Bump anndata to 0.12.16 and mudata to 0.3.8

Author: DriesSchaumont

CHANGELOG.md

@@ -50,7 +50,9 @@
 
 * `workflows/multiomics/process_samples`: refactored to use a shared `process_singlesample_base` subworkflow, which is also used by the new `process_singlesample` workflow to avoid code duplication (PR #1147).
 
-* Bump anndata to `0.12.11` (PR #1174).
+* Bump anndata to `0.12.16` (PR #1174 and PR #).
+
+* Bump mudata to `0.3.8` (PR #).
 
 * Add missing `example` fields to several component and workflow configurations (PR #1067).
 

src/base/requirements/anndata.yaml

@@ -1,4 +1,4 @@
 packages:
-  - anndata~=0.12.11
+  - anndata~=0.12.16
   - awkward #Required for reading VDJ data stored in AIRR format
-  - scipy!=1.17.* # Pinning scipy because https://github.com/scverse/anndata/issues/339
+  - scipy~=1.17.1 # Exclude scipy 1.17.0 because https://github.com/scverse/anndata/issues/339

src/base/requirements/anndata_mudata.yaml

@@ -1,5 +1,5 @@
 __merge__: [/src/base/requirements/anndata.yaml, .]
 packages:
-  - mudata~=0.3.2
+  - mudata~=0.3.8
 script: |
     exec("try:\n  import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  assert int(version(\"zarr\").partition(\".\")[0]) > 2")

src/convert/from_h5ad_to_h5mu/script.py

@@ -38,6 +38,7 @@
     pass
 
 # Set var index names to avoid https://github.com/scverse/mudata/issues/146
+# TODO: Will be fixed in mudata 0.3.9
 for key, name in var_index_names.items():
     mudata.mod[key].var.index.name = name