From f5719b0ce77f00e77ffecc3896373894e6d18dad Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Mar 2026 18:57:08 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: v2.3.10 → v2.4.6](https://github.com/biomejs/pre-commit/compare/v2.3.10...v2.4.6)
- [github.com/astral-sh/ruff-pre-commit: v0.14.11 → v0.15.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.11...v0.15.5)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7b5c4676..12ecdfaa 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,11 +7,11 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/biomejs/pre-commit
-      rev: v2.3.10
+      rev: v2.4.6
       hooks:
           - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.14.11
+      rev: v0.15.5
       hooks:
           - id: ruff-check
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]

From e3415eb42f6e958d432e484d811d65957630c7af Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Mar 2026 18:57:30 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 biomni/tool/cancer_biology.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/biomni/tool/cancer_biology.py b/biomni/tool/cancer_biology.py
index c512bbea..4824a271 100644
--- a/biomni/tool/cancer_biology.py
+++ b/biomni/tool/cancer_biology.py
@@ -1233,8 +1233,9 @@ def norm_chr(x):
                     r_end = r["end"]
                     r_start = r["start"]
                     overlaps["ov_len"] = overlaps.apply(
-                        lambda row, r_end=r_end, r_start=r_start: min(row[end_col], r_end)
-                        - max(row[start_col], r_start),
+                        lambda row, r_end=r_end, r_start=r_start: (
+                            min(row[end_col], r_end) - max(row[start_col], r_start)
+                        ),
                         axis=1,
                     )
                     best = overlaps.sort_values("ov_len", ascending=False).iloc[0]