From fcd33993efc6ae67a84e6c4602ae31d0e673cb89 Mon Sep 17 00:00:00 2001
From: shinthor <44301097+shinthor@users.noreply.github.com>
Date: Tue, 2 Jul 2024 16:55:10 -0400
Subject: [PATCH 1/2] add the layer argument for sc.tl.score_genes_cell_cycle

---
 src/scanpy/tools/_score_genes.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/scanpy/tools/_score_genes.py b/src/scanpy/tools/_score_genes.py
index a743abff3..a9520e9d5 100644
--- a/src/scanpy/tools/_score_genes.py
+++ b/src/scanpy/tools/_score_genes.py
@@ -207,6 +207,7 @@ def score_genes_cell_cycle(
     s_genes: Sequence[str],
     g2m_genes: Sequence[str],
     copy: bool = False,
+    layer: str | None = None,
     **kwargs,
 ) -> AnnData | None:
     """\
@@ -226,6 +227,8 @@ def score_genes_cell_cycle(
         List of genes associated with G2M phase.
     copy
         Copy `adata` or modify it inplace.
+    layer
+        Key from `adata.layers` whose value will be used to perform tests on.
     **kwargs
         Are passed to :func:`~scanpy.tl.score_genes`. `ctrl_size` is not
         possible, as it's set as `min(len(s_genes), len(g2m_genes))`.
@@ -254,7 +257,7 @@ def score_genes_cell_cycle(
     adata = adata.copy() if copy else adata
     ctrl_size = min(len(s_genes), len(g2m_genes))
     for genes, name in [(s_genes, "S_score"), (g2m_genes, "G2M_score")]:
-        score_genes(adata, genes, score_name=name, ctrl_size=ctrl_size, **kwargs)
+        score_genes(adata, genes, score_name=name, ctrl_size=ctrl_size, layer=layer, **kwargs)
     scores = adata.obs[["S_score", "G2M_score"]]
 
     # default phase is S

From a00fd76f94caf7ced5b603fb6aee08ad7de8b073 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 5 Jul 2024 11:36:20 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/scanpy/tools/_score_genes.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/scanpy/tools/_score_genes.py b/src/scanpy/tools/_score_genes.py
index a9520e9d5..35ceedac5 100644
--- a/src/scanpy/tools/_score_genes.py
+++ b/src/scanpy/tools/_score_genes.py
@@ -257,7 +257,9 @@ def score_genes_cell_cycle(
     adata = adata.copy() if copy else adata
     ctrl_size = min(len(s_genes), len(g2m_genes))
     for genes, name in [(s_genes, "S_score"), (g2m_genes, "G2M_score")]:
-        score_genes(adata, genes, score_name=name, ctrl_size=ctrl_size, layer=layer, **kwargs)
+        score_genes(
+            adata, genes, score_name=name, ctrl_size=ctrl_size, layer=layer, **kwargs
+        )
     scores = adata.obs[["S_score", "G2M_score"]]
 
     # default phase is S