Fixup: Fix doc test, Anndata/Scanpy incompatibility

aeisenbarth · aeisenbarth · commit cc15f064b60c · 2026-02-22T18:26:34.000+01:00
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -31,7 +31,11 @@ Plain AnnData with ScanPy
 SquidPy
 -------
 
+.. note:: Example may not work
+   SquidPy (0.4.1) is not anymore compatible with the dependencies used in this project.
+
 .. testcode::
+   :skipif: True
 
    from metaspace_converter import metaspace_to_anndata
    import squidpy as sq
diff --git a/pyproject.toml b/pyproject.toml
@@ -55,7 +55,7 @@ docs = [
     # For example code in documentation
     "scanpy~=1.11.5",
     "spatialdata-plot~=0.2.9",
-    "squidpy~=1.4.1",
+    #"squidpy~=1.4.1", # Has not been updated to anndata>0.10.9, which is incompatible with SpatialData
 ]
 
 [project.urls]

Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ docs = [`
`55`	`55`	`# For example code in documentation`
`56`	`56`	`"scanpy~=1.11.5",`
`57`	`57`	`"spatialdata-plot~=0.2.9",`
`58`		`- "squidpy~=1.4.1",`
	`58`	`+ #"squidpy~=1.4.1", # Has not been updated to anndata>0.10.9, which is incompatible with SpatialData`
`59`	`59`	`]`
`60`	`60`
`61`	`61`	`[project.urls]`