Merge pull request #17480 from bernt-matthias/topic/del-print #26555
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: 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: ['3.7'] | |
| 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@v3 | |
| with: | |
| path: 'galaxy root' | |
| - uses: actions/setup-node@v3 | |
| 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@v3 | |
| with: | |
| repository: galaxyproject/galaxy-test-data | |
| path: galaxy-test-data | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache venv dir | |
| uses: actions/cache@v3 | |
| id: pip-cache | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} | |
| - name: Move test data | |
| run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/' | |
| - name: Install planemo | |
| run: pip install planemo | |
| - name: Determine converters to check | |
| run: | | |
| ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt | |
| echo "Skipping checks for the following converters:" | |
| ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip | |
| echo "Checking only the following converters:" | |
| cat tool_list.txt | |
| - name: Lint converters | |
| run: | | |
| mapfile -t TOOL_ARRAY < tool_list.txt | |
| planemo lint --skip citations,stdio,help --report_level warn "${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@v3 | |
| if: failure() | |
| with: | |
| name: Converter test results (${{ matrix.python-version }}) | |
| path: tool_test_output.html |