From ec2c3593a12a3beaf798e233cfb916a1c985d05e Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Sat, 17 Oct 2026 04:57:55 -0400 Subject: [PATCH 01/13] docs: say save/save_array/save_group write to a store, not the local file system (#4520) The three docstrings, inherited from Zarr 2, opened with "to the local file system". The functions take a StoreLike and a storage_options argument, and work with every store the library supports. The wording was being read as a design limitation of the functions (see the discussion in #3976), which it is not. --- changes/4520.doc.md | 1 + src/zarr/api/asynchronous.py | 6 +++--- src/zarr/api/synchronous.py | 6 +++--- 3 files changed, 7 insertions(+), 6 deletions(-) create mode 100644 changes/4520.doc.md diff --git a/changes/4520.doc.md b/changes/4520.doc.md new file mode 100644 index 0000000000..1c3ad1a06d --- /dev/null +++ b/changes/4520.doc.md @@ -0,0 +1 @@ +Correct the docstrings of `zarr.save`, `zarr.save_array` and `zarr.save_group` to say the functions write to any store. Previously the docstrings stated the functions wrote to only the local file system, which was inaccurate. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 5725b3d13a..39e7cdd9d4 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -457,7 +457,7 @@ async def save( storage_options: dict[str, Any] | None = None, **kwargs: Any, # TODO: type kwargs as valid args to save ) -> None: - """Convenience function to save an array or group of arrays to the local file system. + """Convenience function to save an array or group of arrays to a store. Parameters ---------- @@ -504,7 +504,7 @@ async def save_array( storage_options: dict[str, Any] | None = None, **kwargs: Any, # TODO: type kwargs as valid args to create ) -> None: - """Convenience function to save a NumPy array to the local file system, following a + """Convenience function to save a NumPy array to a store, following a similar API to the NumPy save() function. Parameters @@ -559,7 +559,7 @@ async def save_group( storage_options: dict[str, Any] | None = None, **kwargs: NDArrayLike, ) -> None: - """Convenience function to save several NumPy arrays to the local file system, following a + """Convenience function to save several NumPy arrays to a store, following a similar API to the NumPy savez()/savez_compressed() functions. Parameters diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 524f719742..b383085bda 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -263,7 +263,7 @@ def save( storage_options: dict[str, Any] | None = None, **kwargs: Any, # TODO: type kwargs as valid args to async_api.save ) -> None: - """Save an array or group of arrays to the local file system. + """Save an array or group of arrays to a store. Parameters ---------- @@ -304,7 +304,7 @@ def save_array( storage_options: dict[str, Any] | None = None, **kwargs: Any, # TODO: type kwargs as valid args to async_api.save_array ) -> None: - """Save a NumPy array to the local file system. + """Save a NumPy array to a store. Follows a similar API to the NumPy save() function. @@ -347,7 +347,7 @@ def save_group( storage_options: dict[str, Any] | None = None, **kwargs: NDArrayLike, ) -> None: - """Save several NumPy arrays to the local file system. + """Save several NumPy arrays to a store. Follows a similar API to the NumPy savez()/savez_compressed() functions. From 21ca97364ff9adebb88684edfed88718d8b70926 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Sun, 18 Oct 2026 18:44:58 +0200 Subject: [PATCH 02/13] perf(zarr-metadata): read a document in one refine walk, with lazy model keys Reading a v3 array document took about 8x as long as zarr-python's own parser, and a consolidated group with 200 arrays 200 times that. The cost was repeated work, not the compiled type checker: each extension point was refined to JSON inside `resolve` and the whole document refined again to build the model's document; every field was frozen into views and its JSON-text key computed at construction whether or not the model was ever compared; `Scope.format` recomputed its answer on every call, and `as_kind` and `kind_of` walked `get_origin` and the MRO on every field. Now a document is refined once: `read_array_v3`, `read_array_v2` and the group reader refine each member where they read it, hand the refined value to `resolve_refined`, and assemble the document the model holds from what was refined, in the document's order, each consolidated child document among them. A model's key and its claims are computed the first time `==`, `hash` or `claims` asks, as `Keyed._model_key`; a scope's format is computed once per scope; a kind is looked up once per way it is named and once per definition class; `well_named` remembers each name; `json_text` reuses one encoder; `frozen` and `_refine` tell the types `json.loads` builds apart by type before falling back to the ABC checks; `_put_back` walks nothing when a configuration holds no nested field; `one_of` checks a set; and the `get_args` calls in `storage_of`, the float fill-value rules and `ValidationProblem` are hoisted to constants. Every problem is reported as before, with the same `loc`, `kind`, message and `input`: a corpus of 25,780 documents (the three benchmark documents, the test fixtures, and systematic mutations of each member) read identically on both sides. The one change in behavior is that a definition's `canonical` is first asked when a model is first compared, not when it is built. Per read, best of ten `timeit` repeats, Python 3.12, PYTHONHASHSEED=0, documents as zarr 3.4.1 writes them: ZarrV3ArrayMetadata.from_json 194.1 us -> 72.5 us (2.7x) ZarrV2ArrayMetadata.from_json 75.0 us -> 18.2 us (4.1x) ZarrV3GroupMetadata, 200 children 37.4 ms -> 14.7 ms (2.5x) The benchmark is `tests/benchmarks/read_documents.py`, run as `python -m tests.benchmarks.read_documents`; a smoke test reads each case once so it keeps working. Assisted-by: ClaudeCode:claude-fable-5-1 --- .../zarr-metadata/src/zarr_metadata/_json.py | 143 +++++++++++----- .../src/zarr_metadata/_typed_json.py | 7 +- .../src/zarr_metadata/model/_array.py | 45 +++-- .../src/zarr_metadata/model/_group.py | 161 ++++++++++-------- .../src/zarr_metadata/model/_keyed.py | 31 +++- .../src/zarr_metadata/model/_validation.py | 106 ++++++++++-- .../src/zarr_metadata/v3/_common.py | 4 +- .../src/zarr_metadata/v3/_definition.py | 101 ++++++++--- .../src/zarr_metadata/v3/_registry.py | 8 +- .../src/zarr_metadata/v3/data_type/_float.py | 9 +- .../tests/benchmarks/__init__.py | 1 + .../tests/benchmarks/read_documents.py | 131 ++++++++++++++ .../tests/benchmarks/test_read_documents.py | 15 ++ .../tests/model/test_construction.py | 31 ++++ .../zarr-metadata/tests/model/test_group.py | 9 + .../tests/model/test_refine_json.py | 37 +++- .../tests/v3/test_definitions.py | 60 +++++++ packages/zarr-metadata/tests/v3/test_kinds.py | 8 + 18 files changed, 717 insertions(+), 190 deletions(-) create mode 100644 packages/zarr-metadata/tests/benchmarks/__init__.py create mode 100644 packages/zarr-metadata/tests/benchmarks/read_documents.py create mode 100644 packages/zarr-metadata/tests/benchmarks/test_read_documents.py diff --git a/packages/zarr-metadata/src/zarr_metadata/_json.py b/packages/zarr-metadata/src/zarr_metadata/_json.py index dee2807796..61c0887343 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_json.py +++ b/packages/zarr-metadata/src/zarr_metadata/_json.py @@ -39,6 +39,10 @@ """ +PROBLEM_KINDS: Final[tuple[ProblemKind, ...]] = get_args(ProblemKind) +"""The kinds a problem is one of, as `ValidationProblem` checks its own.""" + + JSON_DEPTH: Final = 256 """How many levels of nesting a reader walks. @@ -152,8 +156,8 @@ def __post_init__(self) -> None: msg = f"a ValidationProblem's message is a string, got {message!r}" raise TypeError(msg) kind = cast("object", self.kind) - if not isinstance(kind, str) or kind not in get_args(ProblemKind): - msg = f"a ValidationProblem's kind is one of {get_args(ProblemKind)!r}, got {kind!r}" + if not isinstance(kind, str) or kind not in PROBLEM_KINDS: + msg = f"a ValidationProblem's kind is one of {PROBLEM_KINDS!r}, got {kind!r}" raise TypeError(msg) ctx = cast("object", self.ctx) if isinstance(ctx, _Ctx): @@ -308,7 +312,7 @@ def is_object(value: object) -> TypeGuard[Mapping[object, object]]: What `isinstance(value, Mapping)` says, narrowed to a mapping of `object`, which the bare check leaves unknown to a type checker. """ - return isinstance(value, Mapping) + return type(value) is dict or isinstance(value, Mapping) def refined_object(value: object) -> dict[str, JSONValue]: @@ -412,6 +416,8 @@ def within( A problem not below `at` is a `TypeError`: a reader that located one from the wrong root would otherwise report it in the wrong place. """ + if len(problems) == 0: + return () for problem in problems: if problem.loc[: len(at)] != at: msg = f"a problem at {problem.loc!r} does not sit below {at!r}" @@ -421,33 +427,56 @@ def within( def _refine(value: object, loc: tuple[str | int, ...], *, finite: bool) -> _Refined: """`refine_json`, a non-finite number being JSON unless `finite`.""" - if isinstance(value, float): - if not finite or math.isfinite(value): - return float(value), () - return None, ( - ValidationProblem(loc, f"non-finite float {value!r} is not JSON", "invalid_value"), - ) - if isinstance(value, int) and not isinstance(value, bool) and not _writable(value): - message = ( - f"an integer of {value.bit_length()} bits has more digits than JSON text holds " - "here, as sys.get_int_max_str_digits bounds it" - ) - return None, (ValidationProblem(loc, message, "invalid_value"),) - if isinstance(value, bool) or value is None: + # The types `json.loads` builds, told apart by type alone: what nearly + # every value is, so the subclass checks below are reached by the rest + # -- a `StrEnum` member, an `IntEnum` member, a mapping proxy. + if type(value) is str or type(value) is bool or value is None: return value, () - if isinstance(value, str): - # A subclass -- a `StrEnum` member -- as the string JSON writes for it. - return str.__str__(value), () - if isinstance(value, int): - return int(value), () - if (past := nested_past_the_levels(value, loc)) is not None: - return None, (past,) - if is_object(value): + if type(value) is int: + if _writable(value): + return value, () + return None, (ValidationProblem(loc, _too_many_digits(value), "invalid_value"),) + if type(value) is float: + if not finite or math.isfinite(value): + return value, () + return None, (_not_finite(value, loc),) + cls = type(value) + if cls is dict: + mapping = True + elif cls is list or cls is tuple: + mapping = False + else: + if isinstance(value, float): + if not finite or math.isfinite(value): + return float(value), () + return None, (_not_finite(value, loc),) + if isinstance(value, int) and not isinstance(value, bool) and not _writable(value): + return None, (ValidationProblem(loc, _too_many_digits(value), "invalid_value"),) + if isinstance(value, bool): + return value, () + if isinstance(value, str): + # A subclass -- a `StrEnum` member -- as the string JSON writes for it. + return str.__str__(value), () + if isinstance(value, int): + return int(value), () + mapping = is_object(value) + if not mapping and not is_array(value): + return None, ( + ValidationProblem( + loc, + f"not a JSON-serializable value: {shown_by_python(value)}", + "invalid_type", + ), + ) + # A container: judged where it sits, as `nested_past_the_levels` judges one. + if len(loc) >= JSON_DEPTH: + return None, (ValidationProblem(loc, _PAST_THE_LEVELS, "invalid_value"),) + if mapping: # Walked here rather than through `_refine_members`, so that each # level of nesting costs one frame, `JSON_DEPTH` of them at most. members: dict[str, JSONValue] = {} found_in_members: list[ValidationProblem] = [] - for key, item in value.items(): + for key, item in cast("Mapping[object, object]", value).items(): if not isinstance(key, str): found_in_members.append( ValidationProblem( @@ -460,19 +489,26 @@ def _refine(value: object, loc: tuple[str | int, ...], *, finite: bool) -> _Refi if len(found) == 0: members[key] = member return (members if len(found_in_members) == 0 else None), tuple(found_in_members) - if is_array(value): - entries: list[JSONValue] = [] - found_in_entries: list[ValidationProblem] = [] - for index, item in enumerate(value): - entry, found = _refine(item, (*loc, index), finite=finite) - found_in_entries.extend(found) - if len(found) == 0: - entries.append(entry) - return (tuple(entries) if len(found_in_entries) == 0 else None), tuple(found_in_entries) - return None, ( - ValidationProblem( - loc, f"not a JSON-serializable value: {shown_by_python(value)}", "invalid_type" - ), + entries: list[JSONValue] = [] + found_in_entries: list[ValidationProblem] = [] + for index, item in enumerate(cast("Sequence[object]", value)): + entry, found = _refine(item, (*loc, index), finite=finite) + found_in_entries.extend(found) + if len(found) == 0: + entries.append(entry) + return (tuple(entries) if len(found_in_entries) == 0 else None), tuple(found_in_entries) + + +def _not_finite(value: float, loc: tuple[str | int, ...]) -> ValidationProblem: + """The problem a non-finite number at `loc` is, where JSON holds no such number.""" + return ValidationProblem(loc, f"non-finite float {value!r} is not JSON", "invalid_value") + + +def _too_many_digits(value: int) -> str: + """What is wrong with an integer the interpreter will not write: its size.""" + return ( + f"an integer of {value.bit_length()} bits has more digits than JSON text holds " + "here, as sys.get_int_max_str_digits bounds it" ) @@ -494,7 +530,7 @@ def json_text(value: JSONValue) -> str: `0.0` and `NaN` for no value at all, but what a document writes: two values written alike are one value to every reader. """ - return json.dumps(value, sort_keys=True, ensure_ascii=False, default=_as_object) + return _TEXT_ENCODER.encode(value) def _as_object(value: object) -> dict[object, object]: @@ -505,6 +541,10 @@ def _as_object(value: object) -> dict[object, object]: raise TypeError(msg) +_TEXT_ENCODER: Final = json.JSONEncoder(sort_keys=True, ensure_ascii=False, default=_as_object) +"""The encoder `json_text` writes with: what `json.dumps` builds for those arguments on every call, built once.""" + + def shown(value: object) -> str: """`value` as a problem's message shows it: as the JSON a document writes, `null` and `[1, 2]`, or by its repr when it is not JSON; what the interpreter will not write, an integer of too many digits or a value nested too deep, by saying so.""" if isinstance(value, int) and not isinstance(value, bool) and not _writable(value): @@ -651,15 +691,32 @@ def frozen(value: JSONValue) -> JSONValue: Shares the scalars with `value`, and copies nothing else than the containers a view needs. What a model shows of its document. """ - if isinstance(value, Mapping): + cls = type(value) + if cls in _SCALARS: + return value + if cls is dict or isinstance(value, Mapping): + members = cast("Mapping[str, JSONValue]", value) return cast( - "JSONValue", MappingProxyType({key: frozen(item) for key, item in value.items()}) + "JSONValue", + MappingProxyType( + { + key: item if type(item) in _SCALARS else frozen(item) + for key, item in members.items() + } + ), + ) + if cls is tuple or cls is list or isinstance(value, (tuple, list)): + return tuple( + item if type(item) in _SCALARS else frozen(item) + for item in cast("Sequence[JSONValue]", value) ) - if isinstance(value, (tuple, list)): - return tuple(frozen(item) for item in value) return value +_SCALARS: Final[frozenset[type]] = frozenset({str, int, float, bool, type(None)}) +"""The types a JSON scalar is held as, which a read-only view shares as they are.""" + + def copied(value: JSONValue) -> JSONValue: """`value` in containers of its own, sharing nothing with it: each object a new `dict`, each array a new one of its type. diff --git a/packages/zarr-metadata/src/zarr_metadata/_typed_json.py b/packages/zarr-metadata/src/zarr_metadata/_typed_json.py index 3d7bdd0f2c..454f774642 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_typed_json.py +++ b/packages/zarr-metadata/src/zarr_metadata/_typed_json.py @@ -574,8 +574,13 @@ def one_of(allowed: tuple[object, ...]) -> Parser: right type, the wrong value. """ + # Each value with its type, since `True == 1` and `1.0 == 1` in Python + # and not in JSON; a value nothing hashes, an object or an array, is + # none of them. + admitted = frozenset((type(entry), entry) for entry in allowed) + def parse(value: object, loc: Loc) -> Parsed: - if not any(value == entry and type(value) is type(entry) for entry in allowed): + if not _hashable(value) or (type(value), value) not in admitted: return value, (outside_of(loc, value, allowed),) return value, () diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_array.py b/packages/zarr-metadata/src/zarr_metadata/model/_array.py index 5350b10cdd..c6ea483d8e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_array.