Add some more numpydoc rules/associated fixes (#2399)

* Add GL09 validation

* Add SS02 rule

* Add SS04

* Enable PR02 rule

Author: dstansby

pyproject.toml

@@ -329,4 +329,15 @@ ignore = [
 
 [tool.numpydoc_validation]
 # See https://numpydoc.readthedocs.io/en/latest/validation.html#built-in-validation-checks for list of checks
-checks = ["GL06", "GL07", "GL10", "PR03", "PR05", "PR06"]
+checks = [
+    "GL06",
+    "GL07",
+    "GL09",
+    "GL10",
+    "SS02",
+    "SS04",
+    "PR02",
+    "PR03",
+    "PR05",
+    "PR06",
+]

src/zarr/abc/codec.py

@@ -85,7 +85,7 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self:
 
         Parameters
         ----------
-        chunk_spec : ArraySpec
+        array_spec : ArraySpec
 
         Returns
         -------
@@ -99,11 +99,11 @@ def validate(self, *, shape: ChunkCoords, dtype: np.dtype[Any], chunk_grid: Chun
 
         Parameters
         ----------
-        shape: ChunkCoords
+        shape : ChunkCoords
             The array shape
-        dtype: np.dtype[Any]
+        dtype : np.dtype[Any]
             The array data type
-        chunk_grid: ChunkGrid
+        chunk_grid : ChunkGrid
             The array chunk grid
         """
         ...
@@ -292,11 +292,11 @@ def validate(self, *, shape: ChunkCoords, dtype: np.dtype[Any], chunk_grid: Chun
 
         Parameters
         ----------
-        shape: ChunkCoords
+        shape : ChunkCoords
             The array shape
-        dtype: np.dtype[Any]
+        dtype : np.dtype[Any]
             The array data type
-        chunk_grid: ChunkGrid
+        chunk_grid : ChunkGrid
             The array chunk grid
         """
         ...
@@ -308,7 +308,7 @@ def compute_encoded_size(self, byte_length: int, array_spec: ArraySpec) -> int:
 
         Parameters
         ----------
-        input_byte_length : int
+        byte_length : int
         array_spec : ArraySpec
 
         Returns
@@ -327,7 +327,7 @@ async def decode(
 
         Parameters
         ----------
-        chunks_and_specs : Iterable[tuple[Buffer | None, ArraySpec]]
+        chunk_bytes_and_specs : Iterable[tuple[Buffer | None, ArraySpec]]
             Ordered set of encoded chunks with their accompanying chunk spec.
 
         Returns
@@ -346,7 +346,7 @@ async def encode(
 
         Parameters
         ----------
-        chunks_and_specs : Iterable[tuple[NDBuffer | None, ArraySpec]]
+        chunk_arrays_and_specs : Iterable[tuple[NDBuffer | None, ArraySpec]]
             Ordered set of to-be-encoded chunks with their accompanying chunk spec.
 
         Returns

src/zarr/abc/store.py

@@ -162,7 +162,7 @@ def with_mode(self, mode: AccessModeLiteral) -> Self:
 
         Parameters
         ----------
-        mode: AccessModeLiteral
+        mode : AccessModeLiteral
             The new mode to use.
 
         Returns

src/zarr/api/asynchronous.py

@@ -68,7 +68,7 @@
 
 
 def _get_shape_chunks(a: ArrayLike | Any) -> tuple[ChunkCoords | None, ChunkCoords | None]:
-    """helper function to get the shape and chunks from an array-like object"""
+    """Helper function to get the shape and chunks from an array-like object"""
     shape = None
     chunks = None
 
@@ -86,7 +86,7 @@ def _get_shape_chunks(a: ArrayLike | Any) -> tuple[ChunkCoords | None, ChunkCoor
 
 
 def _like_args(a: ArrayLike, kwargs: dict[str, Any]) -> dict[str, Any]:
-    """set default values for shape and chunks if they are not present in the array-like object"""
+    """Set default values for shape and chunks if they are not present in the array-like object"""
 
     new = kwargs.copy()
 
