link zarr.core.config in docstrings

Author: brokkoli71

src/zarr/api/asynchronous.py

@@ -839,20 +839,20 @@ async def create(
         - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``.
         - For Unicode strings, the default is ``VLenUTF8Codec``.
         - For bytes or objects, the default is ``VLenBytesCodec``.
-        These defaults can be changed using the `array.v3_default_codecs` variable in the Zarr config.
+        These defaults can be changed using the ``array.v3_default_codecs`` variable in :mod:`zarr.core.config`.
     compressor : Codec, optional
         Primary compressor to compress chunk data.
         V2 only. V3 arrays should use ``codecs`` instead.
         If neither ``compressor`` nor ``filters`` are provided, a default compressor will be used:
         - For numeric arrays, the default is ``ZstdCodec``.
         - For Unicode strings, the default is ``VLenUTF8Codec``.
         - For bytes or objects, the default is ``VLenBytesCodec``.
-        These defaults can be changed using the `array.v2_default_compressor` variable in the Zarr config.
+        These defaults can be changed using the ``array.v2_default_compressor`` variable in :mod:`zarr.core.config`.
     fill_value : object
         Default value to use for uninitialized portions of the array.
     order : {'C', 'F'}, optional
         Memory layout to be used within each chunk.
-        If not specified, default is taken from the Zarr config ``array.order``.
+        If not specified, default is taken from the Zarr config ```array.order```.
     store : Store or str
         Store or path to directory in file system or name of zip file.
     synchronizer : object, optional

src/zarr/core/array.py

@@ -424,19 +424,19 @@ async def create(
             - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v3_default_codecs` variable in the Zarr config.
+            These defaults can be changed using the ``array.v3_default_codecs`` variable in :mod:`zarr.core.config`.
         dimension_names : Iterable[str], optional
             The names of the dimensions (default is None).
             V3 only. V2 arrays should not use this parameter.
         chunks : ShapeLike, optional
             The shape of the array's chunks.
-            V2 only. V3 arrays should use :attr:`chunk_shape` instead.
+            V2 only. V3 arrays should use ``chunk_shape`` instead.
             If not specified, default are guessed based on the shape and dtype.
         dimension_separator : Literal[".", "/"], optional
             The dimension separator (default is ".").
             V2 only. V3 arrays should use ``chunk_key_encoding`` instead.
         order : Literal["C", "F"], optional
-            The order of the array (default is specified in the Zarr config `array.order`).
+            The order of the array (default is specified by ``array.order`` in :mod:`zarr.core.config`).
         filters : list[dict[str, JSON]], optional
             Sequence of filters to use to encode chunk data prior to compression.
             V2 only. V3 arrays should use ``codecs`` instead. If neither ``compressor``
@@ -449,7 +449,7 @@ async def create(
             - For numeric arrays, the default is ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v2_default_compressor` variable in the Zarr config.
+            These defaults can be changed using the ``array.v2_default_compressor`` variable in :mod:`zarr.core.config`.
         overwrite : bool, optional
             Whether to raise an error if the store already exists (default is False).
         data : npt.ArrayLike, optional
@@ -1516,19 +1516,19 @@ def create(
             - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v3_default_codecs` variable in the Zarr config.
+            These defaults can be changed using the ``array.v3_default_codecs`` variable in :mod:`zarr.core.config`.
         dimension_names : Iterable[str], optional
             The names of the dimensions (default is None).
             V3 only. V2 arrays should not use this parameter.
         chunks : ChunkCoords, optional
             The shape of the array's chunks.
-            V2 only. V3 arrays should use :attr:`chunk_shape` instead.
+            V2 only. V3 arrays should use ``chunk_shape`` instead.
             If not specified, default are guessed based on the shape and dtype.
         dimension_separator : Literal[".", "/"], optional
             The dimension separator (default is ".").
             V2 only. V3 arrays should use ``chunk_key_encoding`` instead.
         order : Literal["C", "F"], optional
-            The order of the array (default is specified in the Zarr config `array.order`).
+            The order of the array (default is specified by ``array.order`` in :mod:`zarr.core.config`).
         filters : list[dict[str, JSON]], optional
             Sequence of filters to use to encode chunk data prior to compression.
             V2 only. V3 arrays should use ``codecs`` instead. If neither ``compressor``
@@ -1541,7 +1541,7 @@ def create(
             - For numeric arrays, the default is ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v2_default_compressor` variable in the Zarr config.
+            These defaults can be changed using the ``array.v2_default_compressor`` variable in :mod:`zarr.core.config`.
         overwrite : bool, optional
             Whether to raise an error if the store already exists (default is False).
 

src/zarr/core/config.py

@@ -1,3 +1,15 @@
+"""
+The config module is responsible for managing the configuration of zarr and  is based on the Donfig python library.
+For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, first register the implementations
+in the registry and then select them in the config.
+e.g. an implementation of the bytes codec in a class "your.module.NewBytesCodec", requires the value of codecs.bytes
+to be "your.module.NewBytesCodec".
+Donfig can be configured programmatically, by environment variables, or from YAML files in standard locations
+e.g. export ZARR_CODECS__BYTES="your.module.NewBytesCodec"
+(for more information see github.com/pytroll/donfig)
+Default values below point to the standard implementations of zarr-python
+"""
+
 from __future__ import annotations
 
 from typing import Any, Literal, cast
@@ -10,7 +22,7 @@ class BadConfigError(ValueError):
 
 
 class Config(DConfig):  # type: ignore[misc]
-    """Will collect configuration from config files and environment variables
+    """The Config will collect configuration from config files and environment variables
 
     Example environment variables:
     Grabs environment variables of the form "ZARR_FOO__BAR_BAZ=123" and
@@ -28,15 +40,6 @@ def reset(self) -> None:
         self.refresh()
 
