mne-tools/mne-python

7.8

Adjusted Score

7.8

Raw Score

100%

Time Factor

2026-08-29

Last Push

3.5K

Stars

Python

Language

680.0K

Lines of Code

8.7K

Files

3.8K

Pattern Hits

2026-08-29

Scan Date

0.00

HC Hit Rate

What These Metrics Mean

Adjusted Score: Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score: The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor: The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits: Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate: High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files: Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

Longitudinal tracking requires multiple scan runs. Once this repository is re-scanned after new commits land, this chart will visualise how the synthetic code signal evolves over time — enabling you to detect whether AI authorship is growing, stabilising, or being actively corrected by human engineers.

No multi-scan history yet — run the scanner again to build trend data.

Severity Breakdown

Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.

CRITICAL 14HIGH 19MEDIUM 659LOW 3080

Directory Score Breakdown

This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.

Pattern Findings

The scanner identified 3772 distinct pattern matches across 20 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.

Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.

Decorative Section Separators483 hits · 1446 pts

Severity	File	Line	Snippet	Context
MEDIUM	mne/io/edf/edf.py	915	# -------------------------------------------------------------------------	COMMENT
MEDIUM	mne/io/edf/edf.py	1371	# ---------------------------------------------------------------------	COMMENT
MEDIUM	mne/io/edf/edf.py	1483	# -----------------------------------------------------------------	COMMENT
MEDIUM	mne/io/edf/edf.py	1509	# ---------------------------------------------------------------------	COMMENT
MEDIUM	mne/io/edf/edf.py	1736	# -----------------------------------------------------------------	COMMENT
MEDIUM	mne/io/kit/constants.py	147	# -----------------	COMMENT
MEDIUM	mne/tests/test_annotations.py	1510	# -------------------------------------------------------------------------	COMMENT
MEDIUM	mne/tests/test_annotations.py	1522	# -------------------------------------------------------------------------	COMMENT
MEDIUM	mne/tests/test_annotations.py	1536	# -------------------------------------------------------------------------	COMMENT
MEDIUM	mne/tests/test_annotations.py	1550	# -------------------------------------------------------------------------	COMMENT
MEDIUM	mne/tests/test_annotations.py	1564	# -------------------------------------------------------------------------	COMMENT
MEDIUM	mne/viz/ica.py	307	# ----------	COMMENT
MEDIUM	mne/viz/ica.py	548	# -------------------------	COMMENT
MEDIUM	mne/viz/ica.py	591	# ------------	COMMENT
MEDIUM	mne/viz/backends/_qt.py	805	# ------------------------------------	COMMENT
MEDIUM	mne/viz/backends/_qt.py	807	# ------------------------------------	COMMENT
MEDIUM	mne/viz/backends/_abstract.py	714	# -------------------	COMMENT
MEDIUM	mne/viz/backends/_abstract.py	716	# -------------------	COMMENT
MEDIUM	mne/viz/backends/_abstract.py	1024	# -------------------	COMMENT
MEDIUM	mne/viz/backends/_abstract.py	1026	# -------------------	COMMENT
MEDIUM	mne/viz/backends/_abstract.py	1062	# ------------------------------------	COMMENT
MEDIUM	mne/viz/backends/_abstract.py	1064	# ------------------------------------	COMMENT
MEDIUM	mne/viz/backends/_notebook.py	789	# ------------------------------------	COMMENT
MEDIUM	mne/viz/backends/_notebook.py	791	# ------------------------------------	COMMENT
MEDIUM	mne/viz/tests/test_topomap.py	395	# ---------------------------------------------------	COMMENT
MEDIUM	mne/viz/tests/test_topomap.py	1174	# -----------	COMMENT
MEDIUM	mne/viz/tests/test_ica.py	130	# ----------------	COMMENT
MEDIUM	mne/viz/tests/test_ica.py	145	# ---------------	COMMENT
MEDIUM⚡	mne/stats/cluster_level.py	887	# -------------------------------------------------------------	COMMENT
MEDIUM⚡	mne/stats/cluster_level.py	999	# -------------------------------------------------------------------	COMMENT
MEDIUM	examples/inverse/mixed_norm_inverse.py	168	# ----------	COMMENT
MEDIUM	examples/inverse/psf_ctf_vertices_lcmv.py	83	# ------------------------------------------------------------	COMMENT
MEDIUM	examples/inverse/psf_ctf_vertices_lcmv.py	115	# --------------------------------------------------------	COMMENT
MEDIUM	examples/inverse/rap_music.py	60	# ----------	COMMENT
MEDIUM	examples/inverse/resolution_metrics_eegmeg.py	99	# -------------	COMMENT
MEDIUM	examples/inverse/resolution_metrics_eegmeg.py	197	# ----------	COMMENT
MEDIUM	examples/inverse/resolution_metrics.py	90	# -----------------	COMMENT
MEDIUM	examples/inverse/resolution_metrics.py	180	# ----------	COMMENT
MEDIUM	examples/inverse/psf_ctf_label_leakage.py	41	# ------------------------------------------	COMMENT
MEDIUM	examples/inverse/psf_ctf_label_leakage.py	65	# --------------------------------------------------	COMMENT
MEDIUM	examples/inverse/psf_ctf_label_leakage.py	90	# ------------------------------------------------------------	COMMENT
MEDIUM	examples/inverse/psf_ctf_label_leakage.py	119	# ---------------------------------------------------------	COMMENT
MEDIUM	examples/inverse/psf_ctf_label_leakage.py	158	# --------------------------	COMMENT
MEDIUM	examples/inverse/psf_ctf_label_leakage.py	168	# -------------------------------	COMMENT
MEDIUM	examples/inverse/trap_music.py	60	# ----------	COMMENT
MEDIUM	examples/inverse/mne_cov_power.py	41	# -----------------------------	COMMENT
MEDIUM	examples/inverse/mne_cov_power.py	55	# --------------	COMMENT
MEDIUM	examples/inverse/mne_cov_power.py	82	# ----------------------------	COMMENT
MEDIUM	examples/inverse/mne_cov_power.py	124	# ------------------------------------	COMMENT
MEDIUM	examples/inverse/mixed_source_space_inverse.py	44	# -----------------------	COMMENT
MEDIUM	examples/inverse/mixed_source_space_inverse.py	91	# ---------------------	COMMENT
MEDIUM	examples/inverse/mixed_source_space_inverse.py	108	# ----------------------	COMMENT
MEDIUM	examples/inverse/mixed_source_space_inverse.py	136	# ------------------------	COMMENT
MEDIUM	examples/inverse/mixed_source_space_inverse.py	154	# ------------------------------	COMMENT
MEDIUM⚡	examples/inverse/mixed_source_space_inverse.py	173	# ----------------	COMMENT
MEDIUM⚡	examples/inverse/mixed_source_space_inverse.py	179	# ---------------	COMMENT
MEDIUM⚡	examples/inverse/mixed_source_space_inverse.py	185	# --------------	COMMENT
MEDIUM	examples/inverse/morph_surface_stc.py	56	# -----------------------------------------	COMMENT
MEDIUM	examples/inverse/morph_surface_stc.py	100	# --------------------------------------	COMMENT
MEDIUM	examples/inverse/morph_surface_stc.py	109	# ------------	COMMENT
423 more matches not shown…

