Backport PR #2633 on branch 0.13.x (docs: adapt to type alias changes) (#2640)

Author: flying-sheep

.github/workflows/check-pr.yml

@@ -57,7 +57,7 @@ jobs:
     name: Check for release notes
     runs-on: ubuntu-latest
     needs: check-milestone
-    if: github.event.pull_request.user.login != 'pre-commit-ci[bot]' && github.event.pull_request.user.login != 'dependabot[bot]' && needs.check-milestone.outputs.no-relnotes-reason == '' && !contains(fromJSON('["style","refactor","test","build","ci"]'), needs.check-milestone.outputs.type)
+    if: github.event.pull_request.user.login != 'pre-commit-ci[bot]' && github.event.pull_request.user.login != 'dependabot[bot]' && needs.check-milestone.outputs.no-relnotes-reason == '' && !contains(fromJSON('["style","refactor","test","build","ci","docs"]'), needs.check-milestone.outputs.type)
     steps:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with: { filter: "blob:none", fetch-depth: 0, persist-credentials: false }

docs/conf.py

@@ -95,6 +95,14 @@ def setup(app: Sphinx) -> None:
     app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
     app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
 
+    # https://github.com/mkdocstrings/python/issues/339
+    from sphinx.domains import ObjType
+    from sphinx.domains.python import PythonDomain
+
+    PythonDomain.object_types.setdefault(
+        "typealias", ObjType("type alias", "type", "obj")
+    )
+
     # TODO: move to scanpydoc
     if TYPE_CHECKING:
         from docutils.nodes import TextElement, reference
@@ -153,12 +161,8 @@ def res(
     },
     # Can’t use `set_module` for `type`s. When moving out of .experimental, define in actual location.
     "anndata._types.StorageType": "anndata.experimental.StorageType",
-    # https://github.com/theislab/scanpydoc/issues/254
-    "anndata.typing.Index1D": "anndata.typing.Index1D",
-    "anndata.typing.Index": "anndata.typing.Index",
-    "anndata.typing.RWAble": "anndata.typing.RWAble",
-    "anndata.typing.AxisStorable": "anndata.typing.AxisStorable",
-    "anndata.typing.InMemoryArray": "anndata.typing.InMemoryArray",
+    #### zarr
+    "zarr.core.group.StoreLike": "zarr.storage.StoreLike",
     #### h5py
     "h5py._hl.group.Group": "h5py.Group",
     "h5py._hl.files.File": "h5py.File",

pyproject.toml

@@ -60,19 +60,20 @@ dev = [
     { include-group = "dev-doc" },
 ]
 doc = [
-    "sphinx>=9.1.0",
-    "sphinx-book-theme>=1.1.0",
-    "sphinx-autodoc-typehints>=3.6.2",
-    "sphinx-issues>=5.0.1",
-    "sphinx-copybutton",
-    "sphinxext.opengraph",
+    "awkward>=2.6.3",
+    "ipython",                             # For syntax highlighting in notebooks
     "myst-nb>=1.4",
+    "myst-parser",
     "scanpydoc[theme,typehints] >=0.17.1",
     "scverse-misc[sphinx]",
-    "awkward>=2.6.3",
-    "IPython",                             # For syntax highlighting in notebooks
-    "myst-parser",
+    "sphinx>=9.1",
+    "sphinx-book-theme>=1.1",
+    # TODO: drop URL once https://github.com/tox-dev/sphinx-autodoc-typehints/pull/766 is released
+    "sphinx-autodoc-typehints @ git+https://github.com/tox-dev/sphinx-autodoc-typehints@refs/pull/766/head",
     "sphinx-design",
+    "sphinx-issues>=5.0.1",
+    "sphinx-copybutton",
+    "sphinxext.opengraph",
     "anndata[dask]",
     "pandas>=3",
     "mudata",