mirror of
https://github.com/galaxyproject/galaxy.git
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dependabot[bot]
7817a9cc0a
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 5. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
72 lines
2.5 KiB
YAML
72 lines
2.5 KiB
YAML
name: Converter tests
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on:
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push:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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- 'packages/**'
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pull_request:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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- 'packages/**'
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schedule:
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# Run at midnight UTC every Tuesday
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- cron: '0 0 * * 2'
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env:
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GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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test:
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name: Test
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.9']
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steps:
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- if: github.event_name == 'schedule'
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run: |
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echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
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echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
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- uses: actions/checkout@v5
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with:
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path: 'galaxy root'
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persist-credentials: false
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- name: Clone galaxyproject/galaxy-test-data
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uses: actions/checkout@v5
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with:
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repository: galaxyproject/galaxy-test-data
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path: galaxy-test-data
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persist-credentials: false
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- uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: 'galaxy root/requirements.txt'
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- name: Move test data
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run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
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- name: Install planemo
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run: pip install planemo
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- name: Determine converters to check
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run: |
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ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt
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echo "Skipping checks for the following converters:"
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ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip
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echo "Checking only the following converters:"
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cat tool_list.txt
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- name: Lint converters
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run: |
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mapfile -t TOOL_ARRAY < tool_list.txt
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planemo lint --skip CitationsMissing,HelpEmpty,HelpMissing --report_level warn "${TOOL_ARRAY[@]}"
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- name: Run tests
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run: |
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mapfile -t TOOL_ARRAY < tool_list.txt
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planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
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- uses: actions/upload-artifact@v5
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if: failure()
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with:
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name: Converter test results (${{ matrix.python-version }})
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path: tool_test_output.html
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