 
-# The config module is responsible for managing the configuration of zarr and  is based on the Donfig python library.
-# For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, first register the implementations
-# in the registry and then select them in the config.
-# e.g. an implementation of the bytes codec in a class "your.module.NewBytesCodec", requires the value of codecs.bytes
-# to be "your.module.NewBytesCodec".
-# Donfig can be configured programmatically, by environment variables, or from YAML files in standard locations
-# e.g. export ZARR_CODECS__BYTES="your.module.NewBytesCodec"
-# (for more information see github.com/pytroll/donfig)
-# Default values below point to the standard implementations of zarr-python
 config = Config(
     "zarr",
     defaults=[

src/zarr/core/group.py

@@ -1049,18 +1049,18 @@ async def create_array(
             - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v3_default_codecs` variable in the Zarr config.
+            These defaults can be changed using the ``array.v3_default_codecs`` variable in :mod:`zarr.core.config`.
         dimension_names : Iterable[str] | None = None
             The names of the dimensions of the array. V3 only.
         chunks : ChunkCoords | None = None
             The shape of the chunks of the array.
-            V2 only. V3 arrays should use :attr:`chunk_shape` instead.
+            V2 only. V3 arrays should use ``chunk_shape`` instead.
             If not specified, default are guessed based on the shape and dtype.
         dimension_separator : Literal[".", "/"] | None = None
             The delimiter used for the chunk keys. (default: ".")
             V2 only. V3 arrays should use ``chunk_key_encoding`` instead.
         order : Literal["C", "F"] | None = None
-            The memory order of the array (default is specified in the Zarr config `array.order`).
+            The memory order of the array (default is specified by ``array.order`` in :mod:`zarr.core.config`).
         filters : list[dict[str, JSON]] | None = None
             Sequence of filters to use to encode chunk data prior to compression.
             V2 only. V3 arrays should use ``codecs`` instead. If neither ``compressor``
@@ -1073,7 +1073,7 @@ async def create_array(
             - For numeric arrays, the default is ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v2_default_compressor` variable in the Zarr config.
+            These defaults can be changed using the ``array.v2_default_compressor`` variable in :mod:`zarr.core.config`.
         overwrite : bool = False
             If True, a pre-existing array or group at the path of this array will
             be overwritten. If False, the presence of a pre-existing array or group is
@@ -2270,18 +2270,18 @@ def create_array(
             - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v3_default_codecs` variable in the Zarr config.
+            These defaults can be changed using the ``array.v3_default_codecs`` variable in :mod:`zarr.core.config`.
         dimension_names : Iterable[str] | None = None
             The names of the dimensions of the array. V3 only.
         chunks : ChunkCoords | None = None
             The shape of the chunks of the array.
-            V2 only. V3 arrays should use :attr:`chunk_shape` instead.
+            V2 only. V3 arrays should use ``chunk_shape`` instead.
             If not specified, default are guessed based on the shape and dtype.
         dimension_separator : Literal[".", "/"] | None = None
             The delimiter used for the chunk keys. (default: ".")
             V2 only. V3 arrays should use ``chunk_key_encoding`` instead.
         order : Literal["C", "F"] | None = None
-            The memory order of the array (default is specified in the Zarr config `array.order`).
+            The memory order of the array (default is specified by ``array.order`` in :mod:`zarr.core.config`).
         filters : list[dict[str, JSON]] | None = None
             Sequence of filters to use to encode chunk data prior to compression.
             V2 only. V3 arrays should use ``codecs`` instead. If neither ``compressor``
@@ -2294,7 +2294,7 @@ def create_array(
             - For numeric arrays, the default is ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v2_default_compressor` variable in the Zarr config.
+            These defaults can be changed using the ``array.v2_default_compressor`` variable in :mod:`zarr.core.config`.
         overwrite : bool = False
             If True, a pre-existing array or group at the path of this array will
             be overwritten. If False, the presence of a pre-existing array or group is
@@ -2634,18 +2634,18 @@ def array(
             - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v3_default_codecs` variable in the Zarr config.
+            These defaults can be changed using the ``array.v3_default_codecs`` variable in :mod:`zarr.core.config`.
         dimension_names : Iterable[str] | None = None
             The names of the dimensions of the array. V3 only.
         chunks : ChunkCoords | None = None
             The shape of the chunks of the array.
-            V2 only. V3 arrays should use :attr:`chunk_shape` instead.
+            V2 only. V3 arrays should use ``chunk_shape`` instead.
             If not specified, default are guessed based on the shape and dtype.
         dimension_separator : Literal[".", "/"] | None = None
             The delimiter used for the chunk keys. (default: ".")
             V2 only. V3 arrays should use ``chunk_key_encoding`` instead.
         order : Literal["C", "F"] | None = None
-            The memory order of the array (default is specified in the Zarr config `array.order`).
+            The memory order of the array (default is specified by ``array.order`` in :mod:`zarr.core.config`).
         filters : list[dict[str, JSON]] | None = None
             Sequence of filters to use to encode chunk data prior to compression.
             V2 only. V3 arrays should use ``codecs`` instead. If neither ``compressor``
@@ -2658,7 +2658,7 @@ def array(
             - For numeric arrays, the default is ``ZstdCodec``.
             - For Unicode strings, the default is ``VLenUTF8Codec``.
             - For bytes or objects, the default is ``VLenBytesCodec``.
-            These defaults can be changed using the `array.v2_default_compressor` variable in the Zarr config.
+            These defaults can be changed using the ``array.v2_default_compressor`` variable in :mod:`zarr.core.config`.
         overwrite : bool = False
             If True, a pre-existing array or group at the path of this array will
             be overwritten. If False, the presence of a pre-existing array or group is