CI: replace flake8 by ruff check

.github/workflows/contrib.yml

@@ -7,7 +7,7 @@ defaults:
 
 jobs:
   stable:
-    name: Run flake8
+    name: Run ruff
     runs-on: ubuntu-latest
 
     steps:
@@ -20,4 +20,4 @@ jobs:
         with:
           python-version: 3
       - name: Lint EddyMotion
-        run: pipx run flake8-pyproject
+        run: pipx run ruff check

pyproject.toml

@@ -136,18 +136,54 @@ exclude = '''
 profile = 'black'
 skip_gitignore = true
 
-[tool.flake8]
-max-line-length = 99
-doctests = false
-exclude = ["*build/", "docs/"]
-select = "C,E,F,W,B,B950"
-ignore = "N802,N806,W503,E203"
-per-file-ignores = [
-    "*/__init__.py: F401",
-    "docs/conf.py: E265",
-    "/^\\s*\\.\\. _.*?: http/: E501"
+[tool.ruff]
+line-length = 99
+
+[tool.ruff.lint]
+extend-select = [
+  "F",
+  "E",
+  "W",
+  "I",
+  "UP",
+  "YTT",
+  "S",
+  "BLE",
+  "B",
+  "A",
+  # "CPY",
+  "C4",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "FA",
+  "ISC",
+  "ICN",
+  "PT",
+  "Q",
+]
+ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+  "S603",
 ]
 
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+"docs/source/conf.py" = ["A001"]
+"mriqc/bin/nib_hash.py" = ["S324"]
+"mriqc/config.py" = ["S105"]
+"mriqc/conftest.py" = ["PT004"]
+"mriqc/engine/plugin.py" = ["BLE001"]
+"mriqc/utils/debug.py" = ["A002", "T100"]
+
+[tool.ruff.format]
+quote-style = "single"
+
 [tool.pytest.ini_options]
 pythonpath = "src/ test/"
 norecursedirs = [".*", "_*"]