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_array.py @@ -19,7 +19,6 @@ frozen, is_object, json_text, - refined_object, with_input, ) from zarr_metadata._sentinel import UNSET @@ -30,6 +29,7 @@ StoreKey, ZarrV2ArrayMetadataReading, ZarrV3ArrayMetadataReading, + array_document_v2, dimension_lengths, dump_store_json, load_store_json, @@ -150,15 +150,19 @@ class ZarrV3ArrayMetadata(Keyed): @property def claims(self) -> Claims: - """What the reading claimed of each name the document writes, keyed as the scope files it.""" - return self._claims + """What the reading claimed of each name the document writes, keyed as the scope files it; computed the first time it is asked for.""" + try: + return self._claims + except AttributeError: + self._claims = MappingProxyType(claims_of(self._reading.fields())) + return self._claims def __init__(self, document: object, context: ZarrV3Context | None = None) -> None: scope = scoped(context, CORE_AND_EXTENSIONS) reading, members = read_array_v3(document, scope) if members is None: raise MetadataValidationError(reading.problems) - self._adopt(refined_object(document), scope, reading, members) + self._adopt(members.document, scope, reading, members) @classmethod def _of( @@ -192,8 +196,6 @@ def _adopt( frozen(members.attributes), frozen(members.extra_fields), ) - self._key = self._key_of() - self._claims = MappingProxyType(claims_of(reading.fields())) # --- the pair --------------------------------------------------------- @@ -335,7 +337,7 @@ def with_context(self, context: ZarrV3Context | None = None) -> ZarrV3ArrayMetad The reading is kept when `context` reads every claim identically. """ scope = scoped(context, CORE_AND_EXTENSIONS) - if scope.disagreements(self._claims).agrees: + if scope.disagreements(self.claims).agrees: return self._of(self._document, scope, self._reading, self._members) return type(self)(self._document, context=scope) @@ -350,7 +352,7 @@ def refined_in(self, context: ZarrV3Context | None = None) -> ZarrV3ArrayMetadat problem. `with_context` reads the document in any scope. """ scope = scoped(context, CORE_AND_EXTENSIONS) - found = scope.disagreements(self._claims) + found = scope.disagreements(self.claims) if len(found.conflicts) != 0: raise ScopeConflictError(located_conflicts(self._reading.fields(), found.conflicts)) return self.with_context(scope) @@ -504,8 +506,7 @@ def read_array_metadata_v3( reading, members = read_array_v3(value, scope) if members is None: return reading - document = refined_object(value) - model = ZarrV3ArrayMetadata._of(document, scope, reading, members) # pyright: ignore[reportPrivateUsage] + model = ZarrV3ArrayMetadata._of(members.document, scope, reading, members) # pyright: ignore[reportPrivateUsage] return model.reading @@ -524,10 +525,7 @@ def read_array_metadata_v2( reading, members = read_array_v2(value, scope) if members is None: return reading - document = refined_object(value) - if "dimension_separator" not in document: - document = {**document, "dimension_separator": "."} - model = ZarrV2ArrayMetadata._of(document, scope, reading, members) # pyright: ignore[reportPrivateUsage] + model = ZarrV2ArrayMetadata._of(array_document_v2(members), scope, reading, members) # pyright: ignore[reportPrivateUsage] return model.reading @@ -576,18 +574,19 @@ class ZarrV2ArrayMetadata(Keyed): @property def claims(self) -> Claims: - """What the reading claimed of each typestr and codec id the document writes, keyed as the scope files them.""" - return self._claims + """What the reading claimed of each typestr and codec id the document writes, keyed as the scope files them; computed the first time it is asked for.""" + try: + return self._claims + except AttributeError: + self._claims = MappingProxyType(claims_of(self._reading.fields())) + return self._claims def __init__(self, document: object, context: ZarrV2Context | None = None) -> None: scope = scoped(context, CORE_V2) reading, members = read_array_v2(document, scope) if members is None: raise MetadataValidationError(reading.problems) - held = refined_object(document) - if "dimension_separator" not in held: - held = {**held, "dimension_separator": "."} - self._adopt(held, scope, reading, members) + self._adopt(array_document_v2(members), scope, reading, members) @classmethod def _of( @@ -619,8 +618,6 @@ def _adopt( UNSET if members.attributes is UNSET else frozen(members.attributes), frozen(members.extra_fields), ) - self._key = self._key_of() - self._claims = MappingProxyType(claims_of(reading.fields())) # --- the pair --------------------------------------------------------- @@ -791,7 +788,7 @@ def with_context(self, context: ZarrV2Context | None = None) -> ZarrV2ArrayMetad The reading is kept when `context` reads every claim identically. """ scope = scoped(context, CORE_V2) - if scope.disagreements(self._claims).agrees: + if scope.disagreements(self.claims).agrees: return self._of(self._document, scope, self._reading, self._members) return type(self)(self._document, context=scope) @@ -804,7 +801,7 @@ def refined_in(self, context: ZarrV2Context | None = None) -> ZarrV2ArrayMetadat when a definition `context` claims refuses what was written. """ scope = scoped(context, CORE_V2) - found = scope.disagreements(self._claims) + found = scope.disagreements(self.claims) if len(found.conflicts) != 0: raise ScopeConflictError(located_conflicts(self._reading.fields(), found.conflicts)) return self.with_context(scope) diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_group.py b/packages/zarr-metadata/src/zarr_metadata/model/_group.py index db9d751a47..63d575d828 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_group.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_group.py @@ -50,6 +50,7 @@ ArrayMembersV3, StoreKey, ZarrV3ArrayMetadataReading, + array_document_v2, attributes_of, check_literal, dump_store_json, @@ -58,7 +59,6 @@ members_past_the_levels, missing_keys, other_members, - parse_group_metadata_v2, read_array_v2, read_array_v3, reading_of, @@ -172,15 +172,19 @@ class ZarrV3GroupMetadata(Keyed): @property def claims(self) -> Claims: - """What the reading claimed of each name the document and its consolidated documents write, keyed as the scope files it.""" - return self._claims + """What the reading claimed of each name the document and its consolidated documents write, keyed as the scope files it; computed the first time it is asked for.""" + try: + return self._claims + except AttributeError: + self._claims = MappingProxyType(claims_of(self._reading.fields())) + return self._claims def __init__(self, document: object, context: ZarrV3Context | None = None) -> None: scope = scoped(context, CORE_AND_EXTENSIONS) reading, members = read_group_v3(document, scope) if members is None or len(reading.problems) != 0: raise MetadataValidationError(reading.problems) - self._adopt(refined_object(documents_for(document)), scope, reading, members) + self._adopt(_document_of(members), scope, reading, members) @classmethod def _of( @@ -218,8 +222,7 @@ def _adopt( self._consolidated: ZarrV3ConsolidatedMetadata | UNSET = UNSET else: member = object_at(document, ZARR_V3_CONSOLIDATED_METADATA_KEY) - documents = object_at(member, "metadata") - models = _nested_models(documents, context, reading.consolidated, members.consolidated) + models = _nested_models(context, reading.consolidated, members.consolidated) # One model per document, of this scope: each nested reading # holds the model the group holds. held = MappingProxyType( @@ -236,8 +239,6 @@ def _adopt( self._reading = dataclasses.replace( reading, consolidated=MappingProxyType(dict(held)), metadata=self ) - self._key = self._key_of() - self._claims = MappingProxyType(claims_of(reading.fields())) # --- the pair --------------------------------------------------------- @@ -275,7 +276,7 @@ def _key_of(self) -> tuple[object, ...]: members = self._members return ( json_text(members.attributes), - UNSET if consolidated is UNSET else consolidated._key, + UNSET if consolidated is UNSET else consolidated._model_key, json_text(members.extra_fields), ) @@ -330,7 +331,7 @@ def update(self, **members: Unpack[ZarrV3GroupMetadataUpdate]) -> ZarrV3GroupMet def with_context(self, context: ZarrV3Context | None = None) -> ZarrV3GroupMetadata: """This document read in `context`, whatever that changes; `MetadataValidationError` when it has a problem there. The reading is kept when `context` reads every claim identically.""" scope = scoped(context, CORE_AND_EXTENSIONS) - if scope.disagreements(self._claims).agrees: + if scope.disagreements(self.claims).agrees: return self._of(self._document, scope, self._reading, self._members) return type(self)(self._document, context=scope) @@ -343,7 +344,7 @@ def refined_in(self, context: ZarrV3Context | None = None) -> ZarrV3GroupMetadat name `context` claims refuses what was written under it. """ scope = scoped(context, CORE_AND_EXTENSIONS) - found = scope.disagreements(self._claims) + found = scope.disagreements(self.claims) if len(found.conflicts) != 0: raise ScopeConflictError(located_conflicts(self._reading.fields(), found.conflicts)) return self.with_context(scope) @@ -424,14 +425,12 @@ def __init__(self, member: object, context: ZarrV3Context | None = None) -> None scope = scoped(context, CORE_AND_EXTENSIONS) # The member sits under a group's key wherever it is read, so the # levels a reader walks are counted from there, as in the group. - readings, members, problems = _read_consolidated_v3( + readings, members, document, problems = _read_consolidated_v3( member, scope, (ZARR_V3_CONSOLIDATED_METADATA_KEY,) ) - if len(problems) != 0: + if len(problems) != 0 or document is None: raise MetadataValidationError(problems) - document = refined_object(_member_documents_for(member)) - documents = object_at(document, "metadata") - self._adopt(document, scope, _nested_models(documents, scope, readings, members)) + self._adopt(document, scope, _nested_models(scope, readings, members)) @classmethod def _of( @@ -454,7 +453,6 @@ def _adopt( self._document = document self._context = context self._metadata = metadata - self._key = self._key_of() # Hidden from the readings, which hold their own models; see `metadata`. @property @@ -477,7 +475,7 @@ def __repr__(self) -> str: def _key_of(self) -> tuple[object, ...]: """What `==` and `hash` compare of consolidated metadata: each document's key, by its path, in path order.""" return tuple( - (path, node._key) + (path, node._model_key) for path, node in sorted(self.metadata.items(), key=lambda item: item[0]) ) @@ -705,6 +703,8 @@ class GroupMembersV3: """Each member the spec does not define that is JSON.""" consolidated: Mapping[str, ArrayMembersV3 | GroupMembersV3] | UNSET """Each array its consolidated metadata holds that has no problem, and each group, by path; UNSET when it holds none.""" + document: dict[str, JSONValue] | None + """The document, refined, which the model holds: each member as the read refined it, in the order the document writes them, each document its consolidated metadata holds among them; None when the read found a problem.""" def read_group_metadata_v3( @@ -762,19 +762,32 @@ def read_group_v3( raw = doc.get(ZARR_V3_CONSOLIDATED_METADATA_KEY, UNSET) consolidated: dict[str, ZarrV3NodeMetadataReading] = {} held: Mapping[str, ArrayMembersV3 | GroupMembersV3] | UNSET = UNSET + member: dict[str, JSONValue] | None = None if raw is not UNSET: - consolidated, held, inside = _read_consolidated_v3( + consolidated, held, member, inside = _read_consolidated_v3( raw, context, (*at, ZARR_V3_CONSOLIDATED_METADATA_KEY) ) found.extend(_prefix(ZARR_V3_CONSOLIDATED_METADATA_KEY, inside)) reading = ZarrV3GroupMetadataReading(MappingProxyType(consolidated), with_input(found, whole)) - return reading, GroupMembersV3(attributes, extra_fields, held) + document: dict[str, JSONValue] | None = None + if len(found) == 0 and attributes is not None: + # Each member as refined above, in the document's order: what the + # model holds, built of what was read rather than refined again. + refined: dict[str, JSONValue] = { + **extra_fields, + "zarr_format": 3, + "node_type": "group", + "attributes": attributes, + ZARR_V3_CONSOLIDATED_METADATA_KEY: member, + } + document = {key: refined[key] for key in cast("Mapping[str, object]", doc)} + return reading, GroupMembersV3(attributes, extra_fields, held, document) _CONSOLIDATED_MEMBERS: Final = ("kind", "must_understand", "metadata") """The members of an inline `consolidated_metadata`, in the order the convention declares them.""" -_CONSOLIDATED_ENVELOPE: Final[dict[str, object]] = {"kind": "inline", "must_understand": False} +_CONSOLIDATED_ENVELOPE: Final[dict[str, JSONValue]] = {"kind": "inline", "must_understand": False} """What the member declares, by declaration.""" @@ -886,9 +899,10 @@ def _read_consolidated_v3( ) -> tuple[ dict[str, ZarrV3NodeMetadataReading], dict[str, ArrayMembersV3 | GroupMembersV3], + dict[str, JSONValue] | None, tuple[ValidationProblem, ...], ]: - """An inline `consolidated_metadata` member, as `context` read it: each document it holds, read once, as `read_node_metadata_v3` reads one, by its path; the members of each a model can be built of; and every problem, located in the member. + """An inline `consolidated_metadata` member, as `context` read it: each document it holds, read once, as `read_node_metadata_v3` reads one, by its path; the members of each a model can be built of; the member refined, each document as its read refined it, when nothing is wrong, else None; and every problem, located in the member. `at` is where the member sits in the document handed in. Each container the reader descends into -- the member, its `metadata`, each document @@ -900,9 +914,9 @@ def _read_consolidated_v3( value = {**_CONSOLIDATED_ENVELOPE, "metadata": dict(value.metadata)} past = nested_past_the_levels(value, at) if past is not None: - return {}, {}, within((past,), at) + return {}, {}, None, within((past,), at) if not is_object(value): - return {}, {}, (ValidationProblem((), "expected an object", "invalid_type"),) + return {}, {}, None, (ValidationProblem((), "expected an object", "invalid_type"),) env = value # Missing members are reported in the order the envelope declares them. problems: list[ValidationProblem] = [ @@ -949,7 +963,24 @@ def _read_consolidated_v3( key, readings[key], members.get(key), readings, members, node_types ) ) - return readings, members, tuple(problems) + refined: dict[str, JSONValue] | None = None + if len(problems) == 0: + # Nothing is wrong, so every entry has members, and a document; + # the envelope in the member's order, by declaration. + documents = { + path: _document_of(members[path]) for path in cast("Mapping[str, object]", entries) + } + held: dict[str, JSONValue] = {**_CONSOLIDATED_ENVELOPE, "metadata": documents} + refined = {key: held[key] for key in cast("Mapping[str, object]", env)} + return readings, members, refined, tuple(problems) + + +def _document_of(members: ArrayMembersV3 | GroupMembersV3) -> dict[str, JSONValue]: + """The document `members`, a node's a read found nothing wrong with, holds refined; `TypeError` for a group's with a problem, which such a read rules out.""" + if members.document is None: + msg = "expected the members of a document a read found nothing wrong with" + raise TypeError(msg) + return members.document def _key_problems(key: str) -> list[ValidationProblem]: @@ -1105,19 +1136,17 @@ def _with_models( context: Context, at: Loc = (), ) -> ZarrV3GroupMetadataReading: - """`reading`, holding the model of each document its consolidated metadata holds that has no problem, and its own when it has none: each built from `value`, the document this read read, in `context`. - - A document with a problem a reader walks past -- a key that is no - string, a value that is no JSON, a level past the cap -- refines to - nothing as a whole; each