keep up with mainline

Author: d-v-b

zarr/storage.py

@@ -60,6 +60,7 @@
     normalize_shape,
     normalize_storage_path,
     retry_call,
+    ensure_contiguous_ndarray_or_bytes,
 )
 
 from zarr._storage.absstore import ABSStore  # noqa: F401
@@ -1422,13 +1423,19 @@ def __getitem__(self, key):
     def setitems(self, values):
         if self.mode == "r":
             raise ReadOnlyError()
-        values = {self._normalize_key(key): val for key, val in values.items()}
+
+        # Normalize keys and make sure the values are bytes
+        values = {
+            self._normalize_key(key): ensure_contiguous_ndarray_or_bytes(val)
+            for key, val in values.items()
+        }
         self.map.setitems(values)
 
     def __setitem__(self, key, value):
         if self.mode == "r":
             raise ReadOnlyError()
         key = self._normalize_key(key)
+        value = ensure_contiguous_ndarray_or_bytes(value)
         path = self.dir_path(key)
         try:
             if self.fs.isdir(path):

zarr/tests/test_core.py

@@ -31,6 +31,7 @@
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 from pkg_resources import parse_version
 
+import zarr
 from zarr._storage.store import (
     BaseStore,
     v3_api_available,
@@ -3046,3 +3047,25 @@ def test_array_mismatched_store_versions():
         Array(store_v3, path="dataset", read_only=False, chunk_store=chunk_store_v2)
     with pytest.raises(ValueError):
         Array(store_v2, path="dataset", read_only=False, chunk_store=chunk_store_v3)
+
+
+@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
+def test_issue_1279(tmpdir):
+    """See <https://github.com/zarr-developers/zarr-python/issues/1279>"""
+
+    data = np.arange(25).reshape((5, 5))
+    ds = zarr.create(
+        shape=data.shape,
+        chunks=(5, 5),
+        dtype=data.dtype,
+        compressor=(None),
+        store=FSStore(url=str(tmpdir), mode="a"),
+        order="F",
+    )
+
+    ds[:] = data
+
+    ds_reopened = zarr.open_array(store=FSStore(url=str(tmpdir), mode="r"))
+
+    written_data = ds_reopened[:]
+    assert_array_equal(data, written_data)

zarr/util.py

@@ -5,17 +5,22 @@
 from textwrap import TextWrapper
 import mmap
 import time
+from typing import Any, Callable, Dict, Optional, Tuple, Union
 
 import numpy as np
 from asciitree import BoxStyle, LeftAligned
 from asciitree.traversal import Traversal
 from collections.abc import Iterable
-from numcodecs.compat import ensure_text, ensure_ndarray_like
+from numcodecs.compat import (
+    ensure_text,
+    ensure_ndarray_like,
+    ensure_bytes,
+    ensure_contiguous_ndarray_like,
+)
+from numcodecs.ndarray_like import NDArrayLike
 from numcodecs.registry import codec_registry
 from numcodecs.blosc import cbuffer_sizes, cbuffer_metainfo
 
-from typing import Any, Callable, Dict, Optional, Tuple, Union
-
 
 def flatten(arg: Iterable) -> Iterable:
     for element in arg:
@@ -690,3 +695,28 @@ def all_equal(value: Any, array: Any):
             # using == raises warnings from numpy deprecated pattern, but
             # using np.equal() raises type errors for structured dtypes...
             return np.all(value == array)
+
+
+def ensure_contiguous_ndarray_or_bytes(buf) -> Union[NDArrayLike, bytes]:
+    """Convenience function to coerce `buf` to ndarray-like array or bytes.
+
+    First check if `buf` can be zero-copy converted to a contiguous array.
+    If not, `buf` will be copied to a newly allocated `bytes` object.
+
+    Parameters
+    ----------
+    buf : ndarray-like, array-like, or bytes-like
+        A numpy array like object such as numpy.ndarray, cupy.ndarray, or
+        any object exporting a buffer interface.
+
+    Returns
+    -------
+    arr : NDArrayLike or bytes
+        A ndarray-like or bytes object
+    """
+
+    try:
+        return ensure_contiguous_ndarray_like(buf)
+    except TypeError:
+        # An error is raised if `buf` couldn't be zero-copy converted
+        return ensure_bytes(buf)