Update tests for libraries API change in Galaxy 23.1 #7
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |