From 8e8abb4e59295d9a31831a18f057f9cf4310c60e Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Mon, 27 May 2024 17:37:35 +0100
Subject: [PATCH 1/9] Automatically generate API reference

---
 docs/api.rst             | 22 ------------------
 docs/api/attrs.rst       | 16 -------------
 docs/api/codecs.rst      | 23 ------------------
 docs/api/convenience.rst | 14 -----------
 docs/api/core.rst        |  5 ----
 docs/api/creation.rst    | 15 ------------
 docs/api/hierarchy.rst   | 41 --------------------------------
 docs/api/n5.rst          |  5 ----
 docs/api/storage.rst     | 50 ----------------------------------------
 docs/api/sync.rst        |  6 -----
 docs/conf.py             | 15 ++++++++----
 docs/index.rst           |  2 +-
 pyproject.toml           |  2 +-
 13 files changed, 13 insertions(+), 203 deletions(-)
 delete mode 100644 docs/api.rst
 delete mode 100644 docs/api/attrs.rst
 delete mode 100644 docs/api/codecs.rst
 delete mode 100644 docs/api/convenience.rst
 delete mode 100644 docs/api/core.rst
 delete mode 100644 docs/api/creation.rst
 delete mode 100644 docs/api/hierarchy.rst
 delete mode 100644 docs/api/n5.rst
 delete mode 100644 docs/api/storage.rst
 delete mode 100644 docs/api/sync.rst

