Update filter x (#324)

* update filters * fix return * add releasenote * update notebooks for counts * update multi_notebook
scverse · Feb 18, 2025 · 621e7de · 621e7de
1 parent d4ce145
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diff --git a/docs/release-notes/0.12.0.md b/docs/release-notes/0.12.0.md
@@ -0,0 +1,14 @@
+### 0.12.0 {small}`the-future`
+
+```{rubric} Features
+```
+* Updates `pp.filter_genes` & `pp.filter_cells` to be closer to the `scanpy` implementation {pr}`324` {smaller}`S Dicks`
+
+```{rubric} Performance
+```
+
+```{rubric} Bug fixes
+```
+
+```{rubric} Misc
+```
diff --git a/docs/release-notes/index.md b/docs/release-notes/index.md
@@ -2,6 +2,10 @@
 
 # Release notes
 
+## Version 0.12.0
+```{include} /release-notes/0.12.0.md
+```
+
 ## Version 0.11.0
 ```{include} /release-notes/0.11.1.md
 ```

diff --git a/notebooks b/notebooks
diff --git a/src/rapids_singlecell/preprocessing/_scrublet/__init__.py b/src/rapids_singlecell/preprocessing/_scrublet/__init__.py
@@ -187,10 +187,8 @@ def _run_scrublet(ad_obs: AnnData, ad_sim: AnnData | None = None):
         # counts and simulating doublets
 
         if ad_sim is None:
-            pp.filter_genes(ad_obs, min_count=3, verbose=False)
-            pp.filter_cells(
-                ad_obs, min_count=3, qc_var="n_genes_by_counts", verbose=False
-            )
+            pp.filter_genes(ad_obs, min_cells=3, verbose=False)
+            pp.filter_cells(ad_obs, min_genes=3, verbose=False)
 
             # Doublet simulation will be based on the un-normalised counts, but on the
             # selection of genes following normalisation and variability filtering. So
+6 −5		demo_gpu-PR.ipynb
+2 −2		demo_gpu-seuratv3-brain-1M.ipynb
+2 −2		demo_gpu-seuratv3.ipynb
+2 −2		demo_gpu.ipynb
+3 −3		multi_gpu_show.ipynb