Process biomodels into 'final'. #132
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| name: Process biomodels into 'final'. | |
| on: | |
| # push: | |
| workflow_dispatch: | |
| jobs: | |
| fixEntries: | |
| name: Fix the entries of BioModels and commit to the repository | |
| strategy: | |
| matrix: | |
| job: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| submodules: recursive | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Setup pip cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: /opt/hostedtoolcache/Python | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install pip and setuptools | |
| run: | | |
| python -m pip install pip==23.0.0 | |
| python -m pip install pip==23.0.0 | |
| - uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'adopt' | |
| java-version: '15' | |
| - name: Install Systems Biology Format Converter (SBFC) | |
| run: | | |
| cd /tmp | |
| wget https://sourceforge.net/projects/sbfc/files/sbfc/sbfc-1.3.7.zip/download -O sbfc-1.3.7.zip | |
| unzip sbfc-1.3.7.zip | |
| mv sbfc-1.3.7 /opt/ | |
| rm sbfc-1.3.7.zip | |
| echo "/opt/sbfc-1.3.7" >> $GITHUB_PATH | |
| - name: Install Octave | |
| run: | | |
| sudo apt update -y | |
| sudo apt-get install -y --no-install-recommends octave | |
| - name: Install Scilab | |
| run: sudo apt-get install -y --no-install-recommends scilab | |
| - name: Install XPP | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y --no-install-recommends xppaut | |
| - name: Install BioModels QC | |
| working-directory: biomodels-qc | |
| run: | | |
| python -m pip install cython | |
| python -m pip install . | |
| - name: Install requirements | |
| run: python -m pip install -r requirements.txt | |
| - name: Fix entries | |
| run: python fix-entries.py --convert-files --validate-sbml --num-jobs 20 --job ${{ matrix.job }} | |
| - name: Setup Git | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "Center for Reproducible Biomodeling Modeling Bot" | |
| git config pull.rebase false | |
| - id: commit-final-entries | |
| name: Commit changes to the fixed entries | |
| run: | | |
| git stash | |
| git pull | |
| set +e | |
| git stash pop | |
| chmod a+x git_add.bat | |
| ./git_add.bat | |
| git pull | |
| git commit -m "Automated update fixed versions of entries" | |
| if [[ $? = 0 ]]; then | |
| finalEntriesChanged=1 | |
| else | |
| finalEntriesChanged=0 | |
| fi | |
| echo "finalEntriesChanged=$finalEntriesChanged" >> $GITHUB_OUTPUT | |
| - name: Push the changes to the fixed entries | |
| if: steps.commit-final-entries.outputs.finalEntriesChanged == '1' | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: ${{ github.ref }} |