Merge branch 'main' into feat/default-buffer

Author: d-v-b

.github/workflows/check_changelogs.yml

@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@681c641aba71e4a1c380be3ab5e12ad51f415867 # v7.1.6
+        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0
 
       - name: Check changelog entries
         run: uv run --no-sync python ci/check_changelog_entries.py

changes/3648.misc.md

@@ -0,0 +1 @@
+Fix deprecation of setting a shape on an array directly in ``numpy`` 2.5+.

src/zarr/_compat.py

@@ -2,10 +2,16 @@
 from collections.abc import Callable
 from functools import wraps
 from inspect import Parameter, signature
-from typing import Any, TypeVar
+from typing import TYPE_CHECKING, Any, TypeVar
+
+import numpy as np
+from packaging.version import Version
 
 from zarr.errors import ZarrFutureWarning
 
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+
 T = TypeVar("T")
 
 # Based off https://github.com/scikit-learn/scikit-learn/blob/e87b32a81c70abed8f2e97483758eb64df8255e9/sklearn/utils/validation.py#L63
@@ -68,3 +74,37 @@ def inner_f(*args: Any, **kwargs: Any) -> T:
         return _inner_deprecate_positional_args(func)
 
     return _inner_deprecate_positional_args  # type: ignore[return-value]
+
+
+def _reshape_view(arr: "NDArray[Any]", shape: tuple[int, ...]) -> "NDArray[Any]":
+    """Reshape an array without copying data.
+
+    This function provides compatibility across NumPy versions for reshaping arrays
+    as views. On NumPy >= 2.1, it uses ``reshape(copy=False)`` which explicitly
+    fails if a view cannot be created. On older versions, it uses direct shape
+    assignment which has the same behavior but is deprecated in 2.5+.
+
+    Parameters
+    ----------
+    arr : NDArray
+        The array to reshape.
+    shape : tuple of int
+        The new shape.
+
+    Returns
+    -------
+    NDArray
+        A reshaped view of the array.
+
+    Raises
+    ------
+    AttributeError
+        If a view cannot be created (the array is not contiguous) on NumPy < 2.1.
+    ValueError
+        If a view cannot be created (the array is not contiguous) on NumPy >= 2.1.
+    """
+    if Version(np.__version__) >= Version("2.1"):
+        return arr.reshape(shape, copy=False)  # type: ignore[call-overload, no-any-return]
+    else:
+        arr.shape = shape
+        return arr

src/zarr/codecs/vlen_utf8.py

@@ -6,6 +6,7 @@
 import numpy as np
 from numcodecs.vlen import VLenBytes, VLenUTF8
 
+from zarr._compat import _reshape_view
 from zarr.abc.codec import ArrayBytesCodec
 from zarr.core.buffer import Buffer, NDBuffer
 from zarr.core.common import JSON, parse_named_configuration
@@ -50,7 +51,7 @@ async def _decode_single(
         raw_bytes = chunk_bytes.as_array_like()
         decoded = _vlen_utf8_codec.decode(raw_bytes)
         assert decoded.dtype == np.object_
-        decoded.shape = chunk_spec.shape
+        decoded = _reshape_view(decoded, chunk_spec.shape)
         as_string_dtype = decoded.astype(chunk_spec.dtype.to_native_dtype(), copy=False)
         return chunk_spec.prototype.nd_buffer.from_numpy_array(as_string_dtype)
 
@@ -95,7 +96,7 @@ async def _decode_single(
         raw_bytes = chunk_bytes.as_array_like()
         decoded = _vlen_bytes_codec.decode(raw_bytes)
         assert decoded.dtype == np.object_
-        decoded.shape = chunk_spec.shape
+        decoded = _reshape_view(decoded, chunk_spec.shape)
         return chunk_spec.prototype.nd_buffer.from_numpy_array(decoded)
 
     async def _encode_single(