Docstring corrections and lint modernization

changes/168.doc.md

@@ -0,0 +1 @@
+Corrected docstring examples in `v2.py` and `v3.py` (and experimental equivalents): fixed copy-pasted v2 output in a v3 example, missing commas, wrong import aliases, a `zarr_format=2` in a v3 example, "codices" → "codecs", "Compare am" → "Compare an", and a truncated sentence in the `to_zarr` docstring. Also fixed `V2ChunkKeyEncoding` to reference the correct config TypedDict, and modernized lint: `for` loops instead of list-comprehension side effects, `dict(data)` instead of `dict(data).copy()`, single-item `in` tests to equality, and raw strings in `pytest.raises(match=…)` calls.

src/pydantic_zarr/core.py

@@ -100,7 +100,8 @@ def ensure_member_name(data: Any) -> str:
 
 def ensure_key_no_path(data: Any) -> Any:
     if isinstance(data, Mapping):
-        [ensure_member_name(key) for key in data]
+        for key in data:
+            ensure_member_name(key)
     return data
 
 

src/pydantic_zarr/experimental/core.py

@@ -98,7 +98,8 @@ def ensure_member_name(data: Any) -> str:
 
 def ensure_key_no_path(data: Any) -> Any:
     if isinstance(data, Mapping):
-        [ensure_member_name(key) for key in data]
+        for key in data:
+            ensure_member_name(key)
     return data
 
 

src/pydantic_zarr/experimental/v2.py

@@ -399,7 +399,7 @@ def like(
         exclude: IncEx = None,
     ) -> bool:
         """
-        Compare am `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
+        Compare an `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
         fields to exclude or include in the comparison. Models are first converted to `dict` via the
         `model_dump` method of `pydantic.BaseModel`, then compared with the `==` operator.
 
@@ -1152,7 +1152,7 @@ def from_flat_group(data: Mapping[str, ArraySpec | BaseGroupSpec]) -> GroupSpec:
     # populates member_groups
     submember_by_parent_name: dict[str, dict[str, ArraySpec | BaseGroupSpec]] = {}
     # copy the input to ensure that mutations are contained inside this function
-    data_copy = dict(data).copy()
+    data_copy = dict(data)
     # Get the root node
     try:
         # The root node is a GroupSpec with the key ""

src/pydantic_zarr/experimental/v3.py

@@ -219,7 +219,7 @@ class ArraySpec(NodeSpec):
     fill_value: FillValue
         The fill value for this array.
     codecs: Sequence[NamedConfig]
-        The sequence of codices for this array.
+        The sequence of codecs for this array.
     storage_transformers: Optional[Sequence[NamedConfig]]
         An optional sequence of `NamedConfig` objects that define the storage
         transformers for this array.
@@ -457,7 +457,7 @@ def like(
         exclude: IncEx = None,
     ) -> bool:
         """
-        Compare am `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
+        Compare an `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
         fields to exclude or include in the comparison. Models are first converted to `dict` via the
         `model_dump` method of `pydantic.BaseModel`, then compared with the `==` operator.
 
@@ -1186,7 +1186,7 @@ def from_flat_group(
     # populates member_groups
     submember_by_parent_name: dict[str, dict[str, ArraySpec | BaseGroupSpec]] = {}
     # copy the input to ensure that mutations are contained inside this function
-    data_copy = dict(data).copy()
+    data_copy = dict(data)
     # Get the root node
     try:
         # The root node is a GroupSpec with the key ""
@@ -1262,9 +1262,9 @@ def auto_fill_value(data: object) -> FillValue:
             return False
         elif kind in ["i", "u"]:
             return 0
-        elif kind in ["f"]:
+        elif kind == "f":
             return "NaN"
-        elif kind in ["c"]:
+        elif kind == "c":
             return ("NaN", "NaN")
         else:
             raise ValueError(f"Cannot determine default fill value for data type {kind}")

src/pydantic_zarr/v2.py

@@ -416,7 +416,7 @@ def like(
         exclude: IncEx = None,
     ) -> bool:
         """
-        Compare am `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
+        Compare an `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
         fields to exclude or include in the comparison. Models are first converted to `dict` via the
         `model_dump` method of `pydantic.BaseModel`, then compared with the `==` operator.
 