@@ -121,7 +121,7 @@ def _like_args(a: ArrayLike, kwargs: dict[str, Any]) -> dict[str, Any]:
 def _handle_zarr_version_or_format(
     *, zarr_version: ZarrFormat | None, zarr_format: ZarrFormat | None
 ) -> ZarrFormat | None:
-    """handle the deprecated zarr_version kwarg and return zarr_format"""
+    """Handle the deprecated zarr_version kwarg and return zarr_format"""
     if zarr_format is not None and zarr_version is not None and zarr_format != zarr_version:
         raise ValueError(
             f"zarr_format {zarr_format} does not match zarr_version {zarr_version}, please only set one"
@@ -135,7 +135,7 @@ def _handle_zarr_version_or_format(
 
 
 def _default_zarr_version() -> ZarrFormat:
-    """return the default zarr_version"""
+    """Return the default zarr_version"""
     return cast(ZarrFormat, int(config.get("default_zarr_version", 3)))
 
 
@@ -152,9 +152,9 @@ async def consolidate_metadata(
 
     Parameters
     ----------
-    store: StoreLike
+    store : StoreLike
         The store-like object whose metadata you wish to consolidate.
-    path: str, optional
+    path : str, optional
         A path to a group in the store to consolidate at. Only children
         below that group will be consolidated.
 
@@ -341,13 +341,13 @@ async def save(
     ----------
     store : Store or str
         Store or path to directory in file system or name of zip file.
-    args : ndarray
+    *args : ndarray
         NumPy arrays with data to save.
     zarr_format : {2, 3, None}, optional
         The zarr format to use when saving.
     path : str or None, optional
         The path within the group where the arrays will be saved.
-    kwargs
+    **kwargs
         NumPy arrays with data to save.
     """
     zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
@@ -386,7 +386,7 @@ async def save_array(
     storage_options : dict
         If using an fsspec URL to create the store, these will be passed to
         the backend implementation. Ignored otherwise.
-    kwargs
+    **kwargs
         Passed through to :func:`create`, e.g., compressor.
     """
     zarr_format = (
@@ -423,7 +423,7 @@ async def save_group(
     ----------
     store : Store or str
         Store or path to directory in file system or name of zip file.
-    args : ndarray
+    *args : ndarray
         NumPy arrays with data to save.
     zarr_format : {2, 3, None}, optional
         The zarr format to use when saving.
@@ -432,7 +432,7 @@ async def save_group(
     storage_options : dict
         If using an fsspec URL to create the store, these will be passed to
         the backend implementation. Ignored otherwise.
-    kwargs
+    **kwargs
         NumPy arrays with data to save.
     """
     zarr_format = (
@@ -479,7 +479,7 @@ async def array(
     ----------
     data : array_like
         The data to fill the array with.
-    kwargs
+    **kwargs
         Passed through to :func:`create`.
 
     Returns

src/zarr/core/array.py

@@ -184,8 +184,6 @@ class AsyncArray(Generic[T_ArrayMetadata]):
         The metadata of the array.
     store_path : StorePath
         The path to the Zarr store.
-    codec_pipeline : CodecPipeline, optional
-        The codec pipeline used for encoding and decoding chunks, by default None.
     order : {'C', 'F'}, optional
         The order of the array data in memory, by default None.
 
@@ -857,9 +855,9 @@ def _iter_chunk_coords(
 
         Parameters
         ----------
-        origin: Sequence[int] | None, default=None
+        origin : Sequence[int] | None, default=None
             The origin of the selection relative to the array's chunk grid.
-        selection_shape: Sequence[int] | None, default=None
+        selection_shape : Sequence[int] | None, default=None
             The shape of the selection in chunk grid coordinates.
 
         Yields
@@ -878,9 +876,9 @@ def _iter_chunk_keys(
 
         Parameters
         ----------
-        origin: Sequence[int] | None, default=None
+        origin : Sequence[int] | None, default=None
             The origin of the selection relative to the array's chunk grid.
-        selection_shape: Sequence[int] | None, default=None
+        selection_shape : Sequence[int] | None, default=None
             The shape of the selection in chunk grid coordinates.
 
