fix(array): thread order parameter through to Array.__init__ (#2417)

Author: jhamman

src/zarr/api/asynchronous.py

@@ -712,7 +712,7 @@ async def create(
     dtype: npt.DTypeLike | None = None,
     compressor: dict[str, JSON] | None = None,  # TODO: default and type change
     fill_value: Any | None = 0,  # TODO: need type
-    order: MemoryOrder | None = None,  # TODO: default change
+    order: MemoryOrder | None = None,
     store: str | StoreLike | None = None,
     synchronizer: Any | None = None,
     overwrite: bool = False,
@@ -761,6 +761,7 @@ async def create(
         Default value to use for uninitialized portions of the array.
     order : {'C', 'F'}, optional
         Memory layout to be used within each chunk.
+        Default is set in Zarr's config (`array.order`).
     store : Store or str
         Store or path to directory in file system or name of zip file.
     synchronizer : object, optional
@@ -834,12 +835,6 @@ async def create(
         else:
             chunk_shape = shape
 
-    if order is not None:
-        warnings.warn(
-            "order is deprecated, use config `array.order` instead",
-            DeprecationWarning,
-            stacklevel=2,
-        )
     if synchronizer is not None:
         warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2)
     if chunk_store is not None:
@@ -889,6 +884,7 @@ async def create(
         codecs=codecs,
         dimension_names=dimension_names,
         attributes=attributes,
+        order=order,
         **kwargs,
     )
 

src/zarr/core/array.py

@@ -33,6 +33,7 @@
     ZARRAY_JSON,
     ZATTRS_JSON,
     ChunkCoords,
+    MemoryOrder,
     ShapeLike,
     ZarrFormat,
     concurrent_map,
@@ -203,29 +204,29 @@ class AsyncArray(Generic[T_ArrayMetadata]):
     metadata: T_ArrayMetadata
     store_path: StorePath
     codec_pipeline: CodecPipeline = field(init=False)
-    order: Literal["C", "F"]
+    order: MemoryOrder
 
     @overload
     def __init__(
         self: AsyncArray[ArrayV2Metadata],
         metadata: ArrayV2Metadata | ArrayV2MetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None: ...
 
     @overload
     def __init__(
         self: AsyncArray[ArrayV3Metadata],
         metadata: ArrayV3Metadata | ArrayV3MetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None: ...
 
     def __init__(
         self,
         metadata: ArrayMetadata | ArrayMetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None:
         if isinstance(metadata, dict):
             zarr_format = metadata["zarr_format"]
@@ -261,7 +262,7 @@ async def create(
         attributes: dict[str, JSON] | None = None,
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -350,7 +351,7 @@ async def create(
         # v2 only
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -382,7 +383,7 @@ async def create(
         # v2 only
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -422,7 +423,6 @@ async def create(
             V2 only. V3 arrays cannot have a dimension separator.
         order : Literal["C", "F"], optional
             The order of the array (default is None).
-            V2 only. V3 arrays should not have 'order' parameter.
         filters : list[dict[str, JSON]], optional
             The filters used to compress the data (default is None).
             V2 only. V3 arrays should not have 'filters' parameter.
@@ -471,10 +471,6 @@ async def create(
                 raise ValueError(
                     "dimension_separator cannot be used for arrays with version 3. Use chunk_key_encoding instead."
                 )
-            if order is not None:
-                raise ValueError(
-                    "order cannot be used for arrays with version 3. Use a transpose codec instead."
-                )
             if filters is not None:
                 raise ValueError(
                     "filters cannot be used for arrays with version 3. Use array-to-array codecs instead."
@@ -494,6 +490,7 @@ async def create(
                 dimension_names=dimension_names,
                 attributes=attributes,
                 exists_ok=exists_ok,
+                order=order,
             )
         elif zarr_format == 2:
             if dtype is str or dtype == "str":
@@ -545,6 +542,7 @@ async def _create_v3(
         dtype: npt.DTypeLike,
         chunk_shape: ChunkCoords,
         fill_value: Any | None = None,
+        order: MemoryOrder | None = None,
         chunk_key_encoding: (
             ChunkKeyEncoding
             | tuple[Literal["default"], Literal[".", "/"]]
@@ -588,7 +586,7 @@ async def _create_v3(
             attributes=attributes or {},
         )
 