@@ -713,14 +713,14 @@ def to_flat(self, root_path: str = "") -> dict[str, AnyArraySpec | AnyGroupSpec]
         Examples
         --------
 
-        >>> from pydantic_zarr.v2 import to_flat, GroupSpec
+        >>> from pydantic_zarr.v2 import GroupSpec
         >>> g1 = GroupSpec(members=None, attributes={'foo': 'bar'})
-        >>> to_flat(g1)
+        >>> g1.to_flat()
         {'': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
-        >>> to_flat(g1 root_path='baz')
+        >>> g1.to_flat(root_path='baz')
         {'baz': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
-        >>> to_flat(GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}))
-        {'/g1': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None), '': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
+        >>> GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}).to_flat()
+        {'': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None), '/g1': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
         """
         return to_flat(self, root_path=root_path)
 
@@ -838,7 +838,7 @@ def to_zarr(
     overwrite : bool, default = False
         Whether to overwrite existing objects in storage to create the Zarr group or array.
     **kwargs
-        Additional keyword arguments will be
+        Additional keyword arguments will be passed to member `to_zarr` calls and `zarr.create`.
 
     Returns
     -------
@@ -883,14 +883,14 @@ def to_flat(
     Examples
     --------
 
-    >>> from pydantic_zarr.v2 import flatten, GroupSpec
+    >>> from pydantic_zarr.v2 import to_flat, GroupSpec
     >>> g1 = GroupSpec(members=None, attributes={'foo': 'bar'})
     >>> to_flat(g1)
     {'': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
-    >>> to_flat(g1 root_path='baz')
+    >>> to_flat(g1, root_path='baz')
     {'baz': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
     >>> to_flat(GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}))
-    {'/g1': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None), '': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
+    {'': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None), '/g1': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
     """
     result = {}
     model_copy: AnyArraySpec | AnyGroupSpec
@@ -983,7 +983,7 @@ def from_flat_group(data: Mapping[str, AnyArraySpec | AnyGroupSpec]) -> AnyGroup
     # populates member_groups
     submember_by_parent_name: dict[str, dict[str, AnyArraySpec | AnyGroupSpec]] = {}
     # copy the input to ensure that mutations are contained inside this function
-    data_copy = dict(data).copy()
+    data_copy = dict(data)
     # Get the root node
     try:
         # The root node is a GroupSpec with the key ""

src/pydantic_zarr/v3.py

@@ -125,7 +125,7 @@ class V2ChunkKeyEncodingConfig(TypedDict):
     separator: Literal[".", "/"]
 
 
-V2ChunkKeyEncoding = NamedConfig[Literal["v2"], DefaultChunkKeyEncodingConfig]
+V2ChunkKeyEncoding = NamedConfig[Literal["v2"], V2ChunkKeyEncodingConfig]
 
