Merge pull request #27 from opencobra/develop

Regular merge of develop

Author: laurentheirendt

.artenolis.yml

@@ -7,7 +7,7 @@ before_install:
     - CURRENT_DIR=`pwd`;
 
     # remove the cloned repository even after failure
-    - rm -rf ~/MATLAB.devTools.CI;
+    - rm -rf $ARTENOLIS_DATA_PATH/repos/MATLAB.devTools.CI;
 
     # change to the current directory
     - cd $CURRENT_DIR;
@@ -20,9 +20,9 @@ script:
     - cd $CURRENT_DIR;
 
     # before launching the tests, make sure that the upstream repository is changed
-    - cd;
-    - rm -rf ~/MATLAB.devTools.CI;
-    - git clone [email protected]:uni-lu/MATLAB.devTools.CI.git;
+    - cd $ARTENOLIS_DATA_PATH/repos/;
+    - rm -rf MATLAB.devTools.CI;
+    - git clone [email protected]:LCSB-BioCore/MATLAB.devTools.CI.git;
     - cd MATLAB.devTools.CI;
     - git remote -v;
     - eval "$(ssh-agent -s)";
@@ -50,16 +50,23 @@ script:
     # launch the tests
     - sh ./.artenolis/runtests.sh;
 
-    - cd ~/fork-MATLAB.devTools.CI;
-    - git reset --hard origin/develop;
-
 after_success:
 
-    # remove the cloned fork-repo
-    - if [ "$MATLAB_VER" == "R2016b" ]; then
+    # submit coverage report
+    - if [[ "$MATLAB_VER" == "R2018b" && "$ARCH" == "Linux" ]]; then
       bash <(curl -s https://codecov.io/bash) -f "!*.lst";
-      export PATH="/home/sbg-jenkins/.local/bin":$PATH;
+      fi
+
+    # deploy the documentation
+    - if [[ "$MATLAB_VER" == "R2018b" && "$JENKINS_PULL_REQUEST" != "True" ]]; then
+      export PATH="/home/jenkins/.local/bin":$PATH;
       cd $CURRENT_DIR;
       pip install --upgrade --user -r docs/requirements.txt;
       python -c "from documenter.deploy import Documentation; doc = Documentation('github.com/opencobra/MATLAB.devTools', ci='jenkins'); doc.deploy()";
       fi
+
+after_script:
+
+    # reset the fork
+    - cd $ARTENOLIS_DATA_PATH/repos/fork-MATLAB.devTools.CI;
+    - git reset --hard origin/develop;

.artenolis/runtests.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
 cd ./test
-/mnt/prince-data/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash -r "launchTests;" < inputCI.txt;
+$ARTENOLIS_SOFT_PATH/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash -r "launchTests;" < inputCI.txt;
 CODE=$?
 exit $CODE

.gitignore

@@ -36,5 +36,7 @@ Temporary Items
 [Dd]esktop.ini
 
 # Documentation related files
+docs/.documenter.enc
+docs/.documenter
 docs/source/_static/json/functions.json
 *.pyc

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "external/rdir"]
 	path = external/rdir
-	url = https://github.com/uni-lu/rdir.git
+	url = https://github.com/LCSB-BioCore/rdir.git

README.rst

@@ -9,9 +9,9 @@
    </h1>
 
 +----------------+----------------+---------------+--------------+
-| MATLAB R2016b  | MATLAB R2015b  | Code Coverage | Code Grade   |
+| MATLAB R2018b  | MATLAB R2017b  | Code Coverage | Code Grade   |
 +================+================+===============+==============+
-| |Build Status| | |Build Status| | |codecov|     | |Code grade| |
+| |bs2018|       | |bs2017|       | |codecov|     | |Code grade| |
 +----------------+----------------+---------------+--------------+
 
 .. begin-description-marker
@@ -207,19 +207,19 @@ paper of The COBRA Toolbox shall we cited when referring to the ``MATLAB.devTool
     A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter,
     Bernhard Ø. Palsson, Ines Thiele, Ronan M.T. Fleming, **Creation and
     analysis of biochemical constraint-based models: the COBRA Toolbox
-    v3.0** (submitted), 2017,
-    `arXiv:1710.04038 <https://arxiv.org/abs/1710.04038>`__.
+    v3.0**, Nature Protocols, volume 14, pages 639–702, 2019
+    `doi.org/10.1038/s41596-018-0098-2 <https://doi.org/10.1038/s41596-018-0098-2>`__.
 
