feat: move hashsolo to sc.pp

docs/api/preprocessing.md

@@ -76,6 +76,16 @@ Also see {ref}`data integration tools <data-integration>` and external {ref}`ext
    pp.scrublet_simulate_doublets
 ```
 
+## Sample demultiplexing
+
+```{eval-rst}
+.. autosummary::
+   :nosignatures:
+   :toctree: generated/
+
+   pp.hashsolo
+```
+
 ## Neighbors
 
 ```{eval-rst}

docs/conf.py

@@ -184,6 +184,7 @@
     "pp.filter_cells": (["np", "sp", "da"], []),
     "pp.filter_genes": (["np", "sp", "da"], []),
     "pp.harmony_integrate": (["np"], []),
+    "pp.hashsolo": (["np", "sp"], []),
     "pp.highly_variable_genes": (["np", "sp", "da"], ["da[sp[csc]]"]),
     "pp.log1p": (["np", "sp", "da"], []),
     "pp.neighbors": (["np", "sp"], []),

docs/external/preprocessing.md

@@ -7,6 +7,7 @@
 
 Previously found here, but now part of scanpy’s main API:
 - {func}`scanpy.pp.harmony_integrate`
+- {func}`scanpy.pp.hashsolo`
 - {func}`scanpy.pp.scrublet`
 - {func}`scanpy.pp.scrublet_simulate_doublets`
 

docs/release-notes/4303.feat.md

@@ -0,0 +1,3 @@
+Move {func}`scanpy.external.pp.hashsolo` into scanpy’s main API as {func}`scanpy.pp.hashsolo` and deprecate the old location.
+The new function takes {mod}`anndata.acc` references, so the hashing counts can live in {attr}`~anndata.AnnData.obs`, in the data matrix (e.g. `A.X[:, ["Hash1", "Hash2"]]`), or all together in {attr}`~anndata.AnnData.obsm` (e.g. `A.obsm["hto"]`),
+and writes its results to `.obs[key_added]` and `.obsm[key_added]` instead of six unnamespaced `.obs` columns {smaller}`P Angerer`