diff --git a/docs/api.rst b/docs/api.rst
deleted file mode 100644
index 2b6e7ea516..0000000000
--- a/docs/api.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-API reference
-=============
-
-.. toctree::
-    :maxdepth: 3
-
-    api/creation
-    api/core
-    api/hierarchy
-    api/storage
-    api/n5
-    api/convenience
-    api/codecs
-    api/attrs
-    api/sync
-
-Indices and tables
-------------------
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/docs/api/attrs.rst b/docs/api/attrs.rst
deleted file mode 100644
index 067b45fac6..0000000000
--- a/docs/api/attrs.rst
+++ /dev/null
@@ -1,16 +0,0 @@
-The Attributes class (``zarr.v2.attrs``)
-========================================
-.. module:: zarr.v2.attrs
-
-.. autoclass:: Attributes
-
-    .. automethod:: __getitem__
-    .. automethod:: __setitem__
-    .. automethod:: __delitem__
-    .. automethod:: __iter__
-    .. automethod:: __len__
-    .. automethod:: keys
-    .. automethod:: asdict
-    .. automethod:: put
-    .. automethod:: update
-    .. automethod:: refresh
diff --git a/docs/api/codecs.rst b/docs/api/codecs.rst
deleted file mode 100644
index 454c5ccd20..0000000000
--- a/docs/api/codecs.rst
+++ /dev/null
@@ -1,23 +0,0 @@
-Compressors and filters (``zarr.v2.codecs``)
-============================================
-.. module:: zarr.codecs
-
-This module contains compressor and filter classes for use with Zarr. Please note that this module
-is provided for backwards compatibility with previous versions of Zarr. From Zarr version 2.2
-onwards, all codec classes have been moved to a separate package called Numcodecs_. The two
-packages (Zarr and Numcodecs_) are designed to be used together. For example, a Numcodecs_ codec
-class can be used as a compressor for a Zarr array::
-
-    >>> import zarr.v2
-    >>> from numcodecs import Blosc
-    >>> z = zarr.v2.zeros(1000000, compressor=Blosc(cname='zstd', clevel=1, shuffle=Blosc.SHUFFLE))
-
-Codec classes can also be used as filters. See the tutorial section on :ref:`tutorial_filters`
-for more information.
-
-Please note that it is also relatively straightforward to define and register custom codec
-classes. See the Numcodecs `codec API <https://numcodecs.readthedocs.io/en/latest/abc.html>`_ and
-`codec registry <https://numcodecs.readthedocs.io/en/latest/registry.html>`_ documentation for more
-information.
-
-.. _Numcodecs: https://numcodecs.readthedocs.io/
diff --git a/docs/api/convenience.rst b/docs/api/convenience.rst
deleted file mode 100644
index 1ff26452fa..0000000000
--- a/docs/api/convenience.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-Convenience functions (``zarr.v2.convenience``)
-===============================================
-.. automodule:: zarr.v2.convenience
-.. autofunction:: open
-.. autofunction:: save
-.. autofunction:: load
-.. autofunction:: save_array
-.. autofunction:: save_group
-.. autofunction:: copy
-.. autofunction:: copy_all
-.. autofunction:: copy_store
-.. autofunction:: tree
-.. autofunction:: consolidate_metadata
-.. autofunction:: open_consolidated
diff --git a/docs/api/core.rst b/docs/api/core.rst
deleted file mode 100644
index aacd03e2a5..0000000000
--- a/docs/api/core.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-The Array class (``zarr.v2.core``)
-==================================
-
-.. automodapi:: zarr.v2.core
-   :no-heading:
diff --git a/docs/api/creation.rst b/docs/api/creation.rst
deleted file mode 100644
index ad0a2ead49..0000000000
--- a/docs/api/creation.rst
+++ /dev/null
@@ -1,15 +0,0 @@
-Array creation (``zarr.v2.creation``)
-=====================================
-.. module:: zarr.v2.creation
-.. autofunction:: create
-.. autofunction:: empty
-.. autofunction:: zeros
-.. autofunction:: ones
-.. autofunction:: full
-.. autofunction:: array
-.. autofunction:: open_array
-.. autofunction:: empty_like
-.. autofunction:: zeros_like
-.. autofunction:: ones_like
-.. autofunction:: full_like
-.. autofunction:: open_like
diff --git a/docs/api/hierarchy.rst b/docs/api/hierarchy.rst
deleted file mode 100644
index 5d9280af1e..0000000000
--- a/docs/api/hierarchy.rst
+++ /dev/null
@@ -1,41 +0,0 @@
-Groups (``zarr.v2.hierarchy``)
-==============================
-.. module:: zarr.v2.hierarchy
-
-.. autofunction:: group
-.. autofunction:: open_group
-
-.. autoclass:: Group
-
-    .. automethod:: __len__
-    .. automethod:: __iter__
-    .. automethod:: __contains__
-    .. automethod:: __getitem__
-    .. automethod:: __enter__
-    .. automethod:: __exit__
-    .. automethod:: group_keys
-    .. automethod:: groups
-    .. automethod:: array_keys
-    .. automethod:: arrays
-    .. automethod:: visit
-    .. automethod:: visitkeys
-    .. automethod:: visitvalues
-    .. automethod:: visititems
-    .. automethod:: tree
-    .. automethod:: create_group
-    .. automethod:: require_group
-    .. automethod:: create_groups
-    .. automethod:: require_groups
-    .. automethod:: create_dataset
-    .. automethod:: require_dataset
-    .. automethod:: create
-    .. automethod:: empty
-    .. automethod:: zeros
-    .. automethod:: ones
-    .. automethod:: full
-    .. automethod:: array
-    .. automethod:: empty_like
-    .. automethod:: zeros_like
-    .. automethod:: ones_like
-    .. automethod:: full_like
-    .. automethod:: move
diff --git a/docs/api/n5.rst b/docs/api/n5.rst
deleted file mode 100644
index 22e490bad4..0000000000
--- a/docs/api/n5.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-N5 (``zarr.v2.n5``)
-===================
-.. automodule:: zarr.v2.n5
-
-.. autoclass:: N5Store
diff --git a/docs/api/storage.rst b/docs/api/storage.rst
deleted file mode 100644
index d0ebd8a429..0000000000
--- a/docs/api/storage.rst
+++ /dev/null
@@ -1,50 +0,0 @@
-Storage (``zarr.v2.storage``)
-=============================
-.. automodule:: zarr.v2.storage
-
-.. autoclass:: MemoryStore
-.. autoclass:: DirectoryStore
-.. autoclass:: TempStore
-.. autoclass:: NestedDirectoryStore
-.. autoclass:: ZipStore
-
-    .. automethod:: close
-    .. automethod:: flush
-
-.. autoclass:: DBMStore
-
-    .. automethod:: close
-    .. automethod:: flush
-
-.. autoclass:: LMDBStore
-
-    .. automethod:: close
-    .. automethod:: flush
-
-.. autoclass:: SQLiteStore
-
-    .. automethod:: close
-
-.. autoclass:: MongoDBStore
-.. autoclass:: RedisStore
-.. autoclass:: LRUStoreCache
-
-    .. automethod:: invalidate
-    .. automethod:: invalidate_values
-    .. automethod:: invalidate_keys
-
-.. autoclass:: ABSStore
-
-.. autoclass:: FSStore
-
-.. autoclass:: ConsolidatedMetadataStore
-
-.. autofunction:: init_array
-.. autofunction:: init_group
-.. autofunction:: contains_array
-.. autofunction:: contains_group
-.. autofunction:: listdir
-.. autofunction:: rmdir
-.. autofunction:: getsize
-.. autofunction:: rename
-.. autofunction:: migrate_1to2
diff --git a/docs/api/sync.rst b/docs/api/sync.rst
deleted file mode 100644
index ff961543af..0000000000
--- a/docs/api/sync.rst
+++ /dev/null
@@ -1,6 +0,0 @@
-Synchronization (``zarr.v2.sync``)
-==================================
-.. module:: zarr.v2.sync
-
-.. autoclass:: ThreadSynchronizer
-.. autoclass:: ProcessSynchronizer
diff --git a/docs/conf.py b/docs/conf.py
index 318843a9fb..1a20ff2cc2 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -42,7 +42,7 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
-    "sphinx_automodapi.automodapi",
+    'autoapi.extension',
     "numpydoc",
     "sphinx_issues",
     "sphinx_copybutton",
@@ -53,8 +53,15 @@
 numpydoc_class_members_toctree = False
 issues_github_path = "zarr-developers/zarr-python"
 
