Merge branch 'generate-zip' into develop

NalaMaria24 · Dec 14, 2017 · 1657f6d · 1657f6d
2 parents 9d8a2f8 + a904f6f
commit 1657f6d
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Showing 76 changed files with 131 additions and 161 deletions.
diff --git a/.ci/generateZip.sh b/.ci/generateZip.sh
@@ -0,0 +1,56 @@
+#!/bin/sh
+
+# script called at the end of a build on a -branches platform,
+# generates a .zip file of the working directory,
+# and puts it to the webserver.
+
+echo "-- Generation of zip of workspace directory -- "
+echo " > Architecture:   $ARCH"
+echo " > MATLAB version: $MATLAB_VER"
+echo " > Branch:         $GIT_BRANCH"
+
+if [ "$ARCH" = "Linux" ] && [ "$MATLAB_VER" = "R2016b" ] && [ "$GIT_BRANCH" = "origin/master" ]; then
+
+    # make a clean local temporary release directory
+    rm -rf /tmp/releaseCT && mkdir /tmp/releaseCT
+    echo " > New temporary folder created: /tmp/releaseCT"
+
+    # clone from local repository
+    git clone file:///mnt/prince-data/jenkins/workspace/COBRAToolbox-branches-auto-linux/MATLAB_VER/$MATLAB_VER/label/linux /tmp/releaseCT --depth 1
+    echo " > Workspace cloned"
+
+    # change to the local temporary release directory
+    cd /tmp/releaseCT
+
+    # set the remote URL
+    git remote set-url origin https://github.com/opencobra/cobratoolbox.git
+    echo " > Remote set"
+
+    # clone submodules
+    git submodule update --init --remote --depth 1
+    echo " > Submodules cloned"
+
+    # retrieve the SHA1 of the detached head
+    lastCommit=$(git rev-parse --short HEAD)
+    echo " > Last commit determined as $lastCommit"
+
+    # zip the entire directory
+    zip -qr /mnt/prince-data/releases/the_COBRA_Toolbox-$lastCommit.zip .
+    echo " > Workspace zipped"
+
+    # move the zip file to /mnt/isilon-dat/releases
+    scp -P 8022 /mnt/prince-data/releases/the_COBRA_Toolbox-$lastCommit.zip jenkins@prince-server.lcsb.uni.lux:/mnt/isilon-dat/releases
+    echo " > .zip file sent to prince-server"
+
+    # update the symbolic link
+    ssh -p8022 jenkins@prince-server.lcsb.uni.lux -o TCPKeepAlive=no "cd /mnt/isilon-dat/releases && rm the_COBRA_Toolbox.zip && ln -s the_COBRA_Toolbox-$lastCommit.zip the_COBRA_Toolbox.zip"
+    echo " > .zip alias set on prince-server"
+
+    # remove the local zip file
+    rm /mnt/prince-data/releases/the_COBRA_Toolbox-$lastCommit.zip
+
+    # provide an output message
+    echo " > Local .zip file removed"
+    echo "-- Done. The zip file can be downloaded from https://prince.lcsb.uni.lu/releases/the_COBRA_Toolbox-$lastCommit.zip --"
+
+fi
diff --git a/.gitignore b/.gitignore
@@ -78,6 +78,9 @@ EcoliModelSamples_3.mat
 EcoliModelSamples_4.mat
 modelRedTmp.mat
 sampleCbModelTmp.mat
+test/verifiedTests/analysis/testEnumerateOptimal/MILPProblem.mat
+test/verifiedTests/analysis/testThermo/MILPProblem.mat
+test/verifiedTests/design/MILPProblem.mat
 
 # shared libraries
 *.so
@@ -146,3 +149,6 @@ output/
 # directory for windows when rmdir fails
 test/verifiedTests/base/testIO/m_model_collection
 tutorials/additionalTutorials/optKnock/Results/
+
+# .documenter file
+docs/.documenter
diff --git a/.travis.yml b/.travis.yml
@@ -22,5 +22,6 @@ after_success:
       export here=`pwd`;
       python ~/github_stats.py $here/docs/source/list_contributors.rst;
       python -c "from documenter.deploy import Documentation; doc = Documentation('github.com/opencobra/cobratoolbox', local_upstream='$here', ci='jenkins'); doc.deploy()";
+      bash .ci/generateZip.sh;
       fi
       fi
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 <br>
 
