chore: Configure ruff in its own file, add precommit hooks (#72)

Author: bendhouseart

.pre-commit-config.yaml

@@ -6,6 +6,7 @@ repos:
     rev: v6.0.0
     hooks:
       - id: trailing-whitespace
+        exclude: .gitignore
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-json

pyproject.toml

@@ -99,61 +99,12 @@ exclude_lines = [
 [tool.black]
 exclude = ".*"
 
-[tool.ruff]
-line-length = 99
-extend-exclude = [
-  "_version.py",
-  "tests/data",
-]
-
-[tool.ruff.lint]
-extend-select = [
-  "F",
-  "E",
-  "W",
-  "I",
-  "D",
-  "UP",
-  "YTT",
-  "S",
-  "BLE",
-  "B",
-  "A",
-  # "CPY",
-  "C4",
-  "DTZ",
-  "T10",
-  # "EM",
-  "EXE",
-  "ISC",
-  "ICN",
-  "PT",
-  "Q",
-]
-ignore = [
-  "ISC001",
-  "D105",
-  "D107",
-  "D203",
-  "D213",
-]
-
-[tool.ruff.lint.flake8-quotes]
-inline-quotes = "single"
-
-[tool.ruff.lint.extend-per-file-ignores]
-"setup.py" = ["D"]
-"*/test_*.py" = [
-    "S101",
-    "D",
-]
-
-[tool.ruff.format]
-quote-style = "single"
+# Ruff configured in ruff.toml
 
 [dependency-groups]
 dev = [
     "ipython>=8.37.0",
+    "ruff>=0.15.5",
 ]
 test = [
   "pytest >=8",

ruff.toml

@@ -0,0 +1,49 @@
+line-length = 99
+extend-exclude = [
+  "_version.py",  # Auto-generated
+  "tests/data",   # Submodules
+]
+
+[format]
+quote-style = "single"
+line-ending = "lf"
+docstring-code-format = true
+
+[lint]
+extend-select = [
+  "F",    # pyflakes
+  "E",    # pycodestyle errors
+  "W",    # pycodestyle warnings
+  "I",    # isort
+  "D",    # pydocstyle
+  "UP",   # pyupgrade
+  "YTT",  # flake8-2020
+  "S",    # bandit
+  "BLE",  # blind-except
+  "B",    # bugbear
+  "A",    # builtins
+  "C4",   # comprehensions
+  "DTZ",  # datetimez
+  "T10",  # debugger
+  # "EM",   # errmsg
+  "EXE",  # executable
+  "ISC",  # implicit-str-concat
+  "ICN",  # import-conventions
+  "PT",   # pytest-style
+  "Q",    # quotes
+]
+ignore = [
+  "D105",  # undocumented-magic-method
+  "D107",  # undocumented __init__
+  "D203",  # blank line before class docstring
+  "D213",  # multi-line-summary-first-line
+  "Q000",  # double quotes
+  "Q003",  # avoidable-escaped-quote
+]
+
+[lint.extend-per-file-ignores]
+"setup.py" = ["D"]
+"*/test_*.py" = [
+  "S101",  # assert
+  "D",
+]

src/bids_validator/bids_validator.py

@@ -136,16 +136,16 @@ def parse(cls, path: str) -> dict[str, str]:
         --------
         >>> from bids_validator import BIDSValidator
         >>> validator = BIDSValidator()
-        >>> validator.parse("/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz")
+        >>> validator.parse('/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz')
         {'subject': '01', 'datatype': 'anat', 'reconstruction': 'CSD', 'suffix': 'T1w',
          'extension': '.nii.gz'}
-        >>> validator.parse("/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe")
+        >>> validator.parse('/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe')
         {}
-        >>> validator.parse("home/username/my_dataset/participants.tsv")
+        >>> validator.parse('home/username/my_dataset/participants.tsv')
         Traceback (most recent call last):
             ...
         ValueError: Path must be relative to root of a BIDS dataset, ...
-        >>> validator.parse("/participants.tsv")
+        >>> validator.parse('/participants.tsv')
         {'stem': 'participants', 'extension': '.tsv'}
 
         """
@@ -196,10 +196,10 @@ def is_bids(cls, path: str) -> bool:
         >>> from bids_validator import BIDSValidator
         >>> validator = BIDSValidator()
         >>> filepaths = [
-        ...   "/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz",
-        ...   "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe", # wrong extension
-        ...   "home/username/my_dataset/participants.tsv", # not relative to root
-        ...   "/participants.tsv",
+        ...     '/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz',
+        ...     '/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe',  # wrong extension
+        ...     'home/username/my_dataset/participants.tsv',  # not relative to root
+        ...     '/participants.tsv',
         ... ]
         >>> for filepath in filepaths:
         ...     print(validator.is_bids(filepath))

src/bids_validator/test_bids_validator.py

@@ -204,9 +204,7 @@ def test_is_session_level(validator: BIDSValidator, fname: str) -> None:
         '/sub-01/sub-01_acq_dwi.bval',  # missed suffix value
         '/sub-01/sub-01_acq-23-singleband_dwi.bvec',  # redundant -23-
         '/sub-01/anat/sub-01_acq-singleband_dwi.json',  # redundant /anat/
-        (
-            '/sub-01/sub-01_recrod-record_acq-singleband_run-01_dwi.bval'
-        ),  # redundant record-record_
+        '/sub-01/sub-01_recrod-record_acq-singleband_run-01_dwi.bval',  # redundant record-record_
         '/sub_01/sub-01_acq-singleband_run-01_dwi.bvec',  # wrong /sub_01/
         '/sub-01/sub-01_acq-singleband__run-01_dwi.json',  # wrong __
         '/sub-01/ses-test/sub-01_ses_test_dwi.bval',  # wrong ses_test