-automodapi_inheritance_diagram = False
-automodapi_toctreedirnm = "_autoapi"
+autoapi_dirs = ['../src/zarr']
+autoapi_add_toctree_entry = False
+autoapi_root = "api"
+
+def skip_submodules(app, what, name, obj, skip, options):
+    if "v2" in name:
+        skip = True
+    return skip
+
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -166,9 +173,9 @@
 html_logo = "_static/logo1.png"
 
 
-# Add custom css
 def setup(app):
     app.add_css_file("custom.css")
+    app.connect("autoapi-skip-member", skip_submodules)
 
 
 # The name of an image file (relative to this directory) to use as a favicon of
diff --git a/docs/index.rst b/docs/index.rst
index 06f79b7e7c..d1d354a741 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -10,7 +10,7 @@ Zarr-Python
 
     getting_started
     tutorial
-    api
+    api/zarr/index
     spec
     release
     license
diff --git a/pyproject.toml b/pyproject.toml
index 96a884b737..7298524814 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -63,7 +63,7 @@ jupyter = [
 docs = [
     'sphinx',
     'sphinx-autobuild>=2021.3.14',
-    'sphinx-automodapi',
+    'sphinx-autoapi',
     'sphinx_design',
     'sphinx-issues',
     'sphinx-copybutton',

From f9db3766fc7fd8feaa4ae29ee52f0bfe403a3d2b Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Mon, 27 May 2024 17:45:11 +0100
Subject: [PATCH 2/9] Remove old automodapi refs

---
 .gitignore     | 1 -
 pyproject.toml | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 7d32026e13..35957f2c99 100644
--- a/.gitignore
+++ b/.gitignore
@@ -51,7 +51,6 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
-docs/_autoapi/
 
 # PyBuilder
 target/
diff --git a/pyproject.toml b/pyproject.toml
index 7298524814..0accb16463 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -145,7 +145,7 @@ features = ['docs']
 
 [tool.hatch.envs.docs.scripts]
 build = "cd docs && make html"
-serve = "sphinx-autobuild docs docs/_build --ignore 'docs/_autoapi/**/*' --host 0.0.0.0"
+serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0"
 
 [tool.ruff]
 line-length = 100

From 8cc730579b2c79b8f3d83042afcf29b10554249c Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Mon, 27 May 2024 19:43:24 +0100
Subject: [PATCH 3/9] Fix some doc warnings

