chore: handle new zarr dtype API

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     'donfig',
     'pytest',
     'universal_pathlib>=0.2.0',
-    "zarr>=3.0.3,<3.1",
+    "zarr @ git+https://github.com/zarr-developers/zarr-python",
 ]
 
 [project.optional-dependencies]

python/zarrs/pipeline.py

@@ -21,6 +21,7 @@
     from zarr.core.chunk_grids import ChunkGrid
     from zarr.core.common import ChunkCoords
     from zarr.core.indexing import SelectorTuple
+    from zarr.dtype import ZDType
 
 from ._internal import CodecPipelineImpl, codec_metadata_v2_to_v3
 from .utils import (
@@ -134,7 +135,7 @@ def __iter__(self) -> Iterator[Codec]:
         yield from self.codecs
 
     def validate(
-        self, *, shape: ChunkCoords, dtype: np.dtype[Any], chunk_grid: ChunkGrid
+        self, *, shape: ChunkCoords, dtype: ZDType, chunk_grid: ChunkGrid
     ) -> None:
         raise NotImplementedError("validate")
 
@@ -236,7 +237,7 @@ def _raise_error_on_unsupported_batch_dtype(
         # https://github.com/LDeakin/zarrs/blob/0532fe983b7b42b59dbf84e50a2fe5e6f7bad4ce/zarrs_metadata/src/v2_to_v3.rs#L289-L293 for VSUMm
         # Further, our pipeline does not support variable-length objects due to limitations on decode_into, so object/np.dtypes.StringDType is also out
         if any(
-            info.dtype.kind in {"V", "S", "U", "M", "m", "O", "T"}
+            info.dtype.to_native_dtype().kind in {"V", "S", "U", "M", "m", "O", "T"}
             for (_, info, _, _, _) in batch_info
         ):
             raise UnsupportedDataTypeError()

python/zarrs/utils.py

@@ -8,7 +8,6 @@
 import numpy as np
 from zarr.core.array_spec import ArraySpec
 from zarr.core.indexing import SelectorTuple, is_integer
-from zarr.core.metadata.v2 import _default_fill_value
 
 from zarrs._internal import Basic, WithSubset
 
@@ -17,6 +16,7 @@
     from types import EllipsisType
 
     from zarr.abc.store import ByteGetter, ByteSetter
+    from zarr.dtype import ZDType
 
 
 # adapted from https://docs.python.org/3/library/concurrent.futures.html#concurrent.futures.ThreadPoolExecutor
@@ -139,9 +139,9 @@ def get_shape_for_selector(
     return resulting_shape_from_index(shape, selector_tuple, drop_axes, pad=pad)
 
 
-def get_implicit_fill_value(dtype: np.dtype, fill_value: Any) -> Any:
+def get_implicit_fill_value(dtype: ZDType, fill_value: Any) -> Any:
     if fill_value is None:
-        fill_value = _default_fill_value(dtype)
+        fill_value = dtype.default_scalar()
     return fill_value
 
 

src/chunk_item.rs

@@ -68,6 +68,7 @@ impl Basic {
         let chunk_shape = chunk_spec.getattr("shape")?.extract()?;
         let mut dtype: String = chunk_spec
             .getattr("dtype")?
+            .call_method0("to_native_dtype")?
             .call_method0("__str__")?
             .extract()?;
         if dtype == "object" {