[python] Initial work toward PyTorch data loaders #12
Workflow file for this run
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| name: python-tiledbsoma-ml | |
| on: | |
| pull_request: | |
| branches: ["*"] | |
| paths: | |
| - "!**" | |
| - "other_packages/python/tiledbsoma_ml/**" | |
| - ".github/workflows/python-tiledbsoma-ml.yml" | |
| push: | |
| branches: [main] | |
| paths: | |
| - "!**" | |
| - "other_packages/python/tiledbsoma_ml/**" | |
| - ".github/workflows/python-tiledbsoma-ml.yml" | |
| workflow_dispatch: | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Restore pre-commit cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }} | |
| - name: Install pre-commit | |
| run: pip -v install pre-commit | |
| - name: Run pre-commit hooks on all files | |
| run: pre-commit run -v -a | |
| tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| cache-dependency-path: python-spec/requirements-py${{ matrix.python-version }}.txt | |
| - name: Install prereqs | |
| working-directory: ./other_packages/python/tiledbsoma_ml/ | |
| run: | | |
| pip install --upgrade pip wheel pytest pytest-cov setuptools | |
| pip install . | |
| - name: Run tests | |
| run: | | |
| PYTHONPATH=$(pwd)/other_packages/python/tiledbsoma_ml python -m pytest \ | |
| --cov=other_packages/python/tiledbsoma_ml/src \ | |
| --cov-report=xml other_packages/python/tiledbsoma_ml/tests \ | |
| -v | |
| - name: Report coverage to Codecov | |
| if: ${{ matrix.python-version == '3.11' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| flags: python | |
| # Although Codecov isn't supposed to require an auth token for public repos like this one, | |
| # the uploader can be unreliable without one; see | |
| # https://github.com/codecov/codecov-action/issues/557#issuecomment-1216749652 | |
| # As of this writing (8 Nov 2022) the CODECOV_TOKEN was generated by @aaronwolen in his | |
| # Codecov settings page for this repo, then filled into the GitHub Actions secrets. | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| build: | |
| # for now, just do a test build to ensure that it works | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Do build | |
| working-directory: ./other_packages/python/tiledbsoma_ml/ | |
| run: | | |
| pip install --upgrade build pip wheel setuptools setuptools-scm | |
| python -m build . |