MEG: Add git pre-commit configuration

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+        args: [--quiet]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.291
+    hooks:
+      - id: ruff
+        name: ruff mne_bids/
+        files: ^mne_bids/
+      - id: ruff
+        name: ruff examples/
+        # D103: missing docstring in public function
+        # D400: docstring first line must end with period
+        # D205: 1 blank line required between summary line and description
+        args: ["--ignore=D103,D400,D205"]
+        files: ^examples/

CONTRIBUTING.md

@@ -109,7 +109,7 @@ bids-validator --version
 We use [GNU Make](https://www.gnu.org/software/make/) for developing `mne-bids`.
 We recommend that you install GNU Make and make use of our `Makefile` at the root
 of the repository.
-For most Linux and OSX operating systems, GNU Make will be already installed by default.
+For most Linux and macOS operating systems, GNU Make will be already installed by default.
 Windows users can download the [Chocolatey package manager](https://chocolatey.org/)
 and install [GNU Make from their repository](https://community.chocolatey.org/packages/make).
 
@@ -131,6 +131,22 @@ We use [Black](https://github.com/psf/black) to format our code.
 You can simply call `black .` from the root of the `mne-bids` repository
 to automatically convert your code to follow the appropriate style.
 
+### git pre-commit hooks
+
+We suggest installing our git pre-commit hooks to automatically run style
+checks before a commit is created:
+
+```Shell
+pip install pre-commit
+pre-commit install
+```
+
+You can also manually run the hooks via
+
+```Shell
+pre-commit run -a
+```
+
 ## Running tests
 
 We run tests using `pytest`.

mne_bids/path.py

@@ -1981,7 +1981,7 @@ def get_entity_vals(
 
     References
     ----------
-    .. [1] https://bids-specification.rtfd.io/en/latest/common-principles.html#entities  # noqa: E501
+    .. [1] https://bids-specification.rtfd.io/en/latest/common-principles.html#entities
 
     """
     root = _check_fname(

mne_bids/tests/test_dig.py

@@ -1,5 +1,5 @@
-# -*- coding: utf-8 -*-
 """Test the digitizations.
+
 For each supported coordinate frame, implement a test.
 """
 # Authors: Alex Rockhill <aprockhill@mailbox.org>

mne_bids/tests/test_path.py

@@ -355,6 +355,7 @@ def test_parse_ext():
     ],
 )
 def test_get_bids_path_from_fname(fname):
+    """Test get_bids_path_from_fname()."""
     bids_path = get_bids_path_from_fname(fname)
     assert bids_path.basename == Path(fname).name
 
@@ -1039,8 +1040,10 @@ def test_match(return_bids_test_dir):
 
 @testing.requires_testing_data
 def test_find_matching_paths(return_bids_test_dir):
-    """We test by yielding the same results as BIDSPath.match() which
-    is extensively tested above."""
+    """We test by yielding the same results as BIDSPath.match().
+
+    BIDSPath.match() is extensively tested above.
+    """
     bids_root = Path(return_bids_test_dir)
 
     # Check a few exemplary entities
@@ -1336,6 +1339,7 @@ def test_find_emptyroom_no_meas_date(tmp_path):
 
 
 def test_bids_path_label_vs_index_entity():
+    """Test entities that must be strings vs those that may be an int."""
     match = "subject must be an instance of None or str"
     with pytest.raises(TypeError, match=match):
         BIDSPath(subject=1)
@@ -1348,6 +1352,7 @@ def test_bids_path_label_vs_index_entity():
 
 @testing.requires_testing_data
 def test_meg_calibration_fpath(return_bids_test_dir):
+    """Test BIDSPath.meg_calibration_fpath."""
     bids_root = return_bids_test_dir
 
     # File exists, so BIDSPath.meg_calibration_fpath should return a non-None
@@ -1379,6 +1384,7 @@ def test_meg_calibration_fpath(return_bids_test_dir):
 
 @testing.requires_testing_data
 def test_meg_crosstalk_fpath(return_bids_test_dir):
+    """Test BIDSPath.meg_crosstalk_fpath."""
     bids_root = return_bids_test_dir
 
     # File exists, so BIDSPath.crosstalk_fpath should return a non-None
@@ -1410,6 +1416,7 @@ def test_meg_crosstalk_fpath(return_bids_test_dir):
 
 @testing.requires_testing_data
 def test_datasetdescription_with_bidspath(return_bids_test_dir):
+    """Test a BIDSPath can generate a valid path to dataset_description.json."""
     with pytest.raises(ValueError, match="Unallowed"):
         bids_path = BIDSPath(
             root=return_bids_test_dir, suffix="dataset_description", extension=".json"
@@ -1437,6 +1444,7 @@ def test_datasetdescription_with_bidspath(return_bids_test_dir):
 
 
 def test_update_fail_check_no_change():
+    """Test BIDSPath.check works in preventing invalid changes."""
     bids_path = BIDSPath(subject="test")
     try:
         bids_path.update(suffix="ave")

mne_bids/tests/test_read.py

@@ -619,7 +619,7 @@ def test_handle_scans_reading(tmp_path):
 
 @pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 def test_handle_scans_reading_brainvision(tmp_path):
-    """Test stability of BrainVision's different file extensions"""
+    """Test stability of BrainVision's different file extensions."""
     test_scan_eeg = OrderedDict(
         [
             ("filename", [Path("eeg/sub-01_ses-eeg_task-rest_eeg.eeg")]),
@@ -1152,6 +1152,7 @@ def test_handle_non_mne_channel_type(tmp_path):
 @pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @testing.requires_testing_data
 def test_bads_reading(tmp_path):
+    """Test reading bad channels."""
     bids_path = _bids_path.copy().update(root=tmp_path, datatype="meg")
     bads_raw = ["MEG 0112", "MEG 0113"]
     bads_sidecar = ["EEG 053", "MEG 2443"]

mne_bids/utils.py

@@ -529,6 +529,7 @@ def warn(
     module="mne_bids",
     ignore_namespaces=("mne", "mne_bids"),
 ):  # noqa: D103
+    """Emit a warning."""
     _warn(
         message,
         category=category,

pyproject.toml

@@ -0,0 +1,12 @@
+[tool.ruff]
+select = ["E", "F", "W", "D"]
+exclude = ["__init__.py"]
+
+[tool.ruff.pydocstyle]
+convention = "numpy"
+
+[tool.black]
+exclude = "(dist/)|(build/)|(.*\\.ipynb)"
+
+[tool.check-manifest]
+ignore = [".pre-commit-config.yaml"]