From 5e8199de6a661c26d118a3fe90fdb5d7836a6c73 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 18 Aug 2026 10:19:21 -0700 Subject: [PATCH 1/7] test: establish Zarr migration baseline --- .github/workflows/test.yml | 46 + pyproject.toml | 8 + tests/test_zarr_migration.py | 135 + uv.lock | 5115 ++++++++++++++++++++++++++++++++++ 4 files changed, 5304 insertions(+) create mode 100644 .github/workflows/test.yml create mode 100644 tests/test_zarr_migration.py create mode 100644 uv.lock diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..14ca5b4 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,46 @@ +name: Tests + +on: + push: + branches: [main, v2.0] + paths-ignore: + - "docs/**" + - "*.md" + - "LICENSE" + pull_request: + branches: [main, v2.0] + paths-ignore: + - "docs/**" + - "*.md" + - "LICENSE" + 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@v7 + with: + version: "0.7.13" + 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: Run tests + run: uv run --no-sync pytest -q -p no:warnings --cov --cov-branch --cov-report=term-missing tests diff --git a/pyproject.toml b/pyproject.toml index 1683ae9..16bc7c9 100644 --- a/pyproject.toml +++ b/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"] diff --git a/tests/test_zarr_migration.py b/tests/test_zarr_migration.py new file mode 100644 index 0000000..71fe3dc --- /dev/null +++ b/tests/test_zarr_migration.py @@ -0,0 +1,135 @@ +"""Executable baseline for the copick 2 / Zarr 3 migration. + +This module intentionally records the storage assumptions present before the +migration. Later stack layers tighten the inventories as each assumption is +removed, while the feature checksum remains a behavioral regression oracle. +""" + +import ast +import hashlib +from pathlib import Path + +import numpy as np +import pytest +import zarr + +from copick_utils.features.skimage import compute_skimage_features + + +SOURCE_ROOT = Path(__file__).parents[1] / "src" / "copick_utils" +DIRECT_LEVEL_READERS = { + "converters/picks_from_mesh.py", + "converters/segmentation_from_mesh.py", + "converters/segmentation_from_picks.py", + "features/skimage.py", + "logical/distance_operations.py", + "pickers/grid_picker.py", + "process/rescale.py", + "process/validbox.py", +} + + +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") + + +def test_direct_zarr_boundary_inventory_is_complete(): + direct_level_readers = set() + feature_array_creators = set() + + for source in SOURCE_ROOT.rglob("*.py"): + relative = source.relative_to(SOURCE_ROOT).as_posix() + tree = ast.parse(source.read_text()) + for node in ast.walk(tree): + if not isinstance(node, ast.Call) or not isinstance(node.func, ast.Attribute): + continue + if not isinstance(node.func.value, ast.Name) or node.func.value.id != "zarr": + continue + if node.func.attr == "open": + direct_level_readers.add(relative) + elif node.func.attr == "create": + feature_array_creators.add(relative) + + assert direct_level_readers == DIRECT_LEVEL_READERS + assert 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tests/test_zarr_migration.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/test_zarr_migration.py b/tests/test_zarr_migration.py index 71fe3dc..e649888 100644 --- a/tests/test_zarr_migration.py +++ b/tests/test_zarr_migration.py @@ -12,10 +12,8 @@ import numpy as np import pytest import zarr - from copick_utils.features.skimage import compute_skimage_features - SOURCE_ROOT = Path(__file__).parents[1] / "src" / "copick_utils" DIRECT_LEVEL_READERS = { "converters/picks_from_mesh.py", From 026714413629bd5fba026b4b11a3040a5710cfde Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 18 Aug 2026 10:45:58 -0700 Subject: [PATCH 4/7] ci: use stable Python toolchain --- .github/workflows/test.yml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index bd147b6..e586cbf 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -30,9 +30,9 @@ jobs: - uses: actions/checkout@v7 - name: Install uv - uses: astral-sh/setup-uv@v7 + uses: astral-sh/setup-uv@ae62891fec2bb8e7d6c99fc78c9fec3a63790f8d # v10.0.0 with: - version: "0.7.13" + version: "0.12.4" python-version: ${{ matrix.python-version }} - name: Check lockfile @@ -41,5 +41,14 @@ jobs: - name: Install test environment run: uv sync --locked --extra test --extra dev + - name: Verify Python version + run: > + uv run --no-sync python -c + "import sys; v = sys.version_info; + expected = tuple(map(int, '${{ 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 From 816728aaa1bdb17b183023c318b4136ca08dc360 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 18 Aug 2026 10:50:44 -0700 Subject: [PATCH 5/7] test: keep migration checks behavior-focused --- tests/test_zarr_migration.py | 41 ++---------------------------------- 1 file changed, 2 insertions(+), 39 deletions(-) diff --git a/tests/test_zarr_migration.py b/tests/test_zarr_migration.py index e649888..f724f07 100644 --- a/tests/test_zarr_migration.py +++ b/tests/test_zarr_migration.py @@ -1,32 +1,16 @@ """Executable baseline for the copick 2 / Zarr 3 migration. -This module intentionally records the storage assumptions present before the -migration. Later stack layers tighten the inventories as each assumption is -removed, while the feature checksum remains a behavioral regression oracle. +This module records the observable storage behavior present before the +migration so the migrated implementation can be checked against it. """ -import ast import hashlib -from pathlib import Path import numpy as np import pytest import zarr from copick_utils.features.skimage import compute_skimage_features -SOURCE_ROOT = Path(__file__).parents[1] / "src" / "copick_utils" -DIRECT_LEVEL_READERS = { - "converters/picks_from_mesh.py", - "converters/segmentation_from_mesh.py", - "converters/segmentation_from_picks.py", - "features/skimage.py", - "logical/distance_operations.py", - "pickers/grid_picker.py", - "process/rescale.py", - "process/validbox.py", -} - - def _memory_store(): return zarr.storage.MemoryStore() @@ -110,24 +94,3 @@ def test_pre_migration_feature_store_documents_reader_incompatibility(): assert isinstance(root, zarr.Array) with pytest.raises((AttributeError, TypeError, zarr.errors.ContainsArrayError)): zarr.open_group(store=features.zarr(), mode="r") - - -def test_direct_zarr_boundary_inventory_is_complete(): - direct_level_readers = set() - feature_array_creators = set() - - for source in SOURCE_ROOT.rglob("*.py"): - relative = source.relative_to(SOURCE_ROOT).as_posix() - tree = ast.parse(source.read_text()) - for node in ast.walk(tree): - if not isinstance(node, ast.Call) or not isinstance(node.func, ast.Attribute): - continue - if not isinstance(node.func.value, ast.Name) or node.func.value.id != "zarr": - continue - if node.func.attr == "open": - direct_level_readers.add(relative) - elif node.func.attr == "create": - feature_array_creators.add(relative) - - assert direct_level_readers == DIRECT_LEVEL_READERS - assert feature_array_creators == {"features/skimage.py"} From 569e52b895a30f52db818cf77d4fc6ade5d533aa Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 18 Aug 2026 10:57:16 -0700 Subject: [PATCH 6/7] style: format migration fixture --- tests/test_zarr_migration.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/test_zarr_migration.py b/tests/test_zarr_migration.py index f724f07..9ad14ac 100644 --- a/tests/test_zarr_migration.py +++ b/tests/test_zarr_migration.py @@ -11,6 +11,7 @@ import zarr from copick_utils.features.skimage import compute_skimage_features + def _memory_store(): return zarr.storage.MemoryStore() From 78aa3a1149a3d30852dee02dda6e9550859f8f6b Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 18 Aug 2026 14:06:30 -0700 Subject: [PATCH 7/7] ci: run required checks for every pull request --- .github/workflows/test.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e586cbf..6696ba2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -8,10 +8,6 @@ on: - "*.md" - "LICENSE" pull_request: - paths-ignore: - - "docs/**" - - "*.md" - - "LICENSE" workflow_dispatch: concurrency: