Merge branch 'v3' into fix-file-modes

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.5.0'
+    rev: 'v0.5.2'
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

src/zarr/array.py

@@ -715,6 +715,10 @@ def order(self) -> Literal["C", "F"]:
     def read_only(self) -> bool:
         return self._async_array.read_only
 
+    @property
+    def fill_value(self) -> Any:
+        return self.metadata.fill_value
+
     def __array__(
         self, dtype: npt.DTypeLike | None = None, copy: bool | None = None
     ) -> NDArrayLike:

src/zarr/metadata.py

@@ -2,10 +2,10 @@
 
 import json
 from abc import ABC, abstractmethod
-from collections.abc import Iterable
+from collections.abc import Iterable, Sequence
 from dataclasses import dataclass, field, replace
 from enum import Enum
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING, Any, Literal, cast, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -32,7 +32,6 @@
     ChunkCoords,
     ZarrFormat,
     parse_dtype,
-    parse_fill_value,
     parse_named_configuration,
     parse_shapelike,
 )
@@ -189,7 +188,7 @@ def __init__(
         chunk_grid_parsed = ChunkGrid.from_dict(chunk_grid)
         chunk_key_encoding_parsed = ChunkKeyEncoding.from_dict(chunk_key_encoding)
         dimension_names_parsed = parse_dimension_names(dimension_names)
-        fill_value_parsed = parse_fill_value(fill_value)
+        fill_value_parsed = parse_fill_value_v3(fill_value, dtype=data_type_parsed)
         attributes_parsed = parse_attributes(attributes)
         codecs_parsed_partial = parse_codecs(codecs)
 
@@ -255,9 +254,18 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
         return self.chunk_key_encoding.encode_chunk_key(chunk_coords)
 
     def to_buffer_dict(self) -> dict[str, Buffer]:
-        def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
+        def _json_convert(o: Any) -> Any:
             if isinstance(o, np.dtype):
                 return str(o)
+            if np.isscalar(o):
+                # convert numpy scalar to python type, and pass
+                # python types through
+                out = getattr(o, "item", lambda: o)()
+                if isinstance(out, complex):
+                    # python complex types are not JSON serializable, so we use the
+                    # serialization defined in the zarr v3 spec
+                    return [out.real, out.imag]
+                return out
             if isinstance(o, Enum):
                 return o.name
             # this serializes numcodecs compressors
@@ -341,7 +349,7 @@ def __init__(
         order_parsed = parse_indexing_order(order)
         dimension_separator_parsed = parse_separator(dimension_separator)
         filters_parsed = parse_filters(filters)
-        fill_value_parsed = parse_fill_value(fill_value)
+        fill_value_parsed = parse_fill_value_v2(fill_value, dtype=data_type_parsed)
         attributes_parsed = parse_attributes(attributes)
 
         object.__setattr__(self, "shape", shape_parsed)
@@ -371,13 +379,17 @@ def chunks(self) -> ChunkCoords:
 
     def to_buffer_dict(self) -> dict[str, Buffer]:
         def _json_convert(
-            o: np.dtype[Any],
-        ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
+            o: Any,
+        ) -> Any:
             if isinstance(o, np.dtype):
                 if o.fields is None:
                     return o.str
                 else:
                     return o.descr
+            if np.isscalar(o):
+                # convert numpy scalar to python type, and pass
+                # python types through
+                return getattr(o, "item", lambda: o)()
             raise TypeError
 
         zarray_dict = self.to_dict()
@@ -517,3 +529,105 @@ def parse_codecs(data: Iterable[Codec | dict[str, JSON]]) -> tuple[Codec, ...]:
             out += (get_codec_class(name_parsed).from_dict(c),)
 
