test.yaml

name: Tests
on:
  push:
  pull_request:
  schedule:
    # Run at midnight UTC every Tuesday
    - cron: '0 0 * * 2'
concurrency:
  group: test-${{ github.ref }}
  cancel-in-progress: true
jobs:
  test:
    if: github.event_name != 'schedule' || github.repository_owner == 'galaxyproject'
    runs-on: ${{ matrix.os }}
    services:
      postgres:
        image: postgres
        # Provide the password for postgres
        env:
          POSTGRES_PASSWORD: postgres
        # Set health checks to wait until postgres has started
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 5432:5432
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        tox_env: [py38]
        galaxy_version:
          - dev
          - release_24.1
          - release_24.0
          - release_23.2
          - release_23.1
          - release_23.0
          - release_22.05
          - release_22.01
          - release_21.09
          - release_21.05
          - release_21.01
          - release_20.09
          - release_20.05
          - release_20.01
          - release_19.09
          - release_19.05
        include:
          - os: ubuntu-latest
            tox_env: py312
            galaxy_version: dev
          # Cannot test on macOS because service containers are not supported
          # yet: https://github.community/t/github-actions-services-available-on-others-vms/16916
          # - os: macos-latest
          #   tox_env: py38
          #   galaxy_version: dev
    steps:
      - uses: actions/checkout@v4
      - name: Cache pip dir
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: pip-cache-${{ matrix.tox_env }}-${{ matrix.galaxy_version }}
      - name: Calculate Python version for BioBlend from tox_env
        id: get_bioblend_python_version
        run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
      - name: Set up Python for BioBlend
        uses: actions/setup-python@v5
        with:
          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
      - name: Install tox
        run: |
          python3 -m pip install --upgrade pip setuptools
          python3 -m pip install 'tox>=1.8.0' 'virtualenv>=20.0.14'
      - name: Determine Python version for Galaxy
        id: get_galaxy_python_version
        run: |
          case ${{ matrix.galaxy_version }} in
            release_19.05 | release_19.09 | release_20.0? )
              # The minimum Python version supported by the 19.05 and 19.09
              # releases is 2.7, but virtualenv dropped support for creating
              # Python <3.7 environments in v20.22.0 .
              # The minimum Python version supported by the 20.0* releases is
              # 3.5, but the setup-python GitHub action dropped support for
              # Python 3.5 and 3.6 on Ubuntu 22.04, see
              # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
              galaxy_python_version=3.7
              ;;
            release_21.0? )
              # The minimum Python supported version by these releases is 3.6,
              # but same as above.
              galaxy_python_version=3.7
              ;;
            release_22.0? | release_23.? )
              galaxy_python_version=3.7
              ;;
            release_24.? | dev )
              galaxy_python_version=3.8
              ;;
          esac
          echo "galaxy_python_version=$galaxy_python_version" >> $GITHUB_OUTPUT
      - name: Set up Python for Galaxy
        uses: actions/setup-python@v5
        with:
          python-version: ${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }}
      - name: Run tests
        env:
          PGPASSWORD: postgres
          PGPORT: 5432
          PGHOST: localhost
        run: |
          # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
          createdb -U postgres galaxy
          # Run ToolShed tests only once per Python version
          if [ "${{ matrix.galaxy_version }}" = 'dev' ]; then
              export BIOBLEND_TOOLSHED_URL=https://testtoolshed.g2.bx.psu.edu/
          fi
          # Install Galaxy
          GALAXY_DIR=galaxy-${{ matrix.galaxy_version }}
          git clone --depth=1 -b ${{ matrix.galaxy_version }} https://github.com/galaxyproject/galaxy $GALAXY_DIR
          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
          ./run_bioblend_tests.sh -g $GALAXY_DIR -v python${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }} -e ${{ matrix.tox_env }}
      - name: The job has failed
        if: ${{ failure() }}
        run: |
          cat galaxy-${{ matrix.galaxy_version }}/*.log