document its consolidated metadata holds is - then refined on its own, from where it sits in the document handed in - -- `at` is where this one sits -- so the ones without a problem still - have their models, and a listed group with a problem of its own holds - those of its own listing. + """`reading`, holding the model of each document its consolidated metadata holds that has no problem, and its own when it has none: each built of what the read refined, as `members` holds it, in `context`. + + A document with a problem -- a key that is no string, a value that is + no JSON, a level past the cap -- has no model; each document its + consolidated metadata holds was read on its own, from where it sits in + `value`, the document this read read -- `at` is where this one sits -- + so the ones without a problem still have their models, and a listed + group with a problem of its own holds those of its own listing. """ if len(reading.problems) == 0: - document = refined_object(value) - model = ZarrV3GroupMetadata._of(document, context, reading, members) # pyright: ignore[reportPrivateUsage] + model = ZarrV3GroupMetadata._of(_document_of(members), context, reading, members) # pyright: ignore[reportPrivateUsage] return model.reading if members.consolidated is UNSET or not is_object(value): return reading @@ -1128,21 +1157,7 @@ def _with_models( if not is_object(entries): return reading held_entries = entries - documents: dict[str, JSONValue] = {} - for path in members.consolidated: - if path not in held_entries: - continue - entry, problems = refine_user_data( - held_entries[path], (*at, ZARR_V3_CONSOLIDATED_METADATA_KEY, "metadata", path) - ) - if len(problems) == 0 and isinstance(entry, Mapping): - documents[path] = entry - models = _nested_models( - documents, - context, - reading.consolidated, - {path: child for path, child in members.consolidated.items() if path in documents}, - ) + models = _nested_models(context, reading.consolidated, members.consolidated) held = dict(reading.consolidated) for path, child in members.consolidated.items(): nested = reading.consolidated[path] @@ -1168,12 +1183,11 @@ def _with_models( def _nested_models( - documents: Mapping[str, JSONValue], context: Context, readings: Mapping[str, ZarrV3NodeMetadataReading], members: Mapping[str, ArrayMembersV3 | GroupMembersV3], ) -> dict[str, ZarrV3NodeMetadata]: - """The model of each document in `documents`, a `metadata` member's, a model can be built of, in `context`: the one its reading holds already when that is of `context`, else built from its reading and members, not read again.""" + """The model of each document among `members`, a `metadata` member's, a model can be built of, in `context`: the one its reading holds already when that is of `context`, else built from its reading and members, which hold the document refined, not read again.""" models: dict[str, ZarrV3NodeMetadata] = {} for path, child in members.items(): reading = readings[path] @@ -1181,14 +1195,17 @@ def _nested_models( if held is not None and held.context is context: models[path] = held continue - document = object_at(documents, path) - if isinstance(reading, ZarrV3ArrayMetadataReading): + if isinstance(reading, ZarrV3ArrayMetadataReading) and isinstance(child, ArrayMembersV3): models[path] = ZarrV3ArrayMetadata._of( # pyright: ignore[reportPrivateUsage] - document, context, reading, cast("ArrayMembersV3", child) + child.document, context, reading, child ) - elif isinstance(reading, ZarrV3GroupMetadataReading) and len(reading.problems) == 0: + elif ( + isinstance(reading, ZarrV3GroupMetadataReading) + and isinstance(child, GroupMembersV3) + and child.document is not None + ): models[path] = ZarrV3GroupMetadata._of( # pyright: ignore[reportPrivateUsage] - document, context, reading, cast("GroupMembersV3", child) + child.document, context, reading, child ) return models @@ -1291,8 +1308,16 @@ def claims(self) -> Claims: def __init__(self, document: object, context: ZarrV2Context | None = None) -> None: scope = scoped(context, CORE_V2) - parsed = parse_group_metadata_v2(document, context=scope) - self._adopt(refined_object(document), scope, _v2_attributes(parsed)) + problems = validate_group_metadata_v2(document, context=scope) + if len(problems) != 0: + raise MetadataValidationError(problems) + # Refined once: the attributes the model holds are the document's, + # which shares nothing with what was handed in. + refined = refined_object(document) + attributes: dict[str, JSONValue] | UNSET = ( + object_at(refined, "attributes") if "attributes" in refined else UNSET + ) + self._adopt(refined, scope, attributes) @classmethod def _of( @@ -1316,7 +1341,6 @@ def _adopt( self._context = context self._attributes = attributes self._shown = UNSET if attributes is UNSET else frozen(attributes) - self._key = self._key_of() @property def context(self) -> Context: @@ -1382,7 +1406,7 @@ def refined_in(self, context: ZarrV2Context | None = None) -> ZarrV2GroupMetadat def refines(self, other: ZarrV2GroupMetadata) -> bool: """Whether this group holds everything `other` holds: its attributes written alike; False of what is not a v2 group.""" - return type(other) is type(self) and self._key == other._key + return type(other) is type(self) and self._model_key == other._model_key @classmethod def create_default( @@ -1476,7 +1500,6 @@ def _adopt( self._context = context self._nodes = nodes self._shown = frozen(object_at(document, "metadata")) - self._key = self._key_of() @property def context(self) -> Context: @@ -1512,7 +1535,7 @@ def _key_of(self) -> tuple[object, ...]: """What `==` and `hash` compare of v2 consolidated metadata: each node by its path and its own key, and every other entry as JSON text.""" nodes = self._nodes return ( - tuple(sorted((path, node._key) for path, node in nodes.items())), + tuple(sorted((path, node._model_key) for path, node in nodes.items())), self._other_entries_text(), ) @@ -1779,10 +1802,7 @@ def located(found: tuple[ValidationProblem, ...]) -> list[ValidationProblem]: reading, members = read_array_v2(merged, context) if members is None: return None, located(reading.problems) - held = refined_object(merged) - if "dimension_separator" not in held: - held["dimension_separator"] = "." - return ZarrV2ArrayMetadata._of(held, context, reading, members), [] # pyright: ignore[reportPrivateUsage] + return ZarrV2ArrayMetadata._of(array_document_v2(members), context, reading, members), [] # pyright: ignore[reportPrivateUsage] found = validate_group_metadata_v2(merged, context=context) if len(found) != 0: return None, located(found) @@ -1791,8 +1811,3 @@ def located(found: tuple[ValidationProblem, ...]) -> list[ValidationProblem]: object_at(document, "attributes") if "attributes" in document else UNSET ) return ZarrV2GroupMetadata._of(document, context, attributes), [] # pyright: ignore[reportPrivateUsage] - - -def _v2_attributes(document: ZarrV2GroupMetadataJSON) -> dict[str, JSONValue] | UNSET: - """The attributes of the v2 group model of `document`, which `parse_group_metadata_v2` gave: `UNSET` when it holds none.""" - return dict(document["attributes"]) if "attributes" in document else UNSET diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_keyed.py b/packages/zarr-metadata/src/zarr_metadata/model/_keyed.py index f131c7748f..9129ab6fb0 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_keyed.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_keyed.py @@ -1,22 +1,39 @@ -"""What every model compares and hashes by: a key its constructor computes once of everything the model shows.""" +"""What every model compares and hashes by: a key computed once, the first time the model is compared, of everything the model shows.""" class Keyed: - """A model whose `==` and `hash` compare a key computed once, when it is built, of what its document means. + """A model whose `==` and `hash` compare a key computed once of what its document means. - Each model computes its own key in `_key_of` and stores it; two models - are equal when they are of one class and their keys are, so a model of - another class, or anything else, is never equal to one. + Each model computes its own key in `_key_of`; `_model_key` computes it + the first time it is asked for -- by `==`, `hash`, or a model holding + this one -- and keeps it, so a model that is only read pays nothing + for it. Two models are equal when they are of one class and their keys + are, so a model of another class, or anything else, is never equal to + one. """ __slots__ = ("_key",) _key: tuple[object, ...] + def _key_of(self) -> tuple[object, ...]: + """What `==` and `hash` compare of this model: each model's own.""" + raise NotImplementedError + + @property + def _model_key(self) -> tuple[object, ...]: + """The key, computed the first time it is asked for and kept.""" + try: + return self._key + except AttributeError: + key = self._key_of() + self._key = key + return key + def __eq__(self, other: object) -> bool: if type(other) is not type(self): return NotImplemented - return self._key == other._key + return self._model_key == other._model_key def __hash__(self) -> int: - return hash(self._key) + return hash(self._model_key) diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_validation.py b/packages/zarr-metadata/src/zarr_metadata/model/_validation.py index bf7c68d38c..a74d80691a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_validation.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_validation.py @@ -63,8 +63,6 @@ CORE_V2, ZarrV2CodecDefinition, ZarrV2DataTypeDefinition, - resolve_codec_v2, - resolve_dtype_v2, ) from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON from zarr_metadata.v3._definition import ( @@ -80,7 +78,7 @@ field_kind, fields_of, fill_value_problems, - resolve, + resolve_refined, ) from zarr_metadata.v3._pipeline import Stage, read_pipeline from zarr_metadata.v3._registry import ( @@ -474,6 +472,8 @@ class ArrayMembersV3: dimension_names: tuple[str | None, ...] | UNSET attributes: dict[str, JSONValue] extra_fields: dict[str, JSONValue] + document: dict[str, JSONValue] + """The document, refined: each member as the read refined it, in the order the document writes them, which the model holds.""" @dataclass(frozen=True, slots=True) @@ -487,6 +487,8 @@ class ArrayMembersV2: dimension_separator: ZarrV2ArrayDimensionSeparator attributes: dict[str, JSONValue] | UNSET extra_fields: dict[str, JSONValue] + document: dict[str, JSONValue] + """The document, refined: each member as the read refined it, in the order the document writes them, which the model holds.""" @dataclass(frozen=True, slots=True) @@ -559,10 +561,21 @@ def read_array_v3( # configuration, against the definition in `context` that claims its # name. `must_understand: false` keeps its meaning where it has one: an # unknown top-level extension *field*, which a reader really can skip. + # Each member is refined once, here, and what was refined is kept: the + # document the model holds is built of it, so nothing is walked twice. + refined: dict[str, JSONValue] = { + **extra_fields, + "zarr_format": 3, + "node_type": "array", + "shape": shape, + } read: dict[str, ResolvedField[Any]] = {} for key, kind in _EXTENSION_POINTS_V3: if key in doc: - read[key], found = resolve(doc[key], kind, context, (*at, key)) + refined[key], found = refine_json(doc[key], (*at, key)) + read[key], found = resolve_refined( + doc[key], refined[key], found, kind, context, (*at, key) + ) problems.extend(within(found, at)) # The fill value is JSON, and judged by the data type the scope read, # when there is one: a data type nothing in scope claims leaves it @@ -570,6 +583,7 @@ def read_array_v3( fill_value: JSONValue = None if "fill_value" in doc: fill_value, found = refine_json(doc["fill_value"], (*at, "fill_value")) + refined["fill_value"] = fill_value problems.extend(within(found, at)) if len(found) == 0 and "data_type" in read: problems.extend(fill_value_problems(read["data_type"], fill_value, ("fill_value",))) @@ -588,10 +602,16 @@ def read_array_v3( problems.append(ValidationProblem((key,), "expected an array", "invalid_type")) else: listed[key] = [] + items: list[JSONValue] = [] for index, entry in enumerate(entries): - resolved, found = resolve(entry, kind, context, (*at, key, index)) + item, found = refine_json(entry, (*at, key, index)) + items.append(item) + resolved, found = resolve_refined( + entry, item, found, kind, context, (*at, key, index) + ) listed[key].append(resolved) problems.extend(within(found, at)) + refined[key] = tuple(items) # The codecs are read as a pipeline, the first handed the grid's chunks # of the array's data type: in order, each judged against the chunk it # is handed. That holds one array -> bytes codec, so it is not empty. @@ -603,6 +623,7 @@ def read_array_v3( attributes: dict[str, JSONValue] | None = {} if "attributes" in doc: attributes, found = attributes_of(doc["attributes"], at) + refined["attributes"] = attributes problems.extend(found) if "dimension_names" in doc: # Simple typed sequences (dimension_names, shape, chunks) report a single @@ -638,13 +659,19 @@ def read_array_v3( ) if len(problems) != 0 or shape is None or attributes is None: return reading, None - names = doc.get("dimension_names", UNSET) + dimension_names: tuple[str | None, ...] | UNSET = UNSET + if "dimension_names" in doc: + # An array of strings and nulls, as judged above: refined, each + # string as JSON writes it. + dimension_names = cast("tuple[str | None, ...]", refine_json(doc["dimension_names"])[0]) + refined["dimension_names"] = dimension_names members = ArrayMembersV3( shape=shape, fill_value=fill_value, - dimension_names=UNSET if names is UNSET else tuple(cast("Sequence[str | None]", names)), + dimension_names=dimension_names, attributes=attributes, extra_fields=extra_fields, + document={key: refined[key] for key in cast("Mapping[str, object]", doc)}, ) return reading, members @@ -735,22 +762,45 @@ def read_array_v2( "invalid_value", ) ) + # Each member is refined once, here, and what was refined is kept: the + # document the model holds is built of it, so nothing is walked twice. + refined: dict[str, JSONValue] = { + **extra_fields, + "zarr_format": 2, + "shape": shape, + "chunks": chunks, + } dtype: ResolvedField[ZarrV2DataTypeDefinition[Any]] | UNSET = UNSET if "dtype" in doc: # A typestr by its family, field records as a struct. - dtype, found = resolve_dtype_v2(doc["dtype"], context, ("dtype",)) + refined["dtype"], found = refine_json(doc["dtype"], ("dtype",)) + dtype, found = resolve_refined( + doc["dtype"], refined["dtype"], found, ZarrV2DataTypeDefinition, context, ("dtype",) + ) problems.extend(found) - if "order" in doc and doc["order"] not in ("C", "F"): - problems.append(outside_of(("order",), doc["order"], ("C", "F"))) + if "order" in doc: + refined["order"], _ = refine_json(doc["order"]) + if doc["order"] not in ("C", "F"): + problems.append(outside_of(("order",), doc["order"], ("C", "F"))) compressor: ResolvedField[ZarrV2CodecDefinition[Any]] | UNSET | None = UNSET if "compressor" in doc: compressor = None + refined["compressor"] = None if doc["compressor"] is not None: - compressor, found = resolve_codec_v2(doc["compressor"], context, ("compressor",)) + refined["compressor"], found = refine_json(doc["compressor"], ("compressor",)) + compressor, found = resolve_refined( + doc["compressor"], + refined["compressor"], + found, + ZarrV2CodecDefinition, + context, + ("compressor",), + ) problems.extend(found) filters: tuple[ResolvedField[ZarrV2CodecDefinition[Any]], ...] | UNSET | None = UNSET if "filters" in doc: filters = None + refined["filters"] = None entries = doc["filters"] if entries is not None: if not _is_array(entries): @@ -765,26 +815,41 @@ def read_array_v2( # "A list of JSON objects providing codec configurations, or # null" (https://github.com/zarr-developers/zarr-specs/blob/fc7dd9c9beb5a50b87f9b08b00bf50fc0048482f/docs/v2/v2.0.rst#L76-L79): an empty list is a list. read: list[ResolvedField[ZarrV2CodecDefinition[Any]]] = [] + items: list[JSONValue] = [] for index, item in enumerate(entries): - entry, found = resolve_codec_v2(item, context, ("filters", index)) + refined_item, found = refine_json(item, ("filters", index)) + items.append(refined_item) + entry, found = resolve_refined( + item, + refined_item, + found, + ZarrV2CodecDefinition, + context, + ("filters", index), + ) read.append(entry) problems.extend(found) filters = tuple(read) - if "dimension_separator" in doc and doc["dimension_separator"] not in (".", "/"): - problems.append( - outside_of(("dimension_separator",), doc["dimension_separator"], (".", "/")) - ) + refined["filters"] = tuple(items) + if "dimension_separator" in doc: + refined["dimension_separator"], _ = refine_json(doc["dimension_separator"]) + if doc["dimension_separator"] not in (".", "/"): + problems.append( + outside_of(("dimension_separator",), doc["dimension_separator"], (".", "/")) + ) fill_value: JSONValue = None if "fill_value" in doc: # JSON, judged by the dtype the scope read, when there is one: a # dtype nothing in scope claims leaves it unjudged. fill_value, found = refine_json(doc["fill_value"], ("fill_value",)) + refined["fill_value"] = fill_value problems.extend(found) if len(found) == 0 and dtype is not UNSET: problems.extend(fill_value_problems(dtype, fill_value, ("fill_value",))) attributes: dict[str, JSONValue] | UNSET | None = UNSET if "attributes" in doc: attributes, found = attributes_of(doc["attributes"]) + refined["attributes"] = attributes problems.extend(found) reading = ZarrV2ArrayMetadataReading( dtype=dtype, @@ -804,10 +869,19 @@ def read_array_v2( ), attributes=attributes, extra_fields=extra_fields, + document={key: refined[key] for key in cast("Mapping[str, object]", doc)}, ) return reading, members +def array_document_v2(members: ArrayMembersV2) -> dict[str, JSONValue]: + """The document a v2 array model holds: as the read refined it, with the `dimension_separator` a document that writes none means, `.