From 17e74a922b7726296baabdc571e89481ca602774 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:47:35 +0200 Subject: [PATCH 01/55] feat(metadata): scaffold zarr-metadata package structure Co-Authored-By: Claude Opus 4.7 (1M context) --- packages/zarr-metadata/README.md | 15 +++++++ packages/zarr-metadata/pyproject.toml | 40 +++++++++++++++++++ .../src/zarr_metadata/__init__.py | 1 + .../src/zarr_metadata/codec/__init__.py | 1 + .../src/zarr_metadata/dtype/__init__.py | 1 + .../src/zarr_metadata/v2/__init__.py | 1 + .../src/zarr_metadata/v3/__init__.py | 1 + packages/zarr-metadata/tests/__init__.py | 1 + 8 files changed, 61 insertions(+) create mode 100644 packages/zarr-metadata/README.md create mode 100644 packages/zarr-metadata/pyproject.toml create mode 100644 packages/zarr-metadata/src/zarr_metadata/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/__init__.py create mode 100644 packages/zarr-metadata/tests/__init__.py diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md new file mode 100644 index 0000000000..0ee12811e9 --- /dev/null +++ b/packages/zarr-metadata/README.md @@ -0,0 +1,15 @@ +# zarr-metadata + +Spec-defined metadata types for Zarr v2 and v3, distributed as pure-typing +artifacts (TypedDicts, type aliases, unions). No runtime logic, no numpy, +no storage backends. + +`zarr-metadata` is developed in the [zarr-python](https://github.com/zarr-developers/zarr-python) +repository at `packages/zarr-metadata/`. + +## Principle + +Every type that models a spec artifact (v2 or v3 array/group/consolidated +metadata, chunk grids, codec named-config envelopes, dtype shapes) belongs +in `zarr-metadata`. Zarr-python implementation details (runtime codecs, +config dataclasses, numcodecs-derived helpers) stay in `zarr`. diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml new file mode 100644 index 0000000000..103ba5ca8a --- /dev/null +++ b/packages/zarr-metadata/pyproject.toml @@ -0,0 +1,40 @@ +[build-system] +requires = ["hatchling>=1.29.0"] +build-backend = "hatchling.build" + +[project] +name = "zarr-metadata" +version = "0.1.0" +description = "Spec-defined metadata types for Zarr v2 and v3." +readme = "README.md" +requires-python = ">=3.12" +license = "MIT" +authors = [ + { name = "Davis Bennett", email = "davis.v.bennett@gmail.com" }, +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Typing :: Typed", +] +dependencies = [ + "typing_extensions>=4.13", +] + +[project.optional-dependencies] +test = ["pytest"] + +[tool.hatch.build.targets.wheel] +packages = ["src/zarr_metadata"] + +[tool.pyright] +include = ["src"] +enableExperimentalFeatures = true +typeCheckingMode = "strict" +pythonVersion = "3.12" diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py new file mode 100644 index 0000000000..20c8835782 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -0,0 +1 @@ +"""Spec-defined metadata types for Zarr v2 and v3.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py new file mode 100644 index 0000000000..8bcc4770c6 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py @@ -0,0 +1 @@ +"""Zarr codec metadata types.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py new file mode 100644 index 0000000000..311e2f8615 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py @@ -0,0 +1 @@ +"""Zarr dtype metadata types.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py new file mode 100644 index 0000000000..881504cc80 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py @@ -0,0 +1 @@ +"""Zarr v2 metadata types.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py new file mode 100644 index 0000000000..9e95090042 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py @@ -0,0 +1 @@ +"""Zarr v3 metadata types.""" diff --git a/packages/zarr-metadata/tests/__init__.py b/packages/zarr-metadata/tests/__init__.py new file mode 100644 index 0000000000..d886440736 --- /dev/null +++ b/packages/zarr-metadata/tests/__init__.py @@ -0,0 +1 @@ +"""Tests for zarr-metadata.""" From 8da469fe510d8c7a189558e80ad699900957002c Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:48:01 +0200 Subject: [PATCH 02/55] build(metadata): depend on zarr-metadata via local uv workspace source Co-Authored-By: Claude Opus 4.7 (1M context) --- pyproject.toml | 4 + uv.lock | 4037 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 4041 insertions(+) create mode 100644 uv.lock diff --git a/pyproject.toml b/pyproject.toml index b4783b5be3..7a24777bec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,6 +38,7 @@ dependencies = [ 'google-crc32c>=1.5', 'typing_extensions>=4.13', 'donfig>=0.8', + 'zarr-metadata>=0.1, <0.2', ] dynamic = [ @@ -471,3 +472,6 @@ ignore-words-list = "astroid" [project.entry-points.pytest11] zarr = "zarr.testing" + +[tool.uv.sources] +zarr-metadata = { path = "packages/zarr-metadata", editable = true } diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000000..961f59f81f --- /dev/null +++ b/uv.lock @@ 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name = "hypothesis" }, + { name = "numpydoc" }, + { name = "pytest" }, + { name = "pytest-accept" }, + { name = "pytest-asyncio" }, + { name = "pytest-benchmark" }, + { name = "pytest-codspeed" }, + { name = "pytest-cov" }, + { name = "pytest-xdist" }, + { name = "tomlkit" }, + { name = "uv" }, +] + +[[package]] +name = "zarr-metadata" +version = "0.1.0" +source = { editable = "packages/zarr-metadata" } +dependencies = [ + { name = "typing-extensions" }, +] + +[package.metadata] +requires-dist = [ + { name = "pytest", marker = "extra == 'test'" }, + { name = "typing-extensions", specifier = ">=4.13" }, +] +provides-extras = ["test"] From e43bd3673bff6dd08fb42a8c2cb83e01e0cd49f7 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:53:42 +0200 Subject: [PATCH 03/55] feat(metadata): add JSON, NamedConfig, NamedRequiredConfig primitives Co-Authored-By: Claude Opus 4.7 (1M context) --- packages/zarr-metadata/pyproject.toml | 10 +++++ .../src/zarr_metadata/__init__.py | 45 ++++++++++++++++++- 2 files changed, 54 insertions(+), 1 deletion(-) diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 103ba5ca8a..7e31477af0 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -33,6 +33,16 @@ test = ["pytest"] [tool.hatch.build.targets.wheel] packages = ["src/zarr_metadata"] +[tool.numpydoc_validation] +checks = [ + "GL10", + "SS04", + "PR02", + "PR03", + "PR05", + "PR06", +] + [tool.pyright] include = ["src"] enableExperimentalFeatures = true diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 20c8835782..26868f3b05 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -1 +1,44 @@ -"""Spec-defined metadata types for Zarr v2 and v3.""" +""" +Top-level cross-version primitives for Zarr metadata. + +Version-specific types live under ``zarr_metadata.v2`` and ``zarr_metadata.v3``. +Codec and dtype spec types live under ``zarr_metadata.codec`` and +``zarr_metadata.dtype``. +""" + +from collections.abc import Mapping, Sequence +from typing import NotRequired, TypedDict + +from typing_extensions import ReadOnly + +JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None +"""Any valid JSON value.""" + + +class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + Named-config envelope with optional configuration. + + Generic with two parameters: name literal and configuration mapping. + """ + + name: ReadOnly[TName] + configuration: NotRequired[ReadOnly[TConfig]] + + +class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + Named-config envelope with required configuration. + + Generic with two parameters: name literal and configuration mapping. + """ + + name: ReadOnly[TName] + configuration: ReadOnly[TConfig] + + +__all__ = [ + "JSON", + "NamedConfig", + "NamedRequiredConfig", +] From 28efcde93057645274782857e709555b0ec4d4b4 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:54:46 +0200 Subject: [PATCH 04/55] feat(metadata): add v3 array metadata types Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v3/array.py | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/array.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py new file mode 100644 index 0000000000..70d361d1fd --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -0,0 +1,79 @@ +"""Zarr v3 array metadata types.""" + +from collections.abc import Mapping, Sequence +from typing import Literal, NotRequired + +from typing_extensions import TypedDict + +from zarr_metadata import JSON, NamedConfig, NamedRequiredConfig + + +class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] + """ + Extra field on a v3 array metadata document. + + Extras must include ``must_understand: false`` and may carry arbitrary + additional JSON data. + """ + + must_understand: Literal[False] + + +# JSON type for a single dimension's rectilinear spec: +# bare int (uniform shorthand), or list of ints / [value, count] RLE pairs. +RectilinearDimSpec = int | list[int | list[int]] + + +class RegularChunkGridConfig(TypedDict): + """ + Configuration body of a regular chunk grid. + """ + + chunk_shape: Sequence[int] + + +class RectilinearChunkGridConfig(TypedDict): + """ + Configuration body of a rectilinear chunk grid. + """ + + kind: Literal["inline"] + chunk_shapes: Sequence[RectilinearDimSpec] + + +RegularChunkGrid = NamedRequiredConfig[Literal["regular"], RegularChunkGridConfig] +"""Regular chunk grid named-config envelope.""" + +RectilinearChunkGrid = NamedRequiredConfig[Literal["rectilinear"], RectilinearChunkGridConfig] +"""Rectilinear chunk grid named-config envelope.""" + + +class ArrayMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] + """ + Zarr v3 array metadata document (the ``zarr.json`` content for an array). + + Extra keys are permitted if they conform to ``AllowedExtraField``. + """ + + zarr_format: Literal[3] + node_type: Literal["array"] + data_type: str | NamedConfig[str, Mapping[str, JSON]] + shape: tuple[int, ...] + chunk_grid: str | NamedConfig[str, Mapping[str, JSON]] + chunk_key_encoding: str | NamedConfig[str, Mapping[str, JSON]] + fill_value: JSON + codecs: tuple[str | NamedConfig[str, Mapping[str, JSON]], ...] + attributes: NotRequired[Mapping[str, JSON]] + storage_transformers: NotRequired[tuple[str | NamedConfig[str, Mapping[str, JSON]], ...]] + dimension_names: NotRequired[tuple[str | None, ...]] + + +__all__ = [ + "AllowedExtraField", + "ArrayMetadataV3", + "RectilinearChunkGrid", + "RectilinearChunkGridConfig", + "RectilinearDimSpec", + "RegularChunkGrid", + "RegularChunkGridConfig", +] From 23aed894cf3b1977765c90476bd37fb5fe0fcf86 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:55:16 +0200 Subject: [PATCH 05/55] feat(metadata): add v3 consolidated metadata type Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v3/consolidated.py | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py new file mode 100644 index 0000000000..19974a83ca --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py @@ -0,0 +1,30 @@ +"""Zarr v3 consolidated metadata types.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Literal, TypedDict + +if TYPE_CHECKING: + from collections.abc import Mapping + + from zarr_metadata.v3.array import ArrayMetadataV3 + from zarr_metadata.v3.group import GroupMetadataV3 + + +class ConsolidatedMetadataV3(TypedDict): + """ + Inline consolidated metadata embedded in a v3 group. + + The ``metadata`` map contains only v3 array and group entries - v2 + entries are excluded by design. Mixing v2 entries into a v3 + consolidated metadata document is invalid per spec. + """ + + kind: Literal["inline"] + must_understand: Literal[False] + metadata: Mapping[str, ArrayMetadataV3 | GroupMetadataV3] + + +__all__ = [ + "ConsolidatedMetadataV3", +] From 43eefba9304842cee4bffe95356f7904e23da1dc Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:55:44 +0200 Subject: [PATCH 06/55] feat(metadata): add v3 group metadata type Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v3/group.py | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/group.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py new file mode 100644 index 0000000000..46d266b8d0 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -0,0 +1,33 @@ +"""Zarr v3 group metadata types.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Literal, NotRequired + +from typing_extensions import TypedDict + +if TYPE_CHECKING: + from collections.abc import Mapping + + from zarr_metadata import JSON + from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 + +from zarr_metadata.v3.array import AllowedExtraField + + +class GroupMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] + """ + Zarr v3 group metadata document (the ``zarr.json`` content for a group). + + Extra keys are permitted if they conform to ``AllowedExtraField``. + """ + + zarr_format: Literal[3] + node_type: Literal["group"] + attributes: NotRequired[Mapping[str, JSON]] + consolidated_metadata: NotRequired[ConsolidatedMetadataV3] + + +__all__ = [ + "GroupMetadataV3", +] From f26e1bd0301f51af96a89106503f469aee45d2ad Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:55:58 +0200 Subject: [PATCH 07/55] feat(metadata): wire up zarr_metadata.v3 re-exports Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v3/__init__.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py index 9e95090042..c63dc46b57 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py @@ -1 +1,25 @@ """Zarr v3 metadata types.""" + +from zarr_metadata.v3.array import ( + AllowedExtraField, + ArrayMetadataV3, + RectilinearChunkGrid, + RectilinearChunkGridConfig, + RectilinearDimSpec, + RegularChunkGrid, + RegularChunkGridConfig, +) +from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 +from zarr_metadata.v3.group import GroupMetadataV3 + +__all__ = [ + "AllowedExtraField", + "ArrayMetadataV3", + "ConsolidatedMetadataV3", + "GroupMetadataV3", + "RectilinearChunkGrid", + "RectilinearChunkGridConfig", + "RectilinearDimSpec", + "RegularChunkGrid", + "RegularChunkGridConfig", +] From 27b000c0ff65020160e188e79e4321ce800d2ad9 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:56:21 +0200 Subject: [PATCH 08/55] feat(metadata): add faithful v2 array metadata types Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v2/array.py | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/array.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py new file mode 100644 index 0000000000..98fc6b5323 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -0,0 +1,62 @@ +"""Zarr v2 array metadata types.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Literal, NotRequired, TypedDict + +if TYPE_CHECKING: + from collections.abc import Mapping, Sequence + + from zarr_metadata import JSON + + +class DataTypeV2Structured(TypedDict): + """ + A single field entry inside a structured v2 dtype. + + Spec-faithful: ``datatype`` is a numpy-style dtype string; ``shape`` is + present only when the field is a subarray field. + """ + + fieldname: str + datatype: str + shape: NotRequired[Sequence[int]] + + +DataTypeV2 = str | list[DataTypeV2Structured] +"""The v2 dtype representation. + +Simple dtypes are numpy-style strings (e.g. ``" Date: Tue, 21 Apr 2026 14:56:33 +0200 Subject: [PATCH 09/55] feat(metadata): add v2 group metadata type Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v2/group.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/group.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/group.py b/packages/zarr-metadata/src/zarr_metadata/v2/group.py new file mode 100644 index 0000000000..cadd3a8ad2 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/group.py @@ -0,0 +1,19 @@ +"""Zarr v2 group metadata types.""" + +from typing import Literal, TypedDict + + +class GroupMetadataV2(TypedDict): + """ + Zarr v2 group metadata document (the ``.zgroup`` content). + + Attributes live in a sibling ``.zattrs`` file, so they are not part + of this dict. + """ + + zarr_format: Literal[2] + + +__all__ = [ + "GroupMetadataV2", +] From d530cb4e88c5712017d4c057523481a814a21a8f Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:56:46 +0200 Subject: [PATCH 10/55] feat(metadata): add v2 consolidated metadata type (canonical impl, not spec) Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v2/consolidated.py | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py new file mode 100644 index 0000000000..b26dd43bf1 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py @@ -0,0 +1,34 @@ +"""Zarr v2 consolidated metadata (``.zmetadata`` file). + +This module models the de-facto ``.zmetadata`` file used by the reference +Python implementation of Zarr v2. **This is NOT a spec artifact.** There +is no Zarr v2 specification that defines ``.zmetadata``; it is a +canonical-implementation convention. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, TypedDict + +if TYPE_CHECKING: + from collections.abc import Mapping + + from zarr_metadata import JSON + + +class ConsolidatedMetadataV2(TypedDict): + """ + ``.zmetadata`` file contents. + + The ``metadata`` map uses flat path keys (``"foo/bar/.zarray"``, + ``"foo/.zattrs"``, etc.) pointing to the JSON contents of the file at + that path. The keys include the filename suffix, not just the node path. + """ + + zarr_consolidated_format: int + metadata: Mapping[str, JSON] + + +__all__ = [ + "ConsolidatedMetadataV2", +] From 266a8eb251f67dc85a8a8f0519e8c9195ce16b34 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:56:59 +0200 Subject: [PATCH 11/55] feat(metadata): wire up zarr_metadata.v2 re-exports Co-Authored-By: Claude Opus 4.7 (1M context) --- .../zarr-metadata/src/zarr_metadata/v2/__init__.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py index 881504cc80..11dd8521d0 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py @@ -1 +1,13 @@ """Zarr v2 metadata types.""" + +from zarr_metadata.v2.array import ArrayMetadataV2, DataTypeV2, DataTypeV2Structured +from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2 + +__all__ = [ + "ArrayMetadataV2", + "ConsolidatedMetadataV2", + "DataTypeV2", + "DataTypeV2Structured", + "GroupMetadataV2", +] From e431dee13be861f58ebeeaa097fc1c2546817c1b Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:57:41 +0200 Subject: [PATCH 12/55] feat(metadata): add ArrayMetadata, GroupMetadata version-polymorphic unions Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/__init__.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 26868f3b05..6118ab3b0d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -37,8 +37,27 @@ class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): configuration: ReadOnly[TConfig] +# Version-polymorphic unions -- imported after primitives to avoid circular import. +from zarr_metadata.v2.array import ArrayMetadataV2 # noqa: E402 +from zarr_metadata.v2.group import GroupMetadataV2 # noqa: E402 +from zarr_metadata.v3.array import ArrayMetadataV3 # noqa: E402 +from zarr_metadata.v3.group import GroupMetadataV3 # noqa: E402 + +ArrayMetadata = ArrayMetadataV2 | ArrayMetadataV3 +"""Any Zarr array metadata document (v2 or v3).""" + +GroupMetadata = GroupMetadataV2 | GroupMetadataV3 +"""Any Zarr group metadata document (v2 or v3).""" + + __all__ = [ "JSON", + "ArrayMetadata", + "ArrayMetadataV2", + "ArrayMetadataV3", + "GroupMetadata", + "GroupMetadataV2", + "GroupMetadataV3", "NamedConfig", "NamedRequiredConfig", ] From c547f550f295fe440e8a44e0870f8532737804db Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:59:50 +0200 Subject: [PATCH 13/55] feat(metadata): add Codec envelope and blosc codec configurations Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/codec/__init__.py | 20 ++++++- .../src/zarr_metadata/codec/blosc.py | 53 +++++++++++++++++++ 2 files changed, 72 insertions(+), 1 deletion(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/blosc.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py index 8bcc4770c6..b8cd8ef735 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py @@ -1 +1,19 @@ -"""Zarr codec metadata types.""" +""" +Zarr codec named-config envelope and per-codec configuration types. +""" + +from collections.abc import Mapping + +Codec = str | Mapping[str, object] +""" +The widest JSON shape that can specify a codec (v2 or v3). + +For v3, a codec is a named-config envelope (``{"name": ..., "configuration": ...}``); +for v2, a codec is the numcodecs JSON dict. The accepted-input shape is the +union of both. +""" + + +__all__ = [ + "Codec", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py new file mode 100644 index 0000000000..a600507ef3 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py @@ -0,0 +1,53 @@ +""" +Blosc codec configuration types (Zarr v3 spec + numcodecs/v2 form). +""" + +from typing import Literal, NotRequired, TypedDict + +Shuffle = Literal["noshuffle", "shuffle", "bitshuffle"] +"""Blosc shuffle mode names (v3 spec).""" + +CName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] +"""Blosc compressor identifiers.""" + + +class BloscCodecConfigurationNumcodecs(TypedDict): + """ + Blosc configuration for Zarr v2 / numcodecs-flavored callers. + + ``shuffle`` is an integer code (the numcodecs convention) rather than + a named literal. + """ + + cname: CName + clevel: int + shuffle: int + blocksize: int + typesize: NotRequired[int] + + +class BloscCodecConfigurationV1(TypedDict): + """ + Blosc configuration for Zarr v3 spec (version 1 of the blosc codec). + + ``shuffle`` is a named string literal. + """ + + cname: CName + clevel: int + shuffle: Shuffle + blocksize: int + typesize: int + + +BloscCodecConfiguration = BloscCodecConfigurationV1 | BloscCodecConfigurationNumcodecs +"""Any supported blosc configuration shape.""" + + +__all__ = [ + "BloscCodecConfiguration", + "BloscCodecConfigurationNumcodecs", + "BloscCodecConfigurationV1", + "CName", + "Shuffle", +] From 1517cd8a5646999a4721f79ff5d5b8554e46409c Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 14:59:57 +0200 Subject: [PATCH 14/55] feat(metadata): add dtype types (DType, LengthBytesConfig, FixedLengthBytesConfig, TimeConfig) Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/dtype/__init__.py | 21 +++++++++++- .../src/zarr_metadata/dtype/bytes.py | 25 ++++++++++++++ .../src/zarr_metadata/dtype/string.py | 25 ++++++++++++++ .../src/zarr_metadata/dtype/time.py | 34 +++++++++++++++++++ 4 files changed, 104 insertions(+), 1 deletion(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/string.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/time.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py index 311e2f8615..385485720c 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py @@ -1 +1,20 @@ -"""Zarr dtype metadata types.""" +""" +Zarr data type spec types. +""" + +from collections.abc import Mapping, Sequence + +# Wider than the top-level JSON because TypedDicts used for dtype configs +# are assignable to Mapping[str, object], not to Mapping[str, JSON]. +DType = str | int | float | Sequence["DType"] | None | Mapping[str, object] +""" +The widest JSON-like shape that can specify a Zarr data type. + +See ``zarr_metadata.dtype.string``, ``.bytes``, and ``.time`` for specific +per-dtype configuration TypedDicts. +""" + + +__all__ = [ + "DType", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py b/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py new file mode 100644 index 0000000000..c174c2620e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py @@ -0,0 +1,25 @@ +""" +Bytes data type configuration. +""" + +from typing import TypedDict + +from typing_extensions import ReadOnly + + +class FixedLengthBytesConfig(TypedDict): + """ + Configuration for a fixed-length bytes data type in Zarr v3. + + Attributes + ---------- + length_bytes + The length in bytes of the data associated with this configuration. + """ + + length_bytes: ReadOnly[int] + + +__all__ = [ + "FixedLengthBytesConfig", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/string.py b/packages/zarr-metadata/src/zarr_metadata/dtype/string.py new file mode 100644 index 0000000000..52bca1b5dc --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/string.py @@ -0,0 +1,25 @@ +""" +String data type configuration. +""" + +from typing import TypedDict + +from typing_extensions import ReadOnly + + +class LengthBytesConfig(TypedDict): + """ + Configuration for a fixed-length string data type in Zarr v3. + + Attributes + ---------- + length_bytes + The length in bytes of the data associated with this configuration. + """ + + length_bytes: ReadOnly[int] + + +__all__ = [ + "LengthBytesConfig", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/time.py b/packages/zarr-metadata/src/zarr_metadata/dtype/time.py new file mode 100644 index 0000000000..b4e6d1e7aa --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/time.py @@ -0,0 +1,34 @@ +""" +Time data type configuration (datetime64, timedelta64). +""" + +from typing import Literal, TypedDict + +from typing_extensions import ReadOnly + +DateTimeUnit = Literal[ + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "ns", "ps", "fs", "as", "generic" +] +"""Time unit codes used by numpy.datetime64 / numpy.timedelta64.""" + + +class TimeConfig(TypedDict): + """ + Configuration for numpy.timedelta64 or numpy.datetime64 in Zarr v3. + + Attributes + ---------- + unit + A string encoding a unit of time. + scale_factor + The multiplier relative to the unit. + """ + + unit: ReadOnly[DateTimeUnit] + scale_factor: ReadOnly[int] + + +__all__ = [ + "DateTimeUnit", + "TimeConfig", +] From b90fb688629378bf10fbbccb2a07040dcb9d8e5f Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:01:50 +0200 Subject: [PATCH 15/55] test(metadata): smoke + structural tests for the package Co-Authored-By: Claude Opus 4.7 (1M context) --- packages/zarr-metadata/tests/test_imports.py | 110 +++++++++++++++++ .../zarr-metadata/tests/test_structural.py | 114 ++++++++++++++++++ 2 files changed, 224 insertions(+) create mode 100644 packages/zarr-metadata/tests/test_imports.py create mode 100644 packages/zarr-metadata/tests/test_structural.py diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py new file mode 100644 index 0000000000..5e980d07e7 --- /dev/null +++ b/packages/zarr-metadata/tests/test_imports.py @@ -0,0 +1,110 @@ +""" +Smoke test: every public name is importable. +""" + +from __future__ import annotations + + +def test_top_level_imports() -> None: + from zarr_metadata import ( + JSON, + ArrayMetadata, + ArrayMetadataV2, + ArrayMetadataV3, + GroupMetadata, + GroupMetadataV2, + GroupMetadataV3, + NamedConfig, + NamedRequiredConfig, + ) + + _ = ( + JSON, + ArrayMetadata, + ArrayMetadataV2, + ArrayMetadataV3, + GroupMetadata, + GroupMetadataV2, + GroupMetadataV3, + NamedConfig, + NamedRequiredConfig, + ) + + +def test_v2_imports() -> None: + from zarr_metadata.v2 import ( + ArrayMetadataV2, + ConsolidatedMetadataV2, + DataTypeV2, + DataTypeV2Structured, + GroupMetadataV2, + ) + + _ = ( + ArrayMetadataV2, + ConsolidatedMetadataV2, + DataTypeV2, + DataTypeV2Structured, + GroupMetadataV2, + ) + + +def test_v3_imports() -> None: + from zarr_metadata.v3 import ( + AllowedExtraField, + ArrayMetadataV3, + ConsolidatedMetadataV3, + GroupMetadataV3, + RectilinearChunkGrid, + RectilinearChunkGridConfig, + RectilinearDimSpec, + RegularChunkGrid, + RegularChunkGridConfig, + ) + + _ = ( + AllowedExtraField, + ArrayMetadataV3, + ConsolidatedMetadataV3, + GroupMetadataV3, + RectilinearChunkGrid, + RectilinearChunkGridConfig, + RectilinearDimSpec, + RegularChunkGrid, + RegularChunkGridConfig, + ) + + +def test_codec_imports() -> None: + from zarr_metadata.codec import Codec + from zarr_metadata.codec.blosc import ( + BloscCodecConfiguration, + BloscCodecConfigurationNumcodecs, + BloscCodecConfigurationV1, + CName, + Shuffle, + ) + + _ = ( + Codec, + BloscCodecConfiguration, + BloscCodecConfigurationNumcodecs, + BloscCodecConfigurationV1, + CName, + Shuffle, + ) + + +def test_dtype_imports() -> None: + from zarr_metadata.dtype import DType + from zarr_metadata.dtype.bytes import FixedLengthBytesConfig + from zarr_metadata.dtype.string import LengthBytesConfig + from zarr_metadata.dtype.time import DateTimeUnit, TimeConfig + + _ = ( + DType, + FixedLengthBytesConfig, + LengthBytesConfig, + DateTimeUnit, + TimeConfig, + ) diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py new file mode 100644 index 0000000000..af7f3d591b --- /dev/null +++ b/packages/zarr-metadata/tests/test_structural.py @@ -0,0 +1,114 @@ +""" +Sample-dict construction tests for zarr-metadata TypedDicts. + +These don't validate at runtime (TypedDicts have no runtime shape check), +but they let pyright in CI catch shape mismatches. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from zarr_metadata.codec.blosc import BloscCodecConfigurationV1 + from zarr_metadata.dtype.bytes import FixedLengthBytesConfig + from zarr_metadata.dtype.string import LengthBytesConfig + from zarr_metadata.dtype.time import TimeConfig + from zarr_metadata.v2.array import ArrayMetadataV2 + from zarr_metadata.v2.group import GroupMetadataV2 + from zarr_metadata.v3.array import ArrayMetadataV3, RegularChunkGrid + from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 + from zarr_metadata.v3.group import GroupMetadataV3 + + +def test_array_metadata_v3_minimal() -> None: + meta: ArrayMetadataV3 = { + "zarr_format": 3, + "node_type": "array", + "data_type": "float32", + "shape": (100, 100), + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [10, 10]}}, + "chunk_key_encoding": {"name": "default"}, + "fill_value": 0, + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + } + assert meta["zarr_format"] == 3 + + +def test_group_metadata_v3_minimal() -> None: + meta: GroupMetadataV3 = { + "zarr_format": 3, + "node_type": "group", + } + assert meta["zarr_format"] == 3 + + +def test_consolidated_metadata_v3_minimal() -> None: + cm: ConsolidatedMetadataV3 = { + "kind": "inline", + "must_understand": False, + "metadata": {}, + } + assert cm["kind"] == "inline" + + +def test_array_metadata_v2_simple_dtype() -> None: + meta: ArrayMetadataV2 = { + "zarr_format": 2, + "shape": (100, 100), + "chunks": (10, 10), + "dtype": " None: + meta: ArrayMetadataV2 = { + "zarr_format": 2, + "shape": (100,), + "chunks": (10,), + "dtype": [ + {"fieldname": "a", "datatype": " None: + meta: GroupMetadataV2 = {"zarr_format": 2} + assert meta["zarr_format"] == 2 + + +def test_regular_chunk_grid_envelope() -> None: + grid: RegularChunkGrid = { + "name": "regular", + "configuration": {"chunk_shape": [10, 10]}, + } + assert grid["name"] == "regular" + + +def test_blosc_config_v1() -> None: + cfg: BloscCodecConfigurationV1 = { + "cname": "zstd", + "clevel": 5, + "shuffle": "shuffle", + "blocksize": 0, + "typesize": 4, + } + assert cfg["cname"] == "zstd" + + +def test_length_bytes_config() -> None: + cfg: LengthBytesConfig = {"length_bytes": 16} + assert cfg["length_bytes"] == 16 + + +def test_fixed_length_bytes_config() -> None: + cfg: FixedLengthBytesConfig = {"length_bytes": 16} + assert cfg["length_bytes"] == 16 + + +def test_time_config() -> None: + cfg: TimeConfig = {"unit": "ns", "scale_factor": 1} + assert cfg["unit"] == "ns" From bb0183c2cf19bcfdecb08733d136441f9eadc90c Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:06:12 +0200 Subject: [PATCH 16/55] refactor(common): re-export JSON, NamedConfig, NamedRequiredConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/core/common.py | 41 ++++------------------------------------- 1 file changed, 4 insertions(+), 37 deletions(-) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 2279820d7a..866be44b79 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -5,7 +5,7 @@ import math import operator import warnings -from collections.abc import Iterable, Mapping, Sequence +from collections.abc import Iterable, Sequence from enum import Enum from itertools import starmap from typing import ( @@ -13,14 +13,14 @@ Any, Final, Literal, - NotRequired, - TypedDict, cast, overload, ) import numpy as np -from typing_extensions import ReadOnly +from zarr_metadata import JSON as JSON # noqa: TC002 +from zarr_metadata import NamedConfig as NamedConfig # noqa: TC002 +from zarr_metadata import NamedRequiredConfig as NamedRequiredConfig from zarr.core.config import config as zarr_config from zarr.errors import ZarrRuntimeWarning @@ -42,7 +42,6 @@ ChunkCoords = tuple[int, ...] ZarrFormat = Literal[2, 3] NodeType = Literal["array", "group"] -JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None MemoryOrder = Literal["C", "F"] AccessModeLiteral = Literal["r", "r+", "a", "w", "w-"] ANY_ACCESS_MODE: Final = "r", "r+", "a", "w", "w-" @@ -50,38 +49,6 @@ DimensionNames = DimensionNamesLike # for backwards compatibility -class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): - """ - A typed dictionary representing an object with a name and configuration, where the configuration - is an optional mapping of string keys to values, e.g. another typed dictionary or a JSON object. - - This class is generic with two type parameters: the type of the name (``TName``) and the type of - the configuration (``TConfig``). - """ - - name: ReadOnly[TName] - """The name of the object.""" - - configuration: NotRequired[ReadOnly[TConfig]] - """The configuration of the object. Not required.""" - - -class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): - """ - A typed dictionary representing an object with a name and configuration, where the configuration - is a mapping of string keys to values, e.g. another typed dictionary or a JSON object. - - This class is generic with two type parameters: the type of the name (``TName``) and the type of - the configuration (``TConfig``). - """ - - name: ReadOnly[TName] - """The name of the object.""" - - configuration: ReadOnly[TConfig] - """The configuration of the object.""" - - def product(tup: tuple[int, ...]) -> int: return functools.reduce(operator.mul, tup, 1) From fc09be62fb0a0ebec82010c0dbb0d024d198a54b Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:07:44 +0200 Subject: [PATCH 17/55] refactor(metadata): re-export v3 types from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/core/metadata/v3.py | 68 ++++++------------------------------ 1 file changed, 11 insertions(+), 57 deletions(-) diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index a8f2b05518..bf0523d6c7 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -3,9 +3,17 @@ import json from collections.abc import Iterable, Mapping, Sequence from dataclasses import dataclass, field, replace -from typing import TYPE_CHECKING, Any, Final, Literal, NotRequired, TypeGuard, cast - -from typing_extensions import TypedDict +from typing import TYPE_CHECKING, Any, Final, Literal, TypeGuard, cast + +from zarr_metadata.v3.array import ( + AllowedExtraField as AllowedExtraField, + ArrayMetadataV3 as ArrayMetadataJSON_V3, + RectilinearChunkGrid as RectilinearChunkGridMetadataJSON, + RectilinearChunkGridConfig as RectilinearChunkGridMetadataConfig, # noqa: F401 + RectilinearDimSpec as RectilinearDimSpecJSON, + RegularChunkGrid as RegularChunkGridMetadataJSON, + RegularChunkGridConfig as RegularChunkGridMetadataConfig, # noqa: F401 +) from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec from zarr.abc.metadata import Metadata @@ -22,7 +30,6 @@ ChunksLike, DimensionNamesLike, NamedConfig, - NamedRequiredConfig, compress_rle, expand_rle, parse_named_configuration, @@ -138,16 +145,6 @@ def parse_storage_transformers(data: object) -> tuple[dict[str, JSON], ...]: ) -class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] - """ - This class models allowed extra fields in array metadata. - They must have ``must_understand`` set to ``False``, and may contain - arbitrary additional JSON data. - """ - - must_understand: Literal[False] - - def check_allowed_extra_field(data: object) -> TypeGuard[AllowedExtraField]: """ Check if the extra field is allowed according to the Zarr v3 spec. The object @@ -175,28 +172,6 @@ def parse_extra_fields( return dict(data) -# JSON type for a single dimension's rectilinear spec: -# bare int (uniform shorthand), or list of ints / [value, count] RLE pairs. -RectilinearDimSpecJSON = int | list[int | list[int]] - - -class RegularChunkGridMetadataConfig(TypedDict): - chunk_shape: Sequence[int] - - -class RectilinearChunkGridMetadataConfig(TypedDict): - kind: Literal["inline"] - chunk_shapes: Sequence[RectilinearDimSpecJSON] - - -RegularChunkGridMetadataJSON = NamedRequiredConfig[ - Literal["regular"], RegularChunkGridMetadataConfig -] -RectilinearChunkGridMetadataJSON = NamedRequiredConfig[ - Literal["rectilinear"], RectilinearChunkGridMetadataConfig -] - - def _parse_chunk_shape(chunk_shape: Iterable[int]) -> tuple[int, ...]: """Validate and normalize a regular chunk shape. @@ -414,27 +389,6 @@ def parse_chunk_grid( raise ValueError(f"Unknown chunk grid name: {name!r}") -class ArrayMetadataJSON_V3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] - """ - A typed dictionary model for zarr v3 array metadata. - - Extra keys are permitted if they conform to ``AllowedExtraField`` - (i.e. they are mappings with ``must_understand: false``). - """ - - zarr_format: Literal[3] - node_type: Literal["array"] - data_type: str | NamedConfig[str, Mapping[str, JSON]] - shape: tuple[int, ...] - chunk_grid: str | NamedConfig[str, Mapping[str, JSON]] - chunk_key_encoding: str | NamedConfig[str, Mapping[str, JSON]] - fill_value: JSON - codecs: tuple[str | NamedConfig[str, Mapping[str, JSON]], ...] - attributes: NotRequired[Mapping[str, JSON]] - storage_transformers: NotRequired[tuple[str | NamedConfig[str, Mapping[str, JSON]], ...]] - dimension_names: NotRequired[tuple[str | None, ...]] - - """ The names of the fields of the array metadata document defined in the zarr V3 spec. """ From 33bfc99327fc8779500eac89295ff0aa8bc6efa7 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:08:19 +0200 Subject: [PATCH 18/55] refactor(metadata): re-export faithful v2 array metadata type Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/core/metadata/v2.py | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 8626d480a7..50dd7a023c 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -3,7 +3,9 @@ import warnings from collections.abc import Iterable, Sequence from functools import cached_property -from typing import TYPE_CHECKING, Any, TypedDict, cast +from typing import TYPE_CHECKING, Any, cast + +from zarr_metadata.v2.array import ArrayMetadataV2 as ArrayV2MetadataDict # noqa: TC002 from zarr.abc.metadata import Metadata from zarr.abc.numcodec import Numcodec, _is_numcodec @@ -43,15 +45,6 @@ from zarr.core.metadata.common import parse_attributes -class ArrayV2MetadataDict(TypedDict): - """ - A typed dictionary model for Zarr format 2 metadata. - """ - - zarr_format: Literal[2] - attributes: dict[str, JSON] - - # Union of acceptable types for v2 compressors type CompressorLikev2 = dict[str, JSON] | Numcodec | None From 1098718bdb1b080d60c05f4531c0be392410096b Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:08:53 +0200 Subject: [PATCH 19/55] refactor(codecs): re-export blosc codec configurations from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/codecs/blosc.py | 26 +++++--------------------- 1 file changed, 5 insertions(+), 21 deletions(-) diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 62ceff7659..82482abab2 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -4,9 +4,13 @@ from dataclasses import dataclass, field, replace from enum import Enum from functools import cached_property -from typing import TYPE_CHECKING, Final, Literal, NotRequired, TypedDict +from typing import TYPE_CHECKING, Final, Literal import numcodecs +from zarr_metadata.codec.blosc import ( + BloscCodecConfigurationNumcodecs as BloscConfigV2, + BloscCodecConfigurationV1 as BloscConfigV3, +) from numcodecs.blosc import Blosc from packaging.version import Version @@ -30,26 +34,6 @@ """The codec identifiers used in the blosc codec """ -class BloscConfigV2(TypedDict): - """Configuration for the V2 Blosc codec""" - - cname: CName - clevel: int - shuffle: int - blocksize: int - typesize: NotRequired[int] - - -class BloscConfigV3(TypedDict): - """Configuration for the V3 Blosc codec""" - - cname: CName - clevel: int - shuffle: Shuffle - blocksize: int - typesize: int - - class BloscJSON_V3(NamedRequiredConfig[Literal["blosc"], BloscConfigV3]): """ The JSON form of the Blosc codec in Zarr V3. From b437812093a69fa6bafb7777d08f8430fc3297d3 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:09:12 +0200 Subject: [PATCH 20/55] refactor(abc): re-export CodecJSON from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/abc/codec.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index eed2119aff..dc6b1a4a4c 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -10,6 +10,7 @@ from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import NamedConfig, concurrent_map from zarr.core.config import config +from zarr_metadata.codec import Codec as CodecJSON # noqa: TC002 if TYPE_CHECKING: from collections.abc import Awaitable, Callable, Iterable @@ -60,11 +61,6 @@ def _check_codecjson_v2(data: object) -> TypeGuard[CodecJSON_V2[str]]: CodecJSON_V3 = str | NamedConfig[str, Mapping[str, object]] """The JSON representation of a codec for Zarr V3.""" -# The widest type we will *accept* for a codec JSON -# This covers v2 and v3 -CodecJSON = str | Mapping[str, object] -"""The widest type of JSON-like input that could specify a codec.""" - @runtime_checkable class SupportsSyncCodec[CI: CodecInput, CO: CodecOutput](Protocol): From 2578ad8e2e3c45e8894c703cef46472db0841f0b Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:10:16 +0200 Subject: [PATCH 21/55] refactor(dtype): re-export DTypeJSON from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/core/dtype/common.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index 87e46b53d2..b07c1f0f13 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -15,6 +15,7 @@ from zarr.core.common import NamedConfig from zarr.errors import UnstableSpecificationWarning +from zarr_metadata.dtype import DType as DTypeJSON # noqa: TC002 EndiannessStr = Literal["little", "big"] ENDIANNESS_STR: Final = "little", "big" @@ -29,10 +30,6 @@ # These are the ids of the known object codecs for zarr v2. OBJECT_CODEC_IDS: Final = ("vlen-utf8", "vlen-bytes", "vlen-array", "pickle", "json2", "msgpack2") -# This is a wider type than our standard JSON type because we need -# to work with typeddict objects which are assignable to Mapping[str, object] -DTypeJSON = str | int | float | Sequence["DTypeJSON"] | None | Mapping[str, object] - # The DTypeJSON_V2 type exists because ZDType.from_json takes a single argument, which must contain # all the information necessary to decode the data type. Zarr v2 supports multiple distinct # data types that all used the "|O" data type identifier. These data types can only be From 51a1df3202b87a1bae4b7ac7938e1d0083980991 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:10:46 +0200 Subject: [PATCH 22/55] refactor(dtype): re-export LengthBytesConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/core/dtype/npy/string.py | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index 069d0b128d..a74f258b43 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -8,7 +8,6 @@ Literal, Protocol, Self, - TypedDict, TypeGuard, overload, runtime_checkable, @@ -34,6 +33,7 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import ZDType +from zarr_metadata.dtype.string import LengthBytesConfig as LengthBytesConfig # noqa: TC002 if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat @@ -47,19 +47,6 @@ class SupportsStr(Protocol): def __str__(self) -> str: ... -class LengthBytesConfig(TypedDict): - """ - Configuration for a fixed-length string data type in Zarr V3. - - Attributes - ---------- - length_bytes : int - The length in bytes of the data associated with this configuration. - """ - - length_bytes: int - - class FixedLengthUTF32JSON_V2(DTypeConfig_V2[str, None]): """ A wrapper around the JSON representation of the ``FixedLengthUTF32`` data type in Zarr V2. From d06fad47a73e07e428c41ef1f20a51ec43cd3c86 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:11:12 +0200 Subject: [PATCH 23/55] refactor(dtype): re-export FixedLengthBytesConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/core/dtype/npy/bytes.py | 25 ++----------------------- 1 file changed, 2 insertions(+), 23 deletions(-) diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index 2cf5985d69..648c2ef5c6 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -3,7 +3,7 @@ import base64 import re from dataclasses import dataclass -from typing import ClassVar, Literal, Self, TypedDict, TypeGuard, cast, overload +from typing import ClassVar, Literal, Self, TypeGuard, cast, overload import numpy as np @@ -20,32 +20,11 @@ ) from zarr.core.dtype.npy.common import check_json_str from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr_metadata.dtype.bytes import FixedLengthBytesConfig as FixedLengthBytesConfig # noqa: TC002 BytesLike = np.bytes_ | str | bytes | int -class FixedLengthBytesConfig(TypedDict): - """ - A configuration for a data type that takes a ``length_bytes`` parameter. - - Attributes - ---------- - - length_bytes : int - The length in bytes of the data associated with this configuration. - - Examples - -------- - ```python - { - "length_bytes": 12 - } - ``` - """ - - length_bytes: int - - class NullterminatedBytesJSON_V2(DTypeConfig_V2[str, None]): """ A wrapper around the JSON representation of the ``NullTerminatedBytes`` data type in Zarr V2. From a2c2960f3b8c62f2a7c20404a70ba4adbbd54282 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:11:58 +0200 Subject: [PATCH 24/55] refactor(dtype): re-export TimeConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) --- src/zarr/core/dtype/npy/time.py | 25 +------------------------ 1 file changed, 1 insertion(+), 24 deletions(-) diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index c4495e167c..52e2df70ed 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -7,7 +7,6 @@ ClassVar, Literal, Self, - TypedDict, TypeGuard, cast, get_args, @@ -15,7 +14,6 @@ ) import numpy as np -from typing_extensions import ReadOnly from zarr.core.common import NamedConfig from zarr.core.dtype.common import ( @@ -34,6 +32,7 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr_metadata.dtype.time import TimeConfig as TimeConfig # noqa: TC002 if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat @@ -89,28 +88,6 @@ def check_json_time(data: JSON) -> TypeGuard[Literal["NaT"] | int]: return check_json_int(data) or data == "NaT" -class TimeConfig(TypedDict): - """ - The configuration for the numpy.timedelta64 or numpy.datetime64 data type in Zarr V3. - - Attributes - ---------- - unit : ReadOnly[DateTimeUnit] - A string encoding a unit of time. - scale_factor : ReadOnly[int] - A scale factor. - - Examples - -------- - ```python - {"unit": "ms", "scale_factor": 1} - ``` - """ - - unit: ReadOnly[DateTimeUnit] - scale_factor: ReadOnly[int] - - class DateTime64JSON_V3(NamedConfig[Literal["numpy.datetime64"], TimeConfig]): """ The JSON representation of the ``numpy.datetime64`` data type in Zarr V3. From d42a508bbb462a1ff14ba5d4f4758e8860ad2c38 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 15:20:02 +0200 Subject: [PATCH 25/55] refactor(metadata): use tuple[int, ...] for fixed-length fields + typed NumcodecsConfig Spec-defined metadata fields with fixed length and no mutation semantics are typed as tuples, not Sequence. Applies to: - v2 ArrayMetadataV2.shape, .chunks - v2 DataTypeV2Structured.shape - v2 ArrayMetadataV2.filters (tuple of codec configs) - v3 RegularChunkGridConfig.chunk_shape - v3 RectilinearChunkGridConfig.chunk_shapes Adds zarr_metadata.v2.codec.NumcodecsConfig, a TypedDict modeling the v2 spec shape for compressors and filters: a required 'id' field plus arbitrary codec-specific extras. ArrayMetadataV2.compressor and .filters now reference this type instead of an untyped Mapping[str, JSON]. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v2/__init__.py | 2 ++ .../src/zarr_metadata/v2/array.py | 13 +++++----- .../src/zarr_metadata/v2/codec.py | 26 +++++++++++++++++++ .../src/zarr_metadata/v3/array.py | 6 ++--- .../zarr-metadata/tests/test_structural.py | 26 +++++++++++++++++-- 5 files changed, 62 insertions(+), 11 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/codec.