Backport PR scverse#3216: Update notebooks

docs/extensions/canonical_tutorial.py

@@ -0,0 +1,24 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from sphinx.util.docutils import SphinxDirective
+
+if TYPE_CHECKING:
+    from typing import ClassVar
+
+    from docutils import nodes
+    from sphinx.application import Sphinx
+
+
+class CanonicalTutorial(SphinxDirective):
+    """In the scanpy-tutorials repo, this links to the canonical location (here!)."""
+
+    required_arguments: ClassVar = 1
+
+    def run(self) -> list[nodes.Node]:
+        return []
+
+
+def setup(app: Sphinx) -> None:
+    app.add_directive("canonical-tutorial", CanonicalTutorial)

docs/how-to/knn-transformers.ipynb

@@ -1 +1 @@
-../../notebooks/knn-transformers.ipynb
+../../notebooks/how-to/knn-transformers.ipynb

docs/how-to/plotting-with-marsilea.ipynb

@@ -1 +1 @@
-../../notebooks/plotting-with-marsilea.ipynb
+../../notebooks/how-to/plotting-with-marsilea.ipynb