Fix behavior, disorder and qualifier pipes #1554
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| name: Tests and Linting | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| push: | |
| branches: [master] | |
| jobs: | |
| linting: | |
| name: Linting | |
| if: github.event_name == 'pull_request' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| # requites to grab the history of the PR | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v4 | |
| - uses: pre-commit/[email protected] | |
| with: | |
| extra_args: --color=always --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }} | |
| pytest: | |
| name: Pytest | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Cache downloaded resources | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.data/ | |
| key: resources | |
| # - name: Cache pip | |
| # uses: actions/cache@v3 | |
| # with: | |
| # path: ~/.cache/pip | |
| # key: ${{ runner.os }}-python-${{ matrix.python-version }}-pip | |
| - run: echo WEEK=$(date +%V) >>$GITHUB_ENV | |
| shell: bash | |
| - uses: hynek/setup-cached-uv@v1 | |
| with: | |
| cache-suffix: -tests-${{ matrix.python-version }}-${{ env.WEEK }} | |
| - name: Set up Java | |
| uses: actions/setup-java@v2 | |
| with: | |
| distribution: "temurin" # See 'Supported distributions' for available options | |
| java-version: "8" | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| uv venv | |
| pip install poetry | |
| source .venv/bin/activate | |
| uv pip install -e '.[dev,setup]' pytest-xdist pip | |
| - name: Test with Pytest on Python ${{ matrix.python-version }} | |
| env: | |
| UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }} | |
| run: | | |
| source .venv/bin/activate | |
| coverage run -m pytest --ignore tests/test_docs.py # -n auto | |
| # coverage combine | |
| # mv .coverage .coverage.${{ matrix.python-version }} | |
| if: matrix.python-version != '3.9' | |
| - name: Test with Pytest on Python ${{ matrix.python-version }} | |
| env: | |
| UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }} | |
| run: | | |
| source .venv/bin/activate | |
| coverage run -m pytest # -n auto | |
| # coverage combine | |
| # mv .coverage .coverage.${{ matrix.python-version }} | |
| if: matrix.python-version == '3.9' | |
| - name: Upload coverage data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-data-${{ matrix.python-version }} | |
| path: .coverage.* | |
| if-no-files-found: ignore | |
| coverage: | |
| name: Coverage | |
| needs: pytest | |
| uses: aphp/foldedtensor/.github/workflows/coverage.yml@main | |
| with: | |
| base-branch: master | |
| coverage-data-pattern: coverage-data-* | |
| coverage-report: coverage.txt | |
| coverage-badge: coverage.svg | |
| coverage-branch: coverage | |
| documentation: | |
| name: Documentation | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| # cache: 'pip' | |
| - run: echo WEEK=$(date +%V) >>$GITHUB_ENV | |
| shell: bash | |
| - uses: hynek/setup-cached-uv@v1 | |
| with: | |
| cache-suffix: -docs-${{ matrix.python-version }}-${{ env.WEEK }} | |
| - name: Install dependencies | |
| run: | | |
| uv venv | |
| uv pip install '.[dev]' | |
| - name: Build documentation | |
| run: | | |
| source .venv/bin/activate | |
| mkdocs build --clean | |
| simple-installation: | |
| name: Simple installation | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: echo WEEK=$(date +%V) >>$GITHUB_ENV | |
| shell: bash | |
| - uses: hynek/setup-cached-uv@v1 | |
| with: | |
| cache-suffix: -simple-install-${{ matrix.python-version }}-${{ env.WEEK }} | |
| - name: Install library | |
| run: | | |
| uv venv | |
| uv pip install . |