`.""" + document = members.document + if "dimension_separator" not in document: + return {**document, "dimension_separator": "."} + return document + + def validate_array_metadata_v2( value: object, *, context: ZarrV2Context | None = None ) -> tuple[ValidationProblem, ...]: diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/_common.py b/packages/zarr-metadata/src/zarr_metadata/v3/_common.py index 4bbef36526..a0e693919b 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/_common.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/_common.py @@ -7,6 +7,7 @@ the validators from `zarr_metadata.model`. """ +import functools import re from typing import Final, TypeAlias, TypeGuard, cast @@ -93,8 +94,9 @@ def validate_metadata_field_v3( r"""What `well_named` accepts, as a JSON Schema `pattern`: the two patterns it matches whole, `(?![\s\S])` where `$` would take a final newline, as `_RAW_BYTES_SCHEMA_PATTERN` has it.""" +@functools.lru_cache(maxsize=4096) def well_named(name: str) -> bool: - """Whether `name` is an extension name as the spec names one. + """Whether `name` is an extension name as the spec names one; remembered per name, since a document names few and a reader meets each many times. A registered name "MUST start with one lower case letter a-z and then be followed by only lower case letters a-z, numerals 0-9, underscores, diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py b/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py index d849049f72..9fb93cec60 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py @@ -153,6 +153,9 @@ def no_pipelines(*_: object) -> Mapping[str, Chunk]: varies takes a codec of its own. """ +STORAGE_CLASSES: Final[tuple[StorageClass, ...]] = get_args(StorageClass) +"""The storage classes, as `storage_of` checks what a definition gives against them.""" + def single_byte(*_: object) -> StorageClass: """The storage of a data type made of single bytes, which no byte order applies to: `uint8`.""" @@ -682,8 +685,13 @@ class StorageTransformerDefinition(Definition[C], kind=True, format=3): def kind_of(definition: Definition[Any]) -> type[Definition[Any]] | None: """The kind `definition` is: the nearest class in its MRO declared with `kind=True`; None for a definition of no kind, which no scope files.""" - bases: tuple[type[object], ...] = type(definition).__mro__ - return next((base for base in bases if _declares_kind(base)), None) + return _kind_of_class(type(definition)) + + +@functools.cache +def _kind_of_class(cls: type[object]) -> type[Definition[Any]] | None: + """`kind_of` a definition of class `cls`: a walk of its MRO, once per class.""" + return next((base for base in cls.__mro__ if _declares_kind(base)), None) def format_of(kind: type[Definition[Any]]) -> Literal[2, 3]: @@ -700,6 +708,10 @@ def _declares_kind(cls: type[object]) -> TypeGuard[type[Definition[Any]]]: return vars(cls).get("_is_kind") is True and issubclass(cls, Definition) +_KIND_NAMED: dict[object, type[Definition[Any]]] = {} +"""What `as_kind` answered for each way a kind was named -- `CodecDefinition`, `CodecDefinition[Any]` -- which never changes: a class is a kind by its declaration.""" + + def as_kind(kind: object) -> type[Definition[Any]]: """The kind of metadata `kind` names, type arguments dropped; `TypeError` if it names none. @@ -708,8 +720,14 @@ def as_kind(kind: object) -> type[Definition[Any]]: `Definition` or a class that declares no kind, under which nothing is filed: a field read as one would go unjudged. """ + try: + return _KIND_NAMED[kind] + except (KeyError, TypeError): + # Not asked before, or not hashable, which no kind is. + pass origin = get_origin(kind) or kind if isinstance(origin, type) and _declares_kind(origin): + _KIND_NAMED[kind] = origin return origin names = ", ".join(known.__name__ for known in KINDS) msg = ( @@ -979,7 +997,7 @@ def _checked( ) -> tuple[object, Problems, tuple[_NestedField, ...]]: """`value` checked as `shape`: the typed value, every problem, and the fields nested in it, in order, each put back as it was written.""" typed, found, nested = _typed(shape, value, loc) - return _put_back(typed, _as_written), found, nested + return _put_back(typed, _as_written, nested), found, nested def _typed( @@ -1020,14 +1038,23 @@ def _declared(field: _NestedField) -> JSONValue: return {key: value for key, value in envelope.items() if key in ENVELOPE_KEYS} -def _put_back(value: object, put: Callable[[_NestedField], JSONValue]) -> object: - """`value` with each nested field the checker handed back put back as `put` gives it.""" +def _put_back( + value: object, put: Callable[[_NestedField], JSONValue], nested: Sequence[_NestedField] +) -> object: + """`value` with each of `nested`, the fields the checker handed back in it, put back as `put` gives it: `value` itself when there are none.""" + if len(nested) == 0: + return value + return _putting_back(value, put) + + +def _putting_back(value: object, put: Callable[[_NestedField], JSONValue]) -> object: + """`_put_back` of a value that holds nested fields: a walk.""" if isinstance(value, _NestedField): return put(value) if is_tuple(value): - return tuple(_put_back(entry, put) for entry in value) + return tuple(_putting_back(entry, put) for entry in value) if is_object(value): - return {key: _put_back(entry, put) for key, entry in value.items()} + return {key: _putting_back(entry, put) for key, entry in value.items()} return value @@ -1056,11 +1083,16 @@ def asked(definition: Definition[Any], what: str, ask: Callable[[], T], at: Loc try: return ask() except Exception as error: - where = "" if at is None else f", reading {at!r}" - error.add_note(f"raised by the {what} of {definition.name!r}{where}") + error.add_note(_raised_by(definition, what, at)) raise +def _raised_by(definition: Definition[Any], what: str, at: Loc | None) -> str: + """The note an error raised by `definition`'s `what` carries: which definition's function raised it, and where it was reading, when that is known.""" + where = "" if at is None else f", reading {at!r}" + return f"raised by the {what} of {definition.name!r}{where}" + + def ruled( definition: Definition[Any], ask: Callable[[], Iterable[ValidationProblem]], at: Loc ) -> Problems: @@ -1070,7 +1102,13 @@ def ruled( what they declare, and an error one raises says which definition's rules raised it, and where they were reading. """ - found = asked(definition, "rules", lambda: tuple(cast("Iterable[object]", ask())), at) + try: + found = tuple(cast("Iterable[object]", ask())) + except Exception as error: + error.add_note(_raised_by(definition, "rules", at)) + raise + if len(found) == 0: + return () for item in found: if not isinstance(item, ValidationProblem): msg = f"{definition.name!r}: its rules yield ValidationProblem values, got {item!r}" @@ -1078,7 +1116,10 @@ def ruled( return _located(at, cast("tuple[ValidationProblem, ...]", found)) -def _located(prefix: Loc, problems: Iterable[ValidationProblem]) -> Problems: +def _located(prefix: Loc, problems: Sequence[ValidationProblem]) -> Problems: + """`problems`, each located under `prefix`.""" + if len(problems) == 0: + return () return tuple(dataclasses.replace(found, loc=(*prefix, *found.loc)) for found in problems) @@ -1107,7 +1148,7 @@ def _configuration_checked( problems = (*found, *(problem for field in nested for problem in _envelope(field))) if not _usable(problems): return None, problems - return cast("T", _put_back(typed, _declared)), problems + return cast("T", _put_back(typed, _declared, nested)), problems def named_configuration( @@ -1685,13 +1726,13 @@ def storage_of(data_type: ResolvedField[DataTypeDefinition[Any]]) -> StorageClas "storage", lambda: cast("object", definition.storage(read_only(configuration), data_type.nested)), ) - if found is not None and found not in get_args(StorageClass): + if found is not None and found not in STORAGE_CLASSES: msg = ( - f"{definition.name!r}: its storage gives one of {get_args(StorageClass)!r} or None, " + f"{definition.name!r}: its storage gives one of {STORAGE_CLASSES!r} or None, " f"got {found!r}" ) raise TypeError(msg) - return cast("StorageClass | None", found) + return found def chunk_grid_lengths( @@ -1768,14 +1809,33 @@ def resolve( `ChunkKeyEncodingDefinition`, `StorageTransformerDefinition` -- with or without type arguments; anything else is a `TypeError`. """ + refined, problems = refine_json(data, loc) + return resolve_refined(data, refined, problems, kind, context, loc) + + +def resolve_refined( + data: object, + refined: JSONValue | None, + problems: Problems, + kind: type[D], + context: Scope, + loc: Loc = (), +) -> tuple[ResolvedField[D], Problems]: + """`resolve` of `data`, which the caller refined already: `refined` and `problems` are what `refine_json(data, loc)` gave. + + For a reader that refines a document's members once and keeps what it + refined -- the document a model holds is built of it -- rather than + refining each field again here. `problems` says whether `data` is + JSON: when it holds any, `refined` is not read. + """ asked = as_kind(kind) - if context.format is not None and context.format != format_of(asked): + scope_format = context.format + if scope_format is not None and scope_format != format_of(asked): msg = ( f"a {asked.label} is a field of a Zarr v{format_of(asked)} document, read in a scope " - f"of that format or of none, got a v{context.format} scope" + f"of that format or of none, got a v{scope_format} scope" ) raise TypeError(msg) - refined, problems = refine_json(data, loc) if len(problems) != 0: # Not JSON, so not read; its name, if it has one, still says what # claims it, and one the spec does not give an extension is a @@ -1852,7 +1912,10 @@ def _read( # one is its own, reported where it sits, as a document's fields are. sound = _usable(found) and all(_named(field) for field in nested) configuration = ( - cast("Mapping[str, JSONValue]", _put_back(typed, lambda field: written[field.loc])) + cast( + "Mapping[str, JSONValue]", + _put_back(typed, lambda field: written[field.loc], nested), + ) if sound else None ) diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/_registry.py b/packages/zarr-metadata/src/zarr_metadata/v3/_registry.py index 24704c0726..0f77f0e1ff 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/_registry.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/_registry.py @@ -17,7 +17,7 @@ from __future__ import annotations from collections.abc import Mapping -from dataclasses import dataclass +from dataclasses import dataclass, field from types import MappingProxyType from typing import TYPE_CHECKING, Any, Final, Generic, Literal, TypeAlias, TypeGuard, cast @@ -87,10 +87,11 @@ class Context(Generic[F]): """ tables: Tables + _format: Literal[2, 3] | None = field(init=False, repr=False) def __post_init__(self) -> None: # What `of` builds, the constructor refuses to build otherwise: each - # key a kind, and every kind of one format. + # key a kind, and every kind of one format, which is the scope's. formats = sorted({format_of(kind) for kind in self.tables}) if len(formats) > 1: msg = ( @@ -98,11 +99,12 @@ def __post_init__(self) -> None: f"formats {' and '.join(f'v{found}' for found in formats)}" ) raise TypeError(msg) + object.__setattr__(self, "_format", formats[0] if len(formats) == 1 else None) @property def format(self) -> Literal[2, 3] | None: """The Zarr format the definitions in scope read, 2 or 3; None for a scope that files nothing.""" - return next((format_of(kind) for kind in self.tables), None) + return self._format @classmethod def of(cls, *definitions: Definition[Any]) -> Context[Any]: diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/_float.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/_float.py index 595ee23bf4..98fba04b99 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/_float.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/_float.py @@ -23,6 +23,11 @@ FloatSpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] """The named non-finite fill values every IEEE 754 floating-point type takes.""" +FLOAT_SPECIAL_FILL_VALUES: Final[tuple[FloatSpecialFillValue, ...]] = get_args( + FloatSpecialFillValue +) +"""The strings a float fill value may be instead of a number, as the fill value rules take them.""" + def float_fill_value_rules( name: str, hex_form: Callable[[str], str] @@ -47,14 +52,14 @@ class _FloatFillValue: def __call__( self, configuration: EmptyConfiguration, nested: Nested, value: float | str ) -> Iterator[ValidationProblem]: - if not isinstance(value, str) or value in get_args(FloatSpecialFillValue): + if not isinstance(value, str) or value in FLOAT_SPECIAL_FILL_VALUES: return try: self.hex_form(value) except ValueError: yield ValidationProblem( (), - f"expected a number, {choices(get_args(FloatSpecialFillValue))}, or a " + f"expected a number, {choices(FLOAT_SPECIAL_FILL_VALUES)}, or a " f"{self.name} hex string, got {shown(value)}", "invalid_value", ) diff --git a/packages/zarr-metadata/tests/benchmarks/__init__.py b/packages/zarr-metadata/tests/benchmarks/__init__.py new file mode 100644 index 0000000000..cd8617176b --- /dev/null +++ b/packages/zarr-metadata/tests/benchmarks/__init__.py @@ -0,0 +1 @@ +"""Timings of reading documents, and the smoke test that keeps them runnable.""" diff --git a/packages/zarr-metadata/tests/benchmarks/read_documents.py b/packages/zarr-metadata/tests/benchmarks/read_documents.py new file mode 100644 index 0000000000..ef84cb0564 --- /dev/null +++ b/packages/zarr-metadata/tests/benchmarks/read_documents.py @@ -0,0 +1,131 @@ +"""How long reading a metadata document takes, on documents as zarr-python writes them. + +Three documents, each as `zarr==3.4.1` wrote it and round-tripped through +`json.dumps`/`json.loads`, so each holds what a store would hand a reader: + +- a v3 array, `zarr.create_array(store, shape=(100, 100), chunks=(10, 10), + dtype="f8", zarr_format=3)`; +- the same array as v2; +- a v3 group holding 200 `int32` arrays of shape `(10,)`, consolidated + with `zarr.consolidate_metadata`. + +Run from the package directory: + + PYTHONHASHSEED=0 uv run --group test python -m tests.benchmarks.read_documents + +Each case is timed with `timeit`, the best of ten repeats, as a mean per +read in microseconds. `--profile` prints a cProfile of the v3 array +read instead, by cumulative time. `test_read_documents.py` runs each +case once, so the script keeps working as the package changes. +""" + +from __future__ import annotations + +import argparse +import cProfile +import json +import pstats +import timeit +from typing import TYPE_CHECKING, Any + +from zarr_metadata import ZarrV2ArrayMetadata, ZarrV3ArrayMetadata, ZarrV3GroupMetadata + +if TYPE_CHECKING: + from collections.abc import Callable + +V3_ARRAY: dict[str, Any] = { + "shape": [100, 100], + "data_type": "float64", + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [10, 