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py index 11dd8521d0..ea5d08af7b 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py @@ -1,6 +1,7 @@ """Zarr v2 metadata types.""" from zarr_metadata.v2.array import ArrayMetadataV2, DataTypeV2, DataTypeV2Structured +from zarr_metadata.v2.codec import NumcodecsConfig from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 from zarr_metadata.v2.group import GroupMetadataV2 @@ -10,4 +11,5 @@ "DataTypeV2", "DataTypeV2Structured", "GroupMetadataV2", + "NumcodecsConfig", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 98fc6b5323..af7d0511a5 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -5,9 +5,10 @@ from typing import TYPE_CHECKING, Literal, NotRequired, TypedDict if TYPE_CHECKING: - from collections.abc import Mapping, Sequence + from collections.abc import Mapping from zarr_metadata import JSON + from zarr_metadata.v2.codec import NumcodecsConfig class DataTypeV2Structured(TypedDict): @@ -20,7 +21,7 @@ class DataTypeV2Structured(TypedDict): fieldname: str datatype: str - shape: NotRequired[Sequence[int]] + shape: NotRequired[tuple[int, ...]] DataTypeV2 = str | list[DataTypeV2Structured] @@ -44,13 +45,13 @@ class ArrayMetadataV2(TypedDict): """ zarr_format: Literal[2] - shape: Sequence[int] - chunks: Sequence[int] + shape: tuple[int, ...] + chunks: tuple[int, ...] dtype: DataTypeV2 - compressor: NotRequired[Mapping[str, JSON] | None] + compressor: NotRequired[NumcodecsConfig | None] fill_value: NotRequired[JSON] order: NotRequired[Literal["C", "F"]] - filters: NotRequired[Sequence[Mapping[str, JSON]] | None] + filters: NotRequired[tuple[NumcodecsConfig, ...] | None] dimension_separator: NotRequired[Literal[".", "/"]] attributes: NotRequired[Mapping[str, JSON]] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/codec.py b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py new file mode 100644 index 0000000000..f2923a8faa --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py @@ -0,0 +1,26 @@ +""" +Zarr v2 codec configuration shape. + +V2 compressors and filters are numcodecs configuration dicts: a required +``id`` field naming the codec, plus arbitrary codec-specific extra fields. +""" + +from typing_extensions import ReadOnly, TypedDict + +from zarr_metadata import JSON + + +class NumcodecsConfig(TypedDict, extra_items=JSON): # type: ignore[call-arg] + """ + A numcodecs configuration dict, used as a v2 compressor or filter. + + The required ``id`` field names the codec; codec-specific parameters + (e.g. ``cname``, ``clevel`` for blosc) appear as extra fields. + """ + + id: ReadOnly[str] + + +__all__ = [ + "NumcodecsConfig", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index 70d361d1fd..aef1aad281 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -1,6 +1,6 @@ """Zarr v3 array metadata types.""" -from collections.abc import Mapping, Sequence +from collections.abc import Mapping from typing import Literal, NotRequired from typing_extensions import TypedDict @@ -29,7 +29,7 @@ class RegularChunkGridConfig(TypedDict): Configuration body of a regular chunk grid. """ - chunk_shape: Sequence[int] + chunk_shape: tuple[int, ...] class RectilinearChunkGridConfig(TypedDict): @@ -38,7 +38,7 @@ class RectilinearChunkGridConfig(TypedDict): """ kind: Literal["inline"] - chunk_shapes: Sequence[RectilinearDimSpec] + chunk_shapes: tuple[RectilinearDimSpec, ...] RegularChunkGrid = NamedRequiredConfig[Literal["regular"], RegularChunkGridConfig] diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index af7f3d591b..c2bbbf746f 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -15,6 +15,7 @@ from zarr_metadata.dtype.string import LengthBytesConfig from zarr_metadata.dtype.time import TimeConfig from zarr_metadata.v2.array import ArrayMetadataV2 + from zarr_metadata.v2.codec import NumcodecsConfig from zarr_metadata.v2.group import GroupMetadataV2 from zarr_metadata.v3.array import ArrayMetadataV3, RegularChunkGrid from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 @@ -69,7 +70,7 @@ def test_array_metadata_v2_structured_dtype() -> None: "chunks": (10,), "dtype": [ {"fieldname": "a", "datatype": " None: def test_regular_chunk_grid_envelope() -> None: grid: RegularChunkGrid = { "name": "regular", - "configuration": {"chunk_shape": [10, 10]}, + "configuration": {"chunk_shape": (10, 10)}, } assert grid["name"] == "regular" @@ -112,3 +113,24 @@ def test_fixed_length_bytes_config() -> None: def test_time_config() -> None: cfg: TimeConfig = {"unit": "ns", "scale_factor": 1} assert cfg["unit"] == "ns" + + +def test_numcodecs_config_minimal() -> None: + cfg: NumcodecsConfig = {"id": "zstd"} + assert cfg["id"] == "zstd" + + +def test_array_metadata_v2_with_compressor_and_filters() -> None: + compressor: NumcodecsConfig = {"id": "zstd"} + filter0: NumcodecsConfig = {"id": "delta"} + meta: ArrayMetadataV2 = { + "zarr_format": 2, + "shape": (100,), + "chunks": (10,), + "dtype": " Date: Tue, 21 Apr 2026 15:30:13 +0200 Subject: [PATCH 26/55] refactor(metadata): fix explicit re-exports and complete DateTimeUnit migration MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Three fixes: 1. Add missing "μs" unit to zarr_metadata.dtype.time.DateTimeUnit so it matches zarr-python's DateTimeUnit. zarr.core.dtype.npy.common.DateTimeUnit now re-exports from zarr-metadata (downstream consumers like zarr.core.dtype.npy.time pick it up transitively). 2. Replace `from X import Y as LegacyName` with `from X import Y` followed by a module-level `LegacyName: TypeAlias = Y` binding. mypy under `strict = true` rejected the renamed-import form under the explicit- re-export check ("Module 'X' does not explicitly export attribute 'Y'"), affecting 13 call sites across the codebase. The TypeAlias form makes the alias a proper type (mypy uses it in annotations) while preserving runtime introspection (`.__annotations__` access on the aliased TypedDict). Affects: - src/zarr/core/dtype/common.py (DTypeJSON) - src/zarr/core/metadata/v2.py (ArrayV2MetadataDict) - src/zarr/core/metadata/v3.py (ArrayMetadataJSON_V3 + 5 others) 3. noqa: UP040 on the TypeAlias bindings. ruff prefers the `type` keyword (PEP 695), but that wraps the alias in a TypeAliasType which breaks `.__annotations__` lookup used by tests. The 12 remaining "unused type: ignore" mypy errors in v3.py are pre-existing (same count on the pre-refactor state) and unrelated to this work. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/dtype/time.py | 2 +- src/zarr/core/dtype/common.py | 6 +++- src/zarr/core/dtype/npy/common.py | 4 +-- src/zarr/core/metadata/v2.py | 8 +++-- src/zarr/core/metadata/v3.py | 36 +++++++++++++++---- 5 files changed, 42 insertions(+), 14 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/time.py b/packages/zarr-metadata/src/zarr_metadata/dtype/time.py index b4e6d1e7aa..b63e0f60ed 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/time.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/time.py @@ -7,7 +7,7 @@ from typing_extensions import ReadOnly DateTimeUnit = Literal[ - "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "ns", "ps", "fs", "as", "generic" + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" ] """Time unit codes used by numpy.datetime64 / numpy.timedelta64.""" diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index b07c1f0f13..dfe8e53880 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -12,10 +12,14 @@ ) from typing_extensions import ReadOnly +from zarr_metadata.dtype import DType from zarr.core.common import NamedConfig from zarr.errors import UnstableSpecificationWarning -from zarr_metadata.dtype import DType as DTypeJSON # noqa: TC002 + +# This is a wider type than our standard JSON type because we need +# to work with typeddict objects which are assignable to Mapping[str, object] +DTypeJSON = DType EndiannessStr = Literal["little", "big"] ENDIANNESS_STR: Final = "little", "big" diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index f413f5f678..e34d7851e3 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -18,6 +18,7 @@ ) import numpy as np +from zarr_metadata.dtype.time import DateTimeUnit as DateTimeUnit from zarr.core.dtype.common import ( ENDIANNESS_STR, @@ -33,9 +34,6 @@ IntLike = SupportsInt | SupportsIndex | bytes | str FloatLike = SupportsIndex | SupportsFloat | bytes | str ComplexLike = SupportsFloat | SupportsIndex | SupportsComplex | bytes | str | None -DateTimeUnit = Literal[ - "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" -] DATETIME_UNIT: Final = ( "Y", "M", diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 50dd7a023c..0c95696c24 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -3,9 +3,9 @@ import warnings from collections.abc import Iterable, Sequence from functools import cached_property -from typing import TYPE_CHECKING, Any, cast +from typing import TYPE_CHECKING, Any, TypeAlias, cast -from zarr_metadata.v2.array import ArrayMetadataV2 as ArrayV2MetadataDict # noqa: TC002 +from zarr_metadata.v2.array import ArrayMetadataV2 from zarr.abc.metadata import Metadata from zarr.abc.numcodec import Numcodec, _is_numcodec @@ -44,6 +44,10 @@ from zarr.core.config import config, parse_indexing_order from zarr.core.metadata.common import parse_attributes +# Legacy alias preserved for zarr.core internal call sites. +# Using explicit `TypeAlias` rather than the `type` keyword so that runtime +# introspection (e.g. `.__annotations__` on the underlying TypedDict) works. +ArrayV2MetadataDict: TypeAlias = ArrayMetadataV2 # noqa: UP040 # Union of acceptable types for v2 compressors type CompressorLikev2 = dict[str, JSON] | Numcodec | None diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index bf0523d6c7..651c072c27 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -3,16 +3,18 @@ import json from collections.abc import Iterable, Mapping, Sequence from dataclasses import dataclass, field, replace -from typing import TYPE_CHECKING, Any, Final, Literal, TypeGuard, cast +from typing import TYPE_CHECKING, Any, Final, Literal, TypeAlias, TypeGuard, cast from zarr_metadata.v3.array import ( AllowedExtraField as AllowedExtraField, - ArrayMetadataV3 as ArrayMetadataJSON_V3, - RectilinearChunkGrid as RectilinearChunkGridMetadataJSON, - RectilinearChunkGridConfig as RectilinearChunkGridMetadataConfig, # noqa: F401 - RectilinearDimSpec as RectilinearDimSpecJSON, - RegularChunkGrid as RegularChunkGridMetadataJSON, - RegularChunkGridConfig as RegularChunkGridMetadataConfig, # noqa: F401 +) +from zarr_metadata.v3.array import ( + ArrayMetadataV3, + RectilinearChunkGrid, + RectilinearChunkGridConfig, + RectilinearDimSpec, + RegularChunkGrid, + RegularChunkGridConfig, ) from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec @@ -44,6 +46,26 @@ from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError from zarr.registry import get_codec_class +# Legacy aliases preserved for zarr.core internal call sites. +# Using explicit `TypeAlias` rather than the `type` keyword so that runtime +# introspection (e.g. `.__annotations__` on the underlying TypedDict) works. +ArrayMetadataJSON_V3: TypeAlias = ArrayMetadataV3 # noqa: UP040 +RectilinearChunkGridMetadataJSON: TypeAlias = RectilinearChunkGrid # noqa: UP040 +RectilinearChunkGridMetadataConfig: TypeAlias = RectilinearChunkGridConfig # noqa: UP040 +RectilinearDimSpecJSON: TypeAlias = RectilinearDimSpec # noqa: UP040 +RegularChunkGridMetadataJSON: TypeAlias = RegularChunkGrid # noqa: UP040 +RegularChunkGridMetadataConfig: TypeAlias = RegularChunkGridConfig # noqa: UP040 + +__all__ = [ + "AllowedExtraField", + "ArrayMetadataJSON_V3", + "RectilinearChunkGridMetadataConfig", + "RectilinearChunkGridMetadataJSON", + "RectilinearDimSpecJSON", + "RegularChunkGridMetadataConfig", + "RegularChunkGridMetadataJSON", +] + if TYPE_CHECKING: from typing import Self From 99b25718cef47955d1b3bd1ae130bbfed5b6cdaf Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 18:05:17 +0200 Subject: [PATCH 27/55] refactor(metadata): extract primitives to common.py to break import cycle Moves JSON, NamedConfig, NamedRequiredConfig out of zarr_metadata/__init__.py into zarr_metadata/common.py. Submodules (v2/*, v3/*) now import from zarr_metadata.common directly, avoiding the circular import that occurred when v2.codec was loaded during __init__.py execution. Also: - v3.array declares RegularChunkGrid/RectilinearChunkGrid as direct TypedDict classes instead of NamedRequiredConfig aliases, simplifying the types and enabling more precise chunk-grid annotations downstream. - v2.consolidated.ConsolidatedMetadataV2.metadata value type widened to GroupMetadataV2 | ArrayMetadataV2 | JSON. - Added spec links to v2/{array,codec} docstrings. zarr_metadata/__init__.py continues to re-export JSON, NamedConfig, NamedRequiredConfig at the top level so zarr.core.common keeps resolving. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/__init__.py | 49 ++----------------- .../zarr-metadata/src/zarr_metadata/common.py | 37 ++++++++++++++ .../src/zarr_metadata/v2/array.py | 26 +++++----- .../src/zarr_metadata/v2/codec.py | 6 ++- .../src/zarr_metadata/v2/consolidated.py | 8 ++- .../src/zarr_metadata/v3/array.py | 36 ++++++++------ .../src/zarr_metadata/v3/group.py | 2 +- 7 files changed, 87 insertions(+), 77 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/common.py diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 6118ab3b0d..a7d39bec1a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -1,47 +1,8 @@ -""" -Top-level cross-version primitives for Zarr metadata. - -Version-specific types live under ``zarr_metadata.v2`` and ``zarr_metadata.v3``. -Codec and dtype spec types live under ``zarr_metadata.codec`` and -``zarr_metadata.dtype``. -""" - -from collections.abc import Mapping, Sequence -from typing import NotRequired, TypedDict - -from typing_extensions import ReadOnly - -JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None -"""Any valid JSON value.""" - - -class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): - """ - Named-config envelope with optional configuration. - - Generic with two parameters: name literal and configuration mapping. - """ - - name: ReadOnly[TName] - configuration: NotRequired[ReadOnly[TConfig]] - - -class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): - """ - Named-config envelope with required configuration. - - Generic with two parameters: name literal and configuration mapping. - """ - - name: ReadOnly[TName] - configuration: ReadOnly[TConfig] - - -# Version-polymorphic unions -- imported after primitives to avoid circular import. -from zarr_metadata.v2.array import ArrayMetadataV2 # noqa: E402 -from zarr_metadata.v2.group import GroupMetadataV2 # noqa: E402 -from zarr_metadata.v3.array import ArrayMetadataV3 # noqa: E402 -from zarr_metadata.v3.group import GroupMetadataV3 # noqa: E402 +from zarr_metadata.common import JSON, NamedConfig, NamedRequiredConfig +from zarr_metadata.v2.array import ArrayMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2 +from zarr_metadata.v3.array import ArrayMetadataV3 +from zarr_metadata.v3.group import GroupMetadataV3 ArrayMetadata = ArrayMetadataV2 | ArrayMetadataV3 """Any Zarr array metadata document (v2 or v3).""" diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py new file mode 100644 index 0000000000..2d8c3f9a4c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -0,0 +1,37 @@ +""" +Top-level cross-version primitives for Zarr metadata. + +Version-specific types live under ``zarr_metadata.v2`` and ``zarr_metadata.v3``. +Codec and dtype spec types live under ``zarr_metadata.codec`` and +``zarr_metadata.dtype``. +""" + +from collections.abc import Mapping, Sequence +from typing import NotRequired, TypedDict + +from typing_extensions import ReadOnly + +JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None +"""Any valid JSON value.""" + + +class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + Named-config envelope with optional configuration. + + Generic with two parameters: name literal and configuration mapping. + """ + + name: ReadOnly[TName] + configuration: NotRequired[ReadOnly[TConfig]] + + +class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + Named-config envelope with required configuration. + + Generic with two parameters: name literal and configuration mapping. + """ + + name: ReadOnly[TName] + configuration: ReadOnly[TConfig] \ No newline at end of file diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index af7d0511a5..6320be048a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -7,7 +7,7 @@ if TYPE_CHECKING: from collections.abc import Mapping - from zarr_metadata import JSON + from zarr_metadata.common import JSON from zarr_metadata.v2.codec import NumcodecsConfig @@ -15,8 +15,10 @@ class DataTypeV2Structured(TypedDict): """ A single field entry inside a structured v2 dtype. - Spec-faithful: ``datatype`` is a numpy-style dtype string; ``shape`` is + Spec-faithful: `datatype` is a numpy-style dtype string; `shape` is present only when the field is a subarray field. + + See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html#data-type-encoding """ fieldname: str @@ -24,7 +26,7 @@ class DataTypeV2Structured(TypedDict): shape: NotRequired[tuple[int, ...]] -DataTypeV2 = str | list[DataTypeV2Structured] +DataTypeV2 = str | tuple[DataTypeV2Structured, ...] """The v2 dtype representation. Simple dtypes are numpy-style strings (e.g. ``" Date: Tue, 21 Apr 2026 21:30:56 +0200 Subject: [PATCH 28/55] fix(metadata): address review findings MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Three issues surfaced by final code review: 1. Add py.typed marker to zarr-metadata. Without it, PEP 561 makes type checkers treat zarr-metadata as untyped, cascading into ~44 spurious mypy errors in zarr (subclassing Any, unused type: ignore, etc). 2. RegularChunkGrid.configuration was accidentally typed NotRequired when converted from NamedRequiredConfig to a direct TypedDict class. Per spec, chunk_shape is mandatory. Make configuration required. 3. RectilinearDimSpec was declared as tuples but zarr's compress_rle returned lists, and the to_dict producer built lists. Align producers with the declared type: compress_rle now returns list[int | tuple[int, int]], expand_rle accepts both list and tuple RLE pairs, to_dict builds tuples. The tuple shape is correct per spec: each RLE pair is a JSON array of exactly two elements (size, count) — a fixed-cardinality structure that tuple models more faithfully than a mutable list. Mypy error count now matches main (32) with these fixes in place. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../zarr-metadata/src/zarr_metadata/py.typed | 0 .../src/zarr_metadata/v3/array.py | 8 ++++++- src/zarr/core/common.py | 23 ++++++++++++------- src/zarr/core/metadata/v3.py | 6 ++--- 4 files changed, 25 insertions(+), 12 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/py.typed diff --git a/packages/zarr-metadata/src/zarr_metadata/py.typed b/packages/zarr-metadata/src/zarr_metadata/py.typed new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index 4a7e5a73c9..cf3ecaf6ee 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -25,12 +25,15 @@ class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] MetadataField = str | NamedConfig[str, Mapping[str, JSON]] """A string or a {name: str, configuration: {...}} key value pair""" + + class RegularChunkGridConfig(TypedDict): """ Configuration body of a regular chunk grid. See #SPEC_URL """ + chunk_shape: tuple[int, ...] @@ -40,18 +43,21 @@ class RectilinearChunkGridConfig(TypedDict): See #SPEC_URL """ + kind: Literal["inline"] chunk_shapes: tuple[RectilinearDimSpec, ...] class RegularChunkGrid(TypedDict): """Regular chunk grid named-config envelope.""" + name: Literal["regular"] - configuration: NotRequired[RegularChunkGridConfig] + configuration: RegularChunkGridConfig class RectilinearChunkGrid(TypedDict): """Rectilinear chunk grid named-config envelope.""" + name: Literal["rectilinear"] configuration: RectilinearChunkGridConfig diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 866be44b79..281a882bc4 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -211,12 +211,16 @@ def _default_zarr_format() -> ZarrFormat: return cast("ZarrFormat", int(zarr_config.get("default_zarr_format", 3))) -def expand_rle(data: Sequence[int | list[int]]) -> list[int]: +def expand_rle(data: Sequence[int | Sequence[int]]) -> list[int]: """Expand a mixed array of bare integers and RLE pairs. Per the rectilinear chunk grid spec, each element can be: - a bare integer (an explicit edge length) - a two-element array ``[value, count]`` (run-length encoded) + + Accepts both list and tuple forms of the RLE pair so the same routine + can decode JSON-parsed input (lists) and internally-constructed input + (tuples). """ result: list[int] = [] for item in data: @@ -225,7 +229,7 @@ def expand_rle(data: Sequence[int | list[int]]) -> list[int]: if val < 1: raise ValueError(f"Chunk edge length must be >= 1, got {val}") result.append(val) - elif isinstance(item, list) and len(item) == 2: + elif isinstance(item, (list, tuple)) and len(item) == 2: size, count = int(item[0]), int(item[1]) if size < 1: raise ValueError(f"Chunk edge length must be >= 1, got {size}") @@ -237,27 +241,30 @@ def expand_rle(data: Sequence[int | list[int]]) -> list[int]: return result -def compress_rle(sizes: Sequence[int]) -> list[int | list[int]]: +def compress_rle(sizes: Sequence[int]) -> list[int | tuple[int, int]]: """Compress chunk sizes to mixed RLE format per the rectilinear spec. - Runs of length > 1 are emitted as ``[value, count]`` pairs; runs of + Runs of length > 1 are emitted as ``(value, count)`` 2-tuples; runs of length 1 are emitted as bare integers:: - [10, 10, 10, 5] -> [[10, 3], 5] + [10, 10, 10, 5] -> [(10, 3), 5] + + The 2-tuple shape mirrors the spec's "exactly two elements" constraint + on RLE pairs. """ if not sizes: return [] - result: list[int | list[int]] = [] + result: list[int | tuple[int, int]] = [] current = sizes[0] count = 1 for s in sizes[1:]: if s == current: count += 1 else: - result.append([current, count] if count > 1 else current) + result.append((current, count) if count > 1 else current) current = s count = 1 - result.append([current, count] if count > 1 else current) + result.append((current, count) if count > 1 else current) return result diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 651c072c27..2706f6c1b6 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -309,9 +309,9 @@ def to_dict(self) -> RectilinearChunkGridMetadataJSON: # type: ignore[override] rle = compress_rle(dim_spec) # Use RLE only if it's actually shorter if len(rle) < len(dim_spec): - serialized_dims.append(rle) + serialized_dims.append(tuple(rle)) else: - serialized_dims.append(list(dim_spec)) + serialized_dims.append(tuple(dim_spec)) return { "name": "rectilinear", "configuration": { @@ -356,7 +356,7 @@ def from_dict(cls, data: RectilinearChunkGridMetadataJSON) -> Self: # type: ign if dim_spec < 1: raise ValueError(f"Integer chunk edge length must be >= 1, got {dim_spec}") parsed.append(dim_spec) - elif isinstance(dim_spec, list): + elif isinstance(dim_spec, (list, tuple)): parsed.append(tuple(expand_rle(dim_spec))) else: raise TypeError( From 7571dbcd59282695633e016c47fa63a6e287de16 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 22:36:44 +0200 Subject: [PATCH 29/55] refactor(metadata): remove consolidated_metadata from GroupMetadataV3 consolidated_metadata is not in the core Zarr v3 spec as a field on group metadata. It has an (unmerged) extension spec and is implemented by zarr-python, but keeping it out of GroupMetadataV3 is the spec-faithful move. The extra_items=AllowedExtraField on GroupMetadataV3 already permits it to appear at runtime as an extension. ConsolidatedMetadataV3 remains available at zarr_metadata.v3.consolidated for consumers that want to type the extension shape. Also fix two stray lint issues (missing trailing newline in common.py, unused Mapping import in v2/array.py). Co-Authored-By: Claude Opus 4.7 (1M context) --- .../zarr-metadata/src/zarr_metadata/common.py | 2 +- .../src/zarr_metadata/v2/array.py | 4 +- .../src/zarr_metadata/v3/group.py | 2 - packages/zarr-metadata/uv.lock | 93 +++++++++++++++++++ 4 files changed, 95 insertions(+), 6 deletions(-) create mode 100644 packages/zarr-metadata/uv.lock diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py index 2d8c3f9a4c..db0e534726 100644 --- a/packages/zarr-metadata/src/zarr_metadata/common.py +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -34,4 +34,4 @@ class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): """ name: ReadOnly[TName] - configuration: ReadOnly[TConfig] \ No newline at end of file + configuration: ReadOnly[TConfig] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 6320be048a..aac9522039 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -5,8 +5,6 @@ from typing import TYPE_CHECKING, Literal, NotRequired, TypedDict if TYPE_CHECKING: - from collections.abc import Mapping - from zarr_metadata.common import JSON from zarr_metadata.v2.codec import NumcodecsConfig @@ -35,6 +33,7 @@ class DataTypeV2Structured(TypedDict): part of this type. """ + class ArrayMetadataV2(TypedDict): """ Zarr v2 array metadata document (the `.zarray` content). @@ -53,7 +52,6 @@ class ArrayMetadataV2(TypedDict): dimension_separator: NotRequired[Literal[".", "/"]] - __all__ = [ "ArrayMetadataV2", "DataTypeV2", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py index 9d8af1e548..92c02a2ff6 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -10,7 +10,6 @@ from collections.abc import Mapping from zarr_metadata.common import JSON - from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 from zarr_metadata.v3.array import AllowedExtraField @@ -25,7 +24,6 @@ class GroupMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore zarr_format: Literal[3] node_type: Literal["group"] attributes: NotRequired[Mapping[str, JSON]] - consolidated_metadata: NotRequired[ConsolidatedMetadataV3] 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Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit zarr-metadata is a library, not an application — its lockfile pins transitive dev versions that shouldn't be fixed in source. Untrack and gitignore. 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{ url = "https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548", size = 44614, upload-time = "2025-08-25T13:49:24.86Z" }, -] - -[[package]] -name = "zarr-metadata" -version = "0.1.0" -source = { editable = "." } -dependencies = [ - { name = "typing-extensions" }, -] - -[package.optional-dependencies] -test = [ - { name = "pytest" }, -] - -[package.metadata] -requires-dist = [ - { name = "pytest", marker = "extra == 'test'" }, - { name = "typing-extensions", specifier = ">=4.13" }, -] -provides-extras = ["test"] From 08c7643a448ffcf1232b85eb0ad7acaab278dc8c Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 22:49:02 +0200 Subject: [PATCH 31/55] feat(metadata): add v3 codec types for bytes, crc32c, gzip, zstd, transpose, sharding MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adds per-codec TypedDict configurations + name literals + full envelope types for every core v3 codec besides blosc (which is extended in the same style for consistency): - {Codec}CodecName : Literal[""] — the spec "name" value - {Codec}CodecConfiguration : TypedDict — the "configuration" body - {Codec}Codec : NamedRequiredConfig — the full envelope crc32c has no configuration fields, so Crc32cCodec uses NamedConfig (configuration optional) and no Configuration TypedDict is exported. The `V1` suffix is dropped from the Configuration types (except blosc, where V1 + Numcodecs disambiguate two concrete shapes). The other v3 codec specs aren't versioned at the codec level; there's only one shape per codec today, and an incompatible future change would land under a new codec name rather than a v2 of the same name. Also fixes pre-existing v2 test fixtures to include the now-required compressor/fill_value/order/filters fields on ArrayMetadataV2. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/codec/blosc.py | 10 ++ .../src/zarr_metadata/codec/bytes.py | 35 ++++++ .../src/zarr_metadata/codec/crc32c.py | 31 +++++ .../src/zarr_metadata/codec/gzip.py | 35 ++++++ .../src/zarr_metadata/codec/sharding.py | 46 +++++++ .../src/zarr_metadata/codec/transpose.py | 34 +++++ .../src/zarr_metadata/codec/zstd.py | 36 ++++++ .../src/zarr_metadata/v3/array.py | 12 +- .../zarr-metadata/tests/test_structural.py | 116 +++++++++++++++++- 9 files changed, 346 insertions(+), 9 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/bytes.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/gzip.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/sharding.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/transpose.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/codec/zstd.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py index a600507ef3..f42e2148b6 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py @@ -4,6 +4,11 @@ from typing import Literal, NotRequired, TypedDict +from zarr_metadata.common import NamedRequiredConfig + +BloscCodecName = Literal["blosc"] +"""The ``name`` field value of a ``blosc`` codec envelope.""" + Shuffle = Literal["noshuffle", "shuffle", "bitshuffle"] """Blosc shuffle mode names (v3 spec).""" @@ -43,11 +48,16 @@ class BloscCodecConfigurationV1(TypedDict): BloscCodecConfiguration = BloscCodecConfigurationV1 | BloscCodecConfigurationNumcodecs """Any supported blosc configuration shape.""" +BloscCodec = NamedRequiredConfig[BloscCodecName, BloscCodecConfiguration] +"""Full ``blosc`` codec named-config envelope.""" + __all__ = [ + "BloscCodec", "BloscCodecConfiguration", "BloscCodecConfigurationNumcodecs", "BloscCodecConfigurationV1", + "BloscCodecName", "CName", "Shuffle", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py new file mode 100644 index 0000000000..9f130f7f6c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py @@ -0,0 +1,35 @@ +""" +Bytes codec configuration. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/bytes/index.html +""" + +from typing import Literal, NotRequired, TypedDict + +from zarr_metadata.common import NamedRequiredConfig + +BytesCodecName = Literal["bytes"] +"""The ``name`` field value of a ``bytes`` codec envelope.""" + + +class BytesCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 ``bytes`` codec. + + The `endian` field is required for multi-byte data types and absent + for single-byte types. Consumers that always expect a value must + tolerate its absence. + """ + + endian: NotRequired[Literal["little", "big"]] + + +BytesCodec = NamedRequiredConfig[BytesCodecName, BytesCodecConfiguration] +"""Full ``bytes`` codec named-config envelope.""" + + +__all__ = [ + "BytesCodec", + "BytesCodecConfiguration", + "BytesCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py new file mode 100644 index 0000000000..e2e931ba32 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py @@ -0,0 +1,31 @@ +""" +CRC32C codec. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/crc32c/index.html + +The CRC32C codec has no configuration fields, so the envelope's +``configuration`` key is absent. +""" + +from collections.abc import Mapping +from typing import Literal + +from zarr_metadata.common import NamedConfig + +Crc32cCodecName = Literal["crc32c"] +"""The ``name`` field value of a ``crc32c`` codec envelope.""" + + +Crc32cCodec = NamedConfig[Crc32cCodecName, Mapping[str, object]] +"""``crc32c`` codec named-config envelope. + +Per spec, the CRC32C codec has no configuration fields, so the +``configuration`` key is optional and, if present, should be an empty +mapping. +""" + + +__all__ = [ + "Crc32cCodec", + "Crc32cCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py new file mode 100644 index 0000000000..5e4551ed93 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py @@ -0,0 +1,35 @@ +""" +Gzip codec configuration. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/gzip/index.html +""" + +from typing import Literal, NotRequired, TypedDict + +from zarr_metadata.common import NamedRequiredConfig + +GzipCodecName = Literal["gzip"] +"""The ``name`` field value of a ``gzip`` codec envelope.""" + + +class GzipCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 ``gzip`` codec. + + `level` is an integer in the range 0-9; 0 disables compression and 9 + is slowest with the best compression ratio. The spec does not mandate + a default. + """ + + level: NotRequired[int] + + +GzipCodec = NamedRequiredConfig[GzipCodecName, GzipCodecConfiguration] +"""Full ``gzip`` codec named-config envelope.""" + + +__all__ = [ + "GzipCodec", + "GzipCodecConfiguration", + "GzipCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py new file mode 100644 index 0000000000..15b27b31c1 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py @@ -0,0 +1,46 @@ +""" +Sharding codec configuration. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/sharding-indexed/index.html +""" + +from typing import Literal, NotRequired, TypedDict + +from zarr_metadata.codec import Codec +from zarr_metadata.common import NamedRequiredConfig + +ShardingCodecName = Literal["sharding_indexed"] +"""The ``name`` field value of a ``sharding_indexed`` codec envelope.""" + + +class ShardingCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 ``sharding_indexed`` codec. + + `chunk_shape` is the shape of inner chunks along each dimension; + it must evenly divide the shard shape. + + `codecs` is the codec pipeline applied to each inner chunk; exactly + one array-to-bytes codec is required. + + `index_codecs` is the codec pipeline applied to the shard index; + it must be deterministic (no variable-size compression). + + `index_location` defaults to ``"end"`` per the spec. + """ + + chunk_shape: tuple[int, ...] + codecs: tuple[Codec, ...] + index_codecs: tuple[Codec, ...] + index_location: NotRequired[Literal["start", "end"]] + + +ShardingCodec = NamedRequiredConfig[ShardingCodecName, ShardingCodecConfiguration] +"""Full ``sharding_indexed`` codec named-config envelope.""" + + +__all__ = [ + "ShardingCodec", + "ShardingCodecConfiguration", + "ShardingCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py new file mode 100644 index 0000000000..d295ab3f7c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py @@ -0,0 +1,34 @@ +""" +Transpose codec configuration. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/transpose/index.html +""" + +from typing import Literal, TypedDict + +from zarr_metadata.common import NamedRequiredConfig + +TransposeCodecName = Literal["transpose"] +"""The ``name`` field value of a ``transpose`` codec envelope.""" + + +class TransposeCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 ``transpose`` codec. + + `order` is a permutation of the dimension indices 0..n-1 that + specifies the dimension reordering applied during encoding. + """ + + order: tuple[int, ...] + + +TransposeCodec = NamedRequiredConfig[TransposeCodecName, TransposeCodecConfiguration] +"""Full ``transpose`` codec named-config envelope.""" + + +__all__ = [ + "TransposeCodec", + "TransposeCodecConfiguration", + "TransposeCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py new file mode 100644 index 0000000000..f20331abd7 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py @@ -0,0 +1,36 @@ +""" +Zstandard codec configuration. + +See https://github.com/zarr-developers/zarr-specs/pull/256 (unmerged at +time of writing; the configuration shape below reflects the proposed +specification). +""" + +from typing import Literal, TypedDict + +from zarr_metadata.common import NamedRequiredConfig + +ZstdCodecName = Literal["zstd"] +"""The ``name`` field value of a ``zstd`` codec envelope.""" + + +class ZstdCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 ``zstd`` codec. + + Both fields are required per the proposed specification. + """ + + level: int + checksum: bool + + +ZstdCodec = NamedRequiredConfig[ZstdCodecName, ZstdCodecConfiguration] +"""Full ``zstd`` codec named-config envelope.""" + + +__all__ = [ + "ZstdCodec", + "ZstdCodecConfiguration", + "ZstdCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index cf3ecaf6ee..2a9b4971e3 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -31,7 +31,7 @@ class RegularChunkGridConfig(TypedDict): """ Configuration body of a regular chunk grid. - See #SPEC_URL + See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#regular-grids """ chunk_shape: tuple[int, ...] @@ -41,7 +41,7 @@ class RectilinearChunkGridConfig(TypedDict): """ Configuration body of a rectilinear chunk grid. - See #SPEC_URL + See https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear """ kind: Literal["inline"] @@ -49,14 +49,14 @@ class RectilinearChunkGridConfig(TypedDict): class RegularChunkGrid(TypedDict): - """Regular chunk grid named-config envelope.""" + """Regular chunk grid named-config container.""" name: Literal["regular"] configuration: RegularChunkGridConfig class RectilinearChunkGrid(TypedDict): - """Rectilinear chunk grid named-config envelope.""" + """Rectilinear chunk grid named-config container.""" name: Literal["rectilinear"] configuration: RectilinearChunkGridConfig @@ -66,7 +66,9 @@ class ArrayMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore """ Zarr v3 array metadata document (the ``zarr.json`` content for an array). - Extra keys are permitted if they conform to ``AllowedExtraField``. + Extra keys are permitted if they conform to `AllowedExtraField`. + + See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#array-metadata """ zarr_format: Literal[3] diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index c2bbbf746f..0a40c839ca 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -10,7 +10,13 @@ from typing import TYPE_CHECKING if TYPE_CHECKING: - from zarr_metadata.codec.blosc import BloscCodecConfigurationV1 + from zarr_metadata.codec.blosc import BloscCodec, BloscCodecConfigurationV1 + from zarr_metadata.codec.bytes import BytesCodec, BytesCodecConfiguration + from zarr_metadata.codec.crc32c import Crc32cCodec + from zarr_metadata.codec.gzip import GzipCodec, GzipCodecConfiguration + from zarr_metadata.codec.sharding import ShardingCodec, ShardingCodecConfiguration + from zarr_metadata.codec.transpose import TransposeCodec, TransposeCodecConfiguration + from zarr_metadata.codec.zstd import ZstdCodec, ZstdCodecConfiguration from zarr_metadata.dtype.bytes import FixedLengthBytesConfig from zarr_metadata.dtype.string import LengthBytesConfig from zarr_metadata.dtype.time import TimeConfig @@ -59,6 +65,10 @@ def test_array_metadata_v2_simple_dtype() -> None: "shape": (100, 100), "chunks": (10, 10), "dtype": " None: "zarr_format": 2, "shape": (100,), "chunks": (10,), - "dtype": [ + "dtype": ( {"fieldname": "a", "datatype": " None: @@ -129,8 +143,102 @@ def test_array_metadata_v2_with_compressor_and_filters() -> None: "chunks": (10,), "dtype": " None: + cfg: BytesCodecConfiguration = {"endian": "little"} + assert cfg["endian"] == "little" + + +def test_bytes_codec_config_no_endian() -> None: + cfg: BytesCodecConfiguration = {} + assert cfg == {} + + +def test_gzip_codec_config() -> None: + cfg: GzipCodecConfiguration = {"level": 5} + assert cfg["level"] == 5 + + +def test_zstd_codec_config() -> None: + cfg: ZstdCodecConfiguration = {"level": 3, "checksum": False} + assert cfg["level"] == 3 + + +def test_transpose_codec_config() -> None: + cfg: TransposeCodecConfiguration = {"order": (1, 0, 2)} + assert cfg["order"] == (1, 0, 2) + + +def test_sharding_codec_config() -> None: + cfg: ShardingCodecConfiguration = { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ( + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "crc32c"}, + ), + "index_location": "end", + } + assert cfg["chunk_shape"] == (16, 16) + + +def test_bytes_codec_envelope() -> None: + codec: BytesCodec = {"name": "bytes", "configuration": {"endian": "little"}} + assert codec["name"] == "bytes" + + +def test_gzip_codec_envelope() -> None: + codec: GzipCodec = {"name": "gzip", "configuration": {"level": 5}} + assert codec["name"] == "gzip" + + +def test_zstd_codec_envelope() -> None: + codec: ZstdCodec = { + "name": "zstd", + "configuration": {"level": 3, "checksum": False}, + } + assert codec["name"] == "zstd" + + +def test_transpose_codec_envelope() -> None: + codec: TransposeCodec = {"name": "transpose", "configuration": {"order": (1, 0)}} + assert codec["name"] == "transpose" + + +def test_sharding_codec_envelope() -> None: + codec: ShardingCodec = { + "name": "sharding_indexed", + "configuration": { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ({"name": "crc32c"},), + }, + } + assert codec["name"] == "sharding_indexed" + + +def test_crc32c_codec_envelope() -> None: + codec: Crc32cCodec = {"name": "crc32c"} + assert codec["name"] == "crc32c" + + +def test_blosc_codec_envelope() -> None: + codec: BloscCodec = { + "name": "blosc", + "configuration": { + "cname": "zstd", + "clevel": 5, + "shuffle": "shuffle", + "blocksize": 0, + "typesize": 4, + }, + } + assert codec["name"] == "blosc" From 2feb4bead7a80e8ee56273fcbd3a03a8fd313c36 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 22:54:05 +0200 Subject: [PATCH 32/55] refactor(metadata): define codec envelope TypedDicts explicitly Each {Codec}Codec envelope type is now an explicit TypedDict class with `name` and `configuration` fields, rather than a NamedRequiredConfig[...] generic alias. Readable at the call site, surfaces the spec structure directly, and allows a real class-level docstring. Also: - Drop BloscCodecConfigurationNumcodecs from zarr-metadata. numcodecs- shape modeling belongs in zarr-python (which implements that shape), not in zarr-metadata (which is spec-only). - Rename BloscCodecConfigurationV1 to BloscCodecConfiguration, matching the unversioned naming used for the other codecs. - Restore BloscConfigV2 locally in zarr-python for the numcodecs shape. