Merge branch 'main' into fix-obstore-listdir

Author: d-v-b

changes/3700.bugfix.md

@@ -0,0 +1 @@
+CacheStore, LoggingStore and LatencyStore now support with_read_only.

changes/3705.bugfix.md

@@ -0,0 +1 @@
+Fix a performance bug in morton curve generation.

changes/3706.misc.md

@@ -0,0 +1 @@
+Allow NumPy ints as input when declaring a shape.

src/zarr/core/common.py

@@ -21,6 +21,7 @@
     overload,
 )
 
+import numpy as np
 from typing_extensions import ReadOnly
 
 from zarr.core.config import config as zarr_config
@@ -37,7 +38,7 @@
 ZMETADATA_V2_JSON = ".zmetadata"
 
 BytesLike = bytes | bytearray | memoryview
-ShapeLike = Iterable[int] | int
+ShapeLike = Iterable[int | np.integer[Any]] | int | np.integer[Any]
 # For backwards compatibility
 ChunkCoords = tuple[int, ...]
 ZarrFormat = Literal[2, 3]
@@ -185,23 +186,28 @@ def parse_named_configuration(
 
 
 def parse_shapelike(data: ShapeLike) -> tuple[int, ...]:
-    if isinstance(data, int):
+    """
+    Parse a shape-like input into an explicit shape.
+    """
+    if isinstance(data, int | np.integer):
         if data < 0:
             raise ValueError(f"Expected a non-negative integer. Got {data} instead")
-        return (data,)
+        return (int(data),)
     try:
         data_tuple = tuple(data)
     except TypeError as e:
         msg = f"Expected an integer or an iterable of integers. Got {data} instead."
         raise TypeError(msg) from e
 
-    if not all(isinstance(v, int) for v in data_tuple):
+    if not all(isinstance(v, int | np.integer) for v in data_tuple):
         msg = f"Expected an iterable of integers. Got {data} instead."
         raise TypeError(msg)
     if not all(v > -1 for v in data_tuple):
         msg = f"Expected all values to be non-negative. Got {data} instead."
         raise ValueError(msg)
-    return data_tuple
+
+    # cast NumPy scalars to plain python ints
+    return tuple(int(x) for x in data_tuple)
 
 
 def parse_fill_value(data: Any) -> Any:

src/zarr/core/indexing.py

@@ -7,7 +7,7 @@
 from collections.abc import Iterator, Sequence
 from dataclasses import dataclass
 from enum import Enum
-from functools import reduce
+from functools import lru_cache, reduce
 from types import EllipsisType
 from typing import (
     TYPE_CHECKING,
@@ -1467,16 +1467,21 @@ def decode_morton(z: int, chunk_shape: tuple[int, ...]) -> tuple[int, ...]:
     return tuple(out)
 
 
-def morton_order_iter(chunk_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]:
-    i = 0
+@lru_cache
+def _morton_order(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]:
+    n_total = product(chunk_shape)
     order: list[tuple[int, ...]] = []
-    while len(order) < product(chunk_shape):
+    i = 0
+    while len(order) < n_total:
         m = decode_morton(i, chunk_shape)
-        if m not in order and all(x < y for x, y in zip(m, chunk_shape, strict=False)):
+        if all(x < y for x, y in zip(m, chunk_shape, strict=False)):
             order.append(m)
         i += 1
-    for j in range(product(chunk_shape)):
-        yield order[j]
+    return tuple(order)
+
+
+def morton_order_iter(chunk_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]:
+    return iter(_morton_order(tuple(chunk_shape)))
 
 
 def c_order_iter(chunks_per_shard: tuple[int, ...]) -> Iterator[tuple[int, ...]]: