Use Ruff for linting

.github/workflows/code_quality.yml

@@ -17,6 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         tox_env:
+          - lint
           - types
 
     steps:
@@ -38,28 +39,6 @@ jobs:
       - name: Run check for tox env "${{ matrix.tox_env }}"
         run: tox -e ${{ matrix.tox_env }}
 
-
-  flake8:
-    name: Code style
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Checkout repository
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run flake8 hooks
-        run: pre-commit run --all-files flake8
-
   black:
     name: Code formatting
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -6,41 +6,22 @@ repos:
     hooks:
       - id: check-ast                  # Simply check whether the files parse as valid python
       - id: check-case-conflict        # Check for files that would conflict in case-insensitive filesystems
-      - id: check-builtin-literals     # Require literal syntax when initializing empty or zero Python builtin types
-      - id: check-docstring-first      # Checks a common error of defining a docstring after code
       - id: check-merge-conflict       # Check for files that contain merge conflict strings
       - id: check-toml                 # Attempts to load all TOML files to verify syntax
-      - id: check-yaml                 # Attempts to load all yaml files to verify syntax
-      - id: check-vcs-permalinks       # Ensures that links to vcs websites are permalinks
+      - id: check-yaml                 # Attempts to load all YAML files to verify syntax
+      - id: check-vcs-permalinks       # Ensures that links to VCS websites are permalinks
       - id: debug-statements           # Check for debugger imports and py37+ `breakpoint()` calls in python source
       - id: detect-private-key         # Detects the presence of private keys
-      - id: double-quote-string-fixer  # Replaces double quoted strings with single quoted strings
       - id: end-of-file-fixer          # Ensures that a file is either empty, or ends with one newline
       - id: mixed-line-ending          # Replaces or checks mixed line ending
-      - id: trailing-whitespace        # This hook trims trailing whitespace
+      - id: trailing-whitespace        # Trims trailing whitespace
         exclude: setup.cfg
 
-  - repo: https://github.com/psf/black
-    rev: 24.8.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.7
     hooks:
-    - id: black
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
-    hooks:
-      - id: flake8
-        additional_dependencies: [
-          flake8-blind-except,      # check for blind, catch-all "except:" statements
-          flake8-bugbear,           # find likely bugs and design problems
-          flake8-builtins,          # check for python builtins being used as variables or parameters
-          flake8-fixme,             # check for FIXME, TODO and other temporary developer notes
-          flake8-markdown,          # lint Python code blocks in Markdown files using flake8
-          flake8-pep3101,           # check for old string formatting
-          flake8-print,             # check for print statements
-          flake8-use-fstring,       # enforce use of f-string
-          flake8-2020,              # check for misuse of `sys.version` or `sys.version_info`
-          pep8-naming,              # check PEP-8 naming conventions
-        ]
+      - id: ruff
+      # - id: ruff-format
 
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
@@ -59,22 +40,11 @@ repos:
       - id: pyupgrade
         args: ['--py38-plus', '--keep-runtime-typing']
 
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.5.0
-    hooks:
-    - id: setup-cfg-fmt
-      args: ['--include-version-classifiers']
-
   - repo: https://github.com/PyCQA/doc8
     rev: v1.1.2
     hooks:
     - id: doc8
 
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
-    hooks:
-    - id: docformatter
-
 
 ci:
   autoupdate_commit_msg: Autoupdate pre-commit hooks

print_system.py

@@ -1,18 +1,17 @@
-# flake8: noqa
 import platform
 import re
 import sys
 
 import numpy
 import SimpleITK as sitk
 import torch
-import torchio
 
+import torchio as tio
 
 sitk_version = re.findall('SimpleITK Version: (.*?)\n', str(sitk.Version()))[0]
 
 print('Platform:  ', platform.platform())
-print('TorchIO:   ', torchio.__version__)
+print('TorchIO:   ', tio.__version__)
 print('PyTorch:   ', torch.__version__)
 print('SimpleITK: ', sitk_version)
 print('NumPy:     ', numpy.__version__)

pyproject.toml

@@ -56,7 +56,6 @@ dev = [
     "black",
     "bump2version",
     "coverage",
-    "flake8",
     "mypy",
     "parameterized",
     "pre-commit",

src/torchio/transforms/interpolation.py

@@ -1,4 +1,4 @@
-# flake8: noqa: B950
+# noqa: B950
 import enum
 
 import SimpleITK as sitk

tests/data/test_io.py

@@ -5,8 +5,8 @@
 import pytest
 import SimpleITK as sitk
 import torch
-from torchio.data import io
-from torchio.data import ScalarImage
+
+from torchio.data import ScalarImage, io
 
 from ..utils import TorchioTestCase
 
@@ -117,12 +117,12 @@ def test_sitk_to_nib(self):
     def test_sitk_to_affine(self):
         spacing = 1, 2, 3
         direction_lps = -1, 0, 0, 0, -1, 0, 0, 0, 1
-        origin_lps = l, p, s = -10, -20, 30
+        origin_lps = left, posterior, superior = -10, -20, 30
         image = sitk.GetImageFromArray(np.random.rand(10, 20, 30))
         image.SetDirection(direction_lps)
         image.SetSpacing(spacing)
         image.SetOrigin(origin_lps)
-        origin_ras = -l, -p, s
+        origin_ras = -left, -posterior, superior
         fixture = np.diag((*spacing, 1))
         fixture[:3, 3] = origin_ras
         affine = io.get_ras_affine_from_sitk(image)

tox.ini

@@ -17,6 +17,12 @@ commands =
         --cov-report=xml \
         {posargs}
 
+[testenv:lint]
+description = Run code linter
+skip_install = True
+deps = ruff
+commands = ruff check
+
 [testenv:types]
 deps =
     mypy
@@ -26,13 +32,3 @@ commands =
         --install-types \
         --non-interactive \
         src
-
-[flake8]
-max-line-length = 88
-select = C,E,F,W,B,B950
-extend-ignore =
-    N813,
-    E123,
-    W503,
-    E203,
-    E501