 .. end-how-to-cite-marker
 
 
-.. |Build Status| image:: https://prince.lcsb.uni.lu/jenkins/buildStatus/icon?job=devTools-branches-auto/MATLAB_VER=R2016b
-   :target: https://prince.lcsb.uni.lu/jenkins/job/devTools-branches-auto/MATLAB_VER=R2016b/
-.. |Build Status| image:: https://prince.lcsb.uni.lu/jenkins/buildStatus/icon?job=devTools-branches-auto/MATLAB_VER=R2015b
-   :target: https://prince.lcsb.uni.lu/jenkins/job/devTools-branches-auto/MATLAB_VER=R2015b/
+.. |bs2018| image:: https://prince.lcsb.uni.lu/jenkins/job/devTools-branches-auto/MATLAB_VER=R2018b,label=prince-slave-linux-01/badge/icon
+   :target: https://prince.lcsb.uni.lu/jenkins/job/devTools-branches-auto/MATLAB_VER=R2018b,label=prince-slave-linux-01
+.. |bs2017| image:: https://prince.lcsb.uni.lu/jenkins/job/devTools-branches-auto/MATLAB_VER=R2017b,label=prince-slave-linux-01/badge/icon
+   :target: https://prince.lcsb.uni.lu/jenkins/job/devTools-branches-auto/MATLAB_VER=R2017b,label=prince-slave-linux-01
 .. |codecov| image:: https://codecov.io/gh/opencobra/MATLAB.devTools/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/opencobra/MATLAB.devTools/branch/master
-.. |Code grade| image:: https://prince.lcsb.uni.lu/jenkins/userContent/codegrade-MATLABdevTools.svg?maxAge=0
+.. |Code grade| image:: https://prince.lcsb.uni.lu/MATLAB.devTools/codegrade/codegrade.svg?maxAge=0
 
 
 .. begin-screencast-marker
@@ -233,30 +233,30 @@ paper of The COBRA Toolbox shall we cited when referring to the ``MATLAB.devTool
 .. begin-icon-marker
 .. |macos| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/apple.png" height="20px" width="20px" alt="macOS">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/apple.png" height="20px" width="20px" alt="macOS">
 
 .. |linux| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/linux.png" height="20px" width="20px" alt="linux">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/linux.png" height="20px" width="20px" alt="linux">
 
 .. |windows| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/windows.png" height="20px" width="20px" alt="windows">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/windows.png" height="20px" width="20px" alt="windows">
 
 .. |matlab| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/matlab.png" height="20px" width="20px" alt="matlab">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/matlab.png" height="20px" width="20px" alt="matlab">
 
 .. |important| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/warning.png" height="20px" width="20px" alt="bulb">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/warning.png" height="20px" width="20px" alt="bulb">
 
 .. |warning| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/warning.png" height="20px" width="20px" alt="warning">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/warning.png" height="20px" width="20px" alt="warning">
 
 .. |bulb| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/bulb.png" height="20px" width="20px" alt="bulb">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/bulb.png" height="20px" width="20px" alt="bulb">
 
 .. end-icon-marker

docs/requirements.txt

@@ -1,6 +1,6 @@
-git+https://github.com/uni-lu/sphinx.git@develop#egg=sphinx
+git+https://github.com/LCSB-BioCore/sphinx.git@develop#egg=sphinx
 git+https://github.com/syarra/sphinxcontrib-matlabdomain#egg=sphinxcontrib-matlabdomain
 sphinx_rtd_theme
-git+https://github.com/uni-lu/sphinx_julia_theme.git@develop#egg=sphinx_julia_theme
-git+https://github.com/syarra/Documenter.py@develop#egg=documenter
-git+https://github.com/uni-lu/sphinxcontrib-napoleon.git@develop#egg=sphinxcontrib_napoleon
+git+https://github.com/LCSB-BioCore/sphinx_julia_theme.git@develop#egg=sphinx_julia_theme
+git+https://github.com/syarra/Documenter.py@master#egg=documenter
+git+https://github.com/LCSB-BioCore/sphinxcontrib-napoleon.git@develop#egg=sphinxcontrib_napoleon

docs/source/cite.rst

@@ -3,47 +3,47 @@ How to cite
 
 .. include:: ../../README.rst
    :start-after: begin-how-to-cite-marker
-   :end-before: end-how-to-cite-marker 
+   :end-before: end-how-to-cite-marker
 
