Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-compat

Author: TomAugspurger

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
     rev: v1.11.2
     hooks:
       - id: mypy
-        files: src
+        files: src|tests/v3/test_(api|array|buffer).py
         additional_dependencies:
           # Package dependencies
           - asciitree
@@ -35,7 +35,17 @@ repos:
           - numcodecs
           - numpy
           - typing_extensions
+          - universal-pathlib
           # Tests
           - pytest
           # Zarr v2
           - types-redis
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.04.23
+    hooks:
+      - id: sp-repo-review
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal

pyproject.toml

@@ -96,6 +96,7 @@ extra = [
 ]
 optional = [
     'lmdb',
+    'universal-pathlib',
 ]
 
 [project.urls]
@@ -213,6 +214,7 @@ extend-select = [
     "UP",  # pyupgrade
     "RSE",
     "RUF",
+    "TCH", # flake8-type-checking
     "TRY", # tryceratops
 ]
 ignore = [
@@ -259,3 +261,9 @@ filterwarnings = [
 markers = [
     "gpu: mark a test as requiring CuPy and GPU"
 ]
+
+[tool.repo-review]
+ignore = [
+	"PC111",  # fix Python code in documentation - enable later 
+	"PC180",  # for JavaScript - not interested
+]

src/zarr/abc/codec.py

@@ -1,22 +1,22 @@
 from __future__ import annotations
 
 from abc import abstractmethod
-from collections.abc import Awaitable, Callable, Iterable
 from typing import TYPE_CHECKING, Any, Generic, TypeVar
 
-import numpy as np
-
 from zarr.abc.metadata import Metadata
-from zarr.abc.store import ByteGetter, ByteSetter
 from zarr.core.buffer import Buffer, NDBuffer
-from zarr.core.chunk_grids import ChunkGrid
 from zarr.core.common import ChunkCoords, concurrent_map
 from zarr.core.config import config
 
 if TYPE_CHECKING:
+    from collections.abc import Awaitable, Callable, Iterable
+
+    import numpy as np
     from typing_extensions import Self
 
+    from zarr.abc.store import ByteGetter, ByteSetter
     from zarr.core.array_spec import ArraySpec
+    from zarr.core.chunk_grids import ChunkGrid
     from zarr.core.common import JSON
     from zarr.core.indexing import SelectorTuple
 

src/zarr/abc/metadata.py

@@ -6,9 +6,9 @@
 if TYPE_CHECKING:
     from typing_extensions import Self
 
-from dataclasses import dataclass, fields
+    from zarr.core.common import JSON
 
-from zarr.core.common import JSON
+from dataclasses import dataclass, fields
 
 __all__ = ["Metadata"]
 

src/zarr/api/asynchronous.py

@@ -2,16 +2,12 @@
 
 import asyncio
 import warnings
-from collections.abc import Iterable
-from typing import Any, Literal, Union, cast
+from typing import TYPE_CHECKING, Any, Literal, Union, cast
 
 import numpy as np
 import numpy.typing as npt
 
-from zarr.abc.codec import Codec
 from zarr.core.array import Array, AsyncArray
-from zarr.core.buffer import NDArrayLike
-from zarr.core.chunk_key_encodings import ChunkKeyEncoding
 from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
 from zarr.core.group import AsyncGroup
 from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata
@@ -20,6 +16,13 @@
     make_store_path,
 )
 
+if TYPE_CHECKING:
+    from collections.abc import Iterable
+
+    from zarr.abc.codec import Codec
+    from zarr.core.buffer import NDArrayLike
+    from zarr.core.chunk_key_encodings import ChunkKeyEncoding
+
 __all__ = [
     "consolidate_metadata",
     "copy",

src/zarr/api/synchronous.py

@@ -1,15 +1,17 @@
 from __future__ import annotations
 
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 import zarr.api.asynchronous as async_api
 from zarr._compat import _deprecate_positional_args
 from zarr.core.array import Array, AsyncArray
-from zarr.core.buffer import NDArrayLike
-from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, ZarrFormat
 from zarr.core.group import Group
 from zarr.core.sync import sync
-from zarr.store import StoreLike
+
+if TYPE_CHECKING:
+    from zarr.core.buffer import NDArrayLike
+    from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, ZarrFormat
+    from zarr.store import StoreLike
 
 __all__ = [
     "consolidate_metadata",

src/zarr/codecs/_v2.py

@@ -1,16 +1,19 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
+from typing import TYPE_CHECKING
 
 import numcodecs
 from numcodecs.compat import ensure_bytes, ensure_ndarray
 
 from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec
-from zarr.core.array_spec import ArraySpec
 from zarr.core.buffer import Buffer, NDBuffer, default_buffer_prototype
 from zarr.core.common import JSON, to_thread
 from zarr.registry import get_ndbuffer_class
 
+if TYPE_CHECKING:
+    from zarr.core.array_spec import ArraySpec
+
 
 @dataclass(frozen=True)
 class V2Compressor(ArrayBytesCodec):

src/zarr/codecs/blosc.py

@@ -9,15 +9,16 @@
 from numcodecs.blosc import Blosc
 
 from zarr.abc.codec import BytesBytesCodec
-from zarr.core.array_spec import ArraySpec
-from zarr.core.buffer import Buffer
 from zarr.core.buffer.cpu import as_numpy_array_wrapper
 from zarr.core.common import JSON, parse_enum, parse_named_configuration, to_thread
 from zarr.registry import register_codec
 
 if TYPE_CHECKING:
     from typing_extensions import Self
 
+    from zarr.core.array_spec import ArraySpec
+    from zarr.core.buffer import Buffer
+
 
 class BloscShuffle(Enum):
     noshuffle = "noshuffle"

src/zarr/codecs/bytes.py

@@ -8,14 +8,15 @@
 import numpy as np
 
 from zarr.abc.codec import ArrayBytesCodec
-from zarr.core.array_spec import ArraySpec
 from zarr.core.buffer import Buffer, NDArrayLike, NDBuffer
 from zarr.core.common import JSON, parse_enum, parse_named_configuration
 from zarr.registry import register_codec
 
 if TYPE_CHECKING:
     from typing_extensions import Self
 
+    from zarr.core.array_spec import ArraySpec
+
 
 class Endian(Enum):
     big = "big"

src/zarr/codecs/crc32c_.py

@@ -8,14 +8,15 @@
 from crc32c import crc32c
 
 from zarr.abc.codec import BytesBytesCodec
-from zarr.core.array_spec import ArraySpec
-from zarr.core.buffer import Buffer
 from zarr.core.common import JSON, parse_named_configuration
 from zarr.registry import register_codec
 
 if TYPE_CHECKING:
     from typing_extensions import Self
 
+    from zarr.core.array_spec import ArraySpec
+    from zarr.core.buffer import Buffer
+
 
 @dataclass(frozen=True)
 class Crc32cCodec(BytesBytesCodec):