 
 class NodeSpec(StrictBase):
@@ -207,7 +207,7 @@ class ArraySpec(NodeSpec, Generic[TAttr]):
     fill_value: FillValue
         The fill value for this array.
     codecs: Sequence[NamedConfig]
-        The sequence of codices for this array.
+        The sequence of codecs for this array.
     storage_transformers: Optional[Sequence[NamedConfig]]
         An optional sequence of `NamedConfig` objects that define the storage
         transformers for this array.
@@ -350,10 +350,12 @@ def from_zarr(cls, array: zarr.Array) -> Self:
         Examples
         --------
         >>> import zarr
+        >>> import zarr.storage
         >>> from pydantic_zarr.v3 import ArraySpec
-        >>> x = zarr.create((10,10))
+        >>> store = zarr.storage.MemoryStore()
+        >>> x = zarr.create(store=store, shape=(10, 10), zarr_format=3)
         >>> ArraySpec.from_zarr(x)
-        ArraySpec(zarr_format=2, attributes={}, shape=(10, 10), chunks=(10, 10), dtype='<f8', fill_value=0.0, order='C', filters=None, dimension_separator='.', compressor={'id': 'blosc', 'cname': 'lz4', 'clevel': 5, 'shuffle': 1, 'blocksize': 0})
+        ArraySpec(zarr_format=3, node_type='array', attributes={}, shape=(10, 10), data_type='float64', chunk_grid={'name': 'regular', 'configuration': {'chunk_shape': (10, 10)}}, chunk_key_encoding={'name': 'default', 'configuration': {'separator': '/'}}, fill_value=0.0, codecs=({'name': 'bytes', 'configuration': {'endian': 'little'}}, {'name': 'zstd', 'configuration': {'level': 0, 'checksum': False}}), storage_transformers=(), dimension_names=None)
 
         """
         try:
@@ -451,7 +453,7 @@ def like(
         exclude: IncEx = None,
     ) -> bool:
         """
-        Compare am `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
+        Compare an `ArraySpec` to another `ArraySpec` or a `zarr.Array`, parameterized over the
         fields to exclude or include in the comparison. Models are first converted to `dict` via the
         `model_dump` method of `pydantic.BaseModel`, then compared with the `==` operator.
 
@@ -601,14 +603,14 @@ def to_flat(self, root_path: str = "") -> dict[str, AnyArraySpec | AnyGroupSpec]
         Examples
         --------
 
-        >>> from pydantic_zarr.v3 import to_flat, GroupSpec
+        >>> from pydantic_zarr.v3 import GroupSpec
         >>> g1 = GroupSpec(members=None, attributes={'foo': 'bar'})
-        >>> to_flat(g1)
-        {'': GroupSpec(zarr_format=3, attributes={'foo': 'bar'}, members=None)}
-        >>> to_flat(g1 root_path='baz')
-        {'baz': GroupSpec(zarr_format=3, attributes={'foo': 'bar'}, members=None)}
-        >>> to_flat(GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}))
-        {'/g1': GroupSpec(zarr_format=3, attributes={'foo': 'bar'}, members=None), '': GroupSpec(zarr_format=3, attributes={'foo': 'bar'}, members=None)}
+        >>> g1.to_flat()
+        {'': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None)}
+        >>> g1.to_flat(root_path='baz')
+        {'baz': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None)}
+        >>> GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}).to_flat()
+        {'': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None), '/g1': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None)}
         """
         return to_flat(self, root_path=root_path)
 
@@ -968,7 +970,7 @@ def from_flat_group(
     # populates member_groups
     submember_by_parent_name: dict[str, dict[str, ArraySpec[Any] | GroupSpec[Any, Any]]] = {}
     # copy the input to ensure that mutations are contained inside this function
-    data_copy = dict(data).copy()
+    data_copy = dict(data)
     # Get the root node
     try:
         # The root node is a GroupSpec with the key ""
@@ -1041,9 +1043,9 @@ def auto_fill_value(data: object) -> FillValue:
             return False
         elif kind in ["i", "u"]:
             return 0
-        elif kind in ["f"]:
+        elif kind == "f":
             return "NaN"
-        elif kind in ["c"]:
+        elif kind == "c":
             return ("NaN", "NaN")
         else:
             raise ValueError(f"Cannot determine default fill value for data type {kind}")
@@ -1105,14 +1107,14 @@ def to_flat(node: ArraySpec | GroupSpec, root_path: str = "") -> dict[str, Array
     Examples
     --------
 
