add function to check SAMPLE_CLASS and cfDNA existence #857
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: build | |
| on: | |
| push: | |
| branches: [main, develop, 'GEN*', 'gen*'] | |
| pull_request: | |
| release: | |
| types: | |
| - created | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install -y bedtools | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest pytest-cov cython | |
| pip install . | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| # - name: Lint with flake8 | |
| # run: | | |
| # # stop the build if there are Python syntax errors or undefined names | |
| # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| pytest tests/ --cov=genie --cov=genie_registry --cov-report=html | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pytest-results-${{ matrix.python-version }} | |
| path: htmlcov | |
| # Use always() to always run this step to publish test results when there are test failures | |
| if: ${{ always() }} | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: psf/black@stable | |
| deploy: | |
| needs: [test, lint] | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'release' | |
| permissions: | |
| id-token: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel build | |
| - name: Build distributions | |
| run: python -m build | |
| - name: Publish to pypi | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| build-container: | |
| needs: [test, lint] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Docker buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log into registry ${{ env.REGISTRY }} | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract Docker metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| - name: Format tags as registry refs | |
| id: registry_refs | |
| env: | |
| TAGS: ${{ steps.meta.outputs.json }} | |
| run: | | |
| echo tags=$(echo $TAGS | jq '.tags[] | "type=registry,ref=" + . + "_cache"| @text') >> $GITHUB_OUTPUT | |
| - name: Build and push Docker image | |
| id: build-and-push | |
| uses: docker/build-push-action@v5 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| context: . | |
| push: true | |
| provenance: false | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: ${{ steps.registry_refs.outputs.tags }},mode=max | |
| cache-to: ${{ steps.registry_refs.outputs.tags }},mode=max |