[IBCDPE-749] Clarify points in documentation #233
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| # GitHub Actions configuration **EXAMPLE**, | |
| # MODIFY IT ACCORDING TO YOUR NEEDS! | |
| # Reference: https://docs.github.com/en/actions | |
| name: tests | |
| on: | |
| push: | |
| # Avoid using all the resources/limits available by checking only | |
| # relevant branches and tags. Other branches can be checked via PRs. | |
| branches: [main] | |
| tags: ['v[0-9]*', '[0-9]+.[0-9]+*'] # Match tags that resemble a version | |
| pull_request: # Run in every PR | |
| workflow_dispatch: # Allow manually triggering the workflow | |
| schedule: | |
| # Run roughly every 15 days at 00:00 UTC | |
| # (useful to check if updates on dependencies break the package) | |
| - cron: '0 0 1,16 * *' | |
| concurrency: | |
| group: >- | |
| ${{ github.workflow }}-${{ github.ref_type }}- | |
| ${{ github.event.pull_request.number || github.sha }} | |
| cancel-in-progress: false | |
| jobs: | |
| prepare: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| wheel-path: ${{ steps.distribution-paths.outputs.wheel }} | |
| tarball-path: ${{ steps.distribution-paths.outputs.tarball }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: {fetch-depth: 0} # deep clone for setuptools-scm | |
| - uses: actions/setup-python@v4 | |
| with: {python-version: "3.11"} | |
| - name: Run static analysis and format checkers | |
| run: pipx run pre-commit run --all-files --show-diff-on-failure | |
| - name: Install tox-gh plugin | |
| run: python -m pip install tox-gh>=1.2 | |
| - name: Build package distribution files | |
| run: tox -e clean,build | |
| - name: Record the paths of wheel and source tarball distributions | |
| id: distribution-paths | |
| run: | | |
| echo "wheel=$(ls dist/*.whl)" >> $GITHUB_OUTPUT | |
| echo "tarball=$(ls dist/*.tar.gz)" >> $GITHUB_OUTPUT | |
| - name: Store the distribution files for use in other stages | |
| # `tests`, `pypi-publish`, and `docker-publish` will use the same | |
| # pre-built distributions, so we make sure to release the exact | |
| # same package that was tested | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: python-distribution-files | |
| path: dist/ | |
| retention-days: 1 | |
| # Prevent scheduled workflow from ever being paused | |
| - name: Keepalive Workflow | |
| uses: gautamkrishnar/[email protected] | |
| with: | |
| time_elapsed: 44 | |
| test: | |
| needs: prepare | |
| strategy: | |
| matrix: | |
| python: | |
| - "3.10" # oldest Python supported | |
| - "3.11" # newest Python that is stable | |
| platform: | |
| - ubuntu-latest | |
| - macos-latest | |
| env: | |
| OS: ${{ matrix.platform }} | |
| PYTHON: ${{ matrix.python }} | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - uses: actions/download-artifact@v3 | |
| with: {name: python-distribution-files, path: dist/} | |
| - name: Install tox-gh plugin | |
| run: python -m pip install tox-gh>=1.2 | |
| - name: Setup test suite | |
| run: tox -vv --notest | |
| - name: Run tests | |
| env: | |
| # New variables should match a `passenv` pattern under `[testenv]` in tox.ini | |
| SEVENBRIDGES_CONNECTION_URI: ${{ secrets.SEVENBRIDGES_CONNECTION_URI }} | |
| NEXTFLOWTOWER_CONNECTION_URI: ${{ secrets.NEXTFLOWTOWER_CONNECTION_URI }} | |
| SYNAPSE_CONNECTION_URI: ${{ secrets.SYNAPSE_CONNECTION_URI }} | |
| run: >- | |
| tox --installpkg '${{ needs.prepare.outputs.wheel-path }}' | |
| -- -rFEx --durations 10 --color yes | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| # CodeCov can be flaky, so this step is not required for success | |
| fail_ci_if_error: false | |
| files: coverage.xml | |
| # Using matrix pattern from `codecov/codecov-action` README: | |
| # https://github.com/codecov/codecov-action#example-workflowyml-with-codecov-action | |
| env_vars: OS,PYTHON | |
| verbose: true | |
| pypi-publish: | |
| needs: [prepare, test] | |
| if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: {python-version: "3.11"} | |
| - uses: actions/download-artifact@v3 | |
| with: {name: python-distribution-files, path: dist/} | |
| - name: Publish Python Package to PyPI | |
| env: | |
| TWINE_REPOSITORY: pypi | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | |
| run: pipx run --spec 'tox!=3.0' tox -e publish | |
| docker-publish: | |
| needs: [prepare, test] | |
| if: ${{ github.event_name == 'push' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/download-artifact@v3 | |
| with: {name: python-distribution-files, path: dist/} | |
| - uses: docker/setup-qemu-action@v2 | |
| - uses: docker/setup-buildx-action@v2 | |
| - uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: | | |
| ghcr.io/${{ github.repository }} | |
| tags: | | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=semver,pattern={{major}} | |
| type=ref,event=branch | |
| type=sha | |
| - name: Publish Python Package to Docker Hub and GHCR | |
| uses: docker/build-push-action@v3 | |
| with: | |
| platforms: linux/amd64,linux/arm64 | |
| context: . | |
| file: src/docker/Dockerfile | |
| build-args: | | |
| TARBALL_PATH=${{ needs.prepare.outputs.tarball-path }} | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} |