test: establish Zarr migration baseline

.github/workflows/test.yml

@@ -0,0 +1,50 @@
+name: Tests
+
+on:
+  push:
+    branches: [main, v2.0]
+    paths-ignore:
+      - "docs/**"
+      - "*.md"
+      - "LICENSE"
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: locked py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@ae62891fec2bb8e7d6c99fc78c9fec3a63790f8d # v10.0.0
+        with:
+          version: "0.12.4"
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check lockfile
+        run: uv lock --check
+
+      - name: Install test environment
+        run: uv sync --locked --extra test --extra dev
+
+      - name: Verify Python version
+        run: >
+          uv run --no-sync python -c
+          "import sys; v = sys.version_info;
+          expected = tuple(map(int, '${{ matrix.python-version }}'.split('.')));
+          assert (v.major, v.minor) == expected, sys.version;
+          assert v.releaselevel == 'final', sys.version;
+          print(sys.version)"
+
+      - name: Run tests
+        run: uv run --no-sync pytest -q -p no:warnings --cov --cov-branch --cov-report=term-missing tests

pyproject.toml

@@ -50,6 +50,10 @@ Issues = "https://github.com/KyleHarrington/copick-utils/issues"
 Documentation = "https://github.com/KyleHarrington/copick-utils#readme"
 
 [project.optional-dependencies]
+test = [
+    "pytest>=8.4.1",
+    "pytest-cov>=6.2.1",
+]
 dev = [
     "black>=25.1.0",
     "hatchling>=1.25.0",
@@ -165,3 +169,7 @@ exclude_lines = [
   "if __name__ == .__main__.:",
   "if TYPE_CHECKING:",
 ]
+
+[tool.pytest.ini_options]
+minversion = "8.0"
+testpaths = ["tests"]

tests/test_zarr_migration.py

@@ -0,0 +1,97 @@
+"""Executable baseline for the copick 2 / Zarr 3 migration.
+
+This module records the observable storage behavior present before the
+migration so the migrated implementation can be checked against it.
+"""
+
+import hashlib
+
+import numpy as np
+import pytest
+import zarr
+from copick_utils.features.skimage import compute_skimage_features
+
+
+def _memory_store():
+    return zarr.storage.MemoryStore()
+
+
+def _tomogram_store(path="0"):
+    store = _memory_store()
+    group = zarr.group(store=store)
+    data = ((np.indices((5, 6, 7)) * np.array([11, 5, 2])[:, None, None, None]).sum(0) % 17).astype(np.float32)
+    group.create_dataset(path, data=data, chunks=(3, 4, 5))
+    group.attrs["multiscales"] = [{"datasets": [{"path": path}]}]
+    return store, data
+
+
+class _Features:
+    def __init__(self):
+        self.store = _memory_store()
+
+    def zarr(self):
+        return self.store
+
+
+class _Tomogram:
+    def __init__(self, store):
+        self.store = store
+        self.features = None
+
+    def zarr(self):
+        return self.store
+
+    def new_features(self, feature_type):
+        assert feature_type == "golden"
+        self.features = _Features()
+        return self.features
+
+
+@pytest.mark.parametrize("path", ["0", "s0"])
+def test_local_ome_zarr_fixture_declares_its_level_path(path):
+    store, expected = _tomogram_store(path)
+    group = zarr.open_group(store=store, mode="r")
+
+    declared_path = group.attrs["multiscales"][0]["datasets"][0]["path"]
+    np.testing.assert_array_equal(group[declared_path][:], expected)
+
+
+def test_pre_migration_feature_result_is_frozen():
+    """Protect the existing chunk subdivision and boundary behavior."""
+    store, _ = _tomogram_store()
+    features = compute_skimage_features(
+        _Tomogram(store),
+        "golden",
+        None,
+        sigma_min=0.5,
+        sigma_max=0.5,
+        feature_chunk_size=(3, 4, 5),
+    )
+    result = zarr.open(features.zarr(), mode="r")[:]
+
+    assert result.shape == (5, 5, 6, 7)
+    assert result.dtype == np.float32
+    rounded_digest = hashlib.sha256(np.round(result, 5).tobytes()).hexdigest()
+    assert rounded_digest == "8364181d58811d79fe86847872316a97370ed2737aeee6411a38753124305312"
+
+
+def test_pre_migration_feature_store_documents_reader_incompatibility():
+    store, _ = _tomogram_store()
+    features = compute_skimage_features(
+        _Tomogram(store),
+        "golden",
+        None,
+        intensity=True,
+        edges=False,
+        texture=False,
+        sigma_min=0.5,
+        sigma_max=0.5,
+        feature_chunk_size=(3, 4, 5),
+    )
+
+    # The old implementation writes an array at the store root.  CopickFeatures
+    # expects an OME group and therefore cannot resolve a metadata-defined level.
+    root = zarr.open(features.zarr(), mode="r")
+    assert isinstance(root, zarr.Array)
+    with pytest.raises((AttributeError, TypeError, zarr.errors.ContainsArrayError)):
+        zarr.open_group(store=features.zarr(), mode="r")