From 0ff8979d9ca6f109cd8a38f9d4ed0c67e9447525 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Jan 2026 22:08:27 +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:
- https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror
- [github.com/psf/black-pre-commit-mirror: 25.1.0 → 26.1.0](https://github.com/psf/black-pre-commit-mirror/compare/25.1.0...26.1.0)
- [github.com/asottile/blacken-docs: 1.19.1 → 1.20.0](https://github.com/asottile/blacken-docs/compare/1.19.1...1.20.0)
- [github.com/PyCQA/isort: 6.0.0 → 7.0.0](https://github.com/PyCQA/isort/compare/6.0.0...7.0.0)
- [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0)
- [github.com/PyCQA/flake8: 7.1.2 → 7.3.0](https://github.com/PyCQA/flake8/compare/7.1.2...7.3.0)
- [github.com/asottile/pyupgrade: v3.19.1 → v3.21.2](https://github.com/asottile/pyupgrade/compare/v3.19.1...v3.21.2)
---
 .pre-commit-config.yaml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ad1d18d..1d2ff7a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,8 +6,8 @@ default_stages:
     - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: 25.1.0
+    - repo: https://github.com/psf/black-pre-commit-mirror
+      rev: 26.1.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
@@ -15,11 +15,11 @@ repos:
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.19.1
+      rev: 1.20.0
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
-      rev: 6.0.0
+      rev: 7.0.0
       hooks:
           - id: isort
     - repo: https://github.com/asottile/yesqa
@@ -34,7 +34,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v5.0.0
+      rev: v6.0.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -53,7 +53,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 7.1.2
+      rev: 7.3.0
       hooks:
           - id: flake8
             additional_dependencies:
@@ -64,7 +64,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.19.1
+      rev: v3.21.2
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

From 6266c91d73cad39cf869c2ac8083044c6395f256 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Jan 2026 22:08:55 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 ALLCools/clustering/feature_selection/feature_enrichment.py | 2 +-
 ALLCools/plot/genome_track/GtfTrack.py                      | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/ALLCools/clustering/feature_selection/feature_enrichment.py b/ALLCools/clustering/feature_selection/feature_enrichment.py
index e197dee..26e3833 100644
--- a/ALLCools/clustering/feature_selection/feature_enrichment.py
+++ b/ALLCools/clustering/feature_selection/feature_enrichment.py
@@ -241,7 +241,7 @@ def cluster_enriched_features(
             null_values = null_enrichment.iloc[row, :].sort_values()
             values = enrichment.iloc[row, :]
             pvals = 1 - np.searchsorted(null_values, values) / values.shape[0]
-            (_, q, _, _) = multipletests(pvals, alpha, method="fdr_bh")
+            _, q, _, _ = multipletests(pvals, alpha, method="fdr_bh")
             qvals[row, :] = q
         qvals = pd.DataFrame(qvals, index=enrichment.index, columns=enrichment.columns)
 
diff --git a/ALLCools/plot/genome_track/GtfTrack.py b/ALLCools/plot/genome_track/GtfTrack.py
index 4d9e6f6..ed27312 100644
--- a/ALLCools/plot/genome_track/GtfTrack.py
+++ b/ALLCools/plot/genome_track/GtfTrack.py
@@ -181,9 +181,7 @@ class GtfTrack(BedTrack):
 
     SUPPORTED_ENDINGS = ["gtf", "gtf.gz", "gtf.db"]
     TRACK_TYPE = "gtf"
-    OPTIONS_TXT = (
-        GenomeTrack.OPTIONS_TXT
-        + f"""
+    OPTIONS_TXT = GenomeTrack.OPTIONS_TXT + f"""
 # By default the transcript_name is used.
 # If you want to use the gene_name:
 # prefered_name = gene_name
@@ -255,7 +253,6 @@ class GtfTrack(BedTrack):
 # optional. If not given is guessed from the file ending.
 file_type = {TRACK_TYPE}
     """
-    )
 
     DEFAULTS_PROPERTIES = {
         "fontsize": 12,