PolyStore/.github/workflows/tests.yml at main · OpenHCSDev/PolyStore · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
name: Tests

on:
  push:
    branches: [ main, copilot/** ]
  pull_request:
    branches: [ main ]
  workflow_dispatch:

jobs:
  distribution:
    runs-on: ubuntu-latest
    timeout-minutes: 10

    steps:
      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
        with:
          python-version: "3.12"
      - name: Install distribution validators
        run: python -m pip install build "twine>=7,<8" uv
      - name: Verify the generated dependency lock matches declarations
        run: uv lock --check --no-python-downloads
      - name: Build release artifacts
        run: python -m build
      - name: Validate release artifacts
        run: python -m twine check dist/*

  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python-version: ["3.11", "3.12"]

    steps:
      - name: Checkout code
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          # Install the package with dev dependencies
          pip install -e ".[dev]"

      - name: Verify installation
        run: |
          python -c "import polystore; print(f'polystore {polystore.__version__} installed successfully')"
          python -c "from polystore import FileManager, MemoryBackend, DiskBackend; print('All imports successful')"

      - name: Lint with ruff
        run: |
          ruff check src/ tests/ || true

      - name: Format check with black
        run: |
          black --check src/ tests/ || true

      - name: Run tests with coverage
        run: |
          python -m pytest --cov=polystore --cov-report=term-missing --cov-report=xml -v

      - name: Upload coverage to Codecov
        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
        continue-on-error: true
        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
        with:
          file: ./coverage.xml
          fail_ci_if_error: false

  zarr-minimum:
    name: Zarr minimum stack (Python 3.11)
    runs-on: ubuntu-latest
    timeout-minutes: 15
    steps:
      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
        with:
          python-version: "3.11"
      - name: Install the minimum supported Zarr stack
        run: |
          python -m pip install --upgrade pip
          python -m pip install -e ".[dev]" -c tests/constraints/zarr-minimum.txt
          python -m pip check
      - name: Exercise both storage formats and every configured codec
        run: python -m pytest tests/test_zarr_backend.py tests/test_zarr_batch.py tests/test_ome_zarr_storage.py tests/test_ome_zarr_metadata.py --no-cov -v

  imagej-runtime:
    runs-on: ubuntu-latest
    timeout-minutes: 15
    steps:
      - name: Checkout code
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1

      - name: Set up Python 3.12
        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
        with:
          python-version: "3.12"

      - name: Cache the declared JDK and ImageJ artifacts
        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
        with:
          path: ~/.cache/polystore
          key: ${{ runner.os }}-polystore-imagej-${{ hashFiles('src/polystore/imagej_distribution.py', 'src/polystore/imagej_runtime.py') }}

      - name: Install the Bio-Formats integration
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[bioformats,dev]"

      # Tests forbid downloads (tests/conftest.py), so the bundle cache is
      # filled here, outside pytest, when actions/cache restores nothing.
      - name: Prepare the declared Fiji bundle cache
        run: python -c "from polystore.imagej_runtime import FIJI_IMAGEJ_RUNTIME; print(FIJI_IMAGEJ_RUNTIME.distribution.materialize().imagej_directory)"

      - name: Resolve and initialize the declared Fiji runtime
        env:
          POLYSTORE_LIVE_IMAGEJ_TEST: "1"
        run: python -m pytest tests/integration/test_imagej_runtime_live.py --no-cov -v