Hyper-Verbose Identifiers1002 hits · 990 pts

Severity	File	Line	Snippet	Context
LOW	mne/source_estimate.py	468	def _verify_source_estimate_compat(a, b):	CODE
LOW	mne/source_estimate.py	597	def extract_label_time_course(	CODE
LOW	mne/source_estimate.py	831	def _remove_kernel_sens_data_(self):	CODE
LOW	mne/source_estimate.py	3104	def _spatio_temporal_src_adjacency_vol(src, n_times):	CODE
LOW	mne/source_estimate.py	3113	def _spatio_temporal_src_adjacency_surf(src, n_times):	CODE
LOW	mne/source_estimate.py	3157	def spatio_temporal_src_adjacency(src, n_times, dist=None, verbose=None):	CODE
LOW	mne/source_estimate.py	3221	def spatio_temporal_tris_adjacency(tris, n_times, remap_vertices=False, verbose=None):	CODE
LOW	mne/source_estimate.py	3256	def spatio_temporal_dist_adjacency(src, n_times, dist, verbose=None):	CODE
LOW	mne/source_estimate.py	3375	def spatial_inter_hemi_adjacency(src, dist, verbose=None):	CODE
LOW	mne/source_estimate.py	3409	def _get_adjacency_from_edges(edges, n_times, verbose=None):	CODE
LOW	mne/source_estimate.py	3494	def _prepare_label_extraction(stc, labels, src, mode, allow_empty, use_sparse):	CODE
LOW	mne/source_estimate.py	3723	def _gen_extract_label_time_course(	CODE
LOW	mne/source_estimate.py	3822	def extract_label_time_course(	CODE
LOW	mne/source_estimate.py	2481	def extract_label_time_course(	STRING
LOW	mne/transforms.py	697	def get_ras_to_neuromag_trans(nasion, lpa, rpa):	CODE
LOW	mne/transforms.py	750	def _get_transforms_to_coord_frame(info, trans, coord_frame="mri"):	CODE
LOW	mne/transforms.py	1332	def angle_distance_between_rigid(a, b=None, *, angle_units="rad", distance_units="m"):	CODE
LOW	mne/transforms.py	1661	def compute_volume_registration(	CODE
LOW	mne/transforms.py	1710	def _compute_volume_registration(	CODE
LOW	mne/transforms.py	1825	def apply_volume_registration(	CODE
LOW	mne/transforms.py	1912	def apply_volume_registration_points(	CODE
LOW	mne/conftest.py	269	def pytest_collection_modifyitems(items: list[pytest.Item]):	STRING
LOW	mne/conftest.py	761	def renderer_interactive_pyvistaqt(request, options_3d, qt_windows_closed):	CODE
LOW	mne/conftest.py	954	def _all_src_types_inv_evoked(_evoked_cov_sphere, _all_src_types_fwd):	CODE
LOW	mne/conftest.py	1377	def pytest_runtest_makereport(item: pytest.Item, call: pytest.CallInfo):	CODE
LOW	mne/event.py	1344	def _categories_from_acq_pars(self):	CODE
LOW	mne/epochs.py	722	def _check_events_outside_data(self, on_outside, raw):	CODE
LOW	mne/epochs.py	3335	def _diff_input_strings_vs_event_id(input_strings, input_name, event_id):	CODE
LOW	mne/coreg.py	1723	def _nearest_transformed_high_res_mri_idx_hsp(self):	CODE
LOW	mne/coreg.py	1774	def _processed_high_res_mri_points(self):	CODE
LOW	mne/coreg.py	1777	def _get_processed_mri_points(self, res):	CODE
LOW	mne/coreg.py	2091	def compute_dig_mri_distances(self):	CODE
LOW	mne/coreg.py	2141	def _get_fiducials_distance_str(self):	CODE
LOW	mne/_freesurfer.py	212	def get_volume_labels_from_aseg(mgz_fname, return_colors=False, atlas_ids=None):	CODE
LOW	mne/_freesurfer.py	510	def _get_affine_from_lta_info(lines):	CODE
LOW	mne/bem.py	291	def _fwd_bem_ip_modify_solution(solution, ip_solution, ip_mult, n_tri):	CODE
LOW	mne/bem.py	329	def _fwd_bem_linear_collocation_solution(bem):	CODE
LOW	mne/bem.py	381	def _fwd_bem_openmeeg_solution(bem):	CODE
LOW	mne/bem.py	717	def _fwd_eeg_get_multi_sphere_model_coeffs(m, n_terms):	CODE
LOW	mne/bem.py	757	def _compose_linear_fitting_data(mu, u):	CODE
LOW	mne/bem.py	771	def _compute_linear_parameters(mu, u):	CODE
LOW	mne/bem.py	1876	def _write_bem_surfaces_block(fid, surfs):	CODE
LOW	mne/cov.py	886	def _unpack_covariance_inputs(inst):	CODE
LOW	mne/evoked.py	1669	def _check_evokeds_ch_names_times(all_evoked, inplace=False):	CODE
LOW	mne/chpi.py	518	def _magnetic_dipole_objective(	CODE
LOW	mne/chpi.py	533	def _magnetic_dipole_delta_multi(whitened_fwd_svd, B, B2):	CODE
LOW	mne/chpi.py	594	def _fit_coil_order_dev_head_trans(	CODE
LOW	mne/chpi.py	658	def _setup_hpi_amplitude_fitting(	CODE
LOW	mne/cuda.py	189	def _setup_cuda_fft_multiply_repeated(n_jobs, h, n_fft, kind="FFT FIR filtering"):	CODE
LOW	mne/label.py	1907	def _grow_nonoverlapping_labels(	CODE
LOW	mne/parallel.py	157	def _running_in_joblib_context():	CODE
LOW	mne/annotations.py	1169	def _hed_extras_from_hed_annotations(annot):	CODE
LOW	mne/annotations.py	1642	def get_annotations_per_epoch(self, *, with_extras=False):	CODE
LOW	mne/annotations.py	1728	def add_annotations_to_metadata(self, overwrite=False, *, with_extras=True):	CODE
LOW	mne/annotations.py	1882	def _annotations_starts_stops(raw, kinds, name="skip_by_annotation", invert=False):	CODE
LOW	mne/annotations.py	2182	def _read_brainstorm_annotations(fname, orig_time=None):	STRING
LOW	mne/annotations.py	2229	def _read_annotations_txt_parse_header(fname):	STRING
LOW	mne/annotations.py	2378	def _select_annotations_based_on_description(descriptions, event_id, regexp):	CODE
LOW	mne/annotations.py	2413	def _select_events_based_on_id(events, event_desc):	CODE
LOW	mne/rank.py	158	def _estimate_rank_meeg_signals(	CODE
942 more matches not shown…

