MAINT: Use black

.github/workflows/tests.yml

@@ -23,6 +23,7 @@ jobs:
     - uses: actions/setup-python@v4
       with:
         python-version: '3.11'
+    - uses: psf/black@stable
     - uses: pre-commit/[email protected]
 
   pytest:

.pre-commit-config.yaml

@@ -1,9 +1,9 @@
 repos:
-# - repo: https://github.com/psf/black
-#   rev: 23.1.0
-#   hooks:
-#     - id: black
-#       args: [--quiet]
+- repo: https://github.com/psf/black
+  rev: 23.3.0
+  hooks:
+    - id: black
+      args: [--quiet]
 
 # Ruff mne
 - repo: https://github.com/charliermarsh/ruff-pre-commit

azure-pipelines.yml

@@ -57,7 +57,7 @@ stages:
       displayName: Install dependencies
     - bash: |
         make pre-commit
-      displayName: make ruff
+      displayName: make pre-commit
       condition: always()
     - bash: |
         make nesting

ignore_words.txt

@@ -14,6 +14,7 @@ nd
 cas
 thes
 ba
+bu
 ist
 od
 fo
@@ -33,3 +34,4 @@ recuse
 ro
 nam
 shs
+pres

mne/channels/tests/test_montage.py

@@ -223,12 +223,12 @@ def test_documented():
 
     pytest.param(
         partial(read_custom_montage, head_size=None, coord_frame='mri'),
-        ('// MatLab   Sphere coordinates [degrees]         Cartesian coordinates\n'  # noqa: E501
-         '// Label       Theta       Phi    Radius         X         Y         Z       off sphere surface\n'  # noqa: E501
-         'E1      37.700     -14.000       1.000    0.7677    0.5934   -0.2419  -0.00000000000000011\n'  # noqa: E501
-         'E3      51.700      11.000       1.000    0.6084    0.7704    0.1908   0.00000000000000000\n'  # noqa: E501
-         'E31      90.000     -11.000       1.000    0.0000    0.9816   -0.1908   0.00000000000000000\n'  # noqa: E501
-         'E61     158.000     -17.200       1.000   -0.8857    0.3579   -0.2957  -0.00000000000000022'),  # noqa: E501
+        "// MatLab   Sphere coordinates [degrees]         Cartesian coordinates\n"  # noqa: E501
+        "// Label       Theta       Phi    Radius         X         Y         Z       off sphere surface\n"  # noqa: E501
+        "E1      37.700     -14.000       1.000    0.7677    0.5934   -0.2419  -0.00000000000000011\n"  # noqa: E501
+        "E3      51.700      11.000       1.000    0.6084    0.7704    0.1908   0.00000000000000000\n"  # noqa: E501
+        "E31      90.000     -11.000       1.000    0.0000    0.9816   -0.1908   0.00000000000000000\n"  # noqa: E501
+        "E61     158.000     -17.200       1.000   -0.8857    0.3579   -0.2957  -0.00000000000000022",  # noqa: E501
         make_dig_montage(
             ch_pos={
                 'E1': [0.7677, 0.5934, -0.2419],

mne/chpi.py

@@ -847,11 +847,12 @@ def compute_head_pos(info, chpi_locs, dist_limit=0.005, gof_limit=0.98,
         # 1. Check number of good ones
         #
         if len(use_idx) < 3:
-            msg = (_time_prefix(fit_time) + '%s/%s good HPI fits, cannot '
-                   'determine the transformation (%s GOF)!'
-                   % (len(use_idx), n_coils,
-                      ', '.join('%0.2f' % g for g in g_coils)))
-            warn(msg)
+            gofs = ', '.join(f"{g:0.2f}" for g in g_coils)
+            warn(
+                f"{_time_prefix(fit_time)}{len(use_idx)}/{n_coils} "
+                "good HPI fits, cannot determine the transformation "
+                f"({gofs} GOF)!"
+            )
             continue
 
