base64 encode fill value for some dtypes with zarr_format=2 (#2286)

Co-authored-by: Davis Bennett <[email protected]>

Author: TomAugspurger

src/zarr/abc/metadata.py

@@ -22,7 +22,6 @@ def to_dict(self) -> dict[str, JSON]:
         are instances of `Metadata`. Sequences of `Metadata` are similarly recursed into, and
         the output of that recursion is collected in a list.
         """
-        ...
         out_dict = {}
         for field in fields(self):
             key = field.name

src/zarr/core/metadata/v2.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
 
+import base64
 from collections.abc import Iterable
 from enum import Enum
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, cast
 
 if TYPE_CHECKING:
     from typing import Any, Literal, Self
@@ -31,7 +32,7 @@ class ArrayV2Metadata(ArrayMetadata):
     shape: ChunkCoords
     chunk_grid: RegularChunkGrid
     data_type: np.dtype[Any]
-    fill_value: None | int | float = 0
+    fill_value: None | int | float | str | bytes = 0
     order: Literal["C", "F"] = "C"
     filters: tuple[numcodecs.abc.Codec, ...] | None = None
     dimension_separator: Literal[".", "/"] = "."
@@ -140,6 +141,13 @@ def from_dict(cls, data: dict[str, Any]) -> ArrayV2Metadata:
         _data = data.copy()
         # check that the zarr_format attribute is correct
         _ = parse_zarr_format(_data.pop("zarr_format"))
+        dtype = parse_dtype(_data["dtype"])
+
+        if dtype.kind in "SV":
+            fill_value_encoded = _data.get("fill_value")
+            if fill_value_encoded is not None:
+                fill_value = base64.standard_b64decode(fill_value_encoded)
+                _data["fill_value"] = fill_value
 
         # zarr v2 allowed arbitrary keys here.
         # We don't want the ArrayV2Metadata constructor to fail just because someone put an
@@ -155,6 +163,14 @@ def from_dict(cls, data: dict[str, Any]) -> ArrayV2Metadata:
 
     def to_dict(self) -> dict[str, JSON]:
         zarray_dict = super().to_dict()
+
+        if self.dtype.kind in "SV" and self.fill_value is not None:
+            # There's a relationship between self.dtype and self.fill_value
+            # that mypy isn't aware of. The fact that we have S or V dtype here
+            # means we should have a bytes-type fill_value.
+            fill_value = base64.standard_b64encode(cast(bytes, self.fill_value)).decode("ascii")
+            zarray_dict["fill_value"] = fill_value
+
         _ = zarray_dict.pop("chunk_grid")
         zarray_dict["chunks"] = self.chunk_grid.chunk_shape
 

tests/v3/test_v2.py

@@ -1,3 +1,4 @@
+import json
 from collections.abc import Iterator
 
 import numpy as np
@@ -6,6 +7,9 @@
 from numcodecs.blosc import Blosc
 
 import zarr
+import zarr.core.buffer.cpu
+import zarr.core.metadata
+import zarr.storage
 from zarr import Array
 from zarr.storage import MemoryStore, StorePath
 
@@ -46,3 +50,37 @@ def test_codec_pipeline() -> None:
     result = array[:]
     expected = np.ones(1)
     np.testing.assert_array_equal(result, expected)
+
+
+@pytest.mark.parametrize("dtype", ["|S", "|V"])
+async def test_v2_encode_decode(dtype):
+    store = zarr.storage.MemoryStore(mode="w")
+    g = zarr.group(store=store, zarr_format=2)
+    g.create_array(
+        name="foo",
+        shape=(3,),
+        chunks=(3,),
+        dtype=dtype,
+        fill_value=b"X",
+    )
+
+    result = await store.get("foo/.zarray", zarr.core.buffer.default_buffer_prototype())
+    assert result is not None
+
+    serialized = json.loads(result.to_bytes())
+    expected = {
+        "chunks": [3],
+        "compressor": None,
+        "dtype": f"{dtype}0",
+        "fill_value": "WA==",
+        "filters": None,
+        "order": "C",
+        "shape": [3],
+        "zarr_format": 2,
+        "dimension_separator": ".",
+    }
+    assert serialized == expected
+
+    data = zarr.open_array(store=store, path="foo")[:]
+    expected = np.full((3,), b"X", dtype=dtype)
+    np.testing.assert_equal(data, expected)