Over-Commented Block831 hits · 793 pts

Severity	File	Line	Snippet	Context
LOW	mne/transforms.py	961		COMMENT
LOW	mne/transforms.py	981	#	COMMENT
LOW	mne/transforms.py	1441	assert quats.ndim == 2 and quats.shape[1] in (3, 4)	COMMENT
LOW	mne/_transforms_numba.py	81		COMMENT
LOW	mne/coreg.py	1181	mri_transforms_dirname.format(subjects_dir=subjects_dir, subject=subject_to),	COMMENT
LOW	mne/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/morph.py	801	)	COMMENT
LOW	mne/_surface_numba.py	101	run_all=True,	COMMENT
LOW	mne/label.py	3041	vertices belonging to label ``li``.	COMMENT
LOW	mne/dipole.py	1201	def _fit_confidence(*, rd, Q, ori, whitener, fwd_data, sensors):	COMMENT
LOW	mne/dipole.py	1361	# Tested minimizers:	COMMENT
LOW	mne/dipole.py	1681	if "eeg" in ch_types:	COMMENT
LOW	mne/time_frequency/spectrum.py	941	data = _psd_from_mt(data, self.weights)	COMMENT
LOW	mne/time_frequency/psd.py	21	#	COMMENT
LOW	mne/time_frequency/multitaper.py	141	# the variance of the timeseries	COMMENT
LOW	mne/time_frequency/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/beamformer/_compute_beamformer.py	381	#	COMMENT
LOW	mne/beamformer/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/datasets/config.py	101	MNE_DATASETS = dict()	COMMENT
LOW	mne/datasets/_infant/base.py	61	# Code used to create the lists:	COMMENT
LOW	mne/datasets/_phantom/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/datasets/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/datasets/_fsaverage/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/ant/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/nirx/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/curry/curry.py	821	if isinstance(events, np.ndarray): # if there are events	COMMENT
LOW	mne/io/curry/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/egi/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/edf/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/boxy/boxy.py	241		COMMENT
LOW	mne/io/boxy/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/bci2k/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/bci2k/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/nicolet/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/artemis123/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/array/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/snirf/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/persyst/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/eximia/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/ctf/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/nedf/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/tests/data/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/mef/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/eeglab/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/eyelink/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/bti/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/cnt/_utils.py	61	# unsigned char KeyBoard; /* range 0-11 corresponding to fcn keys +1 */	COMMENT
LOW	mne/io/cnt/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/fieldtrip/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/fiff/raw.py	121	"properly and that split and original files were not "	COMMENT
LOW	mne/io/fiff/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/brainvision/brainvision.py	921	# for newer BV files, the unit is specified for every channel separated by a	COMMENT
LOW	mne/io/brainvision/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/io/neuralynx/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/tests/test_morph.py	601	)	COMMENT
LOW	mne/simulation/metrics/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/simulation/tests/__init__.py	1	# Authors: The MNE-Python contributors.	COMMENT
LOW	mne/utils/check.py	141	#	COMMENT
LOW	mne/decoding/time_delaying_ridge.py	81	# it's faster to create the Toeplitz ourselves than use	COMMENT
771 more matches not shown…

Deep Nesting461 hits · 440 pts

Severity	File	Line	Context
LOW	mne/source_estimate.py	236	CODE
LOW	mne/source_estimate.py	392	CODE
LOW	mne/source_estimate.py	3494	CODE
LOW	mne/source_estimate.py	3723	CODE
LOW	mne/transforms.py	578	CODE
LOW	mne/transforms.py	1591	CODE
LOW	mne/transforms.py	1710	CODE
LOW	mne/transforms.py	2211	CODE
LOW	mne/misc.py	6	CODE
LOW	mne/event.py	36	CODE
LOW	mne/event.py	85	CODE
LOW	mne/event.py	1275	CODE
LOW	mne/fixes.py	656	CODE
LOW	mne/fixes.py	774	CODE
LOW	mne/baseline.py	35	CODE
LOW	mne/baseline.py	149	CODE
LOW	mne/epochs.py	266	CODE
LOW	mne/epochs.py	335	CODE
LOW	mne/epochs.py	3116	CODE
LOW	mne/epochs.py	4095	CODE
LOW	mne/epochs.py	4160	CODE
LOW	mne/epochs.py	4245	CODE
LOW	mne/epochs.py	4727	CODE
LOW	mne/epochs.py	852	CODE
LOW	mne/epochs.py	1720	CODE
LOW	mne/epochs.py	2075	CODE
LOW	mne/epochs.py	2518	CODE
LOW	mne/coreg.py	824	CODE
LOW	mne/coreg.py	1041	CODE
LOW	mne/coreg.py	1341	CODE
LOW	mne/morph_map.py	112	CODE
LOW	mne/morph.py	961	CODE
LOW	mne/morph.py	1263	CODE
LOW	mne/morph.py	605	CODE
LOW	mne/bem.py	215	CODE
LOW	mne/bem.py	1179	CODE
LOW	mne/bem.py	2393	CODE
LOW	mne/cov.py	902	CODE
LOW	mne/cov.py	1311	CODE
LOW	mne/cov.py	1984	CODE
LOW	mne/cov.py	2452	CODE
LOW	mne/evoked.py	1669	CODE
LOW	mne/evoked.py	1886	CODE
LOW	mne/evoked.py	289	CODE
LOW	mne/evoked.py	1083	CODE
LOW	mne/_surface_numba.py	88	CODE
LOW	mne/chpi.py	419	CODE
LOW	mne/chpi.py	905	CODE
LOW	mne/chpi.py	1229	CODE
LOW	mne/proj.py	380	CODE
LOW	mne/label.py	1273	CODE
LOW	mne/label.py	1551	CODE
LOW	mne/label.py	2018	CODE
LOW	mne/label.py	2675	CODE
LOW	mne/filter.py	42	CODE
LOW	mne/filter.py	671	CODE
LOW	mne/filter.py	1067	CODE
LOW	mne/filter.py	1450	CODE
LOW	mne/filter.py	2169	CODE
LOW	mne/dipole.py	692	CODE
401 more matches not shown…

