TestTools #11
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| name: TestTools | |
| on: | |
| schedule: | |
| - cron: '0 0 * * 1' | |
| jobs: | |
| list: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: 'List repos' | |
| id: set-matrix | |
| run: echo "matrix=$(find tools -mindepth 1 -maxdepth 1 -type d | jq -R -s -c 'split("\n")[:-1] | map(split("/")[-1])')" >> "${GITHUB_OUTPUT}" | |
| skip: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: 'List repos' | |
| id: set-matrix | |
| run: | | |
| matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_tools_skip.txt) | |
| echo "Number of repos: ${matrix}" | |
| echo "matrix=$matrix" >> "${GITHUB_OUTPUT}" | |
| test: | |
| needs: [list, skip] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| repo: ${{ fromJson(needs.list.outputs.matrix) }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: "Setup python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' # caching pip dependencies | |
| cache-dependency-path: | | |
| env/requirements.txt | |
| - name: 'Install packages' | |
| run: | | |
| pip install -r env/requirements.txt | |
| - name: 'Prepare output' | |
| run: | | |
| mkdir -p "log/${{ matrix.repo }}" | |
| - name: 'Wrapper Lint' | |
| run: | | |
| planemo lint "tools/${{ matrix.repo }}" | |
| - name: 'Shed lint' | |
| run: | | |
| planemo shed_lint --urls --xsd --ensure_metadata "tools/${{ matrix.repo }}" | |
| ./scripts/shed_lint.py -i "tools/${{ matrix.repo }}" | |
| - name: 'Prepare' | |
| run: | | |
| mkdir -p "log/${{ matrix.repo }}" | |
| - name: 'Test tool' | |
| if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }} | |
| timeout-minutes: 120 | |
| continue-on-error: true | |
| run: | | |
| planemo test \ | |
| --biocontainers \ | |
| --no_dependency_resolution \ | |
| --no_conda_auto_init \ | |
| --galaxy_source https://github.com/galaxyproject/galaxy \ | |
| --galaxy_branch release_22.05 \ | |
| --galaxy_python_version 3.7 \ | |
| "tools/${{ matrix.repo }}" | |
| mv tool_test_output.json "log/${{ matrix.repo }}" | |
| - name: 'Prepare artefact' | |
| run: | | |
| zip -r -9 log.zip log | |
| - name: 'Upload Artifact Version' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: log-artifact-${{ matrix.repo }} | |
| path: log.zip | |
| - name: 'Aggregate results' | |
| if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }} | |
| run: | | |
| ./scripts/aggregate_test.py -i . |