Update Python dependencies #291
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| name: Converter tests | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| pull_request: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| schedule: | |
| # Run at midnight UTC every Tuesday | |
| - cron: '0 0 * * 2' | |
| env: | |
| GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Test | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| steps: | |
| - if: github.event_name == 'schedule' | |
| run: | | |
| echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV | |
| echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV | |
| - 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' | |
| - name: Clone galaxyproject/galaxy-test-data | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: galaxyproject/galaxy-test-data | |
| path: galaxy-test-data | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| cache-dependency-path: 'galaxy root/requirements.txt' | |
| - name: Move test data | |
| run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/' | |
| - name: Install planemo | |
| run: pip install planemo | |
| - name: Determine converters to check | |
| run: | | |
| ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt | |
| echo "Skipping checks for the following converters:" | |
| ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip | |
| echo "Checking only the following converters:" | |
| cat tool_list.txt | |
| - name: Lint converters | |
| run: | | |
| mapfile -t TOOL_ARRAY < tool_list.txt | |
| planemo lint --skip citations,stdio,help --report_level warn "${TOOL_ARRAY[@]}" | |
| - name: Run tests | |
| run: | | |
| mapfile -t TOOL_ARRAY < tool_list.txt | |
| planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}" | |
| - uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: Converter test results (${{ matrix.python-version }}) | |
| path: tool_test_output.html |