Use Ruff instead of other lint/formatting tools

.pre-commit-config.yaml

@@ -1,57 +1,14 @@
+ci:
+  autoupdate_schedule: quarterly
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.12.1
-  hooks:
-  - id: black
-    name: black
-    description: "Black: The uncompromising Python code formatter"
-    entry: black
-    language: python
-    language_version: python3
-    minimum_pre_commit_version: 2.9.2
-    require_serial: true
-    types_or: [python, pyi]
-  - id: black-jupyter
-    name: black-jupyter
-    description:
-      "Black: The uncompromising Python code formatter (with Jupyter Notebook support)"
-    entry: black
-    language: python
-    minimum_pre_commit_version: 2.9.2
-    require_serial: true
-    types_or: [python, pyi, jupyter]
-    additional_dependencies: [".[jupyter]"]
-
-- repo: https://github.com/pycqa/flake8
-  rev: 7.0.0
-  hooks:
-  - id: flake8
-    additional_dependencies:
-    - flake8-bugbear
-    - flake8-comprehensions
-    - flake8-simplify
-
-- repo: https://gitlab.com/kennon.mckeever/nbhooks
-  rev: 1.0.1
-  hooks:
-  - id: nb-ensure-clean
-    name: nb-ensure-clean
-    description: Ensure that committed Jupyter notebooks contain no outputs.
-    entry: nb-ensure-clean
-    files: \.ipynb$
-    language: python
-
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
-  hooks:
-  - id: pyupgrade
-    args: [--py310-plus]
-
-- repo: https://github.com/asottile/reorder-python-imports
-  rev: v3.12.0
-  hooks:
-  - id: reorder-python-imports
-    args: [--py310-plus, --add-import, "from __future__ import annotations"]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.8.1
+  hooks:
+    # Run the linter
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter
+    - id: ruff-format
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
@@ -75,20 +32,10 @@ repos:
           .gitignore
         )
 
-- repo: https://github.com/PyCQA/pydocstyle
-  rev: 6.3.0
-  hooks:
-  - id: pydocstyle
-    files: bmipy/.*\.py$
-    args:
-    - --convention=numpy
-    - --add-select=D417
-    additional_dependencies: [".[toml]"]
-
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: v1.8.0
   hooks:
   - id: mypy
-    language_version: python3.12
-    additional_dependencies: [types-all]
+    #language_version: python3.12
+    #additional_dependencies: [types-all]
     files: src/.*\.py$

noxfile.py

@@ -1,3 +1,5 @@
+"""Nox configuration."""
+
 from __future__ import annotations
 
 import os

pyproject.toml

@@ -65,6 +65,29 @@ where = [
 [tool.coverage.run]
 relative_files = true
 
+[tool.ruff.lint]
+select = [
+    "B",       # flake8-bugbear
+    "C4",      # flake8-comprehensions
+    "C90",     # mccabe
+    "D",       # pydocstyle
+    "E", "W",  # pycodestyle
+    "F",       # Pyflakes
+    "FA",      # flake8-future-annotations
+    "I",       # isort
+    # "SIM",   # flake8-simplify
+    "UP",      # pyupgrade
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**.py" = ["D"]
+
+[tool.ruff.lint.mccabe]
+max-complexity = 18
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
 [tool.mypy]
 check_untyped_defs = true
 disallow_any_generics = true

src/bmipy/__init__.py

@@ -1,4 +1,5 @@
 """The Basic Model Interface (BMI) for Python."""
+
 from __future__ import annotations
 
 from bmipy._version import __version__

src/bmipy/__main__.py

@@ -1,4 +1,5 @@
 """The bmipy-render command."""
+
 from __future__ import annotations
 
 from bmipy._cmd import main

src/bmipy/_cmd.py

@@ -1,4 +1,5 @@
 """Command line interface that create template BMI implementations."""
+
 from __future__ import annotations
 
 import argparse

src/bmipy/_template.py

@@ -4,8 +4,7 @@
 import os
 import re
 import textwrap
-from collections import defaultdict
-from collections import OrderedDict
+from collections import OrderedDict, defaultdict
 
 from bmipy.bmi import Bmi
 

src/bmipy/bmi.py

@@ -3,10 +3,10 @@
 This language specification is derived from the Scientific Interface
 Definition Language (SIDL) file `bmi.sidl <https://github.com/csdms/bmi>`_.
 """
+
 from __future__ import annotations
 
-from abc import ABC
-from abc import abstractmethod
+from abc import ABC, abstractmethod
 from typing import Any
 
 import numpy as np

tests/cli_test.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import pytest
+
 from bmipy._cmd import main
 
 

tests/template_test.py

@@ -1,8 +1,8 @@
 from __future__ import annotations
 
 import pytest
-from bmipy._template import dedent_docstring
-from bmipy._template import render_function_signature
+
+from bmipy._template import dedent_docstring, render_function_signature
 
 
 @pytest.mark.parametrize(