Use ruff

.pre-commit-config.yaml

@@ -5,15 +5,9 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
--   repo: https://github.com/psf/black
-    rev: 23.3.0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
     hooks:
-    -   id: black
--   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-    -   id: isort
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-    -   id: flake8
+    -   id: ruff
+        args: [--fix, --show-fixes]
+    -   id: ruff-format

pycdhit/__init__.py

@@ -4,7 +4,7 @@
 from ._commands import *  # noqa: F403
 from ._io import *  # noqa: F403
 
-VERSION = "1.1.2"
+VERSION = "1.1.3"
 
 __all__ = [  # noqa: F405
     "CommandBase",

pyproject.toml

@@ -28,9 +28,7 @@ dynamic = ["version"]
 [project.optional-dependencies]
 dev = [
     "pre-commit==3.3.2",
-    "black==23.3.0",
-    "flake8==6.0.0",
-    "isort==5.12.0",
+    "ruff==0.6.9",
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
     "notebook>=6.5.4",
@@ -47,5 +45,9 @@ packages = ["pycdhit"]
 [tool.setuptools.dynamic]
 version = {attr = "pycdhit.VERSION"}
 
-[tool.black]
+[tool.ruff]
 line-length = 79
+extend-exclude = ["*.ipynb"]
+
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F", "I"]