tests #45
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| 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 * *" | |
| permissions: | |
| contents: read | |
| concurrency: | |
| group: >- | |
| ${{ github.workflow }}-${{ github.ref_type }}- | |
| ${{ github.event.pull_request.number || github.sha }} | |
| cancel-in-progress: true | |
| jobs: | |
| # https://docs.github.com/en/actions/using-jobs/setting-default-values-for-jobs | |
| pre_job: | |
| # continue-on-error: true # Uncomment once integration is finished | |
| runs-on: ubuntu-latest | |
| # Map a step output to a job output | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@v5 | |
| with: | |
| # All of these options are optional, so you can remove them if you are happy with the defaults | |
| concurrent_skipping: "never" | |
| skip_after_successful_duplicate: "true" | |
| paths_ignore: '["**/README.md", "**/docs/**"]' | |
| do_not_skip: '["pull_request", "workflow_dispatch", "schedule"]' | |
| prepare: | |
| needs: pre_job | |
| if: needs.pre_job.outputs.should_skip != 'true' | |
| runs-on: ubuntu-latest | |
| outputs: | |
| wheel-distribution: ${{ steps.wheel-distribution.outputs.path }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: { fetch-depth: 0 } # deep clone for setuptools-scm | |
| - uses: actions/setup-python@v4 | |
| id: setup-python | |
| with: { python-version: "3.11" } | |
| - name: Run static analysis and format checkers | |
| run: pipx run pre-commit run --all-files --show-diff-on-failure | |
| - name: Build package distribution files | |
| run: >- | |
| pipx run --python '${{ steps.setup-python.outputs.python-path }}' | |
| tox -e clean,build | |
| - name: Record the path of wheel distribution | |
| id: wheel-distribution | |
| run: echo "path=$(ls dist/*.whl)" >> $GITHUB_OUTPUT | |
| - name: Store the distribution files for use in other stages | |
| # `tests` and `publish` will use the same pre-built distributions, | |
| # so we make sure to release the exact same package that was tested | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: python-distribution-files | |
| path: dist/ | |
| retention-days: 1 | |
| download_big_testdata: | |
| needs: pre_job | |
| if: needs.pre_job.outputs.should_skip != 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download test data | |
| run: >- | |
| pip install requests && python tests/specific_analyses/e03_download_intraassay_zenodo_zip.py | |
| - name: Store the test data for use in other stages | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: example_data | |
| path: example_data/ | |
| retention-days: 1 | |
| # Starting point from: https://coderefinery.github.io/documentation/gh_workflow/ | |
| docs: | |
| needs: | |
| - pre_job | |
| - prepare | |
| if: needs.pre_job.outputs.should_skip != 'true' | |
| permissions: | |
| contents: write | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| id: setup-python | |
| with: | |
| python-version: "3.8" | |
| - name: Retrieve pre-built distribution files | |
| uses: actions/download-artifact@v3 | |
| with: { name: python-distribution-files, path: dist/ } | |
| - name: Install pandoc and build documentation | |
| run: | | |
| sudo apt-get install pandoc | |
| pipx run --python '${{ steps.setup-python.outputs.python-path }}' tox -e docs | |
| - name: Deploy to GitHub Pages | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: docs/_build/html | |
| test: | |
| needs: | |
| - pre_job | |
| - prepare | |
| - download_big_testdata | |
| if: needs.pre_job.outputs.should_skip != 'true' | |
| strategy: | |
| matrix: | |
| python: | |
| - "3.8" # oldest Python supported by PSF | |
| - "3.11" # newest Python that is stable | |
| platform: | |
| - ubuntu-latest | |
| # - macos-latest # graphviz would not install (2023-12-08) | |
| - windows-latest | |
| fail-fast: false # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstrategyfail-fast | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # https://github.com/marketplace/actions/setup-graphviz | |
| - name: Setup Graphviz | |
| uses: ts-graphviz/setup-graphviz@v1 | |
| - uses: actions/setup-python@v4 | |
| id: setup-python | |
| with: | |
| python-version: ${{ matrix.python }} | |
| # https://docs.github.com/en/actions/using-workflows/storing-workflow-data-as-artifacts#passing-data-between-jobs-in-a-workflow | |
| - name: Retrieve pre-built distribution files | |
| uses: actions/download-artifact@v3 | |
| with: { name: python-distribution-files, path: dist/ } | |
| - name: Retrieve downloaded big test files | |
| uses: actions/download-artifact@v3 | |
| with: { name: example_data, path: example_data/ } | |
| - name: Run tests | |
| run: >- | |
| pipx run --python '${{ steps.setup-python.outputs.python-path }}' | |
| tox -e coverage_githubCI --installpkg '${{ needs.prepare.outputs.wheel-distribution }}' -- -rFEx --durations 10 --color yes | |
| - name: Generate coverage report | |
| run: pipx run coverage lcov -o coverage.lcov | |
| - name: Upload partial coverage report | |
| uses: coverallsapp/github-action@master | |
| with: | |
| path-to-lcov: coverage.lcov | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| flag-name: ${{ matrix.platform }} - py${{ matrix.python }} | |
| parallel: true | |
| finalize: | |
| needs: | |
| - pre_job | |
| - test | |
| if: needs.pre_job.outputs.should_skip != 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Finalize coverage report | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel-finished: true | |
| publish: | |
| needs: | |
| - pre_job | |
| - finalize | |
| if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }} && needs.pre_job.outputs.should_skip != 'true' | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: { python-version: "3.11" } | |
| - name: Retrieve pre-built distribution files | |
| uses: actions/download-artifact@v3 | |
| with: { name: python-distribution-files, path: dist/ } | |
| - name: Publish Package | |
| env: | |
| # TODO: Set your PYPI_TOKEN as a secret using GitHub UI | |
| # - https://pypi.org/help/#apitoken | |
| # - https://docs.github.com/en/actions/security-guides/encrypted-secrets | |
| TWINE_REPOSITORY: pypi | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | |
| run: pipx run tox -e publish |