fix: keep fill value and attributes in from_array (#4288)

`from_array` discards both `fill_value` and `attributes`.

An explicit `fill_value=None` now means the dtype's default scalar (v3) or a
null fill value (v2), consistent with `create_array`, and an empty
`attributes` dict opts out of copying the source's attributes.

Fixes #4287

Author: paraseba

changes/4288.bugfix.md

@@ -0,0 +1,3 @@
+`zarr.from_array` now defaults to the fill value and the attributes of the source array. Previously both were silently discarded: the array was created with the data type's default scalar and no attributes.
+
+An explicit `fill_value=None` now selects the data type's default scalar (Zarr format 3) or a null fill value (Zarr format 2), consistently with `create_array`, and an empty `attributes` dict creates the array with no attributes.

src/zarr/api/synchronous.py

@@ -1105,6 +1105,8 @@ def from_array(
     fill_value : Any, optional
         Fill value for the array.
         If not specified, defaults to the fill value of the data array.
+        Pass `None` explicitly to use the default scalar of the data type
+        (Zarr format 3) or a null fill value (Zarr format 2) instead.
     order : {"C", "F"}, optional
         The memory order of the array (default is "C").
         For Zarr format 2, this parameter sets the memory order of the array.
@@ -1118,6 +1120,7 @@ def from_array(
     attributes : dict, optional
         Attributes for the array.
         If not specified, defaults to the attributes of the data array.
+        Pass an empty dict to create the array with no attributes.
     chunk_key_encoding : ChunkKeyEncoding, optional
         A specification of how the chunk keys are represented in storage.
         For Zarr format 3, the default is `{"name": "default", "separator": "/"}}`.

src/zarr/core/array.py

@@ -4179,6 +4179,8 @@ async def from_array(
     fill_value : Any, optional
         Fill value for the array.
         If not specified, defaults to the fill value of the data array.
+        Pass `None` explicitly to use the default scalar of the data type
+        (Zarr format 3) or a null fill value (Zarr format 2) instead.
     order : {"C", "F"}, optional
         The memory order of the array (default is "C").
         For Zarr format 2, this parameter sets the memory order of the array.
@@ -4192,6 +4194,7 @@ async def from_array(
     attributes : dict, optional
         Attributes for the array.
         If not specified, defaults to the attributes of the data array.
+        Pass an empty dict to create the array with no attributes.
     chunk_key_encoding : ChunkKeyEncoding, optional
         A specification of how the chunk keys are represented in storage.
         For Zarr format 3, the default is `{"name": "default", "separator": "/"}}`.
@@ -4276,6 +4279,7 @@ async def from_array(
         zarr_format,
         chunk_key_encoding,
         dimension_names,
+        attributes,
     ) = _parse_keep_array_attr(
         data=data,
         chunks=chunks,
@@ -4288,6 +4292,7 @@ async def from_array(
         zarr_format=zarr_format,
         chunk_key_encoding=chunk_key_encoding,
         dimension_names=dimension_names,
+        attributes=attributes,
     )
     if not hasattr(data, "dtype") or not hasattr(data, "shape"):
         data = np.array(data)
@@ -4772,6 +4777,7 @@ def _parse_keep_array_attr(
     zarr_format: ZarrFormat | None,
     chunk_key_encoding: ChunkKeyEncodingLike | None,
     dimension_names: DimensionNamesLike,
+    attributes: dict[str, JSON] | None,
 ) -> tuple[
     ChunksLike | Literal["auto"],
     ShardsLike | None,
@@ -4783,6 +4789,7 @@ def _parse_keep_array_attr(
     ZarrFormat,
     ChunkKeyEncodingLike | None,
     DimensionNamesLike,
+    dict[str, JSON] | None,
 ]:
     if isinstance(data, Array):
         if chunks == "keep":
@@ -4809,7 +4816,7 @@ def _parse_keep_array_attr(
                 serializer = cast("SerializerLike", data.serializer)
             else:
                 serializer = "auto"
-        if fill_value is None:
+        if fill_value is DEFAULT_FILL_VALUE:
             fill_value = data.fill_value
 
         if data.metadata.zarr_format == 2 and zarr_format == 3 and data.order == "F":
@@ -4830,6 +4837,8 @@ def _parse_keep_array_attr(
                 chunk_key_encoding = data.metadata.chunk_key_encoding
         if dimension_names is None and data.metadata.zarr_format == 3:
             dimension_names = data.metadata.dimension_names
+        if attributes is None:
+            attributes = dict(data.attrs)
     else:
         if chunks == "keep":
             chunks = "auto"
@@ -4856,6 +4865,7 @@ def _parse_keep_array_attr(
         zarr_format,
         chunk_key_encoding,
         dimension_names,
+        attributes,
     )
 
