feat(dynacell): HF demo + eval metrics/perf refactor + pix2pix3d leaves + dataset notebook #74
Workflow file for this run
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| name: Test | |
| on: | |
| push: | |
| branches: [main, modular-viscy-staging] | |
| pull_request: | |
| branches: [main, modular-viscy-staging] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }} | |
| jobs: | |
| test: | |
| name: Test (${{ matrix.package }}, Python ${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ["3.12", "3.13"] | |
| package: [viscy-transforms, viscy-models] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v5 | |
| - name: Set up uv with Python ${{ matrix.python-version }} | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| enable-cache: true | |
| cache-suffix: ${{ matrix.os }}-${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: uv sync --frozen --all-extras --dev | |
| working-directory: packages/${{ matrix.package }} | |
| - name: Run tests with coverage | |
| run: uv run --frozen pytest --cov=src/ --cov-report=term-missing | |
| working-directory: packages/${{ matrix.package }} | |
| test-data: | |
| name: Test Data (Python ${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ["3.12", "3.13"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v5 | |
| - name: Set up uv with Python ${{ matrix.python-version }} | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| enable-cache: true | |
| cache-suffix: ${{ matrix.os }}-${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: uv sync --frozen --all-extras --dev | |
| working-directory: packages/viscy-data | |
| - name: Run tests with coverage | |
| run: uv run --frozen pytest --cov=viscy_data --cov-report=term-missing | |
| working-directory: packages/viscy-data | |
| test-data-extras: | |
| name: Test Data Extras (Python 3.13, ubuntu-latest) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v5 | |
| - name: Set up uv with Python 3.13 | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: "3.13" | |
| enable-cache: true | |
| cache-suffix: ubuntu-latest-3.13 | |
| - name: Install dependencies | |
| run: uv sync --frozen --all-extras --dev | |
| working-directory: packages/viscy-data | |
| - name: Run tests with coverage | |
| run: uv run --frozen pytest --cov=viscy_data --cov-report=term-missing | |
| working-directory: packages/viscy-data | |
| test-applications: | |
| name: Test (${{ matrix.application }}, Python 3.13, ubuntu-latest) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| application: [dynaclr, cytoland, airtable, qc] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v5 | |
| - name: Set up uv with Python 3.13 | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: "3.13" | |
| enable-cache: true | |
| cache-suffix: ubuntu-latest-3.13 | |
| - name: Install dependencies | |
| run: uv sync --frozen --all-extras --dev | |
| working-directory: applications/${{ matrix.application }} | |
| - name: Run tests | |
| run: uv run --frozen pytest | |
| working-directory: applications/${{ matrix.application }} | |
| test-dynacell-configs: | |
| name: Test dynacell benchmark configs (Python 3.13, ubuntu-latest) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v5 | |
| - name: Set up uv with Python 3.13 | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: "3.13" | |
| enable-cache: true | |
| cache-suffix: ubuntu-latest-3.13 | |
| - name: Install dynacell with eval deps + test group (CPU) | |
| # The eval-pipeline tests import dynacell.evaluation.pipeline, a hard | |
| # consumer of the eval stack (cubic, cellpose, …). cubic is CPU-capable | |
| # (falls back to numpy/scikit-image without CUDA), so the eval extra | |
| # installs and runs on a GPU-less runner. eval_gpu (cupy/cucim) is NOT | |
| # installed — those are the only CUDA-only deps. | |
| run: uv sync --frozen --extra eval --group test | |
| working-directory: applications/dynacell | |
| - name: Run benchmark-schema + submit-tool + eval-runtime tests | |
| # test_benchmark_config_composition + test_submit_benchmark_job cover | |
| # config composition + the launcher. test_runtime + the two | |
| # test_evaluation_pipeline_parallel* suites cover the runtime module, | |
| # the FovResult pickle contract, and evaluate_predictions end-to-end | |
| # (serial vs spawn-process) on a tiny iohub fixture + prebuilt mask | |
| # cache (target_name=er + require_complete_cache=true short-circuit the | |
| # segmenter + feature-extractor model loads — but pipeline import still | |
| # needs the eval stack). test_evaluation_grouped drives the | |
| # multi-condition driver against the same cache-only fixture. | |
| run: | | |
| uv run --frozen pytest \ | |
| tests/test_benchmark_config_composition.py \ | |
| tests/test_submit_benchmark_job.py \ | |
| tests/test_runtime.py \ | |
| tests/test_evaluation_pipeline_parallel.py \ | |
| tests/test_evaluation_pipeline_parallel_cpu.py \ | |
| tests/test_evaluation_grouped.py \ | |
| -v | |
| working-directory: applications/dynacell | |
| check: | |
| name: All tests pass | |
| if: always() | |
| needs: [test, test-data, test-data-extras, test-applications, test-dynacell-configs] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Verify all test jobs succeeded | |
| uses: re-actors/alls-green@release/v1 | |
| with: | |
| jobs: ${{ toJSON(needs) }} |