10]}}, + "chunk_key_encoding": {"name": "default", "configuration": {"separator": "/"}}, + "fill_value": 0.0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "zstd", "configuration": {"level": 0, "checksum": False}}, + ], + "attributes": {}, + "zarr_format": 3, + "node_type": "array", + "storage_transformers": [], +} + +V2_ARRAY: dict[str, Any] = { + "shape": [100, 100], + "chunks": [10, 10], + "dtype": " tuple[str, dict[str, Any]]: + return f"a{index}", { + "shape": [10], + "data_type": "int32", + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [10]}}, + "chunk_key_encoding": {"name": "default", "configuration": {"separator": "/"}}, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "zstd", "configuration": {"level": 0, "checksum": False}}, + ], + "attributes": {}, + "zarr_format": 3, + "node_type": "array", + "storage_transformers": [], + } + + +V3_GROUP: dict[str, Any] = { + "attributes": {}, + "zarr_format": 3, + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": dict(_child(index) for index in range(200)), + }, + "node_type": "group", +} + + +def _round_tripped(document: dict[str, Any]) -> dict[str, Any]: + return json.loads(json.dumps(document)) + + +CASES: tuple[tuple[str, Callable[[], object], int], ...] = ( + ("ZarrV3ArrayMetadata.from_json", lambda: ZarrV3ArrayMetadata.from_json(_V3_ARRAY), 2000), + ("ZarrV2ArrayMetadata.from_json", lambda: ZarrV2ArrayMetadata.from_json(_V2_ARRAY), 2000), + ( + "ZarrV3GroupMetadata.from_json, 200 consolidated arrays", + lambda: ZarrV3GroupMetadata.from_json(_V3_GROUP), + 10, + ), +) + +_V3_ARRAY = _round_tripped(V3_ARRAY) +_V2_ARRAY = _round_tripped(V2_ARRAY) +_V3_GROUP = _round_tripped(V3_GROUP) + + +def main() -> None: + parser = argparse.ArgumentParser(description="How long reading a metadata document takes.") + parser.add_argument("--profile", action="store_true", help="profile the v3 array read") + parser.add_argument("--repeat", type=int, default=10, help="timeit repeats; the best is shown") + arguments = parser.parse_args() + if arguments.profile: + profiler = cProfile.Profile() + profiler.runcall(lambda: [ZarrV3ArrayMetadata.from_json(_V3_ARRAY) for _ in range(1000)]) + pstats.Stats(profiler).sort_stats("cumulative").print_stats(45) + return + for name, read, number in CASES: + read() # compile the checkers and warm every cache, as a process reading many documents has + best = min(timeit.repeat(read, number=number, repeat=arguments.repeat)) + print(f"{name}: {best / number * 1e6:.1f} us") + + +if __name__ == "__main__": + main() diff --git a/packages/zarr-metadata/tests/benchmarks/test_read_documents.py b/packages/zarr-metadata/tests/benchmarks/test_read_documents.py new file mode 100644 index 0000000000..9aaf100cbe --- /dev/null +++ b/packages/zarr-metadata/tests/benchmarks/test_read_documents.py @@ -0,0 +1,15 @@ +"""Each benchmark case reads: the script does not rot as the package changes.""" + +from __future__ import annotations + +import pytest + +from tests.benchmarks.read_documents import CASES + + +@pytest.mark.parametrize( + ("name", "read"), [(name, read) for name, read, _ in CASES], ids=[name for name, _, _ in CASES] +) +def test_each_case_reads(name: str, read: object) -> None: + assert callable(read) + assert read() is not None diff --git a/packages/zarr-metadata/tests/model/test_construction.py b/packages/zarr-metadata/tests/model/test_construction.py index 185b6740cb..914416fe3a 100644 --- a/packages/zarr-metadata/tests/model/test_construction.py +++ b/packages/zarr-metadata/tests/model/test_construction.py @@ -26,6 +26,7 @@ ZarrV3ConsolidatedMetadata, ZarrV3GroupMetadata, ) +from zarr_metadata.v3.codec.gzip import GZIP_CODEC, GzipCodecConfiguration from zarr_metadata.v3.data_type.int8 import INT8_DATA_TYPE from zarr_metadata.v3.definition import ( CORE_AND_EXTENSIONS, @@ -308,3 +309,33 @@ def test_error_consolidated_metadata_paths_are_strings() -> None: assert [(found.loc, found.kind) for found in raised.value.problems] == [ (("metadata",), "invalid_type") ] + + +def test_a_model_s_key_is_computed_when_it_is_first_compared() -> None: + """`==` and `hash` compare a key of what the document means, computed the first time either is asked for and kept: a model that is only read never asks a definition for its `canonical` spelling.""" + asked: list[int] = [] + + def counting(configuration: GzipCodecConfiguration) -> GzipCodecConfiguration: + asked.append(1) + return configuration + + scope = CORE_AND_EXTENSIONS.extended_with(dataclasses.replace(GZIP_CODEC, canonical=counting)) + document = { + "zarr_format": 3, + "node_type": "array", + "shape": [4], + "data_type": "int8", + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [4]}}, + "chunk_key_encoding": {"name": "default", "configuration": {"separator": "/"}}, + "fill_value": 0, + "codecs": [{"name": "bytes"}, {"name": "gzip", "configuration": {"level": 1}}], + } + model = ZarrV3ArrayMetadata(document, scope) + assert model.to_json()["codecs"][1] == {"name": "gzip", "configuration": {"level": 1}} + assert asked == [] + other = ZarrV3ArrayMetadata(document, scope) + assert model == other + assert len(asked) == 2 + assert hash(model) == hash(other) + assert model != ZarrV3ArrayMetadata({**document, "fill_value": 1}, scope) + assert len(asked) == 3 diff --git a/packages/zarr-metadata/tests/model/test_group.py b/packages/zarr-metadata/tests/model/test_group.py index d9c5bf99e4..c984759ce6 100644 --- a/packages/zarr-metadata/tests/model/test_group.py +++ b/packages/zarr-metadata/tests/model/test_group.py @@ -25,6 +25,7 @@ ) from zarr_metadata.model._array import ZarrV3ArrayMetadata, ZarrV3ArrayMetadataUpdate from zarr_metadata.model._group import ( + GroupMembersV3, ZarrV2ConsolidatedMetadata, ZarrV2GroupMetadata, ZarrV2GroupMetadataUpdate, @@ -1462,3 +1463,11 @@ def test_the_group_guard_asks_tuples_of_the_documents_the_group_lists() -> None: ) ) assert not is_group_metadata_v3(nested) + + +def test_error_a_model_is_built_only_of_members_a_read_found_nothing_wrong_with() -> None: + """The members of a group read with a problem hold no document; a model built of them is a `TypeError`, not a model of nothing.""" + from zarr_metadata.model._group import _document_of + + with pytest.raises(TypeError, match="nothing wrong with"): + _document_of(GroupMembersV3(None, {}, UNSET, None)) diff --git a/packages/zarr-metadata/tests/model/test_refine_json.py b/packages/zarr-metadata/tests/model/test_refine_json.py index d5594d4ebd..61f0d71465 100644 --- a/packages/zarr-metadata/tests/model/test_refine_json.py +++ b/packages/zarr-metadata/tests/model/test_refine_json.py @@ -3,7 +3,8 @@ from __future__ import annotations import math -from collections import OrderedDict +from collections import OrderedDict, UserDict +from types import MappingProxyType from typing import TYPE_CHECKING, cast import pytest @@ -216,3 +217,37 @@ class Score(float): {"zarr_format": Format.THREE, "node_type": NodeType.GROUP} ) assert model.to_json() == {"zarr_format": 3, "node_type": "group"} + + +def test_a_mapping_or_sequence_of_another_type_is_refined_as_a_dict_or_list_is() -> None: + """A mapping proxy, a `UserDict`, a subclass of `dict` or `list`, a tuple: refined to the JSON the dict or list it holds refines to, and judged the same, each problem where it sits.""" + + class Listed(list[object]): + pass + + class Mapped(dict[str, object]): + pass + + held: dict[str, object] = {"a": [1, {"b": (2, 3)}], "c": "x", "d": [True, None, 2.5]} + expected = refine_json(held) + assert expected == ({"a": (1, {"b": (2, 3)}), "c": "x", "d": (True, None, 2.5)}, ()) + for other in ( + MappingProxyType(held), + UserDict(held), + Mapped(held), + {**held, "a": Listed(cast("list[object]", held["a"]))}, + ): + assert refine_json(other) == expected + bad: dict[str, object] = {"a": [1, {"b": math.nan}], "c": {1, 2}} + for other in ( + bad, + MappingProxyType(bad), + Mapped(bad), + {**bad, "a": Listed([1, {"b": math.nan}])}, + ): + refined, problems = refine_json(other) + assert refined is None + assert [(p.loc, p.kind) for p in problems] == [ + (("a", 1, "b"), "invalid_value"), + (("c",), "invalid_type"), + ] diff --git a/packages/zarr-metadata/tests/v3/test_definitions.py b/packages/zarr-metadata/tests/v3/test_definitions.py index 21f9fb2262..1642904ee1 100644 --- a/packages/zarr-metadata/tests/v3/test_definitions.py +++ b/packages/zarr-metadata/tests/v3/test_definitions.py @@ -16,6 +16,7 @@ from annotated_types import Ge, Predicate from typing_extensions import TypedDict +from zarr_metadata._json import refine_json from zarr_metadata._sentinel import UNSET from zarr_metadata.model import ( is_metadata_field_v3, @@ -26,10 +27,12 @@ from zarr_metadata.typed_json import ( check, ) +from zarr_metadata.v2.definition import CORE_V2 from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON from zarr_metadata.v3._definition import ( canonical_of, configuration_of, + resolve_refined, ) from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON from zarr_metadata.v3.chunk_grid.regular import REGULAR_CHUNK_GRID @@ -1474,3 +1477,60 @@ def test_a_field_holding_fields_is_copied_and_pickled_whole() -> None: assert again == field assert type(again) is type(field) assert again.nested == field.nested + + +@pytest.mark.parametrize( + "field", + [ + "crc32c", + {"name": "gzip", "configuration": {"level": 1}}, + {"name": "gzip", "configuration": {"level": 12}}, + {"name": "gzip", "configuration": {"level": 1}, "must_understand": False}, + {"name": "acme.x", "configuration": {"a": [1, {"b": None}]}}, + {"name": "BAD NAME"}, + {"name": "sharding_indexed", "configuration": {**SHARD, "index_location": "x"}}, + {"configuration": {}}, + ], + ids=[ + "bare", + "read", + "refused", + "envelope", + "unclaimed", + "ill-named", + "nested-refused", + "nameless", + ], +) +def test_a_field_its_caller_refined_reads_as_resolve_reads_it(field: object) -> None: + """`resolve_refined` is `resolve` for a caller that refined the field already: the same field, the same problems, located the same, with the same `input`.""" + refined, problems = refine_json(field, ("codecs", 0)) + assert problems == () + expected = resolve(field, CodecDefinition, CORE, ("codecs", 0)) + found = resolve_refined(field, refined, problems, CodecDefinition, CORE, ("codecs", 0)) + assert found == expected + assert [(p.loc, p.kind, p.input) for p in found[1]] == [ + (p.loc, p.kind, p.input) for p in expected[1] + ] + + +def test_error_a_field_its_caller_found_not_to_be_json_is_refused_unread() -> None: + """What `refine_json` found wrong is the field's problems, and the field is refused as not JSON, its name still saying what claims it, as `resolve` refuses one.""" + field = {"name": "gzip", "configuration": {"level": {1, 2}}} + refined, problems = refine_json(field, ("codecs", 0)) + assert refined is None + resolved, found = resolve_refined( + field, refined, problems, CodecDefinition, CORE, ("codecs", 0) + ) + assert resolved == RefusedField( + json=UNSET, name="gzip", read_as=CodecDefinition, definition=GZIP_CODEC + ) + assert [(p.loc, p.kind) for p in found] == [ + (("codecs", 0, "configuration", "level"), "invalid_type") + ] + assert (resolved, found) == resolve(field, CodecDefinition, CORE, ("codecs", 0)) + + +def test_error_a_refined_field_is_not_read_in_a_scope_of_the_other_format() -> None: + with pytest.raises(TypeError, match="got a v2 scope"): + resolve_refined("gzip", "gzip", (), CodecDefinition, CORE_V2) diff --git a/packages/zarr-metadata/tests/v3/test_kinds.py b/packages/zarr-metadata/tests/v3/test_kinds.py index af05932bed..db4ededff5 100644 --- a/packages/zarr-metadata/tests/v3/test_kinds.py +++ b/packages/zarr-metadata/tests/v3/test_kinds.py @@ -260,3 +260,11 @@ def test_error_a_field_is_read_in_a_scope_of_its_format() -> None: resolve("int32", DataTypeDefinition, CORE_V2) field, _ = resolve(" None: + """A field is read as a kind, a class: a list or a dict given for one is refused as any other non-kind is, not with the `TypeError` hashing it raises.""" + with pytest.raises(TypeError, match="is not a kind of metadata"): + as_kind(["codec"]) + with pytest.raises(TypeError, match="is not a kind of metadata"): + as_kind({"kind": CodecDefinition}) From c777c9b326ecf5d59eaf845d7dccc449985224d7 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Sun, 18 Oct 2026 18:46:19 +0200 Subject: [PATCH 03/13] docs(zarr-metadata): the fragment for the faster read Assisted-by: ClaudeCode:claude-fable-5-1 --- packages/zarr-metadata/changes/407.feature.md | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 packages/zarr-metadata/changes/407.feature.md diff --git a/packages/zarr-metadata/changes/407.feature.md b/packages/zarr-metadata/changes/407.feature.md new file mode 100644 index 0000000000..b39bdc0274 --- /dev/null +++ b/packages/zarr-metadata/changes/407.feature.md @@ -0,0 +1,7 @@ +Reading a metadata document is 2.5 to 4 times faster: a document is refined +to JSON once, the model holds what was refined, and a model's key -- what +`==` and `hash` compare -- is computed the first time the model is compared +rather than when it is built, so a definition's `canonical` is first asked +then. Every problem is reported as before, with the same `loc`, `kind`, +message and `input`. The timings and the benchmark are in +`tests/benchmarks/read_documents.py`. From 3d73e290b2d8004c6ceff5d3711e13a1371c8442 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 20 Oct 2026 22:12:55 +0200 Subject: [PATCH 04/13] chore(deps): bump aiohttp from 3.14.3 to 3.14.4 (#4529) --- updated-dependencies: - dependency-name: aiohttp dependency-version: 3.14.4 dependency-type: indirect ... 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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- uv.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/uv.lock b/uv.lock index d4671fd93c..82c1592ca0 100644 --- a/uv.lock +++ b/uv.lock @@ -479,11 +479,11 @@ wheels = [ [[package]] name = "certifi" -version = "2026.4.22" +version = "2026.10.19" source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/25/ee/6caf7a40c36a1220410afe15a1cc64993a1f864871f698c0f93acb72842a/certifi-2026.4.22.tar.gz", hash = "sha256:8d455352a37b71bf76a79caa83a3d6c25afee4a385d632127b6afb3963f1c580", size = 137077, upload-time = "2026-04-22T11:26:11.191Z" } +sdist = { url = "https://files.pythonhosted.org/packages/a6/bd/1436c50cc46699de0230fbaacc1d1de7bfec413176099949e9d5112e88f2/certifi-2026.10.19.tar.gz", hash = "sha256:035c1e85572b141bf1c3a3eff0e33a8eb74917522f2559075ff8d2fea780a1ae", size = 137598, upload-time = "2026-10-20T02:24:16.604Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/22/30/7cd8fdcdfbc5b869528b079bfb76dcdf6056b1a2097a662e5e8c04f42965/certifi-2026.4.22-py3-none-any.whl", hash = "sha256:3cb2210c8f88ba2318d29b0388d1023c8492ff72ecdde4ebdaddbb13a31b1c4a", size = 135707, upload-time = "2026-04-22T11:26:09.372Z" }, + { url = "https://files.pythonhosted.org/packages/c4/51/29046e48f693c54e5b7412216d447a1d8362c9653148d98c02cdf65fa733/certifi-2026.10.19-py3-none-any.whl", hash = "sha256:42d35340cc5b9ba78e818ddbff0c5b1c2b779de448a340fd1b989f5fa8670e1b", size = 136464, upload-time = "2026-10-20T02:24:15.072Z" }, ] [[package]] From 1dca23fbd2db5f8af7818f8de051f9c7fccb886c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 21 Oct 2026 18:43:40 +0200 Subject: [PATCH 06/13] ci(docs): fix the Read the Docs sub-site builds and skip filters (#4543) * ci(docs): fix the Read the Docs sub-site builds and skip filters The zarr-indexing, zarr-metadata and zarr-http-server docs sites install their docs group with pip on Read the Docs, without a lockfile, so pymdown-extensions floated to 12.3, whose Highlight extension API the pinned mkdocstrings 1.0.6 cannot drive (Highlight.