Merge pull request #1456 from opencobra/develop

Regular merge of develop
opencobra · Apr 2, 2019 · 2ed83d1 · 2ed83d1
2 parents f3fe20d + a02a346
commit 2ed83d1
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diff --git a/.artenolis.yml b/.artenolis.yml
@@ -22,16 +22,16 @@ after_success:
 
     # deploy documentation
     - if [[ "$MATLAB_VER" == "R2017b" && "$ARCH" == "Linux" && "$JENKINS_PULL_REQUEST" != "True" ]]; then
-      export PATH="/home/sbg-jenkins/.local/bin":$PATH;
+      export PATH="/home/jenkins/.local/bin":$PATH;
       pip install --upgrade --user -r docs/requirements.txt;
-      python ~/github_stats.py $(pwd)/docs/source/list_contributors.rst;
+      python $ARTENOLIS_SCRIPTS_PATH/src/github_stats.py $(pwd)/docs/source/list_contributors.rst;
       export GIT_LOCAL_BRANCH=${GIT_BRANCH##origin/};
       echo $GIT_LOCAL_BRANCH;
-      ssh -t sbg-jenkins@10.184.148.14 'GIT_LOCAL_BRANCH='"'$GIT_LOCAL_BRANCH'"' && echo $GIT_LOCAL_BRANCH && cd ~/tmp/COBRA.tutorials && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH';
-      ssh -t sbg-jenkins@10.184.148.14 'GIT_LOCAL_BRANCH='"'$GIT_LOCAL_BRANCH'"' && echo $GIT_LOCAL_BRANCH && cd ~/tmp/cobratoolbox && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH && git submodule update --init';
-      ssh -t sbg-jenkins@10.184.148.14 'GIT_LOCAL_BRANCH='"'$GIT_LOCAL_BRANCH'"' && echo $GIT_LOCAL_BRANCH && cd ~/tmp/cobratoolbox && ~/tmp/cobratoolbox/docs/prepareTutorials.sh -c=~/tmp/cobratoolbox -t=~/tmp/COBRA.tutorials -p=~/tmp -m=html,pdf,png';
-      cd ~/tmp/COBRA.tutorials && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH;
-      cd ~/tmp/cobratoolbox && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH && git submodule update --init;
+      scp "$(pwd)/.artenolis/deployTutorials.sh" jenkins@lcsbs-mac-pro.uni.lux:$ARTENOLIS_ROOT_PATH_MAC/scratch/.;
+      ssh -t jenkins@lcsbs-mac-pro.uni.lux 'source ~/.profile && GIT_LOCAL_BRANCH='"'$GIT_LOCAL_BRANCH'"' && sh $ARTENOLIS_ROOT_PATH_MAC/scratch/deployTutorials.sh';
+      scp -r jenkins@lcsbs-mac-pro.uni.lux:$ARTENOLIS_ROOT_PATH_MAC/scratch/tutorials $ARTENOLIS_DATA_PATH/cobratoolbox/.;
+      cd $ARTENOLIS_DATA_PATH/repos/COBRA.tutorials && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH;
+      cd $ARTENOLIS_DATA_PATH/repos/cobratoolbox && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH && git submodule update --init;
       python -c "from documenter.deploy import Documentation; doc = Documentation('github.com/opencobra/cobratoolbox', local_upstream='$(pwd)', ci='jenkins'); doc.deploy()";
       bash .artenolis/generateZip.sh;
       fi
diff --git a/.artenolis/deployTutorials.sh b/.artenolis/deployTutorials.sh
@@ -0,0 +1,22 @@
+# DESCRIPTION:
+#   deploy tutorials of the COBRA Toolbox
+
+# set the local branch
+echo $GIT_LOCAL_BRANCH
+
+# update the cobra tutorials repository
+cd $ARTENOLIS_ROOT_PATH_MAC/repos/COBRA.tutorials
+git stash
+git checkout $GIT_LOCAL_BRANCH
+git pull origin $GIT_LOCAL_BRANCH
+
+# update the cobratoolbox repository
+cd $ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox
+git stash
+git checkout $GIT_LOCAL_BRANCH
+git pull origin $GIT_LOCAL_BRANCH
+git submodule update --init
+
+# generate and deploy the tutorials
+cd $ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox
+$ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox/docs/prepareTutorials.sh -c=$ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox -t=$ARTENOLIS_ROOT_PATH_MAC/repos/COBRA.tutorials -p=$ARTENOLIS_ROOT_PATH_MAC/scratch -m=html,pdf,png
diff --git a/.artenolis/generateZip.sh b/.artenolis/generateZip.sh
@@ -51,6 +51,6 @@ if [ "$ARCH" = "Linux" ] && [ "$MATLAB_VER" = "R2016b" ] && [ "$GIT_BRANCH" = "o
 