AI Structural Patterns333 hits · 300 pts

Severity	File	Line	Context
LOW	mne/source_estimate.py	152	CODE
LOW	mne/source_estimate.py	3895	CODE
LOW	mne/source_estimate.py	749	CODE
LOW	mne/source_estimate.py	2297	CODE
LOW	mne/source_estimate.py	2373	CODE
LOW	mne/source_estimate.py	2442	CODE
LOW	mne/source_estimate.py	2818	CODE
LOW	mne/transforms.py	798	CODE
LOW	mne/transforms.py	2070	CODE
LOW	mne/event.py	478	CODE
LOW	mne/event.py	592	CODE
LOW	mne/fixes.py	342	CODE
LOW	mne/epochs.py	4966	CODE
LOW	mne/epochs.py	463	CODE
LOW	mne/epochs.py	1364	CODE
LOW	mne/epochs.py	1428	CODE
LOW	mne/epochs.py	1571	CODE
LOW	mne/epochs.py	1720	CODE
LOW	mne/epochs.py	1996	CODE
LOW	mne/epochs.py	2682	CODE
LOW	mne/epochs.py	2747	CODE
LOW	mne/epochs.py	2882	CODE
LOW	mne/epochs.py	3707	CODE
LOW	mne/epochs.py	3845	CODE
LOW	mne/epochs.py	3906	CODE
LOW	mne/coreg.py	328	CODE
LOW	mne/coreg.py	609	CODE
LOW	mne/coreg.py	824	CODE
LOW	mne/coreg.py	1964	CODE
LOW	mne/morph.py	44	CODE
LOW	mne/bem.py	130	CODE
LOW	mne/bem.py	1179	CODE
LOW	mne/bem.py	2393	CODE
LOW	mne/cov.py	587	CODE
LOW	mne/cov.py	902	CODE
LOW	mne/cov.py	1503	CODE
LOW	mne/cov.py	1886	CODE
LOW	mne/cov.py	1984	CODE
LOW	mne/cov.py	2215	CODE
LOW	mne/cov.py	2281	CODE
LOW	mne/cov.py	330	CODE
LOW	mne/cov.py	1590	CODE
LOW	mne/cov.py	1750	CODE
LOW	mne/evoked.py	529	CODE
LOW	mne/evoked.py	584	CODE
LOW	mne/evoked.py	636	CODE
LOW	mne/evoked.py	682	CODE
LOW	mne/evoked.py	753	CODE
LOW	mne/evoked.py	841	CODE
LOW	mne/evoked.py	1083	CODE
LOW	mne/evoked.py	1234	CODE
LOW	mne/evoked.py	1300	CODE
LOW	mne/evoked.py	1362	CODE
LOW	mne/chpi.py	1716	CODE
LOW	mne/proj.py	238	CODE
LOW	mne/proj.py	284	CODE
LOW	mne/label.py	2269	CODE
LOW	mne/label.py	2675	CODE
LOW	mne/label.py	2935	CODE
LOW	mne/label.py	233	CODE
273 more matches not shown…

