MAINT: use ruff for linting and formatting

.github/workflows/python-style.yml

@@ -0,0 +1,17 @@
+name: Python Style
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v1

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-added-large-files
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.7.1
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

examples/snr_adjustment.py

@@ -3,7 +3,6 @@
 """
 
 import mne
-import numpy as np
 import matplotlib.pyplot as plt
 
 from pathlib import Path

pyproject.toml

@@ -31,8 +31,10 @@ Issues = "https://github.com/ctrltz/meegsim/issues"
 dev = [
     "harmoni",
     "mock",
+    "pre-commit",
     "pytest",
-    "pytest-cov"
+    "pytest-cov",
+    "ruff"
 ]
 docs = [
     "intersphinx-registry",

src/meegsim/_check.py

@@ -252,7 +252,7 @@ def check_names(names, n_sources, existing):
             raise ValueError(f"Expected all names to be strings, got {actual_type}: {name}")
 
         if not name:
-            raise ValueError(f"All names should not be empty")
+            raise ValueError("All names should not be empty")
 
         if name.startswith('auto'):
             raise ValueError(f"Name {name} should not start with auto, this prefix "

src/meegsim/sources.py

@@ -8,7 +8,7 @@
 import numpy as np
 import mne
 
-from .utils import vertices_to_mne, get_sfreq, _extract_hemi
+from .utils import vertices_to_mne, _extract_hemi
 
 
 class _BaseSource:

src/meegsim/utils.py

@@ -119,9 +119,9 @@ def _extract_hemi(src):
     if src['id'] == FIFF.FIFFV_MNE_SURF_RIGHT_HEMI:
         return 'rh'
 
-    raise ValueError(f"Unexpected ID for the provided surface source space. "
-                     f"Please check the code that was used to generate and/or "
-                     f"manipulate the src, it should not change the 'id' field.")
+    raise ValueError("Unexpected ID for the provided surface source space. "
+                     "Please check the code that was used to generate and/or "
+                     "manipulate the src, it should not change the 'id' field.")
 
 
 def get_sfreq(times):

tests/test_configuration.py

@@ -105,12 +105,12 @@ def test_sourceconfiguration_to_raw(apply_forward_mock):
     apply_forward_mock.assert_called()
     stc = apply_forward_mock.call_args.args[1]
     assert np.all(stc.data == 1e-6), \
-        f"Default scaling factor was not applied correctly"
-    assert raw == 0, f"Output of apply_forward_raw should not be changed"
+        "Default scaling factor was not applied correctly"
+    assert raw == 0, "Output of apply_forward_raw should not be changed"
 
     raw = sc.to_raw([], [], scaling_factor=10)
     apply_forward_mock.assert_called()
     stc = apply_forward_mock.call_args.args[1]
     assert np.all(stc.data == 10), \
-        f"Custom scaling factor was not applied correctly"
-    assert raw == 0, f"Output of apply_forward_raw should not be changed"
+        "Custom scaling factor was not applied correctly"
+    assert raw == 0, "Output of apply_forward_raw should not be changed"

tests/test_simulate.py

@@ -46,7 +46,7 @@ def test_sourcesimulator_add_point_sources():
     assert len(sim._sources) == 8, \
         f"Expected eight sources to be created, got {len(sim._sources)}"
     assert all([name in sim._sources for name in custom_names]), \
-        f"Provided source names were not used properly"
+        "Provided source names were not used properly"
 
     # Add one group with already existing names
     with pytest.raises(ValueError):
@@ -92,7 +92,7 @@ def test_sourcesimulator_add_patch_sources():
     assert len(sim._sources) == 4, \
         f"Expected four sources to be created, got {len(sim._sources)}"
     assert all([name in sim._sources for name in custom_names]), \
-        f"Provided source names were not used properly"
+        "Provided source names were not used properly"
 
     # Add one group with already existing names
     with pytest.raises(ValueError):
@@ -354,7 +354,7 @@ def test_simulate():
                                            src, times=times, fwd=None, random_state=0)
 
         assert len(simulate_mock.call_args_list) == 3, \
-            f"Expected three calls of PointSourceGroup.simulate method"
+            "Expected three calls of PointSourceGroup.simulate method"
 
         random_states = [kall.kwargs['random_state'] == 0
                          for kall in simulate_mock.call_args_list]

tests/test_sources.py

@@ -1,4 +1,3 @@
-import unittest
 from unittest.mock import MagicMock, patch
 
 import numpy as np
@@ -61,7 +60,7 @@ def test_pointsource_to_stc(src_idx, vertno):
     assert vertno in stc.vertices[src_idx], \
         f"Expected the vertex to be put in src {src_idx}, but it is not there"
     assert np.allclose(stc.data, waveform), \
-        f"The source waveform should not change during conversion to stc"
+        "The source waveform should not change during conversion to stc"
 
 
 @pytest.mark.parametrize("tstep", [0.01, 0.025, 0.05])
@@ -220,7 +219,7 @@ def test_patchsource_to_stc(src_idx, vertno):
     assert np.all(vertno in stc.vertices[src_idx]), \
         f"Expected all vertno to be put in src {src_idx}"
     assert np.allclose(stc.data, waveform), \
-        f"The source waveform should not change during conversion to stc"
+        "The source waveform should not change during conversion to stc"
 
 
 def test_patchsource_to_stc_bad_src_raises():