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: ${{ matrix.os }}
    services:
      postgres:
        # Use PostgreSQL 11 to workaround https://github.com/sqlalchemy/sqlalchemy/issues/4919
        # for Galaxy 18.05, 18.09 and 19.01
        image: postgres:11
        # Provide the password for postgres
        env:
          POSTGRES_PASSWORD: postgres
        # Set health checks to wait until postgres has started
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 5432:5432
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        tox_env: [py36]
        galaxy_version:
          - dev
          - release_21.09
          - release_21.05
          - release_21.01
          - release_20.09
          - release_20.05
          - release_20.01
          - release_19.09
          - release_19.05
          - release_19.01
          - release_18.09
          - release_18.05
          - release_18.01
          - release_17.09
        include:
          - os: ubuntu-latest
            tox_env: py310
            galaxy_version: dev
          - os: ubuntu-latest
            tox_env: py39
            galaxy_version: dev
          - os: ubuntu-latest
            tox_env: py38
            galaxy_version: dev
          - os: ubuntu-latest
            tox_env: py37
            galaxy_version: dev
          # Cannot test on macOS because service containers are not supported
          # yet: https://github.community/t/github-actions-services-available-on-others-vms/16916
          # - os: macos-latest
          #   tox_env: py36
          #   galaxy_version: dev
    steps:
      - uses: actions/checkout@v2
      - name: Cache pip dir
        uses: actions/cache@v2
        with:
          path: ~/.cache/pip
          key: pip-cache-${{ matrix.tox_env }}-${{ matrix.galaxy_version }}
      - name: Calculate Python version for BioBlend from tox_env
        id: get_bioblend_python_version
        run: echo "::set-output name=bioblend_python_version::$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')"
      - name: Set up Python for BioBlend
        uses: actions/setup-python@v2
        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 ${{ matrix.galaxy_version }} in
            release_17.09 | release_18.0* | release_19.0* )
              galaxy_python_version=2.7
              ;;
            release_20.0* )
              galaxy_python_version=3.5
              ;;
            release_21.0* )
              galaxy_python_version=3.6
              ;;
            release_22.0* | dev )
              galaxy_python_version=3.7
          esac
          echo "::set-output name=galaxy_python_version::$galaxy_python_version"
      - name: Set up Python for Galaxy
        uses: actions/setup-python@v2
        with:
          python-version: ${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }}
      - name: Run tests
        env:
          PGPASSWORD: postgres
          PGPORT: 5432
          PGHOST: localhost
        run: |
          # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
          createdb -U postgres galaxy
          # Install Galaxy
          wget https://github.com/galaxyproject/galaxy/archive/${{ matrix.galaxy_version }}.tar.gz
          tar xvzf ${{ matrix.galaxy_version }}.tar.gz | tail
          cd galaxy-${{ matrix.galaxy_version }}
          export GALAXY_DIR=$PWD
          export GALAXY_PYTHON=python${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }}
          export GALAXY_VERSION=${{ matrix.galaxy_version }}
          # Export GALAXY_CONFIG_FILE environment variable to be used by run_galaxy.sh
          export GALAXY_CONFIG_FILE=config/galaxy.ini
          # Export BIOBLEND_ environment variables to be used in BioBlend tests
          export BIOBLEND_GALAXY_MASTER_API_KEY=$(LC_ALL=C tr -dc A-Za-z0-9 < /dev/urandom | head -c 32)
          export BIOBLEND_GALAXY_USER_EMAIL=${USER}@localhost.localdomain
          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
          eval "echo \"$(cat "${{ github.workspace }}/tests/template_galaxy.ini")\"" > "$GALAXY_CONFIG_FILE"
          # Update psycopg2 requirement to a version compatible with glibc 2.26 for Galaxy releases 16.01-18.01, see https://github.com/psycopg/psycopg2-wheels/issues/2
          sed -i.bak -e 's/psycopg2==2.6.1/psycopg2==2.7.3.1/' lib/galaxy/dependencies/conditional-requirements.txt
          # Start Galaxy and wait for successful server start
          export GALAXY_SKIP_CLIENT_BUILD=1
          GALAXY_RUN_ALL=1 "${{ github.workspace }}/run_galaxy.sh" --daemon --wait
          export BIOBLEND_GALAXY_URL=http://localhost:8080
          cd "${{ github.workspace }}"
          tox -e ${{ matrix.tox_env }}
      - name: The job has failed
        if: ${{ failure() }}
        run: |
          cat galaxy-${{ matrix.galaxy_version }}/main.log