         #

mne/conftest.py

@@ -101,8 +101,8 @@ def pytest_configure(config):
         first_kind = 'error'
     else:
         first_kind = 'always'
-    warning_lines = r"""
-    {0}::
+    warning_lines = f"    {first_kind}::"
+    warning_lines += r"""
     # matplotlib->traitlets (notebook)
     ignore:Passing unrecognized arguments to super.*:DeprecationWarning
     # notebook tests
@@ -142,7 +142,7 @@ def pytest_configure(config):
     ignore:pkg_resources is deprecated as an API.*:DeprecationWarning
     # h5py
     ignore:`product` is deprecated as of NumPy.*:DeprecationWarning
-    """.format(first_kind)  # noqa: E501
+    """  # noqa: E501
     for warning_line in warning_lines.split('\n'):
         warning_line = warning_line.strip()
         if warning_line and not warning_line.startswith('#'):

mne/coreg.py

@@ -23,11 +23,17 @@
 from .io._digitization import _get_data_as_dict_from_dig
 # keep get_mni_fiducials for backward compat (no burden to keep in this
 # namespace, too)
-from ._freesurfer import (_read_mri_info, get_mni_fiducials,  # noqa: F401
-                          estimate_head_mri_t)  # noqa: F401
+from ._freesurfer import (
+    _read_mri_info,
+    get_mni_fiducials,
+    estimate_head_mri_t,  # noqa: F401
+)
 from .label import read_label, Label
-from .source_space import (add_source_space_distances, read_source_spaces,  # noqa: E501,F401
-                           write_source_spaces)
+from .source_space import (
+    add_source_space_distances,
+    read_source_spaces,  # noqa: F401
+    write_source_spaces,
+)
 from .surface import (read_surface, write_surface, _normalize_vectors,
                       complete_surface_info, decimate_surface,
                       _DistanceQuery)

mne/io/kit/tests/test_kit.py

@@ -69,8 +69,9 @@ def test_data(tmp_path):
     # check functionality
     raw_mrk = read_raw_kit(sqd_path, [mrk2_path, mrk3_path], elp_txt_path,
                            hsp_txt_path)
-    assert raw_mrk.info['description'] == \
-        'NYU 160ch System since Jan24 2009 (34) V2R004 EQ1160C'
+    assert (
+        raw_mrk.info['description'] == 'NYU 160ch System since Jan24 2009 (34) V2R004 EQ1160C'  # noqa: E501
+    )
     raw_py = _test_raw_reader(read_raw_kit, input_fname=sqd_path, mrk=mrk_path,
                               elp=elp_txt_path, hsp=hsp_txt_path,
                               stim=list(range(167, 159, -1)), slope='+',
@@ -123,8 +124,9 @@ def test_data(tmp_path):
     # KIT-UMD data
     _test_raw_reader(read_raw_kit, input_fname=sqd_umd_path, test_rank='less')
     raw = read_raw_kit(sqd_umd_path)
-    assert raw.info['description'] == \
-        'University of Maryland/Kanazawa Institute of Technology/160-channel MEG System (53) V2R004 PQ1160R'  # noqa: E501
+    assert (
+        raw.info['description'] == 'University of Maryland/Kanazawa Institute of Technology/160-channel MEG System (53) V2R004 PQ1160R'  # noqa: E501
+    )
     assert_equal(raw.info['kit_system_id'], KIT.SYSTEM_UMD_2014_12)
     # check number/kind of channels
     assert_equal(len(raw.info['chs']), 193)
@@ -135,8 +137,9 @@ def test_data(tmp_path):
 
     # KIT Academia Sinica
     raw = read_raw_kit(sqd_as_path, slope='+')
-    assert raw.info['description'] == \
-        'Academia Sinica/Institute of Linguistics//Magnetoencephalograph System (261) V2R004 PQ1160R-N2'  # noqa: E501
+    assert (
+        raw.info['description'] == 'Academia Sinica/Institute of Linguistics//Magnetoencephalograph System (261) V2R004 PQ1160R-N2'  # noqa: E501
+    )
     assert_equal(raw.info['kit_system_id'], KIT.SYSTEM_AS_2008)
     assert_equal(raw.info['chs'][100]['ch_name'], 'MEG 101')
     assert_equal(raw.info['chs'][100]['kind'], FIFF.FIFFV_MEG_CH)
@@ -374,7 +377,9 @@ def test_berlin():
     """Test data from Berlin."""
     # gh-8535
     raw = read_raw_kit(berlin_path)
-    assert raw.info['description'] == 'Physikalisch Technische Bundesanstalt, Berlin/128-channel MEG System (124) V2R004 PQ1128R-N2'  # noqa: E501
+    assert (
+        raw.info['description'] == 'Physikalisch Technische Bundesanstalt, Berlin/128-channel MEG System (124) V2R004 PQ1128R-N2'  # noqa: E501
+    )
     assert raw.info['kit_system_id'] == 124
     assert raw.info['highpass'] == 0.
     assert raw.info['lowpass'] == 200.

mne/io/tests/test_raw.py

@@ -739,9 +739,15 @@ def test_describe_print():
     assert re.match(
         r'<Raw | test_raw.fif, 376 x 14400 (24\.0 s), '
         r'~3\.. MB, data not loaded>', s[0]) is not None, s[0]
-    assert s[1] == " ch  name      type  unit         min         Q1     median         Q3        max"  # noqa
-    assert s[2] == "  0  MEG 0113  GRAD  fT/cm    -221.80     -38.57      -9.64      19.29     414.67"  # noqa
-    assert s[-1] == "375  EOG 061   EOG   µV       -231.41     271.28     277.16     285.66     334.69"  # noqa
+    assert (
+        s[1] == " ch  name      type  unit         min         Q1     median         Q3        max"  # noqa: E501
+    )
+    assert (
+        s[2] == "  0  MEG 0113  GRAD  fT/cm    -221.80     -38.57      -9.64      19.29     414.67"  # noqa: E501
+    )
+    assert (
+        s[-1] == "375  EOG 061   EOG   µV       -231.41     271.28     277.16     285.66     334.69"  # noqa: E501
+    )
 
 
 @requires_pandas

mne/io/tests/test_reference.py

@@ -329,7 +329,8 @@ def test_set_eeg_reference_rest():
     # load('leadfield.mat', 'G');
     # dat_ref = ft_preproc_rereference(dat, 'all', 'rest', true, G);
     # sprintf('%g ', dat_ref(:, 171));
-    want = np.array('-3.3265e-05 -3.2419e-05 -3.18758e-05 -3.24079e-05 -3.39801e-05 -3.40573e-05 -3.24163e-05 -3.26896e-05 -3.33814e-05 -3.54734e-05 -3.51289e-05 -3.53229e-05 -3.51532e-05 -3.53149e-05 -3.4505e-05 -3.03462e-05 -2.81848e-05 -3.08895e-05 -3.27158e-05 -3.4605e-05 -3.47728e-05 -3.2459e-05 -3.06552e-05 -2.53255e-05 -2.69671e-05 -2.83425e-05 -3.12836e-05 -3.30965e-05 -3.34099e-05 -3.32766e-05 -3.32256e-05 -3.36385e-05 -3.20796e-05 -2.7108e-05 -2.47054e-05 -2.49589e-05 -2.7382e-05 -3.09774e-05 -3.12003e-05 -3.1246e-05 -3.07572e-05 -2.64942e-05 -2.25505e-05 -2.67194e-05 -2.86e-05 -2.94903e-05 -2.96249e-05 -2.92653e-05 -2.86472e-05 -2.81016e-05 -2.69737e-05 -2.48076e-05 -3.00473e-05 -2.73404e-05 -2.60153e-05 -2.41608e-05 -2.61937e-05 -2.5539e-05 -2.47104e-05 -2.35194e-05'.split(' '), float)  # noqa: E501
+    data_array = "-3.3265e-05 -3.2419e-05 -3.18758e-05 -3.24079e-05 -3.39801e-05 -3.40573e-05 -3.24163e-05 -3.26896e-05 -3.33814e-05 -3.54734e-05 -3.51289e-05 -3.53229e-05 -3.51532e-05 -3.53149e-05 -3.4505e-05 -3.03462e-05 -2.81848e-05 -3.08895e-05 -3.27158e-05 -3.4605e-05 -3.47728e-05 -3.2459e-05 -3.06552e-05 -2.53255e-05 -2.69671e-05 -2.83425e-05 -3.12836e-05 -3.30965e-05 -3.34099e-05 -3.32766e-05 -3.32256e-05 -3.36385e-05 -3.20796e-05 -2.7108e-05 -2.47054e-05 -2.49589e-05 -2.7382e-05 -3.09774e-05 -3.12003e-05 -3.1246e-05 -3.07572e-05 -2.64942e-05 -2.25505e-05 -2.67194e-05 -2.86e-05 -2.94903e-05 -2.96249e-05 -2.92653e-05 -2.86472e-05 -2.81016e-05 -2.69737e-05 -2.48076e-05 -3.00473e-05 -2.73404e-05 -2.60153e-05 -2.41608e-05 -2.61937e-05 -2.5539e-05 -2.47104e-05 -2.35194e-05"  # noqa: E501
+    want = np.array(data_array.split(" "), float)
     norm = np.linalg.norm(want)
     idx = np.argmin(np.abs(evoked.times - 0.083))
     assert idx == 170

