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scverse · Dec 18, 2023 · 4ef04f2 · 4ef04f2
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diff --git a/docs/release-notes/1.9.7.md b/docs/release-notes/1.9.7.md
@@ -7,3 +7,4 @@
 - Fix {func}`scanpy.pl.violin` usage of `seaborn.catplot` {pr}`2739` {smaller}`E Roellin`
 - Fix {func}`scanpy.pp.highly_variable_genes` to handle the combinations of `inplace` and `subset` consistently {pr}`2757` {smaller}`E Roellin`
 - Replace usage of various deprecated functionality from {mod}`anndata` and {mod}`pandas` {pr}`2678` {pr}`2779` {smaller}`P Angerer`
+- Allow to use default `n_top_genes` when using {func}`scanpy.pp.highly_variable_genes` flavor `'seurat_v3'` {pr}`2782` {smaller}`P Angerer`
diff --git a/scanpy/tests/test_highly_variable_genes.py b/scanpy/tests/test_highly_variable_genes.py
@@ -387,12 +387,16 @@ def test_higly_variable_genes_compare_to_seurat_v3():
     seu = pd.Index(seurat_hvg_info_batch["x"].values)
     assert len(seu.intersection(df.index)) / 4000 > 0.95
 
+
+@needs.skmisc
+def test_higly_variable_genes_seurat_v3_warning():
+    pbmc = pbmc3k()[:200].copy()
     sc.pp.log1p(pbmc)
     with pytest.warns(
         UserWarning,
         match="`flavor='seurat_v3'` expects raw count data, but non-integers were found.",
     ):
-        sc.pp.highly_variable_genes(pbmc, n_top_genes=1000, flavor="seurat_v3")
+        sc.pp.highly_variable_genes(pbmc, flavor="seurat_v3")
 
 
 def test_filter_genes_dispersion_compare_to_seurat():