 
 .. |macos| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/apple.png" height="20px" width="20px" alt="macOS">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/apple.png" height="20px" width="20px" alt="macOS">
 
 
 .. |linux| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/linux.png" height="20px" width="20px" alt="linux">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/linux.png" height="20px" width="20px" alt="linux">
 
 
 .. |windows| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/apple.png" height="20px" width="20px" alt="windows">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/windows.png" height="20px" width="20px" alt="windows">
 
 
 .. |warning| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/warning.png" height="20px" width="20px" alt="warning">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/warning.png" height="20px" width="20px" alt="warning">
 
 
 .. |matlab| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/matlab.png" height="20px" width="20px" alt="matlab">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/matlab.png" height="20px" width="20px" alt="matlab">
 
 
 .. |tada| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/tada.png" height="20px" width="20px" alt="tada">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/tada.png" height="20px" width="20px" alt="tada">
 
 
 .. |thumbsup| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/thumbsUP.png" height="20px" width="20px" alt="thumbsup">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/thumbsUP.png" height="20px" width="20px" alt="thumbsup">
 
 
 .. |bulb| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/bulb.png" height="20px" width="20px" alt="bulb">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/bulb.png" height="20px" width="20px" alt="bulb">
 
 
 .. |tutorials| raw:: html
@@ -54,7 +54,7 @@ How to cite
 .. |latest| raw:: html
 
    <a href="https://opencobra.github.io/cobratoolbox/latest"><img src="https://img.shields.io/badge/COBRA-docs-blue.svg?maxAge=0"></a>
-   
+
 
 .. |forum| raw:: html
 

docs/source/contr_cobratoolbox.rst

@@ -204,7 +204,7 @@ directory `fork-cobratoolbox`. You can do so by typing:
 If there are changes listed, publish them by selecting procedure ``[3]`` of the
 contribute menu.
 
-.. |branchModel| image:: https://prince.lcsb.uni.lu/img/figure6.png
+.. |branchModel| image:: https://prince.lcsb.uni.lu/MATLAB.devTools/img/figure6.png
 
 .. include:: ../../README.rst
    :start-after: begin-icon-marker

docs/source/funding.rst

@@ -19,10 +19,10 @@ Funding
     <table width="100%" class="noBorder">
        <tr class="noBorder">
        <td class="noBorderImg" width="30%">
-           <div style="align-center;"><a href="http://www.ncer-pd.lu/index.php/en/"><img src="https://prince.lcsb.uni.lu/img/logos/ncer.png" alt="" width="80%"></a></div>
+           <div style="align-center;"><a href="http://www.ncer-pd.lu/index.php/en/"><img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/ncer.png" alt="" width="80%"></a></div>
        </td>
        <td class="noBorderImg" width="30%">
-            <div style="align-center;"><a href="http://www.ncer-pd.lu/index.php/en/"><img src="https://prince.lcsb.uni.lu/img/logos/fnr.png" alt="" width="80%"></a></div>
+            <div style="align-center;"><a href="http://www.ncer-pd.lu/index.php/en/"><img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/fnr.png" alt="" width="80%"></a></div>
        </td>
        <td class="noBorder" width="40%">
        National Centre of Excellence in Research (NCER) on Parkinson’s disease.
@@ -33,7 +33,7 @@ Funding
     <table width="100%" class="noBorder">
         <tr class="noBorder">
         <td class="noBorderImg" width="60%">
-            <div style="align-center;"><a href="https://energy.gov"><img src="https://prince.lcsb.uni.lu/img/logos/doe.png" alt="" width="80%"></a></div>
+            <div style="align-center;"><a href="https://energy.gov"><img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/doe.png" alt="" width="80%"></a></div>
         </td>
         <td class="noBorder" width="40%">
         U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429
@@ -49,10 +49,10 @@ Funding
     <br><br>
     <ul class="featureslogo">
        <li>
-           <div style="align-center;"><a href="http://wwwen.uni.lu/lcsb/"><img src="https://prince.lcsb.uni.lu/img/logos/largelcsb.png" alt="" width="100%"></a></div>
+           <div style="align-center;"><a href="http://wwwen.uni.lu/lcsb/"><img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/largelcsb.png" alt="" width="100%"></a></div>
        </li>
        <li>
-           <div style="align-center;"><a href="http://www.uni.lu"><img src="https://prince.lcsb.uni.lu/img/logos/largeul.png" alt="" width="100%"></a></div>
+           <div style="align-center;"><a href="http://www.uni.lu"><img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/largeul.png" alt="" width="100%"></a></div>
        </li>
     </ul>
    </p>

