[MNT] move pre-commit config to ruff

.pre-commit-config.yaml

@@ -18,41 +18,19 @@ repos:
       - id: name-tests-test
         args: ["--django"]
 
-  - repo: https://github.com/pycqa/isort
-    rev: 8.0.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.1
     hooks:
-      - id: isort
-        name: isort
-
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 26.3.1
-    hooks:
-      - id: black
-        language_version: python3
+      - id: ruff-format
+      - id: ruff-check
+        args: [--fix]
 
   - repo: https://github.com/asottile/blacken-docs
     rev: 1.20.0
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==22.3.0]
 
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.3.0
-    hooks:
-      - id: flake8
-        exclude: docs/source/conf.py, __pycache__
-        additional_dependencies:
-          [
-            flake8-bugbear,
-            flake8-builtins,
-            flake8-quotes>=3.3.2,
-            flake8-comprehensions,
-            pandas-vet,
-            flake8-print,
-            pep8-naming,
-            doc8,
-          ]
-
   - repo: https://github.com/pycqa/pydocstyle
     rev: 6.3.0
     hooks:
@@ -62,15 +40,8 @@ repos:
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.9.1
     hooks:
-      - id: nbqa-isort
-        args: [--nbqa-mutate, --nbqa-dont-skip-bad-cells]
-        additional_dependencies: [isort==5.6.4]
-      - id: nbqa-black
-        args: [--nbqa-mutate, --nbqa-dont-skip-bad-cells]
-        additional_dependencies: [black>=22.3.0]
-      - id: nbqa-flake8
-        args: [--nbqa-dont-skip-bad-cells, "--extend-ignore=E402,E203"]
-        additional_dependencies: [flake8==3.8.3]
+      - id: nbqa-ruff
+        args: [--nbqa-mutate]
 
   - repo: https://github.com/PyCQA/bandit
     rev: 1.9.4

docs/source/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # copyright: skbase developers, BSD-3-Clause License (see LICENSE file)
 """Configure skbase Sphinx documentation."""
 
@@ -298,7 +297,7 @@ def find_source():
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/{.major}".format(sys.version_info), None),
+    "python": (f"https://docs.python.org/{sys.version_info.major}", None),
     "scikit-learn": ("https://scikit-learn.org/stable/", None),
     "sktime": ("https://www.sktime.net/en/stable/", None),
 }

pyproject.toml

@@ -47,18 +47,9 @@ dev = [
 
 linters = [
     "mypy",
-    "isort",
-    "flake8",
-    "black",
+    "ruff",
     "pydocstyle",
     "nbqa",
-    "flake8-bugbear",
-    "flake8-builtins",
-    "flake8-quotes",
-    "flake8-comprehensions",
-    "pandas-vet",
-    "flake8-print",
-    "pep8-naming",
     "doc8",
 ]
 
@@ -112,16 +103,6 @@ addopts = [
     "--cov-report=html",
 ]
 
-[tool.isort]
-profile = "black"
-src_paths = ["skbase/*"]
-multi_line_output = 3
-known_first_party = ["skbase"]
-
-[tool.black]
-line-length = 88
-extend-exclude = "^/setup.py docs/conf.py"
-
 [tool.pydocstyle]
 convention = "numpy"
 
@@ -137,6 +118,79 @@ max-line-length = 88
 ignore = ["D004"]
 ignore_path = ["docs/_build", "docs/source/api_reference/auto_generated"]
 
