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Merge pull request #1 from effigies/maint/style-and-precommit
chore: Add ruff and pre-commit configurations, apply
2 parents 0a0915a + 52e4d95 commit cdd1f92

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-70
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lines changed

‎.pre-commit-config.yaml

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

‎pyproject.toml

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

‎src/bids_validator/__init__.py

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@@ -1,6 +1,9 @@
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"""BIDS validator common Python package."""
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23
from .bids_validator import BIDSValidator
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35
__all__ = ['BIDSValidator']
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from . import _version
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__version__ = _version.get_versions()['version']

‎src/bids_validator/bids_validator.py

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@@ -1,4 +1,5 @@
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"""Validation class for BIDS projects."""
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23
import logging
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import os
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import re
@@ -139,8 +140,10 @@ def parse(cls, path):
139140
path = path.replace(os.sep, '/')
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141142
if not path.startswith('/'):
142-
raise ValueError("Path must be relative to root of a BIDS dataset,"
143-
" and must include a leading forward slash `/`.")
143+
raise ValueError(
144+
'Path must be relative to root of a BIDS dataset,'
145+
' and must include a leading forward slash `/`.'
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)
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145148
for regex in cls.regexes:
146149
match = re.match(regex, path[1:])

‎src/bids_validator/test_bids_validator.py

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@@ -7,18 +7,16 @@
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88
import os
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10-
import pytest
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import datalad.api
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import pytest
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from bids_validator import BIDSValidator
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HOME = os.path.expanduser('~')
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1717
TEST_DATA_DICT = {
18-
'eeg_matchingpennies': (
19-
'https://gin.g-node.org/sappelhoff/eeg_matchingpennies'
20-
),
21-
}
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'eeg_matchingpennies': ('https://gin.g-node.org/sappelhoff/eeg_matchingpennies'),
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}
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2321
EXCLUDE_KEYWORDS = ['git', 'datalad', 'sourcedata', 'bidsignore']
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@@ -61,94 +59,112 @@ def test_datasets(validator, fname):
6159
assert validator.is_bids(fname)
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6361

64-
@pytest.mark.parametrize('fname, matches', [
65-
('/T1w.json', True),
66-
('/dataset_description.json', True),
67-
('/README', True),
68-
('/CHANGES', True),
69-
('/participants.tsv', True),
70-
('/sub-01/anat/sub-01_T1w.nii.gz', False),
71-
])
62+
@pytest.mark.parametrize(
63+
('fname', 'matches'),
64+
[
65+
('/T1w.json', True),
66+
('/dataset_description.json', True),
67+
('/README', True),
68+
('/CHANGES', True),
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('/participants.tsv', True),
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('/sub-01/anat/sub-01_T1w.nii.gz', False),
71+
],
72+
)
7273
def test_top_level(validator, fname, matches):
7374
"""Test that is_top_level returns true for top-level files."""
7475
assert validator.is_top_level(fname) is matches
7576

7677

77-
@pytest.mark.parametrize('fname, matches', [
78-
('/sourcedata/unstructured_data.nii.gz', True),
79-
('/sourcedata/dicom_dir/xyz.dcm', True),
80-
('/code/my_analysis/analysis.py', True),
81-
('/derivatives/preproc/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz', True),
82-
('/stimuli/pic.jpg', True),
83-
('/sub-01/anat/sub-01_T1w.nii.gz', False),
84-
])
78+
@pytest.mark.parametrize(
79+
('fname', 'matches'),
80+
[
81+
('/sourcedata/unstructured_data.nii.gz', True),
82+
('/sourcedata/dicom_dir/xyz.dcm', True),
83+
('/code/my_analysis/analysis.py', True),
84+
('/derivatives/preproc/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz', True),
85+
('/stimuli/pic.jpg', True),
86+
('/sub-01/anat/sub-01_T1w.nii.gz', False),
87+
],
88+
)
8589
def test_associated_data(validator, fname, matches):
8690
"""Test that is_associated_data returns true for associated data."""
8791
assert validator.is_associated_data(fname) is matches
8892