__init__() missing argument 'md'). No zarr-indexing build has succeeded since. Pin pymdown-extensions to 11.0.1, the version the repo-root uv.lock resolves to, and refresh the package lockfiles. The post_checkout skip filters compared the PR head against the tip of main with a two-dot diff, so any PR that was behind main appeared to touch every package and built every site. Compare against the merge base instead, after fetching full history into the shallow checkout. Also exclude zarr-http-server from the root site's filter, as the other two packages already were. Assisted-by: ClaudeCode:claude-fable-5.1 Co-Authored-By: Claude Fable 5.1 * docs: add changelog entry for #4543 Assisted-by: ClaudeCode:claude-fable-5.1 Co-Authored-By: Claude Fable 5.1 --------- Co-authored-by: Claude Fable 5.1 --- .readthedocs.yaml | 21 ++++++++++++++++++--- changes/4543.misc.md | 1 + packages/zarr-http-server/.readthedocs.yaml | 14 ++++++++++++-- packages/zarr-http-server/pyproject.toml | 4 ++++ packages/zarr-http-server/uv.lock | 2 ++ packages/zarr-indexing/.readthedocs.yaml | 14 ++++++++++++-- packages/zarr-indexing/pyproject.toml | 4 ++++ packages/zarr-indexing/uv.lock | 2 ++ packages/zarr-metadata/.readthedocs.yaml | 14 ++++++++++++-- packages/zarr-metadata/pyproject.toml | 4 ++++ packages/zarr-metadata/uv.lock | 8 +++++--- 11 files changed, 76 insertions(+), 12 deletions(-) create mode 100644 changes/4543.misc.md diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 872eb2be80..d079f62d5a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,12 +10,27 @@ build: # that have their own Read the Docs projects. Exit code 183 cancels the # build and reports success to the Git provider. Scoped to PR builds # ("external" versions) because origin/main is only a meaningful diff - # base there. Read the Docs strips shell quoting from commands, so the + # base there. Compare against the merge base (origin/main...HEAD), not + # against the tip of main: a two-dot diff also reports everything that + # landed on main after the PR branched, which made every PR that was + # behind main build every site. The checkout is shallow, so fetch the + # full history first; without a merge base the diff fails and the build + # runs, which is the safe default. Read the Docs strips shell quoting from commands, so the # exclude pathspecs must use the quote-free :! form, not ':(exclude)'. + # The diff is taken against the merge base (origin/main...HEAD), not + # against the tip of main: a two-dot diff also reports everything that + # landed on main after the PR branched, which made every PR that was + # behind main build every site. The checkout is shallow, so fetch the + # full history first; without a merge base the diff fails and the build + # runs, which is the safe default. - | - if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- :!packages/zarr-metadata :!packages/zarr-indexing; + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ]; then - exit 183; + git fetch --quiet --unshallow origin main pull/$READTHEDOCS_VERSION_NAME/head || true; + if git diff --quiet origin/main...HEAD -- :!packages/zarr-metadata :!packages/zarr-indexing :!packages/zarr-http-server; + then + exit 183; + fi fi install: - pip install --upgrade pip diff --git a/changes/4543.misc.md b/changes/4543.misc.md new file mode 100644 index 0000000000..54be050e61 --- /dev/null +++ b/changes/4543.misc.md @@ -0,0 +1 @@ +Fixed the Read the Docs builds of the zarr-indexing, zarr-metadata and zarr-http-server documentation sites, which failed after an unpinned `pymdown-extensions` release, and made pull request builds of those sites skip when the pull request does not change the package. diff --git a/packages/zarr-http-server/.readthedocs.yaml b/packages/zarr-http-server/.readthedocs.yaml index 09cf295794..4490a0c3e1 100644 --- a/packages/zarr-http-server/.readthedocs.yaml +++ b/packages/zarr-http-server/.readthedocs.yaml @@ -15,10 +15,20 @@ build: # to PR builds ("external" versions) because origin/main is only a # meaningful diff base there. The shared docs config and header script # live outside the package directory but change this site too. + # The diff is taken against the merge base (origin/main...HEAD), not + # against the tip of main: a two-dot diff also reports everything that + # landed on main after the PR branched, which made every PR that was + # behind main build every site. The checkout is shallow, so fetch the + # full history first; without a merge base the diff fails and the build + # runs, which is the safe default. - | - if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- packages/zarr-http-server packages/mkdocs-base.yml packages/source-version.js; + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ]; then - exit 183; + git fetch --quiet --unshallow origin main pull/$READTHEDOCS_VERSION_NAME/head || true; + if git diff --quiet origin/main...HEAD -- packages/zarr-http-server packages/mkdocs-base.yml packages/source-version.js; + then + exit 183; + fi fi install: - pip install --upgrade pip diff --git a/packages/zarr-http-server/pyproject.toml b/packages/zarr-http-server/pyproject.toml index 1d312cf93f..f7a46eda90 100644 --- a/packages/zarr-http-server/pyproject.toml +++ b/packages/zarr-http-server/pyproject.toml @@ -70,6 +70,10 @@ docs = [ "mkdocs-material==9.7.7", "mkdocs==1.6.1", "mkdocstrings==1.0.6", + # pymdown-extensions 12.3 changed the Highlight extension API; mkdocstrings 1.0.6 + # cannot drive it (Highlight.__init__() missing argument "md"). Match the + # version in the repo-root uv.lock until mkdocstrings is bumped everywhere. + "pymdown-extensions==11.0.1", "mkdocstrings-python==2.0.8", "griffe-inherited-docstrings==1.1.3", # mkdocstrings uses ruff to format rendered signatures diff --git a/packages/zarr-http-server/uv.lock b/packages/zarr-http-server/uv.lock index 673dc54645..77bb5a0baf 100644 --- a/packages/zarr-http-server/uv.lock +++ b/packages/zarr-http-server/uv.lock @@ -2156,6 +2156,7 @@ docs = [ { name = "mkdocs-material" }, { name = "mkdocstrings" }, { name = "mkdocstrings-python" }, + { name = "pymdown-extensions" }, { name = "ruff" }, ] examples = [ @@ -2186,6 +2187,7 @@ docs = [ { name = "mkdocs-material", specifier = "==9.7.7" }, { name = "mkdocstrings", specifier = "==1.0.6" }, { name = "mkdocstrings-python", specifier = "==2.0.8" }, + { name = "pymdown-extensions", specifier = "==11.0.1" }, { name = "ruff", specifier = "==0.16.8" }, ] examples = [ diff --git a/packages/zarr-indexing/.readthedocs.yaml b/packages/zarr-indexing/.readthedocs.yaml index 4228d267ca..6577440275 100644 --- a/packages/zarr-indexing/.readthedocs.yaml +++ b/packages/zarr-indexing/.readthedocs.yaml @@ -15,10 +15,20 @@ build: # to PR builds ("external" versions) because origin/main is only a # meaningful diff base there. The shared docs config and header script # live outside the package directory but change this site too. + # The diff is taken against the merge base (origin/main...HEAD), not + # against the tip of main: a two-dot diff also reports everything that + # landed on main after the PR branched, which made every PR that was + # behind main build every site. The checkout is shallow, so fetch the + # full history first; without a merge base the diff fails and the build + # runs, which is the safe default. - | - if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- packages/zarr-indexing packages/mkdocs-base.yml packages/source-version.js; + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ]; then - exit 183; + git fetch --quiet --unshallow origin main pull/$READTHEDOCS_VERSION_NAME/head || true; + if git diff --quiet origin/main...HEAD -- packages/zarr-indexing packages/mkdocs-base.yml packages/source-version.js; + then + exit 183; + fi fi install: - pip install --upgrade pip diff --git a/packages/zarr-indexing/pyproject.toml b/packages/zarr-indexing/pyproject.toml index da7bee34aa..50a63832ea 100644 --- a/packages/zarr-indexing/pyproject.toml +++ b/packages/zarr-indexing/pyproject.toml @@ -61,6 +61,10 @@ docs = [ "mkdocs-material==9.7.7", "mkdocs==1.6.1", "mkdocstrings==1.0.6", + # pymdown-extensions 12.3 changed the Highlight extension API; mkdocstrings 1.0.6 + # cannot drive it (Highlight.__init__() missing argument "md"). Match the + # version in the repo-root uv.lock until mkdocstrings is bumped everywhere. + "pymdown-extensions==11.0.1", "mkdocstrings-python==2.0.8", "griffe-inherited-docstrings==1.1.3", # mkdocstrings uses ruff to format rendered signatures diff --git a/packages/zarr-indexing/uv.lock b/packages/zarr-indexing/uv.lock index 1a4a90e2ba..37a98a5694 100644 --- a/packages/zarr-indexing/uv.lock +++ b/packages/zarr-indexing/uv.lock @@ -740,6 +740,7 @@ docs = [ { name = "mkdocs-material" }, { name = "mkdocstrings" }, { name = "mkdocstrings-python" }, + { name = "pymdown-extensions" }, { name = "ruff" }, ] test = [ @@ -761,6 +762,7 @@ docs = [ { name = "mkdocs-material", specifier = "==9.7.7" }, { name = "mkdocstrings", specifier = "==1.0.6" }, { name = "mkdocstrings-python", specifier = "==2.0.8" }, + { name = "pymdown-extensions", specifier = "==11.0.1" }, { name = "ruff", specifier = "==0.16.8" }, ] test = [ diff --git a/packages/zarr-metadata/.readthedocs.yaml b/packages/zarr-metadata/.readthedocs.yaml index b67e76948c..5e6f993a3e 100644 --- a/packages/zarr-metadata/.readthedocs.yaml +++ b/packages/zarr-metadata/.readthedocs.yaml @@ -15,10 +15,20 @@ build: # to PR builds ("external" versions) because origin/main is only a # meaningful diff base there. The shared docs config and header script # live outside the package directory but change this site too. + # The diff is taken against the merge base (origin/main...HEAD), not + # against the tip of main: a two-dot diff also reports everything that + # landed on main after the PR branched, which made every PR that was + # behind main build every site. The checkout is shallow, so fetch the + # full history first; without a merge base the diff fails and the build + # runs, which is the safe default. - | - if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- packages/zarr-metadata packages/mkdocs-base.yml packages/source-version.js; + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ]; then - exit 183; + git fetch --quiet --unshallow origin main pull/$READTHEDOCS_VERSION_NAME/head || true; + if git diff --quiet origin/main...HEAD -- packages/zarr-metadata packages/mkdocs-base.yml packages/source-version.js; + then + exit 183; + fi fi install: - pip install --upgrade pip diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 31d548bf2a..109f5b48df 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -56,6 +56,10 @@ docs = [ "mkdocs-material==9.7.7", "mkdocs==1.6.1", "mkdocstrings==1.0.6", + # pymdown-extensions 12.3 changed the Highlight extension API; mkdocstrings 1.0.6 + # cannot drive it (Highlight.__init__() missing argument "md"). 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Debian currently ships numcodecs 0.17.0, which zarr excludes (GHSA-jqc8-qjfv-5m6r), and the job failed through the pickle opt-in tests instead of saying so. Install zarr with its dependencies resolved and run pip check, so an image that does not satisfy pyproject.toml fails at install time. Debian stays a source of prebuilt s390x binaries only. Build a satisfying numcodecs from source in the image, where the compile is cached as a layer, using Debian's meson, Cython and numpy so nothing else compiles under emulation. Assisted-by: ClaudeCode:claude-fable-5.1 Co-Authored-By: Claude Fable 5.1 * docs: add changelog entry for #4547 Assisted-by: ClaudeCode:claude-fable-5.1 Co-Authored-By: Claude Fable 5.1 --------- Co-authored-by: Claude Fable 5.1 --- .github/workflows/big-endian.yml | 5 ++++- changes/4547.misc.md | 1 + ci/big-endian/Dockerfile | 23 +++++++++++++++++++---- 3 files changed, 24 insertions(+), 5 deletions(-) create mode 100644 changes/4547.misc.md diff --git a/.github/workflows/big-endian.yml b/.github/workflows/big-endian.yml index 0119f04ffa..7bf78eacf5 100644 --- a/.github/workflows/big-endian.yml +++ b/.github/workflows/big-endian.yml @@ -57,7 +57,10 @@ jobs: run: | docker run --rm --platform linux/s390x -v "$PWD":/src:ro zarr-big-endian bash -euc ' cp -r /src /work && cd /work - pip install -q --no-deps --no-build-isolation . + # Resolve dependencies against pyproject.toml rather than trusting whatever the + # image provides, then fail if any installed package falls outside the constraints. + pip install -q --no-build-isolation . + pip check python -c "import sys; assert sys.byteorder == \"big\", sys.byteorder" python -m pytest -p no:cacheprovider --hypothesis-profile ci -n auto \ tests/test_dtype tests/test_dtype_registry.py \ diff --git a/changes/4547.misc.md b/changes/4547.misc.md new file mode 100644 index 0000000000..f98644f479 --- /dev/null +++ b/changes/4547.misc.md @@ -0,0 +1 @@ +The big-endian (s390x) CI job now installs zarr with its dependencies resolved against `pyproject.toml` and runs `pip check`, instead of trusting whatever versions the Debian-based test image provides. The image builds a numcodecs that satisfies zarr's constraints from source where Debian's package does not. diff --git a/ci/big-endian/Dockerfile b/ci/big-endian/Dockerfile index 973ce698be..8c70535fc7 100644 --- a/ci/big-endian/Dockerfile +++ b/ci/big-endian/Dockerfile @@ -1,11 +1,20 @@ # Test image for a big-endian host (s390x, run under QEMU by .github/workflows/big-endian.yml). -# Debian packages supply numpy and numcodecs, so nothing heavy compiles under emulation; -# this is also the environment Debian tests zarr in. Debian does not package Google's -# crc32c library, so it is built here for the google-crc32c C extension. +# +# Debian packages are used as a source of prebuilt binaries for s390x, which PyPI does not +# have, so that numpy and friends do not compile under emulation. They do not define the +# test environment: zarr's pyproject.toml does. The workflow installs zarr with its +# dependencies resolved and runs `pip check`, so a Debian package that falls outside the +# declared constraints fails the job at install time instead of through unrelated-looking +# test failures. Anything Debian cannot satisfy is built here from source so the compile is +# cached as an image layer rather than repeated in every job. +# +# Debian does not package Google's crc32c library, so it is built here for the +# google-crc32c C extension. FROM debian:sid RUN apt-get update -qq && apt-get install -y -qq --no-install-recommends \ - build-essential cmake git python3 python3-dev python3-pip python3-venv \ + build-essential cmake cython3 git meson ninja-build pkgconf python3 python3-dev \ + python3-mesonpy python3-pip python3-setuptools-scm python3-venv \ python3-crc32c python3-donfig python3-fsspec python3-hatch-vcs python3-hatchling \ python3-hypothesis python3-numcodecs python3-numpy python3-numpydoc python3-packaging \ python3-pytest python3-pytest-asyncio python3-pytest-benchmark python3-pytest-xdist \ @@ -24,3 +33,9 @@ RUN git clone -q --depth 1 --branch 1.1.2 https://github.com/google/crc32c /tmp/ RUN python3 -m venv --system-site-packages /venv ENV PATH=/venv/bin:$PATH RUN pip install -q --no-binary google-crc32c google-crc32c msgspec pytest-accept +# Debian sid ships numcodecs 0.17.0, which zarr excludes (see pyproject.toml; GHSA-jqc8-qjfv-5m6r), +# and PyPI has no s390x wheels, so build a satisfying numcodecs from source into the venv, where +# it shadows the Debian package. Built without isolation so the Debian meson, Cython and numpy +# are used instead of compiling a build-time numpy under emulation. Remove once Debian ships a +# version that satisfies zarr's constraint; `pip check` in the workflow will say when it does not. +RUN pip install -q --no-binary numcodecs --no-build-isolation "numcodecs>=0.16.6,!=0.17.0" From 63a681d419670ac0e6eb26cd08ceaf64941f2d18 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 21 Oct 2026 19:08:45 +0200 Subject: [PATCH 08/13] chore(deps): bump pillow from 12.3.0 to 13.0.0 (#4540) Bumps [pillow](https://github.com/python-pillow/Pillow) from 12.3.0 to 13.0.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/12.3.0...13.0.0) --- updated-dependencies: - dependency-name: pillow dependency-version: 13.0.0 dependency-type: indirect ... 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notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.12.21...0.13.4) --- updated-dependencies: - dependency-name: uv dependency-version: 0.13.4 dependency-type: direct:development ... 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[actions/download-artifact](https://github.com/actions/download-artifact) | `8.0.1` | `8.0.2` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.6.4` | `0.7.1` | Updates `astral-sh/setup-uv` from 10.2.0 to 10.3.