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Merge pull request #1456 from opencobra/develop
Regular merge of develop
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‎.artenolis.yml

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@@ -22,16 +22,16 @@ after_success:
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# deploy documentation
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- if [[ "$MATLAB_VER" == "R2017b" && "$ARCH" == "Linux" && "$JENKINS_PULL_REQUEST" != "True" ]]; then
25-
export PATH="/home/sbg-jenkins/.local/bin":$PATH;
25+
export PATH="/home/jenkins/.local/bin":$PATH;
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pip install --upgrade --user -r docs/requirements.txt;
27-
python ~/github_stats.py $(pwd)/docs/source/list_contributors.rst;
27+
python $ARTENOLIS_SCRIPTS_PATH/src/github_stats.py $(pwd)/docs/source/list_contributors.rst;
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export GIT_LOCAL_BRANCH=${GIT_BRANCH##origin/};
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echo $GIT_LOCAL_BRANCH;
30-
ssh -t sbg-jenkins@10.184.148.14 'GIT_LOCAL_BRANCH='"'$GIT_LOCAL_BRANCH'"' && echo $GIT_LOCAL_BRANCH && cd ~/tmp/COBRA.tutorials && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH';
31-
ssh -t sbg-jenkins@10.184.148.14 'GIT_LOCAL_BRANCH='"'$GIT_LOCAL_BRANCH'"' && echo $GIT_LOCAL_BRANCH && cd ~/tmp/cobratoolbox && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH && git submodule update --init';
32-
ssh -t sbg-jenkins@10.184.148.14 'GIT_LOCAL_BRANCH='"'$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';
33-
cd ~/tmp/COBRA.tutorials && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH;
34-
cd ~/tmp/cobratoolbox && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH && git submodule update --init;
30+
scp "$(pwd)/.artenolis/deployTutorials.sh" jenkins@lcsbs-mac-pro.uni.lux:$ARTENOLIS_ROOT_PATH_MAC/scratch/.;
31+
ssh -t jenkins@lcsbs-mac-pro.uni.lux 'source ~/.profile && GIT_LOCAL_BRANCH='"'$GIT_LOCAL_BRANCH'"' && sh $ARTENOLIS_ROOT_PATH_MAC/scratch/deployTutorials.sh';
32+
scp -r jenkins@lcsbs-mac-pro.uni.lux:$ARTENOLIS_ROOT_PATH_MAC/scratch/tutorials $ARTENOLIS_DATA_PATH/cobratoolbox/.;
33+
cd $ARTENOLIS_DATA_PATH/repos/COBRA.tutorials && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH;
34+
cd $ARTENOLIS_DATA_PATH/repos/cobratoolbox && git stash && git checkout $GIT_LOCAL_BRANCH && git pull origin $GIT_LOCAL_BRANCH && git submodule update --init;
3535
python -c "from documenter.deploy import Documentation; doc = Documentation('github.com/opencobra/cobratoolbox', local_upstream='$(pwd)', ci='jenkins'); doc.deploy()";
3636
bash .artenolis/generateZip.sh;
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fi

‎.artenolis/deployTutorials.sh

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@@ -0,0 +1,22 @@
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# DESCRIPTION:
2+
# deploy tutorials of the COBRA Toolbox
3+
4+
# set the local branch
5+
echo $GIT_LOCAL_BRANCH
6+
7+
# update the cobra tutorials repository
8+
cd $ARTENOLIS_ROOT_PATH_MAC/repos/COBRA.tutorials
9+
git stash
10+
git checkout $GIT_LOCAL_BRANCH
11+
git pull origin $GIT_LOCAL_BRANCH
12+
13+
# update the cobratoolbox repository
14+
cd $ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox
15+
git stash
16+
git checkout $GIT_LOCAL_BRANCH
17+
git pull origin $GIT_LOCAL_BRANCH
18+
git submodule update --init
19+
20+
# generate and deploy the tutorials
21+
cd $ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox
22+
$ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox/docs/prepareTutorials.sh -c=$ARTENOLIS_ROOT_PATH_MAC/repos/cobratoolbox -t=$ARTENOLIS_ROOT_PATH_MAC/repos/COBRA.tutorials -p=$ARTENOLIS_ROOT_PATH_MAC/scratch -m=html,pdf,png