8993

90-
@pytest.mark.parametrize('fname, matches', [
91-
('/sub-01/ses-1/sub-01_ses-1_scans.tsv', True),
92-
('/sub-01/ses-1/sub-01_ses-1_scans.json', True),
93-
('/sub-01/sub-01_scans.tsv', True),
94-
('/sub-01/sub-01_scans.json', True),
95-
('/sub-01/ses-1/sub-01_ses-1_task-rest_bold.json', True),
96-
('/sub-01/sub-01_task-rest_bold.json', True),
97-
('/sub-01/ses-1/sub-01_ses-1_asl.json', True),
98-
('/sub-01/sub-01_asl.json', True),
99-
('/sub-01/ses-1/sub-01_ses-1_pet.json', True),
100-
('/sub-01/sub-01_pet.json', True),
101-
('/sub-01/ses-1/sub-01_ses-1_proc-test_channels.tsv', True),
102-
('/sub-01/ses-1/sub-01_ses-1_channels.json', True),
103-
('/sub-01/sub-01_proc-test_channels.tsv', True),
104-
('/sub-01/sub-01_channels.json', True),
105-
('/sub-01/ses-1/sub-01_ses-1_space-CapTrak_electrodes.tsv', True),
106-
('/sub-01/ses-1/sub-01_ses-1_coordsystem.json', True),
107-
('/sub-01/sub-01_space-CapTrak_electrodes.tsv', True),
108-
('/sub-01/sub-01_coordsystem.json', True),
109-
('/sub-01/ses-1/sub-01_ses-1_motion.json', True),
110-
('/sub-01/sub-01_motion.json', True),
111-
('/sub-01/ses-1/sub-01_ses-1_TEM.json', True),
112-
('/sub-01/sub-01_TEM.json', True),
113-
('/sub-01/ses-1/sub-01_ses-1_nirs.json', True),
114-
('/sub-01/sub-01_nirs.json', True),
115-
# Mismatch sessions
116-
('/sub-01/sub-01_ses-1_scans.tsv', False),
117-
('/sub-01/sub-01_ses-1_scans.json', False),
118-
('/sub-01/ses-1/sub-01_ses-2_scans.tsv', False),
119-
# File-level
120-
('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', False),
121-
('/sub-01/anat/sub-01_T1w.nii.gz', False),
122-
])
94+
@pytest.mark.parametrize(
95+
('fname', 'matches'),
96+
[
97+
('/sub-01/ses-1/sub-01_ses-1_scans.tsv', True),
98+
('/sub-01/ses-1/sub-01_ses-1_scans.json', True),
99+
('/sub-01/sub-01_scans.tsv', True),
100+
('/sub-01/sub-01_scans.json', True),
101+
('/sub-01/ses-1/sub-01_ses-1_task-rest_bold.json', True),
102+
('/sub-01/sub-01_task-rest_bold.json', True),
103+
('/sub-01/ses-1/sub-01_ses-1_asl.json', True),
104+
('/sub-01/sub-01_asl.json', True),
105+
('/sub-01/ses-1/sub-01_ses-1_pet.json', True),
106+
('/sub-01/sub-01_pet.json', True),
107+
('/sub-01/ses-1/sub-01_ses-1_proc-test_channels.tsv', True),
108+
('/sub-01/ses-1/sub-01_ses-1_channels.json', True),
109+
('/sub-01/sub-01_proc-test_channels.tsv', True),
110+
('/sub-01/sub-01_channels.json', True),
111+
('/sub-01/ses-1/sub-01_ses-1_space-CapTrak_electrodes.tsv', True),
112+
('/sub-01/ses-1/sub-01_ses-1_coordsystem.json', True),
113+
('/sub-01/sub-01_space-CapTrak_electrodes.tsv', True),
114+
('/sub-01/sub-01_coordsystem.json', True),
115+
('/sub-01/ses-1/sub-01_ses-1_motion.json', True),
116+
('/sub-01/sub-01_motion.json', True),
117+
('/sub-01/ses-1/sub-01_ses-1_TEM.json', True),
118+
('/sub-01/sub-01_TEM.json', True),
119+
('/sub-01/ses-1/sub-01_ses-1_nirs.json', True),
120+
('/sub-01/sub-01_nirs.json', True),
121+
# Mismatch sessions
122+
('/sub-01/sub-01_ses-1_scans.tsv', False),
123+
('/sub-01/sub-01_ses-1_scans.json', False),
124+
('/sub-01/ses-1/sub-01_ses-2_scans.tsv', False),
125+
# File-level
126+
('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', False),
127+
('/sub-01/anat/sub-01_T1w.nii.gz', False),
128+
],
129+
)
123130
def test_session_level(validator, fname, matches):
124131
"""Test that is_session_level returns true for session level files."""
125132
assert validator.is_session_level(fname) is matches
126133

127134

128-
@pytest.mark.parametrize('fname, matches', [
129-
('/sub-01/sub-01_sessions.tsv', True),
130-
('/sub-01/sub-01_sessions.json', True),
131-
('/sub-01/anat/sub-01_T1w.nii.gz', False),
132-
])
135+
@pytest.mark.parametrize(
136+
('fname', 'matches'),
137+
[
138+
('/sub-01/sub-01_sessions.tsv', True),
139+
('/sub-01/sub-01_sessions.json', True),
140+
('/sub-01/anat/sub-01_T1w.nii.gz', False),
141+
],
142+
)
133143
def test_subject_level(validator, fname, matches):
134144
"""Test that is_subject_level returns true for subject level files."""
135145
assert validator.is_subject_level(fname) is matches
136146

137147

138-
@pytest.mark.parametrize('fname, matches', [
139-
('/phenotype/measure.tsv', True),
140-
('/phenotype/measure.json', True),
141-
('/sub-01/anat/sub-01_T1w.nii.gz', False),
142-
])
148+
@pytest.mark.parametrize(
149+
('fname', 'matches'),
150+
[
151+
('/phenotype/measure.tsv', True),
152+
('/phenotype/measure.json', True),
153+
('/sub-01/anat/sub-01_T1w.nii.gz', False),
154+
],
155+
)
143156
def test_phenotpic(validator, fname, matches):
144157
"""Test that is_phenotypic returns true for phenotypic files."""
145158
assert validator.is_phenotypic(fname) is matches
146159

147160

148-
@pytest.mark.parametrize('fname, matches', [
149-
('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', True),
150-
('/sub-01/anat/sub-01_T1w.nii.gz', True),
151-
])
161+
@pytest.mark.parametrize(
162+
('fname', 'matches'),
163+
[
164+
('/sub-01/ses-1/func/sub-01_ses-1_task-rest_bold.nii.gz', True),
165+
('/sub-01/anat/sub-01_T1w.nii.gz', True),
166+
],
167+
)
152168
def test_file_level(validator, fname, matches):
153169
"""Test that is_file returns true for file level files."""
154170
assert validator.is_file(fname) is matches

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