Backport PR #2352: docs: update scverse-misc to 0.1 (#2510)

.gitignore

@@ -24,8 +24,9 @@ __pycache__/
 .ipynb_checkpoints
 
 # docs
-/docs/generated/
 /docs/_build/
+/docs/generated/*
+!/docs/generated/anndata.types.ExtensionNamespace.rst
 
 # IDEs
 /.idea/

docs/api.md

@@ -214,12 +214,14 @@ Types used by the former:
 Types used by the former:
 
 ```{eval-rst}
-.. autosummary::
-   :toctree: generated/
+.. toctree::
+   :hidden:
 
-   types.ExtensionNamespace
+   generated/anndata.types.ExtensionNamespace
 ```
 
+{class}`scverse_misc.ExtensionNamespace`
+
 (errors-api)=
 
 ## Errors and warnings
@@ -241,6 +243,7 @@ Types used by the former:
 
    settings
    settings.override
+   settings.reset
 ```
 
 (types-api)=

docs/conf.py

@@ -58,6 +58,7 @@
     "sphinx_design",
     "sphinxext.opengraph",
     "scanpydoc",  # needs to be before linkcode
+    "scverse_misc.sphinx_ext",
     "sphinx.ext.linkcode",
     "IPython.sphinxext.ipython_console_highlighting",
     *(p.stem for p in _extension_dir.glob("*.py")),
@@ -136,11 +137,11 @@ def res(
     pandas=("https://pandas.pydata.org/pandas-docs/version/2.3", None),
     python=("https://docs.python.org/3", None),
     scipy=("https://docs.scipy.org/doc/scipy", None),
+    scverse_misc=("https://scverse-misc.readthedocs.io/stable", None),
     sklearn=("https://scikit-learn.org/stable", None),
     xarray=("https://docs.xarray.dev/en/stable", None),
     zarr=("https://zarr.readthedocs.io/en/stable/", None),
     zarrs=("https://zarrs-python.readthedocs.io/en/stable/", None),
-    scverse_misc=("https://scverse-misc.readthedocs.io/stable", None),
     annbatch=("https://annbatch.readthedocs.io/en/stable/", None),
 )
 
@@ -175,6 +176,10 @@ def res(
     "awkward.highlevel.Array": "ak.Array",
     "numpy.int64": ("py:attr", "numpy.int64"),
     "numpy.dtypes.StringDType": ("py:attr", "numpy.dtypes.StringDType"),
+    "numpy._typing._array_like.NDArray": ("py:data", "numpy.typing.NDArray"),
+    # For some reason after https://github.com/numpy/numpy/commit/cc5aaf2cc744dfbc0a16c1d20607853874307333
+    # sphinx is still looking for this type here even though our min bound is 1.26
+    "numpy._typing._array_like.GenericAlias": ("py:class", "types.GenericAlias"),
     "pandas.DataFrame.iloc": ("py:attr", "pandas.DataFrame.iloc"),
     "pandas.DataFrame.loc": ("py:attr", "pandas.DataFrame.loc"),
     "pandas.core.series.Series": "pandas.Series",

docs/generated/anndata.types.ExtensionNamespace.rst

@@ -0,0 +1,5 @@
+anndata.types.ExtensionNamespace
+================================
+
+.. version-deprecated:: 0.13.0
+   Use :class:`scverse_misc.ExtensionNamespace` instead

pyproject.toml

@@ -70,6 +70,7 @@ doc = [
     "sphinxext.opengraph",
     "myst-nb",
     "scanpydoc[theme,typehints] >=0.17.1",
+    "scverse-misc[sphinx]",
     "awkward>=2.6.3",
     "IPython",                             # For syntax highlighting in notebooks
     "myst-parser",

src/anndata/_core/extensions.py

@@ -1,12 +1,24 @@
 from __future__ import annotations
 
+import sys
+import warnings
+
 from scverse_misc import make_register_namespace_decorator
 
 from .anndata import AnnData
 
 __all__ = ["register_anndata_namespace"]
 
 
-register_anndata_namespace = make_register_namespace_decorator(
-    AnnData, "adata", "register_anndata_namespace", "numpy"
-)
+if sys.version_info >= (3, 12):
+    register_anndata_namespace = make_register_namespace_decorator(AnnData, "adata")
+else:
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            r".*argument is deprecated and will be removed in the future",
+            DeprecationWarning,
+        )
+        register_anndata_namespace = make_register_namespace_decorator(
+            AnnData, "adata", "register_anndata_namespace", "numpy"
+        )

src/anndata/experimental/pytorch/_annloader.py

@@ -120,6 +120,9 @@ def compose_convert(arr):
 
 
 # AnnLoader has the same arguments as DataLoader, but uses BatchIndexSampler by default
+@deprecated(
+    Deprecation("0.12.17", "Use :class:`annbatch.Loader` instead of `AnnLoader`")
+)
 class AnnLoader(DataLoader):
     """\
     PyTorch DataLoader for AnnData objects.
@@ -128,9 +131,6 @@ class AnnLoader(DataLoader):
     :class:`~anndata.experimental.AnnCollection` object or from an `AnnCollectionView` object.
     Takes care of the required conversions.
 
-    .. deprecated:: 0.12.17
-        Use :class:`annbatch.Loader` instead.
-
     Parameters
     ----------
     adatas
@@ -152,9 +152,6 @@ class AnnLoader(DataLoader):
         arguments for `AnnCollection` initialization.
     """
 
-    @deprecated(
-        Deprecation("0.12.17", "Use {class}`annbatch.Loader` instead of `AnnLoader`")
-    )
     @old_positionals("batch_size", "shuffle", "use_default_converter", "use_cuda")
     def __init__(
         self,