---
 docs/conf.py              |  7 +------
 docs/index.rst            |  2 +-
 src/zarr/buffer.py        | 30 +++++++++++++++---------------
 src/zarr/store/local.py   |  1 +
 src/zarr/testing/utils.py |  4 ++--
 5 files changed, 20 insertions(+), 24 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 1a20ff2cc2..8ccb4e5ee0 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -56,11 +56,7 @@
 autoapi_dirs = ['../src/zarr']
 autoapi_add_toctree_entry = False
 autoapi_root = "api"
-
-def skip_submodules(app, what, name, obj, skip, options):
-    if "v2" in name:
-        skip = True
-    return skip
+autoapi_ignore = ["*v2*"]
 
 
 # Add any paths that contain templates here, relative to this directory.
@@ -175,7 +171,6 @@ def skip_submodules(app, what, name, obj, skip, options):
 
 def setup(app):
     app.add_css_file("custom.css")
-    app.connect("autoapi-skip-member", skip_submodules)
 
 
 # The name of an image file (relative to this directory) to use as a favicon of
diff --git a/docs/index.rst b/docs/index.rst
index d1d354a741..c495ba4c5f 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -80,7 +80,7 @@ Zarr is a file storage format for chunked, compressed, N-dimensional arrays base
 
         +++
 
-        .. button-ref:: api
+        .. button-ref:: api/zarr/index
             :expand:
             :color: dark
             :click-parent:
diff --git a/src/zarr/buffer.py b/src/zarr/buffer.py
index 1a34d9f290..add6c51354 100644
--- a/src/zarr/buffer.py
+++ b/src/zarr/buffer.py
@@ -85,8 +85,8 @@ def all(self) -> bool: ...
     def __eq__(self, other: Any) -> Self:  # type: ignore[explicit-override, override]
         """Element-wise equal
 
-        Notice
-        ------
+        Notes
+        -----
         Type checkers such as mypy complains because the return type isn't a bool like
         its supertype "object", which violates the Liskov substitution principle.
         This is true, but since NumPy's ndarray is defined as an element-wise equal,
@@ -115,8 +115,8 @@ class Buffer:
     array-like instance can be copied/converted to a regular Numpy array
     (host memory).
 
-    Note
-    ----
+    Notes
+    -----
     This buffer is untyped, so all indexing and sizes are in bytes.
 
     Parameters
@@ -186,8 +186,8 @@ def as_array_like(self) -> ArrayLike:
     def as_numpy_array(self) -> npt.NDArray[Any]:
         """Returns the buffer as a NumPy array (host memory).
 
-        Warning
-        -------
+        Notes
+        -----
         Might have to copy data, consider using `.as_array_like()` instead.
 
         Returns
@@ -199,8 +199,8 @@ def as_numpy_array(self) -> npt.NDArray[Any]:
     def to_bytes(self) -> bytes:
         """Returns the buffer as `bytes` (host memory).
 
-        Warning
-        -------
+        Warnings
+        --------
         Will always copy data, only use this method for small buffers such as metadata
         buffers. If possible, use `.as_numpy_array()` or `.as_array_like()` instead.
 
@@ -242,8 +242,8 @@ class NDBuffer:
     ndarray-like instance can be copied/converted to a regular Numpy array
     (host memory).
 
-    Note
-    ----
+    Notes
+    -----
     The two buffer classes Buffer and NDBuffer are very similar. In fact, Buffer
     is a special case of NDBuffer where dim=1, stride=1, and dtype="b". However,
     in order to use Python's type system to differentiate between the contiguous
@@ -288,8 +288,8 @@ def create(
         -------
             New buffer representing a new ndarray_like object
 
-        Developer Notes
-        ---------------
+        Notes
+        -----
         A subclass can overwrite this method to create a ndarray-like object
         other then the default Numpy array.
         """
@@ -342,8 +342,8 @@ def as_ndarray_like(self) -> NDArrayLike:
     def as_numpy_array(self) -> npt.NDArray[Any]:
         """Returns the buffer as a NumPy array (host memory).
 
-        Warning
-        -------
+        Warnings
+        --------
         Might have to copy data, consider using `.as_ndarray_like()` instead.
 
