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Merge pull request #27 from opencobra/develop
Regular merge of develop
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@@ -7,7 +7,7 @@ before_install: | |
| - CURRENT_DIR=`pwd`; | ||
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| # remove the cloned repository even after failure | ||
| - rm -rf ~/MATLAB.devTools.CI; | ||
| - rm -rf $ARTENOLIS_DATA_PATH/repos/MATLAB.devTools.CI; | ||
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| # change to the current directory | ||
| - cd $CURRENT_DIR; | ||
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@@ -20,9 +20,9 @@ script: | |
| - cd $CURRENT_DIR; | ||
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| # 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)"; | ||
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@@ -50,16 +50,23 @@ script: | |
| # launch the tests | ||
| - sh ./.artenolis/runtests.sh; | ||
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| - cd ~/fork-MATLAB.devTools.CI; | ||
| - git reset --hard origin/develop; | ||
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| after_success: | ||
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| # 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 | ||
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| # 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 | ||
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| after_script: | ||
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| # reset the fork | ||
| - cd $ARTENOLIS_DATA_PATH/repos/fork-MATLAB.devTools.CI; | ||
| - git reset --hard origin/develop; | ||
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| @@ -1,5 +1,5 @@ | ||
| #!/bin/sh | ||
| cd ./test | ||
| /mnt/prince-data/MATLAB/$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 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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| Original file line number | Diff line number | Diff line change |
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@@ -122,10 +122,10 @@ shell). On **Windows**, start ``GUI Bash``. Then type | |
| Please replace ``"yourGitHubUsername"`` and ``"[email protected]"`` | ||
| with your respective credentials. | ||
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| .. |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 | ||
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| .. |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 | ||
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| .. include:: ../../README.rst | ||
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@@ -3,7 +3,7 @@ COBRA.tutorials | |
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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"> | ||
| <img src="https://prince.lcsb.uni.lu/MATLAB.devTools/img/warning.png" height="20px" width="20px" alt="warning"> | ||
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| |warning| This section is tailored to users who feel comfortable using | ||
| the terminal (or shell). It is recommended for other users | ||
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@@ -18,25 +18,25 @@ Fork and checkout your branch | |
| 1. Fork the `COBRA.tutorials repository <https://www.github.com/opencobra/COBRA.tutorials>`__ on Github. | ||
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| 2. Clone the forked repository to ``fork-COBRA.tutorials`` located in a directory of your choice: | ||
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| .. code-block:: console | ||
| $ git clone [email protected]:<userName>/COBRA.tutorials.git fork-COBRA.tutorials.git | ||
| 3. Change to the directory ``fork-COBRA.tutorials``: | ||
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| .. code-block:: console | ||
| $ cd fork-COBRA.tutorials.git/ | ||
| 4. Set the upstream to the ``opencobra/COBRA.tutorials`` repository: | ||
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| .. code-block:: console | ||
| $ git remote add upstream [email protected]:opencobra/COBRA.tutorials.git | ||
| 5. Fetch from the upstream repository | ||
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| .. code-block:: console | ||
| $ git fetch upstream | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| cobrabot | ||
| /home/sbg-jenkins/ | ||
| artenobot | ||
| /mnt/artenolis-data/repos/ | ||
| y | ||
| n | ||
| testFile1 | ||
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