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Merge pull request #27 from opencobra/develop
Regular merge of develop
2 parents 96b3764 + dd99406 commit 3a2b995

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15 files changed

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‎.artenolis.yml

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

‎.artenolis/runtests.sh

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

‎.gitignore

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[Dd]esktop.ini
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# Documentation related files
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docs/.documenter.enc
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docs/.documenter
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docs/source/_static/json/functions.json
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*.pyc

‎.gitmodules

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

‎README.rst

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

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

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.. include:: ../../README.rst
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:end-before: end-how-to-cite-marker
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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/jenkins/userContent/tada.png" height="20px" width="20px" alt="tada">
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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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.. |tutorials| raw:: html
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.. |latest| raw:: html
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<a href="https://opencobra.github.io/cobratoolbox/latest"><img src="https://img.shields.io/badge/COBRA-docs-blue.svg?maxAge=0"></a>
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‎docs/source/contr_cobratoolbox.rst

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If there are changes listed, publish them by selecting procedure ``[3]`` of the
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contribute menu.
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.. |branchModel| image:: https://prince.lcsb.uni.lu/img/figure6.png
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.. |branchModel| image:: https://prince.lcsb.uni.lu/MATLAB.devTools/img/figure6.png
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.. include:: ../../README.rst
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‎docs/source/funding.rst

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<table width="100%" class="noBorder">
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<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>
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<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>
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<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>
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<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>
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National Centre of Excellence in Research (NCER) on Parkinson’s disease.
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<table width="100%" class="noBorder">
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<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>
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<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>
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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
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<br><br>
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<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>
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<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>
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<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>
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<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>
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‎docs/source/index.rst

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‎docs/source/prerequisites.rst

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‎docs/source/troubleshooting/cobratutorials.rst

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‎test/inputCI.txt

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y
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testFile1

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