     # provide an output message
     echo " > Local .zip file removed"
-    echo "-- Done. The zip file can be downloaded from https://prince.lcsb.uni.lu/releases/theCOBRAToolbox-$lastCommit.zip --"
+    echo "-- Done. The zip file can be downloaded from https://prince.lcsb.uni.lu/cobratoolbox/releases/theCOBRAToolbox-$lastCommit.zip --"
 
 fi
diff --git a/.artenolis/runtests.sh b/.artenolis/runtests.sh
@@ -6,12 +6,14 @@ normal=$(tput sgr0)
 red=$(tput setaf 1)
 green=$(tput setaf 2)
 
+currentBranch="${GIT_BRANCH##origin/}"
+
 echo "Checking if the test suite should be run..."
 if [[ ! -z $GIT_PREVIOUS_SUCCESSFUL_COMMIT ]]; then
    commitHashs=($(git cherry $GIT_PREVIOUS_SUCCESSFUL_COMMIT HEAD 2>&1))
 else
    echo " -- environment variable GIT_PREVIOUS_SUCCESSFUL_COMMIT is not set (or empty)."
-   commitHashs=($(git log develop..HEAD -q --pretty=%H 2>&1))
+   commitHashs=($(git log develop..$currentBranch -q --pretty=%H 2>&1))
 fi
 
 # check if all commit messages contains only [documentation]
@@ -43,7 +45,7 @@ if [[ "$artenolisForce" = false ]]; then
     if [[ ! -z $GIT_PREVIOUS_SUCCESSFUL_COMMIT ]]; then
     modifiedFiles=($(git diff --name-only $GIT_PREVIOUS_SUCCESSFUL_COMMIT HEAD 2>&1))
     else
-    modifiedFiles=($(git log develop..HEAD -q --pretty=%H | tail -1 2>&1))
+    modifiedFiles=($(git log develop..$currentBranch -q --pretty=%H | tail -1 2>&1))
     fi
 
     onlyDocFiles=true
@@ -69,20 +71,20 @@ else
 fi
 
 if [ "$ARCH" == "Linux" ]; then
-    /mnt/prince-data/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash < test/testAll.m
+    $ARTENOLIS_SOFT_PATH/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash < test/testAll.m
 
 elif [ "$ARCH" == "macOS" ]; then
     caffeinate -u &
-    /Applications/MATLAB_$MATLAB_VER.app/bin/matlab -nodesktop -nosplash < test/testAll.m
+    /Applications/MATLAB_$MATLAB_VER.app/bin/matlab -nodisplay -nosplash < test/testAll.m
 
 elif [ "$ARCH" == "windows" ]; then
     # change to the build directory
     echo " -- changing to the build directory --"
-    cd "D:\\jenkins\\workspace\\$CI_PROJECT_NAME\\MATLAB_VER\\$MATLAB_VER\\label\\$ARCHVERSION"
+    cd "$ARTENOLIS_DATA_PATH\jenkins\\workspace\\$CI_PROJECT_NAME\\MATLAB_VER\\$MATLAB_VER\\label\\$NODE_LABELS"
 
     echo " -- launching MATLAB --"
     unset Path
-    nohup "D:\\MATLAB\\$MATLAB_VER\\\bin\\matlab.exe" -nojvm -nodesktop -nosplash -useStartupFolderPref -logfile output.log -wait -r "restoredefaultpath; cd D:\\jenkins\\workspace\\$CI_PROJECT_NAME\\MATLAB_VER\\$MATLAB_VER\\label\\$ARCHVERSION; cd test; testAll;" & PID=$!
+    nohup "$ARTENOLIS_SOFT_PATH\MATLAB\\$MATLAB_VER\\\bin\\matlab.exe" -nojvm -nodesktop -nosplash -useStartupFolderPref -logfile output.log -wait -r "restoredefaultpath; cd $ARTENOLIS_DATA_PATH\jenkins\\workspace\\$CI_PROJECT_NAME\\MATLAB_VER\\$MATLAB_VER\\label\\$NODE_LABELS; cd test; testAll;" & PID=$!
 