Self-Referential Comments88 hits · 274 pts

Severity	File	Line	Snippet	Context
MEDIUM	.extended_metadata.yaml	1	# This file contains additional metadata about MNE-Python, beyond what is contained in `pyproject.toml`.	COMMENT
MEDIUM	mne/cov.py	1909	# Create the projection operator	COMMENT
MEDIUM	mne/evoked.py	2142	# Create the file and save the essentials	COMMENT
MEDIUM	mne/annotations.py	1807	# Create a new Annotations column that is instantiated as an empty	COMMENT
MEDIUM	mne/beamformer/tests/test_dics.py	77	# Create an info object that holds information about the sensors	COMMENT
MEDIUM	mne/beamformer/tests/test_dics.py	95	# Define a single epoch (weird baseline but shouldn't matter)	COMMENT
MEDIUM	mne/beamformer/tests/test_dics.py	730	# Create a DICS beamformer and convert the EpochsTFR to source space.	COMMENT
MEDIUM	mne/datasets/utils.py	331	# This function is designed primarily to be used by CircleCI, to:	COMMENT
MEDIUM	mne/io/base.py	3226	# Create the file and save the essentials	COMMENT
MEDIUM	mne/io/snirf/tests/test_snirf.py	652	# Create a clean copy and ensure it loads without error	COMMENT
MEDIUM	mne/io/ctf/info.py	197	# Create the channel position information	COMMENT
MEDIUM⚡	mne/io/ctf/tests/test_ctf.py	81	# Create a dummy .eeg file so we can test our reading/application of it	COMMENT
MEDIUM⚡	mne/io/ctf/tests/test_ctf.py	90	# Create a bad file	COMMENT
MEDIUM⚡	mne/io/ctf/tests/test_ctf.py	94	# Create a good file	COMMENT
MEDIUM	mne/io/ctf/tests/test_ctf.py	115	# Create a version with no hc, starting out with EEG pos (error)	COMMENT
MEDIUM	mne/io/kit/kit.py	227	# Create a synthetic stim channel	COMMENT
MEDIUM	mne/tests/test_source_estimate.py	2066	# Create a sample _BaseSourceEstimate object	COMMENT
MEDIUM	mne/utils/_bunch.py	11	# Create a Bunch class that acts like a struct (mybunch.key = val)	COMMENT
MEDIUM	mne/utils/tests/test_config.py	302	# Create a unique key/value pair.	COMMENT
MEDIUM	mne/decoding/receptive_field.py	233	# Define the slice that we should use in the middle	COMMENT
MEDIUM	mne/decoding/receptive_field.py	553	# Create a correlation scikit-learn-style scorer	COMMENT
MEDIUM	mne/decoding/tests/test_base.py	129	# Define a classifier, an invertible transformer and an non-invertible one.	COMMENT
MEDIUM	mne/viz/topomap.py	789	# Define the outline of the head, ears and nose	COMMENT
MEDIUM	mne/viz/evoked.py	2153	# The following functions are all helpers for plot_compare_evokeds. #	COMMENT
MEDIUM	mne/viz/ui_events.py	291	# Create the event channel if it doesn't exist yet	COMMENT
MEDIUM	mne/viz/topo.py	243	# Create a PolyCollection for the axis backgrounds	COMMENT
MEDIUM	mne/_fiff/proj.py	1290	# Create the projector	COMMENT
MEDIUM	mne/_fiff/compensator.py	40	# Create the preselector	COMMENT
MEDIUM	mne/_fiff/compensator.py	50	# Create the postselector (zero entries for channels not found)	COMMENT
MEDIUM	mne/_fiff/reference.py	438	# Creating an average reference may fail. In this case, make	COMMENT
MEDIUM	mne/gui/_dipolefit.py	971	# Create a coordinate system where X and Y are tangential to the helmet	COMMENT
MEDIUM	mne/report/report.py	3497	# Create the figure once and reuse it for performance reasons	COMMENT
MEDIUM	mne/preprocessing/_regress.py	92	# Create an EOGRegression object and load the given betas into it.	COMMENT
MEDIUM	mne/preprocessing/xdawn.py	477	# Define the components to keep	COMMENT
MEDIUM	mne/preprocessing/eyetracking/_pupillometry.py	98	# Create an empty boolean mask	COMMENT
MEDIUM	…e/preprocessing/eyetracking/tests/test_pupillometry.py	34	# Create a dummy stim channel	COMMENT
MEDIUM	mne/preprocessing/nirs/_tddr.py	67	# This function is the reference implementation for the TDDR algorithm for	COMMENT
MEDIUM	mne/source_space/_source_space.py	2114	# Define the sphere which fits the surface	COMMENT
MEDIUM	mne/source_space/_source_space.py	2902	# Create a list of Label	COMMENT
MEDIUM	mne/source_space/tests/test_source_space.py	1047	# The following code was used to generate small-src.fif.gz.	COMMENT
MEDIUM	mne/minimum_norm/inverse.py	435	# Create the file and save the essentials	COMMENT
MEDIUM⚡	mne/minimum_norm/inverse.py	678	# Create the diagonal matrix for computing the regularized inverse	COMMENT
MEDIUM⚡	mne/minimum_norm/inverse.py	683	# Create the projection operator	COMMENT
MEDIUM⚡	mne/minimum_norm/inverse.py	692	# Create the whitener	COMMENT
MEDIUM	mne/stats/parametric.py	12	# The following function is a rewriting of scipy.stats.f_oneway	COMMENT
MEDIUM	mne/stats/cluster_level.py	768	# Create the leftmost column as 0,0,...,1,1,...	COMMENT
MEDIUM	mne/forward/_compute_forward.py	359	# The following code is equivalent to this, but saves memory	COMMENT
MEDIUM	mne/forward/_make_forward.py	181	# Create the result	COMMENT
MEDIUM	mne/forward/tests/test_make_forward.py	779	# Create a new Dipole object with the dipole fits	COMMENT
MEDIUM	mne/channels/interpolation.py	549	# Create a new instance for the interpolated EEG channels	COMMENT
MEDIUM	mne/channels/montage.py	1852	# Create a mapping from column name to index	STRING
MEDIUM	mne/channels/tests/test_interpolation.py	518	# Create a target montage	COMMENT
MEDIUM	mne/channels/tests/test_layout.py	335	# Create a grid of points. Box size should be (0.1, 0.1).	COMMENT
MEDIUM	mne/channels/tests/test_layout.py	340	# Create a random set of points. This should never break the function.	COMMENT
MEDIUM	examples/visualization/evoked_topomap.py	132	# Define a threshold and create the mask	COMMENT
MEDIUM	examples/visualization/brain.py	127	# Create a screenshot for exporting the brain image	COMMENT
MEDIUM	examples/datasets/hf_sef_data.py	31	# Create a highpass filtered version	COMMENT
MEDIUM	examples/datasets/limo_data.py	166	# Create a dictionary containing the evoked responses	COMMENT
MEDIUM⚡	examples/simulation/plot_stc_metrics.py	62	# Define main parameters of sources	COMMENT
MEDIUM	examples/simulation/plot_stc_metrics.py	95	# Define the time course of the activity	COMMENT
28 more matches not shown…

Unused Imports222 hits · 220 pts

Severity	File	Line	Context
LOW	mne/conftest.py	1230	CODE
LOW	mne/conftest.py	1232	CODE
LOW	mne/conftest.py	1233	CODE
LOW	mne/conftest.py	1234	CODE
LOW	mne/epochs.py	118	CODE
LOW	mne/epochs.py	119	CODE
LOW	mne/epochs.py	120	CODE
LOW	mne/epochs.py	123	CODE
LOW	mne/epochs.py	124	CODE
LOW	mne/epochs.py	127	CODE
LOW	mne/epochs.py	131	CODE
LOW	mne/coreg.py	26	CODE
LOW	mne/coreg.py	47	CODE
LOW	mne/coreg.py	47	CODE
LOW	mne/coreg.py	47	CODE
LOW	mne/coreg.py	47	CODE
LOW	mne/evoked.py	75	CODE
LOW	mne/evoked.py	76	CODE
LOW	mne/evoked.py	77	CODE
LOW	mne/evoked.py	77	CODE
LOW	mne/evoked.py	78	CODE
LOW	mne/evoked.py	79	CODE
LOW	mne/evoked.py	81	CODE
LOW	mne/evoked.py	82	CODE
LOW	mne/evoked.py	84	CODE
LOW	mne/evoked.py	84	CODE
LOW	mne/evoked.py	84	CODE
LOW	mne/datasets/limo/__init__.py	7	CODE
LOW	mne/datasets/limo/__init__.py	7	CODE
LOW	mne/datasets/_infant/__init__.py	5	CODE
LOW	mne/datasets/misc/__init__.py	7	CODE
LOW	mne/datasets/misc/__init__.py	7	CODE
LOW	mne/datasets/eegbci/__init__.py	7	CODE
LOW	mne/datasets/eegbci/__init__.py	7	CODE
LOW	mne/datasets/eegbci/__init__.py	7	CODE
LOW	mne/datasets/opm/__init__.py	7	CODE
LOW	mne/datasets/opm/__init__.py	7	CODE
LOW	mne/datasets/sleep_physionet/__init__.py	5	CODE
LOW	mne/datasets/sleep_physionet/__init__.py	5	CODE
LOW	mne/datasets/sleep_physionet/__init__.py	5	CODE
LOW	mne/datasets/refmeg_noise/__init__.py	7	CODE
LOW	mne/datasets/refmeg_noise/__init__.py	7	CODE
LOW	mne/datasets/brainstorm/__init__.py	7	CODE
LOW	mne/datasets/brainstorm/__init__.py	7	CODE
LOW	mne/datasets/brainstorm/__init__.py	7	CODE
LOW	mne/datasets/brainstorm/__init__.py	7	CODE
LOW	mne/datasets/brainstorm/__init__.py	7	CODE
LOW	mne/datasets/phantom_kernel/__init__.py	7	CODE
LOW	mne/datasets/phantom_kernel/__init__.py	7	CODE
LOW	mne/datasets/ucl_opm_auditory/__init__.py	7	CODE
LOW	mne/datasets/ucl_opm_auditory/__init__.py	7	CODE
LOW	mne/datasets/spm_face/__init__.py	7	CODE
LOW	mne/datasets/spm_face/__init__.py	7	CODE
LOW	mne/datasets/spm_face/__init__.py	7	CODE
LOW	mne/datasets/spm_face/__init__.py	7	CODE
LOW	mne/datasets/phantom_kit/__init__.py	7	CODE
LOW	mne/datasets/phantom_kit/__init__.py	7	CODE
LOW	mne/datasets/ssvep/__init__.py	7	CODE
LOW	mne/datasets/ssvep/__init__.py	7	CODE
LOW	mne/datasets/lite_data/__init__.py	7	CODE
162 more matches not shown…

