From f4ac87347a1603d1d8b39576e72dac83aab1ff10 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 22:24:58 +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/asottile/reorder-python-imports: v3.12.0 → v3.16.0](https://github.com/asottile/reorder-python-imports/compare/v3.12.0...v3.16.0)
- [github.com/asottile/add-trailing-comma: v3.2.0 → v4.0.0](https://github.com/asottile/add-trailing-comma/compare/v3.2.0...v4.0.0)
- [github.com/asottile/pyupgrade: v3.20.0 → v3.21.2](https://github.com/asottile/pyupgrade/compare/v3.20.0...v3.21.2)
- https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror
- [github.com/psf/black-pre-commit-mirror: 23.12.1 → 26.1.0](https://github.com/psf/black-pre-commit-mirror/compare/23.12.1...26.1.0)
---
 .pre-commit-config.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c77d8eb..ee4e5f5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
+    rev: v3.16.0
     hooks:
     -   id: reorder-python-imports
         args: ["--py38-plus"]
@@ -14,17 +14,17 @@ repos:
         exclude: ^docs/
 
 -   repo: https://github.com/asottile/add-trailing-comma
-    rev: v3.2.0
+    rev: v4.0.0
     hooks:
     -   id: add-trailing-comma
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.20.0
+    rev: v3.21.2
     hooks:
     -   id: pyupgrade
 
--   repo: https://github.com/psf/black
-    rev: 23.12.1
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.1.0
     hooks:
     -   id: black
         args: ["--safe", "-l120"]

From 6c4a6acf44513340a167a8475a8d2b3d5b77f0ac 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 22:25:08 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 geneplexus/__init__.py            | 1 -
 geneplexus/_config/__init__.py    | 1 +
 geneplexus/_config/config.py      | 1 +
 geneplexus/_config/logger_util.py | 1 +
 geneplexus/cli.py                 | 1 +
 geneplexus/download.py            | 1 +
 geneplexus/geneplexus.py          | 1 +
 geneplexus/util.py                | 1 +
 8 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/geneplexus/__init__.py b/geneplexus/__init__.py
index 5b72b77..2db64e2 100644
--- a/geneplexus/__init__.py
+++ b/geneplexus/__init__.py
@@ -124,6 +124,5 @@
 from . import util
 from .geneplexus import GenePlexus
 
-
 __version__ = "3.0.0"
 __all__ = ["download", "GenePlexus", "util", "config"]
diff --git a/geneplexus/_config/__init__.py b/geneplexus/_config/__init__.py
index eeb3ffe..add5578 100644
--- a/geneplexus/_config/__init__.py
+++ b/geneplexus/_config/__init__.py
@@ -1,4 +1,5 @@
 """Basic configurations."""
+
 from . import config
 from .logger_util import make_logger
 
diff --git a/geneplexus/_config/config.py b/geneplexus/_config/config.py
index 7e0e614..d9a2a4b 100644
--- a/geneplexus/_config/config.py
+++ b/geneplexus/_config/config.py
@@ -1,4 +1,5 @@
 """Global variables used by the GenePlexus library."""
+
 import os.path as osp
 import pathlib
 from typing import Any
diff --git a/geneplexus/_config/logger_util.py b/geneplexus/_config/logger_util.py
index 8c5933f..074a080 100644
--- a/geneplexus/_config/logger_util.py
+++ b/geneplexus/_config/logger_util.py
@@ -1,4 +1,5 @@
 """Logger utilities."""
+
 import logging
 from contextlib import contextmanager
 from typing import Optional
diff --git a/geneplexus/cli.py b/geneplexus/cli.py
index 7723169..f354c4e 100644
--- a/geneplexus/cli.py
+++ b/geneplexus/cli.py
@@ -1,4 +1,5 @@
 """Command line interface for the GenePlexus pipeline."""
+
 import argparse
 import atexit
 import json
diff --git a/geneplexus/download.py b/geneplexus/download.py
index a478198..49721fd 100755
--- a/geneplexus/download.py
+++ b/geneplexus/download.py
@@ -1,4 +1,5 @@
 """Data download module."""
+
 import io
 import os
 import os.path as osp
diff --git a/geneplexus/geneplexus.py b/geneplexus/geneplexus.py
index 287912c..9219898 100755
--- a/geneplexus/geneplexus.py
+++ b/geneplexus/geneplexus.py
@@ -1,4 +1,5 @@
 """GenePlexus API."""
+
 import os
 import os.path as osp
 import tempfile
diff --git a/geneplexus/util.py b/geneplexus/util.py
index 03dafbe..1fb29fc 100755
--- a/geneplexus/util.py
+++ b/geneplexus/util.py
@@ -1,4 +1,5 @@
 """Utilities including file and path handling."""
+
 import functools
 import json
 import os