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/codec/blosc.py | 43 +++++-------------- .../src/zarr_metadata/codec/bytes.py | 13 +++--- .../src/zarr_metadata/codec/crc32c.py | 21 ++++----- .../src/zarr_metadata/codec/gzip.py | 13 +++--- .../src/zarr_metadata/codec/sharding.py | 18 ++++---- .../src/zarr_metadata/codec/transpose.py | 13 +++--- .../src/zarr_metadata/codec/zstd.py | 11 ++--- packages/zarr-metadata/tests/test_imports.py | 43 +++++++++++++++++-- .../zarr-metadata/tests/test_structural.py | 4 +- src/zarr/codecs/blosc.py | 22 +++++++--- 10 files changed, 117 insertions(+), 84 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py index f42e2148b6..5969e9cea2 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py @@ -1,42 +1,23 @@ """ -Blosc codec configuration types (Zarr v3 spec + numcodecs/v2 form). -""" +Blosc codec types. -from typing import Literal, NotRequired, TypedDict +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/blosc/index.html +""" -from zarr_metadata.common import NamedRequiredConfig +from typing import Literal, TypedDict BloscCodecName = Literal["blosc"] """The ``name`` field value of a ``blosc`` codec envelope.""" Shuffle = Literal["noshuffle", "shuffle", "bitshuffle"] -"""Blosc shuffle mode names (v3 spec).""" +"""Blosc shuffle mode names.""" CName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] """Blosc compressor identifiers.""" -class BloscCodecConfigurationNumcodecs(TypedDict): - """ - Blosc configuration for Zarr v2 / numcodecs-flavored callers. - - ``shuffle`` is an integer code (the numcodecs convention) rather than - a named literal. - """ - - cname: CName - clevel: int - shuffle: int - blocksize: int - typesize: NotRequired[int] - - -class BloscCodecConfigurationV1(TypedDict): - """ - Blosc configuration for Zarr v3 spec (version 1 of the blosc codec). - - ``shuffle`` is a named string literal. - """ +class BloscCodecConfiguration(TypedDict): + """Configuration for the Zarr v3 ``blosc`` codec.""" cname: CName clevel: int @@ -45,18 +26,16 @@ class BloscCodecConfigurationV1(TypedDict): typesize: int -BloscCodecConfiguration = BloscCodecConfigurationV1 | BloscCodecConfigurationNumcodecs -"""Any supported blosc configuration shape.""" +class BloscCodec(TypedDict): + """Full ``blosc`` codec named-config envelope.""" -BloscCodec = NamedRequiredConfig[BloscCodecName, BloscCodecConfiguration] -"""Full ``blosc`` codec named-config envelope.""" + name: BloscCodecName + configuration: BloscCodecConfiguration __all__ = [ "BloscCodec", "BloscCodecConfiguration", - "BloscCodecConfigurationNumcodecs", - "BloscCodecConfigurationV1", "BloscCodecName", "CName", "Shuffle", diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py index 9f130f7f6c..274da69c2b 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py @@ -1,13 +1,11 @@ """ -Bytes codec configuration. +Bytes codec types. See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/bytes/index.html """ from typing import Literal, NotRequired, TypedDict -from zarr_metadata.common import NamedRequiredConfig - BytesCodecName = Literal["bytes"] """The ``name`` field value of a ``bytes`` codec envelope.""" @@ -16,7 +14,7 @@ class BytesCodecConfiguration(TypedDict): """ Configuration for the Zarr v3 ``bytes`` codec. - The `endian` field is required for multi-byte data types and absent + The ``endian`` field is required for multi-byte data types and absent for single-byte types. Consumers that always expect a value must tolerate its absence. """ @@ -24,8 +22,11 @@ class BytesCodecConfiguration(TypedDict): endian: NotRequired[Literal["little", "big"]] -BytesCodec = NamedRequiredConfig[BytesCodecName, BytesCodecConfiguration] -"""Full ``bytes`` codec named-config envelope.""" +class BytesCodec(TypedDict): + """Full ``bytes`` codec named-config envelope.""" + + name: BytesCodecName + configuration: BytesCodecConfiguration __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py index e2e931ba32..b60aedca09 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py @@ -1,5 +1,5 @@ """ -CRC32C codec. +CRC32C codec types. See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/crc32c/index.html @@ -7,22 +7,23 @@ ``configuration`` key is absent. """ -from collections.abc import Mapping -from typing import Literal +from typing import Literal, NotRequired, TypedDict -from zarr_metadata.common import NamedConfig +from zarr_metadata.common import JSON Crc32cCodecName = Literal["crc32c"] """The ``name`` field value of a ``crc32c`` codec envelope.""" -Crc32cCodec = NamedConfig[Crc32cCodecName, Mapping[str, object]] -"""``crc32c`` codec named-config envelope. +class Crc32cCodec(TypedDict): + """``crc32c`` codec named-config envelope. -Per spec, the CRC32C codec has no configuration fields, so the -``configuration`` key is optional and, if present, should be an empty -mapping. -""" + Per spec the codec has no configuration fields. ``configuration`` is + optional and, if present, should be an empty mapping. + """ + + name: Crc32cCodecName + configuration: NotRequired[dict[str, JSON]] __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py index 5e4551ed93..082d36a4f4 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py @@ -1,13 +1,11 @@ """ -Gzip codec configuration. +Gzip codec types. See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/gzip/index.html """ from typing import Literal, NotRequired, TypedDict -from zarr_metadata.common import NamedRequiredConfig - GzipCodecName = Literal["gzip"] """The ``name`` field value of a ``gzip`` codec envelope.""" @@ -16,7 +14,7 @@ class GzipCodecConfiguration(TypedDict): """ Configuration for the Zarr v3 ``gzip`` codec. - `level` is an integer in the range 0-9; 0 disables compression and 9 + ``level`` is an integer in the range 0-9; 0 disables compression and 9 is slowest with the best compression ratio. The spec does not mandate a default. """ @@ -24,8 +22,11 @@ class GzipCodecConfiguration(TypedDict): level: NotRequired[int] -GzipCodec = NamedRequiredConfig[GzipCodecName, GzipCodecConfiguration] -"""Full ``gzip`` codec named-config envelope.""" +class GzipCodec(TypedDict): + """Full ``gzip`` codec named-config envelope.""" + + name: GzipCodecName + configuration: GzipCodecConfiguration __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py index 15b27b31c1..796aa893fd 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py @@ -1,5 +1,5 @@ """ -Sharding codec configuration. +Sharding codec types. See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/sharding-indexed/index.html """ @@ -7,7 +7,6 @@ from typing import Literal, NotRequired, TypedDict from zarr_metadata.codec import Codec -from zarr_metadata.common import NamedRequiredConfig ShardingCodecName = Literal["sharding_indexed"] """The ``name`` field value of a ``sharding_indexed`` codec envelope.""" @@ -17,16 +16,16 @@ class ShardingCodecConfiguration(TypedDict): """ Configuration for the Zarr v3 ``sharding_indexed`` codec. - `chunk_shape` is the shape of inner chunks along each dimension; + ``chunk_shape`` is the shape of inner chunks along each dimension; it must evenly divide the shard shape. - `codecs` is the codec pipeline applied to each inner chunk; exactly + ``codecs`` is the codec pipeline applied to each inner chunk; exactly one array-to-bytes codec is required. - `index_codecs` is the codec pipeline applied to the shard index; + ``index_codecs`` is the codec pipeline applied to the shard index; it must be deterministic (no variable-size compression). - `index_location` defaults to ``"end"`` per the spec. + ``index_location`` defaults to ``"end"`` per the spec. """ chunk_shape: tuple[int, ...] @@ -35,8 +34,11 @@ class ShardingCodecConfiguration(TypedDict): index_location: NotRequired[Literal["start", "end"]] -ShardingCodec = NamedRequiredConfig[ShardingCodecName, ShardingCodecConfiguration] -"""Full ``sharding_indexed`` codec named-config envelope.""" +class ShardingCodec(TypedDict): + """Full ``sharding_indexed`` codec named-config envelope.""" + + name: ShardingCodecName + configuration: ShardingCodecConfiguration __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py index d295ab3f7c..7a861819bf 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py @@ -1,13 +1,11 @@ """ -Transpose codec configuration. +Transpose codec types. See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/transpose/index.html """ from typing import Literal, TypedDict -from zarr_metadata.common import NamedRequiredConfig - TransposeCodecName = Literal["transpose"] """The ``name`` field value of a ``transpose`` codec envelope.""" @@ -16,15 +14,18 @@ class TransposeCodecConfiguration(TypedDict): """ Configuration for the Zarr v3 ``transpose`` codec. - `order` is a permutation of the dimension indices 0..n-1 that + ``order`` is a permutation of the dimension indices 0..n-1 that specifies the dimension reordering applied during encoding. """ order: tuple[int, ...] -TransposeCodec = NamedRequiredConfig[TransposeCodecName, TransposeCodecConfiguration] -"""Full ``transpose`` codec named-config envelope.""" +class TransposeCodec(TypedDict): + """Full ``transpose`` codec named-config envelope.""" + + name: TransposeCodecName + configuration: TransposeCodecConfiguration __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py index f20331abd7..9f5153ee7f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py @@ -1,5 +1,5 @@ """ -Zstandard codec configuration. +Zstandard codec types. See https://github.com/zarr-developers/zarr-specs/pull/256 (unmerged at time of writing; the configuration shape below reflects the proposed @@ -8,8 +8,6 @@ from typing import Literal, TypedDict -from zarr_metadata.common import NamedRequiredConfig - ZstdCodecName = Literal["zstd"] """The ``name`` field value of a ``zstd`` codec envelope.""" @@ -25,8 +23,11 @@ class ZstdCodecConfiguration(TypedDict): checksum: bool -ZstdCodec = NamedRequiredConfig[ZstdCodecName, ZstdCodecConfiguration] -"""Full ``zstd`` codec named-config envelope.""" +class ZstdCodec(TypedDict): + """Full ``zstd`` codec named-config envelope.""" + + name: ZstdCodecName + configuration: ZstdCodecConfiguration __all__ = [ diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index 5e980d07e7..338b70df77 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -78,20 +78,55 @@ def test_v3_imports() -> None: def test_codec_imports() -> None: from zarr_metadata.codec import Codec from zarr_metadata.codec.blosc import ( + BloscCodec, BloscCodecConfiguration, - BloscCodecConfigurationNumcodecs, - BloscCodecConfigurationV1, + BloscCodecName, CName, Shuffle, ) + from zarr_metadata.codec.bytes import ( + BytesCodec, + BytesCodecConfiguration, + BytesCodecName, + ) + from zarr_metadata.codec.crc32c import Crc32cCodec, Crc32cCodecName + from zarr_metadata.codec.gzip import GzipCodec, GzipCodecConfiguration, GzipCodecName + from zarr_metadata.codec.sharding import ( + ShardingCodec, + ShardingCodecConfiguration, + ShardingCodecName, + ) + from zarr_metadata.codec.transpose import ( + TransposeCodec, + TransposeCodecConfiguration, + TransposeCodecName, + ) + from zarr_metadata.codec.zstd import ZstdCodec, ZstdCodecConfiguration, ZstdCodecName _ = ( Codec, + BloscCodec, BloscCodecConfiguration, - BloscCodecConfigurationNumcodecs, - BloscCodecConfigurationV1, + BloscCodecName, + BytesCodec, + BytesCodecConfiguration, + BytesCodecName, CName, + Crc32cCodec, + Crc32cCodecName, + GzipCodec, + GzipCodecConfiguration, + GzipCodecName, + ShardingCodec, + ShardingCodecConfiguration, + ShardingCodecName, Shuffle, + TransposeCodec, + TransposeCodecConfiguration, + TransposeCodecName, + ZstdCodec, + ZstdCodecConfiguration, + ZstdCodecName, ) diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index 0a40c839ca..804a30f130 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -10,7 +10,7 @@ from typing import TYPE_CHECKING if TYPE_CHECKING: - from zarr_metadata.codec.blosc import BloscCodec, BloscCodecConfigurationV1 + from zarr_metadata.codec.blosc import BloscCodec, BloscCodecConfiguration from zarr_metadata.codec.bytes import BytesCodec, BytesCodecConfiguration from zarr_metadata.codec.crc32c import Crc32cCodec from zarr_metadata.codec.gzip import GzipCodec, GzipCodecConfiguration @@ -104,7 +104,7 @@ def test_regular_chunk_grid_envelope() -> None: def test_blosc_config_v1() -> None: - cfg: BloscCodecConfigurationV1 = { + cfg: BloscCodecConfiguration = { "cname": "zstd", "clevel": 5, "shuffle": "shuffle", diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 82482abab2..4488cb94e0 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -4,21 +4,33 @@ from dataclasses import dataclass, field, replace from enum import Enum from functools import cached_property -from typing import TYPE_CHECKING, Final, Literal +from typing import TYPE_CHECKING, Final, Literal, NotRequired, TypedDict import numcodecs -from zarr_metadata.codec.blosc import ( - BloscCodecConfigurationNumcodecs as BloscConfigV2, - BloscCodecConfigurationV1 as BloscConfigV3, -) from numcodecs.blosc import Blosc from packaging.version import Version +from zarr_metadata.codec.blosc import BloscCodecConfiguration as BloscConfigV3 from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, NamedRequiredConfig, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasItemSize + +class BloscConfigV2(TypedDict): + """Blosc configuration in the numcodecs/v2 form. + + ``shuffle`` is an integer code (the numcodecs convention) rather than + a named literal as in v3. + """ + + cname: Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] + clevel: int + shuffle: int + blocksize: int + typesize: NotRequired[int] + + if TYPE_CHECKING: from typing import Self From a12fe70ba56f9927039e423acdaa141781f8981a Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 22:57:43 +0200 Subject: [PATCH 33/55] feat(metadata): add Final string constants for codec names and enum-valued fields Each codec now exports SCREAMING_CASE Final constants alongside the Literal types. Downstream packages can reference the spec-defined strings without retyping magic strings. Codec names: BLOSC_CODEC_NAME, BYTES_CODEC_NAME, CRC32C_CODEC_NAME, GZIP_CODEC_NAME, SHARDING_CODEC_NAME, TRANSPOSE_CODEC_NAME, ZSTD_CODEC_NAME. Enum-valued field values: - Blosc: BLOSC_SHUFFLE_{NOSHUFFLE,SHUFFLE,BITSHUFFLE}, BLOSC_CNAME_{LZ4,LZ4HC,BLOSCLZ,SNAPPY,ZLIB,ZSTD} - Bytes: BYTES_ENDIAN_{LITTLE,BIG} (also extracts the existing Literal into a new `Endian` alias) - Sharding: SHARDING_INDEX_LOCATION_{START,END} (and `IndexLocation` Literal alias) Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/codec/blosc.py | 28 +++++++- .../src/zarr_metadata/codec/bytes.py | 19 +++++- .../src/zarr_metadata/codec/crc32c.py | 8 ++- .../src/zarr_metadata/codec/gzip.py | 8 ++- .../src/zarr_metadata/codec/sharding.py | 19 +++++- .../src/zarr_metadata/codec/transpose.py | 8 ++- .../src/zarr_metadata/codec/zstd.py | 8 ++- .../zarr-metadata/tests/test_structural.py | 68 +++++++++++++++++++ 8 files changed, 150 insertions(+), 16 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py index 5969e9cea2..630af8beab 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py @@ -4,14 +4,28 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/blosc/index.html """ -from typing import Literal, TypedDict +from typing import Final, Literal, TypedDict -BloscCodecName = Literal["blosc"] +BLOSC_CODEC_NAME: Final = "blosc" """The ``name`` field value of a ``blosc`` codec envelope.""" +BloscCodecName = Literal["blosc"] +"""Literal type of the ``name`` field of a ``blosc`` codec envelope.""" + +BLOSC_SHUFFLE_NOSHUFFLE: Final = "noshuffle" +BLOSC_SHUFFLE_SHUFFLE: Final = "shuffle" +BLOSC_SHUFFLE_BITSHUFFLE: Final = "bitshuffle" + Shuffle = Literal["noshuffle", "shuffle", "bitshuffle"] """Blosc shuffle mode names.""" +BLOSC_CNAME_LZ4: Final = "lz4" +BLOSC_CNAME_LZ4HC: Final = "lz4hc" +BLOSC_CNAME_BLOSCLZ: Final = "blosclz" +BLOSC_CNAME_SNAPPY: Final = "snappy" +BLOSC_CNAME_ZLIB: Final = "zlib" +BLOSC_CNAME_ZSTD: Final = "zstd" + CName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] """Blosc compressor identifiers.""" @@ -34,6 +48,16 @@ class BloscCodec(TypedDict): __all__ = [ + "BLOSC_CNAME_BLOSCLZ", + "BLOSC_CNAME_LZ4", + "BLOSC_CNAME_LZ4HC", + "BLOSC_CNAME_SNAPPY", + "BLOSC_CNAME_ZLIB", + "BLOSC_CNAME_ZSTD", + "BLOSC_CODEC_NAME", + "BLOSC_SHUFFLE_BITSHUFFLE", + "BLOSC_SHUFFLE_NOSHUFFLE", + "BLOSC_SHUFFLE_SHUFFLE", "BloscCodec", "BloscCodecConfiguration", "BloscCodecName", diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py index 274da69c2b..42bf0cd9ce 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py @@ -4,11 +4,20 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/bytes/index.html """ -from typing import Literal, NotRequired, TypedDict +from typing import Final, Literal, NotRequired, TypedDict -BytesCodecName = Literal["bytes"] +BYTES_CODEC_NAME: Final = "bytes" """The ``name`` field value of a ``bytes`` codec envelope.""" +BytesCodecName = Literal["bytes"] +"""Literal type of the ``name`` field of a ``bytes`` codec envelope.""" + +BYTES_ENDIAN_LITTLE: Final = "little" +BYTES_ENDIAN_BIG: Final = "big" + +Endian = Literal["little", "big"] +"""Byte order of multi-byte numeric data.""" + class BytesCodecConfiguration(TypedDict): """ @@ -19,7 +28,7 @@ class BytesCodecConfiguration(TypedDict): tolerate its absence. """ - endian: NotRequired[Literal["little", "big"]] + endian: NotRequired[Endian] class BytesCodec(TypedDict): @@ -30,7 +39,11 @@ class BytesCodec(TypedDict): __all__ = [ + "BYTES_CODEC_NAME", + "BYTES_ENDIAN_BIG", + "BYTES_ENDIAN_LITTLE", "BytesCodec", "BytesCodecConfiguration", "BytesCodecName", + "Endian", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py index b60aedca09..c4fbfda270 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py @@ -7,13 +7,16 @@ ``configuration`` key is absent. """ -from typing import Literal, NotRequired, TypedDict +from typing import Final, Literal, NotRequired, TypedDict from zarr_metadata.common import JSON -Crc32cCodecName = Literal["crc32c"] +CRC32C_CODEC_NAME: Final = "crc32c" """The ``name`` field value of a ``crc32c`` codec envelope.""" +Crc32cCodecName = Literal["crc32c"] +"""Literal type of the ``name`` field of a ``crc32c`` codec envelope.""" + class Crc32cCodec(TypedDict): """``crc32c`` codec named-config envelope. @@ -27,6 +30,7 @@ class Crc32cCodec(TypedDict): __all__ = [ + "CRC32C_CODEC_NAME", "Crc32cCodec", "Crc32cCodecName", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py index 082d36a4f4..eb0fa3a070 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py @@ -4,11 +4,14 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/gzip/index.html """ -from typing import Literal, NotRequired, TypedDict +from typing import Final, Literal, NotRequired, TypedDict -GzipCodecName = Literal["gzip"] +GZIP_CODEC_NAME: Final = "gzip" """The ``name`` field value of a ``gzip`` codec envelope.""" +GzipCodecName = Literal["gzip"] +"""Literal type of the ``name`` field of a ``gzip`` codec envelope.""" + class GzipCodecConfiguration(TypedDict): """ @@ -30,6 +33,7 @@ class GzipCodec(TypedDict): __all__ = [ + "GZIP_CODEC_NAME", "GzipCodec", "GzipCodecConfiguration", "GzipCodecName", diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py index 796aa893fd..25eaae2651 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py @@ -4,13 +4,22 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/sharding-indexed/index.html """ -from typing import Literal, NotRequired, TypedDict +from typing import Final, Literal, NotRequired, TypedDict from zarr_metadata.codec import Codec -ShardingCodecName = Literal["sharding_indexed"] +SHARDING_CODEC_NAME: Final = "sharding_indexed" """The ``name`` field value of a ``sharding_indexed`` codec envelope.""" +ShardingCodecName = Literal["sharding_indexed"] +"""Literal type of the ``name`` field of a ``sharding_indexed`` codec envelope.""" + +SHARDING_INDEX_LOCATION_START: Final = "start" +SHARDING_INDEX_LOCATION_END: Final = "end" + +IndexLocation = Literal["start", "end"] +"""Position of the shard index within the encoded shard.""" + class ShardingCodecConfiguration(TypedDict): """ @@ -31,7 +40,7 @@ class ShardingCodecConfiguration(TypedDict): chunk_shape: tuple[int, ...] codecs: tuple[Codec, ...] index_codecs: tuple[Codec, ...] - index_location: NotRequired[Literal["start", "end"]] + index_location: NotRequired[IndexLocation] class ShardingCodec(TypedDict): @@ -42,6 +51,10 @@ class ShardingCodec(TypedDict): __all__ = [ + "SHARDING_CODEC_NAME", + "SHARDING_INDEX_LOCATION_END", + "SHARDING_INDEX_LOCATION_START", + "IndexLocation", "ShardingCodec", "ShardingCodecConfiguration", "ShardingCodecName", diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py index 7a861819bf..88ab646d64 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py @@ -4,11 +4,14 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/transpose/index.html """ -from typing import Literal, TypedDict +from typing import Final, Literal, TypedDict -TransposeCodecName = Literal["transpose"] +TRANSPOSE_CODEC_NAME: Final = "transpose" """The ``name`` field value of a ``transpose`` codec envelope.""" +TransposeCodecName = Literal["transpose"] +"""Literal type of the ``name`` field of a ``transpose`` codec envelope.""" + class TransposeCodecConfiguration(TypedDict): """ @@ -29,6 +32,7 @@ class TransposeCodec(TypedDict): __all__ = [ + "TRANSPOSE_CODEC_NAME", "TransposeCodec", "TransposeCodecConfiguration", "TransposeCodecName", diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py index 9f5153ee7f..fa72b10a1c 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py @@ -6,11 +6,14 @@ specification). """ -from typing import Literal, TypedDict +from typing import Final, Literal, TypedDict -ZstdCodecName = Literal["zstd"] +ZSTD_CODEC_NAME: Final = "zstd" """The ``name`` field value of a ``zstd`` codec envelope.""" +ZstdCodecName = Literal["zstd"] +"""Literal type of the ``name`` field of a ``zstd`` codec envelope.""" + class ZstdCodecConfiguration(TypedDict): """ @@ -31,6 +34,7 @@ class ZstdCodec(TypedDict): __all__ = [ + "ZSTD_CODEC_NAME", "ZstdCodec", "ZstdCodecConfiguration", "ZstdCodecName", diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index 804a30f130..2eb87ed043 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -242,3 +242,71 @@ def test_blosc_codec_envelope() -> None: }, } assert codec["name"] == "blosc" + + +def test_codec_name_constants() -> None: + """Final constants carry the same string values as the Literal types.""" + from zarr_metadata.codec.blosc import BLOSC_CODEC_NAME + from zarr_metadata.codec.bytes import BYTES_CODEC_NAME + from zarr_metadata.codec.crc32c import CRC32C_CODEC_NAME + from zarr_metadata.codec.gzip import GZIP_CODEC_NAME + from zarr_metadata.codec.sharding import SHARDING_CODEC_NAME + from zarr_metadata.codec.transpose import TRANSPOSE_CODEC_NAME + from zarr_metadata.codec.zstd import ZSTD_CODEC_NAME + + assert BLOSC_CODEC_NAME == "blosc" + assert BYTES_CODEC_NAME == "bytes" + assert CRC32C_CODEC_NAME == "crc32c" + assert GZIP_CODEC_NAME == "gzip" + assert SHARDING_CODEC_NAME == "sharding_indexed" + assert TRANSPOSE_CODEC_NAME == "transpose" + assert ZSTD_CODEC_NAME == "zstd" + + +def test_blosc_enum_value_constants() -> None: + """Blosc shuffle and cname constants can be used as codec config values.""" + from zarr_metadata.codec.blosc import ( + BLOSC_CNAME_ZSTD, + BLOSC_SHUFFLE_BITSHUFFLE, + ) + + cfg: BloscCodecConfiguration = { + "cname": BLOSC_CNAME_ZSTD, + "clevel": 5, + "shuffle": BLOSC_SHUFFLE_BITSHUFFLE, + "blocksize": 0, + "typesize": 4, + } + assert cfg["cname"] == "zstd" + assert cfg["shuffle"] == "bitshuffle" + + +def test_bytes_endian_constants() -> None: + from zarr_metadata.codec.bytes import BYTES_ENDIAN_BIG, BYTES_ENDIAN_LITTLE + + cfg_little: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_LITTLE} + cfg_big: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_BIG} + assert cfg_little["endian"] == "little" + assert cfg_big["endian"] == "big" + + +def test_sharding_index_location_constants() -> None: + from zarr_metadata.codec.sharding import ( + SHARDING_INDEX_LOCATION_END, + SHARDING_INDEX_LOCATION_START, + ) + + cfg_end: ShardingCodecConfiguration = { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ({"name": "crc32c"},), + "index_location": SHARDING_INDEX_LOCATION_END, + } + cfg_start: ShardingCodecConfiguration = { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ({"name": "crc32c"},), + "index_location": SHARDING_INDEX_LOCATION_START, + } + assert cfg_end["index_location"] == "end" + assert cfg_start["index_location"] == "start" From ec22950ddf2647315a07ed7ac450bb069f3f0176 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 23:03:07 +0200 Subject: [PATCH 34/55] docs(metadata): say "codec metadata" instead of "codec envelope" Rewords docstrings and test names throughout the package: the {Codec}Codec TypedDict describes a codec's JSON metadata, not a "named-config envelope." Less jargon, consistent with the package name. Identifier names are unchanged (still BloscCodec, GzipCodec, etc.). Also renames v3/array.py chunk-grid docstrings for consistency (Regular/Rectilinear ChunkGrid "metadata" rather than "named-config container"), and updates the README. Co-Authored-By: Claude Opus 4.7 (1M context) --- packages/zarr-metadata/README.md | 4 ++-- .../src/zarr_metadata/codec/__init__.py | 8 ++++---- .../src/zarr_metadata/codec/blosc.py | 18 +++++++++--------- .../src/zarr_metadata/codec/bytes.py | 6 +++--- .../src/zarr_metadata/codec/crc32c.py | 10 +++++----- .../src/zarr_metadata/codec/gzip.py | 6 +++--- .../src/zarr_metadata/codec/sharding.py | 6 +++--- .../src/zarr_metadata/codec/transpose.py | 6 +++--- .../src/zarr_metadata/codec/zstd.py | 6 +++--- .../src/zarr_metadata/v3/array.py | 4 ++-- packages/zarr-metadata/tests/test_imports.py | 8 ++++---- .../zarr-metadata/tests/test_structural.py | 16 ++++++++-------- 12 files changed, 49 insertions(+), 49 deletions(-) diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md index 0ee12811e9..2e4b44ae1a 100644 --- a/packages/zarr-metadata/README.md +++ b/packages/zarr-metadata/README.md @@ -10,6 +10,6 @@ repository at `packages/zarr-metadata/`. ## Principle Every type that models a spec artifact (v2 or v3 array/group/consolidated -metadata, chunk grids, codec named-config envelopes, dtype shapes) belongs -in `zarr-metadata`. Zarr-python implementation details (runtime codecs, +metadata, chunk grids, codec metadata, dtype shapes) belongs in +`zarr-metadata`. Zarr-python implementation details (runtime codecs, config dataclasses, numcodecs-derived helpers) stay in `zarr`. diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py index b8cd8ef735..8c7d1769de 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py @@ -1,5 +1,5 @@ """ -Zarr codec named-config envelope and per-codec configuration types. +Zarr codec metadata types. """ from collections.abc import Mapping @@ -8,9 +8,9 @@ """ The widest JSON shape that can specify a codec (v2 or v3). -For v3, a codec is a named-config envelope (``{"name": ..., "configuration": ...}``); -for v2, a codec is the numcodecs JSON dict. The accepted-input shape is the -union of both. +For v3, a codec is a ``{"name": ..., "configuration": ...}`` mapping (or +a bare ``str`` shorthand); for v2, a codec is the numcodecs JSON dict. +The accepted-input shape is the union of both. """ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py index 630af8beab..0c96599bd8 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py @@ -7,16 +7,16 @@ from typing import Final, Literal, TypedDict BLOSC_CODEC_NAME: Final = "blosc" -"""The ``name`` field value of a ``blosc`` codec envelope.""" +"""The ``name`` field value of the ``blosc`` codec.""" BloscCodecName = Literal["blosc"] -"""Literal type of the ``name`` field of a ``blosc`` codec envelope.""" +"""Literal type of the ``name`` field of the ``blosc`` codec.""" BLOSC_SHUFFLE_NOSHUFFLE: Final = "noshuffle" BLOSC_SHUFFLE_SHUFFLE: Final = "shuffle" BLOSC_SHUFFLE_BITSHUFFLE: Final = "bitshuffle" -Shuffle = Literal["noshuffle", "shuffle", "bitshuffle"] +BloscShuffle = Literal["noshuffle", "shuffle", "bitshuffle"] """Blosc shuffle mode names.""" BLOSC_CNAME_LZ4: Final = "lz4" @@ -26,22 +26,22 @@ BLOSC_CNAME_ZLIB: Final = "zlib" BLOSC_CNAME_ZSTD: Final = "zstd" -CName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] +BloscCName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] """Blosc compressor identifiers.""" class BloscCodecConfiguration(TypedDict): """Configuration for the Zarr v3 ``blosc`` codec.""" - cname: CName + cname: BloscCName clevel: int - shuffle: Shuffle + shuffle: BloscShuffle blocksize: int typesize: int class BloscCodec(TypedDict): - """Full ``blosc`` codec named-config envelope.""" + """``blosc`` codec metadata.""" name: BloscCodecName configuration: BloscCodecConfiguration @@ -58,9 +58,9 @@ class BloscCodec(TypedDict): "BLOSC_SHUFFLE_BITSHUFFLE", "BLOSC_SHUFFLE_NOSHUFFLE", "BLOSC_SHUFFLE_SHUFFLE", + "BloscCName", "BloscCodec", "BloscCodecConfiguration", "BloscCodecName", - "CName", - "Shuffle", + "BloscShuffle", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py index 42bf0cd9ce..b4643c12eb 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py @@ -7,10 +7,10 @@ from typing import Final, Literal, NotRequired, TypedDict BYTES_CODEC_NAME: Final = "bytes" -"""The ``name`` field value of a ``bytes`` codec envelope.""" +"""The ``name`` field value of the ``bytes`` codec.""" BytesCodecName = Literal["bytes"] -"""Literal type of the ``name`` field of a ``bytes`` codec envelope.""" +"""Literal type of the ``name`` field of the ``bytes`` codec.""" BYTES_ENDIAN_LITTLE: Final = "little" BYTES_ENDIAN_BIG: Final = "big" @@ -32,7 +32,7 @@ class BytesCodecConfiguration(TypedDict): class BytesCodec(TypedDict): - """Full ``bytes`` codec named-config envelope.""" + """``bytes`` codec metadata.""" name: BytesCodecName configuration: BytesCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py index c4fbfda270..3926c775cd 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py @@ -3,8 +3,8 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/crc32c/index.html -The CRC32C codec has no configuration fields, so the envelope's -``configuration`` key is absent. +The CRC32C codec has no configuration fields, so the ``configuration`` +key is absent from the metadata. """ from typing import Final, Literal, NotRequired, TypedDict @@ -12,14 +12,14 @@ from zarr_metadata.common import JSON CRC32C_CODEC_NAME: Final = "crc32c" -"""The ``name`` field value of a ``crc32c`` codec envelope.""" +"""The ``name`` field value of the ``crc32c`` codec.""" Crc32cCodecName = Literal["crc32c"] -"""Literal type of the ``name`` field of a ``crc32c`` codec envelope.""" +"""Literal type of the ``name`` field of the ``crc32c`` codec.""" class Crc32cCodec(TypedDict): - """``crc32c`` codec named-config envelope. + """``crc32c`` codec metadata. Per spec the codec has no configuration fields. ``configuration`` is optional and, if present, should be an empty mapping. diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py index eb0fa3a070..adc14c410e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py @@ -7,10 +7,10 @@ from typing import Final, Literal, NotRequired, TypedDict GZIP_CODEC_NAME: Final = "gzip" -"""The ``name`` field value of a ``gzip`` codec envelope.""" +"""The ``name`` field value of the ``gzip`` codec.""" GzipCodecName = Literal["gzip"] -"""Literal type of the ``name`` field of a ``gzip`` codec envelope.""" +"""Literal type of the ``name`` field of the ``gzip`` codec.""" class GzipCodecConfiguration(TypedDict): @@ -26,7 +26,7 @@ class GzipCodecConfiguration(TypedDict): class GzipCodec(TypedDict): - """Full ``gzip`` codec named-config envelope.""" + """``gzip`` codec metadata.""" name: GzipCodecName configuration: GzipCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py index 25eaae2651..403eec8fa5 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py @@ -9,10 +9,10 @@ from zarr_metadata.codec import Codec SHARDING_CODEC_NAME: Final = "sharding_indexed" -"""The ``name`` field value of a ``sharding_indexed`` codec envelope.""" +"""The ``name`` field value of the ``sharding_indexed`` codec.""" ShardingCodecName = Literal["sharding_indexed"] -"""Literal type of the ``name`` field of a ``sharding_indexed`` codec envelope.""" +"""Literal type of the ``name`` field of the ``sharding_indexed`` codec.""" SHARDING_INDEX_LOCATION_START: Final = "start" SHARDING_INDEX_LOCATION_END: Final = "end" @@ -44,7 +44,7 @@ class ShardingCodecConfiguration(TypedDict): class ShardingCodec(TypedDict): - """Full ``sharding_indexed`` codec named-config envelope.""" + """``sharding_indexed`` codec metadata.""" name: ShardingCodecName configuration: ShardingCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py index 88ab646d64..a73ac8144b 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py @@ -7,10 +7,10 @@ from typing import Final, Literal, TypedDict TRANSPOSE_CODEC_NAME: Final = "transpose" -"""The ``name`` field value of a ``transpose`` codec envelope.""" +"""The ``name`` field value of the ``transpose`` codec.""" TransposeCodecName = Literal["transpose"] -"""Literal type of the ``name`` field of a ``transpose`` codec envelope.""" +"""Literal type of the ``name`` field of the ``transpose`` codec.""" class TransposeCodecConfiguration(TypedDict): @@ -25,7 +25,7 @@ class TransposeCodecConfiguration(TypedDict): class TransposeCodec(TypedDict): - """Full ``transpose`` codec named-config envelope.""" + """``transpose`` codec metadata.""" name: TransposeCodecName configuration: TransposeCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py index fa72b10a1c..232dc82015 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py @@ -9,10 +9,10 @@ from typing import Final, Literal, TypedDict ZSTD_CODEC_NAME: Final = "zstd" -"""The ``name`` field value of a ``zstd`` codec envelope.""" +"""The ``name`` field value of the ``zstd`` codec.""" ZstdCodecName = Literal["zstd"] -"""Literal type of the ``name`` field of a ``zstd`` codec envelope.""" +"""Literal type of the ``name`` field of the ``zstd`` codec.""" class ZstdCodecConfiguration(TypedDict): @@ -27,7 +27,7 @@ class ZstdCodecConfiguration(TypedDict): class ZstdCodec(TypedDict): - """Full ``zstd`` codec named-config envelope.""" + """``zstd`` codec metadata.""" name: ZstdCodecName configuration: ZstdCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index 2a9b4971e3..beb296e3fb 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -49,14 +49,14 @@ class RectilinearChunkGridConfig(TypedDict): class RegularChunkGrid(TypedDict): - """Regular chunk grid named-config container.""" + """Regular chunk grid metadata.""" name: Literal["regular"] configuration: RegularChunkGridConfig class RectilinearChunkGrid(TypedDict): - """Rectilinear chunk grid named-config container.""" + """Rectilinear chunk grid metadata.""" name: Literal["rectilinear"] configuration: RectilinearChunkGridConfig diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index 338b70df77..3020a26599 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -78,11 +78,11 @@ def test_v3_imports() -> None: def test_codec_imports() -> None: from zarr_metadata.codec import Codec from zarr_metadata.codec.blosc import ( + BloscCName, BloscCodec, BloscCodecConfiguration, BloscCodecName, - CName, - Shuffle, + BloscShuffle, ) from zarr_metadata.codec.bytes import ( BytesCodec, @@ -111,7 +111,7 @@ def test_codec_imports() -> None: BytesCodec, BytesCodecConfiguration, BytesCodecName, - CName, + BloscCName, Crc32cCodec, Crc32cCodecName, GzipCodec, @@ -120,7 +120,7 @@ def test_codec_imports() -> None: ShardingCodec, ShardingCodecConfiguration, ShardingCodecName, - Shuffle, + BloscShuffle, TransposeCodec, TransposeCodecConfiguration, TransposeCodecName, diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index 2eb87ed043..29f85c608e 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -95,7 +95,7 @@ def test_group_metadata_v2_minimal() -> None: assert meta["zarr_format"] == 2 -def test_regular_chunk_grid_envelope() -> None: +def test_regular_chunk_grid_metadata() -> None: grid: RegularChunkGrid = { "name": "regular", "configuration": {"chunk_shape": (10, 10)}, @@ -190,17 +190,17 @@ def test_sharding_codec_config() -> None: assert cfg["chunk_shape"] == (16, 16) -def test_bytes_codec_envelope() -> None: +def test_bytes_codec_metadata() -> None: codec: BytesCodec = {"name": "bytes", "configuration": {"endian": "little"}} assert codec["name"] == "bytes" -def test_gzip_codec_envelope() -> None: +def test_gzip_codec_metadata() -> None: codec: GzipCodec = {"name": "gzip", "configuration": {"level": 5}} assert codec["name"] == "gzip" -def test_zstd_codec_envelope() -> None: +def test_zstd_codec_metadata() -> None: codec: ZstdCodec = { "name": "zstd", "configuration": {"level": 3, "checksum": False}, @@ -208,12 +208,12 @@ def test_zstd_codec_envelope() -> None: assert codec["name"] == "zstd" -def test_transpose_codec_envelope() -> None: +def test_transpose_codec_metadata() -> None: codec: TransposeCodec = {"name": "transpose", "configuration": {"order": (1, 0)}} assert codec["name"] == "transpose" -def test_sharding_codec_envelope() -> None: +def test_sharding_codec_metadata() -> None: codec: ShardingCodec = { "name": "sharding_indexed", "configuration": { @@ -225,12 +225,12 @@ def test_sharding_codec_envelope() -> None: assert codec["name"] == "sharding_indexed" -def test_crc32c_codec_envelope() -> None: +def test_crc32c_codec_metadata() -> None: codec: Crc32cCodec = {"name": "crc32c"} assert codec["name"] == "crc32c" -def test_blosc_codec_envelope() -> None: +def test_blosc_codec_metadata() -> None: codec: BloscCodec = { "name": "blosc", "configuration": { From 275bf558d4a86412e94a6e39ba8b6daec96dc888 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 23:05:10 +0200 Subject: [PATCH 35/55] docs(metadata): use single-backtick markdown code formatting Convert all double-backtick RST-style inline code in zarr-metadata docstrings to single-backtick markdown style. The package's documentation will be rendered by mkdocs, which expects markdown, so single backticks render correctly as inline code. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/codec/__init__.py | 4 ++-- .../src/zarr_metadata/codec/blosc.py | 8 ++++---- .../src/zarr_metadata/codec/bytes.py | 10 +++++----- .../src/zarr_metadata/codec/crc32c.py | 10 +++++----- .../src/zarr_metadata/codec/gzip.py | 10 +++++----- .../src/zarr_metadata/codec/sharding.py | 16 ++++++++-------- .../src/zarr_metadata/codec/transpose.py | 10 +++++----- .../src/zarr_metadata/codec/zstd.py | 8 ++++---- .../zarr-metadata/src/zarr_metadata/common.py | 6 +++--- .../src/zarr_metadata/dtype/__init__.py | 2 +- .../zarr-metadata/src/zarr_metadata/v2/array.py | 2 +- .../zarr-metadata/src/zarr_metadata/v2/codec.py | 7 ++++--- .../src/zarr_metadata/v2/consolidated.py | 13 ++++++------- .../zarr-metadata/src/zarr_metadata/v2/group.py | 4 ++-- .../zarr-metadata/src/zarr_metadata/v3/array.py | 4 ++-- .../src/zarr_metadata/v3/consolidated.py | 2 +- .../zarr-metadata/src/zarr_metadata/v3/group.py | 4 ++-- 17 files changed, 60 insertions(+), 60 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py index 8c7d1769de..97b3a69551 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py @@ -8,8 +8,8 @@ """ The widest JSON shape that can specify a codec (v2 or v3). -For v3, a codec is a ``{"name": ..., "configuration": ...}`` mapping (or -a bare ``str`` shorthand); for v2, a codec is the numcodecs JSON dict. +For v3, a codec is a `{"name": ..., "configuration": ...}` mapping (or +a bare `str` shorthand); for v2, a codec is the numcodecs JSON dict. The accepted-input shape is the union of both. """ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py index 0c96599bd8..1cd79f3d43 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py @@ -7,10 +7,10 @@ from typing import Final, Literal, TypedDict BLOSC_CODEC_NAME: Final = "blosc" -"""The ``name`` field value of the ``blosc`` codec.""" +"""The `name` field value of the `blosc` codec.""" BloscCodecName = Literal["blosc"] -"""Literal type of the ``name`` field of the ``blosc`` codec.""" +"""Literal type of the `name` field of the `blosc` codec.""" BLOSC_SHUFFLE_NOSHUFFLE: Final = "noshuffle" BLOSC_SHUFFLE_SHUFFLE: Final = "shuffle" @@ -31,7 +31,7 @@ class BloscCodecConfiguration(TypedDict): - """Configuration for the Zarr v3 ``blosc`` codec.""" + """Configuration for the Zarr v3 `blosc` codec.""" cname: BloscCName clevel: int @@ -41,7 +41,7 @@ class BloscCodecConfiguration(TypedDict): class BloscCodec(TypedDict): - """``blosc`` codec metadata.""" + """`blosc` codec metadata.""" name: BloscCodecName configuration: BloscCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py index b4643c12eb..76e057c48b 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py @@ -7,10 +7,10 @@ from typing import Final, Literal, NotRequired, TypedDict BYTES_CODEC_NAME: Final = "bytes" -"""The ``name`` field value of the ``bytes`` codec.""" +"""The `name` field value of the `bytes` codec.""" BytesCodecName = Literal["bytes"] -"""Literal type of the ``name`` field of the ``bytes`` codec.""" +"""Literal type of the `name` field of the `bytes` codec.""" BYTES_ENDIAN_LITTLE: Final = "little" BYTES_ENDIAN_BIG: Final = "big" @@ -21,9 +21,9 @@ class BytesCodecConfiguration(TypedDict): """ - Configuration for the Zarr v3 ``bytes`` codec. + Configuration for the Zarr v3 `bytes` codec. - The ``endian`` field is required for multi-byte data types and absent + The `endian` field is required for multi-byte data types and absent for single-byte types. Consumers that always expect a value must tolerate its absence. """ @@ -32,7 +32,7 @@ class BytesCodecConfiguration(TypedDict): class BytesCodec(TypedDict): - """``bytes`` codec metadata.""" + """`bytes` codec metadata.""" name: BytesCodecName configuration: BytesCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py index 3926c775cd..573e56b356 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py @@ -3,7 +3,7 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/crc32c/index.html -The CRC32C codec has no configuration fields, so the ``configuration`` +The CRC32C codec has no configuration fields, so the `configuration` key is absent from the metadata. """ @@ -12,16 +12,16 @@ from zarr_metadata.common import JSON CRC32C_CODEC_NAME: Final = "crc32c" -"""The ``name`` field value of the ``crc32c`` codec.""" +"""The `name` field value of the `crc32c` codec.""" Crc32cCodecName = Literal["crc32c"] -"""Literal type of the ``name`` field of the ``crc32c`` codec.""" +"""Literal type of the `name` field of the `crc32c` codec.""" class Crc32cCodec(TypedDict): - """``crc32c`` codec metadata. + """`crc32c` codec metadata. - Per spec the codec has no configuration fields. ``configuration`` is + Per spec the codec has no configuration fields. `configuration` is optional and, if present, should be an empty mapping. """ diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py index adc14c410e..16d9c5c5d1 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py @@ -7,17 +7,17 @@ from typing import Final, Literal, NotRequired, TypedDict GZIP_CODEC_NAME: Final = "gzip" -"""The ``name`` field value of the ``gzip`` codec.""" +"""The `name` field value of the `gzip` codec.""" GzipCodecName = Literal["gzip"] -"""Literal type of the ``name`` field of the ``gzip`` codec.""" +"""Literal type of the `name` field of the `gzip` codec.""" class GzipCodecConfiguration(TypedDict): """ - Configuration for the Zarr v3 ``gzip`` codec. + Configuration for the Zarr v3 `gzip` codec. - ``level`` is an integer in the range 0-9; 0 disables compression and 9 + `level` is an integer in the range 0-9; 0 disables compression and 9 is slowest with the best compression ratio. The spec does not mandate a default. """ @@ -26,7 +26,7 @@ class GzipCodecConfiguration(TypedDict): class GzipCodec(TypedDict): - """``gzip`` codec metadata.""" + """`gzip` codec metadata.""" name: GzipCodecName configuration: GzipCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py index 403eec8fa5..a7c9c6d950 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py @@ -9,10 +9,10 @@ from zarr_metadata.codec import Codec SHARDING_CODEC_NAME: Final = "sharding_indexed" -"""The ``name`` field value of the ``sharding_indexed`` codec.""" +"""The `name` field value of the `sharding_indexed` codec.""" ShardingCodecName = Literal["sharding_indexed"] -"""Literal type of the ``name`` field of the ``sharding_indexed`` codec.""" +"""Literal type of the `name` field of the `sharding_indexed` codec.""" SHARDING_INDEX_LOCATION_START: Final = "start" SHARDING_INDEX_LOCATION_END: Final = "end" @@ -23,18 +23,18 @@ class ShardingCodecConfiguration(TypedDict): """ - Configuration for the Zarr v3 ``sharding_indexed`` codec. + Configuration for the Zarr v3 `sharding_indexed` codec. - ``chunk_shape`` is the shape of inner chunks along each dimension; + `chunk_shape` is the shape of inner chunks along each dimension; it must evenly divide the shard shape. - ``codecs`` is the codec pipeline applied to each inner chunk; exactly + `codecs` is the codec pipeline applied to each inner chunk; exactly one array-to-bytes codec is required. - ``index_codecs`` is the codec pipeline applied to the shard index; + `index_codecs` is the codec pipeline applied to the shard index; it must be deterministic (no variable-size compression). - ``index_location`` defaults to ``"end"`` per the spec. + `index_location` defaults to `"end"` per the spec. """ chunk_shape: tuple[int, ...] @@ -44,7 +44,7 @@ class ShardingCodecConfiguration(TypedDict): class ShardingCodec(TypedDict): - """``sharding_indexed`` codec metadata.""" + """`sharding_indexed` codec metadata.""" name: ShardingCodecName configuration: ShardingCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py index a73ac8144b..ef792670c5 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py @@ -7,17 +7,17 @@ from typing import Final, Literal, TypedDict TRANSPOSE_CODEC_NAME: Final = "transpose" -"""The ``name`` field value of the ``transpose`` codec.""" +"""The `name` field value of the `transpose` codec.""" TransposeCodecName = Literal["transpose"] -"""Literal type of the ``name`` field of the ``transpose`` codec.""" +"""Literal type of the `name` field of the `transpose` codec.""" class TransposeCodecConfiguration(TypedDict): """ - Configuration for the Zarr v3 ``transpose`` codec. + Configuration for the Zarr v3 `transpose` codec. - ``order`` is a permutation of the dimension indices 0..n-1 that + `order` is a permutation of the dimension indices 0..n-1 that specifies the dimension reordering applied during encoding. """ @@ -25,7 +25,7 @@ class TransposeCodecConfiguration(TypedDict): class TransposeCodec(TypedDict): - """``transpose`` codec metadata.""" + """`transpose` codec metadata.""" name: TransposeCodecName configuration: TransposeCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py index 232dc82015..a659ca4cf1 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py @@ -9,15 +9,15 @@ from typing import Final, Literal, TypedDict ZSTD_CODEC_NAME: Final = "zstd" -"""The ``name`` field value of the ``zstd`` codec.""" +"""The `name` field value of the `zstd` codec.""" ZstdCodecName = Literal["zstd"] -"""Literal type of the ``name`` field of the ``zstd`` codec.""" +"""Literal type of the `name` field of the `zstd` codec.""" class ZstdCodecConfiguration(TypedDict): """ - Configuration for the Zarr v3 ``zstd`` codec. + Configuration for the Zarr v3 `zstd` codec. Both fields are required per the proposed specification. """ @@ -27,7 +27,7 @@ class ZstdCodecConfiguration(TypedDict): class ZstdCodec(TypedDict): - """``zstd`` codec metadata.""" + """`zstd` codec metadata.""" name: ZstdCodecName configuration: ZstdCodecConfiguration diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py index db0e534726..c160634493 100644 --- a/packages/zarr-metadata/src/zarr_metadata/common.py +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -1,9 +1,9 @@ """ Top-level cross-version primitives for Zarr metadata. -Version-specific types live under ``zarr_metadata.v2`` and ``zarr_metadata.v3``. -Codec and dtype spec types live under ``zarr_metadata.codec`` and -``zarr_metadata.dtype``. +Version-specific types live under `zarr_metadata.v2` and `zarr_metadata.v3`. +Codec and dtype spec types live under `zarr_metadata.codec` and +`zarr_metadata.dtype`. """ from collections.abc import Mapping, Sequence diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py index 385485720c..a62bc7de59 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py @@ -10,7 +10,7 @@ """ The widest JSON-like shape that can specify a Zarr data type. -See ``zarr_metadata.dtype.string``, ``.bytes``, and ``.time`` for specific +See `zarr_metadata.dtype.string`, `.bytes`, and `.time` for specific per-dtype configuration TypedDicts. """ diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index aac9522039..cbcbccc0e2 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -27,7 +27,7 @@ class DataTypeV2Structured(TypedDict): DataTypeV2 = str | tuple[DataTypeV2Structured, ...] """The v2 dtype representation. -Simple dtypes are numpy-style strings (e.g. ``" Date: Tue, 21 Apr 2026 23:22:14 +0200 Subject: [PATCH 36/55] feat(metadata): add v3 spec data type metadata Models the spec-defined v3 data types from zarr-specs core and zarr-extensions: * `dtype/primitive.py` (NEW) - Final constants and `PrimitiveDTypeName` Literal union for all 14 core v3 primitives (bool, int8..int64, uint8..uint64, float16..float64, complex64, complex128). * `dtype/bytes.py` - adds `BYTES_DTYPE_NAME` and `BytesDTypeName` for the variable-length `bytes` extension; adds `NullTerminatedBytes` envelope TypedDict for `null_terminated_bytes` (zarr-extensions). Retains `FixedLengthBytesConfig` (re-exported by zarr-python). * `dtype/string.py` - adds `STRING_DTYPE_NAME`/`StringDTypeName` for the `string` extension; adds `FixedLengthUtf32` envelope. Retains `LengthBytesConfig`. * `dtype/time.py` - adds `NumpyDatetime64` and `NumpyTimedelta64` envelopes plus name constants/literals. The shared `TimeConfig` body is preserved. * `dtype/struct.py` (NEW) - the `struct` extension type, with `StructField`, `StructConfig`, and `Struct` envelope. Fields hold recursive `DType` values, supporting nested structs. The `r` raw-bytes type from the core spec is parameterised on bit count, not a single literal name, so it isn't given a TypedDict; consumers match it against the wider `DType` alias. Tests updated and extended for the new types and constants. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/codec/bytes.py | 4 +- .../src/zarr_metadata/dtype/__init__.py | 9 +- .../src/zarr_metadata/dtype/bytes.py | 43 +++++++-- .../src/zarr_metadata/dtype/primitive.py | 62 +++++++++++++ .../src/zarr_metadata/dtype/string.py | 43 +++++++-- .../src/zarr_metadata/dtype/struct.py | 56 ++++++++++++ .../src/zarr_metadata/dtype/time.py | 43 ++++++++- packages/zarr-metadata/tests/test_imports.py | 91 ++++++++++++++++++- .../zarr-metadata/tests/test_structural.py | 90 +++++++++++++++++- 9 files changed, 412 insertions(+), 29 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/struct.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py index 76e057c48b..fe6e7b2579 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py @@ -23,9 +23,7 @@ class BytesCodecConfiguration(TypedDict): """ Configuration for the Zarr v3 `bytes` codec. - The `endian` field is required for multi-byte data types and absent - for single-byte types. Consumers that always expect a value must - tolerate its absence. + The `endian` field is required for multi-byte data types. """ endian: NotRequired[Endian] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py index a62bc7de59..3c908decff 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py @@ -10,8 +10,13 @@ """ The widest JSON-like shape that can specify a Zarr data type. -See `zarr_metadata.dtype.string`, `.bytes`, and `.time` for specific -per-dtype configuration TypedDicts. +See the submodules for specific per-dtype types: + +- `zarr_metadata.dtype.primitive` -- core v3 primitives (bool, int*, uint*, float*, complex*) +- `zarr_metadata.dtype.bytes` -- `bytes`, `null_terminated_bytes` +- `zarr_metadata.dtype.string` -- `string`, `fixed_length_utf32` +- `zarr_metadata.dtype.time` -- `numpy.datetime64`, `numpy.timedelta64` +- `zarr_metadata.dtype.struct` -- `struct` """ diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py b/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py index c174c2620e..f20090ed55 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py @@ -1,25 +1,54 @@ """ -Bytes data type configuration. +Bytes-shaped Zarr v3 data types. + +This module covers: + +- `bytes` (variable-length bytes, bare string, zarr-extensions) +- `null_terminated_bytes` (fixed-length NUL-terminated, envelope, zarr-extensions) + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types """ -from typing import TypedDict +from typing import Final, Literal, TypedDict from typing_extensions import ReadOnly +BYTES_DTYPE_NAME: Final = "bytes" +"""The `data_type` value for the variable-length `bytes` type.""" + +BytesDTypeName = Literal["bytes"] +"""Literal type of the `data_type` field for `bytes`.""" + +NULL_TERMINATED_BYTES_DTYPE_NAME: Final = "null_terminated_bytes" +"""The `name` field value of the `null_terminated_bytes` data type.""" + +NullTerminatedBytesDTypeName = Literal["null_terminated_bytes"] +"""Literal type of the `name` field of the `null_terminated_bytes` data type.""" + class FixedLengthBytesConfig(TypedDict): """ - Configuration for a fixed-length bytes data type in Zarr v3. + Configuration for fixed-length bytes-shaped data types. - Attributes - ---------- - length_bytes - The length in bytes of the data associated with this configuration. + Used by `null_terminated_bytes` (and any other fixed-length bytes + extension). `length_bytes` is the allocated byte count per element. """ length_bytes: ReadOnly[int] +class NullTerminatedBytes(TypedDict): + """`null_terminated_bytes` data type metadata.""" + + name: NullTerminatedBytesDTypeName + configuration: FixedLengthBytesConfig + + __all__ = [ + "BYTES_DTYPE_NAME", + "NULL_TERMINATED_BYTES_DTYPE_NAME", + "BytesDTypeName", "FixedLengthBytesConfig", + "NullTerminatedBytes", + "NullTerminatedBytesDTypeName", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py b/packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py new file mode 100644 index 0000000000..2f51e5a112 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py @@ -0,0 +1,62 @@ +""" +Primitive Zarr v3 data types. + +All primitives are spec-defined as bare-string `data_type` values -- they +carry no configuration. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#data-types +""" + +from typing import Final, Literal + +BOOL_DTYPE_NAME: Final = "bool" +INT8_DTYPE_NAME: Final = "int8" +INT16_DTYPE_NAME: Final = "int16" +INT32_DTYPE_NAME: Final = "int32" +INT64_DTYPE_NAME: Final = "int64" +UINT8_DTYPE_NAME: Final = "uint8" +UINT16_DTYPE_NAME: Final = "uint16" +UINT32_DTYPE_NAME: Final = "uint32" +UINT64_DTYPE_NAME: Final = "uint64" +FLOAT16_DTYPE_NAME: Final = "float16" +FLOAT32_DTYPE_NAME: Final = "float32" +FLOAT64_DTYPE_NAME: Final = "float64" +COMPLEX64_DTYPE_NAME: Final = "complex64" +COMPLEX128_DTYPE_NAME: Final = "complex128" + +PrimitiveDTypeName = Literal[ + "bool", + "int8", + "int16", + "int32", + "int64", + "uint8", + "uint16", + "uint32", + "uint64", + "float16", + "float32", + "float64", + "complex64", + "complex128", +] +"""Literal union of every core v3 primitive data type name.""" + + +__all__ = [ + "BOOL_DTYPE_NAME", + "COMPLEX64_DTYPE_NAME", + "COMPLEX128_DTYPE_NAME", + "FLOAT16_DTYPE_NAME", + "FLOAT32_DTYPE_NAME", + "FLOAT64_DTYPE_NAME", + "INT8_DTYPE_NAME", + "INT16_DTYPE_NAME", + "INT32_DTYPE_NAME", + "INT64_DTYPE_NAME", + "UINT8_DTYPE_NAME", + "UINT16_DTYPE_NAME", + "UINT32_DTYPE_NAME", + "UINT64_DTYPE_NAME", + "PrimitiveDTypeName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/string.py b/packages/zarr-metadata/src/zarr_metadata/dtype/string.py index 52bca1b5dc..337436418c 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/string.