Update cellxgene schema version to 5.2.0 #2965
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: Python cellxgene_census package unit tests | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - "api/r/**" | |
| push: | |
| branches: [main] | |
| # If a new commit is pushed, cancel the jobs from previous commits. | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| CELLXGENE_CENSUS_USERAGENT: "CZI-test" | |
| jobs: | |
| unit_tests_python_api: | |
| strategy: | |
| fail-fast: false # Don't stop the workflow if one of the jobs fails | |
| matrix: | |
| os: [sc-dev-64g-runner, macos-latest] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| exclude: | |
| - os: macos-latest | |
| python-version: "3.12" | |
| runs-on: ${{matrix.os}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| cache-dependency-path: | | |
| api/**/pyproject.toml | |
| api/**/requirements*.txt | |
| - name: Install dependencies (including experimental) | |
| run: | | |
| python -m pip install -U pip setuptools wheel | |
| pip install --use-pep517 accumulation-tree # Geneformer dependency needs --use-pep517 for Cython | |
| GIT_CLONE_PROTECTION_ACTIVE=false pip install -r ./api/python/cellxgene_census/scripts/requirements-dev.txt | |
| pip install -e './api/python/cellxgene_census/[experimental]' | |
| - name: Report Dependency Versions | |
| run: pip list | |
| - name: Test with pytest (API, main tests) | |
| run: | | |
| PYTHONPATH=. coverage run --parallel-mode -m pytest -v -rP --durations=20 ./api/python/cellxgene_census/tests/ | |
| - name: Test with pytest (API, experimental) | |
| run: | | |
| PYTHONPATH=. coverage run --parallel-mode -m pytest -v -rP --durations=20 --experimental ./api/python/cellxgene_census/tests/experimental | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-api-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: ./.coverage* | |
| include-hidden-files: true | |
| if-no-files-found: "error" | |
| retention-days: 3 | |
| unit_tests_builder: | |
| strategy: | |
| matrix: | |
| os: [sc-dev-64g-runner] | |
| python-version: ["3.11"] | |
| runs-on: ${{matrix.os}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| cache-dependency-path: | | |
| tools/**/pyproject.toml | |
| tools/**/requirements*.txt | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install -U pip setuptools wheel | |
| pip install -e ./tools/cellxgene_census_builder/ | |
| pip install -r ./tools/scripts/requirements-dev.txt | |
| - name: Test with pytest (builder) | |
| run: | | |
| # Run with and without Numba JIT. This gives a more accurate representation of code coverage | |
| PYTHONPATH=. coverage run --parallel-mode -m pytest -v -s -rP ./tools/cellxgene_census_builder/tests/ | |
| PYTHONPATH=. NUMBA_DISABLE_JIT=1 coverage run --parallel-mode -m pytest -v -s -rP ./tools/cellxgene_census_builder/tests/ | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-builder-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: ./.coverage* | |
| include-hidden-files: true | |
| if-no-files-found: "error" | |
| retention-days: 3 | |
| submit-codecoverage: | |
| needs: | |
| - unit_tests_builder | |
| - unit_tests_python_api | |
| runs-on: [self-hosted, Linux, X64] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| pattern: coverage-* | |
| merge-multiple: true | |
| path: . | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| cache: "pip" | |
| - name: install requirements | |
| run: | | |
| pip install coverage | |
| - name: coverage report | |
| run: | | |
| coverage combine | |
| coverage xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| env_vars: OS,PYTHON | |
| files: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella |