Enable ruff/isort rules (I) and fix issues

bench/compress_normal.py

@@ -1,9 +1,9 @@
 import sys
 import timeit
 
+import line_profiler
 import numpy as np
 
-import line_profiler
 import zarr
 from zarr import blosc
 

docs/release.rst

@@ -26,6 +26,9 @@ Unreleased
 Enhancements
 ~~~~~~~~~~~~
 
+* Enable ruff/isort rules (I) and fix issues.
+  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1704`.
+
 Docs
 ~~~~
 

pyproject.toml

@@ -105,7 +105,8 @@ exclude = [
 
 [tool.ruff.lint]
 extend-select = [
-    "B"
+    "B",
+    "I"
 ]
 
 [tool.black]

zarr/_storage/absstore.py

@@ -1,19 +1,20 @@
 """This module contains storage classes related to Azure Blob Storage (ABS)"""
 
-from typing import Optional
 import warnings
+from typing import Optional
 
 from numcodecs.compat import ensure_bytes
-from zarr.util import normalize_storage_path
+
 from zarr._storage.store import (
+    V3_DEPRECATION_MESSAGE,
+    Store,
+    StoreV3,
     _get_metadata_suffix,
     data_root,
     meta_root,
-    Store,
-    StoreV3,
-    V3_DEPRECATION_MESSAGE,
 )
 from zarr.types import DIMENSION_SEPARATOR
+from zarr.util import normalize_storage_path
 
 __doctest_requires__ = {
     ("ABSStore", "ABSStore.*"): ["azure.storage.blob"],

zarr/_storage/store.py

@@ -7,10 +7,10 @@
 from string import ascii_letters, digits
 from typing import Any, Dict, List, Mapping, Optional, Sequence, Tuple, Union
 
-from zarr.meta import Metadata2, Metadata3
-from zarr.util import normalize_storage_path
 from zarr.context import Context
+from zarr.meta import Metadata2, Metadata3
 from zarr.types import ZARR_VERSION
+from zarr.util import normalize_storage_path
 
 # v2 store keys
 array_meta_key = ".zarray"

zarr/_storage/v3.py

@@ -3,39 +3,36 @@
 from collections import OrderedDict
 from collections.abc import MutableMapping
 from threading import Lock
-from typing import Union, Dict, Any, Optional
-
-from zarr.errors import (
-    MetadataError,
-    ReadOnlyError,
-)
-from zarr.util import buffer_size, json_loads, normalize_storage_path
-from zarr.types import DIMENSION_SEPARATOR
+from typing import Any, Dict, Optional, Union
 
 from zarr._storage.absstore import ABSStoreV3  # noqa: F401
 from zarr._storage.store import (  # noqa: F401
+    BaseStore,
+    Store,
+    StoreV3,
     _get_hierarchy_metadata,
     _get_metadata_suffix,
     _listdir_from_keys,
+    _path_to_prefix,
+    _prefix_to_array_key,
+    _prefix_to_group_key,
     _rename_from_keys,
     _rename_metadata_v3,
     _rmdir_from_keys,
     _rmdir_from_keys_v3,
-    _path_to_prefix,
-    _prefix_to_array_key,
-    _prefix_to_group_key,
     array_meta_key,
     attrs_key,
     data_root,
     group_meta_key,
     meta_root,
-    BaseStore,
-    Store,
-    StoreV3,
+)
+from zarr.errors import (
+    MetadataError,
+    ReadOnlyError,
 )
 from zarr.storage import (
-    DBMStore,
     ConsolidatedMetadataStore,
+    DBMStore,
     DirectoryStore,
     FSStore,
     KVStore,
@@ -48,6 +45,8 @@
     ZipStore,
     _getsize,
 )
+from zarr.types import DIMENSION_SEPARATOR
+from zarr.util import buffer_size, json_loads, normalize_storage_path
 
 __doctest_requires__ = {
     ("RedisStore", "RedisStore.*"): ["redis"],

zarr/_storage/v3_storage_transformers.py

@@ -1,15 +1,14 @@
 import functools
 import itertools
 import os
-from typing import NamedTuple, Tuple, Optional, Union, Iterator
+from typing import Iterator, NamedTuple, Optional, Tuple, Union
 
-from numcodecs.compat import ensure_bytes
 import numpy as np
+from numcodecs.compat import ensure_bytes
 
 from zarr._storage.store import StorageTransformer, StoreV3, _rmdir_from_keys_v3
-from zarr.util import normalize_storage_path
 from zarr.types import DIMENSION_SEPARATOR
-
+from zarr.util import normalize_storage_path
 
 MAX_UINT_64 = 2**64 - 1
 

zarr/convenience.py

@@ -4,29 +4,27 @@
 import os
 import re
 from collections.abc import Mapping, MutableMapping
+from typing import Union
 
-from zarr._storage.store import data_root, meta_root, assert_zarr_v3_api_available
+from zarr._storage.store import assert_zarr_v3_api_available, data_root, meta_root
+from zarr._storage.v3 import ConsolidatedMetadataStoreV3
 from zarr.core import Array
 from zarr.creation import array as _create_array
 from zarr.creation import open_array
 from zarr.errors import CopyError, PathNotFoundError
-from zarr.hierarchy import Group
+from zarr.hierarchy import Group, open_group
 from zarr.hierarchy import group as _create_group
-from zarr.hierarchy import open_group
 from zarr.meta import json_dumps, json_loads
 from zarr.storage import (
+    BaseStore,
+    ConsolidatedMetadataStore,
     _get_metadata_suffix,
     contains_array,
     contains_group,
     normalize_store_arg,
-    BaseStore,
-    ConsolidatedMetadataStore,
 )
-from zarr._storage.v3 import ConsolidatedMetadataStoreV3
 from zarr.util import TreeViewer, buffer_size, normalize_storage_path
 
-from typing import Union
-
 StoreLike = Union[BaseStore, MutableMapping, str, None]
 
 _builtin_open = open  # builtin open is later shadowed by a local open function

zarr/core.py

@@ -14,17 +14,17 @@
 from zarr.attrs import Attributes
 from zarr.codecs import AsType, get_codec
 from zarr.context import Context
-from zarr.errors import ArrayNotFoundError, ReadOnlyError, ArrayIndexError
+from zarr.errors import ArrayIndexError, ArrayNotFoundError, ReadOnlyError
 from zarr.indexing import (
     BasicIndexer,
+    BlockIndex,
+    BlockIndexer,
     CoordinateIndexer,
     MaskIndexer,
     OIndex,
     OrthogonalIndexer,
-    VIndex,
-    BlockIndex,
-    BlockIndexer,
     PartialChunkIterator,
+    VIndex,
     check_fields,
     check_no_multi_fields,
     ensure_tuple,
@@ -36,28 +36,28 @@
     pop_fields,
 )
 from zarr.storage import (
+    KVStore,
     _get_hierarchy_metadata,
     _prefix_to_array_key,
-    KVStore,
     getsize,
     listdir,
     normalize_store_arg,
 )
 from zarr.util import (
     ConstantMap,
-    all_equal,
     InfoReporter,
+    PartialReadBuffer,
+    UncompressedPartialReadBufferV3,
+    all_equal,
     check_array_shape,
+    ensure_ndarray_like,
     human_readable_size,
     is_total_slice,
     nolock,
     normalize_chunks,
     normalize_resize_args,
     normalize_shape,
     normalize_storage_path,
-    PartialReadBuffer,
-    UncompressedPartialReadBufferV3,
-    ensure_ndarray_like,
 )
 
 __all__ = ["Array"]

zarr/creation.py

@@ -1,13 +1,13 @@
 from collections.abc import MutableMapping
-from typing import Optional, Tuple, Union, Sequence
+from typing import Optional, Sequence, Tuple, Union
 from warnings import warn
 
 import numpy as np
 import numpy.typing as npt
 from numcodecs.abc import Codec
 from numcodecs.registry import codec_registry
 
