Backport PR #2782: Fix Seurat n_top_genes default (#2783)

docs/release-notes/1.9.7.md

@@ -6,3 +6,5 @@
 - Specify correct version of `matplotlib` dependency {pr}`2733` {smaller}`P Fisher`
 - 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`

scanpy/preprocessing/_highly_variable_genes.py

@@ -1,5 +1,8 @@
+from __future__ import annotations
+
 import warnings
-from typing import Literal, Optional
+from inspect import signature
+from typing import Literal, Optional, cast
 
 import numpy as np
 import pandas as pd
@@ -301,13 +304,13 @@ def _highly_variable_genes_single_batch(
 
 def highly_variable_genes(
     adata: AnnData,
-    layer: Optional[str] = None,
-    n_top_genes: Optional[int] = None,
-    min_disp: Optional[float] = 0.5,
-    max_disp: Optional[float] = np.inf,
-    min_mean: Optional[float] = 0.0125,
-    max_mean: Optional[float] = 3,
-    span: Optional[float] = 0.3,
+    layer: str | None = None,
+    n_top_genes: int | None = None,
+    min_disp: float | None = 0.5,
+    max_disp: float | None = np.inf,
+    min_mean: float | None = 0.0125,
+    max_mean: float | None = 3,
+    span: float = 0.3,
     n_bins: int = 20,
     flavor: Literal["seurat", "cell_ranger", "seurat_v3"] = "seurat",
     subset: bool = False,
@@ -432,6 +435,9 @@ def highly_variable_genes(
         )
 
     if flavor == "seurat_v3":
+        if n_top_genes is None:
+            sig = signature(_highly_variable_genes_seurat_v3)
+            n_top_genes = cast(int, sig.parameters["n_top_genes"].default)
         return _highly_variable_genes_seurat_v3(
             adata,
             layer=layer,