Merge remote-tracking branch 'origin/main' into fix/1143-hvg-store-seuratv3-details

* origin/main:
  Set `.var` index names in `from_h5ad_to_h5mu` (#1184)

Author: lazappi

CHANGELOG.md

@@ -60,6 +60,8 @@
 
 * `dataflow/split_h5mu`: pin scipy version to 1.16.3 to avoid regression that corrupts large sparse matrix indexing (PR #1153).
 
+* `convert/from_h5ad_h5mu`: store and reset var index names to avoid issues with a change in mudata (PR #1184).
+
 * `feature_annotation/highly_variable_features_scanpy`: always store details of highly variable features, regardless of the features used (PR #1186)
 
 # openpipelines 4.0.4

src/convert/from_h5ad_to_h5mu/script.py

@@ -29,13 +29,18 @@
 }
 
 logger.info("Converting to mudata")
+var_index_names = {key: adata.var.index.name for key, adata in data.items()}
 mudata = mu.MuData(data)
 
 try:
     mudata.var_names_make_unique()
 except (TypeError, ValueError):
     pass
 
+# Set var index names to avoid https://github.com/scverse/mudata/issues/146
+for key, name in var_index_names.items():
+    mudata.mod[key].var.index.name = name
+
 logger.info("Writing to %s.", par["output"])
 mudata.write_h5mu(par["output"], compression=par["output_compression"])