         Returns
@@ -431,7 +431,7 @@ def as_numpy_array_wrapper(
 
     Returns
     -------
-        The result of `func` converted to a `prototype.buffer`
+        The result of `func` converted to a `Buffer`
     """
     return prototype.buffer.from_bytes(func(buf.as_numpy_array()))
 
diff --git a/src/zarr/store/local.py b/src/zarr/store/local.py
index 9238700445..5915559900 100644
--- a/src/zarr/store/local.py
+++ b/src/zarr/store/local.py
@@ -109,6 +109,7 @@ async def get_partial_values(
     ) -> list[Buffer | None]:
         """
         Read byte ranges from multiple keys.
+
         Parameters
         ----------
         key_ranges: List[Tuple[str, Tuple[int, int]]]
diff --git a/src/zarr/testing/utils.py b/src/zarr/testing/utils.py
index 04b05d1b1c..67c6c72de7 100644
--- a/src/zarr/testing/utils.py
+++ b/src/zarr/testing/utils.py
@@ -7,8 +7,8 @@
 def assert_bytes_equal(b1: Buffer | BytesLike | None, b2: Buffer | BytesLike | None) -> None:
     """Help function to assert if two bytes-like or Buffers are equal
 
-    Warning
-    -------
+    Warnings
+    --------
     Always copies data, only use for testing and debugging
     """
     if isinstance(b1, Buffer):

From e33b5ddef4d4691d16712d62643adcdcc3c0294d Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Mon, 27 May 2024 21:13:15 +0100
Subject: [PATCH 4/9] Skip private modules

---
 docs/conf.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/conf.py b/docs/conf.py
index 8ccb4e5ee0..ad8b1e896d 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -58,6 +58,11 @@
 autoapi_root = "api"
 autoapi_ignore = ["*v2*"]
 
+def skip_private_modules(app, what: str, name: str, obj, skip: bool, options) -> bool:
+    if what == "module" and "._" in name:
+       return True
+    return False
+
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -171,6 +176,7 @@
 
 def setup(app):
     app.add_css_file("custom.css")
+    app.connect("autoapi-skip-member", skip_private_modules)
 
 
 # The name of an image file (relative to this directory) to use as a favicon of

From 7be27bab4e725fde1d5a43a12a0307c999cc5f95 Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Mon, 27 May 2024 21:20:28 +0100
Subject: [PATCH 5/9] Skip all private objects

---
 docs/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index ad8b1e896d..678c7c57ca 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -59,7 +59,7 @@
 autoapi_ignore = ["*v2*"]
 
 def skip_private_modules(app, what: str, name: str, obj, skip: bool, options) -> bool:
-    if what == "module" and "._" in name:
+    if "._" in name:
        return True
     return False
 

From c11a8e9d8b054c98361fc375cb7c10bebd0fe72d Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Fri, 7 Jun 2024 18:07:39 +0100
Subject: [PATCH 6/9] Add API ref page for zarr namespace

---
 docs/api/index.rst | 7 +++++++
 docs/api/zarr.rst  | 5 +++++
 docs/conf.py       | 7 ++++++-
 docs/index.rst     | 4 ++--
 4 files changed, 20 insertions(+), 3 deletions(-)
 create mode 100644 docs/api/index.rst
 create mode 100644 docs/api/zarr.rst

diff --git a/docs/api/index.rst b/docs/api/index.rst
new file mode 100644
index 0000000000..58ea531905
--- /dev/null
+++ b/docs/api/index.rst
@@ -0,0 +1,7 @@
+API Reference
+=============
+
+.. toctree::
+    :maxdepth: 1
+
+    zarr
diff --git a/docs/api/zarr.rst b/docs/api/zarr.rst
new file mode 100644
index 0000000000..8a9216f19e
--- /dev/null
+++ b/docs/api/zarr.rst
@@ -0,0 +1,5 @@
+zarr
+====
+
+.. autoapimodule:: zarr
+    :members:
diff --git a/docs/conf.py b/docs/conf.py
index 678c7c57ca..b2e31cb94f 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -15,6 +15,9 @@
 
 import os
 import sys
+from typing import Any
+
+import sphinx.application
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -22,6 +25,7 @@
 #
 # The short X.Y version.
 import zarr
+import sphinx
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -55,10 +59,11 @@
 
 autoapi_dirs = ['../src/zarr']
 autoapi_add_toctree_entry = False
+autoapi_generate_api_docs = False
 autoapi_root = "api"
 autoapi_ignore = ["*v2*"]
 