     return out
+
+
+def parse_fill_value_v2(fill_value: Any, dtype: np.dtype[Any]) -> Any:
+    """
+    Parse a potential fill value into a value that is compatible with the provided dtype.
+
+    This is a light wrapper around zarr.v2.util.normalize_fill_value.
+
+    Parameters
+    ----------
+    fill_value: Any
+        A potential fill value.
+    dtype: np.dtype[Any]
+        A numpy dtype.
+
+    Returns
+        An instance of `dtype`, or `None`, or any python object (in the case of an object dtype)
+    """
+    from zarr.v2.util import normalize_fill_value
+
+    return normalize_fill_value(fill_value=fill_value, dtype=dtype)
+
+
+BOOL = np.bool_
+BOOL_DTYPE = np.dtypes.BoolDType
+
+INTEGER_DTYPE = (
+    np.dtypes.Int8DType
+    | np.dtypes.Int16DType
+    | np.dtypes.Int32DType
+    | np.dtypes.Int64DType
+    | np.dtypes.UByteDType
+    | np.dtypes.UInt16DType
+    | np.dtypes.UInt32DType
+    | np.dtypes.UInt64DType
+)
+
+INTEGER = np.int8 | np.int16 | np.int32 | np.int64 | np.uint8 | np.uint16 | np.uint32 | np.uint64
+FLOAT_DTYPE = np.dtypes.Float16DType | np.dtypes.Float32DType | np.dtypes.Float64DType
+FLOAT = np.float16 | np.float32 | np.float64
+COMPLEX_DTYPE = np.dtypes.Complex64DType | np.dtypes.Complex128DType
+COMPLEX = np.complex64 | np.complex128
+# todo: r* dtypes
+
+
+@overload
+def parse_fill_value_v3(fill_value: Any, dtype: BOOL_DTYPE) -> BOOL: ...
+
+
+@overload
+def parse_fill_value_v3(fill_value: Any, dtype: INTEGER_DTYPE) -> INTEGER: ...
+
+
+@overload
+def parse_fill_value_v3(fill_value: Any, dtype: FLOAT_DTYPE) -> FLOAT: ...
+
+
+@overload
+def parse_fill_value_v3(fill_value: Any, dtype: COMPLEX_DTYPE) -> COMPLEX: ...
+
+
+def parse_fill_value_v3(
+    fill_value: Any, dtype: BOOL_DTYPE | INTEGER_DTYPE | FLOAT_DTYPE | COMPLEX_DTYPE
+) -> BOOL | INTEGER | FLOAT | COMPLEX:
+    """
+    Parse `fill_value`, a potential fill value, into an instance of `dtype`, a data type.
+    If `fill_value` is `None`, then this function will return the result of casting the value 0
+    to the provided data type. Otherwise, `fill_value` will be cast to the provided data type.
+
+    Note that some numpy dtypes use very permissive casting rules. For example,
+    `np.bool_({'not remotely a bool'})` returns `True`. Thus this function should not be used for
+    validating that the provided fill value is a valid instance of the data type.
+
+    Parameters
+    ----------
+    fill_value: Any
+        A potential fill value.
+    dtype: BOOL_DTYPE | INTEGER_DTYPE | FLOAT_DTYPE | COMPLEX_DTYPE
+        A numpy data type that models a data type defined in the Zarr V3 specification.
+
+    Returns
+    -------
+    A scalar instance of `dtype`
+    """
+    if fill_value is None:
+        return dtype.type(0)
+    if isinstance(fill_value, Sequence) and not isinstance(fill_value, str):
+        if dtype in (np.complex64, np.complex128):
+            dtype = cast(COMPLEX_DTYPE, dtype)
+            if len(fill_value) == 2:
+                # complex datatypes serialize to JSON arrays with two elements
+                return dtype.type(complex(*fill_value))
+            else:
+                msg = (
+                    f"Got an invalid fill value for complex data type {dtype}."
+                    f"Expected a sequence with 2 elements, but {fill_value} has "
+                    f"length {len(fill_value)}."
+                )
+                raise ValueError(msg)
+        msg = f"Cannot parse non-string sequence {fill_value} as a scalar with type {dtype}."
+        raise TypeError(msg)
+    return dtype.type(fill_value)