 <p align="center">
-  <img class="readme_logo" src="docs/source/_static/images/logos/logo.png" height="160px"/>
+  <img class="readme_logo" src="https://prince.lcsb.uni.lu/img/logos/logo.png" height="160px"/>
 </p>
 
 The COBRA Toolbox <br> COnstraint-Based Reconstruction and Analysis Toolbox

diff --git a/docs/prepareTutorials.sh b/docs/prepareTutorials.sh
@@ -51,7 +51,7 @@ buildTutorialList(){
 }
 
 createLocalVariables(){
-    tutorial=$1    
+    tutorial=$1
     tutorialDir=${tutorial%/*}
     tutorialName=${tutorial##*/}
     tutorialName="${tutorialName%.*}"
@@ -61,16 +61,16 @@ createLocalVariables(){
     else
         tutorialTitle="tutorialNoName"
     fi
- 
+
     echo_time "  - $tutorialTitle ($tutorialName) $tutorialFolder"
- 
+
     foo="${tutorialName:9}"
     tutorialLongTitle="${tutorialName:0:8}${foo^}"
     readmePath="$cobraToolBoxPath/tutorials/$tutorialFolder"
     htmlPath="$cobraToolBoxPath/docs/source/_static/tutorials"
     rstPath="$cobraToolBoxPath/docs/source/tutorials" # should be changed later to mimic structure of the src folder.
     pngPath="$pdfPath/tutorials/$tutorialFolder"
- 
+
     pdfHyperlink="https://prince.lcsb.uni.lu/userContent/tutorials/$tutorialFolder/$tutorialName.pdf"
     pngHyperlink="https://prince.lcsb.uni.lu/userContent/tutorials/$tutorialFolder/$tutorialName.png"
     htmlHyperlink="https://prince.lcsb.uni.lu/cobratoolbox/tutorials/$tutorialFolder/iframe_$tutorialName.html"
@@ -235,7 +235,7 @@ if [ $buildPNG = true ] || [ $buildMD = true ] || [ $buildRST = true ]; then
         if [ $buildMD = true ]; then
             mkdir -p $readmePath
             echo "<p align=\"center\">" > $readmePath/README.md
-            echo "    <a href=\"$pdfHyperlink\" title=\"Download PDF file\" target=\"_blank\"><img src=\"https://cdn.rawgit.com/opencobra/cobratoolbox/master/docs/source/_static/images/icon_pdf.png\" height=\"90px\"></a>&nbsp;&nbsp;&nbsp;<a href=\"$mlxHyperlink\" title=\"Download Live Script file\" target=\"_blank\"><img src=\"https://cdn.rawgit.com/opencobra/cobratoolbox/master/docs/source/_static/images/icon_mlx.png\" height=\"90px\"></a>&nbsp;&nbsp;&nbsp;<a href=\"$mHyperlink\" title=\"Download MATLAB file\" target=\"_blank\"><img src=\"https://cdn.rawgit.com/opencobra/cobratoolbox/master/docs/source/_static/images/icon_m.png\" height=\"90px\"></a>&nbsp;&nbsp;&nbsp;<a href=\"https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html\" title=\"Tutorials\"><img src=\"https://cdn.rawgit.com/opencobra/cobratoolbox/master/docs/source/_static/images/icon_tut.png\" height=\"90px\"></a>" >> $readmePath/README.md
+            echo "    <a href=\"$pdfHyperlink\" title=\"Download PDF file\" target=\"_blank\"><img src=\"https://prince.lcsb.uni.lu/img/icon_pdf.png\" height=\"90px\"></a>&nbsp;&nbsp;&nbsp;<a href=\"$mlxHyperlink\" title=\"Download Live Script file\" target=\"_blank\"><img src=\"https://prince.lcsb.uni.lu/img/icon_mlx.png\" height=\"90px\"></a>&nbsp;&nbsp;&nbsp;<a href=\"$mHyperlink\" title=\"Download MATLAB file\" target=\"_blank\"><img src=\"https://prince.lcsb.uni.lu/img/icon_m.png\" height=\"90px\"></a>&nbsp;&nbsp;&nbsp;<a href=\"https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html\" title=\"Tutorials\"><img src=\"https://prince.lcsb.uni.lu/img/icon_tut.png\" height=\"90px\"></a>" >> $readmePath/README.md
             echo "<br><br>" >> $readmePath/README.md
             echo "</p>" >> $readmePath/README.md
 