+[tool.ruff]
+line-length = 88
+extend-exclude = ["setup.py", "docs/source/conf.py"]
+target-version = "py310"
+extend-include = ["*.ipynb"]
+
+[tool.ruff.lint]
+select = [
+    "D",  # pydocstyle
+    "E",  # pycodestyle errors
+    "W",  # pycodestyle warnings
+    "F",  # pyflakes
+    "I",  # isort
+    "UP",  # pyupgrade
+    "B",  # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "PIE",  # flake8-pie
+    "T20",  # flake8-print
+    "RET",  # flake8-return
+    "SIM",  # flake8-simplify
+    "TID",  # flake8-tidy-imports
+    "TCH",  # flake8-type-checking
+    "RUF",  # Ruff-specific rules
+]
+ignore = [
+    "E203",  # Whitespace before punctuation
+    "E402",  # Module import not at top of file
+    "E501",  # Line too long
+    "E731",  # Do not assign a lambda expression, use a def
+    "RET504",  # Unnecessary variable assignment before `return` statement
+    "S101",  # Use of `assert` detected
+    "C408",  # Unnecessary dict call - rewrite as a literal
+    "UP031",  # Use format specifier instead of %
+    "UP009",  # UTF-8 encoding declaration is unnecessary
+    "S102",  # Use of exec
+    "C414",  # Unnecessary `list` call within `sorted()`
+    "S301",  # pickle and modules that wrap it can be unsafe
+    "C416",  # Unnecessary list comprehension - rewrite as a generator
+    "S310",  # Audit URL open for permitted schemes
+    "S202",  # Uses of `tarfile.extractall()`
+    "S307",  # Use of possibly insecure function
+    "C417",  # Unnecessary `map` usage (rewrite using a generator expression)
+    "S605",  # Starting a process with a shell, possible injection detected
+    "E741",  # Ambiguous variable name
+    "S107",  # Possible hardcoded password
+    "S105",  # Possible hardcoded password
+    "PT018",  # Checks for assertions that combine multiple independent condition
+    "S602",  # sub process call with shell=True unsafe
+    "C419",  # Unnecessary list comprehension, some are flagged yet are not
+    "C409",  # Unnecessary `list` literal passed to `tuple()` (rewrite as a `tuple` literal)
+    "S113",  # Probable use of httpx call without timeout
+]
+allowed-confusables = ["σ"]
+
+[tool.ruff.lint.per-file-ignores]
+"setup.py" = ["S101"]
+"**/__init__.py" = [
+    "F401",  # unused import
+]
+"**/tests/**" = [
+    "D",  # docstring
+    "S605",  # Starting a process with a shell: seems safe, but may be changed in the future; consider rewriting without `shell`
+    "S607",  # Starting a process with a partial executable path
+    "RET504",  # Unnecessary variable assignment before `return` statement
+    "PT004",  # Fixture `tmpdir_unittest_fixture` does not return anything, add leading underscore
+    "PT011",  # `pytest.raises(ValueError)` is too broad, set the `match` parameter or use a more specific exception
+    "PT012",  # `pytest.raises()` block should contain a single simple statement
+    "PT019",  # Fixture `_` without value is injected as parameter, use `@pytest.mark.usefixtures` instead
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
 [tool.bandit]
 exclude_dirs = ["*/tests/*", "*/testing/*"]
 

skbase/_exceptions.py

@@ -5,20 +5,18 @@
 # conditions see https://github.com/scikit-learn/scikit-learn/blob/main/COPYING
 """Custom exceptions used in ``skbase``."""
 
-from typing import List
-
-__author__: List[str] = ["fkiraly", "mloning", "rnkuhns"]
-__all__: List[str] = ["FixtureGenerationError", "NotFittedError"]
+__author__: list[str] = ["fkiraly", "mloning", "rnkuhns"]
+__all__: list[str] = ["FixtureGenerationError", "NotFittedError"]
 
 
 class FixtureGenerationError(Exception):
     """Raised when a fixture fails to generate."""
 
-    def __init__(self, fixture_name="", err=None):  # noqa: B042
+    def __init__(self, fixture_name="", err=None):
         self.fixture_name = fixture_name
         self.err = err
         msg = f"fixture {fixture_name} failed to generate. {err}"
-        super().__init__(msg)  # noqa: B042
+        super().__init__(msg)
 
 
 class NotFittedError(ValueError, AttributeError):

skbase/base/__init__.py

@@ -7,8 +7,6 @@
 sktime design principles in your project.
 """
 
-from typing import List
-
 from skbase.base._base import BaseEstimator, BaseObject
 from skbase.base._meta import (
     BaseMetaEstimator,
@@ -17,12 +15,12 @@
     BaseMetaObjectMixin,
 )
 
-__author__: List[str] = ["mloning", "RNKuhns", "fkiraly"]
-__all__: List[str] = [
-    "BaseObject",
+__author__: list[str] = ["mloning", "RNKuhns", "fkiraly"]
+__all__: list[str] = [
     "BaseEstimator",
     "BaseMetaEstimator",
-    "BaseMetaObject",
     "BaseMetaEstimatorMixin",
+    "BaseMetaObject",
     "BaseMetaObjectMixin",
+    "BaseObject",
 ]