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 +136,33 @@ 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]
+select = [
+  "F",
+  "E",
+  "C",
+  "W",
+  "B",
+]
+ignore = [
+  "E203"
 ]
 
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "double"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/__init__.py" = ["F401"]
+"docs/conf.py" = ["E265"]
+"/^\\s*\\.\\. _.*?: http/" = ["E501"]
+"src/eddymotion/estimator.py" = ["C901"]
+
+[tool.ruff.format]
+quote-style = "double"
+
 [tool.pytest.ini_options]
 pythonpath = "src/ test/"
 norecursedirs = [".*", "_*"]

src/eddymotion/data/dmri.py

@@ -253,7 +253,8 @@ def load(
         if bvec_file and bval_file:
             warn(
                 "Gradients table file and b-vec/val files are defined; "
-                "dismissing b-vec/val files."
+                "dismissing b-vec/val files.",
+                stacklevel=2
             )
     elif bvec_file and bval_file:
         grad = np.vstack(

src/eddymotion/model/base.py

@@ -90,7 +90,7 @@ class BaseModel:
         "_models",
         "_datashape",
     )
-    _modelargs = tuple()
+    _modelargs = ()
 
     def __init__(self, gtab, S0=None, mask=None, b_max=None, **kwargs):
         """Base initialization."""

src/eddymotion/viz.py

@@ -343,7 +343,7 @@ def plot_carpet(
         segmentation_masked = segmentation_reshaped[segmentation_reshaped > 0]
 
         if segment_labels is not None:
-            segments = dict()
+            segments = {}
             labels = list(segment_labels.keys())
             for label in labels:
                 indices = np.array([], dtype=int)
@@ -395,7 +395,7 @@ def get_segment_labels(filepath, keywords, delimiter=" ", index_position=0, labe
           'Cerebral_Cortex': [3, 42],
           'Ventricle': [4, 14, 15, 43, 72]}
     """
-    segment_labels = dict()
+    segment_labels = {}
 
     with open(filepath, "r") as f:
         labels = f.read()