Hallucination Indicators14 hits · 165 pts

Severity	File	Line	Snippet	Context
CRITICAL	mne/viz/_mpl_figure.py	212	self.mne.parent_fig.mne.child_figs.remove(self)	CODE
CRITICAL	mne/viz/_mpl_figure.py	360	self.mne.parent_fig.mne.child_figs.remove(self)	CODE
CRITICAL	mne/viz/_mpl_figure.py	1443	self.mne.fig_annotation.mne.radio_ax.set_title(	CODE
CRITICAL⚡	mne/viz/utils.py	1492	self.cidpress = self.cbar.ax.figure.canvas.mpl_connect(	CODE
CRITICAL⚡	mne/viz/utils.py	1495	self.cidrelease = self.cbar.ax.figure.canvas.mpl_connect(	CODE
CRITICAL⚡	mne/viz/utils.py	1498	self.cidmotion = self.cbar.ax.figure.canvas.mpl_connect(	CODE
CRITICAL⚡	mne/viz/utils.py	1501	self.keypress = self.cbar.ax.figure.canvas.mpl_connect(	CODE
CRITICAL⚡	mne/viz/utils.py	1504	self.scroll = self.cbar.ax.figure.canvas.mpl_connect(	CODE
CRITICAL	mne/viz/utils.py	1611	self.cbar.ax.figure.canvas.draw()	CODE
CRITICAL	mne/viz/_figure.py	217	durations = self.mne.inst.annotations.duration.copy()	CODE
CRITICAL	mne/viz/_brain/tests/test_brain.py	941	fp = np.array(brain._renderer.figure.plotter.renderer.ComputeVisiblePropBounds())	CODE
CRITICAL	mne/report/js_and_css/jquery-3.6.0.min.js	2	!function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):f	CODE
CRITICAL	…d_css/bootstrap-table/bootstrap-table-copy-rows.min.js	10	!function(t,e){"object"==typeof exports&&"undefined"!=typeof module?e(require("jquery")):"function"==typeof define&&defi	CODE
CRITICAL	…_and_css/bootstrap-table/bootstrap-table-export.min.js	10	!function(t,e){"object"==typeof exports&&"undefined"!=typeof module?e(require("jquery")):"function"==typeof define&&defi	CODE

