Merge branch 'main' into fix/unbreak-chunks-initialized

Author: d-v-b

.pre-commit-config.yaml

@@ -37,6 +37,7 @@ repos:
           - obstore>=0.5.1
           # Tests
           - pytest
+          - hypothesis
   - repo: https://github.com/scientific-python/cookie
     rev: 2025.01.22
     hooks:

changes/2950.bufgix.rst

@@ -0,0 +1 @@
+Specifying the memory order of Zarr format 2 arrays using the ``order`` keyword argument has been fixed.

changes/2962.fix.rst

@@ -0,0 +1 @@
+Internally use `typesize` constructor parameter for :class:`numcodecs.blosc.Blosc` to improve compression ratios back to the v2-package levels.

changes/2978.bugfix.rst

@@ -0,0 +1 @@
+Fixed sharding with GPU buffers.

changes/2998.bugfix.md

@@ -0,0 +1 @@
+Fix structured `dtype` fill value serialization for consolidated metadata

changes/3027.misc.rst

@@ -0,0 +1 @@
+Simplified scalar indexing of size-1 arrays.

changes/3045.bugfix.rst

@@ -0,0 +1 @@
+Fixed the typing of ``dimension_names`` arguments throughout so that it now accepts iterables that contain `None` alongside `str`.

docs/user-guide/arrays.rst

@@ -209,8 +209,8 @@ prints additional diagnostics, e.g.::
    Serializer         : BytesCodec(endian=<Endian.little: 'little'>)
    Compressors        : (BloscCodec(typesize=4, cname=<BloscCname.zstd: 'zstd'>, clevel=3, shuffle=<BloscShuffle.bitshuffle: 'bitshuffle'>, blocksize=0),)
    No. bytes          : 400000000 (381.5M)
-   No. bytes stored   : 9696520
-   Storage ratio      : 41.3
+   No. bytes stored   : 3558573
+   Storage ratio      : 112.4
    Chunks Initialized : 100
 
 .. note::

pyproject.toml

@@ -83,7 +83,7 @@ test = [
 remote_tests = [
     'zarr[remote]',
     "botocore",
-    "s3fs",
+    "s3fs>=2023.10.0",
     "moto[s3,server]",
     "requests",
 ]
@@ -104,7 +104,7 @@ docs = [
     # Optional dependencies to run examples
     'numcodecs[msgpack]',
     'rich',
-    's3fs',
+    's3fs>=2023.10.0',
     'astroid<4'
 ]
 
@@ -348,27 +348,27 @@ python_version = "3.11"
 ignore_missing_imports = true
 namespace_packages = false
 
-
 strict = true
 warn_unreachable = true
-
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 
+
 [[tool.mypy.overrides]]
 module = [
-    "zarr.v2.*",
+    "tests.package_with_entrypoint.*",
+    "zarr.testing.stateful",
+    "tests.test_codecs.test_transpose",
+    "tests.test_config"
 ]
-ignore_errors = true
+strict = false
 
+# TODO: Move the next modules up to the strict = false section
+# and fix the errors
 [[tool.mypy.overrides]]
 module = [
-    "zarr.testing.stateful",  # lots of hypothesis decorator errors
-    "tests.package_with_entrypoint.*",
     "tests.test_codecs.test_codecs",
-    "tests.test_codecs.test_transpose",
     "tests.test_metadata.*",
     "tests.test_store.*",
-    "tests.test_config",
     "tests.test_group",
     "tests.test_indexing",
     "tests.test_properties",

src/zarr/api/asynchronous.py

@@ -16,6 +16,7 @@
     JSON,
     AccessModeLiteral,
     ChunkCoords,
+    DimensionNames,
     MemoryOrder,
     ZarrFormat,
     _default_zarr_format,
@@ -865,7 +866,7 @@ async def create(
         | None
     ) = None,
     codecs: Iterable[Codec | dict[str, JSON]] | None = None,
-    dimension_names: Iterable[str] | None = None,
+    dimension_names: DimensionNames = None,
     storage_options: dict[str, Any] | None = None,
     config: ArrayConfigLike | None = None,
     **kwargs: Any,
@@ -1040,15 +1041,13 @@ async def create(
             )
             warnings.warn(UserWarning(msg), stacklevel=1)
         config_dict["write_empty_chunks"] = write_empty_chunks
-    if order is not None:
-        if config is not None:
-            msg = (
-                "Both order and config keyword arguments are set. "
-                "This is redundant. When both are set, order will be ignored and "
-                "config will be used."
-            )
-            warnings.warn(UserWarning(msg), stacklevel=1)
-        config_dict["order"] = order
+    if order is not None and config is not None:
+        msg = (
+            "Both order and config keyword arguments are set. "
+            "This is redundant. When both are set, order will be ignored and "
+            "config will be used."
+        )
+        warnings.warn(UserWarning(msg), stacklevel=1)
 
     config_parsed = ArrayConfig.from_dict(config_dict)
 
@@ -1062,6 +1061,7 @@ async def create(
         overwrite=overwrite,
         filters=filters,
         dimension_separator=dimension_separator,
+        order=order,
         zarr_format=zarr_format,
         chunk_shape=chunk_shape,
         chunk_key_encoding=chunk_key_encoding,