diff --git a/.ci/get_workflow_status.py b/.ci/get_workflow_status.py
index e2e8926bd692..875345c2efde 100644
--- a/.ci/get_workflow_status.py
+++ b/.ci/get_workflow_status.py
@@ -6,6 +6,7 @@
 
 TRIGGER_PHRASE: Code phrase that triggers workflow.
 """
+
 import json
 from os import environ
 from sys import argv, exit
diff --git a/.nuget/create_nuget.py b/.nuget/create_nuget.py
index ec954dae7ca3..1e6258dbcdb3 100644
--- a/.nuget/create_nuget.py
+++ b/.nuget/create_nuget.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 """Script for generating files with NuGet package metadata."""
+
 import datetime
 import sys
 from pathlib import Path
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8ffb6a8f8f2f..6c8732a01416 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ exclude: |
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -25,7 +25,7 @@ repos:
         args: ["--settings-path", "python-package/pyproject.toml"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.2.1
+    rev: v0.4.7
     hooks:
       # Run the linter.
       - id: ruff
diff --git a/docs/conf.py b/docs/conf.py
index 2780f47d913f..f8bd29a69922 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -17,6 +17,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute.
 """Sphinx configuration file."""
+
 import datetime
 import os
 import sys
diff --git a/helpers/check_dynamic_dependencies.py b/helpers/check_dynamic_dependencies.py
index fcf41ea52701..087061d9575c 100644
--- a/helpers/check_dynamic_dependencies.py
+++ b/helpers/check_dynamic_dependencies.py
@@ -12,6 +12,7 @@
 * GLIBCXX: https://gcc.gnu.org/onlinedocs/libstdc++/manual/abi.html
 * OMP/GOMP: https://github.com/gcc-mirror/gcc/blob/master/libgomp/libgomp.map
 """
+
 import re
 import sys
 from pathlib import Path
diff --git a/helpers/parameter_generator.py b/helpers/parameter_generator.py
index fb1749638bca..15db36da2bb2 100644
--- a/helpers/parameter_generator.py
+++ b/helpers/parameter_generator.py
@@ -6,6 +6,7 @@
 along with parameters description in LightGBM/docs/Parameters.rst file
 from the information in LightGBM/include/LightGBM/config.h file.
 """
+
 import re
 from collections import defaultdict
 from pathlib import Path
diff --git a/python-package/lightgbm/__init__.py b/python-package/lightgbm/__init__.py
index ae38a6169a22..600f71284159 100644
--- a/python-package/lightgbm/__init__.py
+++ b/python-package/lightgbm/__init__.py
@@ -3,6 +3,7 @@
 
 Contributors: https://github.com/microsoft/LightGBM/graphs/contributors.
 """
+
 from pathlib import Path
 
 from .basic import Booster, Dataset, Sequence, register_logger
diff --git a/python-package/lightgbm/basic.py b/python-package/lightgbm/basic.py
index 8e33d0ab56f2..5bfb8dcbbb58 100644
--- a/python-package/lightgbm/basic.py
+++ b/python-package/lightgbm/basic.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 """Wrapper for C API of LightGBM."""
+
 import abc
 import ctypes
 import inspect
diff --git a/python-package/lightgbm/callback.py b/python-package/lightgbm/callback.py
index e776ea953bd1..ae1e72c549d4 100644
--- a/python-package/lightgbm/callback.py
+++ b/python-package/lightgbm/callback.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 """Callbacks library."""
+
 from collections import OrderedDict
 from dataclasses import dataclass
 from functools import partial
diff --git a/python-package/lightgbm/dask.py b/python-package/lightgbm/dask.py
index 928fe51bddce..e15979bc40db 100644
--- a/python-package/lightgbm/dask.py
+++ b/python-package/lightgbm/dask.py
@@ -6,6 +6,7 @@
 
 It is based on dask-lightgbm, which was based on dask-xgboost.
 """
+
 import operator
 import socket
 from collections import defaultdict
diff --git a/python-package/lightgbm/engine.py b/python-package/lightgbm/engine.py
index 74b211f4a426..5f93824458d4 100644
--- a/python-package/lightgbm/engine.py
+++ b/python-package/lightgbm/engine.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 """Library with training routines of LightGBM."""
+
 import copy
 import json
 import warnings
diff --git a/python-package/lightgbm/libpath.py b/python-package/lightgbm/libpath.py
index 09eb946e3c45..a55e7362ab44 100644
--- a/python-package/lightgbm/libpath.py
+++ b/python-package/lightgbm/libpath.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 """Find the path to LightGBM dynamic library files."""
+
 from pathlib import Path
 from platform import system
 from typing import List
diff --git a/python-package/lightgbm/plotting.py b/python-package/lightgbm/plotting.py
index 9bcc1b928ffd..1c7bda5c68b6 100644
--- a/python-package/lightgbm/plotting.py
+++ b/python-package/lightgbm/plotting.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 """Plotting library."""
+
 import math
 from copy import deepcopy
 from io import BytesIO
diff --git a/python-package/lightgbm/sklearn.py b/python-package/lightgbm/sklearn.py
index 1ea7b47c5462..9f1a62f542ca 100644
--- a/python-package/lightgbm/sklearn.py
+++ b/python-package/lightgbm/sklearn.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 """Scikit-learn wrapper interface for LightGBM."""
+
 import copy
 from inspect import signature
 from pathlib import Path