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/c18668ad3cf93ea998bef934396af7bb5c839dc7...1c37ad07a6a961277cf70c0d37d6f313000f5884) Updates `CodSpeedHQ/action` from 5.2.1 to 5.5.0 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/373d6868929f444bc08d901fd0eb0ad52a8875ea...821a40cd6c80e3cfe387caf55668287addd808da) Updates `actions/upload-artifact` from 7.0.1 to 7.0.2 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/043fb46d1a93c77aae656e7c1c64a875d1fc6a0a...cf430e030ddbb5b0abf93d22962f4752f3646cd9) Updates `actions/download-artifact` from 8.0.1 to 8.0.2 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c...9000827ccba6bdab643e8b6fd33ac0654aef8333) Updates `zizmorcore/zizmor-action` from 0.6.4 to 0.7.1 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/cc914d7f3750a2d13d75c7f184a1060aa0e9d482...85b2b9fb8e3325e7a23d7d0a9d7ba5ae0f999e3e) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 10.3.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 5.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.7.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 2 +- .github/workflows/codspeed.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/downstream.yml | 4 ++-- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/lint.yml | 2 +- .github/workflows/releases.yml | 6 +++--- .github/workflows/test.yml | 8 ++++---- .github/workflows/zarr-http-server-release.yml | 10 +++++----- .github/workflows/zarr-http-server.yml | 8 ++++---- .github/workflows/zarr-indexing-release.yml | 10 +++++----- .github/workflows/zarr-indexing.yml | 8 ++++---- .github/workflows/zarr-metadata-release.yml | 10 +++++----- .github/workflows/zarr-metadata.yml | 8 ++++---- .github/workflows/zizmor.yml | 2 +- 16 files changed, 43 insertions(+), 43 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index bfc7096edb..b6613c0ed7 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -22,7 +22,7 @@ jobs: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install just uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1 diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index a58ce40a9d..73846ede18 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -41,7 +41,7 @@ jobs: repo: casey/just version: 1.58.0 - name: Run the benchmarks - uses: CodSpeedHQ/action@373d6868929f444bc08d901fd0eb0ad52a8875ea # v5.2.1 + uses: CodSpeedHQ/action@821a40cd6c80e3cfe387caf55668287addd808da # v5.5.0 env: ZARR_BENCHMARK_CLEAR_CACHE: '1' with: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 3e6b468452..88c0f11577 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -22,7 +22,7 @@ jobs: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + - uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install just uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1 with: diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 35b06b740c..0972aded63 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -45,7 +45,7 @@ jobs: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install xarray and test dependencies working-directory: xarray @@ -106,7 +106,7 @@ jobs: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install numcodecs with test-zarr-main group working-directory: numcodecs diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index f223e0ca17..86f7add71b 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -62,7 +62,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install Hatch uses: pypa/hatch@f647ed70d49adb885f53a27d1c7f5bdaeacf2c60 with: diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index eb9b5fb008..b6b67fae29 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -60,7 +60,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install Hatch uses: pypa/hatch@f647ed70d49adb885f53a27d1c7f5bdaeacf2c60 with: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index ed9e95a144..5c64d851c3 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -27,7 +27,7 @@ jobs: with: python-version: "3.12" - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Install just diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 0865314915..c57e67aa8e 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -43,7 +43,7 @@ jobs: version: '1.16.5' - name: Build wheel and sdist run: hatch build - - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: releases path: dist @@ -53,7 +53,7 @@ jobs: needs: [build_artifacts] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: releases path: dist @@ -76,7 +76,7 @@ jobs: attestations: write # Required for artifact attestation artifact-metadata: write # Required for artifact attestation metadata steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: releases path: dist diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index dea37533b2..e8b00543c8 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -66,7 +66,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Install just @@ -119,7 +119,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Install just @@ -158,7 +158,7 @@ jobs: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Install just @@ -187,7 +187,7 @@ jobs: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Install just diff --git a/.github/workflows/zarr-http-server-release.yml b/.github/workflows/zarr-http-server-release.yml index 5070c6deb2..bbae0d35b0 100644 --- a/.github/workflows/zarr-http-server-release.yml +++ b/.github/workflows/zarr-http-server-release.yml @@ -35,7 +35,7 @@ jobs: - name: Build run: hatch build - - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: zarr-http-server-dist path: packages/zarr-http-server/dist @@ -45,13 +45,13 @@ jobs: needs: [build] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-http-server-dist path: dist - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: false @@ -104,7 +104,7 @@ jobs: id-token: write # required for OIDC trusted publishing attestations: write # required for artifact attestations steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-http-server-dist path: dist @@ -129,7 +129,7 @@ jobs: id-token: write attestations: write steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-http-server-dist path: dist diff --git a/.github/workflows/zarr-http-server.yml b/.github/workflows/zarr-http-server.yml index f6ffd96cb8..8a74d259b0 100644 --- a/.github/workflows/zarr-http-server.yml +++ b/.github/workflows/zarr-http-server.yml @@ -53,7 +53,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Set up Python ${{ matrix.python-version }} @@ -83,7 +83,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install just uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1 with: @@ -104,7 +104,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Set up Python @@ -131,7 +131,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Install just diff --git a/.github/workflows/zarr-indexing-release.yml b/.github/workflows/zarr-indexing-release.yml index f70f78d157..ba046bd0ce 100644 --- a/.github/workflows/zarr-indexing-release.yml +++ b/.github/workflows/zarr-indexing-release.yml @@ -35,7 +35,7 @@ jobs: - name: Build run: hatch build - - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: zarr-indexing-dist path: packages/zarr-indexing/dist @@ -45,13 +45,13 @@ jobs: needs: [build] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-indexing-dist path: dist - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: false @@ -104,7 +104,7 @@ jobs: id-token: write # required for OIDC trusted publishing attestations: write # required for artifact attestations steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-indexing-dist path: dist @@ -129,7 +129,7 @@ jobs: id-token: write attestations: write steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-indexing-dist path: dist diff --git a/.github/workflows/zarr-indexing.yml b/.github/workflows/zarr-indexing.yml index c44d7446da..a20363a533 100644 --- a/.github/workflows/zarr-indexing.yml +++ b/.github/workflows/zarr-indexing.yml @@ -46,7 +46,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Install just @@ -86,7 +86,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install just uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1 with: @@ -108,7 +108,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Set up Python @@ -136,7 +136,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Install just diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index fb97c662f4..a118967fd7 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -35,7 +35,7 @@ jobs: - name: Build run: hatch build - - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: zarr-metadata-dist path: packages/zarr-metadata/dist @@ -45,13 +45,13 @@ jobs: needs: [build] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-metadata-dist path: dist - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: false @@ -104,7 +104,7 @@ jobs: id-token: write # required for OIDC trusted publishing attestations: write # required for artifact attestations steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-metadata-dist path: dist @@ -129,7 +129,7 @@ jobs: id-token: write attestations: write steps: - - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: name: zarr-metadata-dist path: dist diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml index 16b19181a7..256e712811 100644 --- a/.github/workflows/zarr-metadata.yml +++ b/.github/workflows/zarr-metadata.yml @@ -45,7 +45,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Install just @@ -72,7 +72,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 - name: Install just uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1 with: @@ -93,7 +93,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Install just @@ -117,7 +117,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0 + uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0 with: enable-cache: true - name: Install just diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 19bdb461ea..ae7dd9d8b2 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -32,4 +32,4 @@ jobs: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@cc914d7f3750a2d13d75c7f184a1060aa0e9d482 # v0.6.4 + uses: zizmorcore/zizmor-action@85b2b9fb8e3325e7a23d7d0a9d7ba5ae0f999e3e # v0.7.1 From 52858775c85cea28ab0406446ef9932e6821e545 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Thu, 22 Oct 2026 13:11:34 +0200 Subject: [PATCH 12/13] docs(zarr-metadata): the faster-read fragment is #4490's, which it lands in Assisted-by: ClaudeCode:claude-fable-5-1 --- .../zarr-metadata/changes/{407.feature.md => 4490.feature.1.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename packages/zarr-metadata/changes/{407.feature.md => 4490.feature.1.md} (100%) diff --git a/packages/zarr-metadata/changes/407.feature.md b/packages/zarr-metadata/changes/4490.feature.1.md similarity index 100% rename from packages/zarr-metadata/changes/407.feature.md rename to packages/zarr-metadata/changes/4490.feature.1.md From 20d6b0b606d244342691c1d7230715cfbd587685 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Thu, 22 Oct 2026 13:44:24 +0200 Subject: [PATCH 13/13] fix(zarr-metadata): what two reviews of the faster read found A v2 `order` or `dimension_separator` that only compares equal to "C" or "." without being a string was written back as null once the document was built of what the read refined; both are now judged as refined, so such a value is refused as any other outside the set is. A document writing the `UNSET` sentinel at `consolidated_metadata` was taken for one without the member and written as null; the member is read whenever the key is present. A `ZarrV3ConsolidatedMetadata` given as the member is read in its document's order, so the group writes it as the member wrote it. `_located` takes the problems a kind's `envelope_problems` yields lazily, as it did before. `one_of` is as it was, since its frozenset drifted at the edges for a 1% gain. The kind caches are bounded. The group reader copies listed models only on the problem path, and the depth rule `_refine` applies inline is stated once, in `_past_the_levels`. A test per case, and one showing that a `canonical` that raises does so when the model is first compared, with its note. Assisted-by: ClaudeCode:claude-fable-5-1 --- .../zarr-metadata/changes/4490.feature.1.md | 6 +++- .../zarr-metadata/src/zarr_metadata/_json.py | 22 ++++++++---- .../src/zarr_metadata/_typed_json.py | 7 +--- .../src/zarr_metadata/model/_group.py | 35 +++++++++--------- .../src/zarr_metadata/model/_validation.py | 16 +++++---- .../src/zarr_metadata/v3/_definition.py | 36 ++++++++++--------- .../tests/model/test_construction.py | 24 +++++++++++++ .../zarr-metadata/tests/model/test_group.py | 31 ++++++++++++++++ .../model/test_read_array_metadata_v2.py | 30 ++++++++++++++++ packages/zarr-metadata/tests/v3/test_kinds.py | 31 ++++++++++++++++ 10 files changed, 184 insertions(+), 54 deletions(-) diff --git a/packages/zarr-metadata/changes/4490.feature.1.md b/packages/zarr-metadata/changes/4490.feature.1.md index b39bdc0274..84da29a3aa 100644 --- a/packages/zarr-metadata/changes/4490.feature.1.md +++ b/packages/zarr-metadata/changes/4490.feature.1.md @@ -3,5 +3,9 @@ to JSON once, the model holds what was refined, and a model's key -- what `==` and `hash` compare -- is computed the first time the model is compared rather than when it is built, so a definition's `canonical` is first asked then. Every problem is reported as before, with the same `loc`, `kind`, -message and `input`. The timings and the benchmark are in +message and `input`. The typed members a model shows are the refined values +throughout: `dimension_names`, a v2 group's `attributes`, and a v2 array's +`order` and `dimension_separator`, which are now judged as refined, so a +value that only compares equal to `"C"` or `"."` without being a string is +refused. The timings and the benchmark are in `tests/benchmarks/read_documents.py`. diff --git a/packages/zarr-metadata/src/zarr_metadata/_json.py b/packages/zarr-metadata/src/zarr_metadata/_json.py index 61c0887343..c6e061b976 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_json.py +++ b/packages/zarr-metadata/src/zarr_metadata/_json.py @@ -395,16 +395,23 @@ def refine_user_data( def nested_past_the_levels(value: object, loc: tuple[str | int, ...]) -> ValidationProblem | None: """The problem `value` is when it is a container -- an object or an array -- at `loc`, past the levels a reader walks, `JSON_DEPTH` of them; None for a scalar, or within them. - `_refine` asks it of every value it reaches, and a reader of each - container it walks without refining -- a document's members, the - consolidated metadata it descends into -- so a chain of documents is - bounded as any other nesting is, and every container is judged where - it sits, as `refine_json` of the whole document would judge it. + `_refine` judges each container it reaches by this rule, as + `_past_the_levels` states it for a value known to be one, and a reader + of each container it walks without refining -- a document's members, + the consolidated metadata it descends into -- asks this, so a chain of + documents is bounded as any other nesting is, and every container is + judged where it sits, as `refine_json` of the whole document would + judge it. """ if len(loc) < JSON_DEPTH or isinstance(value, (str, int, float, bool)) or value is None: return None if not isinstance(value, (Mapping, Sequence)) or isinstance(value, (bytes, bytearray)): return None + return _past_the_levels(loc) + + +def _past_the_levels(loc: tuple[str | int, ...]) -> ValidationProblem: + """The problem a container at `loc`, past the levels a reader walks, is: what `nested_past_the_levels` finds, for a value known to be a container.""" return ValidationProblem(loc, _PAST_THE_LEVELS, "invalid_value") @@ -468,9 +475,10 @@ def _refine(value: object, loc: tuple[str | int, ...], *, finite: bool) -> _Refi "invalid_type", ), ) - # A container: judged where it sits, as `nested_past_the_levels` judges one. + # A container: judged where it sits, by the rule `nested_past_the_levels` + # states, which `_refine` reaches only for a container. if len(loc) >= JSON_DEPTH: - return None, (ValidationProblem(loc, _PAST_THE_LEVELS, "invalid_value"),) + return None, (_past_the_levels(loc),) if mapping: # Walked here rather than through `_refine_members`, so that each # level of nesting costs one frame, `JSON_DEPTH` of them at most. diff --git a/packages/zarr-metadata/src/zarr_metadata/_typed_json.py b/packages/zarr-metadata/src/zarr_metadata/_typed_json.py index 454f774642..3d7bdd0f2c 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_typed_json.py +++ b/packages/zarr-metadata/src/zarr_metadata/_typed_json.py @@ -574,13 +574,8 @@ def one_of(allowed: tuple[object, ...]) -> Parser: right type, the wrong value. """ - # Each value with its type, since `True == 1` and `1.0 == 1` in Python - # and not in JSON; a value nothing hashes, an object or an array, is - # none of them. - admitted = frozenset((type(entry), entry) for entry in allowed) - def parse(value: object, loc: Loc) -> Parsed: - if not _hashable(value) or (type(value), value) not in admitted: + if not any(value == entry and type(value) is type(entry) for entry in allowed): return value, (outside_of(loc, value, allowed),) return value, () diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_group.py b/packages/zarr-metadata/src/zarr_metadata/model/_group.py index 63d575d828..6f5f9951a1 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_group.