-from zarr._storage.store import DEFAULT_ZARR_VERSION
+from zarr._storage.store import DEFAULT_ZARR_VERSION, StorageTransformer
 from zarr.core import Array
 from zarr.errors import (
     ArrayNotFoundError,
@@ -22,9 +22,8 @@
     normalize_storage_path,
     normalize_store_arg,
 )
-from zarr._storage.store import StorageTransformer
 from zarr.sync import Synchronizer
-from zarr.types import ZARR_VERSION, DIMENSION_SEPARATOR, MEMORY_ORDER, MetaArray, PathLike
+from zarr.types import DIMENSION_SEPARATOR, MEMORY_ORDER, ZARR_VERSION, MetaArray, PathLike
 from zarr.util import normalize_dimension_separator
 
 

zarr/hierarchy.py

@@ -4,12 +4,13 @@
 import numpy as np
 
 from zarr._storage.store import (
+    DEFAULT_ZARR_VERSION,
     _get_metadata_suffix,
+    assert_zarr_v3_api_available,
     data_root,
     meta_root,
-    DEFAULT_ZARR_VERSION,
-    assert_zarr_v3_api_available,
 )
+from zarr._storage.v3 import MemoryStoreV3
 from zarr.attrs import Attributes
 from zarr.core import Array
 from zarr.creation import (
@@ -25,17 +26,17 @@
     zeros_like,
 )
 from zarr.errors import (
+    ArrayNotFoundError,
     ContainsArrayError,
     ContainsGroupError,
-    ArrayNotFoundError,
     GroupNotFoundError,
     ReadOnlyError,
 )
 from zarr.storage import (
-    _get_hierarchy_metadata,
-    _prefix_to_group_key,
     BaseStore,
     MemoryStore,
+    _get_hierarchy_metadata,
+    _prefix_to_group_key,
     attrs_key,
     contains_array,
     contains_group,
@@ -46,7 +47,6 @@
     rename,
     rmdir,
 )
-from zarr._storage.v3 import MemoryStoreV3
 from zarr.util import (
     InfoReporter,
     TreeViewer,

zarr/indexing.py

@@ -5,13 +5,12 @@
 
 import numpy as np
 
-
 from zarr.errors import (
     ArrayIndexError,
+    BoundsCheckError,
     NegativeStepError,
-    err_too_many_indices,
     VindexInvalidSelectionError,
-    BoundsCheckError,
+    err_too_many_indices,
 )
 
 

zarr/meta.py

@@ -1,6 +1,8 @@
 import base64
 import itertools
 from collections.abc import Mapping
+from typing import TYPE_CHECKING, Any, List, Optional, Union, cast
+from typing import Mapping as MappingType
 
 import numcodecs
 import numpy as np
@@ -9,8 +11,6 @@
 from zarr.errors import MetadataError
 from zarr.util import json_dumps, json_loads
 
-from typing import cast, Union, Any, List, Mapping as MappingType, Optional, TYPE_CHECKING
-
 if TYPE_CHECKING:  # pragma: no cover
     from zarr._storage.store import StorageTransformer
 
@@ -458,8 +458,8 @@ def _encode_storage_transformer_metadata(
 
     @classmethod
     def _decode_storage_transformer_metadata(cls, meta: Mapping) -> "StorageTransformer":
-        from zarr.tests.test_storage_v3 import DummyStorageTransfomer
         from zarr._storage.v3_storage_transformers import ShardingStorageTransformer
+        from zarr.tests.test_storage_v3 import DummyStorageTransfomer
 
         # This might be changed to a proper registry in the future
         KNOWN_STORAGE_TRANSFORMERS = [DummyStorageTransfomer, ShardingStorageTransformer]

zarr/n5.py

@@ -4,17 +4,16 @@
 import os
 import struct
 import sys
-from typing import Any, Dict, Optional, cast
 import warnings
+from typing import Any, Dict, Optional, cast
 
 import numpy as np
 from numcodecs.abc import Codec
 from numcodecs.compat import ndarray_copy
 from numcodecs.registry import get_codec, register_codec
 
 from .meta import ZARR_FORMAT, json_dumps, json_loads
-from .storage import FSStore
-from .storage import NestedDirectoryStore, _prog_ckey, _prog_number, normalize_storage_path
+from .storage import FSStore, NestedDirectoryStore, _prog_ckey, _prog_number, normalize_storage_path
 from .storage import array_meta_key as zarr_array_meta_key
 from .storage import attrs_key as zarr_attrs_key
 from .storage import group_meta_key as zarr_group_meta_key