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/string.py @@ -1,25 +1,54 @@ """ -String data type configuration. +String-shaped Zarr v3 data types. + +This module covers: + +- `string` (variable-length utf-8, bare string, zarr-extensions) +- `fixed_length_utf32` (fixed-length utf-32, envelope, zarr-extensions) + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types """ -from typing import TypedDict +from typing import Final, Literal, TypedDict from typing_extensions import ReadOnly +STRING_DTYPE_NAME: Final = "string" +"""The `data_type` value for the variable-length `string` type.""" + +StringDTypeName = Literal["string"] +"""Literal type of the `data_type` field for `string`.""" + +FIXED_LENGTH_UTF32_DTYPE_NAME: Final = "fixed_length_utf32" +"""The `name` field value of the `fixed_length_utf32` data type.""" + +FixedLengthUtf32DTypeName = Literal["fixed_length_utf32"] +"""Literal type of the `name` field of the `fixed_length_utf32` data type.""" + class LengthBytesConfig(TypedDict): """ - Configuration for a fixed-length string data type in Zarr v3. + Configuration for fixed-length string-shaped data types. - Attributes - ---------- - length_bytes - The length in bytes of the data associated with this configuration. + Used by `fixed_length_utf32`. `length_bytes` is the allocated byte count + per element; for utf-32 this must be a multiple of 4. """ length_bytes: ReadOnly[int] +class FixedLengthUtf32(TypedDict): + """`fixed_length_utf32` data type metadata.""" + + name: FixedLengthUtf32DTypeName + configuration: LengthBytesConfig + + __all__ = [ + "FIXED_LENGTH_UTF32_DTYPE_NAME", + "STRING_DTYPE_NAME", + "FixedLengthUtf32", + "FixedLengthUtf32DTypeName", "LengthBytesConfig", + "StringDTypeName", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py b/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py new file mode 100644 index 0000000000..42b3bc7b33 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py @@ -0,0 +1,56 @@ +""" +Structured (heterogeneous) Zarr v3 data type. + +See https://github.com/zarr-developers/zarr-extensions/blob/main/data-types/struct/README.md +""" + +from typing import Final, Literal, TypedDict + +from typing_extensions import ReadOnly + +from zarr_metadata.dtype import DType + +STRUCT_DTYPE_NAME: Final = "struct" +"""The `name` field value of the `struct` data type.""" + +StructDTypeName = Literal["struct"] +"""Literal type of the `name` field of the `struct` data type.""" + + +class StructField(TypedDict): + """ + A single field entry inside a structured dtype. + + Attributes + ---------- + name + The field name (must be unique within a struct and non-empty). + data_type + The field's data type. Recursive: may be a bare-string primitive + or a named-config envelope including another `struct`. + """ + + name: ReadOnly[str] + data_type: ReadOnly[DType] + + +class StructConfig(TypedDict): + """Configuration for the `struct` data type.""" + + fields: ReadOnly[tuple[StructField, ...]] + + +class Struct(TypedDict): + """`struct` data type metadata.""" + + name: StructDTypeName + configuration: StructConfig + + +__all__ = [ + "STRUCT_DTYPE_NAME", + "Struct", + "StructConfig", + "StructDTypeName", + "StructField", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/time.py b/packages/zarr-metadata/src/zarr_metadata/dtype/time.py index b63e0f60ed..df2305239e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/time.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/time.py @@ -1,11 +1,28 @@ """ -Time data type configuration (datetime64, timedelta64). +Time-shaped Zarr v3 data types. + +This module covers `numpy.datetime64` and `numpy.timedelta64`, both defined +in the zarr-extensions registry. + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types """ -from typing import Literal, TypedDict +from typing import Final, Literal, TypedDict from typing_extensions import ReadOnly +NUMPY_DATETIME64_DTYPE_NAME: Final = "numpy.datetime64" +"""The `name` field value of the `numpy.datetime64` data type.""" + +NumpyDatetime64DTypeName = Literal["numpy.datetime64"] +"""Literal type of the `name` field of the `numpy.datetime64` data type.""" + +NUMPY_TIMEDELTA64_DTYPE_NAME: Final = "numpy.timedelta64" +"""The `name` field value of the `numpy.timedelta64` data type.""" + +NumpyTimedelta64DTypeName = Literal["numpy.timedelta64"] +"""Literal type of the `name` field of the `numpy.timedelta64` data type.""" + DateTimeUnit = Literal[ "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" ] @@ -14,7 +31,7 @@ class TimeConfig(TypedDict): """ - Configuration for numpy.timedelta64 or numpy.datetime64 in Zarr v3. + Configuration shared by `numpy.datetime64` and `numpy.timedelta64`. Attributes ---------- @@ -28,7 +45,27 @@ class TimeConfig(TypedDict): scale_factor: ReadOnly[int] +class NumpyDatetime64(TypedDict): + """`numpy.datetime64` data type metadata.""" + + name: NumpyDatetime64DTypeName + configuration: TimeConfig + + +class NumpyTimedelta64(TypedDict): + """`numpy.timedelta64` data type metadata.""" + + name: NumpyTimedelta64DTypeName + configuration: TimeConfig + + __all__ = [ + "NUMPY_DATETIME64_DTYPE_NAME", + "NUMPY_TIMEDELTA64_DTYPE_NAME", "DateTimeUnit", + "NumpyDatetime64", + "NumpyDatetime64DTypeName", + "NumpyTimedelta64", + "NumpyTimedelta64DTypeName", "TimeConfig", ] diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index 3020a26599..d5ca6160e5 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -132,14 +132,97 @@ def test_codec_imports() -> None: def test_dtype_imports() -> None: from zarr_metadata.dtype import DType - from zarr_metadata.dtype.bytes import FixedLengthBytesConfig - from zarr_metadata.dtype.string import LengthBytesConfig - from zarr_metadata.dtype.time import DateTimeUnit, TimeConfig + from zarr_metadata.dtype.bytes import ( + BYTES_DTYPE_NAME, + NULL_TERMINATED_BYTES_DTYPE_NAME, + BytesDTypeName, + FixedLengthBytesConfig, + NullTerminatedBytes, + NullTerminatedBytesDTypeName, + ) + from zarr_metadata.dtype.primitive import ( + BOOL_DTYPE_NAME, + COMPLEX64_DTYPE_NAME, + COMPLEX128_DTYPE_NAME, + FLOAT16_DTYPE_NAME, + FLOAT32_DTYPE_NAME, + FLOAT64_DTYPE_NAME, + INT8_DTYPE_NAME, + INT16_DTYPE_NAME, + INT32_DTYPE_NAME, + INT64_DTYPE_NAME, + UINT8_DTYPE_NAME, + UINT16_DTYPE_NAME, + UINT32_DTYPE_NAME, + UINT64_DTYPE_NAME, + PrimitiveDTypeName, + ) + from zarr_metadata.dtype.string import ( + FIXED_LENGTH_UTF32_DTYPE_NAME, + STRING_DTYPE_NAME, + FixedLengthUtf32, + FixedLengthUtf32DTypeName, + LengthBytesConfig, + StringDTypeName, + ) + from zarr_metadata.dtype.struct import ( + STRUCT_DTYPE_NAME, + Struct, + StructConfig, + StructDTypeName, + StructField, + ) + from zarr_metadata.dtype.time import ( + NUMPY_DATETIME64_DTYPE_NAME, + NUMPY_TIMEDELTA64_DTYPE_NAME, + DateTimeUnit, + NumpyDatetime64, + NumpyDatetime64DTypeName, + NumpyTimedelta64, + NumpyTimedelta64DTypeName, + TimeConfig, + ) _ = ( DType, + BOOL_DTYPE_NAME, + BYTES_DTYPE_NAME, + BytesDTypeName, + COMPLEX64_DTYPE_NAME, + COMPLEX128_DTYPE_NAME, + DateTimeUnit, + FIXED_LENGTH_UTF32_DTYPE_NAME, + FLOAT16_DTYPE_NAME, + FLOAT32_DTYPE_NAME, + FLOAT64_DTYPE_NAME, FixedLengthBytesConfig, + FixedLengthUtf32, + FixedLengthUtf32DTypeName, + INT8_DTYPE_NAME, + INT16_DTYPE_NAME, + INT32_DTYPE_NAME, + INT64_DTYPE_NAME, LengthBytesConfig, - DateTimeUnit, + NULL_TERMINATED_BYTES_DTYPE_NAME, + NUMPY_DATETIME64_DTYPE_NAME, + NUMPY_TIMEDELTA64_DTYPE_NAME, + NullTerminatedBytes, + NullTerminatedBytesDTypeName, + NumpyDatetime64, + NumpyDatetime64DTypeName, + NumpyTimedelta64, + NumpyTimedelta64DTypeName, + PrimitiveDTypeName, + STRING_DTYPE_NAME, + STRUCT_DTYPE_NAME, + StringDTypeName, + Struct, + StructConfig, + StructDTypeName, + StructField, TimeConfig, + UINT8_DTYPE_NAME, + UINT16_DTYPE_NAME, + UINT32_DTYPE_NAME, + UINT64_DTYPE_NAME, ) diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index 29f85c608e..02206aa388 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -17,9 +17,10 @@ from zarr_metadata.codec.sharding import ShardingCodec, ShardingCodecConfiguration from zarr_metadata.codec.transpose import TransposeCodec, TransposeCodecConfiguration from zarr_metadata.codec.zstd import ZstdCodec, ZstdCodecConfiguration - from zarr_metadata.dtype.bytes import FixedLengthBytesConfig - from zarr_metadata.dtype.string import LengthBytesConfig - from zarr_metadata.dtype.time import TimeConfig + from zarr_metadata.dtype.bytes import FixedLengthBytesConfig, NullTerminatedBytes + from zarr_metadata.dtype.string import FixedLengthUtf32, LengthBytesConfig + from zarr_metadata.dtype.struct import Struct + from zarr_metadata.dtype.time import NumpyDatetime64, NumpyTimedelta64, TimeConfig from zarr_metadata.v2.array import ArrayMetadataV2 from zarr_metadata.v2.codec import NumcodecsConfig from zarr_metadata.v2.group import GroupMetadataV2 @@ -310,3 +311,86 @@ def test_sharding_index_location_constants() -> None: } assert cfg_end["index_location"] == "end" assert cfg_start["index_location"] == "start" + + +def test_primitive_dtype_names() -> None: + from zarr_metadata.dtype.primitive import ( + BOOL_DTYPE_NAME, + COMPLEX128_DTYPE_NAME, + FLOAT32_DTYPE_NAME, + INT32_DTYPE_NAME, + UINT64_DTYPE_NAME, + ) + + assert BOOL_DTYPE_NAME == "bool" + assert INT32_DTYPE_NAME == "int32" + assert UINT64_DTYPE_NAME == "uint64" + assert FLOAT32_DTYPE_NAME == "float32" + assert COMPLEX128_DTYPE_NAME == "complex128" + + +def test_null_terminated_bytes_dtype_metadata() -> None: + dtype: NullTerminatedBytes = { + "name": "null_terminated_bytes", + "configuration": {"length_bytes": 16}, + } + assert dtype["name"] == "null_terminated_bytes" + assert dtype["configuration"]["length_bytes"] == 16 + + +def test_fixed_length_utf32_dtype_metadata() -> None: + dtype: FixedLengthUtf32 = { + "name": "fixed_length_utf32", + "configuration": {"length_bytes": 32}, + } + assert dtype["name"] == "fixed_length_utf32" + + +def test_numpy_datetime64_dtype_metadata() -> None: + dtype: NumpyDatetime64 = { + "name": "numpy.datetime64", + "configuration": {"unit": "ns", "scale_factor": 1}, + } + assert dtype["name"] == "numpy.datetime64" + + +def test_numpy_timedelta64_dtype_metadata() -> None: + dtype: NumpyTimedelta64 = { + "name": "numpy.timedelta64", + "configuration": {"unit": "s", "scale_factor": 1}, + } + assert dtype["name"] == "numpy.timedelta64" + + +def test_struct_dtype_metadata() -> None: + dtype: Struct = { + "name": "struct", + "configuration": { + "fields": ( + {"name": "x", "data_type": "float32"}, + {"name": "y", "data_type": "float32"}, + ), + }, + } + assert dtype["name"] == "struct" + assert len(dtype["configuration"]["fields"]) == 2 + + +def test_struct_dtype_metadata_nested() -> None: + """Struct fields can hold envelope data types, including another struct.""" + inner: Struct = { + "name": "struct", + "configuration": { + "fields": ({"name": "r", "data_type": "uint8"},), + }, + } + outer: Struct = { + "name": "struct", + "configuration": { + "fields": ( + {"name": "coord", "data_type": "float64"}, + {"name": "color", "data_type": inner}, + ), + }, + } + assert outer["configuration"]["fields"][1]["name"] == "color" From 9554ca3d9d1125490faabd247f666a400f9f54eb Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 23:46:11 +0200 Subject: [PATCH 37/55] refactor(metadata): per-dtype modules with fill-value types and validators Restructure `zarr_metadata.dtype.*` so each spec data type lives in its own module, mirroring the per-codec layout in `zarr_metadata.codec.*` and the per-dtype directory layout in zarr-extensions. New per-type modules (one per spec data type): bool.py, int8/16/32/64.py, uint8/16/32/64.py, float16/32/64.py, complex64/128.py, bytes.py, string.py, numpy_datetime64.py, numpy_timedelta64.py, struct.py, raw.py Each module exports: - {DTYPE}_DTYPE_NAME (Final str) - {DType}DTypeName (Literal) - For envelope types: a {DType} TypedDict + a {DType}Configuration - {DType}FillValue alias for the JSON shape of `fill_value` Removed `null_terminated_bytes` and `fixed_length_utf32` from zarr-metadata: they are not in zarr-specs or zarr-extensions; they are zarr-python-specific. Their `LengthBytesConfig` and `FixedLengthBytesConfig` TypedDicts now live locally in zarr-python at src/zarr/core/dtype/npy/{string,bytes}.py. zarr.core.dtype.npy.common now imports `DateTimeUnit` from `zarr_metadata.dtype.numpy_datetime64`. zarr.core.dtype.npy.time imports `TimeConfig` (aliased from `NumpyDatetime64Configuration`). NewType + validating-constructor pattern for non-literal spec strings: - HexFloat{16,32,64} for the float hex-string fill values - Base64Bytes for the `bytes` base64 fill value - RawBytesDTypeName for the `r` parameterised name These make spec-format constraints visible to the type system; the matching validating constructors (e.g. `hex_float32`) are the only runtime logic in the package and are minimal regex checks. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/dtype/bool.py | 23 +++ .../src/zarr_metadata/dtype/bytes.py | 52 +++---- .../src/zarr_metadata/dtype/complex128.py | 37 +++++ .../src/zarr_metadata/dtype/complex64.py | 37 +++++ .../src/zarr_metadata/dtype/float16.py | 53 +++++++ .../src/zarr_metadata/dtype/float32.py | 53 +++++++ .../src/zarr_metadata/dtype/float64.py | 54 +++++++ .../src/zarr_metadata/dtype/int16.py | 23 +++ .../src/zarr_metadata/dtype/int32.py | 23 +++ .../src/zarr_metadata/dtype/int64.py | 23 +++ .../src/zarr_metadata/dtype/int8.py | 23 +++ .../zarr_metadata/dtype/numpy_datetime64.py | 61 ++++++++ .../dtype/{time.py => numpy_timedelta64.py} | 42 ++---- .../src/zarr_metadata/dtype/primitive.py | 62 -------- .../src/zarr_metadata/dtype/raw.py | 45 ++++++ .../src/zarr_metadata/dtype/string.py | 45 +----- .../src/zarr_metadata/dtype/struct.py | 19 ++- .../src/zarr_metadata/dtype/uint16.py | 23 +++ .../src/zarr_metadata/dtype/uint32.py | 23 +++ .../src/zarr_metadata/dtype/uint64.py | 23 +++ .../src/zarr_metadata/dtype/uint8.py | 23 +++ packages/zarr-metadata/tests/test_imports.py | 140 ++++++++++++------ .../zarr-metadata/tests/test_structural.py | 113 ++++++++------ src/zarr/core/dtype/npy/bytes.py | 16 +- src/zarr/core/dtype/npy/common.py | 2 +- src/zarr/core/dtype/npy/string.py | 15 +- src/zarr/core/dtype/npy/time.py | 4 +- 27 files changed, 802 insertions(+), 255 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/bool.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/complex128.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/complex64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/float16.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/float32.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/float64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/int16.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/int32.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/int64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/int8.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/numpy_datetime64.py rename packages/zarr-metadata/src/zarr_metadata/dtype/{time.py => numpy_timedelta64.py} (54%) delete mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/raw.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/uint16.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/uint32.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/uint64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/dtype/uint8.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/bool.py b/packages/zarr-metadata/src/zarr_metadata/dtype/bool.py new file mode 100644 index 0000000000..48042b612a --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/bool.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `bool` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +BOOL_DTYPE_NAME: Final = "bool" +"""The `data_type` value for the `bool` type.""" + +BoolDTypeName = Literal["bool"] +"""Literal type of the `data_type` field for `bool`.""" + +BoolFillValue = bool +"""Permitted JSON shape of the `fill_value` field for `bool`: a JSON boolean.""" + + +__all__ = [ + "BOOL_DTYPE_NAME", + "BoolDTypeName", + "BoolFillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py b/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py index f20090ed55..1295f22234 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py @@ -1,17 +1,11 @@ """ -Bytes-shaped Zarr v3 data types. +Zarr `bytes` data type (variable-length raw bytes, zarr-extensions). -This module covers: - -- `bytes` (variable-length bytes, bare string, zarr-extensions) -- `null_terminated_bytes` (fixed-length NUL-terminated, envelope, zarr-extensions) - -See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/bytes """ -from typing import Final, Literal, TypedDict - -from typing_extensions import ReadOnly +import re +from typing import Final, Literal, NewType BYTES_DTYPE_NAME: Final = "bytes" """The `data_type` value for the variable-length `bytes` type.""" @@ -19,36 +13,36 @@ BytesDTypeName = Literal["bytes"] """Literal type of the `data_type` field for `bytes`.""" -NULL_TERMINATED_BYTES_DTYPE_NAME: Final = "null_terminated_bytes" -"""The `name` field value of the `null_terminated_bytes` data type.""" +Base64Bytes = NewType("Base64Bytes", str) +"""A standard-alphabet base64-encoded byte sequence.""" -NullTerminatedBytesDTypeName = Literal["null_terminated_bytes"] -"""Literal type of the `name` field of the `null_terminated_bytes` data type.""" +_BASE64_RE: Final = re.compile(r"^[A-Za-z0-9+/]*={0,2}$") -class FixedLengthBytesConfig(TypedDict): - """ - Configuration for fixed-length bytes-shaped data types. +def base64_bytes(value: str) -> Base64Bytes: + """Validate `value` as a Base64Bytes and brand it. - Used by `null_terminated_bytes` (and any other fixed-length bytes - extension). `length_bytes` is the allocated byte count per element. + Raises ValueError if `value` is not standard-alphabet base64 + (length must be a multiple of 4 once padded; only `A-Z`, `a-z`, + `0-9`, `+`, `/`, and trailing `=` padding are permitted). """ - - length_bytes: ReadOnly[int] + if len(value) % 4 != 0 or not _BASE64_RE.fullmatch(value): + raise ValueError(f"Expected standard-alphabet base64, got {value!r}") + return Base64Bytes(value) -class NullTerminatedBytes(TypedDict): - """`null_terminated_bytes` data type metadata.""" +BytesFillValue = tuple[int, ...] | Base64Bytes +"""Permitted JSON shape of the `fill_value` field for `bytes`. - name: NullTerminatedBytesDTypeName - configuration: FixedLengthBytesConfig +Either a JSON array of integers in `[0, 255]` (one per byte), or a +`Base64Bytes` string encoding the byte sequence. +""" __all__ = [ "BYTES_DTYPE_NAME", - "NULL_TERMINATED_BYTES_DTYPE_NAME", + "Base64Bytes", "BytesDTypeName", - "FixedLengthBytesConfig", - "NullTerminatedBytes", - "NullTerminatedBytesDTypeName", + "BytesFillValue", + "base64_bytes", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/complex128.py b/packages/zarr-metadata/src/zarr_metadata/dtype/complex128.py new file mode 100644 index 0000000000..97bc14c08c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/complex128.py @@ -0,0 +1,37 @@ +""" +Zarr v3 `complex128` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +from zarr_metadata.dtype.float64 import Float64FillValue + +COMPLEX128_DTYPE_NAME: Final = "complex128" +"""The `data_type` value for the `complex128` type.""" + +Complex128DTypeName = Literal["complex128"] +"""Literal type of the `data_type` field for `complex128`.""" + +Complex128Component = Float64FillValue +"""One real or imaginary component of a `complex128` fill value. + +Same shape as a `float64` fill value: a JSON number, a named sentinel, +or a `HexFloat64` string. +""" + +Complex128FillValue = tuple[Complex128Component, Complex128Component] +"""Permitted JSON shape of the `fill_value` field for `complex128`. + +A two-element JSON array `[real, imag]` where each component is a +`Complex128Component`. +""" + + +__all__ = [ + "COMPLEX128_DTYPE_NAME", + "Complex128Component", + "Complex128DTypeName", + "Complex128FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/complex64.py b/packages/zarr-metadata/src/zarr_metadata/dtype/complex64.py new file mode 100644 index 0000000000..61772dd33c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/complex64.py @@ -0,0 +1,37 @@ +""" +Zarr v3 `complex64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +from zarr_metadata.dtype.float32 import Float32FillValue + +COMPLEX64_DTYPE_NAME: Final = "complex64" +"""The `data_type` value for the `complex64` type.""" + +Complex64DTypeName = Literal["complex64"] +"""Literal type of the `data_type` field for `complex64`.""" + +Complex64Component = Float32FillValue +"""One real or imaginary component of a `complex64` fill value. + +Same shape as a `float32` fill value: a JSON number, a named sentinel, +or a `HexFloat32` string. +""" + +Complex64FillValue = tuple[Complex64Component, Complex64Component] +"""Permitted JSON shape of the `fill_value` field for `complex64`. + +A two-element JSON array `[real, imag]` where each component is a +`Complex64Component`. +""" + + +__all__ = [ + "COMPLEX64_DTYPE_NAME", + "Complex64Component", + "Complex64DTypeName", + "Complex64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/float16.py b/packages/zarr-metadata/src/zarr_metadata/dtype/float16.py new file mode 100644 index 0000000000..dac9eed09b --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/float16.py @@ -0,0 +1,53 @@ +""" +Zarr v3 `float16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT16_DTYPE_NAME: Final = "float16" +"""The `data_type` value for the `float16` type.""" + +Float16DTypeName = Literal["float16"] +"""Literal type of the `data_type` field for `float16`.""" + +Float16SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat16 = NewType("HexFloat16", str) +"""A 6-character hex string (`0x` + 4 hex digits) encoding the +unsigned-integer representation of a float16.""" + +_HEX_FLOAT16_RE: Final = re.compile(r"^0x[0-9a-fA-F]{4}$") + + +def hex_float16(value: str) -> HexFloat16: + """Validate `value` as a HexFloat16 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 4 hex + digits. + """ + if not _HEX_FLOAT16_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 4 hex digits, got {value!r}") + return HexFloat16(value) + + +Float16FillValue = float | int | Float16SpecialFillValue | HexFloat16 +"""Permitted JSON shape of the `fill_value` field for `float16`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat16` (`0xYYYY` string encoding +the unsigned-integer representation of the IEEE 754 value). +""" + + +__all__ = [ + "FLOAT16_DTYPE_NAME", + "Float16DTypeName", + "Float16FillValue", + "Float16SpecialFillValue", + "HexFloat16", + "hex_float16", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/float32.py b/packages/zarr-metadata/src/zarr_metadata/dtype/float32.py new file mode 100644 index 0000000000..37bc19243e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/float32.py @@ -0,0 +1,53 @@ +""" +Zarr v3 `float32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT32_DTYPE_NAME: Final = "float32" +"""The `data_type` value for the `float32` type.""" + +Float32DTypeName = Literal["float32"] +"""Literal type of the `data_type` field for `float32`.""" + +Float32SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat32 = NewType("HexFloat32", str) +"""A 10-character hex string (`0x` + 8 hex digits) encoding the +unsigned-integer representation of a float32.""" + +_HEX_FLOAT32_RE: Final = re.compile(r"^0x[0-9a-fA-F]{8}$") + + +def hex_float32(value: str) -> HexFloat32: + """Validate `value` as a HexFloat32 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 8 hex + digits. + """ + if not _HEX_FLOAT32_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 8 hex digits, got {value!r}") + return HexFloat32(value) + + +Float32FillValue = float | int | Float32SpecialFillValue | HexFloat32 +"""Permitted JSON shape of the `fill_value` field for `float32`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat32` (`0xYYYYYYYY` string +encoding the unsigned-integer representation of the IEEE 754 value). +""" + + +__all__ = [ + "FLOAT32_DTYPE_NAME", + "Float32DTypeName", + "Float32FillValue", + "Float32SpecialFillValue", + "HexFloat32", + "hex_float32", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/float64.py b/packages/zarr-metadata/src/zarr_metadata/dtype/float64.py new file mode 100644 index 0000000000..28e77568af --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/float64.py @@ -0,0 +1,54 @@ +""" +Zarr v3 `float64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT64_DTYPE_NAME: Final = "float64" +"""The `data_type` value for the `float64` type.""" + +Float64DTypeName = Literal["float64"] +"""Literal type of the `data_type` field for `float64`.""" + +Float64SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat64 = NewType("HexFloat64", str) +"""An 18-character hex string (`0x` + 16 hex digits) encoding the +unsigned-integer representation of a float64.""" + +_HEX_FLOAT64_RE: Final = re.compile(r"^0x[0-9a-fA-F]{16}$") + + +def hex_float64(value: str) -> HexFloat64: + """Validate `value` as a HexFloat64 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 16 hex + digits. + """ + if not _HEX_FLOAT64_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 16 hex digits, got {value!r}") + return HexFloat64(value) + + +Float64FillValue = float | int | Float64SpecialFillValue | HexFloat64 +"""Permitted JSON shape of the `fill_value` field for `float64`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat64` (`0xYYYYYYYYYYYYYYYY` +string encoding the unsigned-integer representation of the IEEE 754 +value). +""" + + +__all__ = [ + "FLOAT64_DTYPE_NAME", + "Float64DTypeName", + "Float64FillValue", + "Float64SpecialFillValue", + "HexFloat64", + "hex_float64", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int16.py b/packages/zarr-metadata/src/zarr_metadata/dtype/int16.py new file mode 100644 index 0000000000..e0488ab56e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/int16.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT16_DTYPE_NAME: Final = "int16" +"""The `data_type` value for the `int16` type.""" + +Int16DTypeName = Literal["int16"] +"""Literal type of the `data_type` field for `int16`.""" + +Int16FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int16`: a JSON integer in [-32768, 32767].""" + + +__all__ = [ + "INT16_DTYPE_NAME", + "Int16DTypeName", + "Int16FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int32.py b/packages/zarr-metadata/src/zarr_metadata/dtype/int32.py new file mode 100644 index 0000000000..762561a4b1 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/int32.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT32_DTYPE_NAME: Final = "int32" +"""The `data_type` value for the `int32` type.""" + +Int32DTypeName = Literal["int32"] +"""Literal type of the `data_type` field for `int32`.""" + +Int32FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int32`: a JSON integer in [-2**31, 2**31 - 1].""" + + +__all__ = [ + "INT32_DTYPE_NAME", + "Int32DTypeName", + "Int32FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int64.py b/packages/zarr-metadata/src/zarr_metadata/dtype/int64.py new file mode 100644 index 0000000000..4699d4681c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/int64.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT64_DTYPE_NAME: Final = "int64" +"""The `data_type` value for the `int64` type.""" + +Int64DTypeName = Literal["int64"] +"""Literal type of the `data_type` field for `int64`.""" + +Int64FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int64`: a JSON integer in [-2**63, 2**63 - 1].""" + + +__all__ = [ + "INT64_DTYPE_NAME", + "Int64DTypeName", + "Int64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int8.py b/packages/zarr-metadata/src/zarr_metadata/dtype/int8.py new file mode 100644 index 0000000000..84a788a963 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/int8.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int8` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT8_DTYPE_NAME: Final = "int8" +"""The `data_type` value for the `int8` type.""" + +Int8DTypeName = Literal["int8"] +"""Literal type of the `data_type` field for `int8`.""" + +Int8FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int8`: a JSON integer in [-128, 127].""" + + +__all__ = [ + "INT8_DTYPE_NAME", + "Int8DTypeName", + "Int8FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/numpy_datetime64.py b/packages/zarr-metadata/src/zarr_metadata/dtype/numpy_datetime64.py new file mode 100644 index 0000000000..d6e77a7fb7 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/numpy_datetime64.py @@ -0,0 +1,61 @@ +""" +Zarr `numpy.datetime64` data type (zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.datetime64 +""" + +from typing import Final, Literal, TypedDict + +from typing_extensions import ReadOnly + +NUMPY_DATETIME64_DTYPE_NAME: Final = "numpy.datetime64" +"""The `name` field value of the `numpy.datetime64` data type.""" + +NumpyDatetime64DTypeName = Literal["numpy.datetime64"] +"""Literal type of the `name` field of the `numpy.datetime64` data type.""" + +DateTimeUnit = Literal[ + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" +] +"""Time unit codes used by numpy.datetime64.""" + + +class NumpyDatetime64Configuration(TypedDict): + """ + Configuration for the `numpy.datetime64` data type. + + Attributes + ---------- + unit + A string encoding a unit of time. + scale_factor + The multiplier relative to the unit. + """ + + unit: ReadOnly[DateTimeUnit] + scale_factor: ReadOnly[int] + + +class NumpyDatetime64(TypedDict): + """`numpy.datetime64` data type metadata.""" + + name: NumpyDatetime64DTypeName + configuration: NumpyDatetime64Configuration + + +NumpyDatetime64FillValue = int | Literal["NaT"] +"""Permitted JSON shape of the `fill_value` field for `numpy.datetime64`. + +Either a JSON integer (count of `unit * scale_factor` since the epoch), +or the string `"NaT"` (equivalent to the integer `-2**63`). +""" + + +__all__ = [ + "NUMPY_DATETIME64_DTYPE_NAME", + "DateTimeUnit", + "NumpyDatetime64", + "NumpyDatetime64Configuration", + "NumpyDatetime64DTypeName", + "NumpyDatetime64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/time.py b/packages/zarr-metadata/src/zarr_metadata/dtype/numpy_timedelta64.py similarity index 54% rename from packages/zarr-metadata/src/zarr_metadata/dtype/time.py rename to packages/zarr-metadata/src/zarr_metadata/dtype/numpy_timedelta64.py index df2305239e..535b231490 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/time.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/numpy_timedelta64.py @@ -1,22 +1,13 @@ """ -Time-shaped Zarr v3 data types. +Zarr `numpy.timedelta64` data type (zarr-extensions). -This module covers `numpy.datetime64` and `numpy.timedelta64`, both defined -in the zarr-extensions registry. - -See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.timedelta64 """ from typing import Final, Literal, TypedDict from typing_extensions import ReadOnly -NUMPY_DATETIME64_DTYPE_NAME: Final = "numpy.datetime64" -"""The `name` field value of the `numpy.datetime64` data type.""" - -NumpyDatetime64DTypeName = Literal["numpy.datetime64"] -"""Literal type of the `name` field of the `numpy.datetime64` data type.""" - NUMPY_TIMEDELTA64_DTYPE_NAME: Final = "numpy.timedelta64" """The `name` field value of the `numpy.timedelta64` data type.""" @@ -26,12 +17,12 @@ DateTimeUnit = Literal[ "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" ] -"""Time unit codes used by numpy.datetime64 / numpy.timedelta64.""" +"""Time unit codes used by numpy.timedelta64.""" -class TimeConfig(TypedDict): +class NumpyTimedelta64Configuration(TypedDict): """ - Configuration shared by `numpy.datetime64` and `numpy.timedelta64`. + Configuration for the `numpy.timedelta64` data type. Attributes ---------- @@ -45,27 +36,26 @@ class TimeConfig(TypedDict): scale_factor: ReadOnly[int] -class NumpyDatetime64(TypedDict): - """`numpy.datetime64` data type metadata.""" - - name: NumpyDatetime64DTypeName - configuration: TimeConfig - - class NumpyTimedelta64(TypedDict): """`numpy.timedelta64` data type metadata.""" name: NumpyTimedelta64DTypeName - configuration: TimeConfig + configuration: NumpyTimedelta64Configuration + + +NumpyTimedelta64FillValue = int | Literal["NaT"] +"""Permitted JSON shape of the `fill_value` field for `numpy.timedelta64`. + +Either a JSON integer (a count of `unit * scale_factor`), or the string +`"NaT"` (equivalent to the integer `-2**63`). +""" __all__ = [ - "NUMPY_DATETIME64_DTYPE_NAME", "NUMPY_TIMEDELTA64_DTYPE_NAME", "DateTimeUnit", - "NumpyDatetime64", - "NumpyDatetime64DTypeName", "NumpyTimedelta64", + "NumpyTimedelta64Configuration", "NumpyTimedelta64DTypeName", - "TimeConfig", + "NumpyTimedelta64FillValue", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py b/packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py deleted file mode 100644 index 2f51e5a112..0000000000 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/primitive.py +++ /dev/null @@ -1,62 +0,0 @@ -""" -Primitive Zarr v3 data types. - -All primitives are spec-defined as bare-string `data_type` values -- they -carry no configuration. - -See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#data-types -""" - -from typing import Final, Literal - -BOOL_DTYPE_NAME: Final = "bool" -INT8_DTYPE_NAME: Final = "int8" -INT16_DTYPE_NAME: Final = "int16" -INT32_DTYPE_NAME: Final = "int32" -INT64_DTYPE_NAME: Final = "int64" -UINT8_DTYPE_NAME: Final = "uint8" -UINT16_DTYPE_NAME: Final = "uint16" -UINT32_DTYPE_NAME: Final = "uint32" -UINT64_DTYPE_NAME: Final = "uint64" -FLOAT16_DTYPE_NAME: Final = "float16" -FLOAT32_DTYPE_NAME: Final = "float32" -FLOAT64_DTYPE_NAME: Final = "float64" -COMPLEX64_DTYPE_NAME: Final = "complex64" -COMPLEX128_DTYPE_NAME: Final = "complex128" - -PrimitiveDTypeName = Literal[ - "bool", - "int8", - "int16", - "int32", - "int64", - "uint8", - "uint16", - "uint32", - "uint64", - "float16", - "float32", - "float64", - "complex64", - "complex128", -] -"""Literal union of every core v3 primitive data type name.""" - - -__all__ = [ - "BOOL_DTYPE_NAME", - "COMPLEX64_DTYPE_NAME", - "COMPLEX128_DTYPE_NAME", - "FLOAT16_DTYPE_NAME", - "FLOAT32_DTYPE_NAME", - "FLOAT64_DTYPE_NAME", - "INT8_DTYPE_NAME", - "INT16_DTYPE_NAME", - "INT32_DTYPE_NAME", - "INT64_DTYPE_NAME", - "UINT8_DTYPE_NAME", - "UINT16_DTYPE_NAME", - "UINT32_DTYPE_NAME", - "UINT64_DTYPE_NAME", - "PrimitiveDTypeName", -] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/raw.py b/packages/zarr-metadata/src/zarr_metadata/dtype/raw.py new file mode 100644 index 0000000000..0b6cb0cc42 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/raw.py @@ -0,0 +1,45 @@ +""" +Zarr v3 `r` raw-bytes data type (parameterised by bit count). + +The `data_type` value is a string of the form `r` where `N` is a +positive multiple of 8 (e.g. `r8`, `r16`, `r24`). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html +""" + +import re +from typing import Final, NewType + +RawBytesDTypeName = NewType("RawBytesDTypeName", str) +"""A spec-conformant `r` raw-bytes name (e.g. `"r8"`, `"r16"`).""" + +_RAW_BYTES_RE: Final = re.compile(r"^r(\d+)$") + + +def raw_bytes_dtype_name(value: str) -> RawBytesDTypeName: + """Validate `value` as a `r` raw-bytes name and brand it. + + Raises ValueError if `value` is not `r` followed by a positive + multiple of 8. + """ + match = _RAW_BYTES_RE.fullmatch(value) + if match is None: + raise ValueError(f"Expected 'r' followed by a positive integer, got {value!r}") + bits = int(match.group(1)) + if bits == 0 or bits % 8 != 0: + raise ValueError(f"Expected 'r' where N is a positive multiple of 8, got {value!r}") + return RawBytesDTypeName(value) + + +RawBytesFillValue = tuple[int, ...] +"""Permitted JSON shape of the `fill_value` field for `r`. + +A JSON array of N/8 integers in `[0, 255]` (one per byte). +""" + + +__all__ = [ + "RawBytesDTypeName", + "RawBytesFillValue", + "raw_bytes_dtype_name", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/string.py b/packages/zarr-metadata/src/zarr_metadata/dtype/string.py index 337436418c..82347cde9f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/string.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/string.py @@ -1,54 +1,23 @@ """ -String-shaped Zarr v3 data types. +Zarr `string` data type (variable-length utf-8, zarr-extensions). -This module covers: - -- `string` (variable-length utf-8, bare string, zarr-extensions) -- `fixed_length_utf32` (fixed-length utf-32, envelope, zarr-extensions) - -See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/string """ -from typing import Final, Literal, TypedDict - -from typing_extensions import ReadOnly +from typing import Final, Literal STRING_DTYPE_NAME: Final = "string" -"""The `data_type` value for the variable-length `string` type.""" +"""The `data_type` value for the `string` type.""" StringDTypeName = Literal["string"] """Literal type of the `data_type` field for `string`.""" -FIXED_LENGTH_UTF32_DTYPE_NAME: Final = "fixed_length_utf32" -"""The `name` field value of the `fixed_length_utf32` data type.""" - -FixedLengthUtf32DTypeName = Literal["fixed_length_utf32"] -"""Literal type of the `name` field of the `fixed_length_utf32` data type.""" - - -class LengthBytesConfig(TypedDict): - """ - Configuration for fixed-length string-shaped data types. - - Used by `fixed_length_utf32`. `length_bytes` is the allocated byte count - per element; for utf-32 this must be a multiple of 4. - """ - - length_bytes: ReadOnly[int] - - -class FixedLengthUtf32(TypedDict): - """`fixed_length_utf32` data type metadata.""" - - name: FixedLengthUtf32DTypeName - configuration: LengthBytesConfig +StringFillValue = str +"""Permitted JSON shape of the `fill_value` field for `string`: a JSON unicode string.""" __all__ = [ - "FIXED_LENGTH_UTF32_DTYPE_NAME", "STRING_DTYPE_NAME", - "FixedLengthUtf32", - "FixedLengthUtf32DTypeName", - "LengthBytesConfig", "StringDTypeName", + "StringFillValue", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py b/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py index 42b3bc7b33..20b0b1e925 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py @@ -1,13 +1,15 @@ """ -Structured (heterogeneous) Zarr v3 data type. +Zarr `struct` data type (heterogeneous record, zarr-extensions). See https://github.com/zarr-developers/zarr-extensions/blob/main/data-types/struct/README.md """ +from collections.abc import Mapping from typing import Final, Literal, TypedDict from typing_extensions import ReadOnly +from zarr_metadata.common import JSON from zarr_metadata.dtype import DType STRUCT_DTYPE_NAME: Final = "struct" @@ -34,7 +36,7 @@ class StructField(TypedDict): data_type: ReadOnly[DType] -class StructConfig(TypedDict): +class StructConfiguration(TypedDict): """Configuration for the `struct` data type.""" fields: ReadOnly[tuple[StructField, ...]] @@ -44,13 +46,22 @@ class Struct(TypedDict): """`struct` data type metadata.""" name: StructDTypeName - configuration: StructConfig + configuration: StructConfiguration + + +StructFillValue = Mapping[str, JSON] +"""Permitted JSON shape of the `fill_value` field for `struct`. + +A JSON object mapping each field name to that field's fill value. Field +fill values are themselves shaped per the field's `data_type`, recursively. +""" __all__ = [ "STRUCT_DTYPE_NAME", "Struct", - "StructConfig", + "StructConfiguration", "StructDTypeName", "StructField", + "StructFillValue", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint16.py b/packages/zarr-metadata/src/zarr_metadata/dtype/uint16.py new file mode 100644 index 0000000000..541f3ecb29 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/uint16.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT16_DTYPE_NAME: Final = "uint16" +"""The `data_type` value for the `uint16` type.""" + +Uint16DTypeName = Literal["uint16"] +"""Literal type of the `data_type` field for `uint16`.""" + +Uint16FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint16`: a JSON integer in [0, 65535].""" + + +__all__ = [ + "UINT16_DTYPE_NAME", + "Uint16DTypeName", + "Uint16FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint32.py b/packages/zarr-metadata/src/zarr_metadata/dtype/uint32.py new file mode 100644 index 0000000000..6aaca8cdb8 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/uint32.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT32_DTYPE_NAME: Final = "uint32" +"""The `data_type` value for the `uint32` type.""" + +Uint32DTypeName = Literal["uint32"] +"""Literal type of the `data_type` field for `uint32`.""" + +Uint32FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint32`: a JSON integer in [0, 2**32 - 1].""" + + +__all__ = [ + "UINT32_DTYPE_NAME", + "Uint32DTypeName", + "Uint32FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint64.py b/packages/zarr-metadata/src/zarr_metadata/dtype/uint64.py new file mode 100644 index 0000000000..80bfafcabb --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/uint64.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT64_DTYPE_NAME: Final = "uint64" +"""The `data_type` value for the `uint64` type.""" + +Uint64DTypeName = Literal["uint64"] +"""Literal type of the `data_type` field for `uint64`.""" + +Uint64FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint64`: a JSON integer in [0, 2**64 - 1].""" + + +__all__ = [ + "UINT64_DTYPE_NAME", + "Uint64DTypeName", + "Uint64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint8.py b/packages/zarr-metadata/src/zarr_metadata/dtype/uint8.py new file mode 100644 index 0000000000..8410b60727 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/dtype/uint8.