-        array = cls(metadata=metadata, store_path=store_path)
+        array = cls(metadata=metadata, store_path=store_path, order=order)
         await array._save_metadata(metadata, ensure_parents=True)
         return array
 
@@ -602,16 +600,17 @@ async def _create_v2(
         chunks: ChunkCoords,
         dimension_separator: Literal[".", "/"] | None = None,
         fill_value: None | float = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         attributes: dict[str, JSON] | None = None,
         exists_ok: bool = False,
     ) -> AsyncArray[ArrayV2Metadata]:
         if not exists_ok:
             await ensure_no_existing_node(store_path, zarr_format=2)
+
         if order is None:
-            order = "C"
+            order = parse_indexing_order(config.get("array.order"))
 
         if dimension_separator is None:
             dimension_separator = "."
@@ -627,7 +626,7 @@ async def _create_v2(
             filters=filters,
             attributes=attributes,
         )
-        array = cls(metadata=metadata, store_path=store_path)
+        array = cls(metadata=metadata, store_path=store_path, order=order)
         await array._save_metadata(metadata, ensure_parents=True)
         return array
 
@@ -1179,7 +1178,7 @@ def create(
         # v2 only
         chunks: ChunkCoords | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -1370,7 +1369,7 @@ def store_path(self) -> StorePath:
         return self._async_array.store_path
 
     @property
-    def order(self) -> Literal["C", "F"]:
+    def order(self) -> MemoryOrder:
         return self._async_array.order
 
     @property

src/zarr/core/array_spec.py

@@ -1,11 +1,11 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 
-from zarr.core.common import parse_fill_value, parse_order, parse_shapelike
+from zarr.core.common import MemoryOrder, parse_fill_value, parse_order, parse_shapelike
 
 if TYPE_CHECKING:
     from zarr.core.buffer import BufferPrototype
@@ -17,15 +17,15 @@ class ArraySpec:
     shape: ChunkCoords
     dtype: np.dtype[Any]
     fill_value: Any
-    order: Literal["C", "F"]
+    order: MemoryOrder
     prototype: BufferPrototype
 
     def __init__(
         self,
         shape: ChunkCoords,
         dtype: np.dtype[Any],
         fill_value: Any,
-        order: Literal["C", "F"],
+        order: MemoryOrder,
         prototype: BufferPrototype,
     ) -> None:
         shape_parsed = parse_shapelike(shape)

src/zarr/core/metadata/v2.py

@@ -25,7 +25,7 @@
 from zarr.core.array_spec import ArraySpec
 from zarr.core.chunk_grids import RegularChunkGrid
 from zarr.core.chunk_key_encodings import parse_separator
-from zarr.core.common import ZARRAY_JSON, ZATTRS_JSON, parse_shapelike
+from zarr.core.common import ZARRAY_JSON, ZATTRS_JSON, MemoryOrder, parse_shapelike
 from zarr.core.config import config, parse_indexing_order
 from zarr.core.metadata.common import parse_attributes
 
@@ -45,7 +45,7 @@ class ArrayV2Metadata(Metadata):
     chunks: tuple[int, ...]
     dtype: np.dtype[Any]
     fill_value: None | int | float | str | bytes = 0
-    order: Literal["C", "F"] = "C"
+    order: MemoryOrder = "C"
     filters: tuple[numcodecs.abc.Codec, ...] | None = None
     dimension_separator: Literal[".", "/"] = "."
     compressor: numcodecs.abc.Codec | None = None
@@ -59,7 +59,7 @@ def __init__(
         dtype: npt.DTypeLike,
         chunks: ChunkCoords,
         fill_value: Any,
-        order: Literal["C", "F"],
+        order: MemoryOrder,
         dimension_separator: Literal[".", "/"] = ".",
         compressor: numcodecs.abc.Codec | dict[str, JSON] | None = None,
         filters: Iterable[numcodecs.abc.Codec | dict[str, JSON]] | None = None,
@@ -185,7 +185,7 @@ def to_dict(self) -> dict[str, JSON]:
         return zarray_dict
 