diff --git a/docs/source/_static/images/icon1.png b/docs/source/_static/images/icon1.png
diff --git a/docs/source/_static/images/icon2.png b/docs/source/_static/images/icon2.png
diff --git a/docs/source/_static/images/icon3.png b/docs/source/_static/images/icon3.png
diff --git a/docs/source/_static/images/icon4.png b/docs/source/_static/images/icon4.png
diff --git a/docs/source/_static/images/icon5.png b/docs/source/_static/images/icon5.png
diff --git a/docs/source/_static/images/icon6.png b/docs/source/_static/images/icon6.png
diff --git a/docs/source/_static/images/icon7.png b/docs/source/_static/images/icon7.png
diff --git a/docs/source/_static/images/icon_analysis.png b/docs/source/_static/images/icon_analysis.png
diff --git a/docs/source/_static/images/icon_base.png b/docs/source/_static/images/icon_base.png
diff --git a/docs/source/_static/images/icon_design.png b/docs/source/_static/images/icon_design.png
diff --git a/docs/source/_static/images/icon_di.png b/docs/source/_static/images/icon_di.png
diff --git a/docs/source/_static/images/icon_external.png b/docs/source/_static/images/icon_external.png
diff --git a/docs/source/_static/images/icon_m.png b/docs/source/_static/images/icon_m.png
diff --git a/docs/source/_static/images/icon_mlx.png b/docs/source/_static/images/icon_mlx.png
diff --git a/docs/source/_static/images/icon_pdf.png b/docs/source/_static/images/icon_pdf.png
diff --git a/docs/source/_static/images/icon_reconstruction.png b/docs/source/_static/images/icon_reconstruction.png
diff --git a/docs/source/_static/images/icon_tut.png b/docs/source/_static/images/icon_tut.png
diff --git a/docs/source/_static/images/icon_visualization.png b/docs/source/_static/images/icon_visualization.png
diff --git a/docs/source/_static/images/installation_git_windows_0.png b/docs/source/_static/images/installation_git_windows_0.png
diff --git a/docs/source/_static/images/installation_git_windows_1.png b/docs/source/_static/images/installation_git_windows_1.png
diff --git a/docs/source/_static/images/logos/doe.png b/docs/source/_static/images/logos/doe.png
diff --git a/docs/source/_static/images/logos/eu.svg b/docs/source/_static/images/logos/eu.svg
diff --git a/docs/source/_static/images/logos/fnr.png b/docs/source/_static/images/logos/fnr.png
diff --git a/docs/source/_static/images/logos/github.png b/docs/source/_static/images/logos/github.png
diff --git a/docs/source/_static/images/logos/largelcsb.png b/docs/source/_static/images/logos/largelcsb.png
diff --git a/docs/source/_static/images/logos/largeul.png b/docs/source/_static/images/logos/largeul.png
diff --git a/docs/source/_static/images/logos/logo.png b/docs/source/_static/images/logos/logo.png
diff --git a/docs/source/_static/images/logos/ncer.png b/docs/source/_static/images/logos/ncer.png
diff --git a/docs/source/_static/images/logos/sysmedpd.png b/docs/source/_static/images/logos/sysmedpd.png
diff --git a/docs/source/_templates/README.html b/docs/source/_templates/README.html
@@ -2,36 +2,36 @@ <h1 align="center">The COnstraint-Based Reconstruction <br>and Analysis Toolbox<
 <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/images/logos/github.png" height="40px"></a>.
+    View The COBRA Toolbox <strong>source code</strong> on <a href="https://github.com/opencobra/cobratoolbox/"><img src="https://prince.lcsb.uni.lu/img/logos/github.png" height="40px"></a>.
 </div>
 <br>
 <br>
 <div class="wrapper">
     <ul class="metro">
         <li class="small-tile-text color_class1 scale-10">
             <a class="tile" href="https://opencobra.github.io/cobratoolbox/latest/installation.html">
-                <img src="_static/images/icon1.png" height="110px">
+                <img src="https://prince.lcsb.uni.lu/img/icon1.png" height="110px">
             </a>
             <div>Installation</div>
         </li>
         &nbsp;&nbsp;&nbsp;&nbsp;
         <li class="small-tile-text color_class2 scale-10">
             <a class="tile" href="https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html">
-            <img src="_static/images/icon2.png" height="110px">
+            <img src="https://prince.lcsb.uni.lu/img/icon2.png" height="110px">
             </a>
               <div>Tutorials</div>
         </li>
         &nbsp;&nbsp;&nbsp;&nbsp;
         <li class="small-tile-text color_class3 scale-10">
             <a class="tile" href="https://opencobra.github.io/cobratoolbox/latest/contributing.html">
-            <img src="_static/images/icon3.png" height="110px">
+            <img src="https://prince.lcsb.uni.lu/img/icon3.png" height="110px">
             </a>
               <div>Contributing</div>
         </li>
         &nbsp;&nbsp;&nbsp;&nbsp;
         <li class="small-tile-text color_class4 scale-10">
             <a class="tile" href="https://opencobra.github.io/cobratoolbox/latest/modules/index.html">
-            <img src="_static/images/icon4.png" height="110px">
+            <img src="https://prince.lcsb.uni.lu/img/icon4.png" height="110px">
             </a>
               <div>Documentation</div>
         </li>