AI Slop Vocabulary73 hits · 163 pts

Severity	File	Line	Snippet	Context
MEDIUM	mne/transforms.py	1453	# But this is not robust to quaternions having sign ambiguity,	COMMENT
MEDIUM	mne/fixes.py	442	# sklearn uses np.linalg for this, but ours is more robust to zero eigenvalues	COMMENT
LOW	mne/epochs.py	2632	# 2b. for non-tag ids, just pass them directly	COMMENT
LOW	mne/rank.py	321	# one, so we cannot just use proc_history[0].	COMMENT
MEDIUM	mne/time_frequency/tfr.py	1287	del self._shape # calculated from self._data henceforth	CODE
MEDIUM	mne/time_frequency/spectrum.py	1224	del self._shape # calculated from self._data henceforth	CODE
LOW	mne/beamformer/tests/test_lcmv.py	172	# just use grads	COMMENT
LOW	mne/io/curry/curry.py	141	# of the acquisition system (which is unknown); therefore, just set	COMMENT
MEDIUM	mne/io/persyst/persyst.py	454	# TODO: utilize state and var_type in code.	COMMENT
LOW	mne/io/tests/test_raw.py	1101	# tmin and tmax just use time_as_index under the hood	COMMENT
LOW	mne/io/fiff/raw.py	433	continue # just use zeros for gaps	CODE
MEDIUM	mne/tests/test_chpi.py	652	"""Wrap to facilitate change diff."""	STRING
MEDIUM	mne/tests/test_rank.py	135	# Now do some more comprehensive tests	COMMENT
MEDIUM	mne/utils/misc.py	354	# but this might be more robust to file-like objects not properly	COMMENT
MEDIUM	mne/utils/config.py	516	# This is a more robust way of getting the user's home folder on	COMMENT
LOW	mne/utils/numerics.py	873	# Adapted from sklearn and stripped down to just use linalg.svd	COMMENT
MEDIUM	mne/decoding/receptive_field.py	527	"""Find the slice to be taken in order to remove missing values."""	STRING
LOW	mne/viz/topomap.py	1030	# rare so for now just use the average value of all extras	COMMENT
LOW	mne/viz/evoked.py	1959	# simply create a new evoked object with the desired channel selection	COMMENT
LOW	mne/viz/_3d.py	755	trans = Transform("head", "mri") # not used so just use identity	CODE
LOW	mne/_fiff/meas_info.py	672	# whatever mapping was provided, now we can just use a dict	COMMENT
LOW	mne/_fiff/meas_info.py	949	# set does not preserve order but dict does, so let's just use it	COMMENT
MEDIUM	mne/_fiff/tests/test_meas_info.py	485	# Use assert_object_equal for comprehensive check	COMMENT
LOW	mne/preprocessing/ecg.py	512	# Raw has start param, can just use int	COMMENT
LOW	mne/preprocessing/ecg.py	520	# Raw has stop param, can just use int	COMMENT
LOW	mne/preprocessing/ica.py	3258	# Here we just use the median rather than the (transformed-back) mean of	COMMENT
MEDIUM	mne/preprocessing/eyetracking/tests/test_calibration.py	262	# Calibration reading should be robust to what we are about to do to this file	COMMENT
MEDIUM	mne/preprocessing/nirs/_tddr.py	117	# Step 3. Iterative estimation of robust weights	COMMENT
MEDIUM	mne/preprocessing/nirs/_tddr.py	143	# Step 4. Apply robust weights to centered derivative	COMMENT
LOW	mne/minimum_norm/spatial_resolution.py	148	# can be quite expensive in memory. So let's just use abs() in place below.	COMMENT
LOW	mne/minimum_norm/_eloreta.py	156	# to work. So let's just set to nan for now.	COMMENT
LOW	mne/stats/cluster_level.py	805	# Here we can just use the hash-table (w/collision detection)	COMMENT
MEDIUM	mne/forward/_lead_dots.py	235	# Accumulate the result, a little bit streamlined version	COMMENT
LOW	mne/channels/channels.py	86	# Our helmet does not match very well, so let's just create it	COMMENT
LOW	mne/channels/tests/test_layout.py	365	# Test specifying both width and height. The function should simply return	COMMENT
MEDIUM	examples/visualization/3d_to_2d.py	70	# with the electrode positions on that image. We use this in conjunction with	COMMENT
LOW	examples/time_frequency/source_power_spectrum_opm.py	99	# For speed, let's just use a 1-layer BEM	COMMENT
MEDIUM	examples/datasets/limo_data.py	162	# Since this is a "visual paradigm" it might be best to look at electrodes	COMMENT
LOW	examples/preprocessing/muscle_detection.py	47	raw.crop(130, 160).load_data() # just use a fraction of data for speed here	CODE
LOW	tutorials/inverse/30_mne_dspm_loreta.py	67	# Let's just use the MEG channels for simplicity.	COMMENT
MEDIUM	tutorials/intro/15_inplace.py	76	# Above we saw an example of using the `~mne.io.Raw.copy` method to facilitate	COMMENT
MEDIUM	tutorials/time-freq/20_sensors_time_frequency.py	119	# bias relative to the mean), which is a more robust measure.	COMMENT
MEDIUM	tutorials/time-freq/20_sensors_time_frequency.py	304	# units of baseline standard deviations. This can facilitate comparison across	COMMENT
LOW	…/stats-source-space/30_cluster_ftest_spatiotemporal.py	78	# just pass the spatial adjacency matrix (instead of spatio-temporal)	COMMENT
LOW	…tats-source-space/60_cluster_rmANOVA_spatiotemporal.py	225	# just pass the spatial adjacency matrix (instead of spatio-temporal).	COMMENT
LOW	…/stats-source-space/20_cluster_1samp_spatiotemporal.py	176	# just pass the spatial adjacency matrix (instead of spatio-temporal).	COMMENT
LOW	tutorials/epochs/50_epochs_to_data_frame.py	82	# :class:`~pandas.DataFrame` is simple: just call :meth:`epochs.to_data_frame()	COMMENT
LOW	tutorials/epochs/60_make_fixed_length_epochs.py	49	# To create fixed length epochs, we simply call the function and provide it	COMMENT
MEDIUM	tutorials/epochs/40_autogenerate_metadata.py	204	# present paradigm stimuli were presented in rapid succession, sometimes	COMMENT
MEDIUM	tutorials/epochs/40_autogenerate_metadata.py	366	# this paradigm; taking the last response (time point zero) and the last	COMMENT
MEDIUM	tutorials/epochs/40_autogenerate_metadata.py	468	# the ERN nicely in the given paradigm.	COMMENT
MEDIUM	tutorials/preprocessing/30_filtering_resampling.py	284	# The following section suggests best practices to mitigate both of these	COMMENT
MEDIUM	tutorials/preprocessing/30_filtering_resampling.py	345	# If for some reason you cannot follow the above-recommended best practices,	COMMENT
MEDIUM	tutorials/preprocessing/15_handling_bad_channels.py	174	# rejection thresholds, which in turn can lead to less robust estimation of the	COMMENT
MEDIUM	tutorials/preprocessing/20_rejecting_bad_data.py	50	# best practices for annotating bad data spans so that they will be excluded	COMMENT
LOW	tutorials/preprocessing/20_rejecting_bad_data.py	190	# of events: simply pass the array via the ``events`` parameter. Existing	COMMENT
LOW	tutorials/preprocessing/10_preprocessing_overview.py	32	raw.crop(0, 60).load_data() # just use a fraction of data for speed here	CODE
MEDIUM	tutorials/preprocessing/10_preprocessing_overview.py	71	# in the sensory response to a stimulus, but the experimental paradigm involves	COMMENT
MEDIUM	tutorials/preprocessing/40_artifact_correction_ica.py	101	# converge faster than FastICA and Infomax, and is more robust than other	COMMENT
MEDIUM	tutorials/preprocessing/25_background_filtering.py	796	# Similarly, in a P300 paradigm reported by	COMMENT
13 more matches not shown…