‎.artenolis/generateZip.sh

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@@ -51,6 +51,6 @@ if [ "$ARCH" = "Linux" ] && [ "$MATLAB_VER" = "R2016b" ] && [ "$GIT_BRANCH" = "o
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# provide an output message
5353
echo " > Local .zip file removed"
54-
echo "-- Done. The zip file can be downloaded from https://prince.lcsb.uni.lu/releases/theCOBRAToolbox-$lastCommit.zip --"
54+
echo "-- Done. The zip file can be downloaded from https://prince.lcsb.uni.lu/cobratoolbox/releases/theCOBRAToolbox-$lastCommit.zip --"
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fi

‎.artenolis/runtests.sh

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@@ -6,12 +6,14 @@ normal=$(tput sgr0)
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red=$(tput setaf 1)
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green=$(tput setaf 2)
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9+
currentBranch="${GIT_BRANCH##origin/}"
10+
911
echo "Checking if the test suite should be run..."
1012
if [[ ! -z $GIT_PREVIOUS_SUCCESSFUL_COMMIT ]]; then
1113
commitHashs=($(git cherry $GIT_PREVIOUS_SUCCESSFUL_COMMIT HEAD 2>&1))
1214
else
1315
echo " -- environment variable GIT_PREVIOUS_SUCCESSFUL_COMMIT is not set (or empty)."
14-
commitHashs=($(git log develop..HEAD -q --pretty=%H 2>&1))
16+
commitHashs=($(git log develop..$currentBranch -q --pretty=%H 2>&1))
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fi
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# check if all commit messages contains only [documentation]
@@ -43,7 +45,7 @@ if [[ "$artenolisForce" = false ]]; then
4345
if [[ ! -z $GIT_PREVIOUS_SUCCESSFUL_COMMIT ]]; then
4446
modifiedFiles=($(git diff --name-only $GIT_PREVIOUS_SUCCESSFUL_COMMIT HEAD 2>&1))
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else
46-
modifiedFiles=($(git log develop..HEAD -q --pretty=%H | tail -1 2>&1))
48+
modifiedFiles=($(git log develop..$currentBranch -q --pretty=%H | tail -1 2>&1))
4749
fi
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onlyDocFiles=true
@@ -69,20 +71,20 @@ else
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fi
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7173
if [ "$ARCH" == "Linux" ]; then
72-
/mnt/prince-data/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash < test/testAll.m
74+
$ARTENOLIS_SOFT_PATH/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash < test/testAll.m
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elif [ "$ARCH" == "macOS" ]; then
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caffeinate -u &
76-
/Applications/MATLAB_$MATLAB_VER.app/bin/matlab -nodesktop -nosplash < test/testAll.m
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/Applications/MATLAB_$MATLAB_VER.app/bin/matlab -nodisplay -nosplash < test/testAll.m
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elif [ "$ARCH" == "windows" ]; then
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# change to the build directory
8082
echo " -- changing to the build directory --"
81-
cd "D:\\jenkins\\workspace\\$CI_PROJECT_NAME\\MATLAB_VER\\$MATLAB_VER\\label\\$ARCHVERSION"
83+
cd "$ARTENOLIS_DATA_PATH\jenkins\\workspace\\$CI_PROJECT_NAME\\MATLAB_VER\\$MATLAB_VER\\label\\$NODE_LABELS"
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echo " -- launching MATLAB --"
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unset Path
85-
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=$!
87+
nohup "$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=$!
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# follow the log file
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tail -n0 -F --pid=$! output.log 2>/dev/null

‎.github/CONTRIBUTING.md

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@@ -14,4 +14,4 @@ How to contribute
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- More information on formatting the documentation is [here](https://opencobra.github.io/cobratoolbox/docs/documentationGuide.html)
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- A guide for reporting an **issue** is [here](https://opencobra.github.io/cobratoolbox/docs/issueGuide.html).
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17-
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.
17+
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.

