fix: byte-order handling for structured dtypes in the bytes codec (#4142)

* fix: byte-order handling for structured dtypes in the bytes codec

The bytes codec neither byte-swapped structured-dtype fields to its
configured endian on encode (numpy reports byteorder '|' for void
dtypes, so the top-level byteorder comparison never detected a
mismatch) nor honored its endian when decoding, silently corrupting
any structured data whose field byte order differed from the stored
one (e.g. virtual references to external big-endian data).

Encode now detects byte-order mismatches by comparing full dtypes via
newbyteorder, and decode reinterprets raw bytes in the stored byte
order before converting to the data type's declared byte order, so the
stored layout (codec state) and the in-memory layout (array data type)
are independent.

Closes #4141

Assisted-by: ClaudeCode:claude-fable-5

* test: fold structured byte-order cases into existing bytes codec tests

Extend test_endian's parametrization with structured dtypes and
test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus
stored-layout and decoded-dtype assertions, instead of adding parallel
test functions for the same properties.

Assisted-by: ClaudeCode:claude-fable-5

* refactor: rename stored_dtype to view_dtype in BytesCodec decode

The variable is the dtype used to view the raw chunk bytes (byte order
from the codec's endian configuration), not a property of the stored
data or of the returned buffer, which always carries the array's
declared dtype.

Assisted-by: ClaudeCode:claude-fable-5

* docs: note that the decode-side byte-order conversion copies the chunk

Assisted-by: ClaudeCode:claude-fable-5

Author: d-v-b

changes/4141.bugfix.md

@@ -0,0 +1 @@
+Fix silent byte-order corruption for structured dtypes with the `bytes` codec: multi-byte fields are now byte-swapped to the codec's configured `endian` on write and decoded honoring it on read, so non-native-endian structured data (e.g. big-endian fields, as produced by virtual references to external data) round-trips correctly.

src/zarr/codecs/bytes.py

@@ -100,14 +100,28 @@ def _decode_sync(
         chunk_spec: ArraySpec,
     ) -> NDBuffer:
         endian_str = self.endian
+        dtype = chunk_spec.dtype.to_native_dtype()
+        # The byte order of the stored data is set by this codec's `endian`
+        # configuration; the byte order of the decoded array is set by the array's
+        # data type. The two are independent: the raw bytes are viewed with a dtype
+        # in the stored byte order, then converted to the declared dtype if needed.
         if isinstance(chunk_spec.dtype, HasEndianness):
-            dtype = replace(chunk_spec.dtype, endianness=endian_str).to_native_dtype()  # type: ignore[call-arg]
+            view_dtype = replace(chunk_spec.dtype, endianness=endian_str).to_native_dtype()  # type: ignore[call-arg]
+        elif isinstance(chunk_spec.dtype, Struct) and endian_str is not None:
+            # Per the struct data type spec, all multi-byte fields are stored in the
+            # byte order configured on this codec.
+            view_dtype = dtype.newbyteorder(endian_str)
         else:
-            dtype = chunk_spec.dtype.to_native_dtype()
+            view_dtype = dtype
         as_array_like = chunk_bytes.as_array_like()
         chunk_array = chunk_spec.prototype.nd_buffer.from_ndarray_like(
-            as_array_like.view(dtype=dtype)  # type: ignore[attr-defined]
+            as_array_like.view(dtype=view_dtype)  # type: ignore[attr-defined]
         )
+        if view_dtype != dtype:
+            # This byte-swapping conversion copies the chunk. The dtype inequality
+            # guard keeps the common case, where the stored and declared byte orders
+            # already match, on the zero-copy view path above.
+            chunk_array = chunk_array.astype(dtype)
 
         # ensure correct chunk shape
         if chunk_array.shape != chunk_spec.shape:
@@ -129,13 +143,14 @@ def _encode_sync(
         chunk_spec: ArraySpec,
     ) -> Buffer | None:
         assert isinstance(chunk_array, NDBuffer)
-        if (
-            chunk_array.dtype.itemsize > 1
-            and self.endian is not None
-            and self.endian != chunk_array.byteorder
-        ):
+        if chunk_array.dtype.itemsize > 1 and self.endian is not None:
+            # Compare full dtypes rather than the top-level byteorder: numpy reports
+            # byteorder '|' for structured dtypes even when their fields are
+            # byte-order-sensitive, so newbyteorder is the only reliable way to
+            # detect (and normalize) a byte-order mismatch.
             new_dtype = chunk_array.dtype.newbyteorder(self.endian)
-            chunk_array = chunk_array.astype(new_dtype)
+            if new_dtype != chunk_array.dtype:
+                chunk_array = chunk_array.astype(new_dtype)
 
         nd_array = chunk_array.as_ndarray_like()
         # Flatten the nd-array (only copy if needed) and reinterpret as bytes

