From 1fbc34f480b9574345aeff12c5c74849dcbbe919 Mon Sep 17 00:00:00 2001 From: Chris Barnes Date: Thu, 10 Sep 2026 09:01:54 +0100 Subject: [PATCH 1/5] Add tests for storage validity i.e. JSON files are JSON, zarr hierarchies are zarr Uses zarrista, which requires py311 --- .python-version | 2 +- pyproject.toml | 4 +++ test/test_valid_storage.py | 50 +++++++++++++++++++++++++++ uv.lock | 70 +++++++++++++++++++++++++++++++++++--- 4 files changed, 121 insertions(+), 5 deletions(-) create mode 100644 test/test_valid_storage.py diff --git a/.python-version b/.python-version index c8cfe39..2c07333 100644 --- a/.python-version +++ b/.python-version @@ -1 +1 @@ -3.10 +3.11 diff --git a/pyproject.toml b/pyproject.toml index 115118f..50c9d6b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,6 +15,7 @@ dependencies = [ [dependency-groups] test = [ "pytest>=9.1.1", + "zarrista>=0.1.0; python_version >= '3.11'", ] dev = ["mypy>=2.1.0", "prek>=0.4.5", "ruff>=0.15.17", {include-group = "test"}] @@ -29,5 +30,8 @@ build-backend = "setuptools.build_meta" oztest = "src/oztest" "oztest.cases" = "cases" +[tool.ruff] +target-version = "py310" + [tool.ruff.lint] extend-select = ["I"] diff --git a/test/test_valid_storage.py b/test/test_valid_storage.py new file mode 100644 index 0000000..12efde9 --- /dev/null +++ b/test/test_valid_storage.py @@ -0,0 +1,50 @@ +import json +from typing import Any + +import pytest + +from oztest.case_filter import Case, CaseFilter + + +def _cases_as_parametrize_kwargs( + filt: CaseFilter, +) -> tuple[tuple[str, ...], list[tuple], dict[str, Any]]: + cases = sorted(c for c, _ in filt) + argnames = ("case",) + argvalues = [(c,) for c in cases] + kwargs = {"ids": [c.slug() for c in cases]} + return (argnames, argvalues, kwargs) + + +def parametrize_cases(filt: CaseFilter): + argnames, argvalues, kwargs = _cases_as_parametrize_kwargs(filt) + + def decorator(test_fn): + return pytest.mark.parametrize(argnames, argvalues, **kwargs)(test_fn) + + return decorator + + +@parametrize_cases(CaseFilter.from_args(kinds=["parse_attributes"])) +def test_attributes_are_json(case: Case): + """Test that the attribute tests are all valid JSON.""" + with case.as_path() as p: + assert p.is_file() + text = p.read_text() + json.loads(text) + + +@parametrize_cases( + CaseFilter.from_args( + kinds=["validate_zarr", "transform_coordinates"], version_spec=">=0.5" + ) +) +def test_zarr_tests_are_zarr(case: Case): + zarrista = pytest.importorskip("zarrista") + with case.as_path() as p: + assert p.is_dir() + store = zarrista.store.FilesystemStore(p) + root = zarrista.Group.open(store) + # not sure whether this will error for malformed nodes, + # or just skip + _ = root.traverse() diff --git a/uv.lock b/uv.lock index ffc507d..8218fb5 100644 --- a/uv.lock +++ b/uv.lock @@ -3,7 +3,8 @@ revision = 3 requires-python = ">=3.10, <4.0" resolution-markers = [ "python_full_version >= '3.15'", - "python_full_version < '3.15'", + "python_full_version >= '3.11' and python_full_version < '3.15'", + "python_full_version < '3.11'", ] [[package]] @@ -69,7 +70,7 @@ name = "exceptiongroup" version = "1.3.1" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "typing-extensions", marker = "python_full_version < '3.13'" }, + { name = "typing-extensions", version = "4.15.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/50/79/66800aadf48771f6b62f7eb014e352e5d06856655206165d775e675a02c9/exceptiongroup-1.3.1.tar.gz", hash = "sha256:8b412432c6055b0b7d14c310000ae93352ed6754f70fa8f7c34141f91c4e3219", size = 30371, upload-time = "2025-11-21T23:01:54.787Z" } wheels = [ @@ -201,7 +202,8 @@ dependencies = [ { name = "mypy-extensions" }, { name = "pathspec" }, { name = "tomli", marker = "python_full_version < '3.11'" }, - { name = "typing-extensions" }, + { name = "typing-extensions", version = "4.15.