         Yields
@@ -901,9 +899,9 @@ def _iter_chunk_regions(
 
         Parameters
         ----------
-        origin: Sequence[int] | None, default=None
+        origin : Sequence[int] | None, default=None
             The origin of the selection relative to the array's chunk grid.
-        selection_shape: Sequence[int] | None, default=None
+        selection_shape : Sequence[int] | None, default=None
             The shape of the selection in chunk grid coordinates.
 
         Yields
@@ -1151,17 +1149,7 @@ async def info(self) -> None:
 
 @dataclass(frozen=True)
 class Array:
-    """Instantiate an array from an initialized store.
-
-    Parameters
-    ----------
-    store : StoreLike
-        The array store that has already been initialized.
-    shape : ChunkCoords
-        The shape of the array.
-    dtype : npt.DTypeLike
-        The dtype of the array.
-    """
+    """Instantiate an array from an initialized store."""
 
     _async_array: AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]
 
@@ -1419,9 +1407,9 @@ def _iter_chunk_coords(
 
         Parameters
         ----------
-        origin: Sequence[int] | None, default=None
+        origin : Sequence[int] | None, default=None
             The origin of the selection relative to the array's chunk grid.
-        selection_shape: Sequence[int] | None, default=None
+        selection_shape : Sequence[int] | None, default=None
             The shape of the selection in chunk grid coordinates.
 
         Yields
@@ -1456,9 +1444,9 @@ def _iter_chunk_keys(
 
         Parameters
         ----------
-        origin: Sequence[int] | None, default=None
+        origin : Sequence[int] | None, default=None
             The origin of the selection relative to the array's chunk grid.
-        selection_shape: Sequence[int] | None, default=None
+        selection_shape : Sequence[int] | None, default=None
             The shape of the selection in chunk grid coordinates.
 
         Yields
@@ -1478,9 +1466,9 @@ def _iter_chunk_regions(
 
         Parameters
         ----------
-        origin: Sequence[int] | None, default=None
+        origin : Sequence[int] | None, default=None
             The origin of the selection relative to the array's chunk grid.
-        selection_shape: Sequence[int] | None, default=None
+        selection_shape : Sequence[int] | None, default=None
             The shape of the selection in chunk grid coordinates.
 
         Yields
@@ -2231,7 +2219,7 @@ def get_mask_selection(
 
         Parameters
         ----------
-        selection : ndarray, bool
+        mask : ndarray, bool
             A Boolean array of the same shape as the array against which the selection is
             being made.
         out : NDBuffer, optional
@@ -2314,7 +2302,7 @@ def set_mask_selection(
 
         Parameters
         ----------
-        selection : ndarray, bool
+        mask : ndarray, bool
             A Boolean array of the same shape as the array against which the selection is
             being made.
         value : npt.ArrayLike

src/zarr/core/buffer/core.py

@@ -308,7 +308,7 @@ class NDBuffer:
 
     Parameters
     ----------
-    ndarray_like
+    array : ndarray_like
         ndarray-like object that is convertible to a regular Numpy array.
     """
 

src/zarr/core/buffer/cpu.py

@@ -138,7 +138,7 @@ class NDBuffer(core.NDBuffer):
 
     Parameters
     ----------
-    ndarray_like
+    array
         ndarray-like object that is convertible to a regular Numpy array.
     """
 

src/zarr/core/buffer/gpu.py

@@ -132,7 +132,7 @@ class NDBuffer(core.NDBuffer):
 
     Parameters
     ----------
-    ndarray_like
+    array
         ndarray-like object that is convertible to a regular Numpy array.
     """
 

src/zarr/core/chunk_grids.py

@@ -42,15 +42,15 @@ def _guess_chunks(
 
     Parameters
     ----------
-    shape: ChunkCoords
+    shape : ChunkCoords
         The chunk shape.
-    typesize: int
+    typesize : int
         The size, in bytes, of each element of the chunk.
-    increment_bytes: int = 256 * 1024
+    increment_bytes : int = 256 * 1024
         The number of bytes used to increment or decrement the target chunk size in bytes.
-    min_bytes: int = 128 * 1024
+    min_bytes : int = 128 * 1024
         The soft lower bound on the final chunk size in bytes.
-    max_bytes: int = 64 * 1024 * 1024
+    max_bytes : int = 64 * 1024 * 1024
         The hard upper bound on the final chunk size in bytes.
 
     Returns