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -190,7 +190,7 @@ 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/images/logos/logo.png'
+html_logo = 'https://prince.lcsb.uni.lu/img/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

diff --git a/docs/source/funding.rst b/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.sysmedpd.eu"><img src="_static/images/logos/sysmedpd.png" alt="" width="80%"></a></div>
+           <div style="align-center;"><a href="http://www.sysmedpd.eu"><img src="https://prince.lcsb.uni.lu/img/logos/sysmedpd.png" alt="" width="80%"></a></div>
        </td>
        <td class="noBorderImg" width="30%">
-            <div style="align-center;"><a href="http://www.sysmedpd.eu"><img src="_static/images/logos/eu.svg" alt="" width="80%"></a></div>
+            <div style="align-center;"><a href="http://www.sysmedpd.eu"><img src="https://prince.lcsb.uni.lu/img/logos/eu.svg" alt="" width="80%"></a></div>
        </td>
        <td class="noBorder" width="40%">
        European Union’s Horizon 2020 research and innovation programme under grant agreement No 668738.
@@ -33,10 +33,10 @@ 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="_static/images/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/img/logos/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="_static/images/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/img/logos/fnr.png" alt="" width="80%"></a></div>
        </td>
        <td class="noBorder" width="40%">
        National Centre of Excellence in Research (NCER) on Parkinson’s disease.
@@ -47,7 +47,7 @@ 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="_static/images/logos/doe.png" alt="" width="80%"></a></div>
+            <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>
         </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
@@ -67,10 +67,10 @@ Funding
     <br><br>
     <ul class="featureslogo">
        <li>
-           <div style="align-center;"><a href="http://wwwen.uni.lu/lcsb/"><img src="_static/images/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/img/logos/largelcsb.png" alt="" width="100%"></a></div>
        </li>
        <li>
-           <div style="align-center;"><a href="http://www.uni.lu"><img src="_static/images/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/img/logos/largeul.png" alt="" width="100%"></a></div>
        </li>
     </ul>
    </p>
diff --git a/docs/source/installation/requirements.md b/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/win). During the installation process, please ensure that you select **Use Git Bash and optional Unix tools 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="../_static/images/installation_git_windows_0.png" height="280px">&nbsp;&nbsp;&nbsp;<img src="../_static/images/installation_git_windows_1.png" height="280px">.
+<img src="https://prince.lcsb.uni.lu/img/installation_git_windows_0.png" height="280px">&nbsp;&nbsp;&nbsp;<img src="https://prince.lcsb.uni.lu/img/installation_git_windows_1.png" height="280px">.
 </div>
diff --git a/docs/source/tutorials/template.rst b/docs/source/tutorials/template.rst
@@ -10,28 +10,28 @@
         <ul class="metro">