tests/test_codecs/test_bytes.py

@@ -33,29 +33,50 @@
 
 
 @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
-@pytest.mark.parametrize("input_dtype", [">u2", "<u2"])
+@pytest.mark.parametrize(
+    "input_dtype",
+    [
+        ">u2",
+        "<u2",
+        [("flux", ">f4"), ("mask", ">i4")],
+        [("flux", "<f4"), ("mask", "<i4")],
+    ],
+    ids=["big-scalar", "little-scalar", "big-struct", "little-struct"],
+)
 @pytest.mark.parametrize("store_endian", ["big", "little"])
 async def test_endian(
     store: Store,
-    input_dtype: Literal[">u2", "<u2"],
+    input_dtype: str | list[tuple[str, str]],
     store_endian: Literal["big", "little"],
 ) -> None:
     """
     The `bytes` codec stores multi-byte data in the byte order configured on the
     codec, regardless of the input array's byte order, and reads it back to the
-    original values. The input-dtype/store-endian cross-product exercises the
-    encode-side byteswap (input byte order != store byte order) and the no-op
-    case alike. Compression is disabled so the stored chunk is the codec's raw
-    output and its byte layout can be asserted directly.
+    original values. For structured dtypes this applies to every multi-byte
+    field, per the `struct` data type spec; the struct cases guard against the
+    endianness bugs from
+    https://github.com/zarr-developers/zarr-python/issues/4141, where the
+    encode path never byte-swapped struct fields (numpy reports byteorder '|'
+    for void dtypes) and the decode path ignored the codec's endian entirely.
+    The input-dtype/store-endian cross-product exercises the encode-side
+    byteswap (input byte order != store byte order) and the no-op case alike.
+    Compression is disabled so the stored chunk is the codec's raw output and
+    its byte layout can be asserted directly.
     """
-    data = np.arange(0, 256, dtype=input_dtype).reshape((16, 16))
+    dtype = np.dtype(input_dtype)
+    if dtype.fields is None:
+        data = np.arange(0, 256, dtype=dtype).reshape((16, 16))
+    else:
+        data = np.zeros((16, 16), dtype=dtype)
+        data["flux"] = np.arange(0, 256).reshape((16, 16))
+        data["mask"] = np.arange(256, 512).reshape((16, 16))
     path = "endian"
     spath = StorePath(store, path)
     a = await zarr.api.asynchronous.create_array(
         spath,
         shape=data.shape,
         chunks=(16, 16),
-        dtype="uint16",
+        dtype=dtype,
         fill_value=0,
         compressors=None,
         serializer=BytesCodec(endian=store_endian),
@@ -66,8 +87,7 @@ async def test_endian(
     # The stored chunk is laid out in the byte order configured on the codec.
     stored = await store.get(f"{path}/c/0/0", prototype=default_buffer_prototype())
     assert stored is not None
-    expected_dtype = ">u2" if store_endian == "big" else "<u2"
-    assert stored.to_bytes() == data.astype(expected_dtype).tobytes()
+    assert stored.to_bytes() == data.astype(dtype.newbyteorder(store_endian)).tobytes()
 
     # ... and the data reads back to the original values.
     readback_data = await _AsyncArrayProxy(a)[:, :].get()
@@ -78,9 +98,27 @@ def test_bytes_codec_supports_sync() -> None:
     assert isinstance(BytesCodec(), SupportsSyncCodec)
 
 
-def test_bytes_codec_sync_roundtrip() -> None:
-    codec = BytesCodec()
-    arr = np.arange(100, dtype="float64")
+@pytest.mark.parametrize("endian", ENDIAN)
+@pytest.mark.parametrize(
+    "native_dtype",
+    [np.dtype("float64"), np.dtype(">u2"), np.dtype([("a", ">f4"), ("b", "<i4")])],
+    ids=["native-scalar", "big-scalar", "mixed-endian-struct"],
+)
+def test_bytes_codec_sync_roundtrip(endian: EndianLiteral, native_dtype: np.dtype[Any]) -> None:
+    """
+    The synchronous encode/decode path round-trips data, and the two byte
+    orders involved are independent: the codec's `endian` configuration governs
+    only the stored byte layout (every multi-byte value, including struct
+    fields, is laid out in the codec's byte order regardless of the input
+    array's byte order), while the decoded buffer's byte order is governed by
+    the array's data type regardless of the codec's. The mixed-endian struct
+    case pins that per-field byte order of the in-memory dtype survives a
+    roundtrip through a single stored byte order.
+    """
+    if native_dtype.fields is None:
+        arr = np.arange(100, dtype=native_dtype)
+    else:
+        arr = np.array([(1.5, 2), (3.5, 4), (5.5, 6), (7.5, 8)], dtype=native_dtype)
     zdtype = get_data_type_from_native_dtype(arr.dtype)
     spec = ArraySpec(
         shape=arr.shape,
@@ -91,11 +129,14 @@ def test_bytes_codec_sync_roundtrip() -> None:
     )
     nd_buf: NDBuffer = default_buffer_prototype().nd_buffer.from_numpy_array(arr)
 
-    codec = codec.evolve_from_array_spec(spec)
+    codec = BytesCodec(endian=endian).evolve_from_array_spec(spec)
 
     encoded = codec._encode_sync(nd_buf, spec)
     assert encoded is not None
+    assert encoded.to_bytes() == arr.astype(native_dtype.newbyteorder(endian)).tobytes()
+
     decoded = codec._decode_sync(encoded, spec)
+    assert decoded.dtype == zdtype.to_native_dtype()
     np.testing.assert_array_equal(arr, decoded.as_numpy_array())