fix-ci.yml

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 "bot@reproduciblebiomodels.org"
          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 }}