Merge branch 'main' into main

AminAlam · Sep 2, 2024 · 6c9f4f6 · 6c9f4f6
2 parents cf0b43d + 3c13495
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diff --git a/docs/extensions/canonical_tutorial.py b/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)
diff --git a/docs/how-to/knn-transformers.ipynb b/docs/how-to/knn-transformers.ipynb
@@ -1 +1 @@
-../../notebooks/knn-transformers.ipynb
+../../notebooks/how-to/knn-transformers.ipynb
diff --git a/docs/how-to/plotting-with-marsilea.ipynb b/docs/how-to/plotting-with-marsilea.ipynb
@@ -1 +1 @@
-../../notebooks/plotting-with-marsilea.ipynb
+../../notebooks/how-to/plotting-with-marsilea.ipynb
diff --git a/notebooks b/notebooks
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		@@ -1 +1 @@
		../../notebooks/knn-transformers.ipynb
		../../notebooks/how-to/knn-transformers.ipynb
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		@@ -1 +1 @@
		../../notebooks/plotting-with-marsilea.ipynb
		../../notebooks/how-to/plotting-with-marsilea.ipynb
+1 −1		.pre-commit-config.yaml
+1 −0		.readthedocs.yml
+1 −1		README.rst
+15 −0		_static/css/custom.css
+9 −0		basic-scrna-tutorial.ipynb
+81 −23		conf.py
+96 −120		dask.ipynb
+8 −0		how-to/knn-transformers.ipynb
+16 −8		how-to/plotting-with-marsilea.ipynb
+7 −3		index.rst
+8 −0		integrating-data-using-ingest.ipynb
+8 −0		paga-paul15.ipynb
+8 −0		pbmc3k.ipynb
+9 −0		plotting/advanced.ipynb
+8 −0		plotting/core.ipynb
+2 −1		pyproject.toml
+8 −0		spatial/basic-analysis.ipynb
+12 −4		spatial/integration-scanorama.ipynb
+26 −18		tutorial_pearson_residuals.ipynb