ADT: Add Biomarker/Pathology GX validation suites #646
Workflow file for this run
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| # This is a basic workflow to help you get started with Actions | |
| name: CI | |
| on: | |
| push: | |
| branches: ["dev"] | |
| # Match tags that resemble a version | |
| tags: ['[0-9]+\.[0-9]+\.[0-9]+'] | |
| pull_request: | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| # test job includes unit tests and coverage | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: { fetch-depth: 0 } # deep clone for setuptools-scm | |
| - uses: actions/setup-python@v5 | |
| with: { python-version: "3.9" } | |
| - name: Run static analysis and format checkers | |
| run: pipx run pre-commit run --all-files --show-diff-on-failure | |
| test: | |
| needs: [pre-commit] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.8" | |
| - "3.9" | |
| # Support for Python 3.10 and 3.11 is temproarily disabled | |
| # - "3.10" | |
| # - "3.11" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| pip install pytest pytest-cov | |
| - name: Test with pytest | |
| run: | | |
| pytest tests/ --cov=agoradatatools --cov-report=html | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pytest-results-${{ matrix.python-version }} | |
| path: htmlcov | |
| # Use always() to always run this step to publish test results when there are test failures | |
| if: ${{ always() }} | |
| # build job includes integration test | |
| build: | |
| needs: [test] | |
| # The type of runner that the job will run on | |
| name: test data processing | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.9" | |
| - run: pip install -U setuptools | |
| - run: pip install . | |
| - run: adt test_config.yaml --upload --platform GITHUB --run_id ${{ github.run_id }} --token ${{secrets.SYNAPSE_PAT}} | |
| ghcr-publish: | |
| needs: [build, test] | |
| if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: | | |
| ghcr.io/${{ github.repository }} | |
| tags: | | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=semver,pattern={{major}} | |
| type=ref,event=branch | |
| type=sha | |
| latest | |
| - name: Publish Docker Image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| build-args: | | |
| TARBALL_PATH=${{ needs.prepare.outputs.tarball-path }} | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} |