-    >>> from pydantic_zarr.v3 import flatten, GroupSpec
+    >>> from pydantic_zarr.v3 import to_flat, GroupSpec
     >>> g1 = GroupSpec(members=None, attributes={'foo': 'bar'})
     >>> to_flat(g1)
-    {'': GroupSpec(zarr_format=3, attributes={'foo': 'bar'}, members=None)}
-    >>> to_flat(g1 root_path='baz')
-    {'baz': GroupSpec(zarr_format=3, attributes={'foo': 'bar'}, members=None)}
+    {'': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None)}
+    >>> to_flat(g1, root_path='baz')
+    {'baz': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None)}
     >>> to_flat(GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}))
-    {'/g1': GroupSpec(zarr_format=3, attributes={'foo': 'bar'}, members=None), '': GroupSpec(zarr_format=2, attributes={'foo': 'bar'}, members=None)}
+    {'': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None), '/g1': GroupSpec(zarr_format=3, node_type='group', attributes={'foo': 'bar'}, members=None)}
     """
     result = {}
     model_copy: AnyArraySpec | AnyGroupSpec

tests/test_pydantic_zarr/test_core.py

@@ -7,7 +7,7 @@
 
 @pytest.mark.parametrize("data", ["/", "///", "a/b/", "a/b/vc"])
 def test_parse_str_no_path(data: str) -> None:
-    with pytest.raises(ValueError, match='Strings containing "/" are invalid.'):
+    with pytest.raises(ValueError, match=r'Strings containing "/" are invalid\.'):
         ensure_member_name(data)
 
 

tests/test_pydantic_zarr/test_experimental/test_v2.py

@@ -430,7 +430,7 @@ class GroupB(GroupSpec):
 
 @pytest.mark.parametrize("data", ["/", "a/b/c"])
 def test_member_name(data: str) -> None:
-    with pytest.raises(ValidationError, match='Strings containing "/" are invalid.'):
+    with pytest.raises(ValidationError, match=r'Strings containing "/" are invalid\.'):
         GroupSpec(attributes={}, members={data: GroupSpec(attributes={}, members={})})
 
 

tests/test_pydantic_zarr/test_experimental/test_v3.py

@@ -145,7 +145,7 @@ def test_arrayspec_no_empty_codecs(arrayspec: ArraySpec) -> None:
     """
 
     with pytest.raises(
-        ValidationError, match="Value error, Invalid length. Expected 1 or more, got 0."
+        ValidationError, match=r"Value error, Invalid length\. Expected 1 or more, got 0\."
     ):
         ArraySpec(**(arrayspec.model_dump() | {"codecs": ()}))  # type: ignore[arg-type]
 
@@ -396,7 +396,7 @@ def test_arrayspec_with_methods_validation(arrayspec) -> None:
         arrayspec.with_dimension_names(("x", "y"))  # 2 names for 1D array
 
     # Test that validation fails with empty codecs
-    with pytest.raises(ValidationError, match="Invalid length. Expected 1 or more, got 0"):
+    with pytest.raises(ValidationError, match=r"Invalid length\. Expected 1 or more, got 0"):
         arrayspec.with_codecs(())
 
 

tests/test_pydantic_zarr/test_v2.py

@@ -524,7 +524,7 @@ def test_from_array(shape: tuple[int, ...], dtype: str | None) -> None:
 
 @pytest.mark.parametrize("data", ["/", "a/b/c"])
 def test_member_name(data: str) -> None:
-    with pytest.raises(ValidationError, match='Strings containing "/" are invalid.'):
+    with pytest.raises(ValidationError, match=r'Strings containing "/" are invalid\.'):
         GroupSpec(attributes={}, members={data: GroupSpec(attributes={}, members={})})
 
 

tests/test_pydantic_zarr/test_v3.py

@@ -105,7 +105,7 @@ def test_arrayspec_no_empty_codecs() -> None:
     """
 
     with pytest.raises(
-        ValidationError, match="Value error, Invalid length. Expected 1 or more, got 0."
+        ValidationError, match=r"Value error, Invalid length\. Expected 1 or more, got 0\."
     ):
         ArraySpec(
             shape=(1,),