docs/source/index.rst

@@ -18,7 +18,7 @@ MATLAB.devTools - Contribute the smart way
     </style>
 
     <div class="alert alert-info" align="center">
-        View MATLAB.devTools <strong>source code</strong> on <a href="https://github.com/opencobra/MATLAB.devTools/"><img src="https://prince.lcsb.uni.lu/img/logos/github.png" style="height: 40px !important;"></a>.
+        View MATLAB.devTools <strong>source code</strong> on <a href="https://github.com/opencobra/MATLAB.devTools/"><img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/github.png" style="height: 40px !important;"></a>.
     </div>
 
 .. include:: ../../README.rst

docs/source/prerequisites.rst

@@ -122,10 +122,10 @@ shell). On **Windows**, start ``GUI Bash``. Then type
 Please replace ``"yourGitHubUsername"`` and ``"[email protected]"``
 with your respective credentials.
 
-.. |windows0| image:: https://prince.lcsb.uni.lu/img/installation_git_windows_0.png
+.. |windows0| image:: https://prince.lcsb.uni.lu/MATLAB.devTools/img/installation_git_windows_0.png
    :width: 280px
 
-.. |windows1| image:: https://prince.lcsb.uni.lu/img/installation_git_windows_1.png
+.. |windows1| image:: https://prince.lcsb.uni.lu/MATLAB.devTools/img/installation_git_windows_1.png
    :width: 280px
 
 .. include:: ../../README.rst

docs/source/troubleshooting/cobratutorials.rst

@@ -3,7 +3,7 @@ COBRA.tutorials
 
 .. |warning| raw:: html
 
-   <img src="https://prince.lcsb.uni.lu/jenkins/userContent/warning.png" height="20px" width="20px" alt="warning">
+   <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/warning.png" height="20px" width="20px" alt="warning">
 
 |warning| This section is tailored to users who feel comfortable using
 the terminal (or shell). It is recommended for other users
@@ -18,25 +18,25 @@ Fork and checkout your branch
 1. Fork the `COBRA.tutorials repository <https://www.github.com/opencobra/COBRA.tutorials>`__ on Github.
 
 2. Clone the forked repository to ``fork-COBRA.tutorials`` located in a directory of your choice:
-  
+
    .. code-block:: console
 
       $ git clone [email protected]:<userName>/COBRA.tutorials.git fork-COBRA.tutorials.git
 
 3. Change to the directory ``fork-COBRA.tutorials``:
-  
+
    .. code-block:: console
 
       $ cd fork-COBRA.tutorials.git/
 
 4. Set the upstream to the ``opencobra/COBRA.tutorials`` repository:
-  
+
    .. code-block:: console
 
       $ git remote add upstream [email protected]:opencobra/COBRA.tutorials.git
 
 5. Fetch from the upstream repository
-  
+
    .. code-block:: console
 
       $ git fetch upstream

test/inputCI.txt

@@ -1,5 +1,5 @@
-cobrabot
-/home/sbg-jenkins/
+artenobot
+/mnt/artenolis-data/repos/
 y
 n
 testFile1