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint8` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT8_DTYPE_NAME: Final = "uint8" +"""The `data_type` value for the `uint8` type.""" + +Uint8DTypeName = Literal["uint8"] +"""Literal type of the `data_type` field for `uint8`.""" + +Uint8FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint8`: a JSON integer in [0, 255].""" + + +__all__ = [ + "UINT8_DTYPE_NAME", + "Uint8DTypeName", + "Uint8FillValue", +] diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index d5ca6160e5..d6953c0ea1 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -132,97 +132,139 @@ def test_codec_imports() -> None: def test_dtype_imports() -> None: from zarr_metadata.dtype import DType - from zarr_metadata.dtype.bytes import ( - BYTES_DTYPE_NAME, - NULL_TERMINATED_BYTES_DTYPE_NAME, - BytesDTypeName, - FixedLengthBytesConfig, - NullTerminatedBytes, - NullTerminatedBytesDTypeName, - ) - from zarr_metadata.dtype.primitive import ( - BOOL_DTYPE_NAME, + from zarr_metadata.dtype.bool import BOOL_DTYPE_NAME, BoolDTypeName, BoolFillValue + from zarr_metadata.dtype.bytes import BYTES_DTYPE_NAME, BytesDTypeName, BytesFillValue + from zarr_metadata.dtype.complex64 import ( COMPLEX64_DTYPE_NAME, + Complex64Component, + Complex64DTypeName, + Complex64FillValue, + ) + from zarr_metadata.dtype.complex128 import ( COMPLEX128_DTYPE_NAME, + Complex128Component, + Complex128DTypeName, + Complex128FillValue, + ) + from zarr_metadata.dtype.float16 import ( FLOAT16_DTYPE_NAME, + Float16DTypeName, + Float16FillValue, + Float16SpecialFillValue, + ) + from zarr_metadata.dtype.float32 import ( FLOAT32_DTYPE_NAME, + Float32DTypeName, + Float32FillValue, + Float32SpecialFillValue, + ) + from zarr_metadata.dtype.float64 import ( FLOAT64_DTYPE_NAME, - INT8_DTYPE_NAME, - INT16_DTYPE_NAME, - INT32_DTYPE_NAME, - INT64_DTYPE_NAME, - UINT8_DTYPE_NAME, - UINT16_DTYPE_NAME, - UINT32_DTYPE_NAME, - UINT64_DTYPE_NAME, - PrimitiveDTypeName, + Float64DTypeName, + Float64FillValue, + Float64SpecialFillValue, ) - from zarr_metadata.dtype.string import ( - FIXED_LENGTH_UTF32_DTYPE_NAME, - STRING_DTYPE_NAME, - FixedLengthUtf32, - FixedLengthUtf32DTypeName, - LengthBytesConfig, - StringDTypeName, + from zarr_metadata.dtype.int8 import INT8_DTYPE_NAME, Int8DTypeName, Int8FillValue + from zarr_metadata.dtype.int16 import INT16_DTYPE_NAME, Int16DTypeName, Int16FillValue + from zarr_metadata.dtype.int32 import INT32_DTYPE_NAME, Int32DTypeName, Int32FillValue + from zarr_metadata.dtype.int64 import INT64_DTYPE_NAME, Int64DTypeName, Int64FillValue + from zarr_metadata.dtype.numpy_datetime64 import ( + NUMPY_DATETIME64_DTYPE_NAME, + NumpyDatetime64, + NumpyDatetime64Configuration, + NumpyDatetime64DTypeName, + NumpyDatetime64FillValue, + ) + from zarr_metadata.dtype.numpy_timedelta64 import ( + NUMPY_TIMEDELTA64_DTYPE_NAME, + NumpyTimedelta64, + NumpyTimedelta64Configuration, + NumpyTimedelta64DTypeName, + NumpyTimedelta64FillValue, ) + from zarr_metadata.dtype.string import STRING_DTYPE_NAME, StringDTypeName, StringFillValue from zarr_metadata.dtype.struct import ( STRUCT_DTYPE_NAME, Struct, - StructConfig, + StructConfiguration, StructDTypeName, StructField, + StructFillValue, ) - from zarr_metadata.dtype.time import ( - NUMPY_DATETIME64_DTYPE_NAME, - NUMPY_TIMEDELTA64_DTYPE_NAME, - DateTimeUnit, - NumpyDatetime64, - NumpyDatetime64DTypeName, - NumpyTimedelta64, - NumpyTimedelta64DTypeName, - TimeConfig, - ) + from zarr_metadata.dtype.uint8 import UINT8_DTYPE_NAME, Uint8DTypeName, Uint8FillValue + from zarr_metadata.dtype.uint16 import UINT16_DTYPE_NAME, Uint16DTypeName, Uint16FillValue + from zarr_metadata.dtype.uint32 import UINT32_DTYPE_NAME, Uint32DTypeName, Uint32FillValue + from zarr_metadata.dtype.uint64 import UINT64_DTYPE_NAME, Uint64DTypeName, Uint64FillValue _ = ( DType, BOOL_DTYPE_NAME, BYTES_DTYPE_NAME, + BoolDTypeName, + BoolFillValue, BytesDTypeName, + BytesFillValue, COMPLEX64_DTYPE_NAME, COMPLEX128_DTYPE_NAME, - DateTimeUnit, - FIXED_LENGTH_UTF32_DTYPE_NAME, + Complex64Component, + Complex64DTypeName, + Complex64FillValue, + Complex128Component, + Complex128DTypeName, + Complex128FillValue, FLOAT16_DTYPE_NAME, FLOAT32_DTYPE_NAME, FLOAT64_DTYPE_NAME, - FixedLengthBytesConfig, - FixedLengthUtf32, - FixedLengthUtf32DTypeName, + Float16DTypeName, + Float16FillValue, + Float16SpecialFillValue, + Float32DTypeName, + Float32FillValue, + Float32SpecialFillValue, + Float64DTypeName, + Float64FillValue, + Float64SpecialFillValue, INT8_DTYPE_NAME, INT16_DTYPE_NAME, INT32_DTYPE_NAME, INT64_DTYPE_NAME, - LengthBytesConfig, - NULL_TERMINATED_BYTES_DTYPE_NAME, + Int8DTypeName, + Int8FillValue, + Int16DTypeName, + Int16FillValue, + Int32DTypeName, + Int32FillValue, + Int64DTypeName, + Int64FillValue, NUMPY_DATETIME64_DTYPE_NAME, NUMPY_TIMEDELTA64_DTYPE_NAME, - NullTerminatedBytes, - NullTerminatedBytesDTypeName, NumpyDatetime64, + NumpyDatetime64Configuration, NumpyDatetime64DTypeName, + NumpyDatetime64FillValue, NumpyTimedelta64, + NumpyTimedelta64Configuration, NumpyTimedelta64DTypeName, - PrimitiveDTypeName, + NumpyTimedelta64FillValue, STRING_DTYPE_NAME, STRUCT_DTYPE_NAME, StringDTypeName, + StringFillValue, Struct, - StructConfig, + StructConfiguration, StructDTypeName, StructField, - TimeConfig, + StructFillValue, UINT8_DTYPE_NAME, UINT16_DTYPE_NAME, UINT32_DTYPE_NAME, UINT64_DTYPE_NAME, + Uint8DTypeName, + Uint8FillValue, + Uint16DTypeName, + Uint16FillValue, + Uint32DTypeName, + Uint32FillValue, + Uint64DTypeName, + Uint64FillValue, ) diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index 02206aa388..f38ca188cc 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -9,6 +9,8 @@ from typing import TYPE_CHECKING +import pytest + if TYPE_CHECKING: from zarr_metadata.codec.blosc import BloscCodec, BloscCodecConfiguration from zarr_metadata.codec.bytes import BytesCodec, BytesCodecConfiguration @@ -17,10 +19,9 @@ from zarr_metadata.codec.sharding import ShardingCodec, ShardingCodecConfiguration from zarr_metadata.codec.transpose import TransposeCodec, TransposeCodecConfiguration from zarr_metadata.codec.zstd import ZstdCodec, ZstdCodecConfiguration - from zarr_metadata.dtype.bytes import FixedLengthBytesConfig, NullTerminatedBytes - from zarr_metadata.dtype.string import FixedLengthUtf32, LengthBytesConfig + from zarr_metadata.dtype.numpy_datetime64 import NumpyDatetime64 + from zarr_metadata.dtype.numpy_timedelta64 import NumpyTimedelta64 from zarr_metadata.dtype.struct import Struct - from zarr_metadata.dtype.time import NumpyDatetime64, NumpyTimedelta64, TimeConfig from zarr_metadata.v2.array import ArrayMetadataV2 from zarr_metadata.v2.codec import NumcodecsConfig from zarr_metadata.v2.group import GroupMetadataV2 @@ -115,21 +116,6 @@ def test_blosc_config_v1() -> None: assert cfg["cname"] == "zstd" -def test_length_bytes_config() -> None: - cfg: LengthBytesConfig = {"length_bytes": 16} - assert cfg["length_bytes"] == 16 - - -def test_fixed_length_bytes_config() -> None: - cfg: FixedLengthBytesConfig = {"length_bytes": 16} - assert cfg["length_bytes"] == 16 - - -def test_time_config() -> None: - cfg: TimeConfig = {"unit": "ns", "scale_factor": 1} - assert cfg["unit"] == "ns" - - def test_numcodecs_config_minimal() -> None: cfg: NumcodecsConfig = {"id": "zstd"} assert cfg["id"] == "zstd" @@ -314,13 +300,11 @@ def test_sharding_index_location_constants() -> None: def test_primitive_dtype_names() -> None: - from zarr_metadata.dtype.primitive import ( - BOOL_DTYPE_NAME, - COMPLEX128_DTYPE_NAME, - FLOAT32_DTYPE_NAME, - INT32_DTYPE_NAME, - UINT64_DTYPE_NAME, - ) + from zarr_metadata.dtype.bool import BOOL_DTYPE_NAME + from zarr_metadata.dtype.complex128 import COMPLEX128_DTYPE_NAME + from zarr_metadata.dtype.float32 import FLOAT32_DTYPE_NAME + from zarr_metadata.dtype.int32 import INT32_DTYPE_NAME + from zarr_metadata.dtype.uint64 import UINT64_DTYPE_NAME assert BOOL_DTYPE_NAME == "bool" assert INT32_DTYPE_NAME == "int32" @@ -329,23 +313,6 @@ def test_primitive_dtype_names() -> None: assert COMPLEX128_DTYPE_NAME == "complex128" -def test_null_terminated_bytes_dtype_metadata() -> None: - dtype: NullTerminatedBytes = { - "name": "null_terminated_bytes", - "configuration": {"length_bytes": 16}, - } - assert dtype["name"] == "null_terminated_bytes" - assert dtype["configuration"]["length_bytes"] == 16 - - -def test_fixed_length_utf32_dtype_metadata() -> None: - dtype: FixedLengthUtf32 = { - "name": "fixed_length_utf32", - "configuration": {"length_bytes": 32}, - } - assert dtype["name"] == "fixed_length_utf32" - - def test_numpy_datetime64_dtype_metadata() -> None: dtype: NumpyDatetime64 = { "name": "numpy.datetime64", @@ -394,3 +361,65 @@ def test_struct_dtype_metadata_nested() -> None: }, } assert outer["configuration"]["fields"][1]["name"] == "color" + + +def test_hex_float16_validator() -> None: + from zarr_metadata.dtype.float16 import hex_float16 + + assert hex_float16("0x7c00") == "0x7c00" + with pytest.raises(ValueError): + hex_float16("0x7c") # too short + with pytest.raises(ValueError): + hex_float16("0X7C00") # uppercase 0X prefix not accepted + with pytest.raises(ValueError): + hex_float16("not hex") + + +def test_hex_float32_validator() -> None: + from zarr_metadata.dtype.float32 import hex_float32 + + assert hex_float32("0x7fc00000") == "0x7fc00000" + with pytest.raises(ValueError): + hex_float32("0x7fc0") # too short + with pytest.raises(ValueError): + hex_float32("not hex") + + +def test_hex_float64_validator() -> None: + from zarr_metadata.dtype.float64 import hex_float64 + + assert hex_float64("0x7ff8000000000000") == "0x7ff8000000000000" + with pytest.raises(ValueError): + hex_float64("0x7ff8") # too short + with pytest.raises(ValueError): + hex_float64("not hex") + + +def test_base64_bytes_validator() -> None: + from zarr_metadata.dtype.bytes import base64_bytes + + assert base64_bytes("SGVsbG8=") == "SGVsbG8=" + assert base64_bytes("") == "" + assert base64_bytes("AAAA") == "AAAA" + + with pytest.raises(ValueError): + base64_bytes("not!base64") + with pytest.raises(ValueError): + base64_bytes("ABC") # length not a multiple of 4 + + +def test_raw_bytes_dtype_name_validator() -> None: + from zarr_metadata.dtype.raw import raw_bytes_dtype_name + + assert raw_bytes_dtype_name("r8") == "r8" + assert raw_bytes_dtype_name("r16") == "r16" + assert raw_bytes_dtype_name("r256") == "r256" + + with pytest.raises(ValueError): + raw_bytes_dtype_name("r3") # not a multiple of 8 + with pytest.raises(ValueError): + raw_bytes_dtype_name("r0") # zero not allowed + with pytest.raises(ValueError): + raw_bytes_dtype_name("R8") # uppercase R not accepted + with pytest.raises(ValueError): + raw_bytes_dtype_name("8") # missing prefix diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index 648c2ef5c6..9cc137240b 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -3,7 +3,7 @@ import base64 import re from dataclasses import dataclass -from typing import ClassVar, Literal, Self, TypeGuard, cast, overload +from typing import ClassVar, Literal, Self, TypedDict, TypeGuard, cast, overload import numpy as np @@ -20,7 +20,19 @@ ) from zarr.core.dtype.npy.common import check_json_str from zarr.core.dtype.wrapper import TBaseDType, ZDType -from zarr_metadata.dtype.bytes import FixedLengthBytesConfig as FixedLengthBytesConfig # noqa: TC002 + + +class FixedLengthBytesConfig(TypedDict): + """ + Configuration for fixed-length bytes data types in Zarr V3. + + `null_terminated_bytes` is a zarr-python-specific extension; the + configuration carries `length_bytes`, the per-element allocated + byte count. + """ + + length_bytes: int + BytesLike = np.bytes_ | str | bytes | int diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index e34d7851e3..4e7bab8e58 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -18,7 +18,7 @@ ) import numpy as np -from zarr_metadata.dtype.time import DateTimeUnit as DateTimeUnit +from zarr_metadata.dtype.numpy_datetime64 import DateTimeUnit as DateTimeUnit from zarr.core.dtype.common import ( ENDIANNESS_STR, diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index a74f258b43..f4e0f9b9a8 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -8,6 +8,7 @@ Literal, Protocol, Self, + TypedDict, TypeGuard, overload, runtime_checkable, @@ -33,7 +34,19 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import ZDType -from zarr_metadata.dtype.string import LengthBytesConfig as LengthBytesConfig # noqa: TC002 + + +class LengthBytesConfig(TypedDict): + """ + Configuration for the fixed-length-utf32 string data type in Zarr V3. + + `fixed_length_utf32` is a zarr-python-specific extension; the + configuration carries `length_bytes`, the per-element byte allocation + (must be a multiple of 4 for utf-32). + """ + + length_bytes: int + if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index 52e2df70ed..ae24823870 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -14,6 +14,9 @@ ) import numpy as np +from zarr_metadata.dtype.numpy_datetime64 import ( + NumpyDatetime64Configuration as TimeConfig, +) from zarr.core.common import NamedConfig from zarr.core.dtype.common import ( @@ -32,7 +35,6 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import TBaseDType, ZDType -from zarr_metadata.dtype.time import TimeConfig as TimeConfig # noqa: TC002 if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat From 8d2bd63ae254333535303775172d1a07ccb544c8 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Apr 2026 23:56:51 +0200 Subject: [PATCH 38/55] refactor(metadata): per-grid and per-encoding modules for chunk_grid + chunk_key_encoding MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Move chunk-grid TypedDicts out of `v3/array.py` into per-type modules, mirroring the per-codec and per-dtype layouts: packages/zarr-metadata/src/zarr_metadata/v3/ ├── chunk_grid/ │ ├── __init__.py │ ├── regular.py # core spec │ └── rectilinear.py # zarr-extensions └── chunk_key_encoding/ ├── __init__.py # ChunkKeySeparator alias ├── default.py # core spec └── v2.py # core spec Each module exports: - {NAME}_NAME (Final str) - {Name} (TypedDict envelope) - {Name}Configuration (TypedDict body) - {Name}Name (Literal type of the `name` field) `v3/array.py` shrinks to just `AllowedExtraField`, `MetadataField`, and `ArrayMetadataV3`. `chunk_grid` and `chunk_key_encoding` fields stay typed as `MetadataField` (str | NamedConfig) -- narrowing them to a specific union belongs in a future validation layer, not in the spec-faithful types layer. Configuration TypedDicts renamed from `*Config` to `*Configuration` to match the dtype/codec naming. zarr.core.metadata.v3 re-exports preserve the legacy `*Config` aliases via `as` imports. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/v3/__init__.py | 16 +---- .../src/zarr_metadata/v3/array.py | 47 +------------- .../zarr_metadata/v3/chunk_grid/__init__.py | 10 +++ .../v3/chunk_grid/rectilinear.py | 44 +++++++++++++ .../zarr_metadata/v3/chunk_grid/regular.py | 34 ++++++++++ .../v3/chunk_key_encoding/__init__.py | 22 +++++++ .../v3/chunk_key_encoding/default.py | 42 +++++++++++++ .../zarr_metadata/v3/chunk_key_encoding/v2.py | 42 +++++++++++++ packages/zarr-metadata/tests/test_imports.py | 62 ++++++++++++++++--- .../zarr-metadata/tests/test_structural.py | 39 +++++++++++- src/zarr/core/metadata/v3.py | 14 +++-- 11 files changed, 301 insertions(+), 71 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py index c63dc46b57..967e570e0e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py @@ -1,14 +1,6 @@ """Zarr v3 metadata types.""" -from zarr_metadata.v3.array import ( - AllowedExtraField, - ArrayMetadataV3, - RectilinearChunkGrid, - RectilinearChunkGridConfig, - RectilinearDimSpec, - RegularChunkGrid, - RegularChunkGridConfig, -) +from zarr_metadata.v3.array import AllowedExtraField, ArrayMetadataV3, MetadataField from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 from zarr_metadata.v3.group import GroupMetadataV3 @@ -17,9 +9,5 @@ "ArrayMetadataV3", "ConsolidatedMetadataV3", "GroupMetadataV3", - "RectilinearChunkGrid", - "RectilinearChunkGridConfig", - "RectilinearDimSpec", - "RegularChunkGrid", - "RegularChunkGridConfig", + "MetadataField", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index f83fde9a81..fdb1d57f8f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -19,47 +19,8 @@ class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] must_understand: Literal[False] -# JSON type for a single dimension's rectilinear spec: -# bare int (uniform shorthand), or list of ints / [value, count] RLE pairs. -RectilinearDimSpec = int | tuple[int | tuple[int, int], ...] - MetadataField = str | NamedConfig[str, Mapping[str, JSON]] -"""A string or a {name: str, configuration: {...}} key value pair""" - - -class RegularChunkGridConfig(TypedDict): - """ - Configuration body of a regular chunk grid. - - See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#regular-grids - """ - - chunk_shape: tuple[int, ...] - - -class RectilinearChunkGridConfig(TypedDict): - """ - Configuration body of a rectilinear chunk grid. - - See https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear - """ - - kind: Literal["inline"] - chunk_shapes: tuple[RectilinearDimSpec, ...] - - -class RegularChunkGrid(TypedDict): - """Regular chunk grid metadata.""" - - name: Literal["regular"] - configuration: RegularChunkGridConfig - - -class RectilinearChunkGrid(TypedDict): - """Rectilinear chunk grid metadata.""" - - name: Literal["rectilinear"] - configuration: RectilinearChunkGridConfig +"""A string or a {name: str, configuration: {...}} key value pair.""" class ArrayMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] @@ -87,9 +48,5 @@ class ArrayMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore __all__ = [ "AllowedExtraField", "ArrayMetadataV3", - "RectilinearChunkGrid", - "RectilinearChunkGridConfig", - "RectilinearDimSpec", - "RegularChunkGrid", - "RegularChunkGridConfig", + "MetadataField", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/__init__.py new file mode 100644 index 0000000000..cfd69c48cf --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/__init__.py @@ -0,0 +1,10 @@ +""" +Zarr v3 chunk grid metadata types. + +Each chunk grid lives in its own submodule: + + - `regular` -- core v3 spec + - `rectilinear` -- zarr-extensions + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-grids +""" diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py new file mode 100644 index 0000000000..db84085ba4 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py @@ -0,0 +1,44 @@ +""" +Rectilinear chunk grid (zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear +""" + +from typing import Final, Literal, TypedDict + +RECTILINEAR_CHUNK_GRID_NAME: Final = "rectilinear" +"""The `name` field value of the rectilinear chunk grid.""" + +RectilinearChunkGridName = Literal["rectilinear"] +"""Literal type of the `name` field of the rectilinear chunk grid.""" + +RectilinearDimSpec = int | tuple[int | tuple[int, int], ...] +"""JSON shape for one dimension's rectilinear spec. + +Either a bare integer (uniform shorthand for a regular dimension within +a rectilinear grid), or a tuple of integers and/or `[value, count]` RLE +pairs. +""" + + +class RectilinearChunkGridConfiguration(TypedDict): + """Configuration for the rectilinear chunk grid.""" + + kind: Literal["inline"] + chunk_shapes: tuple[RectilinearDimSpec, ...] + + +class RectilinearChunkGrid(TypedDict): + """Rectilinear chunk grid metadata.""" + + name: RectilinearChunkGridName + configuration: RectilinearChunkGridConfiguration + + +__all__ = [ + "RECTILINEAR_CHUNK_GRID_NAME", + "RectilinearChunkGrid", + "RectilinearChunkGridConfiguration", + "RectilinearChunkGridName", + "RectilinearDimSpec", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py new file mode 100644 index 0000000000..c55289d37e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py @@ -0,0 +1,34 @@ +""" +Regular chunk grid (Zarr v3 core spec). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#regular-grids +""" + +from typing import Final, Literal, TypedDict + +REGULAR_CHUNK_GRID_NAME: Final = "regular" +"""The `name` field value of the regular chunk grid.""" + +RegularChunkGridName = Literal["regular"] +"""Literal type of the `name` field of the regular chunk grid.""" + + +class RegularChunkGridConfiguration(TypedDict): + """Configuration for the regular chunk grid.""" + + chunk_shape: tuple[int, ...] + + +class RegularChunkGrid(TypedDict): + """Regular chunk grid metadata.""" + + name: RegularChunkGridName + configuration: RegularChunkGridConfiguration + + +__all__ = [ + "REGULAR_CHUNK_GRID_NAME", + "RegularChunkGrid", + "RegularChunkGridConfiguration", + "RegularChunkGridName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py new file mode 100644 index 0000000000..4f1c40a4af --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py @@ -0,0 +1,22 @@ +""" +Zarr v3 chunk key encoding metadata types. + +Each chunk key encoding lives in its own submodule: + + - `default` -- v3 default encoding (`/`-separated) + - `v2` -- v2-compatibility encoding (`.`-separated by default) + +Both are defined by the v3 core spec. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from typing import Literal + +ChunkKeySeparator = Literal["/", "."] +"""The two permitted chunk key separator characters per the v3 core spec.""" + + +__all__ = [ + "ChunkKeySeparator", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py new file mode 100644 index 0000000000..a19ad32778 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py @@ -0,0 +1,42 @@ +""" +Default chunk key encoding (Zarr v3 core spec). + +The chunk key for a chunk with grid index `(k, j, i, ...)` is formed +by appending `ckji...` (where `` is `separator`). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from typing import Final, Literal, NotRequired, TypedDict + +from zarr_metadata.v3.chunk_key_encoding import ChunkKeySeparator + +DEFAULT_CHUNK_KEY_ENCODING_NAME: Final = "default" +"""The `name` field value of the default chunk key encoding.""" + +DefaultChunkKeyEncodingName = Literal["default"] +"""Literal type of the `name` field of the default chunk key encoding.""" + + +class DefaultChunkKeyEncodingConfiguration(TypedDict): + """Configuration for the default chunk key encoding. + + `separator` is optional and defaults to `"/"` per spec. + """ + + separator: NotRequired[ChunkKeySeparator] + + +class DefaultChunkKeyEncoding(TypedDict): + """Default chunk key encoding metadata.""" + + name: DefaultChunkKeyEncodingName + configuration: NotRequired[DefaultChunkKeyEncodingConfiguration] + + +__all__ = [ + "DEFAULT_CHUNK_KEY_ENCODING_NAME", + "DefaultChunkKeyEncoding", + "DefaultChunkKeyEncodingConfiguration", + "DefaultChunkKeyEncodingName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py new file mode 100644 index 0000000000..1864e8c5a2 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py @@ -0,0 +1,42 @@ +""" +V2-compatibility chunk key encoding (Zarr v3 core spec). + +Intended only to allow existing v2 arrays to be converted to v3 without +having to rename chunks. Not recommended for new arrays. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from typing import Final, Literal, NotRequired, TypedDict + +from zarr_metadata.v3.chunk_key_encoding import ChunkKeySeparator + +V2_CHUNK_KEY_ENCODING_NAME: Final = "v2" +"""The `name` field value of the v2 chunk key encoding.""" + +V2ChunkKeyEncodingName = Literal["v2"] +"""Literal type of the `name` field of the v2 chunk key encoding.""" + + +class V2ChunkKeyEncodingConfiguration(TypedDict): + """Configuration for the v2 chunk key encoding. + + `separator` is optional and defaults to `"."` per spec. + """ + + separator: NotRequired[ChunkKeySeparator] + + +class V2ChunkKeyEncoding(TypedDict): + """V2-compatibility chunk key encoding metadata.""" + + name: V2ChunkKeyEncodingName + configuration: NotRequired[V2ChunkKeyEncodingConfiguration] + + +__all__ = [ + "V2_CHUNK_KEY_ENCODING_NAME", + "V2ChunkKeyEncoding", + "V2ChunkKeyEncodingConfiguration", + "V2ChunkKeyEncodingName", +] diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index d6953c0ea1..b99305956f 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -55,11 +55,7 @@ def test_v3_imports() -> None: ArrayMetadataV3, ConsolidatedMetadataV3, GroupMetadataV3, - RectilinearChunkGrid, - RectilinearChunkGridConfig, - RectilinearDimSpec, - RegularChunkGrid, - RegularChunkGridConfig, + MetadataField, ) _ = ( @@ -67,11 +63,63 @@ def test_v3_imports() -> None: ArrayMetadataV3, ConsolidatedMetadataV3, GroupMetadataV3, + MetadataField, + ) + + +def test_v3_chunk_grid_imports() -> None: + from zarr_metadata.v3.chunk_grid.rectilinear import ( + RECTILINEAR_CHUNK_GRID_NAME, + RectilinearChunkGrid, + RectilinearChunkGridConfiguration, + RectilinearChunkGridName, + RectilinearDimSpec, + ) + from zarr_metadata.v3.chunk_grid.regular import ( + REGULAR_CHUNK_GRID_NAME, + RegularChunkGrid, + RegularChunkGridConfiguration, + RegularChunkGridName, + ) + + _ = ( + RECTILINEAR_CHUNK_GRID_NAME, + REGULAR_CHUNK_GRID_NAME, RectilinearChunkGrid, - RectilinearChunkGridConfig, + RectilinearChunkGridConfiguration, + RectilinearChunkGridName, RectilinearDimSpec, RegularChunkGrid, - RegularChunkGridConfig, + RegularChunkGridConfiguration, + RegularChunkGridName, + ) + + +def test_v3_chunk_key_encoding_imports() -> None: + from zarr_metadata.v3.chunk_key_encoding import ChunkKeySeparator + from zarr_metadata.v3.chunk_key_encoding.default import ( + DEFAULT_CHUNK_KEY_ENCODING_NAME, + DefaultChunkKeyEncoding, + DefaultChunkKeyEncodingConfiguration, + DefaultChunkKeyEncodingName, + ) + from zarr_metadata.v3.chunk_key_encoding.v2 import ( + V2_CHUNK_KEY_ENCODING_NAME, + V2ChunkKeyEncoding, + V2ChunkKeyEncodingConfiguration, + V2ChunkKeyEncodingName, + ) + + _ = ( + ChunkKeySeparator, + DEFAULT_CHUNK_KEY_ENCODING_NAME, + DefaultChunkKeyEncoding, + DefaultChunkKeyEncodingConfiguration, + DefaultChunkKeyEncodingName, + V2_CHUNK_KEY_ENCODING_NAME, + V2ChunkKeyEncoding, + V2ChunkKeyEncodingConfiguration, + V2ChunkKeyEncodingName, ) diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index f38ca188cc..229f08f27b 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -25,7 +25,11 @@ from zarr_metadata.v2.array import ArrayMetadataV2 from zarr_metadata.v2.codec import NumcodecsConfig from zarr_metadata.v2.group import GroupMetadataV2 - from zarr_metadata.v3.array import ArrayMetadataV3, RegularChunkGrid + from zarr_metadata.v3.array import ArrayMetadataV3 + from zarr_metadata.v3.chunk_grid.rectilinear import RectilinearChunkGrid + from zarr_metadata.v3.chunk_grid.regular import RegularChunkGrid + from zarr_metadata.v3.chunk_key_encoding.default import DefaultChunkKeyEncoding + from zarr_metadata.v3.chunk_key_encoding.v2 import V2ChunkKeyEncoding from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 from zarr_metadata.v3.group import GroupMetadataV3 @@ -105,6 +109,39 @@ def test_regular_chunk_grid_metadata() -> None: assert grid["name"] == "regular" +def test_rectilinear_chunk_grid_metadata() -> None: + grid: RectilinearChunkGrid = { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": ( + (10, (5, 3), 7), # mixed: bare ints and a [value, count] RLE pair + 100, # uniform shorthand + ), + }, + } + assert grid["name"] == "rectilinear" + + +def test_default_chunk_key_encoding_metadata() -> None: + enc: DefaultChunkKeyEncoding = { + "name": "default", + "configuration": {"separator": "/"}, + } + assert enc["name"] == "default" + + minimal: DefaultChunkKeyEncoding = {"name": "default"} # configuration optional + assert minimal["name"] == "default" + + +def test_v2_chunk_key_encoding_metadata() -> None: + enc: V2ChunkKeyEncoding = { + "name": "v2", + "configuration": {"separator": "."}, + } + assert enc["name"] == "v2" + + def test_blosc_config_v1() -> None: cfg: BloscCodecConfiguration = { "cname": "zstd", diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 2706f6c1b6..f13f3595ef 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -8,13 +8,19 @@ from zarr_metadata.v3.array import ( AllowedExtraField as AllowedExtraField, ) -from zarr_metadata.v3.array import ( - ArrayMetadataV3, +from zarr_metadata.v3.array import ArrayMetadataV3 +from zarr_metadata.v3.chunk_grid.rectilinear import ( RectilinearChunkGrid, - RectilinearChunkGridConfig, RectilinearDimSpec, +) +from zarr_metadata.v3.chunk_grid.rectilinear import ( + RectilinearChunkGridConfiguration as RectilinearChunkGridConfig, +) +from zarr_metadata.v3.chunk_grid.regular import ( RegularChunkGrid, - RegularChunkGridConfig, +) +from zarr_metadata.v3.chunk_grid.regular import ( + RegularChunkGridConfiguration as RegularChunkGridConfig, ) from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec From e6139a64144dac56bdc16c45bf88e2e3188bb487 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 22 Apr 2026 00:04:15 +0200 Subject: [PATCH 39/55] refactor(metadata): move codec/ and dtype/ under v3/ Both directories model v3-spec artifacts, so they belong under the v3/ subpackage alongside v3/array, v3/group, v3/consolidated, v3/chunk_grid, and v3/chunk_key_encoding. The principle is now: anything imported from `zarr_metadata.v3.X` is a v3-spec artifact; anything from `zarr_metadata.v2.X` is a v2-spec artifact; only true cross-version primitives sit at the top level (`zarr_metadata.JSON`, `NamedConfig`, `NamedRequiredConfig`, and the `ArrayMetadata`/`GroupMetadata` unions). Path moves: zarr_metadata.codec.* -> zarr_metadata.v3.codec.* zarr_metadata.dtype.* -> zarr_metadata.v3.dtype.* Internal imports inside the moved modules and zarr-python re-export sites updated accordingly. zarr.abc.codec imports the zarr-metadata Codec alias with a private name to avoid colliding with its own runtime `Codec` union (`ArrayArrayCodec | ArrayBytesCodec | BytesBytesCodec`), then re-exports as `CodecJSON`. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../zarr-metadata/src/zarr_metadata/common.py | 4 +- .../zarr_metadata/{ => v3}/codec/__init__.py | 0 .../src/zarr_metadata/{ => v3}/codec/blosc.py | 0 .../src/zarr_metadata/{ => v3}/codec/bytes.py | 0 .../zarr_metadata/{ => v3}/codec/crc32c.py | 0 .../src/zarr_metadata/{ => v3}/codec/gzip.py | 0 .../zarr_metadata/{ => v3}/codec/sharding.py | 2 +- .../zarr_metadata/{ => v3}/codec/transpose.py | 0 .../src/zarr_metadata/{ => v3}/codec/zstd.py | 0 .../zarr_metadata/{ => v3}/dtype/__init__.py | 10 ++-- .../src/zarr_metadata/{ => v3}/dtype/bool.py | 0 .../src/zarr_metadata/{ => v3}/dtype/bytes.py | 0 .../{ => v3}/dtype/complex128.py | 2 +- .../zarr_metadata/{ => v3}/dtype/complex64.py | 2 +- .../zarr_metadata/{ => v3}/dtype/float16.py | 0 .../zarr_metadata/{ => v3}/dtype/float32.py | 0 .../zarr_metadata/{ => v3}/dtype/float64.py | 0 .../src/zarr_metadata/{ => v3}/dtype/int16.py | 0 .../src/zarr_metadata/{ => v3}/dtype/int32.py | 0 .../src/zarr_metadata/{ => v3}/dtype/int64.py | 0 .../src/zarr_metadata/{ => v3}/dtype/int8.py | 0 .../{ => v3}/dtype/numpy_datetime64.py | 0 .../{ => v3}/dtype/numpy_timedelta64.py | 0 .../src/zarr_metadata/{ => v3}/dtype/raw.py | 0 .../zarr_metadata/{ => v3}/dtype/string.py | 0 .../zarr_metadata/{ => v3}/dtype/struct.py | 2 +- .../zarr_metadata/{ => v3}/dtype/uint16.py | 0 .../zarr_metadata/{ => v3}/dtype/uint32.py | 0 .../zarr_metadata/{ => v3}/dtype/uint64.py | 0 .../src/zarr_metadata/{ => v3}/dtype/uint8.py | 0 packages/zarr-metadata/tests/test_imports.py | 56 ++++++++--------- .../zarr-metadata/tests/test_structural.py | 60 +++++++++---------- src/zarr/abc/codec.py | 6 +- src/zarr/codecs/blosc.py | 2 +- src/zarr/core/dtype/common.py | 2 +- src/zarr/core/dtype/npy/common.py | 2 +- src/zarr/core/dtype/npy/time.py | 2 +- 37 files changed, 78 insertions(+), 74 deletions(-) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/__init__.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/blosc.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/bytes.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/crc32c.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/gzip.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/sharding.py (97%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/transpose.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/codec/zstd.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/__init__.py (54%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/bool.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/bytes.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/complex128.py (93%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/complex64.py (93%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/float16.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/float32.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/float64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/int16.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/int32.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/int64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/int8.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/numpy_datetime64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/numpy_timedelta64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/raw.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/string.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/struct.py (97%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/uint16.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/uint32.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/uint64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/{ => v3}/dtype/uint8.py (100%) diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py index c160634493..557260a8a3 100644 --- a/packages/zarr-metadata/src/zarr_metadata/common.py +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -2,8 +2,8 @@ Top-level cross-version primitives for Zarr metadata. Version-specific types live under `zarr_metadata.v2` and `zarr_metadata.v3`. -Codec and dtype spec types live under `zarr_metadata.codec` and -`zarr_metadata.dtype`. +Codec and dtype spec types live under `zarr_metadata.v3.codec` and +`zarr_metadata.v3.dtype`. """ from collections.abc import Mapping, Sequence diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/codec/__init__.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/codec/blosc.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/codec/bytes.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/codec/crc32c.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/codec/gzip.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding.py similarity index 97% rename from packages/zarr-metadata/src/zarr_metadata/codec/sharding.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding.py index a7c9c6d950..50aa6621eb 100644 --- a/packages/zarr-metadata/src/zarr_metadata/codec/sharding.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding.py @@ -6,7 +6,7 @@ from typing import Final, Literal, NotRequired, TypedDict -from zarr_metadata.codec import Codec +from zarr_metadata.v3.codec import Codec SHARDING_CODEC_NAME: Final = "sharding_indexed" """The `name` field value of the `sharding_indexed` codec.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/codec/transpose.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py diff --git a/packages/zarr-metadata/src/zarr_metadata/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/codec/zstd.py rename to packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/__init__.py similarity index 54% rename from packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/__init__.py index 3c908decff..48e0d82869 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/__init__.py @@ -12,11 +12,11 @@ See the submodules for specific per-dtype types: -- `zarr_metadata.dtype.primitive` -- core v3 primitives (bool, int*, uint*, float*, complex*) -- `zarr_metadata.dtype.bytes` -- `bytes`, `null_terminated_bytes` -- `zarr_metadata.dtype.string` -- `string`, `fixed_length_utf32` -- `zarr_metadata.dtype.time` -- `numpy.datetime64`, `numpy.timedelta64` -- `zarr_metadata.dtype.struct` -- `struct` +- `zarr_metadata.v3.dtype.primitive` -- core v3 primitives (bool, int*, uint*, float*, complex*) +- `zarr_metadata.v3.dtype.bytes` -- `bytes`, `null_terminated_bytes` +- `zarr_metadata.v3.dtype.string` -- `string`, `fixed_length_utf32` +- `zarr_metadata.v3.dtype.time` -- `numpy.datetime64`, `numpy.timedelta64` +- `zarr_metadata.v3.dtype.struct` -- `struct` """ diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/bool.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/bool.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/bool.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/bool.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/bytes.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/bytes.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/bytes.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/complex128.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex128.py similarity index 93% rename from packages/zarr-metadata/src/zarr_metadata/dtype/complex128.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex128.py index 97bc14c08c..7b8d92fa3a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/complex128.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex128.py @@ -6,7 +6,7 @@ from typing import Final, Literal -from zarr_metadata.dtype.float64 import Float64FillValue +from zarr_metadata.v3.dtype.float64 import Float64FillValue COMPLEX128_DTYPE_NAME: Final = "complex128" """The `data_type` value for the `complex128` type.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/complex64.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex64.py similarity index 93% rename from packages/zarr-metadata/src/zarr_metadata/dtype/complex64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex64.py index 61772dd33c..81c8eefbf6 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/complex64.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex64.py @@ -6,7 +6,7 @@ from typing import Final, Literal -from zarr_metadata.dtype.float32 import Float32FillValue +from zarr_metadata.v3.dtype.float32 import Float32FillValue COMPLEX64_DTYPE_NAME: Final = "complex64" """The `data_type` value for the `complex64` type.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/float16.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/float16.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/float16.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/float16.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/float32.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/float32.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/float32.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/float32.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/float64.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/float64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/float64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/float64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int16.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int16.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/int16.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/int16.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int32.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int32.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/int32.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/int32.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int64.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/int64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/int64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/int8.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int8.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/int8.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/int8.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/numpy_datetime64.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_datetime64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/numpy_datetime64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_datetime64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/numpy_timedelta64.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_timedelta64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/numpy_timedelta64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_timedelta64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/raw.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/raw.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/raw.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/raw.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/string.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/string.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/string.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/string.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/struct.py similarity index 97% rename from packages/zarr-metadata/src/zarr_metadata/dtype/struct.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/struct.py index 20b0b1e925..63d0cded7d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/dtype/struct.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/struct.py @@ -10,7 +10,7 @@ from typing_extensions import ReadOnly from zarr_metadata.common import JSON -from zarr_metadata.dtype import DType +from zarr_metadata.v3.dtype import DType STRUCT_DTYPE_NAME: Final = "struct" """The `name` field value of the `struct` data type.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint16.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint16.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/uint16.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint16.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint32.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint32.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/uint32.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint32.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint64.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/uint64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/dtype/uint8.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint8.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/dtype/uint8.py rename to packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint8.py diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index b99305956f..98870c9b32 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -124,32 +124,32 @@ def test_v3_chunk_key_encoding_imports() -> None: def test_codec_imports() -> None: - from zarr_metadata.codec import Codec - from zarr_metadata.codec.blosc import ( + from zarr_metadata.v3.codec import Codec + from zarr_metadata.v3.codec.blosc import ( BloscCName, BloscCodec, BloscCodecConfiguration, BloscCodecName, BloscShuffle, ) - from zarr_metadata.codec.bytes import ( + from zarr_metadata.v3.codec.bytes import ( BytesCodec, BytesCodecConfiguration, BytesCodecName, ) - from zarr_metadata.codec.crc32c import Crc32cCodec, Crc32cCodecName - from zarr_metadata.codec.gzip import GzipCodec, GzipCodecConfiguration, GzipCodecName - from zarr_metadata.codec.sharding import ( + from zarr_metadata.v3.codec.crc32c import Crc32cCodec, Crc32cCodecName + from zarr_metadata.v3.codec.gzip import GzipCodec, GzipCodecConfiguration, GzipCodecName + from zarr_metadata.v3.codec.sharding import ( ShardingCodec, ShardingCodecConfiguration, ShardingCodecName, ) - from zarr_metadata.codec.transpose import ( + from zarr_metadata.v3.codec.transpose import ( TransposeCodec, TransposeCodecConfiguration, TransposeCodecName, ) - from zarr_metadata.codec.zstd import ZstdCodec, ZstdCodecConfiguration, ZstdCodecName + from zarr_metadata.v3.codec.zstd import ZstdCodec, ZstdCodecConfiguration, ZstdCodecName _ = ( Codec, @@ -179,59 +179,59 @@ def test_codec_imports() -> None: def test_dtype_imports() -> None: - from zarr_metadata.dtype import DType - from zarr_metadata.dtype.bool import BOOL_DTYPE_NAME, BoolDTypeName, BoolFillValue - from zarr_metadata.dtype.bytes import BYTES_DTYPE_NAME, BytesDTypeName, BytesFillValue - from zarr_metadata.dtype.complex64 import ( + from zarr_metadata.v3.dtype import DType + from zarr_metadata.v3.dtype.bool import BOOL_DTYPE_NAME, BoolDTypeName, BoolFillValue + from zarr_metadata.v3.dtype.bytes import BYTES_DTYPE_NAME, BytesDTypeName, BytesFillValue + from zarr_metadata.v3.dtype.complex64 import ( COMPLEX64_DTYPE_NAME, Complex64Component, Complex64DTypeName, Complex64FillValue, ) - from zarr_metadata.dtype.complex128 import ( + from zarr_metadata.v3.dtype.complex128 import ( COMPLEX128_DTYPE_NAME, Complex128Component, Complex128DTypeName, Complex128FillValue, ) - from zarr_metadata.dtype.float16 import ( + from zarr_metadata.v3.dtype.float16 import ( FLOAT16_DTYPE_NAME, Float16DTypeName, Float16FillValue, Float16SpecialFillValue, ) - from zarr_metadata.dtype.float32 import ( + from zarr_metadata.v3.dtype.float32 import ( FLOAT32_DTYPE_NAME, Float32DTypeName, Float32FillValue, Float32SpecialFillValue, ) - from zarr_metadata.dtype.float64 import ( + from zarr_metadata.v3.dtype.float64 import ( FLOAT64_DTYPE_NAME, Float64DTypeName, Float64FillValue, Float64SpecialFillValue, ) - from zarr_metadata.dtype.int8 import INT8_DTYPE_NAME, Int8DTypeName, Int8FillValue - from zarr_metadata.dtype.int16 import INT16_DTYPE_NAME, Int16DTypeName, Int16FillValue - from zarr_metadata.dtype.int32 import INT32_DTYPE_NAME, Int32DTypeName, Int32FillValue - from zarr_metadata.dtype.int64 import INT64_DTYPE_NAME, Int64DTypeName, Int64FillValue - from zarr_metadata.dtype.numpy_datetime64 import ( + from zarr_metadata.v3.dtype.int8 import INT8_DTYPE_NAME, Int8DTypeName, Int8FillValue + from zarr_metadata.v3.dtype.int16 import INT16_DTYPE_NAME, Int16DTypeName, Int16FillValue + from zarr_metadata.v3.dtype.int32 import INT32_DTYPE_NAME, Int32DTypeName, Int32FillValue + from zarr_metadata.v3.dtype.int64 import INT64_DTYPE_NAME, Int64DTypeName, Int64FillValue + from zarr_metadata.v3.dtype.numpy_datetime64 import ( NUMPY_DATETIME64_DTYPE_NAME, NumpyDatetime64, NumpyDatetime64Configuration, NumpyDatetime64DTypeName, NumpyDatetime64FillValue, ) - from zarr_metadata.dtype.numpy_timedelta64 import ( + from zarr_metadata.v3.dtype.numpy_timedelta64 import ( NUMPY_TIMEDELTA64_DTYPE_NAME, NumpyTimedelta64, NumpyTimedelta64Configuration, NumpyTimedelta64DTypeName, NumpyTimedelta64FillValue, ) - from zarr_metadata.dtype.string import STRING_DTYPE_NAME, StringDTypeName, StringFillValue - from zarr_metadata.dtype.struct import ( + from zarr_metadata.v3.dtype.string import STRING_DTYPE_NAME, StringDTypeName, StringFillValue + from zarr_metadata.v3.dtype.struct import ( STRUCT_DTYPE_NAME, Struct, StructConfiguration, @@ -239,10 +239,10 @@ def test_dtype_imports() -> None: StructField, StructFillValue, ) - from zarr_metadata.dtype.uint8 import UINT8_DTYPE_NAME, Uint8DTypeName, Uint8FillValue - from zarr_metadata.dtype.uint16 import UINT16_DTYPE_NAME, Uint16DTypeName, Uint16FillValue - from zarr_metadata.dtype.uint32 import UINT32_DTYPE_NAME, Uint32DTypeName, Uint32FillValue - from zarr_metadata.dtype.uint64 import UINT64_DTYPE_NAME, Uint64DTypeName, Uint64FillValue + from zarr_metadata.v3.dtype.uint8 import UINT8_DTYPE_NAME, Uint8DTypeName, Uint8FillValue + from zarr_metadata.v3.dtype.uint16 import UINT16_DTYPE_NAME, Uint16DTypeName, Uint16FillValue + from zarr_metadata.v3.dtype.uint32 import UINT32_DTYPE_NAME, Uint32DTypeName, Uint32FillValue + from zarr_metadata.v3.dtype.uint64 import UINT64_DTYPE_NAME, Uint64DTypeName, Uint64FillValue _ = ( DType, diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index 229f08f27b..dc3cb62604 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -12,16 +12,6 @@ import pytest if TYPE_CHECKING: - from zarr_metadata.codec.blosc import BloscCodec, BloscCodecConfiguration - from zarr_metadata.codec.bytes import BytesCodec, BytesCodecConfiguration - from zarr_metadata.codec.crc32c import Crc32cCodec - from zarr_metadata.codec.gzip import GzipCodec, GzipCodecConfiguration - from zarr_metadata.codec.sharding import ShardingCodec, ShardingCodecConfiguration - from zarr_metadata.codec.transpose import TransposeCodec, TransposeCodecConfiguration - from zarr_metadata.codec.zstd import ZstdCodec, ZstdCodecConfiguration - from zarr_metadata.dtype.numpy_datetime64 import NumpyDatetime64 - from zarr_metadata.dtype.numpy_timedelta64 import NumpyTimedelta64 - from zarr_metadata.dtype.struct import Struct from zarr_metadata.v2.array import ArrayMetadataV2 from zarr_metadata.v2.codec import NumcodecsConfig from zarr_metadata.v2.group import GroupMetadataV2 @@ -30,7 +20,17 @@ from zarr_metadata.v3.chunk_grid.regular import RegularChunkGrid from zarr_metadata.v3.chunk_key_encoding.default import DefaultChunkKeyEncoding from zarr_metadata.v3.chunk_key_encoding.v2 import V2ChunkKeyEncoding + from zarr_metadata.v3.codec.blosc import BloscCodec, BloscCodecConfiguration + from zarr_metadata.v3.codec.bytes import BytesCodec, BytesCodecConfiguration + from zarr_metadata.v3.codec.crc32c import Crc32cCodec + from zarr_metadata.v3.codec.gzip import GzipCodec, GzipCodecConfiguration + from zarr_metadata.v3.codec.sharding import ShardingCodec, ShardingCodecConfiguration + from zarr_metadata.v3.codec.transpose import TransposeCodec, TransposeCodecConfiguration + from zarr_metadata.v3.codec.zstd import ZstdCodec, ZstdCodecConfiguration from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 + from zarr_metadata.v3.dtype.numpy_datetime64 import NumpyDatetime64 + from zarr_metadata.v3.dtype.numpy_timedelta64 import NumpyTimedelta64 + from zarr_metadata.v3.dtype.struct import Struct from zarr_metadata.v3.group import GroupMetadataV3 @@ -270,13 +270,13 @@ def test_blosc_codec_metadata() -> None: def test_codec_name_constants() -> None: """Final constants carry the same string values as the Literal types.""" - from zarr_metadata.codec.blosc import BLOSC_CODEC_NAME - from zarr_metadata.codec.bytes import BYTES_CODEC_NAME - from zarr_metadata.codec.crc32c import CRC32C_CODEC_NAME - from zarr_metadata.codec.gzip import GZIP_CODEC_NAME - from zarr_metadata.codec.sharding import SHARDING_CODEC_NAME - from zarr_metadata.codec.transpose import TRANSPOSE_CODEC_NAME - from zarr_metadata.codec.zstd import ZSTD_CODEC_NAME + from zarr_metadata.v3.codec.blosc import BLOSC_CODEC_NAME + from zarr_metadata.v3.codec.bytes import BYTES_CODEC_NAME + from zarr_metadata.v3.codec.crc32c import CRC32C_CODEC_NAME + from zarr_metadata.v3.codec.gzip import GZIP_CODEC_NAME + from zarr_metadata.v3.codec.sharding import SHARDING_CODEC_NAME + from zarr_metadata.v3.codec.transpose import TRANSPOSE_CODEC_NAME + from zarr_metadata.v3.codec.zstd import ZSTD_CODEC_NAME assert BLOSC_CODEC_NAME == "blosc" assert BYTES_CODEC_NAME == "bytes" @@ -289,7 +289,7 @@ def test_codec_name_constants() -> None: def test_blosc_enum_value_constants() -> None: """Blosc shuffle and cname constants can be used as codec config values.""" - from zarr_metadata.codec.blosc import ( + from zarr_metadata.v3.codec.blosc import ( BLOSC_CNAME_ZSTD, BLOSC_SHUFFLE_BITSHUFFLE, ) @@ -306,7 +306,7 @@ def test_blosc_enum_value_constants() -> None: def test_bytes_endian_constants() -> None: - from zarr_metadata.codec.bytes import BYTES_ENDIAN_BIG, BYTES_ENDIAN_LITTLE + from zarr_metadata.v3.codec.bytes import BYTES_ENDIAN_BIG, BYTES_ENDIAN_LITTLE cfg_little: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_LITTLE} cfg_big: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_BIG} @@ -315,7 +315,7 @@ def test_bytes_endian_constants() -> None: def test_sharding_index_location_constants() -> None: - from zarr_metadata.codec.sharding import ( + from zarr_metadata.v3.codec.sharding import ( SHARDING_INDEX_LOCATION_END, SHARDING_INDEX_LOCATION_START, ) @@ -337,11 +337,11 @@ def test_sharding_index_location_constants() -> None: def test_primitive_dtype_names() -> None: - from zarr_metadata.dtype.bool import BOOL_DTYPE_NAME - from zarr_metadata.dtype.complex128 import COMPLEX128_DTYPE_NAME - from zarr_metadata.dtype.float32 import FLOAT32_DTYPE_NAME - from zarr_metadata.dtype.int32 import INT32_DTYPE_NAME - from zarr_metadata.dtype.uint64 import UINT64_DTYPE_NAME + from zarr_metadata.v3.dtype.bool import BOOL_DTYPE_NAME + from zarr_metadata.v3.dtype.complex128 import COMPLEX128_DTYPE_NAME + from zarr_metadata.v3.dtype.float32 import FLOAT32_DTYPE_NAME + from zarr_metadata.v3.dtype.int32 import INT32_DTYPE_NAME + from zarr_metadata.v3.dtype.uint64 import UINT64_DTYPE_NAME assert BOOL_DTYPE_NAME == "bool" assert INT32_DTYPE_NAME == "int32" @@ -401,7 +401,7 @@ def test_struct_dtype_metadata_nested() -> None: def test_hex_float16_validator() -> None: - from zarr_metadata.dtype.float16 import hex_float16 + from zarr_metadata.v3.dtype.float16 import hex_float16 assert hex_float16("0x7c00") == "0x7c00" with pytest.raises(ValueError): @@ -413,7 +413,7 @@ def test_hex_float16_validator() -> None: def test_hex_float32_validator() -> None: - from zarr_metadata.dtype.float32 import hex_float32 + from zarr_metadata.v3.dtype.float32 import hex_float32 assert hex_float32("0x7fc00000") == "0x7fc00000" with pytest.raises(ValueError): @@ -423,7 +423,7 @@ def test_hex_float32_validator() -> None: def test_hex_float64_validator() -> None: - from zarr_metadata.dtype.float64 import hex_float64 + from zarr_metadata.v3.dtype.float64 import hex_float64 assert hex_float64("0x7ff8000000000000") == "0x7ff8000000000000" with pytest.raises(ValueError): @@ -433,7 +433,7 @@ def test_hex_float64_validator() -> None: def test_base64_bytes_validator() -> None: - from zarr_metadata.dtype.bytes import base64_bytes + from zarr_metadata.v3.dtype.bytes import base64_bytes assert base64_bytes("SGVsbG8=") == "SGVsbG8=" assert base64_bytes("") == "" @@ -446,7 +446,7 @@ def test_base64_bytes_validator() -> None: def test_raw_bytes_dtype_name_validator() -> None: - from zarr_metadata.dtype.raw import raw_bytes_dtype_name + from zarr_metadata.v3.dtype.raw import raw_bytes_dtype_name assert raw_bytes_dtype_name("r8") == "r8" assert raw_bytes_dtype_name("r16") == "r16" diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index dc6b1a4a4c..ed9da448cd 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -5,12 +5,15 @@ from typing import TYPE_CHECKING, Literal, Protocol, TypeGuard, runtime_checkable from typing_extensions import ReadOnly, TypedDict +from zarr_metadata.v3.codec import Codec as _CodecJSON from zarr.abc.metadata import Metadata from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import NamedConfig, concurrent_map from zarr.core.config import config -from zarr_metadata.codec import Codec as CodecJSON # noqa: TC002 + +# Legacy alias preserved for zarr.core internal call sites. +type CodecJSON = _CodecJSON if TYPE_CHECKING: from collections.abc import Awaitable, Callable, Iterable @@ -31,6 +34,7 @@ "BaseCodec", "BytesBytesCodec", "CodecInput", + "CodecJSON", "CodecOutput", "CodecPipeline", "GetResult", diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 4488cb94e0..16548f5b1c 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -9,7 +9,7 @@ import numcodecs from numcodecs.blosc import Blosc from packaging.version import Version -from zarr_metadata.codec.blosc import BloscCodecConfiguration as BloscConfigV3 +from zarr_metadata.v3.codec.blosc import BloscCodecConfiguration as BloscConfigV3 from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index dfe8e53880..e3595666ea 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -12,7 +12,7 @@ ) from typing_extensions import ReadOnly -from zarr_metadata.dtype import DType +from zarr_metadata.v3.dtype import DType from zarr.core.common import NamedConfig from zarr.errors import UnstableSpecificationWarning diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index 4e7bab8e58..3ccabc92ba 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -18,7 +18,7 @@ ) import numpy as np -from zarr_metadata.dtype.numpy_datetime64 import DateTimeUnit as DateTimeUnit +from zarr_metadata.v3.dtype.numpy_datetime64 import DateTimeUnit as DateTimeUnit from zarr.core.dtype.common import ( ENDIANNESS_STR, diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index ae24823870..6d42c662f0 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -14,7 +14,7 @@ ) import numpy as np -from zarr_metadata.dtype.numpy_datetime64 import ( +from zarr_metadata.v3.dtype.numpy_datetime64 import ( NumpyDatetime64Configuration as TimeConfig, ) From ac0304cb51b031901b71bb0d5a0410feadceaa38 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 22 Apr 2026 00:09:18 +0200 Subject: [PATCH 40/55] refactor(metadata): rename v3/dtype/ -> v3/data_type/ Matches the v3 spec field name `data_type` exactly. All imports inside the package and in zarr-python re-export sites updated accordingly. The `DType` type alias keeps its short name (it's the widely understood abbreviation for "data type JSON shape"); only the module path changes. