chore: Add ruff and pre-commit configurations, apply

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+      - id: ruff
+        args: [ --select, ISC001, --fix ]

pyproject.toml

@@ -67,3 +67,47 @@ exclude_lines = [
   "if __name__ == .__main__.:",
   "if TYPE_CHECKING:",
 ]
+
+# Disable black
+[tool.black]
+exclude = ".*"
+
+[tool.ruff]
+line-length = 99
+extend-exclude = ["_version.py"]
+
+[tool.ruff.lint]
+extend-select = [
+  "F",
+  "E",
+  "W",
+  "I",
+  "UP",
+  "YTT",
+  "S",
+  "BLE",
+  "B",
+  "A",
+  # "CPY",
+  "C4",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "ISC",
+  "ICN",
+  "PT",
+  "Q",
+]
+ignore = [
+  "ISC001",
+]
+
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+
+[tool.ruff.format]
+quote-style = "single"

src/bids_validator/__init__.py

@@ -1,6 +1,9 @@
 """BIDS validator common Python package."""
+
 from .bids_validator import BIDSValidator
+
 __all__ = ['BIDSValidator']
 
 from . import _version
+
 __version__ = _version.get_versions()['version']

src/bids_validator/bids_validator.py

@@ -1,4 +1,5 @@
 """Validation class for BIDS projects."""
+
 import logging
 import os
 import re
@@ -139,8 +140,10 @@ def parse(cls, path):
             path = path.replace(os.sep, '/')
 
         if not path.startswith('/'):
-            raise ValueError("Path must be relative to root of a BIDS dataset,"
-                             " and must include a leading forward slash `/`.")
+            raise ValueError(
+                'Path must be relative to root of a BIDS dataset,'
+                ' and must include a leading forward slash `/`.'
+            )
 
         for regex in cls.regexes:
             match = re.match(regex, path[1:])

src/bids_validator/test_bids_validator.py

@@ -7,18 +7,16 @@
 
 import os
 
-import pytest
 import datalad.api
+import pytest
 
 from bids_validator import BIDSValidator
 
 HOME = os.path.expanduser('~')
 
 TEST_DATA_DICT = {
-    'eeg_matchingpennies': (
-        'https://gin.g-node.org/sappelhoff/eeg_matchingpennies'
-    ),
-    }
+    'eeg_matchingpennies': ('https://gin.g-node.org/sappelhoff/eeg_matchingpennies'),
+}
 
 EXCLUDE_KEYWORDS = ['git', 'datalad', 'sourcedata', 'bidsignore']
 
@@ -61,94 +59,112 @@ def test_datasets(validator, fname):
     assert validator.is_bids(fname)
 
 
-@pytest.mark.parametrize('fname, matches', [
-    ('/T1w.json', True),
-    ('/dataset_description.json', True),
-    ('/README', True),
-    ('/CHANGES', True),
-    ('/participants.tsv', True),
-    ('/sub-01/anat/sub-01_T1w.nii.gz', False),
-])
+@pytest.mark.parametrize(
+    ('fname', 'matches'),
+    [
+        ('/T1w.json', True),
+        ('/dataset_description.json', True),
+        ('/README', True),
+        ('/CHANGES', True),
+        ('/participants.tsv', True),
+        ('/sub-01/anat/sub-01_T1w.nii.gz', False),
+    ],
+)
 def test_top_level(validator, fname, matches):
     """Test that is_top_level returns true for top-level files."""
     assert validator.is_top_level(fname) is matches
 
 
-@pytest.mark.parametrize('fname, matches', [
-    ('/sourcedata/unstructured_data.nii.gz', True),
-    ('/sourcedata/dicom_dir/xyz.dcm', True),
-    ('/code/my_analysis/analysis.py', True),
-    ('/derivatives/preproc/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz', True),
-    ('/stimuli/pic.jpg', True),
-    ('/sub-01/anat/sub-01_T1w.nii.gz', False),
-])
+@pytest.mark.parametrize(
+    ('fname', 'matches'),
+    [
+        ('/sourcedata/unstructured_data.nii.gz', True),
+        ('/sourcedata/dicom_dir/xyz.dcm', True),
+        ('/code/my_analysis/analysis.py', True),
+        ('/derivatives/preproc/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz', True),
+        ('/stimuli/pic.jpg', True),
+        ('/sub-01/anat/sub-01_T1w.nii.gz', False),
+    ],
+)
 def test_associated_data(validator, fname, matches):
     """Test that is_associated_data returns true for associated data."""
     assert validator.is_associated_data(fname) is matches
 
 
-@pytest.mark.parametrize('fname, matches', [
-    ('/sub-01/ses-1/sub-01_ses-1_scans.tsv', True),
-    ('/sub-01/ses-1/sub-01_ses-1_scans.json', True),
-    ('/sub-01/sub-01_scans.tsv', True),
-    ('/sub-01/sub-01_scans.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_task-rest_bold.json', True),
-    ('/sub-01/sub-01_task-rest_bold.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_asl.json', True),
-    ('/sub-01/sub-01_asl.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_pet.json', True),
-    ('/sub-01/sub-01_pet.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_proc-test_channels.tsv', True),
-    ('/sub-01/ses-1/sub-01_ses-1_channels.json', True),
-    ('/sub-01/sub-01_proc-test_channels.tsv', True),
-    ('/sub-01/sub-01_channels.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_space-CapTrak_electrodes.tsv', True),
-    ('/sub-01/ses-1/sub-01_ses-1_coordsystem.json', True),
-    ('/sub-01/sub-01_space-CapTrak_electrodes.tsv', True),
-    ('/sub-01/sub-01_coordsystem.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_motion.json', True),
-    ('/sub-01/sub-01_motion.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_TEM.json', True),
-    ('/sub-01/sub-01_TEM.json', True),
-    ('/sub-01/ses-1/sub-01_ses-1_nirs.json', True),
-    ('/sub-01/sub-01_nirs.json', True),
-    # Mismatch sessions
-    ('/sub-01/sub-01_ses-1_scans.tsv', False),
-    ('/sub-01/sub-01_ses-1_scans.json', False),
-    ('/sub-01/ses-1/sub-01_ses-2_scans.tsv', False),
-    # File-level
-    ('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', False),
-    ('/sub-01/anat/sub-01_T1w.nii.gz', False),
-])
+@pytest.mark.parametrize(
+    ('fname', 'matches'),
+    [
+        ('/sub-01/ses-1/sub-01_ses-1_scans.tsv', True),
+        ('/sub-01/ses-1/sub-01_ses-1_scans.json', True),
+        ('/sub-01/sub-01_scans.tsv', True),
+        ('/sub-01/sub-01_scans.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_task-rest_bold.json', True),
+        ('/sub-01/sub-01_task-rest_bold.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_asl.json', True),
+        ('/sub-01/sub-01_asl.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_pet.json', True),
+        ('/sub-01/sub-01_pet.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_proc-test_channels.tsv', True),
+        ('/sub-01/ses-1/sub-01_ses-1_channels.json', True),
+        ('/sub-01/sub-01_proc-test_channels.tsv', True),
+        ('/sub-01/sub-01_channels.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_space-CapTrak_electrodes.tsv', True),
+        ('/sub-01/ses-1/sub-01_ses-1_coordsystem.json', True),
+        ('/sub-01/sub-01_space-CapTrak_electrodes.tsv', True),
+        ('/sub-01/sub-01_coordsystem.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_motion.json', True),
+        ('/sub-01/sub-01_motion.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_TEM.json', True),
+        ('/sub-01/sub-01_TEM.json', True),
+        ('/sub-01/ses-1/sub-01_ses-1_nirs.json', True),
+        ('/sub-01/sub-01_nirs.json', True),
+        # Mismatch sessions
+        ('/sub-01/sub-01_ses-1_scans.tsv', False),
+        ('/sub-01/sub-01_ses-1_scans.json', False),
+        ('/sub-01/ses-1/sub-01_ses-2_scans.tsv', False),
+        # File-level
+        ('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', False),
+        ('/sub-01/anat/sub-01_T1w.nii.gz', False),
+    ],
+)
 def test_session_level(validator, fname, matches):
     """Test that is_session_level returns true for session level files."""
     assert validator.is_session_level(fname) is matches
 
 
-@pytest.mark.parametrize('fname, matches', [
-    ('/sub-01/sub-01_sessions.tsv', True),
-    ('/sub-01/sub-01_sessions.json', True),
-    ('/sub-01/anat/sub-01_T1w.nii.gz', False),
-])
+@pytest.mark.parametrize(
+    ('fname', 'matches'),
+    [
+        ('/sub-01/sub-01_sessions.tsv', True),
+        ('/sub-01/sub-01_sessions.json', True),
+        ('/sub-01/anat/sub-01_T1w.nii.gz', False),
+    ],
+)
 def test_subject_level(validator, fname, matches):
     """Test that is_subject_level returns true for subject level files."""
     assert validator.is_subject_level(fname) is matches
 
 
-@pytest.mark.parametrize('fname, matches', [
-    ('/phenotype/measure.tsv', True),
-    ('/phenotype/measure.json', True),
-    ('/sub-01/anat/sub-01_T1w.nii.gz', False),
-])
+@pytest.mark.parametrize(
+    ('fname', 'matches'),
+    [
+        ('/phenotype/measure.tsv', True),
+        ('/phenotype/measure.json', True),
+        ('/sub-01/anat/sub-01_T1w.nii.gz', False),
+    ],
+)
 def test_phenotpic(validator, fname, matches):
     """Test that is_phenotypic returns true for phenotypic files."""
     assert validator.is_phenotypic(fname) is matches
 
 
-@pytest.mark.parametrize('fname, matches', [
-    ('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', True),
-    ('/sub-01/anat/sub-01_T1w.nii.gz', True),
-])
+@pytest.mark.parametrize(
+    ('fname', 'matches'),
+    [
+        ('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', True),
+        ('/sub-01/anat/sub-01_T1w.nii.gz', True),
+    ],
+)
 def test_file_level(validator, fname, matches):
     """Test that is_file returns true for file level files."""
     assert validator.is_file(fname) is matches