Backport PR scverse#1574 on branch 0.10.x ([pre-commit.ci] pre-commit…

… autoupdate) (scverse#1575)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.5
+    rev: v0.5.6
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

docs/conf.py

@@ -189,3 +189,40 @@ def setup(app: Sphinx):
         "Miscellaneous",
     )
 ]
+
+
+def patch_sphinx_toolbox_autoprotocol():
+    """Compat hack: https://github.com/sphinx-toolbox/sphinx-toolbox/issues/168"""
+
+    from sphinx.ext.autodoc import ObjectMember
+    from sphinx_toolbox.more_autodoc.autoprotocol import ProtocolDocumenter
+
+    if TYPE_CHECKING:
+        from typing import Self
+
+    class ObjectMemberCompat(ObjectMember):
+        @classmethod
+        def from_other(cls, other: ObjectMember) -> Self:
+            return cls(
+                other.__name__,
+                other.object,
+                docstring=other.docstring,
+                class_=other.class_,
+                skipped=other.skipped,
+            )
+
+        def __iter__(self):
+            return iter([self.__name__, self.object])
+
+    filter_orig = ProtocolDocumenter.filter_members
+
+    def filter_members(
+        self, members: list[ObjectMember], want_all: bool
+    ) -> list[tuple[str, object, bool]]:
+        member_tuples = [ObjectMemberCompat.from_other(m) for m in members]
+        return filter_orig(self, member_tuples, want_all)
+
+    ProtocolDocumenter.filter_members = filter_members
+
+
+patch_sphinx_toolbox_autoprotocol()

docs/news.md

@@ -1,6 +1,6 @@
 # Muon paper published {small}`2022-02-02`
 
-Muon has been published in Genome Biology [^cite_bredikhin22].
+Muon has been published in Genome Biology [Bredikhin22]_.
 Muon is a framework for multimodal data built on top of `AnnData`.
 
 Check out [Muon](https://muon.readthedocs.io/en/latest/) and its datastructure [MuData](https://mudata.readthedocs.io/en/latest/).