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Port OME-Zarr and SmartSPIM readers from MATLAB to Python #51
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install dependencies | |
| run: pip install black ruff | |
| - name: Check formatting with black | |
| run: black --check src/ tests/ | |
| - name: Lint with ruff | |
| run: ruff check src/ tests/ | |
| bridge: | |
| name: MATLAB/Python bridge completeness | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Two checkouts, laid out as siblings, because the check compares | |
| # NDR-matlab's +ndr tree against this repo's bridge YAMLs. | |
| # No MATLAB runtime is needed -- it only reads the source tree -- | |
| # so this stays a fast job rather than joining the format-heavy | |
| # test matrix. Mirrors NDI-python's ``bridge`` job by design. | |
| - uses: actions/checkout@v4 | |
| with: | |
| path: NDR-python | |
| - name: Check out NDR-matlab (matching branch, fall back to main) | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: VH-Lab/NDR-matlab | |
| # A bridge entry usually lands on the same feature branch as | |
| # the MATLAB function it records, so check that branch first. | |
| ref: ${{ github.head_ref || github.ref_name }} | |
| # fetch-depth: 0 so the hash-currency test can walk history | |
| # for every file: without it `git log -- <path>` sees only the | |
| # last commit and every recorded hash looks stale. | |
| fetch-depth: 0 | |
| path: NDR-matlab | |
| continue-on-error: true | |
| id: matlab_checkout_branch | |
| - name: Check out NDR-matlab (main fallback) | |
| if: steps.matlab_checkout_branch.outcome == 'failure' | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: VH-Lab/NDR-matlab | |
| ref: main | |
| fetch-depth: 0 | |
| path: NDR-matlab | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install pytest and PyYAML | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest pyyaml | |
| - name: Check bridge completeness and hash currency | |
| working-directory: NDR-python | |
| env: | |
| # Both repos are checked out above, so an absent MATLAB tree | |
| # means the checkout step broke. Fail instead of skipping -- | |
| # a check that could not run must not report a pass. | |
| NDR_BRIDGE_CHECK_STRICT: "1" | |
| NDR_MATLAB_PATH: ${{ github.workspace }}/NDR-matlab | |
| run: pytest tests/test_matlab_bridge_completeness.py -v --tb=short | |
| test: | |
| name: Test (Python ${{ matrix.python-version }}) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install package with dev and formats dependencies | |
| # The formats extra carries neo, pyabf, tdt, tifffile and scipy. | |
| # Without it the reader tests raise ImportError and pass as skips, | |
| # so the readers they cover are never actually exercised. | |
| run: pip install -e ".[dev,formats]" | |
| - name: Run tests | |
| run: pytest tests/ src/ndr/test/ -v --tb=short | |
| ced-integration: | |
| name: CED integration (real sonpipe) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| # CED ships sonpy only for CPython 3.14 on Linux, so the real CLI | |
| # cannot run on the main test matrix. This job is the one place the | |
| # CED reader is exercised end-to-end against a real .smr file; the | |
| # stand-in CLI in tests/test_ced_sonpipe.py covers the bridge itself | |
| # on every supported version. | |
| python-version: "3.14" | |
| - name: Install package with dev and ced dependencies | |
| # The [ced] extra pulls sonpipe from its git URL. Same install as | |
| # `python -m ndr.setup.sonpipe`; downstream packages (NDI-python) use | |
| # the module entry point in their own CI so they don't have to know | |
| # the git URL themselves. | |
| run: pip install -e ".[dev,ced]" | |
| - name: Verify sonpipe and sonpy are usable | |
| # Ask sonpipe where SonFile lives rather than hardcoding a layout. CED | |
| # packages sonpy three different ways depending on wheel and version -- | |
| # sonpy.SonFile, sonpy.sonpy.SonFile, sonpy.lib.SonFile -- and | |
| # sonpipe.sonfile.load_sonpy already resolves all three. Naming one | |
| # directly here is how this step failed the first time. | |
| run: | | |
| sonpipe --version | |
| python -c "from sonpipe.sonfile import load_sonpy; m = load_sonpy(); assert hasattr(m, 'SonFile'); print('sonpy OK via', m.__name__)" | |
| - name: Run the CED format tests against the real CLI | |
| # NDR_REQUIRE_SONPIPE turns the usual skip into a failure, so this job | |
| # cannot pass by quietly reading nothing. | |
| env: | |
| NDR_REQUIRE_SONPIPE: "1" | |
| run: pytest src/ndr/test/format/ced/ tests/test_ced_sonpipe.py -v --tb=short |