href="https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md">this guide</a> in order to configure your system properly.
+     Please follow <a href="https://opencobra.github.io/cobratoolbox/docs/requirements.html">this guide</a> in order to configure your system properly.
    </div>
-   
+
    <div class="alert alert-warning">
        <strong>Solver Installation:</strong>
-       The default solver is <code>glpk</code> (for <code>LP</code> and <code>MILP</code>). You can install <code>TOMLAB</code>, <code>IBM ILOG CPLEX</code>, <code>GUROBI</code>, or <code>MOSEK</code> by following these <strong><a href="https://github.com/opencobra/cobratoolbox/blob/master/.github/SOLVERS.md">detailed instructions</a></strong>.
+       The default solver is <code>glpk</code> (for <code>LP</code> and <code>MILP</code>). You can install <code>TOMLAB</code>, <code>IBM ILOG CPLEX</code>, <code>GUROBI</code>, or <code>MOSEK</code> by following these <strong><a href="https://opencobra.github.io/cobratoolbox/docs/solvers.html">detailed instructions</a></strong>.
    </div>
    <ol>
    <li>
@@ -38,4 +38,4 @@ Binaries and Compatibility
    <p>For convenience, we provide the <a href="http://sbml.org/Software/SBMLToolbox"><code>SBMLToolbox 4.1.0</code></a>, and <a href="https://github.com/blegat/glpkmex"><code>glpk_mex</code></a> in <code>external/toolboxes</code>, <a href="http://sbml.org/Software/libSBML"><code>libSBML-5.13.0-matlab</code></a> in <code>src/io/utilities</code>.</p>
    <p><a href="https://github.com/opencobra/COBRA.binary">Binaries</a> for these libraries are provided in a submodule for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 10.0 (64-bit), and Microsoft Windows 7 (64-bit).<br>
    For unsupported OS, please refer to their respective building instructions (<a href="https://github.com/blegat/glpkmex#instructions-for-compiling-from-source"><code>glpk_mex</code></a>, <a href="http://sbml.org/Software/libSBML/5.13.0/docs//cpp-api/libsbml-installation.html"><code>libSBML</code></a>).</p>
-   <p>Read more on the compatibility with SBML-FBCv2 <a href="https://github.com/opencobra/cobratoolbox/blob/master/.github/NOTES.md">here</a>.</p>
+   <p>Read more on the compatibility with SBML-FBCv2 <a href="https://opencobra.github.io/cobratoolbox/docs/notes.html">here</a>.</p>

docs/source/installation/requirements.md

@@ -39,5 +39,5 @@ In order to install `git`, install the [Xcode Command Line Tools](http://osxdail
 Please download the `git` tools for Windows from [here](https://git-scm.com/download). During the installation process, please ensure that you select **Use Git from the Windows Command Prompt**. In addition, please make sure that you select **Checkout as-is, commit Unix-style line endings**.
 
 <div align="center">
-<img src="assets/installation_git_windows_0.png" height="280px">&nbsp;&nbsp;&nbsp;<img src="assets/installation_git_windows_1.png" height="280px">.
+<img src="../_static/images/installation_git_windows_0.png" height="280px">&nbsp;&nbsp;&nbsp;<img src="../_static/images/installation_git_windows_1.png" height="280px">.
 </div>

docs/source/notes/FAQ.md

@@ -5,7 +5,7 @@ Frequently Asked Questions (FAQ)
 
 **What do all these labels mean?**
 
-A comprehensive list of labels and their description for the issues and pull requests is given [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/LABELS.md).
+A comprehensive list of labels and their description for the issues and pull requests is given [here](https://opencobra.github.io/cobratoolbox/docs/labels.html).
 
 ## Reconstruction
 
@@ -32,9 +32,9 @@ git rm --cached external/lusolMex64bit
 
 When running cobra code in a parfor loop, solvers (and other global variables) are not properly set.  
 
-**Answer**: This is an issue with global variables and the matlab parallel computing toolbox. 
+**Answer**: This is an issue with global variables and the matlab parallel computing toolbox.
 Global variables are not passed on to the workers of a parallel pool.  
-To change cobra global settings for a parfor loop, it is necessary to 
+To change cobra global settings for a parfor loop, it is necessary to
 reinitialize the global variables on each worker. The easiest way to do this is as follows:
 ```Matlab
 global CBT_SOLVER_LP
@@ -45,5 +45,5 @@ parfor 1:2
     optimizeCbModel(model);
 end
 ```
-By requesting the current global variable before the parfor loop and assigning it to a local variable, that variable is passed on to the workers, 
-which can then use it to set up the correct solver (or other variable). 
+By requesting the current global variable before the parfor loop and assigning it to a local variable, that variable is passed on to the workers,
+which can then use it to set up the correct solver (or other variable).

initCobraToolbox.m

@@ -530,7 +530,7 @@ function checkGit()
         end
     else
         fprintf(result_gitVersion);
-        fprintf([' > Please follow the guidelines on how to install git ', hyperlink('https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md.', 'here', 'here: '), '.\n']);
+        fprintf([' > Please follow the guidelines on how to install git ', hyperlink('https://opencobra.github.io/cobratoolbox/docs/requirements.html.', 'here', 'here: '), '.\n']);
         error(' > git is not installed.');
     end
 end
@@ -565,7 +565,7 @@ function checkGit()
     else
         if throwError
             fprintf(result_curl);
-            fprintf([' > Please follow the guidelines on how to install curl ', hyperlink('https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md.', 'here', 'here: '), '.\n']);
+            fprintf([' > Please follow the guidelines on how to install curl ', hyperlink('https://opencobra.github.io/cobratoolbox/docs/requirements.html.', 'here', 'here: '), '.\n']);
             error(' > curl is not installed.');
         else
             if ENV_VARS.printLevel