‎.gitmodules

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ignore = dirty
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[submodule "test/models"]
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path = test/models
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url = https://github.com/cobrabot/COBRA.models
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url = https://github.com/LCSB-BioCore/COBRA.models
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ignore = dirty
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[submodule "external/analysis/Volume-and-Sampling"]
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path = external/analysis/Volume-and-Sampling
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ignore = dirty
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[submodule "external/base/utilities/rdir"]
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path = external/base/utilities/rdir
43-
url = https://github.com/uni-lu/rdir.git
43+
url = https://github.com/LCSB-BioCore/rdir.git
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ignore = dirty
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[submodule "external/analysis/mptoolbox"]
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path = external/analysis/mptoolbox
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url = https://github.com/cobrabot/mptoolbox.git
47+
url = https://github.com/LCSB-BioCore/mptoolbox.git
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ignore = dirty
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[submodule "external/analysis/octave-networks-toolbox"]
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path = external/analysis/octave-networks-toolbox

‎README.rst

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.. raw:: html
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<p align="center">
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<img class="readme_logo" src="https://prince.lcsb.uni.lu/img/logos/logo.png" height="160px"/>
4+
<img class="readme_logo" src="https://prince.lcsb.uni.lu/cobratoolbox/img/logo.png" height="160px"/>
55
</p>
66

77

@@ -15,12 +15,12 @@ The COBRA Toolbox |br| COnstraint-Based Reconstruction and Analysis Toolbox
1515
<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>
1616
<a href="https://opencobra.github.io/cobratoolbox/latest"><img src="https://img.shields.io/badge/COBRA-docs-blue.svg?maxAge=0"></a>
1717
<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>
18-
<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>
19-
<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>
20-
<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>
18+
<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>
19+
<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>
20+
<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>
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<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>
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</div></td>
23-
<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%.">
23+
<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%.">
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<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>
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</tr>
2626
</table>
@@ -55,7 +55,7 @@ Installation
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|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|) -
5757
**not** in |matlab|. Although not recommended, you can download the
58-
repository as a `compressed archive <https://prince.lcsb.uni.lu/releases/theCOBRAToolbox.zip>`__.
58+
repository as a `compressed archive <https://prince.lcsb.uni.lu/cobratoolbox/releases/theCOBRAToolbox.zip>`__.
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2. Change to the folder ``cobratoolbox/`` and run from |matlab|
6161

@@ -136,12 +136,11 @@ instructions
136136
- A guide for reporting an **issue** is `here <https://opencobra.github.io/cobratoolbox/docs/issueGuide.html>`__.
137137

138138
If you want to use ``git`` via the command line interface and need help,
139-
these `training slides <https://uni-lu.github.io/slides/>`__ will get
140-
you started. This
139+
this
141140
`guide <https://www.digitalocean.com/community/tutorials/how-to-create-a-pull-request-on-github>`__
142141
or the official `GitHub
143142
guide <https://help.github.com/articles/creating-a-pull-request/>`__
144-
also come in handy.
143+
come in handy.
145144

146145

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.. end-how-to-contribute-marker
@@ -186,8 +185,8 @@ implemented in The COBRA Toolbox v3.0 [2], was employed.*
186185
A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter,
187186
Bernhard Ø. Palsson, Ines Thiele, Ronan M.T. Fleming, **Creation and
188187
analysis of biochemical constraint-based models: the COBRA Toolbox
189-
v3.0**, accepted in Nature Protocols, 2018,
190-
`arXiv:1710.04038 <https://arxiv.org/abs/1710.04038>`__.
188+
v3.0**, Nature Protocols, volume 14, pages 639–702, 2019
189+
`doi.org/10.1038/s41596-018-0098-2 <https://doi.org/10.1038/s41596-018-0098-2>`__.
191190