 

src/zarr/testing/stateful.py

@@ -152,29 +152,14 @@ def add_array(self, data: DataObject, name: str) -> None:
         )
         note(f"Adding array:  path='{path}'  shape={a.shape}  chunks={a.metadata.chunk_grid}")
 
-        # Recreate the same array in the store under test
-        from zarr.core.metadata.v3 import RectilinearChunkGridMetadata, RegularChunkGridMetadata
-
-        chunk_grid = a.metadata.chunk_grid
-        chunks_param: tuple[int, ...] | list[list[int]]
-        if isinstance(chunk_grid, RectilinearChunkGridMetadata):
-            chunks_param = [
-                list(dim) if isinstance(dim, tuple) else [dim] for dim in chunk_grid.chunk_shapes
-            ]
-        elif isinstance(chunk_grid, RegularChunkGridMetadata):
-            chunks_param = chunk_grid.chunk_shape
-        else:
-            chunks_param = a.chunks
-
-        root = zarr.open_group(store=self.store, mode="a")
-        arr = root.create_array(
-            path,
-            shape=a.shape,
-            chunks=chunks_param,
-            dtype=a.dtype,
-            fill_value=a.fill_value,
-            dimension_names=a.metadata.dimension_names,  # type: ignore[union-attr]
-            compressors=None,
+        # Recreate the same array in the store under test.
+        # The data is copied here rather than by `write_data=True`,
+        # whose shard-wise copy does not support rectilinear chunk grids.
+        arr = zarr.from_array(
+            self.store,
+            data=a,
+            name=path,
+            write_data=False,
         )
         arr[:] = a[:]
         self.all_arrays.add(path)

tests/test_array.py

@@ -1826,6 +1826,69 @@ async def test_from_array_arraylike(
         np.testing.assert_array_equal(result[...], np.full_like(src, fill_value))
 
 
+@pytest.mark.parametrize("store", ["local", "memory"], indirect=True)
+def test_from_array_keeps_fill_value_and_attributes(store: Store, zarr_format: ZarrFormat) -> None:
+    """`from_array` defaults to the fill value and attributes of the source array."""
+    attributes: dict[str, JSON] = {"units": "K"}
+    src = zarr.create_array(
+        store,
+        name="src",
+        shape=(4,),
+        dtype="int32",
+        fill_value=42,
+        attributes=attributes,
+        zarr_format=zarr_format,
+    )
+    src[:] = np.arange(4, dtype="int32")
+
+    result = zarr.from_array({}, data=src)
+    assert result.fill_value == 42
+    assert dict(result.attrs) == attributes
+
+    # A metadata-only copy must read back the source's fill value, not the dtype default.
+    meta_only = zarr.from_array({}, data=src, write_data=False)
+    np.testing.assert_array_equal(meta_only[:], np.full((4,), 42, dtype="int32"))
+
+
+@pytest.mark.parametrize("store", ["memory"], indirect=True)
+def test_from_array_explicit_fill_value_and_attributes_override(
+    store: Store, zarr_format: ZarrFormat
+) -> None:
+    """Explicit `fill_value` / `attributes` arguments take precedence over the source.
+
+    An explicit ``fill_value=None`` selects the dtype's default scalar for Zarr format 3
+    and a null fill value for Zarr format 2, matching `create_array`, rather than being
+    treated as "keep the source's fill value". An empty ``attributes`` dict is likewise
+    honoured, so it is possible to drop the source's attributes.
+    """
+    src = zarr.create_array(
+        store,
+        name="src",
+        shape=(4,),
+        dtype="int32",
+        fill_value=42,
+        attributes={"units": "K"},
+        zarr_format=zarr_format,
+    )
+
+    assert zarr.from_array({}, data=src, fill_value=7).fill_value == 7
+    assert dict(zarr.from_array({}, data=src, attributes={}).attrs) == {}
+    assert dict(zarr.from_array({}, data=src, attributes={"a": 1}).attrs) == {"a": 1}
+
+    explicit_none = zarr.from_array({}, data=src, fill_value=None)
+    if zarr_format == 2:
+        assert explicit_none.fill_value is None
+    else:
+        assert explicit_none.fill_value == 0  # int32 default scalar
+
+
+def test_from_array_arraylike_gains_no_attributes() -> None:
+    """A non-Array source has no attributes or fill value to keep."""
+    result = zarr.from_array({}, data=np.arange(4, dtype="int32"))
+    assert dict(result.attrs) == {}
+    assert result.fill_value == 0
+
+
 def test_from_array_F_order() -> None:
     arr = zarr.create_array(store={}, data=np.array([1]), order="F", zarr_format=2)
     with pytest.warns(