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../zarr-metadata/src/zarr_metadata/common.py | 2 +- .../zarr_metadata/v3/data_type/__init__.py | 25 +++++++++ .../v3/{dtype => data_type}/bool.py | 0 .../v3/{dtype => data_type}/bytes.py | 0 .../v3/{dtype => data_type}/complex128.py | 2 +- .../v3/{dtype => data_type}/complex64.py | 2 +- .../v3/{dtype => data_type}/float16.py | 0 .../v3/{dtype => data_type}/float32.py | 0 .../v3/{dtype => data_type}/float64.py | 0 .../v3/{dtype => data_type}/int16.py | 0 .../v3/{dtype => data_type}/int32.py | 0 .../v3/{dtype => data_type}/int64.py | 0 .../v3/{dtype => data_type}/int8.py | 0 .../{dtype => data_type}/numpy_datetime64.py | 0 .../{dtype => data_type}/numpy_timedelta64.py | 0 .../v3/{dtype => data_type}/raw.py | 0 .../v3/{dtype => data_type}/string.py | 0 .../v3/{dtype => data_type}/struct.py | 2 +- .../v3/{dtype => data_type}/uint16.py | 0 .../v3/{dtype => data_type}/uint32.py | 0 .../v3/{dtype => data_type}/uint64.py | 0 .../v3/{dtype => data_type}/uint8.py | 0 .../src/zarr_metadata/v3/dtype/__init__.py | 25 --------- packages/zarr-metadata/tests/test_imports.py | 56 ++++++++++++------- .../zarr-metadata/tests/test_structural.py | 26 ++++----- src/zarr/core/dtype/common.py | 2 +- src/zarr/core/dtype/npy/common.py | 2 +- src/zarr/core/dtype/npy/time.py | 2 +- 28 files changed, 81 insertions(+), 65 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/bool.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/bytes.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/complex128.py (93%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/complex64.py (93%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/float16.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/float32.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/float64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/int16.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/int32.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/int64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/int8.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/numpy_datetime64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/numpy_timedelta64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/raw.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/string.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/struct.py (97%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/uint16.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/uint32.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/uint64.py (100%) rename packages/zarr-metadata/src/zarr_metadata/v3/{dtype => data_type}/uint8.py (100%) delete mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/dtype/__init__.py diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py index 557260a8a3..2af3398c6a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/common.py +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -3,7 +3,7 @@ Version-specific types live under `zarr_metadata.v2` and `zarr_metadata.v3`. Codec and dtype spec types live under `zarr_metadata.v3.codec` and -`zarr_metadata.v3.dtype`. +`zarr_metadata.v3.data_type`. """ from collections.abc import Mapping, Sequence diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py new file mode 100644 index 0000000000..c126e18ddb --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py @@ -0,0 +1,25 @@ +""" +Zarr v3 data type spec types. + +Each v3 data type has its own submodule: + +- Core primitives: `bool`, `int8`/`16`/`32`/`64`, `uint8`/`16`/`32`/`64`, + `float16`/`32`/`64`, `complex64`/`128`, `raw` (for `r`) +- zarr-extensions: `bytes`, `string`, `numpy_datetime64`, `numpy_timedelta64`, + `struct` + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from collections.abc import Mapping, Sequence + +# Wider than the top-level JSON because TypedDicts used for data type +# configurations are assignable to Mapping[str, object], not to +# Mapping[str, JSON]. +DType = str | int | float | Sequence["DType"] | None | Mapping[str, object] +"""The widest JSON-like shape that can specify a Zarr v3 data type.""" + + +__all__ = [ + "DType", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/bool.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/bool.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/bytes.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex128.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py similarity index 93% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex128.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py index 7b8d92fa3a..3f5827bde6 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex128.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py @@ -6,7 +6,7 @@ from typing import Final, Literal -from zarr_metadata.v3.dtype.float64 import Float64FillValue +from zarr_metadata.v3.data_type.float64 import Float64FillValue COMPLEX128_DTYPE_NAME: Final = "complex128" """The `data_type` value for the `complex128` type.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py similarity index 93% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py index 81c8eefbf6..7409fdd452 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/complex64.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py @@ -6,7 +6,7 @@ from typing import Final, Literal -from zarr_metadata.v3.dtype.float32 import Float32FillValue +from zarr_metadata.v3.data_type.float32 import Float32FillValue COMPLEX64_DTYPE_NAME: Final = "complex64" """The `data_type` value for the `complex64` type.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/float16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/float16.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/float32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/float32.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/float64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/float64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/int16.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/int32.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/int64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/int8.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/int8.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_datetime64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_datetime64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_timedelta64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/numpy_timedelta64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/raw.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/raw.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/string.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/string.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/struct.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py similarity index 97% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/struct.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py index 63d0cded7d..414c88d4c0 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/struct.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py @@ -10,7 +10,7 @@ from typing_extensions import ReadOnly from zarr_metadata.common import JSON -from zarr_metadata.v3.dtype import DType +from zarr_metadata.v3.data_type import DType STRUCT_DTYPE_NAME: Final = "struct" """The `name` field value of the `struct` data type.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint16.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint32.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint64.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint8.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py similarity index 100% rename from packages/zarr-metadata/src/zarr_metadata/v3/dtype/uint8.py rename to packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/dtype/__init__.py deleted file mode 100644 index 48e0d82869..0000000000 --- a/packages/zarr-metadata/src/zarr_metadata/v3/dtype/__init__.py +++ /dev/null @@ -1,25 +0,0 @@ -""" -Zarr data type spec types. -""" - -from collections.abc import Mapping, Sequence - -# Wider than the top-level JSON because TypedDicts used for dtype configs -# are assignable to Mapping[str, object], not to Mapping[str, JSON]. -DType = str | int | float | Sequence["DType"] | None | Mapping[str, object] -""" -The widest JSON-like shape that can specify a Zarr data type. - -See the submodules for specific per-dtype types: - -- `zarr_metadata.v3.dtype.primitive` -- core v3 primitives (bool, int*, uint*, float*, complex*) -- `zarr_metadata.v3.dtype.bytes` -- `bytes`, `null_terminated_bytes` -- `zarr_metadata.v3.dtype.string` -- `string`, `fixed_length_utf32` -- `zarr_metadata.v3.dtype.time` -- `numpy.datetime64`, `numpy.timedelta64` -- `zarr_metadata.v3.dtype.struct` -- `struct` -""" - - -__all__ = [ - "DType", -] diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index 98870c9b32..a4c3f10f26 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -179,59 +179,63 @@ def test_codec_imports() -> None: def test_dtype_imports() -> None: - from zarr_metadata.v3.dtype import DType - from zarr_metadata.v3.dtype.bool import BOOL_DTYPE_NAME, BoolDTypeName, BoolFillValue - from zarr_metadata.v3.dtype.bytes import BYTES_DTYPE_NAME, BytesDTypeName, BytesFillValue - from zarr_metadata.v3.dtype.complex64 import ( + from zarr_metadata.v3.data_type import DType + from zarr_metadata.v3.data_type.bool import BOOL_DTYPE_NAME, BoolDTypeName, BoolFillValue + from zarr_metadata.v3.data_type.bytes import BYTES_DTYPE_NAME, BytesDTypeName, BytesFillValue + from zarr_metadata.v3.data_type.complex64 import ( COMPLEX64_DTYPE_NAME, Complex64Component, Complex64DTypeName, Complex64FillValue, ) - from zarr_metadata.v3.dtype.complex128 import ( + from zarr_metadata.v3.data_type.complex128 import ( COMPLEX128_DTYPE_NAME, Complex128Component, Complex128DTypeName, Complex128FillValue, ) - from zarr_metadata.v3.dtype.float16 import ( + from zarr_metadata.v3.data_type.float16 import ( FLOAT16_DTYPE_NAME, Float16DTypeName, Float16FillValue, Float16SpecialFillValue, ) - from zarr_metadata.v3.dtype.float32 import ( + from zarr_metadata.v3.data_type.float32 import ( FLOAT32_DTYPE_NAME, Float32DTypeName, Float32FillValue, Float32SpecialFillValue, ) - from zarr_metadata.v3.dtype.float64 import ( + from zarr_metadata.v3.data_type.float64 import ( FLOAT64_DTYPE_NAME, Float64DTypeName, Float64FillValue, Float64SpecialFillValue, ) - from zarr_metadata.v3.dtype.int8 import INT8_DTYPE_NAME, Int8DTypeName, Int8FillValue - from zarr_metadata.v3.dtype.int16 import INT16_DTYPE_NAME, Int16DTypeName, Int16FillValue - from zarr_metadata.v3.dtype.int32 import INT32_DTYPE_NAME, Int32DTypeName, Int32FillValue - from zarr_metadata.v3.dtype.int64 import INT64_DTYPE_NAME, Int64DTypeName, Int64FillValue - from zarr_metadata.v3.dtype.numpy_datetime64 import ( + from zarr_metadata.v3.data_type.int8 import INT8_DTYPE_NAME, Int8DTypeName, Int8FillValue + from zarr_metadata.v3.data_type.int16 import INT16_DTYPE_NAME, Int16DTypeName, Int16FillValue + from zarr_metadata.v3.data_type.int32 import INT32_DTYPE_NAME, Int32DTypeName, Int32FillValue + from zarr_metadata.v3.data_type.int64 import INT64_DTYPE_NAME, Int64DTypeName, Int64FillValue + from zarr_metadata.v3.data_type.numpy_datetime64 import ( NUMPY_DATETIME64_DTYPE_NAME, NumpyDatetime64, NumpyDatetime64Configuration, NumpyDatetime64DTypeName, NumpyDatetime64FillValue, ) - from zarr_metadata.v3.dtype.numpy_timedelta64 import ( + from zarr_metadata.v3.data_type.numpy_timedelta64 import ( NUMPY_TIMEDELTA64_DTYPE_NAME, NumpyTimedelta64, NumpyTimedelta64Configuration, NumpyTimedelta64DTypeName, NumpyTimedelta64FillValue, ) - from zarr_metadata.v3.dtype.string import STRING_DTYPE_NAME, StringDTypeName, StringFillValue - from zarr_metadata.v3.dtype.struct import ( + from zarr_metadata.v3.data_type.string import ( + STRING_DTYPE_NAME, + StringDTypeName, + StringFillValue, + ) + from zarr_metadata.v3.data_type.struct import ( STRUCT_DTYPE_NAME, Struct, StructConfiguration, @@ -239,10 +243,22 @@ def test_dtype_imports() -> None: StructField, StructFillValue, ) - from zarr_metadata.v3.dtype.uint8 import UINT8_DTYPE_NAME, Uint8DTypeName, Uint8FillValue - from zarr_metadata.v3.dtype.uint16 import UINT16_DTYPE_NAME, Uint16DTypeName, Uint16FillValue - from zarr_metadata.v3.dtype.uint32 import UINT32_DTYPE_NAME, Uint32DTypeName, Uint32FillValue - from zarr_metadata.v3.dtype.uint64 import UINT64_DTYPE_NAME, Uint64DTypeName, Uint64FillValue + from zarr_metadata.v3.data_type.uint8 import UINT8_DTYPE_NAME, Uint8DTypeName, Uint8FillValue + from zarr_metadata.v3.data_type.uint16 import ( + UINT16_DTYPE_NAME, + Uint16DTypeName, + Uint16FillValue, + ) + from zarr_metadata.v3.data_type.uint32 import ( + UINT32_DTYPE_NAME, + Uint32DTypeName, + Uint32FillValue, + ) + from zarr_metadata.v3.data_type.uint64 import ( + UINT64_DTYPE_NAME, + Uint64DTypeName, + Uint64FillValue, + ) _ = ( DType, diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py index dc3cb62604..5c037a501e 100644 --- a/packages/zarr-metadata/tests/test_structural.py +++ b/packages/zarr-metadata/tests/test_structural.py @@ -28,9 +28,9 @@ from zarr_metadata.v3.codec.transpose import TransposeCodec, TransposeCodecConfiguration from zarr_metadata.v3.codec.zstd import ZstdCodec, ZstdCodecConfiguration from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 - from zarr_metadata.v3.dtype.numpy_datetime64 import NumpyDatetime64 - from zarr_metadata.v3.dtype.numpy_timedelta64 import NumpyTimedelta64 - from zarr_metadata.v3.dtype.struct import Struct + from zarr_metadata.v3.data_type.numpy_datetime64 import NumpyDatetime64 + from zarr_metadata.v3.data_type.numpy_timedelta64 import NumpyTimedelta64 + from zarr_metadata.v3.data_type.struct import Struct from zarr_metadata.v3.group import GroupMetadataV3 @@ -337,11 +337,11 @@ def test_sharding_index_location_constants() -> None: def test_primitive_dtype_names() -> None: - from zarr_metadata.v3.dtype.bool import BOOL_DTYPE_NAME - from zarr_metadata.v3.dtype.complex128 import COMPLEX128_DTYPE_NAME - from zarr_metadata.v3.dtype.float32 import FLOAT32_DTYPE_NAME - from zarr_metadata.v3.dtype.int32 import INT32_DTYPE_NAME - from zarr_metadata.v3.dtype.uint64 import UINT64_DTYPE_NAME + from zarr_metadata.v3.data_type.bool import BOOL_DTYPE_NAME + from zarr_metadata.v3.data_type.complex128 import COMPLEX128_DTYPE_NAME + from zarr_metadata.v3.data_type.float32 import FLOAT32_DTYPE_NAME + from zarr_metadata.v3.data_type.int32 import INT32_DTYPE_NAME + from zarr_metadata.v3.data_type.uint64 import UINT64_DTYPE_NAME assert BOOL_DTYPE_NAME == "bool" assert INT32_DTYPE_NAME == "int32" @@ -401,7 +401,7 @@ def test_struct_dtype_metadata_nested() -> None: def test_hex_float16_validator() -> None: - from zarr_metadata.v3.dtype.float16 import hex_float16 + from zarr_metadata.v3.data_type.float16 import hex_float16 assert hex_float16("0x7c00") == "0x7c00" with pytest.raises(ValueError): @@ -413,7 +413,7 @@ def test_hex_float16_validator() -> None: def test_hex_float32_validator() -> None: - from zarr_metadata.v3.dtype.float32 import hex_float32 + from zarr_metadata.v3.data_type.float32 import hex_float32 assert hex_float32("0x7fc00000") == "0x7fc00000" with pytest.raises(ValueError): @@ -423,7 +423,7 @@ def test_hex_float32_validator() -> None: def test_hex_float64_validator() -> None: - from zarr_metadata.v3.dtype.float64 import hex_float64 + from zarr_metadata.v3.data_type.float64 import hex_float64 assert hex_float64("0x7ff8000000000000") == "0x7ff8000000000000" with pytest.raises(ValueError): @@ -433,7 +433,7 @@ def test_hex_float64_validator() -> None: def test_base64_bytes_validator() -> None: - from zarr_metadata.v3.dtype.bytes import base64_bytes + from zarr_metadata.v3.data_type.bytes import base64_bytes assert base64_bytes("SGVsbG8=") == "SGVsbG8=" assert base64_bytes("") == "" @@ -446,7 +446,7 @@ def test_base64_bytes_validator() -> None: def test_raw_bytes_dtype_name_validator() -> None: - from zarr_metadata.v3.dtype.raw import raw_bytes_dtype_name + from zarr_metadata.v3.data_type.raw import raw_bytes_dtype_name assert raw_bytes_dtype_name("r8") == "r8" assert raw_bytes_dtype_name("r16") == "r16" diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index e3595666ea..7656c3ad33 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -12,7 +12,7 @@ ) from typing_extensions import ReadOnly -from zarr_metadata.v3.dtype import DType +from zarr_metadata.v3.data_type import DType from zarr.core.common import NamedConfig from zarr.errors import UnstableSpecificationWarning diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index 3ccabc92ba..221dafec8f 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -18,7 +18,7 @@ ) import numpy as np -from zarr_metadata.v3.dtype.numpy_datetime64 import DateTimeUnit as DateTimeUnit +from zarr_metadata.v3.data_type.numpy_datetime64 import DateTimeUnit as DateTimeUnit from zarr.core.dtype.common import ( ENDIANNESS_STR, diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index 6d42c662f0..50c2421875 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -14,7 +14,7 @@ ) import numpy as np -from zarr_metadata.v3.dtype.numpy_datetime64 import ( +from zarr_metadata.v3.data_type.numpy_datetime64 import ( NumpyDatetime64Configuration as TimeConfig, ) From b7b055ee8017ef1fc291b341454271a4a8e988b4 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 22 Apr 2026 13:47:39 +0200 Subject: [PATCH 41/55] feat: add zarr-metadata package MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adds packages/zarr-metadata, a sibling PyPI package that contains spec-defined Zarr v2 and v3 metadata types as pure-typing artifacts (TypedDicts, type aliases, Final string constants, NewType validators). No runtime logic beyond minimal regex validators for spec-format-locked strings (hex floats, base64 bytes, raw-bytes name). Layout (anything imported from `zarr_metadata.v3.X` is a v3-spec artifact; from `zarr_metadata.v2.X` is v2-spec; only true cross-version primitives sit at the top level): zarr_metadata/ ├── common.py # JSON, NamedConfig, NamedRequiredConfig ├── __init__.py # ArrayMetadata, GroupMetadata unions ├── v2/ │ ├── array.py, group.py, consolidated.py, codec.py └── v3/ ├── array.py, group.py, consolidated.py ├── chunk_grid/ {regular, rectilinear} ├── chunk_key_encoding/ {default, v2} ├── codec/ {blosc, bytes, crc32c, gzip, │ sharding, transpose, zstd} └── data_type/ {bool, int8/16/32/64, uint8/16/32/64, float16/32/64, complex64/128, bytes, string, numpy_datetime64, numpy_timedelta64, struct, raw} zarr-python source is unchanged in this branch. zarr-metadata is shipped as an independent package; a follow-up PR will adopt it inside zarr-python once the package is published to PyPI. Co-Authored-By: Claude Opus 4.7 (1M context) --- .gitignore | 3 + packages/zarr-metadata/README.md | 15 + packages/zarr-metadata/pyproject.toml | 50 ++ .../src/zarr_metadata/__init__.py | 24 + .../zarr-metadata/src/zarr_metadata/common.py | 37 ++ .../zarr-metadata/src/zarr_metadata/py.typed | 0 .../src/zarr_metadata/v2/__init__.py | 15 + .../src/zarr_metadata/v2/array.py | 59 +++ .../src/zarr_metadata/v2/codec.py | 29 ++ .../src/zarr_metadata/v2/consolidated.py | 37 ++ .../src/zarr_metadata/v2/group.py | 19 + .../src/zarr_metadata/v3/__init__.py | 13 + .../src/zarr_metadata/v3/array.py | 52 ++ .../zarr_metadata/v3/chunk_grid/__init__.py | 10 + .../v3/chunk_grid/rectilinear.py | 44 ++ .../zarr_metadata/v3/chunk_grid/regular.py | 34 ++ .../v3/chunk_key_encoding/__init__.py | 22 + .../v3/chunk_key_encoding/default.py | 42 ++ .../zarr_metadata/v3/chunk_key_encoding/v2.py | 42 ++ .../src/zarr_metadata/v3/codec/__init__.py | 19 + .../src/zarr_metadata/v3/codec/blosc.py | 66 +++ .../src/zarr_metadata/v3/codec/bytes.py | 47 ++ .../src/zarr_metadata/v3/codec/crc32c.py | 36 ++ .../src/zarr_metadata/v3/codec/gzip.py | 40 ++ .../src/zarr_metadata/v3/codec/sharding.py | 61 +++ .../src/zarr_metadata/v3/codec/transpose.py | 39 ++ .../src/zarr_metadata/v3/codec/zstd.py | 41 ++ .../src/zarr_metadata/v3/consolidated.py | 30 ++ .../zarr_metadata/v3/data_type/__init__.py | 25 + .../src/zarr_metadata/v3/data_type/bool.py | 23 + .../src/zarr_metadata/v3/data_type/bytes.py | 48 ++ .../zarr_metadata/v3/data_type/complex128.py | 37 ++ .../zarr_metadata/v3/data_type/complex64.py | 37 ++ .../src/zarr_metadata/v3/data_type/float16.py | 53 ++ .../src/zarr_metadata/v3/data_type/float32.py | 53 ++ .../src/zarr_metadata/v3/data_type/float64.py | 54 ++ .../src/zarr_metadata/v3/data_type/int16.py | 23 + .../src/zarr_metadata/v3/data_type/int32.py | 23 + .../src/zarr_metadata/v3/data_type/int64.py | 23 + .../src/zarr_metadata/v3/data_type/int8.py | 23 + .../v3/data_type/numpy_datetime64.py | 61 +++ .../v3/data_type/numpy_timedelta64.py | 61 +++ .../src/zarr_metadata/v3/data_type/raw.py | 45 ++ .../src/zarr_metadata/v3/data_type/string.py | 23 + .../src/zarr_metadata/v3/data_type/struct.py | 67 +++ .../src/zarr_metadata/v3/data_type/uint16.py | 23 + .../src/zarr_metadata/v3/data_type/uint32.py | 23 + .../src/zarr_metadata/v3/data_type/uint64.py | 23 + .../src/zarr_metadata/v3/data_type/uint8.py | 23 + .../src/zarr_metadata/v3/group.py | 31 ++ packages/zarr-metadata/tests/test_imports.py | 334 +++++++++++++ .../zarr-metadata/tests/test_structural.py | 462 ++++++++++++++++++ 52 files changed, 2524 insertions(+) create mode 100644 packages/zarr-metadata/README.md create mode 100644 packages/zarr-metadata/pyproject.toml create mode 100644 packages/zarr-metadata/src/zarr_metadata/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/common.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/py.typed create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/array.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/codec.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/group.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/array.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/v3/group.py create mode 100644 packages/zarr-metadata/tests/test_imports.py create mode 100644 packages/zarr-metadata/tests/test_structural.py diff --git a/.gitignore b/.gitignore index b79ce264c8..3284865d6c 100644 --- a/.gitignore +++ b/.gitignore @@ -91,3 +91,6 @@ tests/.hypothesis zarr/version.py zarr.egg-info/ + +# zarr-metadata package lockfile (a library, not an app) +packages/zarr-metadata/uv.lock diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md new file mode 100644 index 0000000000..2e4b44ae1a --- /dev/null +++ b/packages/zarr-metadata/README.md @@ -0,0 +1,15 @@ +# zarr-metadata + +Spec-defined metadata types for Zarr v2 and v3, distributed as pure-typing +artifacts (TypedDicts, type aliases, unions). No runtime logic, no numpy, +no storage backends. + +`zarr-metadata` is developed in the [zarr-python](https://github.com/zarr-developers/zarr-python) +repository at `packages/zarr-metadata/`. + +## Principle + +Every type that models a spec artifact (v2 or v3 array/group/consolidated +metadata, chunk grids, codec metadata, dtype shapes) belongs in +`zarr-metadata`. Zarr-python implementation details (runtime codecs, +config dataclasses, numcodecs-derived helpers) stay in `zarr`. diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml new file mode 100644 index 0000000000..7e31477af0 --- /dev/null +++ b/packages/zarr-metadata/pyproject.toml @@ -0,0 +1,50 @@ +[build-system] +requires = ["hatchling>=1.29.0"] +build-backend = "hatchling.build" + +[project] +name = "zarr-metadata" +version = "0.1.0" +description = "Spec-defined metadata types for Zarr v2 and v3." +readme = "README.md" +requires-python = ">=3.12" +license = "MIT" +authors = [ + { name = "Davis Bennett", email = "davis.v.bennett@gmail.com" }, +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Typing :: Typed", +] +dependencies = [ + "typing_extensions>=4.13", +] + +[project.optional-dependencies] +test = ["pytest"] + +[tool.hatch.build.targets.wheel] +packages = ["src/zarr_metadata"] + +[tool.numpydoc_validation] +checks = [ + "GL10", + "SS04", + "PR02", + "PR03", + "PR05", + "PR06", +] + +[tool.pyright] +include = ["src"] +enableExperimentalFeatures = true +typeCheckingMode = "strict" +pythonVersion = "3.12" diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py new file mode 100644 index 0000000000..a7d39bec1a --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -0,0 +1,24 @@ +from zarr_metadata.common import JSON, NamedConfig, NamedRequiredConfig +from zarr_metadata.v2.array import ArrayMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2 +from zarr_metadata.v3.array import ArrayMetadataV3 +from zarr_metadata.v3.group import GroupMetadataV3 + +ArrayMetadata = ArrayMetadataV2 | ArrayMetadataV3 +"""Any Zarr array metadata document (v2 or v3).""" + +GroupMetadata = GroupMetadataV2 | GroupMetadataV3 +"""Any Zarr group metadata document (v2 or v3).""" + + +__all__ = [ + "JSON", + "ArrayMetadata", + "ArrayMetadataV2", + "ArrayMetadataV3", + "GroupMetadata", + "GroupMetadataV2", + "GroupMetadataV3", + "NamedConfig", + "NamedRequiredConfig", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py new file mode 100644 index 0000000000..2af3398c6a --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -0,0 +1,37 @@ +""" +Top-level cross-version primitives for Zarr metadata. + +Version-specific types live under `zarr_metadata.v2` and `zarr_metadata.v3`. +Codec and dtype spec types live under `zarr_metadata.v3.codec` and +`zarr_metadata.v3.data_type`. +""" + +from collections.abc import Mapping, Sequence +from typing import NotRequired, TypedDict + +from typing_extensions import ReadOnly + +JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None +"""Any valid JSON value.""" + + +class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + Named-config envelope with optional configuration. + + Generic with two parameters: name literal and configuration mapping. + """ + + name: ReadOnly[TName] + configuration: NotRequired[ReadOnly[TConfig]] + + +class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + Named-config envelope with required configuration. + + Generic with two parameters: name literal and configuration mapping. + """ + + name: ReadOnly[TName] + configuration: ReadOnly[TConfig] diff --git a/packages/zarr-metadata/src/zarr_metadata/py.typed b/packages/zarr-metadata/src/zarr_metadata/py.typed new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py new file mode 100644 index 0000000000..ea5d08af7b --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py @@ -0,0 +1,15 @@ +"""Zarr v2 metadata types.""" + +from zarr_metadata.v2.array import ArrayMetadataV2, DataTypeV2, DataTypeV2Structured +from zarr_metadata.v2.codec import NumcodecsConfig +from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2 + +__all__ = [ + "ArrayMetadataV2", + "ConsolidatedMetadataV2", + "DataTypeV2", + "DataTypeV2Structured", + "GroupMetadataV2", + "NumcodecsConfig", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py new file mode 100644 index 0000000000..cbcbccc0e2 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -0,0 +1,59 @@ +"""Zarr v2 array metadata types.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Literal, NotRequired, TypedDict + +if TYPE_CHECKING: + from zarr_metadata.common import JSON + from zarr_metadata.v2.codec import NumcodecsConfig + + +class DataTypeV2Structured(TypedDict): + """ + A single field entry inside a structured v2 dtype. + + Spec-faithful: `datatype` is a numpy-style dtype string; `shape` is + present only when the field is a subarray field. + + See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html#data-type-encoding + """ + + fieldname: str + datatype: str + shape: NotRequired[tuple[int, ...]] + + +DataTypeV2 = str | tuple[DataTypeV2Structured, ...] +"""The v2 dtype representation. + +Simple dtypes are numpy-style strings (e.g. `"kji...` (where `` is `separator`). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from typing import Final, Literal, NotRequired, TypedDict + +from zarr_metadata.v3.chunk_key_encoding import ChunkKeySeparator + +DEFAULT_CHUNK_KEY_ENCODING_NAME: Final = "default" +"""The `name` field value of the default chunk key encoding.""" + +DefaultChunkKeyEncodingName = Literal["default"] +"""Literal type of the `name` field of the default chunk key encoding.""" + + +class DefaultChunkKeyEncodingConfiguration(TypedDict): + """Configuration for the default chunk key encoding. + + `separator` is optional and defaults to `"/"` per spec. + """ + + separator: NotRequired[ChunkKeySeparator] + + +class DefaultChunkKeyEncoding(TypedDict): + """Default chunk key encoding metadata.""" + + name: DefaultChunkKeyEncodingName + configuration: NotRequired[DefaultChunkKeyEncodingConfiguration] + + +__all__ = [ + "DEFAULT_CHUNK_KEY_ENCODING_NAME", + "DefaultChunkKeyEncoding", + "DefaultChunkKeyEncodingConfiguration", + "DefaultChunkKeyEncodingName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py new file mode 100644 index 0000000000..1864e8c5a2 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py @@ -0,0 +1,42 @@ +""" +V2-compatibility chunk key encoding (Zarr v3 core spec). + +Intended only to allow existing v2 arrays to be converted to v3 without +having to rename chunks. Not recommended for new arrays. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from typing import Final, Literal, NotRequired, TypedDict + +from zarr_metadata.v3.chunk_key_encoding import ChunkKeySeparator + +V2_CHUNK_KEY_ENCODING_NAME: Final = "v2" +"""The `name` field value of the v2 chunk key encoding.""" + +V2ChunkKeyEncodingName = Literal["v2"] +"""Literal type of the `name` field of the v2 chunk key encoding.""" + + +class V2ChunkKeyEncodingConfiguration(TypedDict): + """Configuration for the v2 chunk key encoding. + + `separator` is optional and defaults to `"."` per spec. + """ + + separator: NotRequired[ChunkKeySeparator] + + +class V2ChunkKeyEncoding(TypedDict): + """V2-compatibility chunk key encoding metadata.""" + + name: V2ChunkKeyEncodingName + configuration: NotRequired[V2ChunkKeyEncodingConfiguration] + + +__all__ = [ + "V2_CHUNK_KEY_ENCODING_NAME", + "V2ChunkKeyEncoding", + "V2ChunkKeyEncodingConfiguration", + "V2ChunkKeyEncodingName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py new file mode 100644 index 0000000000..97b3a69551 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py @@ -0,0 +1,19 @@ +""" +Zarr codec metadata types. +""" + +from collections.abc import Mapping + +Codec = str | Mapping[str, object] +""" +The widest JSON shape that can specify a codec (v2 or v3). + +For v3, a codec is a `{"name": ..., "configuration": ...}` mapping (or +a bare `str` shorthand); for v2, a codec is the numcodecs JSON dict. +The accepted-input shape is the union of both. +""" + + +__all__ = [ + "Codec", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py new file mode 100644 index 0000000000..1cd79f3d43 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py @@ -0,0 +1,66 @@ +""" +Blosc codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/blosc/index.html +""" + +from typing import Final, Literal, TypedDict + +BLOSC_CODEC_NAME: Final = "blosc" +"""The `name` field value of the `blosc` codec.""" + +BloscCodecName = Literal["blosc"] +"""Literal type of the `name` field of the `blosc` codec.""" + +BLOSC_SHUFFLE_NOSHUFFLE: Final = "noshuffle" +BLOSC_SHUFFLE_SHUFFLE: Final = "shuffle" +BLOSC_SHUFFLE_BITSHUFFLE: Final = "bitshuffle" + +BloscShuffle = Literal["noshuffle", "shuffle", "bitshuffle"] +"""Blosc shuffle mode names.""" + +BLOSC_CNAME_LZ4: Final = "lz4" +BLOSC_CNAME_LZ4HC: Final = "lz4hc" +BLOSC_CNAME_BLOSCLZ: Final = "blosclz" +BLOSC_CNAME_SNAPPY: Final = "snappy" +BLOSC_CNAME_ZLIB: Final = "zlib" +BLOSC_CNAME_ZSTD: Final = "zstd" + +BloscCName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] +"""Blosc compressor identifiers.""" + + +class BloscCodecConfiguration(TypedDict): + """Configuration for the Zarr v3 `blosc` codec.""" + + cname: BloscCName + clevel: int + shuffle: BloscShuffle + blocksize: int + typesize: int + + +class BloscCodec(TypedDict): + """`blosc` codec metadata.""" + + name: BloscCodecName + configuration: BloscCodecConfiguration + + +__all__ = [ + "BLOSC_CNAME_BLOSCLZ", + "BLOSC_CNAME_LZ4", + "BLOSC_CNAME_LZ4HC", + "BLOSC_CNAME_SNAPPY", + "BLOSC_CNAME_ZLIB", + "BLOSC_CNAME_ZSTD", + "BLOSC_CODEC_NAME", + "BLOSC_SHUFFLE_BITSHUFFLE", + "BLOSC_SHUFFLE_NOSHUFFLE", + "BLOSC_SHUFFLE_SHUFFLE", + "BloscCName", + "BloscCodec", + "BloscCodecConfiguration", + "BloscCodecName", + "BloscShuffle", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py new file mode 100644 index 0000000000..fe6e7b2579 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py @@ -0,0 +1,47 @@ +""" +Bytes codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/bytes/index.html +""" + +from typing import Final, Literal, NotRequired, TypedDict + +BYTES_CODEC_NAME: Final = "bytes" +"""The `name` field value of the `bytes` codec.""" + +BytesCodecName = Literal["bytes"] +"""Literal type of the `name` field of the `bytes` codec.""" + +BYTES_ENDIAN_LITTLE: Final = "little" +BYTES_ENDIAN_BIG: Final = "big" + +Endian = Literal["little", "big"] +"""Byte order of multi-byte numeric data.""" + + +class BytesCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `bytes` codec. + + The `endian` field is required for multi-byte data types. + """ + + endian: NotRequired[Endian] + + +class BytesCodec(TypedDict): + """`bytes` codec metadata.""" + + name: BytesCodecName + configuration: BytesCodecConfiguration + + +__all__ = [ + "BYTES_CODEC_NAME", + "BYTES_ENDIAN_BIG", + "BYTES_ENDIAN_LITTLE", + "BytesCodec", + "BytesCodecConfiguration", + "BytesCodecName", + "Endian", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py new file mode 100644 index 0000000000..573e56b356 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py @@ -0,0 +1,36 @@ +""" +CRC32C codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/crc32c/index.html + +The CRC32C codec has no configuration fields, so the `configuration` +key is absent from the metadata. +""" + +from typing import Final, Literal, NotRequired, TypedDict + +from zarr_metadata.common import JSON + +CRC32C_CODEC_NAME: Final = "crc32c" +"""The `name` field value of the `crc32c` codec.""" + +Crc32cCodecName = Literal["crc32c"] +"""Literal type of the `name` field of the `crc32c` codec.""" + + +class Crc32cCodec(TypedDict): + """`crc32c` codec metadata. + + Per spec the codec has no configuration fields. `configuration` is + optional and, if present, should be an empty mapping. + """ + + name: Crc32cCodecName + configuration: NotRequired[dict[str, JSON]] + + +__all__ = [ + "CRC32C_CODEC_NAME", + "Crc32cCodec", + "Crc32cCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py new file mode 100644 index 0000000000..16d9c5c5d1 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py @@ -0,0 +1,40 @@ +""" +Gzip codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/gzip/index.html +""" + +from typing import Final, Literal, NotRequired, TypedDict + +GZIP_CODEC_NAME: Final = "gzip" +"""The `name` field value of the `gzip` codec.""" + +GzipCodecName = Literal["gzip"] +"""Literal type of the `name` field of the `gzip` codec.""" + + +class GzipCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `gzip` codec. + + `level` is an integer in the range 0-9; 0 disables compression and 9 + is slowest with the best compression ratio. The spec does not mandate + a default. + """ + + level: NotRequired[int] + + +class GzipCodec(TypedDict): + """`gzip` codec metadata.""" + + name: GzipCodecName + configuration: GzipCodecConfiguration + + +__all__ = [ + "GZIP_CODEC_NAME", + "GzipCodec", + "GzipCodecConfiguration", + "GzipCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding.py new file mode 100644 index 0000000000..50aa6621eb --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding.py @@ -0,0 +1,61 @@ +""" +Sharding codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/sharding-indexed/index.html +""" + +from typing import Final, Literal, NotRequired, TypedDict + +from zarr_metadata.v3.codec import Codec + +SHARDING_CODEC_NAME: Final = "sharding_indexed" +"""The `name` field value of the `sharding_indexed` codec.""" + +ShardingCodecName = Literal["sharding_indexed"] +"""Literal type of the `name` field of the `sharding_indexed` codec.""" + +SHARDING_INDEX_LOCATION_START: Final = "start" +SHARDING_INDEX_LOCATION_END: Final = "end" + +IndexLocation = Literal["start", "end"] +"""Position of the shard index within the encoded shard.""" + + +class ShardingCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `sharding_indexed` codec. + + `chunk_shape` is the shape of inner chunks along each dimension; + it must evenly divide the shard shape. + + `codecs` is the codec pipeline applied to each inner chunk; exactly + one array-to-bytes codec is required. + + `index_codecs` is the codec pipeline applied to the shard index; + it must be deterministic (no variable-size compression). + + `index_location` defaults to `"end"` per the spec. + """ + + chunk_shape: tuple[int, ...] + codecs: tuple[Codec, ...] + index_codecs: tuple[Codec, ...] + index_location: NotRequired[IndexLocation] + + +class ShardingCodec(TypedDict): + """`sharding_indexed` codec metadata.""" + + name: ShardingCodecName + configuration: ShardingCodecConfiguration + + +__all__ = [ + "SHARDING_CODEC_NAME", + "SHARDING_INDEX_LOCATION_END", + "SHARDING_INDEX_LOCATION_START", + "IndexLocation", + "ShardingCodec", + "ShardingCodecConfiguration", + "ShardingCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py new file mode 100644 index 0000000000..ef792670c5 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py @@ -0,0 +1,39 @@ +""" +Transpose codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/transpose/index.html +""" + +from typing import Final, Literal, TypedDict + +TRANSPOSE_CODEC_NAME: Final = "transpose" +"""The `name` field value of the `transpose` codec.""" + +TransposeCodecName = Literal["transpose"] +"""Literal type of the `name` field of the `transpose` codec.""" + + +class TransposeCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `transpose` codec. + + `order` is a permutation of the dimension indices 0..n-1 that + specifies the dimension reordering applied during encoding. + """ + + order: tuple[int, ...] + + +class TransposeCodec(TypedDict): + """`transpose` codec metadata.""" + + name: TransposeCodecName + configuration: TransposeCodecConfiguration + + +__all__ = [ + "TRANSPOSE_CODEC_NAME", + "TransposeCodec", + "TransposeCodecConfiguration", + "TransposeCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py new file mode 100644 index 0000000000..a659ca4cf1 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py @@ -0,0 +1,41 @@ +""" +Zstandard codec types. + +See https://github.com/zarr-developers/zarr-specs/pull/256 (unmerged at +time of writing; the configuration shape below reflects the proposed +specification). +""" + +from typing import Final, Literal, TypedDict + +ZSTD_CODEC_NAME: Final = "zstd" +"""The `name` field value of the `zstd` codec.""" + +ZstdCodecName = Literal["zstd"] +"""Literal type of the `name` field of the `zstd` codec.""" + + +class ZstdCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `zstd` codec. + + Both fields are required per the proposed specification. + """ + + level: int + checksum: bool + + +class ZstdCodec(TypedDict): + """`zstd` codec metadata.""" + + name: ZstdCodecName + configuration: ZstdCodecConfiguration + + +__all__ = [ + "ZSTD_CODEC_NAME", + "ZstdCodec", + "ZstdCodecConfiguration", + "ZstdCodecName", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py new file mode 100644 index 0000000000..7fe4f0b8c2 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py @@ -0,0 +1,30 @@ +"""Zarr v3 consolidated metadata types.