fix: correct conversions for volumes, areas #1795
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Tests and Linting | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| push: | |
| branches: [master] | |
| env: | |
| # UV_INDEX_STRATEGY: "unsafe-first-match" | |
| # UV_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu" | |
| PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu" | |
| jobs: | |
| linting: | |
| name: Linting | |
| if: github.event_name == 'pull_request' | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| # requites to grab the history of the PR | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| cache: 'pip' | |
| - 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-22.04 | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] | |
| 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 }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| pip install poetry | |
| pip install -e '.[dev,setup]' pytest-xdist pip | |
| if: matrix.python-version != '3.10' | |
| # uv venv | |
| # source .venv/bin/activate | |
| # uv pip install -e '.[dev,setup]' pytest-xdist pip | |
| - name: Install dependencies | |
| run: | | |
| pip install poetry | |
| pip install -e '.[dev-no-ml,setup]' pytest-xdist pip | |
| if: matrix.python-version == '3.10' | |
| - name: Test with Pytest on Python ${{ matrix.python-version }} | |
| env: | |
| UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }} | |
| run: | | |
| coverage run -m pytest --ignore tests/test_docs.py # -n auto | |
| # coverage combine | |
| # mv .coverage .coverage.${{ matrix.python-version }} | |
| # source .venv/bin/activate | |
| if: matrix.python-version != '3.9' | |
| - name: Test with Pytest on Python ${{ matrix.python-version }} | |
| env: | |
| UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }} | |
| run: | | |
| coverage run -m pytest # -n auto | |
| # coverage combine | |
| # mv .coverage .coverage.${{ matrix.python-version }} | |
| # source .venv/bin/activate | |
| if: matrix.python-version == '3.9' | |
| - name: Upload coverage data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-data-${{ matrix.python-version }} | |
| path: .coverage.* | |
| if-no-files-found: ignore | |
| include-hidden-files: true | |
| coverage: | |
| name: Coverage | |
| needs: pytest | |
| uses: aphp/foldedtensor/.github/workflows/coverage.yml@main | |
| with: | |
| base-branch: master | |
| coverage-data-pattern: coverage-data-* | |
| coverage-report: coverage.txt | |
| coverage-badge: coverage.svg | |
| coverage-branch: coverage | |
| documentation: | |
| name: Documentation | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| cache: 'pip' | |
| - run: echo WEEK=$(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: | | |
| pip install '.[docs]' | |
| # uv venv | |
| # uv pip install '.[docs]' | |
| - name: Build documentation | |
| run: | | |
| mkdocs build --clean | |
| # source .venv/bin/activate | |
| simple-installation: | |
| name: Simple installation | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - run: echo WEEK=$(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: | | |
| pip install ".[ml]" pytest | |
| pytest tests/pipelines/test_pipelines.py | |
| # uv venv | |
| # uv pip install . |