Update tests for libraries API change in Galaxy 23.1 #210
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| 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: ${{ matrix.os }} | |
| services: | |
| postgres: | |
| image: postgres | |
| # Provide the password for postgres | |
| env: | |
| POSTGRES_PASSWORD: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| - 5432:5432 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| tox_env: [py38] | |
| galaxy_version: | |
| - dev | |
| - release_23.1 | |
| - release_23.0 | |
| - release_22.05 | |
| - release_22.01 | |
| - release_21.09 | |
| - release_21.05 | |
| - release_21.01 | |
| - release_20.09 | |
| - release_20.05 | |
| - release_20.01 | |
| - release_19.09 | |
| - release_19.05 | |
| include: | |
| - os: ubuntu-latest | |
| tox_env: py311 | |
| galaxy_version: dev | |
| # Cannot test on macOS because service containers are not supported | |
| # yet: https://github.community/t/github-actions-services-available-on-others-vms/16916 | |
| # - os: macos-latest | |
| # tox_env: py38 | |
| # galaxy_version: dev | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Cache pip dir | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-cache-${{ 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@v4 | |
| 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 ${{ matrix.galaxy_version }} in | |
| release_19.05 | release_19.09 | release_20.0* ) | |
| # The minimum Python version supported by the 19.05 and 19.09 | |
| # releases is 2.7, but virtualenv dropped support for creating | |
| # Python <3.7 environments in v20.22.0 . | |
| # The minimum Python version supported by the 20.0* releases is | |
| # 3.5, but the setup-python GitHub action dropped support for | |
| # Python 3.5 and 3.6 on Ubuntu 22.04, see | |
| # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877 | |
| galaxy_python_version=3.7 | |
| ;; | |
| release_21.0* ) | |
| # The minimum Python supported version by these releases is 3.6, | |
| # but same as above. | |
| galaxy_python_version=3.7 | |
| ;; | |
| release_22.0* | release_23.* | dev ) | |
| galaxy_python_version=3.7 | |
| esac | |
| echo "galaxy_python_version=$galaxy_python_version" >> $GITHUB_OUTPUT | |
| - name: Set up Python for Galaxy | |
| uses: actions/setup-python@v4 | |
| 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 |