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Literal, TypedDict + +if TYPE_CHECKING: + from collections.abc import Mapping + + from zarr_metadata.v3.array import ArrayMetadataV3 + from zarr_metadata.v3.group import GroupMetadataV3 + + +class ConsolidatedMetadataV3(TypedDict): + """ + Inline consolidated metadata embedded in a v3 group. + + The `metadata` map contains only v3 array and group entries - v2 + entries are excluded by design. Mixing v2 entries into a v3 + consolidated metadata document is invalid per spec. + """ + + kind: Literal["inline"] + must_understand: Literal[False] + metadata: Mapping[str, ArrayMetadataV3 | GroupMetadataV3] + + +__all__ = [ + "ConsolidatedMetadataV3", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py new file mode 100644 index 0000000000..c126e18ddb --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py @@ -0,0 +1,25 @@ +""" +Zarr v3 data type spec types. + +Each v3 data type has its own submodule: + +- Core primitives: `bool`, `int8`/`16`/`32`/`64`, `uint8`/`16`/`32`/`64`, + `float16`/`32`/`64`, `complex64`/`128`, `raw` (for `r`) +- zarr-extensions: `bytes`, `string`, `numpy_datetime64`, `numpy_timedelta64`, + `struct` + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from collections.abc import Mapping, Sequence + +# Wider than the top-level JSON because TypedDicts used for data type +# configurations are assignable to Mapping[str, object], not to +# Mapping[str, JSON]. +DType = str | int | float | Sequence["DType"] | None | Mapping[str, object] +"""The widest JSON-like shape that can specify a Zarr v3 data type.""" + + +__all__ = [ + "DType", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py new file mode 100644 index 0000000000..48042b612a --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `bool` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +BOOL_DTYPE_NAME: Final = "bool" +"""The `data_type` value for the `bool` type.""" + +BoolDTypeName = Literal["bool"] +"""Literal type of the `data_type` field for `bool`.""" + +BoolFillValue = bool +"""Permitted JSON shape of the `fill_value` field for `bool`: a JSON boolean.""" + + +__all__ = [ + "BOOL_DTYPE_NAME", + "BoolDTypeName", + "BoolFillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py new file mode 100644 index 0000000000..1295f22234 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py @@ -0,0 +1,48 @@ +""" +Zarr `bytes` data type (variable-length raw bytes, zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/bytes +""" + +import re +from typing import Final, Literal, NewType + +BYTES_DTYPE_NAME: Final = "bytes" +"""The `data_type` value for the variable-length `bytes` type.""" + +BytesDTypeName = Literal["bytes"] +"""Literal type of the `data_type` field for `bytes`.""" + +Base64Bytes = NewType("Base64Bytes", str) +"""A standard-alphabet base64-encoded byte sequence.""" + +_BASE64_RE: Final = re.compile(r"^[A-Za-z0-9+/]*={0,2}$") + + +def base64_bytes(value: str) -> Base64Bytes: + """Validate `value` as a Base64Bytes and brand it. + + Raises ValueError if `value` is not standard-alphabet base64 + (length must be a multiple of 4 once padded; only `A-Z`, `a-z`, + `0-9`, `+`, `/`, and trailing `=` padding are permitted). + """ + if len(value) % 4 != 0 or not _BASE64_RE.fullmatch(value): + raise ValueError(f"Expected standard-alphabet base64, got {value!r}") + return Base64Bytes(value) + + +BytesFillValue = tuple[int, ...] | Base64Bytes +"""Permitted JSON shape of the `fill_value` field for `bytes`. + +Either a JSON array of integers in `[0, 255]` (one per byte), or a +`Base64Bytes` string encoding the byte sequence. +""" + + +__all__ = [ + "BYTES_DTYPE_NAME", + "Base64Bytes", + "BytesDTypeName", + "BytesFillValue", + "base64_bytes", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py new file mode 100644 index 0000000000..3f5827bde6 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py @@ -0,0 +1,37 @@ +""" +Zarr v3 `complex128` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +from zarr_metadata.v3.data_type.float64 import Float64FillValue + +COMPLEX128_DTYPE_NAME: Final = "complex128" +"""The `data_type` value for the `complex128` type.""" + +Complex128DTypeName = Literal["complex128"] +"""Literal type of the `data_type` field for `complex128`.""" + +Complex128Component = Float64FillValue +"""One real or imaginary component of a `complex128` fill value. + +Same shape as a `float64` fill value: a JSON number, a named sentinel, +or a `HexFloat64` string. +""" + +Complex128FillValue = tuple[Complex128Component, Complex128Component] +"""Permitted JSON shape of the `fill_value` field for `complex128`. + +A two-element JSON array `[real, imag]` where each component is a +`Complex128Component`. +""" + + +__all__ = [ + "COMPLEX128_DTYPE_NAME", + "Complex128Component", + "Complex128DTypeName", + "Complex128FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py new file mode 100644 index 0000000000..7409fdd452 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py @@ -0,0 +1,37 @@ +""" +Zarr v3 `complex64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +from zarr_metadata.v3.data_type.float32 import Float32FillValue + +COMPLEX64_DTYPE_NAME: Final = "complex64" +"""The `data_type` value for the `complex64` type.""" + +Complex64DTypeName = Literal["complex64"] +"""Literal type of the `data_type` field for `complex64`.""" + +Complex64Component = Float32FillValue +"""One real or imaginary component of a `complex64` fill value. + +Same shape as a `float32` fill value: a JSON number, a named sentinel, +or a `HexFloat32` string. +""" + +Complex64FillValue = tuple[Complex64Component, Complex64Component] +"""Permitted JSON shape of the `fill_value` field for `complex64`. + +A two-element JSON array `[real, imag]` where each component is a +`Complex64Component`. +""" + + +__all__ = [ + "COMPLEX64_DTYPE_NAME", + "Complex64Component", + "Complex64DTypeName", + "Complex64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py new file mode 100644 index 0000000000..dac9eed09b --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py @@ -0,0 +1,53 @@ +""" +Zarr v3 `float16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT16_DTYPE_NAME: Final = "float16" +"""The `data_type` value for the `float16` type.""" + +Float16DTypeName = Literal["float16"] +"""Literal type of the `data_type` field for `float16`.""" + +Float16SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat16 = NewType("HexFloat16", str) +"""A 6-character hex string (`0x` + 4 hex digits) encoding the +unsigned-integer representation of a float16.""" + +_HEX_FLOAT16_RE: Final = re.compile(r"^0x[0-9a-fA-F]{4}$") + + +def hex_float16(value: str) -> HexFloat16: + """Validate `value` as a HexFloat16 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 4 hex + digits. + """ + if not _HEX_FLOAT16_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 4 hex digits, got {value!r}") + return HexFloat16(value) + + +Float16FillValue = float | int | Float16SpecialFillValue | HexFloat16 +"""Permitted JSON shape of the `fill_value` field for `float16`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat16` (`0xYYYY` string encoding +the unsigned-integer representation of the IEEE 754 value). +""" + + +__all__ = [ + "FLOAT16_DTYPE_NAME", + "Float16DTypeName", + "Float16FillValue", + "Float16SpecialFillValue", + "HexFloat16", + "hex_float16", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py new file mode 100644 index 0000000000..37bc19243e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py @@ -0,0 +1,53 @@ +""" +Zarr v3 `float32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT32_DTYPE_NAME: Final = "float32" +"""The `data_type` value for the `float32` type.""" + +Float32DTypeName = Literal["float32"] +"""Literal type of the `data_type` field for `float32`.""" + +Float32SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat32 = NewType("HexFloat32", str) +"""A 10-character hex string (`0x` + 8 hex digits) encoding the +unsigned-integer representation of a float32.""" + +_HEX_FLOAT32_RE: Final = re.compile(r"^0x[0-9a-fA-F]{8}$") + + +def hex_float32(value: str) -> HexFloat32: + """Validate `value` as a HexFloat32 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 8 hex + digits. + """ + if not _HEX_FLOAT32_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 8 hex digits, got {value!r}") + return HexFloat32(value) + + +Float32FillValue = float | int | Float32SpecialFillValue | HexFloat32 +"""Permitted JSON shape of the `fill_value` field for `float32`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat32` (`0xYYYYYYYY` string +encoding the unsigned-integer representation of the IEEE 754 value). +""" + + +__all__ = [ + "FLOAT32_DTYPE_NAME", + "Float32DTypeName", + "Float32FillValue", + "Float32SpecialFillValue", + "HexFloat32", + "hex_float32", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py new file mode 100644 index 0000000000..28e77568af --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py @@ -0,0 +1,54 @@ +""" +Zarr v3 `float64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT64_DTYPE_NAME: Final = "float64" +"""The `data_type` value for the `float64` type.""" + +Float64DTypeName = Literal["float64"] +"""Literal type of the `data_type` field for `float64`.""" + +Float64SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat64 = NewType("HexFloat64", str) +"""An 18-character hex string (`0x` + 16 hex digits) encoding the +unsigned-integer representation of a float64.""" + +_HEX_FLOAT64_RE: Final = re.compile(r"^0x[0-9a-fA-F]{16}$") + + +def hex_float64(value: str) -> HexFloat64: + """Validate `value` as a HexFloat64 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 16 hex + digits. + """ + if not _HEX_FLOAT64_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 16 hex digits, got {value!r}") + return HexFloat64(value) + + +Float64FillValue = float | int | Float64SpecialFillValue | HexFloat64 +"""Permitted JSON shape of the `fill_value` field for `float64`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat64` (`0xYYYYYYYYYYYYYYYY` +string encoding the unsigned-integer representation of the IEEE 754 +value). +""" + + +__all__ = [ + "FLOAT64_DTYPE_NAME", + "Float64DTypeName", + "Float64FillValue", + "Float64SpecialFillValue", + "HexFloat64", + "hex_float64", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py new file mode 100644 index 0000000000..e0488ab56e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT16_DTYPE_NAME: Final = "int16" +"""The `data_type` value for the `int16` type.""" + +Int16DTypeName = Literal["int16"] +"""Literal type of the `data_type` field for `int16`.""" + +Int16FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int16`: a JSON integer in [-32768, 32767].""" + + +__all__ = [ + "INT16_DTYPE_NAME", + "Int16DTypeName", + "Int16FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py new file mode 100644 index 0000000000..762561a4b1 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT32_DTYPE_NAME: Final = "int32" +"""The `data_type` value for the `int32` type.""" + +Int32DTypeName = Literal["int32"] +"""Literal type of the `data_type` field for `int32`.""" + +Int32FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int32`: a JSON integer in [-2**31, 2**31 - 1].""" + + +__all__ = [ + "INT32_DTYPE_NAME", + "Int32DTypeName", + "Int32FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py new file mode 100644 index 0000000000..4699d4681c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT64_DTYPE_NAME: Final = "int64" +"""The `data_type` value for the `int64` type.""" + +Int64DTypeName = Literal["int64"] +"""Literal type of the `data_type` field for `int64`.""" + +Int64FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int64`: a JSON integer in [-2**63, 2**63 - 1].""" + + +__all__ = [ + "INT64_DTYPE_NAME", + "Int64DTypeName", + "Int64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py new file mode 100644 index 0000000000..84a788a963 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int8` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT8_DTYPE_NAME: Final = "int8" +"""The `data_type` value for the `int8` type.""" + +Int8DTypeName = Literal["int8"] +"""Literal type of the `data_type` field for `int8`.""" + +Int8FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int8`: a JSON integer in [-128, 127].""" + + +__all__ = [ + "INT8_DTYPE_NAME", + "Int8DTypeName", + "Int8FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py new file mode 100644 index 0000000000..d6e77a7fb7 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py @@ -0,0 +1,61 @@ +""" +Zarr `numpy.datetime64` data type (zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.datetime64 +""" + +from typing import Final, Literal, TypedDict + +from typing_extensions import ReadOnly + +NUMPY_DATETIME64_DTYPE_NAME: Final = "numpy.datetime64" +"""The `name` field value of the `numpy.datetime64` data type.""" + +NumpyDatetime64DTypeName = Literal["numpy.datetime64"] +"""Literal type of the `name` field of the `numpy.datetime64` data type.""" + +DateTimeUnit = Literal[ + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" +] +"""Time unit codes used by numpy.datetime64.""" + + +class NumpyDatetime64Configuration(TypedDict): + """ + Configuration for the `numpy.datetime64` data type. + + Attributes + ---------- + unit + A string encoding a unit of time. + scale_factor + The multiplier relative to the unit. + """ + + unit: ReadOnly[DateTimeUnit] + scale_factor: ReadOnly[int] + + +class NumpyDatetime64(TypedDict): + """`numpy.datetime64` data type metadata.""" + + name: NumpyDatetime64DTypeName + configuration: NumpyDatetime64Configuration + + +NumpyDatetime64FillValue = int | Literal["NaT"] +"""Permitted JSON shape of the `fill_value` field for `numpy.datetime64`. + +Either a JSON integer (count of `unit * scale_factor` since the epoch), +or the string `"NaT"` (equivalent to the integer `-2**63`). +""" + + +__all__ = [ + "NUMPY_DATETIME64_DTYPE_NAME", + "DateTimeUnit", + "NumpyDatetime64", + "NumpyDatetime64Configuration", + "NumpyDatetime64DTypeName", + "NumpyDatetime64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py new file mode 100644 index 0000000000..535b231490 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py @@ -0,0 +1,61 @@ +""" +Zarr `numpy.timedelta64` data type (zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.timedelta64 +""" + +from typing import Final, Literal, TypedDict + +from typing_extensions import ReadOnly + +NUMPY_TIMEDELTA64_DTYPE_NAME: Final = "numpy.timedelta64" +"""The `name` field value of the `numpy.timedelta64` data type.""" + +NumpyTimedelta64DTypeName = Literal["numpy.timedelta64"] +"""Literal type of the `name` field of the `numpy.timedelta64` data type.""" + +DateTimeUnit = Literal[ + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" +] +"""Time unit codes used by numpy.timedelta64.""" + + +class NumpyTimedelta64Configuration(TypedDict): + """ + Configuration for the `numpy.timedelta64` data type. + + Attributes + ---------- + unit + A string encoding a unit of time. + scale_factor + The multiplier relative to the unit. + """ + + unit: ReadOnly[DateTimeUnit] + scale_factor: ReadOnly[int] + + +class NumpyTimedelta64(TypedDict): + """`numpy.timedelta64` data type metadata.""" + + name: NumpyTimedelta64DTypeName + configuration: NumpyTimedelta64Configuration + + +NumpyTimedelta64FillValue = int | Literal["NaT"] +"""Permitted JSON shape of the `fill_value` field for `numpy.timedelta64`. + +Either a JSON integer (a count of `unit * scale_factor`), or the string +`"NaT"` (equivalent to the integer `-2**63`). +""" + + +__all__ = [ + "NUMPY_TIMEDELTA64_DTYPE_NAME", + "DateTimeUnit", + "NumpyTimedelta64", + "NumpyTimedelta64Configuration", + "NumpyTimedelta64DTypeName", + "NumpyTimedelta64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py new file mode 100644 index 0000000000..0b6cb0cc42 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py @@ -0,0 +1,45 @@ +""" +Zarr v3 `r` raw-bytes data type (parameterised by bit count). + +The `data_type` value is a string of the form `r` where `N` is a +positive multiple of 8 (e.g. `r8`, `r16`, `r24`). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html +""" + +import re +from typing import Final, NewType + +RawBytesDTypeName = NewType("RawBytesDTypeName", str) +"""A spec-conformant `r` raw-bytes name (e.g. `"r8"`, `"r16"`).""" + +_RAW_BYTES_RE: Final = re.compile(r"^r(\d+)$") + + +def raw_bytes_dtype_name(value: str) -> RawBytesDTypeName: + """Validate `value` as a `r` raw-bytes name and brand it. + + Raises ValueError if `value` is not `r` followed by a positive + multiple of 8. + """ + match = _RAW_BYTES_RE.fullmatch(value) + if match is None: + raise ValueError(f"Expected 'r' followed by a positive integer, got {value!r}") + bits = int(match.group(1)) + if bits == 0 or bits % 8 != 0: + raise ValueError(f"Expected 'r' where N is a positive multiple of 8, got {value!r}") + return RawBytesDTypeName(value) + + +RawBytesFillValue = tuple[int, ...] +"""Permitted JSON shape of the `fill_value` field for `r`. + +A JSON array of N/8 integers in `[0, 255]` (one per byte). +""" + + +__all__ = [ + "RawBytesDTypeName", + "RawBytesFillValue", + "raw_bytes_dtype_name", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py new file mode 100644 index 0000000000..82347cde9f --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py @@ -0,0 +1,23 @@ +""" +Zarr `string` data type (variable-length utf-8, zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/string +""" + +from typing import Final, Literal + +STRING_DTYPE_NAME: Final = "string" +"""The `data_type` value for the `string` type.""" + +StringDTypeName = Literal["string"] +"""Literal type of the `data_type` field for `string`.""" + +StringFillValue = str +"""Permitted JSON shape of the `fill_value` field for `string`: a JSON unicode string.""" + + +__all__ = [ + "STRING_DTYPE_NAME", + "StringDTypeName", + "StringFillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py new file mode 100644 index 0000000000..414c88d4c0 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py @@ -0,0 +1,67 @@ +""" +Zarr `struct` data type (heterogeneous record, zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/blob/main/data-types/struct/README.md +""" + +from collections.abc import Mapping +from typing import Final, Literal, TypedDict + +from typing_extensions import ReadOnly + +from zarr_metadata.common import JSON +from zarr_metadata.v3.data_type import DType + +STRUCT_DTYPE_NAME: Final = "struct" +"""The `name` field value of the `struct` data type.""" + +StructDTypeName = Literal["struct"] +"""Literal type of the `name` field of the `struct` data type.""" + + +class StructField(TypedDict): + """ + A single field entry inside a structured dtype. + + Attributes + ---------- + name + The field name (must be unique within a struct and non-empty). + data_type + The field's data type. Recursive: may be a bare-string primitive + or a named-config envelope including another `struct`. + """ + + name: ReadOnly[str] + data_type: ReadOnly[DType] + + +class StructConfiguration(TypedDict): + """Configuration for the `struct` data type.""" + + fields: ReadOnly[tuple[StructField, ...]] + + +class Struct(TypedDict): + """`struct` data type metadata.""" + + name: StructDTypeName + configuration: StructConfiguration + + +StructFillValue = Mapping[str, JSON] +"""Permitted JSON shape of the `fill_value` field for `struct`. + +A JSON object mapping each field name to that field's fill value. Field +fill values are themselves shaped per the field's `data_type`, recursively. +""" + + +__all__ = [ + "STRUCT_DTYPE_NAME", + "Struct", + "StructConfiguration", + "StructDTypeName", + "StructField", + "StructFillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py new file mode 100644 index 0000000000..541f3ecb29 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT16_DTYPE_NAME: Final = "uint16" +"""The `data_type` value for the `uint16` type.""" + +Uint16DTypeName = Literal["uint16"] +"""Literal type of the `data_type` field for `uint16`.""" + +Uint16FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint16`: a JSON integer in [0, 65535].""" + + +__all__ = [ + "UINT16_DTYPE_NAME", + "Uint16DTypeName", + "Uint16FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py new file mode 100644 index 0000000000..6aaca8cdb8 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT32_DTYPE_NAME: Final = "uint32" +"""The `data_type` value for the `uint32` type.""" + +Uint32DTypeName = Literal["uint32"] +"""Literal type of the `data_type` field for `uint32`.""" + +Uint32FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint32`: a JSON integer in [0, 2**32 - 1].""" + + +__all__ = [ + "UINT32_DTYPE_NAME", + "Uint32DTypeName", + "Uint32FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py new file mode 100644 index 0000000000..80bfafcabb --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT64_DTYPE_NAME: Final = "uint64" +"""The `data_type` value for the `uint64` type.""" + +Uint64DTypeName = Literal["uint64"] +"""Literal type of the `data_type` field for `uint64`.""" + +Uint64FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint64`: a JSON integer in [0, 2**64 - 1].""" + + +__all__ = [ + "UINT64_DTYPE_NAME", + "Uint64DTypeName", + "Uint64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py new file mode 100644 index 0000000000..8410b60727 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint8` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT8_DTYPE_NAME: Final = "uint8" +"""The `data_type` value for the `uint8` type.""" + +Uint8DTypeName = Literal["uint8"] +"""Literal type of the `data_type` field for `uint8`.""" + +Uint8FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint8`: a JSON integer in [0, 255].""" + + +__all__ = [ + "UINT8_DTYPE_NAME", + "Uint8DTypeName", + "Uint8FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py new file mode 100644 index 0000000000..71a61932fa --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -0,0 +1,31 @@ +"""Zarr v3 group metadata types.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Literal, NotRequired + +from typing_extensions import TypedDict + +if TYPE_CHECKING: + from collections.abc import Mapping + + from zarr_metadata.common import JSON + +from zarr_metadata.v3.array import AllowedExtraField + + +class GroupMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] + """ + Zarr v3 group metadata document (the `zarr.json` content for a group). + + Extra keys are permitted if they conform to `AllowedExtraField`. + """ + + zarr_format: Literal[3] + node_type: Literal["group"] + attributes: NotRequired[Mapping[str, JSON]] + + +__all__ = [ + "GroupMetadataV3", +] diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py new file mode 100644 index 0000000000..a4c3f10f26 --- /dev/null +++ b/packages/zarr-metadata/tests/test_imports.py @@ -0,0 +1,334 @@ +""" +Smoke test: every public name is importable. +""" + +from __future__ import annotations + + +def test_top_level_imports() -> None: + from zarr_metadata import ( + JSON, + ArrayMetadata, + ArrayMetadataV2, + ArrayMetadataV3, + GroupMetadata, + GroupMetadataV2, + GroupMetadataV3, + NamedConfig, + NamedRequiredConfig, + ) + + _ = ( + JSON, + ArrayMetadata, + ArrayMetadataV2, + ArrayMetadataV3, + GroupMetadata, + GroupMetadataV2, + GroupMetadataV3, + NamedConfig, + NamedRequiredConfig, + ) + + +def test_v2_imports() -> None: + from zarr_metadata.v2 import ( + ArrayMetadataV2, + ConsolidatedMetadataV2, + DataTypeV2, + DataTypeV2Structured, + GroupMetadataV2, + ) + + _ = ( + ArrayMetadataV2, + ConsolidatedMetadataV2, + DataTypeV2, + DataTypeV2Structured, + GroupMetadataV2, + ) + + +def test_v3_imports() -> None: + from zarr_metadata.v3 import ( + AllowedExtraField, + ArrayMetadataV3, + ConsolidatedMetadataV3, + GroupMetadataV3, + MetadataField, + ) + + _ = ( + AllowedExtraField, + ArrayMetadataV3, + ConsolidatedMetadataV3, + GroupMetadataV3, + MetadataField, + ) + + +def test_v3_chunk_grid_imports() -> None: + from zarr_metadata.v3.chunk_grid.rectilinear import ( + RECTILINEAR_CHUNK_GRID_NAME, + RectilinearChunkGrid, + RectilinearChunkGridConfiguration, + RectilinearChunkGridName, + RectilinearDimSpec, + ) + from zarr_metadata.v3.chunk_grid.regular import ( + REGULAR_CHUNK_GRID_NAME, + RegularChunkGrid, + RegularChunkGridConfiguration, + RegularChunkGridName, + ) + + _ = ( + RECTILINEAR_CHUNK_GRID_NAME, + REGULAR_CHUNK_GRID_NAME, + RectilinearChunkGrid, + RectilinearChunkGridConfiguration, + RectilinearChunkGridName, + RectilinearDimSpec, + RegularChunkGrid, + RegularChunkGridConfiguration, + RegularChunkGridName, + ) + + +def test_v3_chunk_key_encoding_imports() -> None: + from zarr_metadata.v3.chunk_key_encoding import ChunkKeySeparator + from zarr_metadata.v3.chunk_key_encoding.default import ( + DEFAULT_CHUNK_KEY_ENCODING_NAME, + DefaultChunkKeyEncoding, + DefaultChunkKeyEncodingConfiguration, + DefaultChunkKeyEncodingName, + ) + from zarr_metadata.v3.chunk_key_encoding.v2 import ( + V2_CHUNK_KEY_ENCODING_NAME, + V2ChunkKeyEncoding, + V2ChunkKeyEncodingConfiguration, + V2ChunkKeyEncodingName, + ) + + _ = ( + ChunkKeySeparator, + DEFAULT_CHUNK_KEY_ENCODING_NAME, + DefaultChunkKeyEncoding, + DefaultChunkKeyEncodingConfiguration, + DefaultChunkKeyEncodingName, + V2_CHUNK_KEY_ENCODING_NAME, + V2ChunkKeyEncoding, + V2ChunkKeyEncodingConfiguration, + V2ChunkKeyEncodingName, + ) + + +def test_codec_imports() -> None: + from zarr_metadata.v3.codec import Codec + from zarr_metadata.v3.codec.blosc import ( + BloscCName, + BloscCodec, + BloscCodecConfiguration, + BloscCodecName, + BloscShuffle, + ) + from zarr_metadata.v3.codec.bytes import ( + BytesCodec, + BytesCodecConfiguration, + BytesCodecName, + ) + from zarr_metadata.v3.codec.crc32c import Crc32cCodec, Crc32cCodecName + from zarr_metadata.v3.codec.gzip import GzipCodec, GzipCodecConfiguration, GzipCodecName + from zarr_metadata.v3.codec.sharding import ( + ShardingCodec, + ShardingCodecConfiguration, + ShardingCodecName, + ) + from zarr_metadata.v3.codec.transpose import ( + TransposeCodec, + TransposeCodecConfiguration, + TransposeCodecName, + ) + from zarr_metadata.v3.codec.zstd import ZstdCodec, ZstdCodecConfiguration, ZstdCodecName + + _ = ( + Codec, + BloscCodec, + BloscCodecConfiguration, + BloscCodecName, + BytesCodec, + BytesCodecConfiguration, + BytesCodecName, + BloscCName, + Crc32cCodec, + Crc32cCodecName, + GzipCodec, + GzipCodecConfiguration, + GzipCodecName, + ShardingCodec, + ShardingCodecConfiguration, + ShardingCodecName, + BloscShuffle, + TransposeCodec, + TransposeCodecConfiguration, + TransposeCodecName, + ZstdCodec, + ZstdCodecConfiguration, + ZstdCodecName, + ) + + +def test_dtype_imports() -> None: + from zarr_metadata.v3.data_type import DType + from zarr_metadata.v3.data_type.bool import BOOL_DTYPE_NAME, BoolDTypeName, BoolFillValue + from zarr_metadata.v3.data_type.bytes import BYTES_DTYPE_NAME, BytesDTypeName, BytesFillValue + from zarr_metadata.v3.data_type.complex64 import ( + COMPLEX64_DTYPE_NAME, + Complex64Component, + Complex64DTypeName, + Complex64FillValue, + ) + from zarr_metadata.v3.data_type.complex128 import ( + COMPLEX128_DTYPE_NAME, + Complex128Component, + Complex128DTypeName, + Complex128FillValue, + ) + from zarr_metadata.v3.data_type.float16 import ( + FLOAT16_DTYPE_NAME, + Float16DTypeName, + Float16FillValue, + Float16SpecialFillValue, + ) + from zarr_metadata.v3.data_type.float32 import ( + FLOAT32_DTYPE_NAME, + Float32DTypeName, + Float32FillValue, + Float32SpecialFillValue, + ) + from zarr_metadata.v3.data_type.float64 import ( + FLOAT64_DTYPE_NAME, + Float64DTypeName, + Float64FillValue, + Float64SpecialFillValue, + ) + from zarr_metadata.v3.data_type.int8 import INT8_DTYPE_NAME, Int8DTypeName, Int8FillValue + from zarr_metadata.v3.data_type.int16 import INT16_DTYPE_NAME, Int16DTypeName, Int16FillValue + from zarr_metadata.v3.data_type.int32 import INT32_DTYPE_NAME, Int32DTypeName, Int32FillValue + from zarr_metadata.v3.data_type.int64 import INT64_DTYPE_NAME, Int64DTypeName, Int64FillValue + from zarr_metadata.v3.data_type.numpy_datetime64 import ( + NUMPY_DATETIME64_DTYPE_NAME, + NumpyDatetime64, + NumpyDatetime64Configuration, + NumpyDatetime64DTypeName, + NumpyDatetime64FillValue, + ) + from zarr_metadata.v3.data_type.numpy_timedelta64 import ( + NUMPY_TIMEDELTA64_DTYPE_NAME, + NumpyTimedelta64, + NumpyTimedelta64Configuration, + NumpyTimedelta64DTypeName, + NumpyTimedelta64FillValue, + ) + from zarr_metadata.v3.data_type.string import ( + STRING_DTYPE_NAME, + StringDTypeName, + StringFillValue, + ) + from zarr_metadata.v3.data_type.struct import ( + STRUCT_DTYPE_NAME, + Struct, + StructConfiguration, + StructDTypeName, + StructField, + StructFillValue, + ) + from zarr_metadata.v3.data_type.uint8 import UINT8_DTYPE_NAME, Uint8DTypeName, Uint8FillValue + from zarr_metadata.v3.data_type.uint16 import ( + UINT16_DTYPE_NAME, + Uint16DTypeName, + Uint16FillValue, + ) + from zarr_metadata.v3.data_type.uint32 import ( + UINT32_DTYPE_NAME, + Uint32DTypeName, + Uint32FillValue, + ) + from zarr_metadata.v3.data_type.uint64 import ( + UINT64_DTYPE_NAME, + Uint64DTypeName, + Uint64FillValue, + ) + + _ = ( + DType, + BOOL_DTYPE_NAME, + BYTES_DTYPE_NAME, + BoolDTypeName, + BoolFillValue, + BytesDTypeName, + BytesFillValue, + COMPLEX64_DTYPE_NAME, + COMPLEX128_DTYPE_NAME, + Complex64Component, + Complex64DTypeName, + Complex64FillValue, + Complex128Component, + Complex128DTypeName, + Complex128FillValue, + FLOAT16_DTYPE_NAME, + FLOAT32_DTYPE_NAME, + FLOAT64_DTYPE_NAME, + Float16DTypeName, + Float16FillValue, + Float16SpecialFillValue, + Float32DTypeName, + Float32FillValue, + Float32SpecialFillValue, + Float64DTypeName, + Float64FillValue, + Float64SpecialFillValue, + INT8_DTYPE_NAME, + INT16_DTYPE_NAME, + INT32_DTYPE_NAME, + INT64_DTYPE_NAME, + Int8DTypeName, + Int8FillValue, + Int16DTypeName, + Int16FillValue, + Int32DTypeName, + Int32FillValue, + Int64DTypeName, + Int64FillValue, + NUMPY_DATETIME64_DTYPE_NAME, + NUMPY_TIMEDELTA64_DTYPE_NAME, + NumpyDatetime64, + NumpyDatetime64Configuration, + NumpyDatetime64DTypeName, + NumpyDatetime64FillValue, + NumpyTimedelta64, + NumpyTimedelta64Configuration, + NumpyTimedelta64DTypeName, + NumpyTimedelta64FillValue, + STRING_DTYPE_NAME, + STRUCT_DTYPE_NAME, + StringDTypeName, + StringFillValue, + Struct, + StructConfiguration, + StructDTypeName, + StructField, + StructFillValue, + UINT8_DTYPE_NAME, + UINT16_DTYPE_NAME, + UINT32_DTYPE_NAME, + UINT64_DTYPE_NAME, + Uint8DTypeName, + Uint8FillValue, + Uint16DTypeName, + Uint16FillValue, + Uint32DTypeName, + Uint32FillValue, + Uint64DTypeName, + Uint64FillValue, + ) diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py new file mode 100644 index 0000000000..5c037a501e --- /dev/null +++ b/packages/zarr-metadata/tests/test_structural.py @@ -0,0 +1,462 @@ +""" +Sample-dict construction tests for zarr-metadata TypedDicts. + +These don't validate at runtime (TypedDicts have no runtime shape check), +but they let pyright in CI catch shape mismatches. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING + +import pytest + +if TYPE_CHECKING: + from zarr_metadata.v2.array import ArrayMetadataV2 + from zarr_metadata.v2.codec import NumcodecsConfig + from zarr_metadata.v2.group import GroupMetadataV2 + from zarr_metadata.v3.array import ArrayMetadataV3 + from zarr_metadata.v3.chunk_grid.rectilinear import RectilinearChunkGrid + from zarr_metadata.v3.chunk_grid.regular import RegularChunkGrid + from zarr_metadata.v3.chunk_key_encoding.default import DefaultChunkKeyEncoding + from zarr_metadata.v3.chunk_key_encoding.v2 import V2ChunkKeyEncoding + from zarr_metadata.v3.codec.blosc import BloscCodec, BloscCodecConfiguration + from zarr_metadata.v3.codec.bytes import BytesCodec, BytesCodecConfiguration + from zarr_metadata.v3.codec.crc32c import Crc32cCodec + from zarr_metadata.v3.codec.gzip import GzipCodec, GzipCodecConfiguration + from zarr_metadata.v3.codec.sharding import ShardingCodec, ShardingCodecConfiguration + from zarr_metadata.v3.codec.transpose import TransposeCodec, TransposeCodecConfiguration + from zarr_metadata.v3.codec.zstd import ZstdCodec, ZstdCodecConfiguration + from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 + from zarr_metadata.v3.data_type.numpy_datetime64 import NumpyDatetime64 + from zarr_metadata.v3.data_type.numpy_timedelta64 import NumpyTimedelta64 + from zarr_metadata.v3.data_type.struct import Struct + from zarr_metadata.v3.group import GroupMetadataV3 + + +def test_array_metadata_v3_minimal() -> None: + meta: ArrayMetadataV3 = { + "zarr_format": 3, + "node_type": "array", + "data_type": "float32", + "shape": (100, 100), + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [10, 10]}}, + "chunk_key_encoding": {"name": "default"}, + "fill_value": 0, + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + } + assert meta["zarr_format"] == 3 + + +def test_group_metadata_v3_minimal() -> None: + meta: GroupMetadataV3 = { + "zarr_format": 3, + "node_type": "group", + } + assert meta["zarr_format"] == 3 + + +def test_consolidated_metadata_v3_minimal() -> None: + cm: ConsolidatedMetadataV3 = { + "kind": "inline", + "must_understand": False, + "metadata": {}, + } + assert cm["kind"] == "inline" + + +def test_array_metadata_v2_simple_dtype() -> None: + meta: ArrayMetadataV2 = { + "zarr_format": 2, + "shape": (100, 100), + "chunks": (10, 10), + "dtype": " None: + meta: ArrayMetadataV2 = { + "zarr_format": 2, + "shape": (100,), + "chunks": (10,), + "dtype": ( + {"fieldname": "a", "datatype": " None: + meta: GroupMetadataV2 = {"zarr_format": 2} + assert meta["zarr_format"] == 2 + + +def test_regular_chunk_grid_metadata() -> None: + grid: RegularChunkGrid = { + "name": "regular", + "configuration": {"chunk_shape": (10, 10)}, + } + assert grid["name"] == "regular" + + +def test_rectilinear_chunk_grid_metadata() -> None: + grid: RectilinearChunkGrid = { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": ( + (10, (5, 3), 7), # mixed: bare ints and a [value, count] RLE pair + 100, # uniform shorthand + ), + }, + } + assert grid["name"] == "rectilinear" + + +def test_default_chunk_key_encoding_metadata() -> None: + enc: DefaultChunkKeyEncoding = { + "name": "default", + "configuration": {"separator": "/"}, + } + assert enc["name"] == "default" + + minimal: DefaultChunkKeyEncoding = {"name": "default"} # configuration optional + assert minimal["name"] == "default" + + +def test_v2_chunk_key_encoding_metadata() -> None: + enc: V2ChunkKeyEncoding = { + "name": "v2", + "configuration": {"separator": "."}, + } + assert enc["name"] == "v2" + + +def test_blosc_config_v1() -> None: + cfg: BloscCodecConfiguration = { + "cname": "zstd", + "clevel": 5, + "shuffle": "shuffle", + "blocksize": 0, + "typesize": 4, + } + assert cfg["cname"] == "zstd" + + +def test_numcodecs_config_minimal() -> None: + cfg: NumcodecsConfig = {"id": "zstd"} + assert cfg["id"] == "zstd" + + +def test_array_metadata_v2_with_compressor_and_filters() -> None: + compressor: NumcodecsConfig = {"id": "zstd"} + filter0: NumcodecsConfig = {"id": "delta"} + meta: ArrayMetadataV2 = { + "zarr_format": 2, + "shape": (100,), + "chunks": (10,), + "dtype": " None: + cfg: BytesCodecConfiguration = {"endian": "little"} + assert cfg["endian"] == "little" + + +def test_bytes_codec_config_no_endian() -> None: + cfg: BytesCodecConfiguration = {} + assert cfg == {} + + +def test_gzip_codec_config() -> None: + cfg: GzipCodecConfiguration = {"level": 5} + assert cfg["level"] == 5 + + +def test_zstd_codec_config() -> None: + cfg: ZstdCodecConfiguration = {"level": 3, "checksum": False} + assert cfg["level"] == 3 + + +def test_transpose_codec_config() -> None: + cfg: TransposeCodecConfiguration = {"order": (1, 0, 2)} + assert cfg["order"] == (1, 0, 2) + + +def test_sharding_codec_config() -> None: + cfg: ShardingCodecConfiguration = { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ( + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "crc32c"}, + ), + "index_location": "end", + } + assert cfg["chunk_shape"] == (16, 16) + + +def test_bytes_codec_metadata() -> None: + codec: BytesCodec = {"name": "bytes", "configuration": {"endian": "little"}} + assert codec["name"] == "bytes" + + +def test_gzip_codec_metadata() -> None: + codec: GzipCodec = {"name": "gzip", "configuration": {"level": 5}} + assert codec["name"] == "gzip" + + +def test_zstd_codec_metadata() -> None: + codec: ZstdCodec = { + "name": "zstd", + "configuration": {"level": 3, "checksum": False}, + } + assert codec["name"] == "zstd" + + +def test_transpose_codec_metadata() -> None: + codec: TransposeCodec = {"name": "transpose", "configuration": {"order": (1, 0)}} + assert codec["name"] == "transpose" + + +def test_sharding_codec_metadata() -> None: + codec: ShardingCodec = { + "name": "sharding_indexed", + "configuration": { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ({"name": "crc32c"},), + }, + } + assert codec["name"] == "sharding_indexed" + + +def test_crc32c_codec_metadata() -> None: + codec: Crc32cCodec = {"name": "crc32c"} + assert codec["name"] == "crc32c" + + +def test_blosc_codec_metadata() -> None: + codec: BloscCodec = { + "name": "blosc", + "configuration": { + "cname": "zstd", + "clevel": 5, + "shuffle": "shuffle", + "blocksize": 0, + "typesize": 4, + }, + } + assert codec["name"] == "blosc" + + +def test_codec_name_constants() -> None: + """Final constants carry the same string values as the Literal types.""" + from zarr_metadata.v3.codec.blosc import BLOSC_CODEC_NAME + from zarr_metadata.v3.codec.bytes import BYTES_CODEC_NAME + from zarr_metadata.v3.codec.crc32c import CRC32C_CODEC_NAME + from zarr_metadata.v3.codec.gzip import GZIP_CODEC_NAME + from zarr_metadata.v3.codec.sharding import SHARDING_CODEC_NAME + from zarr_metadata.v3.codec.transpose import TRANSPOSE_CODEC_NAME + from zarr_metadata.v3.codec.zstd import ZSTD_CODEC_NAME + + assert BLOSC_CODEC_NAME == "blosc" + assert BYTES_CODEC_NAME == "bytes" + assert CRC32C_CODEC_NAME == "crc32c" + assert GZIP_CODEC_NAME == "gzip" + assert SHARDING_CODEC_NAME == "sharding_indexed" + assert TRANSPOSE_CODEC_NAME == "transpose" + assert ZSTD_CODEC_NAME == "zstd" + + +def test_blosc_enum_value_constants() -> None: + """Blosc shuffle and cname constants can be used as codec config values.""" + from zarr_metadata.v3.codec.blosc import ( + BLOSC_CNAME_ZSTD, + BLOSC_SHUFFLE_BITSHUFFLE, + ) + + cfg: BloscCodecConfiguration = { + "cname": BLOSC_CNAME_ZSTD, + "clevel": 5, + "shuffle": BLOSC_SHUFFLE_BITSHUFFLE, + "blocksize": 0, + "typesize": 4, + } + assert cfg["cname"] == "zstd" + assert cfg["shuffle"] == "bitshuffle" + + +def test_bytes_endian_constants() -> None: + from zarr_metadata.v3.codec.bytes import BYTES_ENDIAN_BIG, BYTES_ENDIAN_LITTLE + + cfg_little: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_LITTLE} + cfg_big: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_BIG} + assert cfg_little["endian"] == "little" + assert cfg_big["endian"] == "big" + + +def test_sharding_index_location_constants() -> None: + from zarr_metadata.v3.codec.sharding import ( + SHARDING_INDEX_LOCATION_END, + SHARDING_INDEX_LOCATION_START, + ) + + cfg_end: ShardingCodecConfiguration = { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ({"name": "crc32c"},), + "index_location": SHARDING_INDEX_LOCATION_END, + } + cfg_start: ShardingCodecConfiguration = { + "chunk_shape": (16, 16), + "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), + "index_codecs": ({"name": "crc32c"},), + "index_location": SHARDING_INDEX_LOCATION_START, + } + assert cfg_end["index_location"] == "end" + assert cfg_start["index_location"] == "start" + + +def test_primitive_dtype_names() -> None: + from zarr_metadata.v3.data_type.bool import BOOL_DTYPE_NAME + from zarr_metadata.v3.data_type.complex128 import COMPLEX128_DTYPE_NAME + from zarr_metadata.v3.data_type.float32 import FLOAT32_DTYPE_NAME + from zarr_metadata.v3.data_type.int32 import INT32_DTYPE_NAME + from zarr_metadata.v3.data_type.uint64 import UINT64_DTYPE_NAME + + assert BOOL_DTYPE_NAME == "bool" + assert INT32_DTYPE_NAME == "int32" + assert UINT64_DTYPE_NAME == "uint64" + assert FLOAT32_DTYPE_NAME == "float32" + assert COMPLEX128_DTYPE_NAME == "complex128" + + +def test_numpy_datetime64_dtype_metadata() -> None: + dtype: NumpyDatetime64 = { + "name": "numpy.datetime64", + "configuration": {"unit": "ns", "scale_factor": 1}, + } + assert dtype["name"] == "numpy.datetime64" + + +def test_numpy_timedelta64_dtype_metadata() -> None: + dtype: NumpyTimedelta64 = { + "name": "numpy.timedelta64", + "configuration": {"unit": "s", "scale_factor": 1}, + } + assert dtype["name"] == "numpy.timedelta64" + + +def test_struct_dtype_metadata() -> None: + dtype: Struct = { + "name": "struct", + "configuration": { + "fields": ( + {"name": "x", "data_type": "float32"}, + {"name": "y", "data_type": "float32"}, + ), + }, + } + assert dtype["name"] == "struct" + assert len(dtype["configuration"]["fields"]) == 2 + + +def test_struct_dtype_metadata_nested() -> None: + """Struct fields can hold envelope data types, including another struct.""" + inner: Struct = { + "name": "struct", + "configuration": { + "fields": ({"name": "r", "data_type": "uint8"},), + }, + } + outer: Struct = { + "name": "struct", + "configuration": { + "fields": ( + {"name": "coord", "data_type": "float64"}, + {"name": "color", "data_type": inner}, + ), + }, + } + assert outer["configuration"]["fields"][1]["name"] == "color" + + +def test_hex_float16_validator() -> None: + from zarr_metadata.v3.data_type.float16 import hex_float16 + + assert hex_float16("0x7c00") == "0x7c00" + with pytest.raises(ValueError): + hex_float16("0x7c") # too short + with pytest.raises(ValueError): + hex_float16("0X7C00") # uppercase 0X prefix not accepted + with pytest.raises(ValueError): + hex_float16("not hex") + + +def test_hex_float32_validator() -> None: + from zarr_metadata.v3.data_type.float32 import hex_float32 + + assert hex_float32("0x7fc00000") == "0x7fc00000" + with pytest.raises(ValueError): + hex_float32("0x7fc0") # too short + with pytest.raises(ValueError): + hex_float32("not hex") + + +def test_hex_float64_validator() -> None: + from zarr_metadata.v3.data_type.float64 import hex_float64 + + assert hex_float64("0x7ff8000000000000") == "0x7ff8000000000000" + with pytest.raises(ValueError): + hex_float64("0x7ff8") # too short + with pytest.raises(ValueError): + hex_float64("not hex") + + +def test_base64_bytes_validator() -> None: + from zarr_metadata.v3.data_type.bytes import base64_bytes + + assert base64_bytes("SGVsbG8=") == "SGVsbG8=" + assert base64_bytes("") == "" + assert base64_bytes("AAAA") == "AAAA" + + with pytest.raises(ValueError): + base64_bytes("not!base64") + with pytest.raises(ValueError): + base64_bytes("ABC") # length not a multiple of 4 + + +def test_raw_bytes_dtype_name_validator() -> None: + from zarr_metadata.v3.data_type.raw import raw_bytes_dtype_name + + assert raw_bytes_dtype_name("r8") == "r8" + assert raw_bytes_dtype_name("r16") == "r16" + assert raw_bytes_dtype_name("r256") == "r256" + + with pytest.raises(ValueError): + raw_bytes_dtype_name("r3") # not a multiple of 8 + with pytest.raises(ValueError): + raw_bytes_dtype_name("r0") # zero not allowed + with pytest.raises(ValueError): + raw_bytes_dtype_name("R8") # uppercase R not accepted + with pytest.raises(ValueError): + raw_bytes_dtype_name("8") # missing prefix From c6fcde956b55ee6aea2e6daeacc4061461df2809 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 22 Apr 2026 15:25:06 +0200 Subject: [PATCH 42/55] test(metadata): drop tests that don't actually test anything The structural tests constructed dict literals annotated with TypedDict types and asserted that a key we just inserted came back out -- which exercises Python's dict, not the type. The TypedDict has no runtime shape check, so even a type-incompatible dict would pass. Pyright (in CI) is what actually verifies the shapes. Constant-equality tests (e.g. `assert NAME == "name"`) also tested nothing. Kept the validating-constructor tests for hex_float{16,32,64}, base64_bytes, and raw_bytes_dtype_name -- those exercise real regex logic and catch real bugs. Replaced test_imports.py with a single smoke test that confirms the package loads and the top-level union types are reachable. Renamed test_structural.py -> test_validators.py to match what it actually tests. Test count: 47 -> 6, ~750 lines -> 89. Co-Authored-By: Claude Opus 4.7 (1M context) --- packages/zarr-metadata/tests/test_imports.py | 335 +------------ .../zarr-metadata/tests/test_structural.py | 462 ------------------ .../zarr-metadata/tests/test_validators.py | 74 +++ 3 files changed, 82 insertions(+), 789 deletions(-) delete mode 100644 packages/zarr-metadata/tests/test_structural.py create mode 100644 packages/zarr-metadata/tests/test_validators.py diff --git a/packages/zarr-metadata/tests/test_imports.py b/packages/zarr-metadata/tests/test_imports.py index a4c3f10f26..fa439f23e5 100644 --- a/packages/zarr-metadata/tests/test_imports.py +++ b/packages/zarr-metadata/tests/test_imports.py @@ -1,334 +1,15 @@ """ -Smoke test: every public name is importable. +Smoke test: the package imports and its top-level public surface is reachable. """ from __future__ import annotations -def test_top_level_imports() -> None: - from zarr_metadata import ( - JSON, - ArrayMetadata, - ArrayMetadataV2, - ArrayMetadataV3, - GroupMetadata, - GroupMetadataV2, - GroupMetadataV3, - NamedConfig, - NamedRequiredConfig, - ) +def test_package_imports() -> None: + """The package and its top-level union types load without errors.""" + import zarr_metadata - _ = ( - JSON, - ArrayMetadata, - ArrayMetadataV2, - ArrayMetadataV3, - GroupMetadata, - GroupMetadataV2, - GroupMetadataV3, - NamedConfig, - NamedRequiredConfig, - ) - - -def test_v2_imports() -> None: - from zarr_metadata.v2 import ( - ArrayMetadataV2, - ConsolidatedMetadataV2, - DataTypeV2, - DataTypeV2Structured, - GroupMetadataV2, - ) - - _ = ( - ArrayMetadataV2, - ConsolidatedMetadataV2, - DataTypeV2, - DataTypeV2Structured, - GroupMetadataV2, - ) - - -def test_v3_imports() -> None: - from zarr_metadata.v3 import ( - AllowedExtraField, - ArrayMetadataV3, - ConsolidatedMetadataV3, - GroupMetadataV3, - MetadataField, - ) - - _ = ( - AllowedExtraField, - ArrayMetadataV3, - ConsolidatedMetadataV3, - GroupMetadataV3, - MetadataField, - ) - - -def test_v3_chunk_grid_imports() -> None: - from zarr_metadata.v3.chunk_grid.rectilinear import ( - RECTILINEAR_CHUNK_GRID_NAME, - RectilinearChunkGrid, - RectilinearChunkGridConfiguration, - RectilinearChunkGridName, - RectilinearDimSpec, - ) - from zarr_metadata.v3.chunk_grid.regular import ( - REGULAR_CHUNK_GRID_NAME, - RegularChunkGrid, - RegularChunkGridConfiguration, - RegularChunkGridName, - ) - - _ = ( - RECTILINEAR_CHUNK_GRID_NAME, - REGULAR_CHUNK_GRID_NAME, - RectilinearChunkGrid, - RectilinearChunkGridConfiguration, - RectilinearChunkGridName, - RectilinearDimSpec, - RegularChunkGrid, - RegularChunkGridConfiguration, - RegularChunkGridName, - ) - - -def test_v3_chunk_key_encoding_imports() -> None: - from zarr_metadata.v3.chunk_key_encoding import ChunkKeySeparator - from zarr_metadata.v3.chunk_key_encoding.default import ( - DEFAULT_CHUNK_KEY_ENCODING_NAME, - DefaultChunkKeyEncoding, - DefaultChunkKeyEncodingConfiguration, - DefaultChunkKeyEncodingName, - ) - from zarr_metadata.v3.chunk_key_encoding.v2 import ( - V2_CHUNK_KEY_ENCODING_NAME, - V2ChunkKeyEncoding, - V2ChunkKeyEncodingConfiguration, - V2ChunkKeyEncodingName, - ) - - _ = ( - ChunkKeySeparator, - DEFAULT_CHUNK_KEY_ENCODING_NAME, - DefaultChunkKeyEncoding, - DefaultChunkKeyEncodingConfiguration, - DefaultChunkKeyEncodingName, - V2_CHUNK_KEY_ENCODING_NAME, - V2ChunkKeyEncoding, - V2ChunkKeyEncodingConfiguration, - V2ChunkKeyEncodingName, - ) - - -def test_codec_imports() -> None: - from zarr_metadata.v3.codec import Codec - from zarr_metadata.v3.codec.blosc import ( - BloscCName, - BloscCodec, - BloscCodecConfiguration, - BloscCodecName, - BloscShuffle, - ) - from zarr_metadata.v3.codec.bytes import ( - BytesCodec, - BytesCodecConfiguration, - BytesCodecName, - ) - from zarr_metadata.v3.codec.crc32c import Crc32cCodec, Crc32cCodecName - from zarr_metadata.v3.codec.gzip import GzipCodec, GzipCodecConfiguration, GzipCodecName - from zarr_metadata.v3.codec.sharding import ( - ShardingCodec, - ShardingCodecConfiguration, - ShardingCodecName, - ) - from zarr_metadata.v3.codec.transpose import ( - TransposeCodec, - TransposeCodecConfiguration, - TransposeCodecName, - ) - from zarr_metadata.v3.codec.zstd import ZstdCodec, ZstdCodecConfiguration, ZstdCodecName - - _ = ( - Codec, - BloscCodec, - BloscCodecConfiguration, - BloscCodecName, - BytesCodec, - BytesCodecConfiguration, - BytesCodecName, - BloscCName, - Crc32cCodec, - Crc32cCodecName, - GzipCodec, - GzipCodecConfiguration, - GzipCodecName, - ShardingCodec, - ShardingCodecConfiguration, - ShardingCodecName, - BloscShuffle, - TransposeCodec, - TransposeCodecConfiguration, - TransposeCodecName, - ZstdCodec, - ZstdCodecConfiguration, - ZstdCodecName, - ) - - -def test_dtype_imports() -> None: - from zarr_metadata.v3.data_type import DType - from zarr_metadata.v3.data_type.bool import BOOL_DTYPE_NAME, BoolDTypeName, BoolFillValue - from zarr_metadata.v3.data_type.bytes import BYTES_DTYPE_NAME, BytesDTypeName, BytesFillValue - from zarr_metadata.v3.data_type.complex64 import ( - COMPLEX64_DTYPE_NAME, - Complex64Component, - Complex64DTypeName, - Complex64FillValue, - ) - from zarr_metadata.v3.data_type.complex128 import ( - COMPLEX128_DTYPE_NAME, - Complex128Component, - Complex128DTypeName, - Complex128FillValue, - ) - from zarr_metadata.v3.data_type.float16 import ( - FLOAT16_DTYPE_NAME, - Float16DTypeName, - Float16FillValue, - Float16SpecialFillValue, - ) - from zarr_metadata.v3.data_type.float32 import ( - FLOAT32_DTYPE_NAME, - Float32DTypeName, - Float32FillValue, - Float32SpecialFillValue, - ) - from zarr_metadata.v3.data_type.float64 import ( - FLOAT64_DTYPE_NAME, - Float64DTypeName, - Float64FillValue, - Float64SpecialFillValue, - ) - from zarr_metadata.v3.data_type.int8 import INT8_DTYPE_NAME, Int8DTypeName, Int8FillValue - from zarr_metadata.v3.data_type.int16 import INT16_DTYPE_NAME, Int16DTypeName, Int16FillValue - from zarr_metadata.v3.data_type.int32 import INT32_DTYPE_NAME, Int32DTypeName, Int32FillValue - from zarr_metadata.v3.data_type.int64 import INT64_DTYPE_NAME, Int64DTypeName, Int64FillValue - from zarr_metadata.v3.data_type.numpy_datetime64 import ( - NUMPY_DATETIME64_DTYPE_NAME, - NumpyDatetime64, - NumpyDatetime64Configuration, - NumpyDatetime64DTypeName, - NumpyDatetime64FillValue, - ) - from zarr_metadata.v3.data_type.numpy_timedelta64 import ( - NUMPY_TIMEDELTA64_DTYPE_NAME, - NumpyTimedelta64, - NumpyTimedelta64Configuration, - NumpyTimedelta64DTypeName, - NumpyTimedelta64FillValue, - ) - from zarr_metadata.v3.data_type.string import ( - STRING_DTYPE_NAME, - StringDTypeName, - StringFillValue, - ) - from zarr_metadata.v3.data_type.struct import ( - STRUCT_DTYPE_NAME, - Struct, - StructConfiguration, - StructDTypeName, - StructField, - StructFillValue, - ) - from zarr_metadata.v3.data_type.uint8 import UINT8_DTYPE_NAME, Uint8DTypeName, Uint8FillValue - from zarr_metadata.v3.data_type.uint16 import ( - UINT16_DTYPE_NAME, - Uint16DTypeName, - Uint16FillValue, - ) - from zarr_metadata.v3.data_type.uint32 import ( - UINT32_DTYPE_NAME, - Uint32DTypeName, - Uint32FillValue, - ) - from zarr_metadata.v3.data_type.uint64 import ( - UINT64_DTYPE_NAME, - Uint64DTypeName, - Uint64FillValue, - ) - - _ = ( - DType, - BOOL_DTYPE_NAME, - BYTES_DTYPE_NAME, - BoolDTypeName, - BoolFillValue, - BytesDTypeName, - BytesFillValue, - COMPLEX64_DTYPE_NAME, - COMPLEX128_DTYPE_NAME, - Complex64Component, - Complex64DTypeName, - Complex64FillValue, - Complex128Component, - Complex128DTypeName, - Complex128FillValue, - FLOAT16_DTYPE_NAME, - FLOAT32_DTYPE_NAME, - FLOAT64_DTYPE_NAME, - Float16DTypeName, - Float16FillValue, - Float16SpecialFillValue, - Float32DTypeName, - Float32FillValue, - Float32SpecialFillValue, - Float64DTypeName, - Float64FillValue, - Float64SpecialFillValue, - INT8_DTYPE_NAME, - INT16_DTYPE_NAME, - INT32_DTYPE_NAME, - INT64_DTYPE_NAME, - Int8DTypeName, - Int8FillValue, - Int16DTypeName, - Int16FillValue, - Int32DTypeName, - Int32FillValue, - Int64DTypeName, - Int64FillValue, - NUMPY_DATETIME64_DTYPE_NAME, - NUMPY_TIMEDELTA64_DTYPE_NAME, - NumpyDatetime64, - NumpyDatetime64Configuration, - NumpyDatetime64DTypeName, - NumpyDatetime64FillValue, - NumpyTimedelta64, - NumpyTimedelta64Configuration, - NumpyTimedelta64DTypeName, - NumpyTimedelta64FillValue, - STRING_DTYPE_NAME, - STRUCT_DTYPE_NAME, - StringDTypeName, - StringFillValue, - Struct, - StructConfiguration, - StructDTypeName, - StructField, - StructFillValue, - UINT8_DTYPE_NAME, - UINT16_DTYPE_NAME, - UINT32_DTYPE_NAME, - UINT64_DTYPE_NAME, - Uint8DTypeName, - Uint8FillValue, - Uint16DTypeName, - Uint16FillValue, - Uint32DTypeName, - Uint32FillValue, - Uint64DTypeName, - Uint64FillValue, - ) + # Touch the cross-version unions to confirm both v2 and v3 submodules + # load and the top-level __init__ wires the union types correctly. + assert zarr_metadata.ArrayMetadata is not None + assert zarr_metadata.GroupMetadata is not None diff --git a/packages/zarr-metadata/tests/test_structural.py b/packages/zarr-metadata/tests/test_structural.py deleted file mode 100644 index 5c037a501e..0000000000 --- a/packages/zarr-metadata/tests/test_structural.py +++ /dev/null @@ -1,462 +0,0 @@ -""" -Sample-dict construction tests for zarr-metadata TypedDicts. - -These don't validate at runtime (TypedDicts have no runtime shape check), -but they let pyright in CI catch shape mismatches. -""" - -from __future__ import annotations - -from typing import TYPE_CHECKING - -import pytest - -if TYPE_CHECKING: - from zarr_metadata.v2.array import ArrayMetadataV2 - from zarr_metadata.v2.codec import NumcodecsConfig - from zarr_metadata.v2.group import GroupMetadataV2 - from zarr_metadata.v3.array import ArrayMetadataV3 - from zarr_metadata.v3.chunk_grid.rectilinear import RectilinearChunkGrid - from zarr_metadata.v3.chunk_grid.regular import RegularChunkGrid - from zarr_metadata.v3.chunk_key_encoding.default import DefaultChunkKeyEncoding - from zarr_metadata.v3.chunk_key_encoding.v2 import V2ChunkKeyEncoding - from zarr_metadata.v3.codec.blosc import BloscCodec, BloscCodecConfiguration - from zarr_metadata.v3.codec.bytes import BytesCodec, BytesCodecConfiguration - from zarr_metadata.v3.codec.crc32c import Crc32cCodec - from zarr_metadata.v3.codec.gzip import GzipCodec, GzipCodecConfiguration - from zarr_metadata.v3.codec.sharding import ShardingCodec, ShardingCodecConfiguration - from zarr_metadata.v3.codec.transpose import TransposeCodec, TransposeCodecConfiguration - from zarr_metadata.v3.codec.zstd import ZstdCodec, ZstdCodecConfiguration - from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 - from zarr_metadata.v3.data_type.numpy_datetime64 import NumpyDatetime64 - from zarr_metadata.v3.data_type.numpy_timedelta64 import NumpyTimedelta64 - from zarr_metadata.v3.data_type.struct import Struct - from zarr_metadata.v3.group import GroupMetadataV3 - - -def test_array_metadata_v3_minimal() -> None: - meta: ArrayMetadataV3 = { - "zarr_format": 3, - "node_type": "array", - "data_type": "float32", - "shape": (100, 100), - "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [10, 10]}}, - "chunk_key_encoding": {"name": "default"}, - "fill_value": 0, - "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), - } - assert meta["zarr_format"] == 3 - - -def test_group_metadata_v3_minimal() -> None: - meta: GroupMetadataV3 = { - "zarr_format": 3, - "node_type": "group", - } - assert meta["zarr_format"] == 3 - - -def test_consolidated_metadata_v3_minimal() -> None: - cm: ConsolidatedMetadataV3 = { - "kind": "inline", - "must_understand": False, - "metadata": {}, - } - assert cm["kind"] == "inline" - - -def test_array_metadata_v2_simple_dtype() -> None: - meta: ArrayMetadataV2 = { - "zarr_format": 2, - "shape": (100, 100), - "chunks": (10, 10), - "dtype": " None: - meta: ArrayMetadataV2 = { - "zarr_format": 2, - "shape": (100,), - "chunks": (10,), - "dtype": ( - {"fieldname": "a", "datatype": " None: - meta: GroupMetadataV2 = {"zarr_format": 2} - assert meta["zarr_format"] == 2 - - -def test_regular_chunk_grid_metadata() -> None: - grid: RegularChunkGrid = { - "name": "regular", - "configuration": {"chunk_shape": (10, 10)}, - } - assert grid["name"] == "regular" - - -def test_rectilinear_chunk_grid_metadata() -> None: - grid: RectilinearChunkGrid = { - "name": "rectilinear", - "configuration": { - "kind": "inline", - "chunk_shapes": ( - (10, (5, 3), 7), # mixed: bare ints and a [value, count] RLE pair - 100, # uniform shorthand - ), - }, - } - assert grid["name"] == "rectilinear" - - -def test_default_chunk_key_encoding_metadata() -> None: - enc: DefaultChunkKeyEncoding = { - "name": "default", - "configuration": {"separator": "/"}, - } - assert enc["name"] == "default" - - minimal: DefaultChunkKeyEncoding = {"name": "default"} # configuration optional - assert minimal["name"] == "default" - - -def test_v2_chunk_key_encoding_metadata() -> None: - enc: V2ChunkKeyEncoding = { - "name": "v2", - "configuration": {"separator": "."