tests/v3/test_array.py

@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 
 from zarr.array import Array
@@ -34,3 +35,51 @@ def test_array_name_properties_with_group(
     assert spam.path == "bar/spam"
     assert spam.name == "/bar/spam"
     assert spam.basename == "spam"
+
+
+@pytest.mark.parametrize("store", ["memory"], indirect=True)
+@pytest.mark.parametrize("specifiy_fill_value", [True, False])
+@pytest.mark.parametrize("dtype_str", ["bool", "uint8", "complex64"])
+def test_array_v3_fill_value_default(
+    store: MemoryStore, specifiy_fill_value: bool, dtype_str: str
+) -> None:
+    """
+    Test that creating an array with the fill_value parameter set to None, or unspecified,
+    results in the expected fill_value attribute of the array, i.e. 0 cast to the array's dtype.
+    """
+    shape = (10,)
+    default_fill_value = 0
+    if specifiy_fill_value:
+        arr = Array.create(
+            store=store,
+            shape=shape,
+            dtype=dtype_str,
+            zarr_format=3,
+            chunk_shape=shape,
+            fill_value=None,
+        )
+    else:
+        arr = Array.create(
+            store=store, shape=shape, dtype=dtype_str, zarr_format=3, chunk_shape=shape
+        )
+
+    assert arr.fill_value == np.dtype(dtype_str).type(default_fill_value)
+    assert arr.fill_value.dtype == arr.dtype
+
+
+@pytest.mark.parametrize("store", ["memory"], indirect=True)
+@pytest.mark.parametrize("fill_value", [False, 0.0, 1, 2.3])
+@pytest.mark.parametrize("dtype_str", ["bool", "uint8", "float32", "complex64"])
+def test_array_v3_fill_value(store: MemoryStore, fill_value: int, dtype_str: str) -> None:
+    shape = (10,)
+    arr = Array.create(
+        store=store,
+        shape=shape,
+        dtype=dtype_str,
+        zarr_format=3,
+        chunk_shape=shape,
+        fill_value=fill_value,
+    )
+
+    assert arr.fill_value == np.dtype(dtype_str).type(fill_value)
+    assert arr.fill_value.dtype == arr.dtype

tests/v3/test_metadata.py

@@ -1,60 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-import pytest
-
-if TYPE_CHECKING:
-    from collections.abc import Sequence
-    from typing import Any
-
-from zarr.metadata import parse_dimension_names, parse_zarr_format_v2, parse_zarr_format_v3
-
-
-# todo: test
-def test_datatype_enum(): ...
-
-
-# todo: test
-# this will almost certainly be a collection of tests
-def test_array_metadata_v3(): ...
-
-
-# todo: test
-# this will almost certainly be a collection of tests
-def test_array_metadata_v2(): ...
-
-
-@pytest.mark.parametrize("data", [None, ("a", "b", "c"), ["a", "a", "a"]])
-def parse_dimension_names_valid(data: Sequence[str] | None) -> None:
-    assert parse_dimension_names(data) == data
-
-
-@pytest.mark.parametrize("data", [(), [1, 2, "a"], {"foo": 10}])
-def parse_dimension_names_invalid(data: Any) -> None:
-    with pytest.raises(TypeError, match="Expected either None or iterable of str,"):
-        parse_dimension_names(data)
-
-
-# todo: test
-def test_parse_attributes() -> None: ...
-
-
-def test_parse_zarr_format_v3_valid() -> None:
-    assert parse_zarr_format_v3(3) == 3
-
-
-@pytest.mark.parametrize("data", [None, 1, 2, 4, 5, "3"])
-def test_parse_zarr_foramt_v3_invalid(data: Any) -> None:
-    with pytest.raises(ValueError, match=f"Invalid value. Expected 3. Got {data}"):
-        parse_zarr_format_v3(data)
-
-
-def test_parse_zarr_format_v2_valid() -> None:
-    assert parse_zarr_format_v2(2) == 2
-
-
-@pytest.mark.parametrize("data", [None, 1, 3, 4, 5, "3"])
-def test_parse_zarr_foramt_v2_invalid(data: Any) -> None:
-    with pytest.raises(ValueError, match=f"Invalid value. Expected 2. Got {data}"):
-        parse_zarr_format_v2(data)

tests/v3/test_metadata/test_v2.py

@@ -0,0 +1,20 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import Any
+
+import pytest
+
+from zarr.metadata import parse_zarr_format_v2
+
+
+def test_parse_zarr_format_valid() -> None:
+    assert parse_zarr_format_v2(2) == 2
+
+
+@pytest.mark.parametrize("data", [None, 1, 3, 4, 5, "3"])
+def test_parse_zarr_format_invalid(data: Any) -> None:
+    with pytest.raises(ValueError, match=f"Invalid value. Expected 2. Got {data}"):
+        parse_zarr_format_v2(data)