             <li class="small-tile-text color_class5 scale-10">
                 <a class="tile" style="width: 90px; height: 90px;" href="#PDFtutorialPath#">
-                    <img src="../_static/images/icon5.png" height="90px">
+                    <img src="https://prince.lcsb.uni.lu/img/icon5.png" height="90px">
                 </a>
                 <div>Download PDF</div>
             </li>
             &nbsp;&nbsp;&nbsp;&nbsp;
             <li class="small-tile-text color_class6 scale-10">
                 <a class="tile" style="width: 90px; height: 90px;" href="#MLXtutorialPath#">
-                <img src="../_static/images/icon6.png" height="90px">
+                <img src="https://prince.lcsb.uni.lu/img/icon6.png" height="90px">
                 </a>
                   <div>Download live Script</div>
             </li>
             &nbsp;&nbsp;&nbsp;&nbsp;
             <li class="small-tile-text color_class7 scale-10">
                 <a class="tile" style="width: 90px; height: 90px;" href="#MtutorialPath#">
-                <img src="../_static/images/icon7.png" height="90px">
+                <img src="https://prince.lcsb.uni.lu/img/icon7.png" height="90px">
                 </a>
                   <div>Download m file</div>
             </li>
             &nbsp;&nbsp;&nbsp;&nbsp;
             <li class="small-tile-text color_class2 scale-10">
                 <a class="tile" style="width: 90px; height: 90px;" href="https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html">
-                <img src="../_static/images/icon2.png" height="90px">
+                <img src="https://prince.lcsb.uni.lu/img/icon2.png" height="90px">
                 </a>
                   <div>Tutorials</div>
             </li>

diff --git a/initCobraToolbox.m b/initCobraToolbox.m
@@ -105,14 +105,6 @@ function initCobraToolbox()
     % check if git is installed
     checkGit();
 
-    % temporary disable ssl verification
-    [status_setSSLVerify, result_setSSLVerify] = system('git config http.sslVerify false');
-
-    if status_setSSLVerify ~= 0
-        fprintf(strrep(result_setSSLVerify, '\', '\\'));
-        warning('Your global git configuration could not be changed.');
-    end
-
     % change to the root of The COBRA Tooolbox
     cd(CBTDIR);
 
@@ -163,6 +155,14 @@ function initCobraToolbox()
         fprintf(' Done.\n');
     end
 
+    % temporary disable ssl verification
+    [status_setSSLVerify, result_setSSLVerify] = system('git config http.sslVerify false');
+
+    if status_setSSLVerify ~= 0
+        fprintf(strrep(result_setSSLVerify, '\', '\\'));
+        warning('Your global git configuration could not be changed.');
+    end
+
     % check curl
     [status_curl, result_curl] = checkCurlAndRemote(false);
 
@@ -181,7 +181,7 @@ function initCobraToolbox()
         end
 
         % Update/initialize submodules
-        [status_gitSubmodule, result_gitSubmodule] = system('git submodule update --init');
+        [status_gitSubmodule, result_gitSubmodule] = system('git submodule update --init --remote --depth 1');
 
         if status_gitSubmodule ~= 0
             fprintf(strrep(result_gitSubmodule, '\', '\\'));