From 1c0f64e2cb505e4bc5adc9d11be1db26aaa5320a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 15 Dec 2025 16:30:49 +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/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/astral-sh/ruff-pre-commit: v0.8.2 → v0.14.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.2...v0.14.9)
---
 .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 a832683..8513aa2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -19,7 +19,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.2
+  rev: v0.14.9
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

From b85229781de25f872d8826854bfb3faa894b2976 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 15 Dec 2025 16:33:13 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/requirements.txt  |  4 ++--
 setup.py               | 10 +++++-----
 tests/conftest.py      |  1 -
 tests/test_real.py     |  2 --
 tests/test_registry.py |  4 +---
 tests/test_txdb.py     |  1 -
 6 files changed, 8 insertions(+), 14 deletions(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index a1b9d2b..c20cf60 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,9 +1,9 @@
+furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-myst-nb
-furo
 sphinx-autodoc-typehints
diff --git a/setup.py b/setup.py
index a21d0a0..1a4cd32 100644
--- a/setup.py
+++ b/setup.py
@@ -1,10 +1,10 @@
 """
-    Setup file for txdb.
-    Use setup.cfg to configure your project.
+Setup file for txdb.
+Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.6.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.6.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 
 from setuptools import setup
diff --git a/tests/conftest.py b/tests/conftest.py
index e807f1c..4702fd9 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -7,7 +7,6 @@
 - https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
-import os
 import sqlite3
 
 import pytest
diff --git a/tests/test_real.py b/tests/test_real.py
index 16aaf87..ab8cc9c 100644
--- a/tests/test_real.py
+++ b/tests/test_real.py
@@ -1,5 +1,3 @@
-import pytest
-
 from txdb import TxDb, TxDbRegistry
 
 __author__ = "Jayaram Kancherla"
diff --git a/tests/test_registry.py b/tests/test_registry.py
index a540c5e..cad84d4 100644
--- a/tests/test_registry.py
+++ b/tests/test_registry.py
@@ -1,10 +1,8 @@
 import sqlite3
-from unittest.mock import MagicMock, patch
 
 import pytest
-from genomicranges import SeqInfo
 
-from txdb import TxDb, TxDbRegistry
+from txdb import TxDbRegistry
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "Jayaram Kancherla"
diff --git a/tests/test_txdb.py b/tests/test_txdb.py
index 231fdf6..2a4e631 100644
--- a/tests/test_txdb.py
+++ b/tests/test_txdb.py
@@ -1,4 +1,3 @@
-import pytest
 from biocframe import BiocFrame
 from genomicranges import GenomicRanges
 from iranges import IRanges