     # follow the log file
     tail -n0 -F --pid=$! output.log 2>/dev/null

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -14,4 +14,4 @@ How to contribute
 - More information on formatting the documentation is [here](https://opencobra.github.io/cobratoolbox/docs/documentationGuide.html)
 - A guide for reporting an **issue** 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.
+If you want to use `git` via the command line interface and need help, 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/) come in handy.
diff --git a/.gitmodules b/.gitmodules
@@ -20,7 +20,7 @@
 	ignore = dirty
 [submodule "test/models"]
 	path = test/models
-	url = https://github.com/cobrabot/COBRA.models
+	url = https://github.com/LCSB-BioCore/COBRA.models
 	ignore = dirty
 [submodule "external/analysis/Volume-and-Sampling"]
 	path = external/analysis/Volume-and-Sampling
@@ -40,11 +40,11 @@
 	ignore = dirty
 [submodule "external/base/utilities/rdir"]
 	path = external/base/utilities/rdir
-	url = https://github.com/uni-lu/rdir.git
+	url = https://github.com/LCSB-BioCore/rdir.git
 	ignore = dirty
 [submodule "external/analysis/mptoolbox"]
 	path = external/analysis/mptoolbox
-	url = https://github.com/cobrabot/mptoolbox.git
+	url = https://github.com/LCSB-BioCore/mptoolbox.git
 	ignore = dirty
 [submodule "external/analysis/octave-networks-toolbox"]
 	path = external/analysis/octave-networks-toolbox

diff --git a/README.rst b/README.rst
@@ -1,7 +1,7 @@
 .. raw:: html
 
    <p align="center">
-     <img class="readme_logo" src="https://prince.lcsb.uni.lu/img/logos/logo.png" height="160px"/>
+     <img class="readme_logo" src="https://prince.lcsb.uni.lu/cobratoolbox/img/logo.png" height="160px"/>
    </p>
 
 
@@ -15,12 +15,12 @@ The COBRA Toolbox |br| COnstraint-Based Reconstruction and Analysis Toolbox
      <td><div align="center"><a href="https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html"><img src="https://img.shields.io/badge/COBRA-tutorials-blue.svg?maxAge=0"></a>
        <a href="https://opencobra.github.io/cobratoolbox/latest"><img src="https://img.shields.io/badge/COBRA-docs-blue.svg?maxAge=0"></a>
        <a href="https://groups.google.com/forum/#!forum/cobra-toolbox"><img src="https://img.shields.io/badge/COBRA-forum-blue.svg?maxAge=0"></a></div></td>
-       <td><div align="center"><a href="https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-linux/"><img src="https://prince.lcsb.uni.lu/badges/linux-cobratoolbox.svg"></a>
-       <a href="https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-macOS/"><img src="https://prince.lcsb.uni.lu/badges/macOS-cobratoolbox.svg"></a>
-       <a href="https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-windows7/"><img src="https://prince.lcsb.uni.lu/badges/windows-cobratoolbox.svg"></a>
+       <td><div align="center"><a href="https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-linux/"><img src="https://prince.lcsb.uni.lu/cobratoolbox/badges/linux.svg"></a>
+       <a href="https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-macOS/"><img src="https://prince.lcsb.uni.lu/cobratoolbox/badges/macOS.svg"></a>
+       <a href="https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-windows7/"><img src="https://prince.lcsb.uni.lu/cobratoolbox/badges/windows.svg"></a>
        <a href="http://opencobra.github.io/cobratoolbox/docs/builds.html"><img src="http://concordion.org/img/benefit-links.png?maxAge=0" height="20px" alt="All continuous integration builds"></a>
        </div></td>
-       <td><div align="center"><img src="https://prince.lcsb.uni.lu/badges/codegrade.svg" alt="Ratio of the number of inefficient code lines and the total number of lines of code (in percent). A: 0-3%, B: 3-6%, C: 6-9%, D: 9-12%, E: 12-15%, F: > 15%.">
+       <td><div align="center"><img src="https://prince.lcsb.uni.lu/cobratoolbox/codegrade/codegrade.svg" alt="Ratio of the number of inefficient code lines and the total number of lines of code (in percent). A: 0-3%, B: 3-6%, C: 6-9%, D: 9-12%, E: 12-15%, F: > 15%.">
        <a href="https://codecov.io/gh/opencobra/cobratoolbox/branch/master"><img src="https://codecov.io/gh/opencobra/cobratoolbox/branch/master/graph/badge.svg?maxAge=0"></a></div></td>
      </tr>
    </table>
@@ -55,7 +55,7 @@ Installation
 
    |warning| Please note the ``--depth=1`` in the clone command. Run this command in ``Terminal`` (on |macos| and |linux|) or in ``Git Bash`` (on |windows|) -
    **not** in |matlab|. Although not recommended, you can download the
-   repository as a `compressed archive <https://prince.lcsb.uni.lu/releases/theCOBRAToolbox.zip>`__.
+   repository as a `compressed archive <https://prince.lcsb.uni.lu/cobratoolbox/releases/theCOBRAToolbox.zip>`__.
 
 2. Change to the folder ``cobratoolbox/`` and run from |matlab|
 
@@ -136,12 +136,11 @@ instructions
 -  A guide for reporting an **issue** 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
+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.
+come in handy.
 
 
 .. end-how-to-contribute-marker
@@ -186,8 +185,8 @@ implemented in The COBRA Toolbox v3.0 [2], was employed.*
     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**, accepted in Nature Protocols, 2018,
-    `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
 
@@ -236,42 +235,42 @@ holder.*
 
 .. |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/cobratoolbox/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/cobratoolbox/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/cobratoolbox/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/cobratoolbox/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/cobratoolbox/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/cobratoolbox/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/cobratoolbox/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/cobratoolbox/img/bulb.png" height="20px" width="20px" alt="bulb">
 
 
 .. |tutorials| raw:: html

diff --git a/docs/Makefile b/docs/Makefile
@@ -53,7 +53,7 @@ html:
 	@echo "Creating modules index page."
 	bash createModulesPage.sh
 	@echo "Copying tutorial html files into source/_static/tutorials/."
-	bash prepareTutorials.sh -t=~/tmp/COBRA.tutorials -c=~/tmp/cobratoolbox -p=~/tmp -m=rst
+	bash prepareTutorials.sh -t=$(ARTENOLIS_DATA_PATH)/repos/COBRA.tutorials -c=$(ARTENOLIS_DATA_PATH)/repos/cobratoolbox -p=$(ARTENOLIS_DATA_PATH)/cobratoolbox -m=rst
 	@echo "Generating list of suggestions for the websearch."
 	python generateJSONList.py
 	@echo
@@ -231,4 +231,4 @@ pseudoxml:
 dummy:
 	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
 	@echo
-	@echo "Build finished. Dummy builder generates no files."
+	@echo "Build finished. Dummy builder generates no files."
diff --git a/docs/createModulesPage.sh b/docs/createModulesPage.sh
@@ -31,7 +31,7 @@ do
     echo ".. raw:: html" >> $rstFunctionPath
     echo "" >> $rstFunctionPath
     echo "   <div class=\"tutorialSectionBox $section\">" >> $rstFunctionPath
-    echo "     <div class=\"sectionLogo\"><img class=\"avatar\" src=\"https://prince.lcsb.uni.lu/img/icon_${section}_wb.png\"></div>" >> $rstFunctionPath
+    echo "     <div class=\"sectionLogo\"><img class=\"avatar\" src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/icon_${section}_wb.png\"></div>" >> $rstFunctionPath
     echo "     <div class=\"sectionTitle\"><h3>${subs[$section]}</h3></div>" >> $rstFunctionPath
     echo "     <div class=\"row\">" >> $rstFunctionPath
     echo "       <div class=\"col-xs-6\">" >> $rstFunctionPath