-def skip_private_modules(app, what: str, name: str, obj, skip: bool, options) -> bool:
+def skip_private_modules(app: sphinx.application.Sphinx, what: str, name: str, obj: Any, skip: bool, options: dict) -> bool:
     if "._" in name:
        return True
     return False
diff --git a/docs/index.rst b/docs/index.rst
index c495ba4c5f..92f9a3df18 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -10,7 +10,7 @@ Zarr-Python
 
     getting_started
     tutorial
-    api/zarr/index
+    api/index
     spec
     release
     license
@@ -80,7 +80,7 @@ Zarr is a file storage format for chunked, compressed, N-dimensional arrays base
 
         +++
 
-        .. button-ref:: api/zarr/index
+        .. button-ref:: api/index
             :expand:
             :color: dark
             :click-parent:

From 4b053758fc4d577770e8d995711838d4b7245cdf Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Fri, 7 Jun 2024 18:13:10 +0100
Subject: [PATCH 7/9] Fix import errors with zarr.v2

---
 docs/conf.py        | 9 +--------
 src/zarr/v2/core.py | 5 ++---
 2 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index b2e31cb94f..e5063299ec 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -61,12 +61,6 @@
 autoapi_add_toctree_entry = False
 autoapi_generate_api_docs = False
 autoapi_root = "api"
-autoapi_ignore = ["*v2*"]
-
-def skip_private_modules(app: sphinx.application.Sphinx, what: str, name: str, obj: Any, skip: bool, options: dict) -> bool:
-    if "._" in name:
-       return True
-    return False
 
 
 # Add any paths that contain templates here, relative to this directory.
@@ -179,9 +173,8 @@ def skip_private_modules(app: sphinx.application.Sphinx, what: str, name: str, o
 html_logo = "_static/logo1.png"
 
 
-def setup(app):
+def setup(app: sphinx.application.Sphinx) -> None:
     app.add_css_file("custom.css")
-    app.connect("autoapi-skip-member", skip_private_modules)
 
 
 # The name of an image file (relative to this directory) to use as a favicon of
diff --git a/src/zarr/v2/core.py b/src/zarr/v2/core.py
index c1223daced..9eeb467d68 100644
--- a/src/zarr/v2/core.py
+++ b/src/zarr/v2/core.py
@@ -8,11 +8,11 @@
 from typing import Any
 
 import numpy as np
-from numcodecs.compat import ensure_bytes
+from numcodecs import AsType, get_codec
+from numcodecs.compat import ensure_bytes, ensure_ndarray_like
 
 from zarr.v2._storage.store import _prefix_to_attrs_key
 from zarr.v2.attrs import Attributes
-from zarr.v2.codecs import AsType, get_codec
 from zarr.v2.context import Context
 from zarr.v2.errors import ArrayNotFoundError, ReadOnlyError, ArrayIndexError
 from zarr.v2.indexing import (
@@ -56,7 +56,6 @@
     normalize_shape,
     normalize_storage_path,
     PartialReadBuffer,
-    ensure_ndarray_like,
 )
 
 __all__ = ["Array"]

From c95d6a1d72596760583bc346c6d2b65908420ec7 Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Fri, 7 Jun 2024 18:16:11 +0100
Subject: [PATCH 8/9] Remove old numpydoc validation

---
 docs/conf.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index e5063299ec..fe605a366a 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -53,8 +53,6 @@
     "sphinx_design",
 ]
 
-numpydoc_show_class_members = False
-numpydoc_class_members_toctree = False
 issues_github_path = "zarr-developers/zarr-python"
 
 autoapi_dirs = ['../src/zarr']

From dfa0caf7bdbb677b1484364420d9b2459c64528c Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Fri, 7 Jun 2024 18:21:41 +0100
Subject: [PATCH 9/9] Use groupwise member order

---
 docs/conf.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/conf.py b/docs/conf.py
index fe605a366a..35afa60577 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -58,6 +58,7 @@
 autoapi_dirs = ['../src/zarr']
 autoapi_add_toctree_entry = False
 autoapi_generate_api_docs = False
+autoapi_member_order = "groupwise"
 autoapi_root = "api"