VisCy/.github/workflows/test.yml at main · mehta-lab/VisCy · GitHub

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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) }}