     def get_chunk_spec(
-        self, _chunk_coords: ChunkCoords, order: Literal["C", "F"], prototype: BufferPrototype
+        self, _chunk_coords: ChunkCoords, order: MemoryOrder, prototype: BufferPrototype
     ) -> ArraySpec:
         return ArraySpec(
             shape=self.chunks,

src/zarr/core/metadata/v3.py

@@ -31,6 +31,7 @@
     JSON,
     ZARR_JSON,
     ChunkCoords,
+    MemoryOrder,
     parse_named_configuration,
     parse_shapelike,
 )
@@ -289,7 +290,7 @@ def ndim(self) -> int:
         return len(self.shape)
 
     def get_chunk_spec(
-        self, _chunk_coords: ChunkCoords, order: Literal["C", "F"], prototype: BufferPrototype
+        self, _chunk_coords: ChunkCoords, order: MemoryOrder, prototype: BufferPrototype
     ) -> ArraySpec:
         assert isinstance(
             self.chunk_grid, RegularChunkGrid

tests/test_api.py

@@ -21,7 +21,7 @@
     save_array,
     save_group,
 )
-from zarr.core.common import ZarrFormat
+from zarr.core.common import MemoryOrder, ZarrFormat
 from zarr.errors import MetadataValidationError
 from zarr.storage._utils import normalize_path
 from zarr.storage.memory import MemoryStore
@@ -206,6 +206,22 @@ def test_open_with_mode_w_minus(tmp_path: pathlib.Path) -> None:
         zarr.open(store=tmp_path, mode="w-")
 
 
+@pytest.mark.parametrize("order", ["C", "F", None])
+@pytest.mark.parametrize("zarr_format", [2, 3])
+def test_array_order(order: MemoryOrder | None, zarr_format: ZarrFormat) -> None:
+    arr = zarr.ones(shape=(2, 2), order=order, zarr_format=zarr_format)
+    expected = order or zarr.config.get("array.order")
+    assert arr.order == expected
+
+    vals = np.asarray(arr)
+    if expected == "C":
+        assert vals.flags.c_contiguous
+    elif expected == "F":
+        assert vals.flags.f_contiguous
+    else:
+        raise AssertionError
+
+
 # def test_lazy_loader():
 #     foo = np.arange(100)
 #     bar = np.arange(100, 0, -1)

tests/test_array.py

@@ -10,7 +10,7 @@
 from zarr.codecs import BytesCodec, VLenBytesCodec
 from zarr.core.array import chunks_initialized
 from zarr.core.buffer.cpu import NDBuffer
-from zarr.core.common import JSON, ZarrFormat
+from zarr.core.common import JSON, MemoryOrder, ZarrFormat
 from zarr.core.group import AsyncGroup
 from zarr.core.indexing import ceildiv
 from zarr.core.sync import sync
@@ -417,3 +417,22 @@ def test_update_attrs(zarr_format: int) -> None:
 
     arr2 = zarr.open_array(store=store, zarr_format=zarr_format)
     assert arr2.attrs["foo"] == "bar"
+
+
+@pytest.mark.parametrize("order", ["C", "F", None])
+@pytest.mark.parametrize("zarr_format", [2, 3])
+@pytest.mark.parametrize("store", ["memory"], indirect=True)
+def test_array_create_order(
+    order: MemoryOrder | None, zarr_format: int, store: MemoryStore
+) -> None:
+    arr = Array.create(store=store, shape=(2, 2), order=order, zarr_format=zarr_format, dtype="i4")
+    expected = order or zarr.config.get("array.order")
+    assert arr.order == expected
+
+    vals = np.asarray(arr)
+    if expected == "C":
+        assert vals.flags.c_contiguous
+    elif expected == "F":
+        assert vals.flags.f_contiguous
+    else:
+        raise AssertionError