ci.yml

name: Continuous integration

on:
  push:
  pull_request:

jobs:
  getVersionNumber:
    name: Get version number
    if: "startsWith(github.ref, 'refs/tags/') && github.actor != 'allcontributors' && !contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ubuntu-22.04
    outputs:
      version: ${{ steps.get-version-number.outputs.version }}
    steps:
      - id: get-version-number
        name: Get version number
        env:
          TAG: ${{ github.ref }}
        run: |
          version="${TAG/refs\/tags\//}"
          echo "version=$version" >> $GITHUB_OUTPUT

  build:
    name: Lint, test, and compile documentation
    if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
    runs-on: ubuntu-22.04
    strategy:
      matrix:
        python-version: [ "3.10" ]
      fail-fast: false
    defaults:
      run:
        shell: bash
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 1

      - name: Configure Git
        run: |
          git config --local user.email "biosimulators.daemon@gmail.com"
          git config --local user.name "biosimulatorsdaemon"
          git config pull.rebase false

      - name: Install Python
        uses: actions/setup-python@v2
        with:
          python-version: '3.10'

      - name: Install pip and setuptools
        run: |
          python -m pip install pip==23.0.0
          python -m pip install pip==23.0.0
          python -m pip --version

      - name: Install Java # for pyNeuroML
        uses: actions/setup-java@v2
        with:
          distribution: 'adopt'
          java-version: '15'

      - name: Install Perl # for BioNetGen
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends perl

      - name: Install XPP
        run: |
          sudo apt-get install -y --no-install-recommends wget make gcc libx11-dev libc6-dev xppaut

      - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
        uses: eWaterCycle/setup-singularity@v6

      # install package
      - name: Set up the environment
        uses: ./.github/actions/setup-poetry-env
        with:
          python-version: ${{ matrix.python-version }}

      # zip COMBINE/OMEX archives
      - name: Zip COMBINE/OMEX archives
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends zipcmp
          poetry run python scripts/zip_examples.py

      - id: commit-archives
        name: Commit zipped COMBINE/OMEX archives
        if: startsWith(github.ref, 'refs/heads/')
        env:
          HEAD: ${{ github.ref }}
        run: |
          git stash || true
          git pull
          set +e
          git stash pop || true
          git add examples/**/*.omex
          git commit -m "chore: Updated COMBINE/OMEX archives [skip ci]"
          if [[ $? = 0 ]]; then
            archivesChanged=1
          else
            archivesChanged=0
          fi
          echo "archivesChanged=$archivesChanged" >> $GITHUB_OUTPUT

          branch="${HEAD/refs\/heads\//}"
          echo "branch=$branch" >> $GITHUB_OUTPUT

      - name: Push the zipped COMBINE/OMEX archives
        if: steps.commit-archives.outputs.archivesChanged == '1' && startsWith(github.ref, 'refs/heads/')
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ steps.commit-archives.outputs.branch }}

      # lint
      - name: Lint the package
        run: poetry run python -m flake8 $GITHUB_WORKSPACE/biosimulators_test_suite

      - name: Run the tests
        uses: GabrielBB/xvfb-action@v1
        env:
          MPLBACKEND: PDF
          # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/  # uncomment to execute tests with the dev deployment
        with:
          run: |
            poetry run python -m pip install --upgrade setuptools
            poetry run python -m pytest tests/ --cov=./biosimulators_test_suite --cov-report=xml

      - name: Upload the coverage report to Codecov
        uses: codecov/codecov-action@v2
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          flags: unittests
          file: ./coverage.xml

      # compile documentation
      - name: Install the requirements for compiling the documentation
        run: poetry install --with docs

      - name: Compile the documentation
        run: |
          poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
          mkdir -p docs-src/_static
          poetry run sphinx-build docs-src docs

      - name: Setup tmate session 3 (if failed)
        uses: mxschmitt/action-tmate@v3
        if: ${{ failure() }}
        timeout-minutes: 40

  release:
    name: Release a new version
    needs: [getVersionNumber, build]
    runs-on: ubuntu-22.04
    outputs:
      docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
          ref: dev

      - name: Configure Git
        run: |
          git config --local user.email "biosimulators.daemon@gmail.com"
          git config --local user.name "biosimulatorsdaemon"
          git config pull.rebase false

      - name: Set up the environment
        uses: ./.github/actions/setup-poetry-env
        with:
          python-version: ${{ matrix.python-version }}

      # compile and push documentation
      - name: Install the requirements for compiling the documentation
        run: poetry install --with docs

      - name: Compile the documentation
        run: |
          poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
          mkdir -p docs-src/_static
          poetry run sphinx-build docs-src docs

      - id: commit-docs
        name: Commit the compiled documentation
        run: |
          git stash
          git pull
          set +e
          git stash pop
          git add docs
          git commit -m "chore: Updated compiled documentation [skip ci]"
          if [[ $? = 0 ]]; then
            changed=1
          else
            changed=0
          fi
          echo "changed=$changed" >> $GITHUB_OUTPUT

      - name: Push the compiled documentation
        if: steps.commit-identifiers-namespaces.outputs.changed == '1' || steps.commit-docs.outputs.changed == '1'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: dev

      # Create GitHub release
      - name: Create GitHub release
        uses: actions/create-release@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          tag_name: ${{ needs.getVersionNumber.outputs.version }}
          release_name: Release ${{ needs.getVersionNumber.outputs.version }}

      # Create PyPI release
      - name: Create packages to upload to PyPI
        run: |
          poetry build

      - name: Upload packages to PyPI
        env:
          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
        run: |
          poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI