[python] Pass in the full context to open_experiment in pytorch loaders #2476
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| 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 | |
| jobs: | |
| unit_tests_python_api: | |
| strategy: | |
| fail-fast: false # Don't stop the workflow if one of the jobs fails | |
| matrix: | |
| os: [single-cell-8c64g-runner, macos-latest] | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| exclude: | |
| - os: macos-latest | |
| python-version: "3.8" | |
| 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* | |
| retention-days: 3 | |
| unit_tests_builder: | |
| strategy: | |
| matrix: | |
| os: [single-cell-8c64g-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* | |
| 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 |