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_group.py @@ -723,7 +723,7 @@ def read_group_metadata_v3( reading, members = read_group_v3(value, scope) if members is None: return reading - return _with_models(reading, members, documents_for(value), scope) + return _with_models(reading, members, value, scope) def read_group_v3( @@ -759,13 +759,17 @@ def read_group_v3( if "attributes" in doc: attributes, problems = attributes_of(doc["attributes"], at) found.extend(problems) - raw = doc.get(ZARR_V3_CONSOLIDATED_METADATA_KEY, UNSET) consolidated: dict[str, ZarrV3NodeMetadataReading] = {} held: Mapping[str, ArrayMembersV3 | GroupMembersV3] | UNSET = UNSET member: dict[str, JSONValue] | None = None - if raw is not UNSET: + if ZARR_V3_CONSOLIDATED_METADATA_KEY in doc: + # Whatever is written there is read, the `UNSET` sentinel among it: + # a document holds no sentinel, and a reader that took one for an + # absent key would write it as null. consolidated, held, member, inside = _read_consolidated_v3( - raw, context, (*at, ZARR_V3_CONSOLIDATED_METADATA_KEY) + doc[ZARR_V3_CONSOLIDATED_METADATA_KEY], + context, + (*at, ZARR_V3_CONSOLIDATED_METADATA_KEY), ) found.extend(_prefix(ZARR_V3_CONSOLIDATED_METADATA_KEY, inside)) reading = ZarrV3GroupMetadataReading(MappingProxyType(consolidated), with_input(found, whole)) @@ -910,8 +914,9 @@ def _read_consolidated_v3( documents is bounded by the levels a reader walks. """ if isinstance(value, ZarrV3ConsolidatedMetadata): - # Another group's member, given whole: its models at their paths. - value = {**_CONSOLIDATED_ENVELOPE, "metadata": dict(value.metadata)} + # Another group's member, given whole: its models at their paths, + # in the member's own order, as its document writes it. + value = {**value._document, "metadata": dict(value.metadata)} # pyright: ignore[reportPrivateUsage] past = nested_past_the_levels(value, at) if past is not None: return {}, {}, None, within((past,), at) @@ -1134,20 +1139,20 @@ def _with_models( members: GroupMembersV3, value: object, context: Context, - at: Loc = (), ) -> ZarrV3GroupMetadataReading: """`reading`, holding the model of each document its consolidated metadata holds that has no problem, and its own when it has none: each built of what the read refined, as `members` holds it, in `context`. A document with a problem -- a key that is no string, a value that is no JSON, a level past the cap -- has no model; each document its - consolidated metadata holds was read on its own, from where it sits in - `value`, the document this read read -- `at` is where this one sits -- - so the ones without a problem still have their models, and a listed - group with a problem of its own holds those of its own listing. + consolidated metadata holds was read on its own, so the ones without + a problem still have their models, and a listed group with a problem + of its own holds those of its own listing, found by walking `value`, + the document this read read, down to it. """ if len(reading.problems) == 0: model = ZarrV3GroupMetadata._of(_document_of(members), context, reading, members) # pyright: ignore[reportPrivateUsage] return model.reading + value = documents_for(value) if members.consolidated is UNSET or not is_object(value): return reading member = value.get(ZARR_V3_CONSOLIDATED_METADATA_KEY) @@ -1172,13 +1177,7 @@ def _with_models( # refused, or one it walked past -- still holds, in its # reading, a model of each document in its own listing that # has none. - held[path] = _with_models( - nested, - child, - held_entries[path], - context, - (*at, ZARR_V3_CONSOLIDATED_METADATA_KEY, "metadata", path), - ) + held[path] = _with_models(nested, child, held_entries[path], context) return dataclasses.replace(reading, consolidated=MappingProxyType(held)) diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_validation.py b/packages/zarr-metadata/src/zarr_metadata/model/_validation.py index a74d80691a..2eda0fd12d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_validation.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_validation.py @@ -779,8 +779,11 @@ def read_array_v2( ) problems.extend(found) if "order" in doc: - refined["order"], _ = refine_json(doc["order"]) - if doc["order"] not in ("C", "F"): + # Judged as refined, so a value that only compares equal to "C" is + # refused as every other value outside the set is. + order, found = refine_json(doc["order"], ("order",)) + refined["order"] = order + if len(found) != 0 or order not in ("C", "F"): problems.append(outside_of(("order",), doc["order"], ("C", "F"))) compressor: ResolvedField[ZarrV2CodecDefinition[Any]] | UNSET | None = UNSET if "compressor" in doc: @@ -832,8 +835,9 @@ def read_array_v2( filters = tuple(read) refined["filters"] = tuple(items) if "dimension_separator" in doc: - refined["dimension_separator"], _ = refine_json(doc["dimension_separator"]) - if doc["dimension_separator"] not in (".", "/"): + separator, found = refine_json(doc["dimension_separator"], ("dimension_separator",)) + refined["dimension_separator"] = separator + if len(found) != 0 or separator not in (".", "/"): problems.append( outside_of(("dimension_separator",), doc["dimension_separator"], (".", "/")) ) @@ -863,9 +867,9 @@ def read_array_v2( shape=shape, chunks=chunks, fill_value=fill_value, - order=cast("ZarrV2ArrayOrder", doc["order"]), + order=cast("ZarrV2ArrayOrder", refined["order"]), dimension_separator=cast( - "ZarrV2ArrayDimensionSeparator", doc.get("dimension_separator", ".") + "ZarrV2ArrayDimensionSeparator", refined.get("dimension_separator", ".") ), attributes=attributes, extra_fields=extra_fields, diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py b/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py index 9fb93cec60..7b716b9a83 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/_definition.py @@ -688,9 +688,9 @@ def kind_of(definition: Definition[Any]) -> type[Definition[Any]] | None: return _kind_of_class(type(definition)) -@functools.cache +@functools.lru_cache(maxsize=256) def _kind_of_class(cls: type[object]) -> type[Definition[Any]] | None: - """`kind_of` a definition of class `cls`: a walk of its MRO, once per class.""" + """`kind_of` a definition of class `cls`: a walk of its MRO, once per class; bounded, so a class built per call is not kept for good.""" return next((base for base in cls.__mro__ if _declares_kind(base)), None) @@ -708,8 +708,13 @@ def _declares_kind(cls: type[object]) -> TypeGuard[type[Definition[Any]]]: return vars(cls).get("_is_kind") is True and issubclass(cls, Definition) -_KIND_NAMED: dict[object, type[Definition[Any]]] = {} -"""What `as_kind` answered for each way a kind was named -- `CodecDefinition`, `CodecDefinition[Any]` -- which never changes: a class is a kind by its declaration.""" +@functools.lru_cache(maxsize=256) +def _kind_named(kind: object) -> type[Definition[Any]] | None: + """The kind `kind` names, type arguments dropped, or None: what `as_kind` answers, once per way a kind is named -- `CodecDefinition`, `CodecDefinition[Any]` -- since a class is a kind by its declaration; bounded, so a class built per call is not kept for good.""" + origin = get_origin(kind) or kind + if isinstance(origin, type) and _declares_kind(origin): + return origin + return None def as_kind(kind: object) -> type[Definition[Any]]: @@ -721,14 +726,12 @@ def as_kind(kind: object) -> type[Definition[Any]]: filed: a field read as one would go unjudged. """ try: - return _KIND_NAMED[kind] - except (KeyError, TypeError): - # Not asked before, or not hashable, which no kind is. - pass - origin = get_origin(kind) or kind - if isinstance(origin, type) and _declares_kind(origin): - _KIND_NAMED[kind] = origin - return origin + found = _kind_named(kind) + except TypeError: + # Not hashable, which no kind is. + found = None + if found is not None: + return found names = ", ".join(known.__name__ for known in KINDS) msg = ( f"{kind!r} is not a kind of metadata; read a field as one of {names}, or as a " @@ -1116,11 +1119,12 @@ def ruled( return _located(at, cast("tuple[ValidationProblem, ...]", found)) -def _located(prefix: Loc, problems: Sequence[ValidationProblem]) -> Problems: - """`problems`, each located under `prefix`.""" - if len(problems) == 0: +def _located(prefix: Loc, problems: Iterable[ValidationProblem]) -> Problems: + """`problems`, each located under `prefix`; a kind's `envelope_problems` may give them lazily.""" + found = tuple(problems) + if len(found) == 0: return () - return tuple(dataclasses.replace(found, loc=(*prefix, *found.loc)) for found in problems) + return tuple(dataclasses.replace(each, loc=(*prefix, *each.loc)) for each in found) def _envelope(field: _NestedField) -> Problems: diff --git a/packages/zarr-metadata/tests/model/test_construction.py b/packages/zarr-metadata/tests/model/test_construction.py index 914416fe3a..df8330f7e5 100644 --- a/packages/zarr-metadata/tests/model/test_construction.py +++ b/packages/zarr-metadata/tests/model/test_construction.py @@ -339,3 +339,27 @@ def counting(configuration: GzipCodecConfiguration) -> GzipCodecConfiguration: assert hash(model) == hash(other) assert model != ZarrV3ArrayMetadata({**document, "fill_value": 1}, scope) assert len(asked) == 3 + + +def test_error_a_canonical_that_raises_is_raised_when_the_model_is_first_compared() -> None: + """A definition's `canonical` is the extension author's code, first asked when a model is first compared: the model builds, and `hash` raises what `canonical` raised, with the note naming the definition.""" + + def refuses(configuration: GzipCodecConfiguration) -> GzipCodecConfiguration: + raise ValueError("no") + + scope = CORE_AND_EXTENSIONS.extended_with(dataclasses.replace(GZIP_CODEC, canonical=refuses)) + document = { + "zarr_format": 3, + "node_type": "array", + "shape": [4], + "data_type": "int8", + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [4]}}, + "chunk_key_encoding": {"name": "default", "configuration": {"separator": "/"}}, + "fill_value": 0, + "codecs": [{"name": "bytes"}, {"name": "gzip", "configuration": {"level": 1}}], + } + model = ZarrV3ArrayMetadata(document, scope) + assert model.to_json()["codecs"][1] == {"name": "gzip", "configuration": {"level": 1}} + with pytest.raises(ValueError, match="no") as raised: + hash(model) + assert raised.value.__notes__ == ["raised by the canonical of 'gzip'"] diff --git a/packages/zarr-metadata/tests/model/test_group.py b/packages/zarr-metadata/tests/model/test_group.py index c984759ce6..9fda7f55f3 100644 --- a/packages/zarr-metadata/tests/model/test_group.py +++ b/packages/zarr-metadata/tests/model/test_group.py @@ -1471,3 +1471,34 @@ def test_error_a_model_is_built_only_of_members_a_read_found_nothing_wrong_with( with pytest.raises(TypeError, match="nothing wrong with"): _document_of(GroupMembersV3(None, {}, UNSET, None)) + + +def test_error_the_unset_sentinel_at_consolidated_metadata_is_not_an_absent_member() -> None: + """`UNSET` is what a reader gives for a key a document does not hold; written at `consolidated_metadata`, it is a value that is no object, as any other such value is, and never written back as null.""" + document = { + "zarr_format": 3, + "node_type": "group", + "attributes": {}, + "consolidated_metadata": UNSET, + } + assert [(found.loc, found.kind) for found in validate_group_metadata_v3(document)] == [ + (("consolidated_metadata",), "invalid_type") + ] + with pytest.raises(MetadataValidationError): + ZarrV3GroupMetadata(document) + + +def test_a_consolidated_model_given_as_the_member_keeps_the_order_its_document_writes() -> None: + """A `ZarrV3ConsolidatedMetadata` given as the member is read as its document, in its document's order, so the group writes it as the member wrote it.""" + array = ZarrV3ArrayMetadata.create_default(shape=(2,)) + member = ZarrV3ConsolidatedMetadata( + {"metadata": {"a": array.to_json()}, "kind": "inline", "must_understand": False} + ) + group = ZarrV3GroupMetadata( + {"zarr_format": 3, "node_type": "group", "consolidated_metadata": member} + ) + written = cast("dict[str, object]", group.to_json()["consolidated_metadata"]) + assert list(written) == ["metadata", "kind", "must_understand"] + assert group == ZarrV3GroupMetadata( + {"zarr_format": 3, "node_type": "group", "consolidated_metadata": member.to_json()} + ) diff --git a/packages/zarr-metadata/tests/model/test_read_array_metadata_v2.py b/packages/zarr-metadata/tests/model/test_read_array_metadata_v2.py index dcd671a3b5..76b71e0dad 100644 --- a/packages/zarr-metadata/tests/model/test_read_array_metadata_v2.py +++ b/packages/zarr-metadata/tests/model/test_read_array_metadata_v2.py @@ -8,6 +8,7 @@ from zarr_metadata._sentinel import UNSET from zarr_metadata.model import ( + MetadataValidationError, ZarrV2ArrayMetadata, is_array_metadata_v2, parse_array_metadata_v2, @@ -123,3 +124,32 @@ def test_the_v2_readers_read_in_the_scope_given() -> None: assert validate_array_metadata_v2(doc) == () found = validate_array_metadata_v2(doc, context=CORE_V2.extended_with(bare)) assert [p.loc for p in found] == [("compressor", "level")] + + +class _EqualTo: + """A value that compares equal to a string without being one.""" + + def __init__(self, text: str) -> None: + self.text = text + + def __eq__(self, other: object) -> bool: + return other == self.text + + __hash__ = None # pyright: ignore[reportAssignmentType] + + +@pytest.mark.parametrize( + ("key", "value"), + [("order", _EqualTo("C")), ("dimension_separator", _EqualTo("."))], + ids=["order", "dimension_separator"], +) +def test_error_a_v2_member_that_only_compares_equal_to_an_allowed_value_is_refused( + key: str, value: object +) -> None: + """`order` and `dimension_separator` are judged as refined: a value that is no string, and only compares equal to one the set allows, is outside the set, of the wrong type, and never a model's.""" + document = {**BASE, key: value} + problems = validate_array_metadata_v2(document) + assert [(found.loc, found.kind) for found in problems] == [((key,), "invalid_type")] + assert read_array_metadata_v2(document).metadata is None + with pytest.raises(MetadataValidationError): + ZarrV2ArrayMetadata(document) diff --git a/packages/zarr-metadata/tests/v3/test_kinds.py b/packages/zarr-metadata/tests/v3/test_kinds.py index db4ededff5..e521018011 100644 --- a/packages/zarr-metadata/tests/v3/test_kinds.py +++ b/packages/zarr-metadata/tests/v3/test_kinds.py @@ -268,3 +268,34 @@ def test_error_what_nothing_hashes_is_not_a_kind() -> None: as_kind(["codec"]) with pytest.raises(TypeError, match="is not a kind of metadata"): as_kind({"kind": CodecDefinition}) + + +class _LazyEnvelope(CodecDefinition[Any], kind=True, format=3): + """A kind whose envelope rule yields its problems rather than returning a tuple of them.""" + + label: ClassVar[str] = "lazy codec" + + @classmethod + def envelope_problems(cls, value: object) -> Any: # noqa: ANN401 - what a kind's author may write + yield from CodecDefinition.envelope_problems(value) + + +def test_a_kind_may_yield_its_envelope_problems() -> None: + """`envelope_problems` is a kind's to write; one that yields its problems is read as one that returns them, with and without a problem to yield.""" + lazy = _LazyEnvelope( + name="gzip", + configuration=GZIP_CODEC.configuration, + kind=GZIP_CODEC.kind, + size=GZIP_CODEC.size, + ) + scope = Context.of(lazy) + read, problems = resolve({"name": "gzip", "configuration": {"level": 1}}, _LazyEnvelope, scope) + assert isinstance(read, AcceptedField) + assert problems == () + refused, problems = resolve( + {"name": "gzip", "configuration": 5}, _LazyEnvelope, scope, ("codecs", 0) + ) + assert isinstance(refused, RefusedField) + assert [(found.loc, found.kind) for found in problems] == [ + (("codecs", 0, "configuration"), "invalid_type") + ]