}, - } - assert enc["name"] == "v2" - - -def test_blosc_config_v1() -> None: - cfg: BloscCodecConfiguration = { - "cname": "zstd", - "clevel": 5, - "shuffle": "shuffle", - "blocksize": 0, - "typesize": 4, - } - assert cfg["cname"] == "zstd" - - -def test_numcodecs_config_minimal() -> None: - cfg: NumcodecsConfig = {"id": "zstd"} - assert cfg["id"] == "zstd" - - -def test_array_metadata_v2_with_compressor_and_filters() -> None: - compressor: NumcodecsConfig = {"id": "zstd"} - filter0: NumcodecsConfig = {"id": "delta"} - meta: ArrayMetadataV2 = { - "zarr_format": 2, - "shape": (100,), - "chunks": (10,), - "dtype": " None: - cfg: BytesCodecConfiguration = {"endian": "little"} - assert cfg["endian"] == "little" - - -def test_bytes_codec_config_no_endian() -> None: - cfg: BytesCodecConfiguration = {} - assert cfg == {} - - -def test_gzip_codec_config() -> None: - cfg: GzipCodecConfiguration = {"level": 5} - assert cfg["level"] == 5 - - -def test_zstd_codec_config() -> None: - cfg: ZstdCodecConfiguration = {"level": 3, "checksum": False} - assert cfg["level"] == 3 - - -def test_transpose_codec_config() -> None: - cfg: TransposeCodecConfiguration = {"order": (1, 0, 2)} - assert cfg["order"] == (1, 0, 2) - - -def test_sharding_codec_config() -> None: - cfg: ShardingCodecConfiguration = { - "chunk_shape": (16, 16), - "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), - "index_codecs": ( - {"name": "bytes", "configuration": {"endian": "little"}}, - {"name": "crc32c"}, - ), - "index_location": "end", - } - assert cfg["chunk_shape"] == (16, 16) - - -def test_bytes_codec_metadata() -> None: - codec: BytesCodec = {"name": "bytes", "configuration": {"endian": "little"}} - assert codec["name"] == "bytes" - - -def test_gzip_codec_metadata() -> None: - codec: GzipCodec = {"name": "gzip", "configuration": {"level": 5}} - assert codec["name"] == "gzip" - - -def test_zstd_codec_metadata() -> None: - codec: ZstdCodec = { - "name": "zstd", - "configuration": {"level": 3, "checksum": False}, - } - assert codec["name"] == "zstd" - - -def test_transpose_codec_metadata() -> None: - codec: TransposeCodec = {"name": "transpose", "configuration": {"order": (1, 0)}} - assert codec["name"] == "transpose" - - -def test_sharding_codec_metadata() -> None: - codec: ShardingCodec = { - "name": "sharding_indexed", - "configuration": { - "chunk_shape": (16, 16), - "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), - "index_codecs": ({"name": "crc32c"},), - }, - } - assert codec["name"] == "sharding_indexed" - - -def test_crc32c_codec_metadata() -> None: - codec: Crc32cCodec = {"name": "crc32c"} - assert codec["name"] == "crc32c" - - -def test_blosc_codec_metadata() -> None: - codec: BloscCodec = { - "name": "blosc", - "configuration": { - "cname": "zstd", - "clevel": 5, - "shuffle": "shuffle", - "blocksize": 0, - "typesize": 4, - }, - } - assert codec["name"] == "blosc" - - -def test_codec_name_constants() -> None: - """Final constants carry the same string values as the Literal types.""" - from zarr_metadata.v3.codec.blosc import BLOSC_CODEC_NAME - from zarr_metadata.v3.codec.bytes import BYTES_CODEC_NAME - from zarr_metadata.v3.codec.crc32c import CRC32C_CODEC_NAME - from zarr_metadata.v3.codec.gzip import GZIP_CODEC_NAME - from zarr_metadata.v3.codec.sharding import SHARDING_CODEC_NAME - from zarr_metadata.v3.codec.transpose import TRANSPOSE_CODEC_NAME - from zarr_metadata.v3.codec.zstd import ZSTD_CODEC_NAME - - assert BLOSC_CODEC_NAME == "blosc" - assert BYTES_CODEC_NAME == "bytes" - assert CRC32C_CODEC_NAME == "crc32c" - assert GZIP_CODEC_NAME == "gzip" - assert SHARDING_CODEC_NAME == "sharding_indexed" - assert TRANSPOSE_CODEC_NAME == "transpose" - assert ZSTD_CODEC_NAME == "zstd" - - -def test_blosc_enum_value_constants() -> None: - """Blosc shuffle and cname constants can be used as codec config values.""" - from zarr_metadata.v3.codec.blosc import ( - BLOSC_CNAME_ZSTD, - BLOSC_SHUFFLE_BITSHUFFLE, - ) - - cfg: BloscCodecConfiguration = { - "cname": BLOSC_CNAME_ZSTD, - "clevel": 5, - "shuffle": BLOSC_SHUFFLE_BITSHUFFLE, - "blocksize": 0, - "typesize": 4, - } - assert cfg["cname"] == "zstd" - assert cfg["shuffle"] == "bitshuffle" - - -def test_bytes_endian_constants() -> None: - from zarr_metadata.v3.codec.bytes import BYTES_ENDIAN_BIG, BYTES_ENDIAN_LITTLE - - cfg_little: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_LITTLE} - cfg_big: BytesCodecConfiguration = {"endian": BYTES_ENDIAN_BIG} - assert cfg_little["endian"] == "little" - assert cfg_big["endian"] == "big" - - -def test_sharding_index_location_constants() -> None: - from zarr_metadata.v3.codec.sharding import ( - SHARDING_INDEX_LOCATION_END, - SHARDING_INDEX_LOCATION_START, - ) - - cfg_end: ShardingCodecConfiguration = { - "chunk_shape": (16, 16), - "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), - "index_codecs": ({"name": "crc32c"},), - "index_location": SHARDING_INDEX_LOCATION_END, - } - cfg_start: ShardingCodecConfiguration = { - "chunk_shape": (16, 16), - "codecs": ({"name": "bytes", "configuration": {"endian": "little"}},), - "index_codecs": ({"name": "crc32c"},), - "index_location": SHARDING_INDEX_LOCATION_START, - } - assert cfg_end["index_location"] == "end" - assert cfg_start["index_location"] == "start" - - -def test_primitive_dtype_names() -> None: - from zarr_metadata.v3.data_type.bool import BOOL_DTYPE_NAME - from zarr_metadata.v3.data_type.complex128 import COMPLEX128_DTYPE_NAME - from zarr_metadata.v3.data_type.float32 import FLOAT32_DTYPE_NAME - from zarr_metadata.v3.data_type.int32 import INT32_DTYPE_NAME - from zarr_metadata.v3.data_type.uint64 import UINT64_DTYPE_NAME - - assert BOOL_DTYPE_NAME == "bool" - assert INT32_DTYPE_NAME == "int32" - assert UINT64_DTYPE_NAME == "uint64" - assert FLOAT32_DTYPE_NAME == "float32" - assert COMPLEX128_DTYPE_NAME == "complex128" - - -def test_numpy_datetime64_dtype_metadata() -> None: - dtype: NumpyDatetime64 = { - "name": "numpy.datetime64", - "configuration": {"unit": "ns", "scale_factor": 1}, - } - assert dtype["name"] == "numpy.datetime64" - - -def test_numpy_timedelta64_dtype_metadata() -> None: - dtype: NumpyTimedelta64 = { - "name": "numpy.timedelta64", - "configuration": {"unit": "s", "scale_factor": 1}, - } - assert dtype["name"] == "numpy.timedelta64" - - -def test_struct_dtype_metadata() -> None: - dtype: Struct = { - "name": "struct", - "configuration": { - "fields": ( - {"name": "x", "data_type": "float32"}, - {"name": "y", "data_type": "float32"}, - ), - }, - } - assert dtype["name"] == "struct" - assert len(dtype["configuration"]["fields"]) == 2 - - -def test_struct_dtype_metadata_nested() -> None: - """Struct fields can hold envelope data types, including another struct.""" - inner: Struct = { - "name": "struct", - "configuration": { - "fields": ({"name": "r", "data_type": "uint8"},), - }, - } - outer: Struct = { - "name": "struct", - "configuration": { - "fields": ( - {"name": "coord", "data_type": "float64"}, - {"name": "color", "data_type": inner}, - ), - }, - } - assert outer["configuration"]["fields"][1]["name"] == "color" - - -def test_hex_float16_validator() -> None: - from zarr_metadata.v3.data_type.float16 import hex_float16 - - assert hex_float16("0x7c00") == "0x7c00" - with pytest.raises(ValueError): - hex_float16("0x7c") # too short - with pytest.raises(ValueError): - hex_float16("0X7C00") # uppercase 0X prefix not accepted - with pytest.raises(ValueError): - hex_float16("not hex") - - -def test_hex_float32_validator() -> None: - from zarr_metadata.v3.data_type.float32 import hex_float32 - - assert hex_float32("0x7fc00000") == "0x7fc00000" - with pytest.raises(ValueError): - hex_float32("0x7fc0") # too short - with pytest.raises(ValueError): - hex_float32("not hex") - - -def test_hex_float64_validator() -> None: - from zarr_metadata.v3.data_type.float64 import hex_float64 - - assert hex_float64("0x7ff8000000000000") == "0x7ff8000000000000" - with pytest.raises(ValueError): - hex_float64("0x7ff8") # too short - with pytest.raises(ValueError): - hex_float64("not hex") - - -def test_base64_bytes_validator() -> None: - from zarr_metadata.v3.data_type.bytes import base64_bytes - - assert base64_bytes("SGVsbG8=") == "SGVsbG8=" - assert base64_bytes("") == "" - assert base64_bytes("AAAA") == "AAAA" - - with pytest.raises(ValueError): - base64_bytes("not!base64") - with pytest.raises(ValueError): - base64_bytes("ABC") # length not a multiple of 4 - - -def test_raw_bytes_dtype_name_validator() -> None: - from zarr_metadata.v3.data_type.raw import raw_bytes_dtype_name - - assert raw_bytes_dtype_name("r8") == "r8" - assert raw_bytes_dtype_name("r16") == "r16" - assert raw_bytes_dtype_name("r256") == "r256" - - with pytest.raises(ValueError): - raw_bytes_dtype_name("r3") # not a multiple of 8 - with pytest.raises(ValueError): - raw_bytes_dtype_name("r0") # zero not allowed - with pytest.raises(ValueError): - raw_bytes_dtype_name("R8") # uppercase R not accepted - with pytest.raises(ValueError): - raw_bytes_dtype_name("8") # missing prefix diff --git a/packages/zarr-metadata/tests/test_validators.py b/packages/zarr-metadata/tests/test_validators.py new file mode 100644 index 0000000000..e910959807 --- /dev/null +++ b/packages/zarr-metadata/tests/test_validators.py @@ -0,0 +1,74 @@ +""" +Tests for the runtime validators in zarr-metadata. + +The TypedDicts and Final constants in this package have no runtime +behavior to test -- pyright (in CI) verifies their shapes. The only +runtime logic is the small set of validating constructors for spec +strings whose constraints can't be expressed as a Literal type. +""" + +from __future__ import annotations + +import pytest + + +def test_hex_float16_validator() -> None: + from zarr_metadata.v3.data_type.float16 import hex_float16 + + assert hex_float16("0x7c00") == "0x7c00" + with pytest.raises(ValueError): + hex_float16("0x7c") # too short + with pytest.raises(ValueError): + hex_float16("0X7C00") # uppercase 0X prefix not accepted + with pytest.raises(ValueError): + hex_float16("not hex") + + +def test_hex_float32_validator() -> None: + from zarr_metadata.v3.data_type.float32 import hex_float32 + + assert hex_float32("0x7fc00000") == "0x7fc00000" + with pytest.raises(ValueError): + hex_float32("0x7fc0") # too short + with pytest.raises(ValueError): + hex_float32("not hex") + + +def test_hex_float64_validator() -> None: + from zarr_metadata.v3.data_type.float64 import hex_float64 + + assert hex_float64("0x7ff8000000000000") == "0x7ff8000000000000" + with pytest.raises(ValueError): + hex_float64("0x7ff8") # too short + with pytest.raises(ValueError): + hex_float64("not hex") + + +def test_base64_bytes_validator() -> None: + from zarr_metadata.v3.data_type.bytes import base64_bytes + + assert base64_bytes("SGVsbG8=") == "SGVsbG8=" + assert base64_bytes("") == "" + assert base64_bytes("AAAA") == "AAAA" + + with pytest.raises(ValueError): + base64_bytes("not!base64") + with pytest.raises(ValueError): + base64_bytes("ABC") # length not a multiple of 4 + + +def test_raw_bytes_dtype_name_validator() -> None: + from zarr_metadata.v3.data_type.raw import raw_bytes_dtype_name + + assert raw_bytes_dtype_name("r8") == "r8" + assert raw_bytes_dtype_name("r16") == "r16" + assert raw_bytes_dtype_name("r256") == "r256" + + with pytest.raises(ValueError): + raw_bytes_dtype_name("r3") # not a multiple of 8 + with pytest.raises(ValueError): + raw_bytes_dtype_name("r0") # zero not allowed + with pytest.raises(ValueError): + raw_bytes_dtype_name("R8") # uppercase R not accepted + with pytest.raises(ValueError): + raw_bytes_dtype_name("8") # missing prefix From c90c9a0dff4637d2f5c857faa7c9c32a9d4dc6fb Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 22 Apr 2026 15:49:48 +0200 Subject: [PATCH 43/55] build(metadata): lower minimum Python to 3.11 zarr-metadata is a typing-only foundational package consumed by libraries; supporting one Python version below the current minimum widens the audience at minimal cost. The only blocker was PEP 695 generic class syntax in `common.py`: class NamedConfig[TName: str, TConfig: ...](TypedDict): Rewritten to the PEP 484 `Generic[T]` form, which works on 3.11+. The two affected classes carry `# noqa: UP046` comments since the ruff rule pushes toward the newer syntax that we deliberately avoid. All other modern features (PEP 604 `X | Y` unions at runtime, `NotRequired`, `extra_items=` via typing_extensions, `ReadOnly`) already work on 3.11. Verified: package imports and all 6 tests pass on Python 3.11. Co-Authored-By: Claude Opus 4.7 (1M context) --- packages/zarr-metadata/pyproject.toml | 5 +++-- .../zarr-metadata/src/zarr_metadata/common.py | 16 +++++++++++++--- 2 files changed, 16 insertions(+), 5 deletions(-) diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 7e31477af0..40dcdc9c17 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -7,7 +7,7 @@ name = "zarr-metadata" version = "0.1.0" description = "Spec-defined metadata types for Zarr v2 and v3." readme = "README.md" -requires-python = ">=3.12" +requires-python = ">=3.11" license = "MIT" authors = [ { name = "Davis Bennett", email = "davis.v.bennett@gmail.com" }, @@ -18,6 +18,7 @@ classifiers = [ "License :: OSI Approved :: MIT License", "Programming Language :: Python", "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", "Programming Language :: Python :: 3.14", @@ -47,4 +48,4 @@ checks = [ include = ["src"] enableExperimentalFeatures = true typeCheckingMode = "strict" -pythonVersion = "3.12" +pythonVersion = "3.11" diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py index 2af3398c6a..03e0394222 100644 --- a/packages/zarr-metadata/src/zarr_metadata/common.py +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -7,7 +7,7 @@ """ from collections.abc import Mapping, Sequence -from typing import NotRequired, TypedDict +from typing import Generic, NotRequired, TypedDict, TypeVar from typing_extensions import ReadOnly @@ -15,22 +15,32 @@ """Any valid JSON value.""" -class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): +TName = TypeVar("TName", bound=str) +TConfig = TypeVar("TConfig", bound=Mapping[str, object]) + + +class NamedConfig(TypedDict, Generic[TName, TConfig]): # noqa: UP046 """ Named-config envelope with optional configuration. Generic with two parameters: name literal and configuration mapping. + + Uses the PEP 484 ``Generic[T]`` form rather than PEP 695 ``[T]`` syntax + so the package supports Python 3.11. """ name: ReadOnly[TName] configuration: NotRequired[ReadOnly[TConfig]] -class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): +class NamedRequiredConfig(TypedDict, Generic[TName, TConfig]): # noqa: UP046 """ Named-config envelope with required configuration. Generic with two parameters: name literal and configuration mapping. + + Uses the PEP 484 ``Generic[T]`` form rather than PEP 695 ``[T]`` syntax + so the package supports Python 3.11. """ name: ReadOnly[TName] From 700d916042c12b0f9e093c7df20a51e42a19679b Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 28 Apr 2026 14:15:17 -0400 Subject: [PATCH 44/55] refactor: remove generic base metadata --- .../src/zarr_metadata/__init__.py | 3 +- .../zarr-metadata/src/zarr_metadata/common.py | 33 +++---------------- .../src/zarr_metadata/v3/array.py | 2 +- 3 files changed, 7 insertions(+), 31 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index a7d39bec1a..857bb6ff08 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -1,4 +1,4 @@ -from zarr_metadata.common import JSON, NamedConfig, NamedRequiredConfig +from zarr_metadata.common import JSON, NamedConfig from zarr_metadata.v2.array import ArrayMetadataV2 from zarr_metadata.v2.group import GroupMetadataV2 from zarr_metadata.v3.array import ArrayMetadataV3 @@ -20,5 +20,4 @@ "GroupMetadataV2", "GroupMetadataV3", "NamedConfig", - "NamedRequiredConfig", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/common.py b/packages/zarr-metadata/src/zarr_metadata/common.py index 03e0394222..7206d0c5cc 100644 --- a/packages/zarr-metadata/src/zarr_metadata/common.py +++ b/packages/zarr-metadata/src/zarr_metadata/common.py @@ -7,41 +7,18 @@ """ from collections.abc import Mapping, Sequence -from typing import Generic, NotRequired, TypedDict, TypeVar - -from typing_extensions import ReadOnly +from typing import NotRequired, TypedDict JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None """Any valid JSON value.""" -TName = TypeVar("TName", bound=str) -TConfig = TypeVar("TConfig", bound=Mapping[str, object]) - - -class NamedConfig(TypedDict, Generic[TName, TConfig]): # noqa: UP046 - """ - Named-config envelope with optional configuration. - - Generic with two parameters: name literal and configuration mapping. - - Uses the PEP 484 ``Generic[T]`` form rather than PEP 695 ``[T]`` syntax - so the package supports Python 3.11. - """ - - name: ReadOnly[TName] - configuration: NotRequired[ReadOnly[TConfig]] - - -class NamedRequiredConfig(TypedDict, Generic[TName, TConfig]): # noqa: UP046 +class NamedConfig(TypedDict): """ - Named-config envelope with required configuration. + Externally-tagged union member for a metadata field. Generic with two parameters: name literal and configuration mapping. - - Uses the PEP 484 ``Generic[T]`` form rather than PEP 695 ``[T]`` syntax - so the package supports Python 3.11. """ - name: ReadOnly[TName] - configuration: ReadOnly[TConfig] + name: str + configuration: NotRequired[Mapping[str, JSON]] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index fdb1d57f8f..c3f050c732 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -19,7 +19,7 @@ class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] must_understand: Literal[False] -MetadataField = str | NamedConfig[str, Mapping[str, JSON]] +MetadataField = str | NamedConfig """A string or a {name: str, configuration: {...}} key value pair.""" From 84d5ca177078012bcc61054d3fb8241a1a0d849d Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 28 Apr 2026 20:48:27 -0400 Subject: [PATCH 45/55] refactor: clean up codecs init --- .../src/zarr_metadata/v3/codec/__init__.py | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py index 97b3a69551..e69de29bb2 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py @@ -1,19 +0,0 @@ -""" -Zarr codec metadata types. -""" - -from collections.abc import Mapping - -Codec = str | Mapping[str, object] -""" -The widest JSON shape that can specify a codec (v2 or v3). - -For v3, a codec is a `{"name": ..., "configuration": ...}` mapping (or -a bare `str` shorthand); for v2, a codec is the numcodecs JSON dict. -The accepted-input shape is the union of both. -""" - - -__all__ = [ - "Codec", -] From c30a768003969a1fd403ce4f9f73c8dd9b4155ed Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 28 Apr 2026 20:49:09 -0400 Subject: [PATCH 46/55] fix: correct v2 structured dtype spec --- .../src/zarr_metadata/v2/array.py | 20 ++++++++----------- 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index cbcbccc0e2..cc646b7ade 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -9,20 +9,15 @@ from zarr_metadata.v2.codec import NumcodecsConfig -class DataTypeV2Structured(TypedDict): - """ - A single field entry inside a structured v2 dtype. - - Spec-faithful: `datatype` is a numpy-style dtype string; `shape` is - present only when the field is a subarray field. - - See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html#data-type-encoding - """ +DataTypeV2Structured = tuple[str, str] | tuple[str, str, tuple[int, ...]] +""" +A single field entry inside a structured v2 dtype. - fieldname: str - datatype: str - shape: NotRequired[tuple[int, ...]] +Spec-faithful: `datatype` is a numpy-style dtype string; `shape` is +present only when the field is a subarray field. +See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html#data-type-encoding +""" DataTypeV2 = str | tuple[DataTypeV2Structured, ...] """The v2 dtype representation. @@ -50,6 +45,7 @@ class ArrayMetadataV2(TypedDict): order: Literal["C", "F"] filters: tuple[NumcodecsConfig, ...] | None dimension_separator: NotRequired[Literal[".", "/"]] + attributes: JSON __all__ = [ From fa66cc9966c8ef486bfca39568485ff0bad21358 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 28 Apr 2026 20:50:49 -0400 Subject: [PATCH 47/55] refactor: drop readonly for numcodecs config --- packages/zarr-metadata/src/zarr_metadata/v2/codec.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/codec.py b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py index b841da29d1..8ed8386f5a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/codec.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py @@ -5,7 +5,7 @@ `id` field naming the codec, plus arbitrary codec-specific extra fields. """ -from typing_extensions import ReadOnly, TypedDict +from typing_extensions import TypedDict from zarr_metadata.common import JSON @@ -21,7 +21,7 @@ class NumcodecsConfig(TypedDict, extra_items=JSON): # type: ignore[call-arg] https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ - id: ReadOnly[str] + id: str __all__ = [ From cf12cdca786289c2cabbb87b01ae6fe8f9b5778e Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 28 Apr 2026 20:52:36 -0400 Subject: [PATCH 48/55] docs: improve docstring --- packages/zarr-metadata/src/zarr_metadata/v3/array.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index c3f050c732..6f765da63d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -20,7 +20,7 @@ class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] MetadataField = str | NamedConfig -"""A string or a {name: str, configuration: {...}} key value pair.""" +"""A string or a {name: str, configuration: {...}} key value pair, where the 'configuration' key may be omitted. """ class ArrayMetadataV3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] From 82e10d65b66629fa13783945af0d17f9b0f5706f Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 28 Apr 2026 20:52:43 -0400 Subject: [PATCH 49/55] fix: use empty typeddict for crc32c config --- .../zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py index 573e56b356..ad828dee52 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py @@ -9,8 +9,6 @@ from typing import Final, Literal, NotRequired, TypedDict -from zarr_metadata.common import JSON - CRC32C_CODEC_NAME: Final = "crc32c" """The `name` field value of the `crc32c` codec.""" @@ -18,6 +16,10 @@ """Literal type of the `name` field of the `crc32c` codec.""" +class Empty(TypedDict, closed=True): # type: ignore[call-arg] + """An empty mapping""" + + class Crc32cCodec(TypedDict): """`crc32c` codec metadata. @@ -26,7 +28,7 @@ class Crc32cCodec(TypedDict): """ name: Crc32cCodecName - configuration: NotRequired[dict[str, JSON]] + configuration: NotRequired[Empty] __all__ = [ From 4b5bd11ad0abe0547f759bb32f5c4414580bfc57 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 29 Apr 2026 07:51:05 -0400 Subject: [PATCH 50/55] fix: remove arbitrary json from consolidated model --- packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py index 487c9e628a..31585a5e92 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py @@ -13,8 +13,6 @@ if TYPE_CHECKING: from collections.abc import Mapping - from zarr_metadata.common import JSON - from .array import ArrayMetadataV2 from .group import GroupMetadataV2 @@ -29,7 +27,7 @@ class ConsolidatedMetadataV2(TypedDict): """ zarr_consolidated_format: int - metadata: Mapping[str, GroupMetadataV2 | ArrayMetadataV2 | JSON] + metadata: Mapping[str, GroupMetadataV2 | ArrayMetadataV2] __all__ = [ From e6e5920d96c7b4e22842cd6268d4c6401f4c8b18 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 29 Apr 2026 10:09:30 -0400 Subject: [PATCH 51/55] fix: don't depend on zarr-metadata yet --- pyproject.toml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7a24777bec..ca9c9d58e7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,6 @@ dependencies = [ 'google-crc32c>=1.5', 'typing_extensions>=4.13', 'donfig>=0.8', - 'zarr-metadata>=0.1, <0.2', ] dynamic = [ @@ -471,7 +470,4 @@ start_string = "\n" ignore-words-list = "astroid" [project.entry-points.pytest11] -zarr = "zarr.testing" - -[tool.uv.sources] -zarr-metadata = { path = "packages/zarr-metadata", editable = true } +zarr = "zarr.testing" \ No newline at end of file From a732fb22689c5b8319e2c6d8caabaf76446e9e57 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 29 Apr 2026 10:09:54 -0400 Subject: [PATCH 52/55] fix: typesize is not required --- packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py index 1cd79f3d43..60b90e13e5 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py @@ -4,7 +4,7 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/blosc/index.html """ -from typing import Final, Literal, TypedDict +from typing import Final, Literal, NotRequired, TypedDict BLOSC_CODEC_NAME: Final = "blosc" """The `name` field value of the `blosc` codec.""" @@ -37,7 +37,7 @@ class BloscCodecConfiguration(TypedDict): clevel: int shuffle: BloscShuffle blocksize: int - typesize: int + typesize: NotRequired[int] class BloscCodec(TypedDict): From 8691138e9dfa77b1c08133e660d316660f4f42a2 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 29 Apr 2026 10:22:00 -0400 Subject: [PATCH 53/55] fix: re-wire zarr-metadata up as a dependency for zarr-python --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index ca9c9d58e7..58f80c57e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -154,6 +154,9 @@ hooks.vcs.version-file = "src/zarr/_version.py" [tool.hatch.envs.test] dependency-groups = ["test"] +extra-dependencies = [ + "zarr-metadata @ {root:uri}/packages/zarr-metadata", +] [tool.hatch.envs.test.env-vars] From a6d0e5e8939dc941237119b7b103ac963a214278 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 29 Apr 2026 10:27:03 -0400 Subject: [PATCH 54/55] chore: revert changes to src/zarr --- pyproject.toml | 5 +- src/zarr/abc/codec.py | 10 +-- src/zarr/codecs/blosc.py | 36 ++++++----- src/zarr/core/common.py | 64 +++++++++++++------ src/zarr/core/dtype/common.py | 9 ++- src/zarr/core/dtype/npy/bytes.py | 23 ++++--- src/zarr/core/dtype/npy/common.py | 4 +- src/zarr/core/dtype/npy/string.py | 26 ++++---- src/zarr/core/dtype/npy/time.py | 27 +++++++- src/zarr/core/metadata/v2.py | 17 ++--- src/zarr/core/metadata/v3.py | 100 ++++++++++++++++++------------ 11 files changed, 200 insertions(+), 121 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 58f80c57e6..b4783b5be3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -154,9 +154,6 @@ hooks.vcs.version-file = "src/zarr/_version.py" [tool.hatch.envs.test] dependency-groups = ["test"] -extra-dependencies = [ - "zarr-metadata @ {root:uri}/packages/zarr-metadata", -] [tool.hatch.envs.test.env-vars] @@ -473,4 +470,4 @@ start_string = "\n" ignore-words-list = "astroid" [project.entry-points.pytest11] -zarr = "zarr.testing" \ No newline at end of file +zarr = "zarr.testing" diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index ed9da448cd..eed2119aff 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -5,16 +5,12 @@ from typing import TYPE_CHECKING, Literal, Protocol, TypeGuard, runtime_checkable from typing_extensions import ReadOnly, TypedDict -from zarr_metadata.v3.codec import Codec as _CodecJSON from zarr.abc.metadata import Metadata from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import NamedConfig, concurrent_map from zarr.core.config import config -# Legacy alias preserved for zarr.core internal call sites. -type CodecJSON = _CodecJSON - if TYPE_CHECKING: from collections.abc import Awaitable, Callable, Iterable from typing import Self @@ -34,7 +30,6 @@ "BaseCodec", "BytesBytesCodec", "CodecInput", - "CodecJSON", "CodecOutput", "CodecPipeline", "GetResult", @@ -65,6 +60,11 @@ def _check_codecjson_v2(data: object) -> TypeGuard[CodecJSON_V2[str]]: CodecJSON_V3 = str | NamedConfig[str, Mapping[str, object]] """The JSON representation of a codec for Zarr V3.""" +# The widest type we will *accept* for a codec JSON +# This covers v2 and v3 +CodecJSON = str | Mapping[str, object] +"""The widest type of JSON-like input that could specify a codec.""" + @runtime_checkable class SupportsSyncCodec[CI: CodecInput, CO: CodecOutput](Protocol): diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 16548f5b1c..62ceff7659 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -9,28 +9,12 @@ import numcodecs from numcodecs.blosc import Blosc from packaging.version import Version -from zarr_metadata.v3.codec.blosc import BloscCodecConfiguration as BloscConfigV3 from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, NamedRequiredConfig, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasItemSize - -class BloscConfigV2(TypedDict): - """Blosc configuration in the numcodecs/v2 form. - - ``shuffle`` is an integer code (the numcodecs convention) rather than - a named literal as in v3. - """ - - cname: Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] - clevel: int - shuffle: int - blocksize: int - typesize: NotRequired[int] - - if TYPE_CHECKING: from typing import Self @@ -46,6 +30,26 @@ class BloscConfigV2(TypedDict): """The codec identifiers used in the blosc codec """ +class BloscConfigV2(TypedDict): + """Configuration for the V2 Blosc codec""" + + cname: CName + clevel: int + shuffle: int + blocksize: int + typesize: NotRequired[int] + + +class BloscConfigV3(TypedDict): + """Configuration for the V3 Blosc codec""" + + cname: CName + clevel: int + shuffle: Shuffle + blocksize: int + typesize: int + + class BloscJSON_V3(NamedRequiredConfig[Literal["blosc"], BloscConfigV3]): """ The JSON form of the Blosc codec in Zarr V3. diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 281a882bc4..2279820d7a 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -5,7 +5,7 @@ import math import operator import warnings -from collections.abc import Iterable, Sequence +from collections.abc import Iterable, Mapping, Sequence from enum import Enum from itertools import starmap from typing import ( @@ -13,14 +13,14 @@ Any, Final, Literal, + NotRequired, + TypedDict, cast, overload, ) import numpy as np -from zarr_metadata import JSON as JSON # noqa: TC002 -from zarr_metadata import NamedConfig as NamedConfig # noqa: TC002 -from zarr_metadata import NamedRequiredConfig as NamedRequiredConfig +from typing_extensions import ReadOnly from zarr.core.config import config as zarr_config from zarr.errors import ZarrRuntimeWarning @@ -42,6 +42,7 @@ ChunkCoords = tuple[int, ...] ZarrFormat = Literal[2, 3] NodeType = Literal["array", "group"] +JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None MemoryOrder = Literal["C", "F"] AccessModeLiteral = Literal["r", "r+", "a", "w", "w-"] ANY_ACCESS_MODE: Final = "r", "r+", "a", "w", "w-" @@ -49,6 +50,38 @@ DimensionNames = DimensionNamesLike # for backwards compatibility +class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + A typed dictionary representing an object with a name and configuration, where the configuration + is an optional mapping of string keys to values, e.g. another typed dictionary or a JSON object. + + This class is generic with two type parameters: the type of the name (``TName``) and the type of + the configuration (``TConfig``). + """ + + name: ReadOnly[TName] + """The name of the object.""" + + configuration: NotRequired[ReadOnly[TConfig]] + """The configuration of the object. Not required.""" + + +class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): + """ + A typed dictionary representing an object with a name and configuration, where the configuration + is a mapping of string keys to values, e.g. another typed dictionary or a JSON object. + + This class is generic with two type parameters: the type of the name (``TName``) and the type of + the configuration (``TConfig``). + """ + + name: ReadOnly[TName] + """The name of the object.""" + + configuration: ReadOnly[TConfig] + """The configuration of the object.""" + + def product(tup: tuple[int, ...]) -> int: return functools.reduce(operator.mul, tup, 1) @@ -211,16 +244,12 @@ def _default_zarr_format() -> ZarrFormat: return cast("ZarrFormat", int(zarr_config.get("default_zarr_format", 3))) -def expand_rle(data: Sequence[int | Sequence[int]]) -> list[int]: +def expand_rle(data: Sequence[int | list[int]]) -> list[int]: """Expand a mixed array of bare integers and RLE pairs. Per the rectilinear chunk grid spec, each element can be: - a bare integer (an explicit edge length) - a two-element array ``[value, count]`` (run-length encoded) - - Accepts both list and tuple forms of the RLE pair so the same routine - can decode JSON-parsed input (lists) and internally-constructed input - (tuples). """ result: list[int] = [] for item in data: @@ -229,7 +258,7 @@ def expand_rle(data: Sequence[int | Sequence[int]]) -> list[int]: if val < 1: raise ValueError(f"Chunk edge length must be >= 1, got {val}") result.append(val) - elif isinstance(item, (list, tuple)) and len(item) == 2: + elif isinstance(item, list) and len(item) == 2: size, count = int(item[0]), int(item[1]) if size < 1: raise ValueError(f"Chunk edge length must be >= 1, got {size}") @@ -241,30 +270,27 @@ def expand_rle(data: Sequence[int | Sequence[int]]) -> list[int]: return result -def compress_rle(sizes: Sequence[int]) -> list[int | tuple[int, int]]: +def compress_rle(sizes: Sequence[int]) -> list[int | list[int]]: """Compress chunk sizes to mixed RLE format per the rectilinear spec. - Runs of length > 1 are emitted as ``(value, count)`` 2-tuples; runs of + Runs of length > 1 are emitted as ``[value, count]`` pairs; runs of length 1 are emitted as bare integers:: - [10, 10, 10, 5] -> [(10, 3), 5] - - The 2-tuple shape mirrors the spec's "exactly two elements" constraint - on RLE pairs. + [10, 10, 10, 5] -> [[10, 3], 5] """ if not sizes: return [] - result: list[int | tuple[int, int]] = [] + result: list[int | list[int]] = [] current = sizes[0] count = 1 for s in sizes[1:]: if s == current: count += 1 else: - result.append((current, count) if count > 1 else current) + result.append([current, count] if count > 1 else current) current = s count = 1 - result.append((current, count) if count > 1 else current) + result.append([current, count] if count > 1 else current) return result diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index 7656c3ad33..87e46b53d2 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -12,15 +12,10 @@ ) from typing_extensions import ReadOnly -from zarr_metadata.v3.data_type import DType from zarr.core.common import NamedConfig from zarr.errors import UnstableSpecificationWarning -# This is a wider type than our standard JSON type because we need -# to work with typeddict objects which are assignable to Mapping[str, object] -DTypeJSON = DType - EndiannessStr = Literal["little", "big"] ENDIANNESS_STR: Final = "little", "big" @@ -34,6 +29,10 @@ # These are the ids of the known object codecs for zarr v2. OBJECT_CODEC_IDS: Final = ("vlen-utf8", "vlen-bytes", "vlen-array", "pickle", "json2", "msgpack2") +# This is a wider type than our standard JSON type because we need +# to work with typeddict objects which are assignable to Mapping[str, object] +DTypeJSON = str | int | float | Sequence["DTypeJSON"] | None | Mapping[str, object] + # The DTypeJSON_V2 type exists because ZDType.from_json takes a single argument, which must contain # all the information necessary to decode the data type. Zarr v2 supports multiple distinct # data types that all used the "|O" data type identifier. These data types can only be diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index 9cc137240b..2cf5985d69 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -21,20 +21,29 @@ from zarr.core.dtype.npy.common import check_json_str from zarr.core.dtype.wrapper import TBaseDType, ZDType +BytesLike = np.bytes_ | str | bytes | int + class FixedLengthBytesConfig(TypedDict): """ - Configuration for fixed-length bytes data types in Zarr V3. + A configuration for a data type that takes a ``length_bytes`` parameter. - `null_terminated_bytes` is a zarr-python-specific extension; the - configuration carries `length_bytes`, the per-element allocated - byte count. - """ + Attributes + ---------- - length_bytes: int + length_bytes : int + The length in bytes of the data associated with this configuration. + Examples + -------- + ```python + { + "length_bytes": 12 + } + ``` + """ -BytesLike = np.bytes_ | str | bytes | int + length_bytes: int class NullterminatedBytesJSON_V2(DTypeConfig_V2[str, None]): diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index 221dafec8f..f413f5f678 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -18,7 +18,6 @@ ) import numpy as np -from zarr_metadata.v3.data_type.numpy_datetime64 import DateTimeUnit as DateTimeUnit from zarr.core.dtype.common import ( ENDIANNESS_STR, @@ -34,6 +33,9 @@ IntLike = SupportsInt | SupportsIndex | bytes | str FloatLike = SupportsIndex | SupportsFloat | bytes | str ComplexLike = SupportsFloat | SupportsIndex | SupportsComplex | bytes | str | None +DateTimeUnit = Literal[ + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" +] DATETIME_UNIT: Final = ( "Y", "M", diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index f4e0f9b9a8..069d0b128d 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -35,19 +35,6 @@ ) from zarr.core.dtype.wrapper import ZDType - -class LengthBytesConfig(TypedDict): - """ - Configuration for the fixed-length-utf32 string data type in Zarr V3. - - `fixed_length_utf32` is a zarr-python-specific extension; the - configuration carries `length_bytes`, the per-element byte allocation - (must be a multiple of 4 for utf-32). - """ - - length_bytes: int - - if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat from zarr.core.dtype.wrapper import TBaseDType @@ -60,6 +47,19 @@ class SupportsStr(Protocol): def __str__(self) -> str: ... +class LengthBytesConfig(TypedDict): + """ + Configuration for a fixed-length string data type in Zarr V3. + + Attributes + ---------- + length_bytes : int + The length in bytes of the data associated with this configuration. + """ + + length_bytes: int + + class FixedLengthUTF32JSON_V2(DTypeConfig_V2[str, None]): """ A wrapper around the JSON representation of the ``FixedLengthUTF32`` data type in Zarr V2. diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index 57d96bdc63..6a864dc889 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -7,6 +7,7 @@ ClassVar, Literal, Self, + TypedDict, TypeGuard, cast, get_args, @@ -14,9 +15,7 @@ ) import numpy as np -from zarr_metadata.v3.data_type.numpy_datetime64 import ( - NumpyDatetime64Configuration as TimeConfig, -) +from typing_extensions import ReadOnly from zarr.core.common import NamedConfig from zarr.core.dtype.common import ( @@ -90,6 +89,28 @@ def check_json_time(data: JSON) -> TypeGuard[Literal["NaT"] | int]: return check_json_int(data) or data == "NaT" +class TimeConfig(TypedDict): + """ + The configuration for the numpy.timedelta64 or numpy.datetime64 data type in Zarr V3. + + Attributes + ---------- + unit : ReadOnly[DateTimeUnit] + A string encoding a unit of time. + scale_factor : ReadOnly[int] + A scale factor. + + Examples + -------- + ```python + {"unit": "ms", "scale_factor": 1} + ``` + """ + + unit: ReadOnly[DateTimeUnit] + scale_factor: ReadOnly[int] + + class DateTime64JSON_V3(NamedConfig[Literal["numpy.datetime64"], TimeConfig]): """ The JSON representation of the ``numpy.datetime64`` data type in Zarr V3. diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 0c95696c24..8626d480a7 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -3,9 +3,7 @@ import warnings from collections.abc import Iterable, Sequence from functools import cached_property -from typing import TYPE_CHECKING, Any, TypeAlias, cast - -from zarr_metadata.v2.array import ArrayMetadataV2 +from typing import TYPE_CHECKING, Any, TypedDict, cast from zarr.abc.metadata import Metadata from zarr.abc.numcodec import Numcodec, _is_numcodec @@ -44,10 +42,15 @@ from zarr.core.config import config, parse_indexing_order from zarr.core.metadata.common import parse_attributes -# Legacy alias preserved for zarr.core internal call sites. -# Using explicit `TypeAlias` rather than the `type` keyword so that runtime -# introspection (e.g. `.__annotations__` on the underlying TypedDict) works. -ArrayV2MetadataDict: TypeAlias = ArrayMetadataV2 # noqa: UP040 + +class ArrayV2MetadataDict(TypedDict): + """ + A typed dictionary model for Zarr format 2 metadata. + """ + + zarr_format: Literal[2] + attributes: dict[str, JSON] + # Union of acceptable types for v2 compressors type CompressorLikev2 = dict[str, JSON] | Numcodec | None diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index f13f3595ef..a8f2b05518 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -3,25 +3,9 @@ import json from collections.abc import Iterable, Mapping, Sequence from dataclasses import dataclass, field, replace -from typing import TYPE_CHECKING, Any, Final, Literal, TypeAlias, TypeGuard, cast +from typing import TYPE_CHECKING, Any, Final, Literal, NotRequired, TypeGuard, cast -from zarr_metadata.v3.array import ( - AllowedExtraField as AllowedExtraField, -) -from zarr_metadata.v3.array import ArrayMetadataV3 -from zarr_metadata.v3.chunk_grid.rectilinear import ( - RectilinearChunkGrid, - RectilinearDimSpec, -) -from zarr_metadata.v3.chunk_grid.rectilinear import ( - RectilinearChunkGridConfiguration as RectilinearChunkGridConfig, -) -from zarr_metadata.v3.chunk_grid.regular import ( - RegularChunkGrid, -) -from zarr_metadata.v3.chunk_grid.regular import ( - RegularChunkGridConfiguration as RegularChunkGridConfig, -) +from typing_extensions import TypedDict from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec from zarr.abc.metadata import Metadata @@ -38,6 +22,7 @@ ChunksLike, DimensionNamesLike, NamedConfig, + NamedRequiredConfig, compress_rle, expand_rle, parse_named_configuration, @@ -52,26 +37,6 @@ from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError from zarr.registry import get_codec_class -# Legacy aliases preserved for zarr.core internal call sites. -# Using explicit `TypeAlias` rather than the `type` keyword so that runtime -# introspection (e.g. `.__annotations__` on the underlying TypedDict) works. -ArrayMetadataJSON_V3: TypeAlias = ArrayMetadataV3 # noqa: UP040 -RectilinearChunkGridMetadataJSON: TypeAlias = RectilinearChunkGrid # noqa: UP040 -RectilinearChunkGridMetadataConfig: TypeAlias = RectilinearChunkGridConfig # noqa: UP040 -RectilinearDimSpecJSON: TypeAlias = RectilinearDimSpec # noqa: UP040 -RegularChunkGridMetadataJSON: TypeAlias = RegularChunkGrid # noqa: UP040 -RegularChunkGridMetadataConfig: TypeAlias = RegularChunkGridConfig # noqa: UP040 - -__all__ = [ - "AllowedExtraField", - "ArrayMetadataJSON_V3", - "RectilinearChunkGridMetadataConfig", - "RectilinearChunkGridMetadataJSON", - "RectilinearDimSpecJSON", - "RegularChunkGridMetadataConfig", - "RegularChunkGridMetadataJSON", -] - if TYPE_CHECKING: from typing import Self @@ -173,6 +138,16 @@ def parse_storage_transformers(data: object) -> tuple[dict[str, JSON], ...]: ) +class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] + """ + This class models allowed extra fields in array metadata. + They must have ``must_understand`` set to ``False``, and may contain + arbitrary additional JSON data. + """ + + must_understand: Literal[False] + + def check_allowed_extra_field(data: object) -> TypeGuard[AllowedExtraField]: """ Check if the extra field is allowed according to the Zarr v3 spec. The object @@ -200,6 +175,28 @@ def parse_extra_fields( return dict(data) +# JSON type for a single dimension's rectilinear spec: +# bare int (uniform shorthand), or list of ints / [value, count] RLE pairs. +RectilinearDimSpecJSON = int | list[int | list[int]] + + +class RegularChunkGridMetadataConfig(TypedDict): + chunk_shape: Sequence[int] + + +class RectilinearChunkGridMetadataConfig(TypedDict): + kind: Literal["inline"] + chunk_shapes: Sequence[RectilinearDimSpecJSON] + + +RegularChunkGridMetadataJSON = NamedRequiredConfig[ + Literal["regular"], RegularChunkGridMetadataConfig +] +RectilinearChunkGridMetadataJSON = NamedRequiredConfig[ + Literal["rectilinear"], RectilinearChunkGridMetadataConfig +] + + def _parse_chunk_shape(chunk_shape: Iterable[int]) -> tuple[int, ...]: """Validate and normalize a regular chunk shape. @@ -315,9 +312,9 @@ def to_dict(self) -> RectilinearChunkGridMetadataJSON: # type: ignore[override] rle = compress_rle(dim_spec) # Use RLE only if it's actually shorter if len(rle) < len(dim_spec): - serialized_dims.append(tuple(rle)) + serialized_dims.append(rle) else: - serialized_dims.append(tuple(dim_spec)) + serialized_dims.append(list(dim_spec)) return { "name": "rectilinear", "configuration": { @@ -362,7 +359,7 @@ def from_dict(cls, data: RectilinearChunkGridMetadataJSON) -> Self: # type: ign if dim_spec < 1: raise ValueError(f"Integer chunk edge length must be >= 1, got {dim_spec}") parsed.append(dim_spec) - elif isinstance(dim_spec, (list, tuple)): + elif isinstance(dim_spec, list): parsed.append(tuple(expand_rle(dim_spec))) else: raise TypeError( @@ -417,6 +414,27 @@ def parse_chunk_grid( raise ValueError(f"Unknown chunk grid name: {name!r}") +class ArrayMetadataJSON_V3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] + """ + A typed dictionary model for zarr v3 array metadata. + + Extra keys are permitted if they conform to ``AllowedExtraField`` + (i.e. they are mappings with ``must_understand: false``). + """ + + zarr_format: Literal[3] + node_type: Literal["array"] + data_type: str | NamedConfig[str, Mapping[str, JSON]] + shape: tuple[int, ...] + chunk_grid: str | NamedConfig[str, Mapping[str, JSON]] + chunk_key_encoding: str | NamedConfig[str, Mapping[str, JSON]] + fill_value: JSON + codecs: tuple[str | NamedConfig[str, Mapping[str, JSON]], ...] + attributes: NotRequired[Mapping[str, JSON]] + storage_transformers: NotRequired[tuple[str | NamedConfig[str, Mapping[str, JSON]], ...]] + dimension_names: NotRequired[tuple[str | None, ...]] + + """ The names of the fields of the array metadata document defined in the zarr V3 spec. """ From b8d67fe06652697e3a925520adb149e3fb6c28f6 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 29 Apr 2026 17:19:33 -0400 Subject: [PATCH 55/55] chore: mypy ignore the new package --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d91b35fa4f..6e6c21b581 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -31,7 +31,7 @@ repos: rev: v1.19.1 hooks: - id: mypy - files: src|tests + files: ^(src|tests)/ additional_dependencies: # Package dependencies - packaging