mne/source_space.py

@@ -31,8 +31,13 @@
                       complete_surface_info, _compute_nearest, fast_cross_3d,
                       _CheckInside)
 # keep get_mni_fiducials here just for easy backward compat
-from ._freesurfer import (_get_mri_info_data, _get_atlas_values,  # noqa: F401
-                          read_freesurfer_lut, get_mni_fiducials, _check_mri)
+from ._freesurfer import (
+    _get_mri_info_data,
+    _get_atlas_values,
+    read_freesurfer_lut,
+    get_mni_fiducials,  # noqa: F401
+    _check_mri,
+)
 from .utils import (get_subjects_dir, check_fname, logger, verbose, fill_doc,
                     _ensure_int, _get_call_line, warn, object_size, sizeof_fmt,
                     _check_fname, _path_like, _check_sphere, _import_nibabel,

mne/tests/test_annotations.py

@@ -987,7 +987,7 @@ def test_io_annotation_txt(dummy_annotation_txt_file, tmp_path_factory,
     pytest.param(None, None, id='None'),
     pytest.param(42, 42.0, id='Scalar'),
     pytest.param(3.14, 3.14, id='Float'),
-    pytest.param((3, 140000), 3.14, id='Scalar touple'),
+    pytest.param((3, 140000), 3.14, id="Scalar tuple"),
     pytest.param('2002-12-03 19:01:11.720100', 1038942071.7201,
                  id='valid iso8601 string'),
     pytest.param('2002-12-03T19:01:11.720100', None,
@@ -1355,7 +1355,7 @@ def test_annotation_ch_names():
     assert raw_2.annotations.ch_names[1] == tuple(raw.ch_names[4:5])
     for ch_drop in raw_2.annotations.ch_names:
         assert all(name in raw_2.ch_names for name in ch_drop)
-    with pytest.raises(ValueError, match='channel name in annotations missin'):
+    with pytest.raises(ValueError, match='channel name in annotations miss'):
         raw_2.set_annotations(annot)
     with pytest.warns(RuntimeWarning, match='channel name in annotations mis'):
         raw_2.set_annotations(annot, on_missing='warn')

mne/tests/test_docstring_parameters.py

@@ -130,7 +130,10 @@ def check_parameters_match(func, cls=None):
         msg = str(exc)
         # E   ValueError: no signature found for builtin type
         #     <class 'mne.forward.forward.Forward'>
-        if inspect.isclass(callable_) and 'no signature found for buil' in msg:
+        if (
+            inspect.isclass(callable_) and
+            "no signature found for builtin type" in msg
+        ):
             pass
         else:
             raise

mne/tests/test_source_estimate.py

@@ -1898,5 +1898,5 @@ def test_label_extraction_subject(kind):
         with pytest.raises(ValueError, match=r'label\.sub.*not match.* stc\.'):
             extract_label_time_course(stc, labels_fs, src)
         stc.subject = None
-        with pytest.raises(ValueError, match=r'label\.sub.*not match.* sourc'):
+        with pytest.raises(ValueError, match=r"label\.sub.*not match.* sour"):
             extract_label_time_course(stc, labels_fs, src)

mne/tests/test_source_space.py

@@ -479,7 +479,7 @@ def test_setup_source_space(tmp_path):
         setup_source_space('sample', spacing='7emm',
                            add_dist=False, subjects_dir=subjects_dir)
     with pytest.raises(ValueError, match='must be a string with values'):
-        setup_source_space('sample', spacing='alls',
+        setup_source_space("sample", spacing="ally",
                            add_dist=False, subjects_dir=subjects_dir)
 