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "typing-extensions", version = "4.16.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/82/15/cca9d88503549ed6fedeaa1d448cdddd542ee8a490232d732e278036fbf2/mypy-2.1.0.tar.gz", hash = "sha256:81e76ad12c2d804512e9b13240d1588316531bfba07558286078bfbce9613633", size = 3898359, upload-time = "2026-05-11T18:37:36.237Z" } wheels = [ @@ -276,9 +278,11 @@ dev = [ { name = "prek" }, { name = "pytest" }, { name = "ruff" }, + { name = "zarrista", marker = "python_full_version >= '3.11'" }, ] test = [ { name = "pytest" }, + { name = "zarrista", marker = "python_full_version >= '3.11'" }, ] [package.metadata] @@ -295,8 +299,12 @@ dev = [ { name = "prek", specifier = ">=0.4.5" }, { name = "pytest", specifier = ">=9.1.1" }, { name = "ruff", specifier = ">=0.15.17" }, + { name = "zarrista", marker = 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Traversable.""" @@ -48,16 +50,40 @@ def case_kind_version_profile_validities( yield (d.name, d) -def _iter_files_recursive(trav, prefix: str = "") -> Iterable[tuple[str, Any]]: - """Recursively walk a Traversable, yielding (relative_path, Traversable) for every file found.""" +def maybe_join(*args: str, sep="/"): + return sep.join(a for a in args if a) + + +def _case_kind_version_validity_names_inner( + trav, prefix: str = "" +) -> Iterable[tuple[str, Any]]: + """Recursively walk a Traversable, yielding (relative_path, Traversable) for every test case found. + + Test cases are either files or the top of a Zarr hierarchy. + """ for item in trav.iterdir(): if item.name.startswith("__") or item.name.startswith("."): continue - rel = f"{prefix}/{item.name}" if prefix else item.name - if item.is_dir(): - yield from _iter_files_recursive(item, rel) + + if is_case(item): + stub = item.name.split(".")[0] + yield (maybe_join(prefix, stub), item) else: - yield (rel, item) + yield from _case_kind_version_validity_names_inner( + item, maybe_join(prefix, item.name) + ) + + +def is_case(trav): + """If the traversible (path) is a file or a directory containing a Zarr metadata file.""" + if trav.is_file(): + return True + + for fname in ZARR_META_FILES: + if trav.joinpath(fname).is_file(): + return True + + return False def case_kind_version_validity_names( @@ -71,9 +97,7 @@ def case_kind_version_validity_names( (e.g. `invalid/image/foo.json`) purely for organisational purposes; that nesting is not itself a filterable attribute. """ - for rel, item in _iter_files_recursive(case_kind_version_validity_trav): - name, _, ext = rel.rpartition(".") - yield (name if ext else rel, item) + yield from _case_kind_version_validity_names_inner(case_kind_version_validity_trav) class OzVersion(Version): @@ -272,6 +296,28 @@ def __init__( self.builtin_cases = builtin_cases self.verbose = verbose + @classmethod + def from_args( + cls, + kinds: list[str] | None = None, + version_spec: str | None = None, + include_profile: list[str] | None = None, + exclude_profile: list[str] | None = None, + include_validity: list[str] | None = None, + exclude_validity: list[str] | None = None, + include_name: list[str] | None = None, + exclude_name: list[str] | None = None, + ): + return cls( + None, + True, + make_kind_filter(kinds), + make_version_filter(version_spec), + make_str_filter(include_profile, exclude_profile), + make_validity_filter(include_validity, exclude_validity), + make_str_filter(include_name, exclude_name), + ) + def _iter_case_roots(self) -> Iterator[tuple[Case, bool]]: if self.builtin_cases: yield from self._iter_kinds() From 2a2ef9341a18c1fa250688a33e072e9d39869ced Mon Sep 17 00:00:00 2001 From: Chris Barnes Date: Thu, 10 Sep 2026 10:56:36 +0100 Subject: [PATCH 3/5] minor refactor --- test/test_valid_storage.py | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/test/test_valid_storage.py b/test/test_valid_storage.py index 12efde9..20abace 100644 --- a/test/test_valid_storage.py +++ b/test/test_valid_storage.py @@ -1,26 +1,21 @@ import json -from typing import Any import pytest from oztest.case_filter import Case, CaseFilter -def _cases_as_parametrize_kwargs( - filt: CaseFilter, -) -> tuple[tuple[str, ...], list[tuple], dict[str, Any]]: +def parametrize_cases(filt: CaseFilter): cases = sorted(c for c, _ in filt) argnames = ("case",) - argvalues = [(c,) for c in cases] - kwargs = {"ids": [c.slug() for c in cases]} - return (argnames, argvalues, kwargs) - - -def parametrize_cases(filt: CaseFilter): - argnames, argvalues, kwargs = _cases_as_parametrize_kwargs(filt) + argvalues: list[tuple[Case]] = [] + ids: list[str] = [] + for c in cases: + argvalues.append((c,)) + ids.append(c.slug()) def decorator(test_fn): - return pytest.mark.parametrize(argnames, argvalues, **kwargs)(test_fn) + return pytest.mark.parametrize(argnames, argvalues, ids=ids)(test_fn) return decorator From 2406523c53ee68b19bcf1fea2b73831714b7ce33 Mon Sep 17 00:00:00 2001 From: Chris Barnes Date: Thu, 10 Sep 2026 16:50:45 +0100 Subject: [PATCH 4/5] Use py312 and zarr-python where necessary --- .python-version | 2 +- README.md | 6 + pyproject.toml | 2 +- test/test_valid_storage.py | 17 +-- uv.lock | 273 +++++++++++++++++++++++++++++++------ 5 files changed, 252 insertions(+), 48 deletions(-) diff --git a/.python-version b/.python-version index 2c07333..e4fba21 100644 --- a/.python-version +++ b/.python-version @@ -1 +1 @@ -3.11 +3.12 diff --git a/README.md b/README.md index 44b839f..37b8ab2 100644 --- a/README.md +++ b/README.md @@ -117,3 +117,9 @@ Run `just pre-commit-install` to install the hooks. CLI functionality is tested using [pytest](https://docs.pytest.org/en/stable/). Run `just test` to run the tests. + +### Python version support + +Some development tooling has tighter python version constraints than `oztest` itself. +Linting and CI covers the full range of `oztest` python support specified in `pyproject.toml`, +but developers should use the python version found in `.python-version`. diff --git a/pyproject.toml b/pyproject.toml index 50c9d6b..50b4c0d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,7 @@ dependencies = [ [dependency-groups] test = [ "pytest>=9.1.1", - "zarrista>=0.1.0; python_version >= '3.11'", + "zarr>=3.3; python_version >= '3.12'", ] dev = ["mypy>=2.1.0", "prek>=0.4.5", "ruff>=0.15.17", {include-group = "test"}] diff --git a/test/test_valid_storage.py b/test/test_valid_storage.py index 20abace..b1c8aaf 100644 --- a/test/test_valid_storage.py +++ b/test/test_valid_storage.py @@ -31,15 +31,16 @@ def test_attributes_are_json(case: Case): @parametrize_cases( CaseFilter.from_args( - kinds=["validate_zarr", "transform_coordinates"], version_spec=">=0.5" + kinds=["validate_zarr", "transform_coordinates"], version_spec=">=0.4" ) ) def test_zarr_tests_are_zarr(case: Case): - zarrista = pytest.importorskip("zarrista") + pytest.importorskip("zarr") + import zarr + with case.as_path() as p: - assert p.is_dir() - store = zarrista.store.FilesystemStore(p) - root = zarrista.Group.open(store) - # not sure whether this will error for malformed nodes, - # or just skip - _ = root.traverse() + root = zarr.open(p, mode="r") + + if isinstance(root, zarr.Group): + for _ in root.members(None): + pass diff --git a/uv.lock b/uv.lock index 8218fb5..4bd3829 100644 --- a/uv.lock +++ b/uv.lock @@ -3,7 +3,8 @@ revision = 3 requires-python = ">=3.10, <4.0" resolution-markers = [ "python_full_version >= '3.15'", - "python_full_version >= '3.11' and python_full_version < '3.15'", + "python_full_version >= '3.12' and python_full_version < '3.15'", + "python_full_version == '3.11.*'", "python_full_version < '3.11'", ] 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