fix: preserve rectilinear grids in from_array

Author: CAOShurong

src/zarr/core/array.py

@@ -101,7 +101,6 @@
     Selection,
     VIndex,
     _iter_grid,
-    _iter_regions,
     check_fields,
     check_no_multi_fields,
     is_pure_fancy_indexing,
@@ -126,6 +125,7 @@
 )
 from zarr.core.metadata.v3 import (
     ChunkGridMetadata,
+    RegularChunkGridMetadata,
     create_chunk_grid_metadata,
     parse_node_type_array,
 )
@@ -4814,13 +4814,24 @@ def _parse_keep_array_attr(
     dict[str, JSON] | None,
 ]:
     if isinstance(data, Array):
+        # ``ChunkGrid.from_metadata`` represents rectilinear dimensions with
+        # uniform edges as ``FixedDimension``. Consequently,
+        # ``data._chunk_grid.is_regular`` does not preserve the grid kind
+        # recorded in v3 metadata, which is what ``chunks='keep'`` must copy.
+        if isinstance(data.metadata, ArrayV3Metadata):
+            metadata_has_regular_grid = isinstance(
+                data.metadata.chunk_grid, RegularChunkGridMetadata
+            )
+        else:
+            # Zarr format 2 always has a regular chunk grid.
+            metadata_has_regular_grid = True
         if chunks == "keep":
-            if data._chunk_grid.is_regular:
+            if metadata_has_regular_grid:
                 chunks = data.chunks
             else:
                 chunks = data.write_chunk_sizes
         if shards == "keep":
-            shards = data.shards if data._chunk_grid.is_regular else None
+            shards = data.shards if metadata_has_regular_grid else None
         if zarr_format is None:
             zarr_format = data.metadata.zarr_format
         if filters == "keep":
@@ -5293,13 +5304,12 @@ def _iter_shard_regions(
         A tuple of slice objects representing the region spanned by each shard in the selection or chunk
         when no shards are present.
     """
-    if array.shards is None:
-        shard_shape = array.chunks
-    else:
-        shard_shape = array.shards
-
-    return _iter_regions(
-        array.shape, shard_shape, origin=origin, selection_shape=selection_shape, trim_excess=True
+    # The array's metadata grid describes the outer storage layout in both
+    # sharded and non-sharded arrays. Using it directly supports rectilinear
+    # grids, for which ``chunks`` and ``shards`` are intentionally undefined.
+    return array._chunk_grid.iter_chunk_regions(
+        origin=origin,
+        selection_shape=selection_shape,
     )
 
 

tests/test_array.py

@@ -7,6 +7,7 @@
 import re
 import sys
 from itertools import accumulate, starmap
+from pathlib import Path
 from typing import TYPE_CHECKING, Any, Literal
 from unittest import mock
 
@@ -72,6 +73,7 @@
 from zarr.core.group import AsyncGroup
 from zarr.core.indexing import BasicIndexer, _iter_grid, _iter_regions
 from zarr.core.metadata.v2 import ArrayV2Metadata
+from zarr.core.metadata.v3 import RectilinearChunkGridMetadata
 from zarr.core.sync import sync
 from zarr.errors import (
     ContainsArrayError,
@@ -1889,6 +1891,35 @@ def test_from_array_arraylike_gains_no_attributes() -> None:
     assert result.fill_value == 0
 
 
+@pytest.mark.parametrize("store_type", ["memory", "local"])
+def test_from_array_keeps_uniform_rectilinear_grid(
+    store_type: Literal["memory", "local"], tmp_path: Path
+) -> None:
+    """``chunks='keep'`` uses the stored v3 grid kind, not its runtime shape."""
+    with zarr.config.set({"array.rectilinear_chunks": True}):
+        if store_type == "memory":
+            source_store: MemoryStore | LocalStore = MemoryStore()
+            destination_store: MemoryStore | LocalStore = MemoryStore()
+        else:
+            source_store = LocalStore(tmp_path / "source.zarr")
+            destination_store = LocalStore(tmp_path / "destination.zarr")
+
+        source = zarr.create_array(
+            store=source_store,
+            shape=(24,),
+            chunks=[[10, 10, 4]],
+            dtype="i4",
+            zarr_format=3,
+        )
+        source[:] = np.arange(24, dtype="i4")
+
+        result = zarr.from_array(store=destination_store, data=source)
+
+    assert isinstance(result.metadata.chunk_grid, RectilinearChunkGridMetadata)
+    assert result.write_chunk_sizes == ((10, 10, 4),)
+    np.testing.assert_array_equal(result[:], source[:])
+
+
 def test_from_array_F_order() -> None:
     arr = zarr.create_array(store={}, data=np.array([1]), order="F", zarr_format=2)
     with pytest.warns(