CI_pull_request.yml

name: CI on pull request
on:
  pull_request:
    branches:
      - main
  schedule:
      - cron: '15 2 * * TUE'  # Also run the full test suite for PRs on the main branch every Tuesday night
jobs:
  lint-and-format:
    name: Lint and check formatting
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.x"
      - uses: pre-commit/action@v3.0.1
  run-full-test-suite:
    name: Run full test suite
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.8", "3.9", "3.10", "3.11"]
        singularity-provider: ["singularity", "apptainer", "singularity-ce"]
        include:
          - singularity-provider: "singularity"
            singularity-version: "3.8.7"
          - singularity-provider: "apptainer"
            singularity-version: "1.1.3"
          - singularity-provider: "singularity-ce"
            singularity-version: "3.9.2"
    steps:
      - name: Checkout code
        uses: actions/checkout@v3
      - name: Attempt to restore Singularity/Apptainer installer from cache
        uses: actions/cache@v3
        id: cache-singularity-installer
        with:
          path: ./singularity_installer.deb
          key: ${{ matrix.os }}-${{ matrix.singularity-provider }}_installer-${{ matrix.singularity-version }}
      - name: Download Singularity ${{ matrix.singularity-version }}
        if: ${{ steps.cache-singularity-installer.outputs.cache-hit != 'true' && matrix.singularity-provider == 'singularity' }}
        run: wget -O singularity_installer.deb https://github.com/apptainer/singularity/releases/download/v${{ matrix.singularity-version }}/singularity-container_${{ matrix.singularity-version }}_amd64.deb
      - name: Download Apptainer ${{ matrix.apptainer-version }}
        if: ${{ steps.cache-singularity-installer.outputs.cache-hit != 'true' && matrix.singularity-provider == 'apptainer' }}
        run: wget -O singularity_installer.deb https://github.com/apptainer/apptainer/releases/download/v${{ matrix.singularity-version }}/apptainer_${{ matrix.singularity-version }}_amd64.deb
      - name: Download SingularityCE ${{ matrix.singularity-version }}
        if: ${{ steps.cache-singularity-installer.outputs.cache-hit != 'true' && matrix.singularity-provider == 'singularity-ce' }}
        run: wget -O singularity_installer.deb https://github.com/sylabs/singularity/releases/download/v${{ matrix.singularity-version }}/singularity-ce_${{ matrix.singularity-version }}-focal_amd64.deb
      - name: Set up Singularity/Apptainer
        run: |
          sudo apt install ./singularity_installer.deb
          singularity --version
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip
          cache-dependency-path: "**/test-requirements.txt"
      - name: Install test dependencies
        run: |
          python3 -m pip install --upgrade pip
          python3 -m pip install -r test-requirements.txt
      - name: Run test suite via pytest
        run: pytest -vv --junitxml=pytest_junit_out.xml
      - name: Archive the test results and coverage
        uses: actions/upload-artifact@v3
        with:
          name: test-results-and-coverage_python${{ matrix.python-version }}_${{ matrix.singularity-provider }}${{ matrix.singularity-version }}
          path: |
            pytest_junit_out.xml
            htmlcov/*