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.. end-how-to-cite-marker
193192
@@ -236,42 +235,42 @@ holder.*
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.. |macos| raw:: html
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239-
<img src="https://prince.lcsb.uni.lu/jenkins/userContent/apple.png" height="20px" width="20px" alt="macOS">
238+
<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/apple.png" height="20px" width="20px" alt="macOS">
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.. |linux| raw:: html
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244-
<img src="https://prince.lcsb.uni.lu/jenkins/userContent/linux.png" height="20px" width="20px" alt="linux">
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<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/linux.png" height="20px" width="20px" alt="linux">
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.. |windows| raw:: html
248247

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<img src="https://prince.lcsb.uni.lu/jenkins/userContent/windows.png" height="20px" width="20px" alt="windows">
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<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/windows.png" height="20px" width="20px" alt="windows">
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.. |warning| raw:: html
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<img src="https://prince.lcsb.uni.lu/jenkins/userContent/warning.png" height="20px" width="20px" alt="warning">
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<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/warning.png" height="20px" width="20px" alt="warning">
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.. |matlab| raw:: html
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<img src="https://prince.lcsb.uni.lu/jenkins/userContent/matlab.png" height="20px" width="20px" alt="matlab">
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<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/matlab.png" height="20px" width="20px" alt="matlab">
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.. |tada| raw:: html
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<img src="https://prince.lcsb.uni.lu/jenkins/userContent/tada.png" height="20px" width="20px" alt="tada">
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<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/tada.png" height="20px" width="20px" alt="tada">
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.. |thumbsup| raw:: html
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<img src="https://prince.lcsb.uni.lu/jenkins/userContent/thumbsUP.png" height="20px" width="20px" alt="thumbsup">
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<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/thumbsUP.png" height="20px" width="20px" alt="thumbsup">
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.. |bulb| raw:: html
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<img src="https://prince.lcsb.uni.lu/jenkins/userContent/bulb.png" height="20px" width="20px" alt="bulb">
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<img src="https://prince.lcsb.uni.lu/cobratoolbox/img/bulb.png" height="20px" width="20px" alt="bulb">
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.. |tutorials| raw:: html

‎docs/Makefile

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@echo "Creating modules index page."
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bash createModulesPage.sh
5555
@echo "Copying tutorial html files into source/_static/tutorials/."
56-
bash prepareTutorials.sh -t=~/tmp/COBRA.tutorials -c=~/tmp/cobratoolbox -p=~/tmp -m=rst
56+
bash prepareTutorials.sh -t=$(ARTENOLIS_DATA_PATH)/repos/COBRA.tutorials -c=$(ARTENOLIS_DATA_PATH)/repos/cobratoolbox -p=$(ARTENOLIS_DATA_PATH)/cobratoolbox -m=rst
5757
@echo "Generating list of suggestions for the websearch."
5858
python generateJSONList.py
5959
@echo
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231231
dummy:
232232
$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
233233
@echo
234-
@echo "Build finished. Dummy builder generates no files."
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@echo "Build finished. Dummy builder generates no files."

‎docs/createModulesPage.sh

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echo ".. raw:: html" >> $rstFunctionPath
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echo "" >> $rstFunctionPath
3333
echo " <div class=\"tutorialSectionBox $section\">" >> $rstFunctionPath
34-
echo " <div class=\"sectionLogo\"><img class=\"avatar\" src=\"https://prince.lcsb.uni.lu/img/icon_${section}_wb.png\"></div>" >> $rstFunctionPath
34+
echo " <div class=\"sectionLogo\"><img class=\"avatar\" src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/icon_${section}_wb.png\"></div>" >> $rstFunctionPath
3535
echo " <div class=\"sectionTitle\"><h3>${subs[$section]}</h3></div>" >> $rstFunctionPath
3636
echo " <div class=\"row\">" >> $rstFunctionPath
3737
echo " <div class=\"col-xs-6\">" >> $rstFunctionPath

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