Allow a posix file source to prefer linking. #4023
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| name: Integration | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| - 'lib/galaxy_test/selenium/**' | |
| pull_request: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| - 'lib/galaxy_test/selenium/**' | |
| schedule: | |
| # Run at midnight UTC every Tuesday | |
| - cron: '0 0 * * 2' | |
| env: | |
| GALAXY_TEST_AMQP_URL: 'amqp://localhost:5672//' | |
| GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8' | |
| GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1' | |
| GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1' | |
| GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT: '1' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Test | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.8'] | |
| chunk: ['0', '1', '2', '3'] | |
| services: | |
| postgres: | |
| image: postgres:13 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: postgres | |
| ports: | |
| - 5432:5432 | |
| rabbitmq: | |
| image: rabbitmq | |
| ports: | |
| - 5672:5672 | |
| steps: | |
| - if: github.event_name == 'schedule' | |
| run: | | |
| echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV | |
| # Skip outputs_to_working_directory: true in integration tests, doesn't work with pulsar | |
| # echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV | |
| - name: Prune unused docker image, volumes and containers | |
| run: docker system prune -a -f | |
| - name: Clean dotnet folder for space | |
| run: rm -Rf /usr/share/dotnet | |
| - name: Install packages | |
| # conntrack: mandatory for later k8s versions | |
| # ffmpeg: ffprobe needed by media datatypes | |
| run: sudo apt-get update && sudo apt-get -y install conntrack ffmpeg | |
| - name: Setup Minikube | |
| uses: medyagh/setup-minikube@latest | |
| with: | |
| driver: none | |
| kubernetes-version: '1.23.0' | |
| - name: Check pods | |
| run: kubectl get pods -A | |
| - uses: actions/checkout@v4 | |
| with: | |
| path: 'galaxy root' | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: '18.12.1' | |
| cache: 'yarn' | |
| cache-dependency-path: 'galaxy root/client/yarn.lock' | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| cache-dependency-path: 'galaxy root/requirements.txt' | |
| - name: Get full Python version | |
| id: full-python-version | |
| shell: bash | |
| run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT | |
| - name: Cache galaxy venv | |
| uses: actions/cache@v4 | |
| with: | |
| path: 'galaxy root/.venv' | |
| key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration | |
| - name: Install Apptainer's singularity | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| - name: Run tests | |
| run: | | |
| . .ci/minikube-test-setup/start_services.sh | |
| ./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }} | |
| working-directory: 'galaxy root' | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| flags: integration | |
| working-directory: 'galaxy root' | |
| - uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: Integration test results (${{ matrix.python-version }}, ${{ matrix.chunk }}) | |
| path: 'galaxy root/run_integration_tests.html' |