     # ico 5 (fsaverage) - write to temp file

mne/transforms.py

@@ -1822,7 +1822,7 @@ def apply_volume_registration(moving, static, reg_affine, sdr_morph=None,
                            moving.shape, moving_affine)
     reg_data = affine_map.transform(moving, interpolation=interpolation)
     if sdr_morph is not None:
-        logger.info('Appling SDR warp ...')
+        logger.info("Applying SDR warp ...")
         reg_data = sdr_morph.transform(
             reg_data, interpolation=interpolation,
             image_world2grid=np.linalg.inv(static_affine),

mne/utils/tests/test_check.py

@@ -204,7 +204,9 @@ def test_suggest():
     sug = _suggest('Left-cerebellum', names)
     assert sug == " Did you mean 'Left-Cerebellum-Cortex'?"
     sug = _suggest('Cerebellum-Cortex', names)
-    assert sug == " Did you mean one of ['Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', 'Left-Cerebral-Cortex']?"  # noqa: E501
+    assert (
+        sug == " Did you mean one of ['Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', 'Left-Cerebral-Cortex']?"  # noqa: E501
+    )
 
 
 def test_on_missing():

mne/viz/backends/_notebook.py

@@ -34,8 +34,14 @@
                         _AbstractWidgetList, _AbstractAction, _AbstractDialog,
                         _AbstractKeyPress)
 from ._pyvista import _PyVistaRenderer, Plotter
-from ._pyvista import (_close_3d_figure, _check_3d_figure, _close_all,  # noqa: F401,E501 analysis:ignore
-                       _set_3d_view, _set_3d_title, _take_3d_screenshot)  # noqa: F401,E501 analysis:ignore
+from ._pyvista import (
+    _close_3d_figure,  # noqa: F401
+    _check_3d_figure,  # noqa: F401
+    _close_all,  # noqa: F401
+    _set_3d_view,  # noqa: F401
+    _set_3d_title,  # noqa: F401
+    _take_3d_screenshot,  # noqa: F401
+)
 from ._utils import _notebook_vtk_works
 
 

mne/viz/backends/_qt.py

@@ -32,9 +32,15 @@
                             QSpinBox, QStyle, QStyleOptionSlider)
 
 from ._pyvista import _PyVistaRenderer
-from ._pyvista import (_close_3d_figure, _check_3d_figure, _close_all,  # noqa: F401,E501 analysis:ignore
-                       _set_3d_view, _set_3d_title, _take_3d_screenshot,  # noqa: F401,E501 analysis:ignore
-                       _is_mesa)  # noqa: F401,E501 analysis:ignore
+from ._pyvista import (
+    _close_3d_figure,  # noqa: F401
+    _check_3d_figure,  # noqa: F401
+    _close_all,  # noqa: F401
+    _set_3d_view,  # noqa: F401
+    _set_3d_title,  # noqa: F401
+    _take_3d_screenshot,  # noqa: F401
+    _is_mesa,  # noqa: F401
+)
 from ._abstract import (_AbstractAppWindow, _AbstractHBoxLayout,
                         _AbstractVBoxLayout, _AbstractGridLayout,
                         _AbstractWidget, _AbstractCanvas,

pyproject.toml

@@ -1,6 +1,5 @@
 [tool.codespell]
 ignore-words = "ignore_words.txt"
-uri-ignore-words-list = "bu"
 builtin = "clear,rare,informal,names,usage"
 skip = "doc/references.bib"
 
@@ -48,3 +47,6 @@ addopts = """--durations=20 --doctest-modules -ra --cov-report= --tb=short \
     --ignore=mne/report/js_and_css \
     --color=yes --capture=sys"""
 junit_family = "xunit2"
+
+[tool.black]
+exclude = "(dist/)|(build/)|(.*\\.ipynb)"

requirements_testing.txt

@@ -11,3 +11,4 @@ tomli; python_version<'3.11'
 twine
 wheel
 pre-commit
+black

tutorials/forward/50_background_freesurfer_mne.py

@@ -128,7 +128,7 @@ def imshow_mri(data, img, vox, xyz, suptitle):
     # Figure out the title based on the code of this axis
     ori_slice = dict(P='Coronal', A='Coronal',
                      I='Axial', S='Axial',
-                     L='Sagittal', R='Saggital')
+                     L='Sagittal', R='Sagittal')
     ori_names = dict(P='posterior', A='anterior',
                      I='inferior', S='superior',
                      L='left', R='right')