Switch from black/isort/... to ruff

WIP

- [ ] Apply changes after the bigger PRs have been merged to avoid conflicts.
- [ ] Re-enable some currently ignored rules

.pre-commit-config.yaml

@@ -4,31 +4,8 @@
 # `pre-commit run --all-files` as by default only changed files are checked
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.10.0
-  hooks:
-  - id: black
-    description: The uncompromising code formatter
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    name: isort (python)
-  - id: isort
-    name: isort (cython)
-    types: [cython]
-  - id: isort
-    name: isort (pyi)
-    types: [pyi]
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.0
-  hooks:
-    - id: nbqa-black
-    - id: nbqa-pyupgrade
-      args: [--py36-plus]
-    - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
     description: Check yaml files for parseable syntax
@@ -44,3 +21,19 @@ repos:
     description: Fix empty lines at ends of files
   - id: detect-private-key
     description: Detects the presence of private keys
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.9
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - pyproject.toml

pyproject.toml

@@ -5,12 +5,47 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
-[tool.black]
+[tool.ruff]
 line-length = 79
-target-version = ['py37', 'py38', 'py39']
-skip-string-normalization = true
+exclude = ["amici_models"]
+extend-include = ["*.ipynb"]
+lint.ignore = [
+    # FIXME: we should be able to remive move of those
+    "D103", # Missing docstring in public function
+    "S101", # Use of assert detected
+    "E501", # Line too long
+    "B028", # No explicit `stacklevel` keyword argument found
+    "C419", # Unnecessary list comprehension
+    "F403", # star import
+    "F821", # undefined name
+    "T201", # print statement
+    "S301", # pickle module used
+    "S102", # Use of exec detected
+    "S307", # Use of possibly insecure function
+    "B026", # Star-arg unpacking after a keyword argument
+    "B006",
+    "B027",
+    "C405",
+    "C416",
+    "E722",
+    "B904",
+    "B007",
+    "F841",
+    "B024",
 
-[tool.isort]
-profile = "black"
-line_length = 79
-multi_line_output = 3
+]
+lint.select = [
+    "F",  # Pyflakes
+    "I",  # isort
+    # "D",  # pydocstyle (PEP 257)  FIXME enable after https://github.com/PEtab-dev/petab_select/pull/67
+    "S",  # flake8-bandit
+    "B",  # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "T20",  # flake8-print
+    "W",  # pycodestyle Warnings
+    "E",  # pycodestyle Errors
+    "UP",  # pyupgrade
+    # "ANN",  # flakes-annotations
+]
+[tool.ruff.lint.pydocstyle]
+convention = "pep257"

tox.ini

@@ -23,18 +23,3 @@ commands =
   coverage report
 description =
   Test basic functionality
-
-[testenv:flake8]
-skip_install = true
-deps =
-    flake8 >= 3.8.3
-    flake8-bandit >= 2.1.2
-    flake8-bugbear >= 20.1.4
-    flake8-colors >= 0.1.6
-    flake8-comprehensions >= 3.2.3
-    flake8-print >= 3.1.4
-    flake8-docstrings >= 1.6.0
-commands =
-    flake8 petab_select test setup.py
-description =
-    Run flake8 with various plugins.