Excessive Try-Catch Wrapping134 hits · 142 pts

Severity	File	Line	Snippet	Context
LOW	mne/conftest.py	133	except Exception:	CODE
LOW	mne/conftest.py	243	except Exception:	STRING
LOW	mne/conftest.py	683	except Exception:	CODE
LOW	mne/conftest.py	1237	except Exception as exc:	CODE
LOW	mne/conftest.py	1274	except Exception:	CODE
MEDIUM	mne/conftest.py	1228	def _nbclient():	CODE
LOW	mne/fixes.py	699	except Exception:	CODE
LOW	mne/fixes.py	704	except Exception:	CODE
LOW	mne/fixes.py	788	except Exception:	CODE
LOW	mne/_numba.py	28	except Exception: # could be ImportError, SystemError, etc.	CODE
LOW	mne/coreg.py	1259	except Exception:	CODE
LOW	mne/morph_map.py	70	except Exception:	CODE
LOW	mne/morph_map.py	151	except Exception as exp:	CODE
LOW	mne/__init__.py	27	except Exception:	CODE
MEDIUM	mne/bem.py	355	def _import_openmeeg(what="compute a BEM solution using OpenMEEG"):	CODE
LOW	mne/bem.py	358	except Exception as exc:	CODE
LOW	mne/bem.py	1502	except Exception: # not our format	CODE
LOW	mne/cuda.py	80	except Exception:	CODE
LOW	mne/cuda.py	137	except Exception as exp:	CODE
LOW	mne/cuda.py	243	except Exception as exp:	CODE
LOW	mne/cuda.py	345	except Exception:	CODE
LOW	mne/filter.py	1812	except Exception:	CODE
LOW	mne/parallel.py	136	except Exception:	CODE
LOW	mne/time_frequency/tfr.py	2043	except Exception as e:	CODE
LOW	mne/io/_preload_cache.py	63	except Exception as exc:	CODE
LOW	mne/io/_read_raw.py	195	except Exception:	CODE
LOW	mne/io/base.py	843	except Exception:	CODE
LOW	mne/io/base.py	1483	except Exception:	CODE
LOW	mne/io/base.py	1574	except Exception:	CODE
LOW	mne/io/base.py	3452	except Exception:	CODE
LOW	mne/io/curry/curry.py	166	except Exception:	CODE
LOW	mne/io/egi/egimff.py	86	except Exception:	CODE
LOW	mne/io/egi/events.py	47	except Exception:	CODE
LOW	mne/io/egi/events.py	61	except Exception as exc:	CODE
LOW⚡	mne/io/edf/edf.py	1128	except Exception:	CODE
LOW⚡	mne/io/edf/edf.py	1138	except Exception:	CODE
LOW⚡	mne/io/edf/edf.py	1145	except Exception:	CODE
LOW	mne/io/edf/edf.py	270	except Exception:	CODE
LOW	mne/io/edf/edf.py	1400	except Exception:	CODE
LOW	mne/io/artemis123/artemis123.py	168	except Exception:	CODE
LOW	mne/io/mef/_utils.py	160	except Exception:	CODE
LOW	mne/io/eeglab/_eeglab.py	124	except Exception:	STRING
LOW	mne/io/cnt/cnt.py	548	except Exception:	CODE
LOW	mne/io/fiff/raw.py	571	except Exception:	CODE
LOW	mne/io/hitachi/hitachi.py	215	except Exception:	CODE
LOW	mne/io/hitachi/hitachi.py	221	except Exception:	CODE
LOW	mne/tests/test_cov.py	316	except Exception as exp:	CODE
LOW	mne/tests/test_docstring_parameters.py	296	except Exception: # e.g., mne.export not having pybv	CODE
LOW	mne/utils/misc.py	250	except Exception:	CODE
LOW	mne/utils/_logging.py	517	except Exception:	STRING
LOW	mne/utils/config.py	668	except Exception as exc:	CODE
LOW	mne/utils/config.py	695	except Exception:	CODE
LOW	mne/utils/config.py	735	except Exception: # pragma: no cover	CODE
LOW	mne/utils/config.py	824	except Exception: # in case someone overrides sys.stdout in an unsafe way	CODE
LOW	mne/utils/config.py	841	except Exception as exc:	CODE
LOW	mne/utils/config.py	848	except Exception as exc:	CODE
LOW	mne/utils/config.py	1004	except Exception:	CODE
LOW	mne/utils/check.py	309	except Exception:	CODE
LOW	mne/utils/check.py	1069	except Exception:	CODE
LOW	mne/utils/check.py	1082	except Exception:	CODE
74 more matches not shown…

Slop Phrases50 hits · 136 pts

Severity	File	Line	Snippet	Context
LOW	mne/label.py	2810	# make sure to add no duplicate color	STRING
LOW	mne/utils/tests/test_check.py	218	# make sure to inform the user that 7 channels were dropped	COMMENT
LOW	mne/viz/topo.py	1251	# make sure to only modify the time courses, not the ticks	COMMENT
MEDIUM	mne/preprocessing/tests/test_css.py	37	# include test for gh-12373, that you can use MAG+EEG if you want	COMMENT
LOW	mne/channels/channels.py	2154	# create new instances and make sure to copy important attributes	COMMENT
MEDIUM⚡	examples/visualization/brain.py	75	# To highlight a region on the brain you can use the ``add_label`` method.	COMMENT
MEDIUM	tutorials/inverse/21_interactive_dipole_fit.py	53	# sources. On the command line there are various options you can use to specify files	COMMENT
MEDIUM	tutorials/inverse/21_interactive_dipole_fit.py	146	# happy with the selection, you can use the "Fit dipole" button as before to fit a	COMMENT
MEDIUM	tutorials/intro/30_info.py	181	# channels in it, you can use the :func:`mne.pick_info` function to pick the	COMMENT
LOW	tutorials/intro/40_sensor_locations.py	52	# computed on a spherical head model, make sure to check out the `eeg_positions`_	COMMENT
MEDIUM	tutorials/intro/50_configure_mne.py	198	# the current Python session, you can use :func:`mne.set_log_level` instead.	COMMENT
MEDIUM	tutorials/intro/50_configure_mne.py	275	# Or you can use :func:`mne.sys_info` directly, which prints to ``stdout`` by	COMMENT
MEDIUM	tutorials/time-freq/20_sensors_time_frequency.py	180	# but you can also use :func:`mne.time_frequency.tfr_multitaper`	COMMENT
MEDIUM	tutorials/time-freq/10_spectrum_class.py	104	# similar to :class:`~mne.Epochs` objects: you can use string values to select	COMMENT
MEDIUM	tutorials/io/60_ctf_bst_auditory.py	223	# saccades) you can use keyword ``reject_by_annotation=False``.	COMMENT
MEDIUM	tutorials/simulation/10_array_objs.py	115	# To create a `~mne.io.Raw` object from scratch, you can use the	COMMENT
MEDIUM	tutorials/simulation/10_array_objs.py	137	# To create an `~mne.Epochs` object from scratch, you can use the	COMMENT
MEDIUM	tutorials/simulation/10_array_objs.py	197	# If you already have data that was averaged across trials, you can use it to	COMMENT
MEDIUM	…/stats-source-space/20_cluster_1samp_spatiotemporal.py	9	conditions across subjects. Here just for demonstration purposes we simulate data from	STRING
MEDIUM	tutorials/epochs/30_epochs_metadata.py	90	# Like any :class:`pandas.DataFrame`, you can modify the data or add columns as	COMMENT
MEDIUM	tutorials/epochs/10_epochs_overview.py	178	# constructor, you can add it later by assigning to the ``event_id``	COMMENT
MEDIUM	tutorials/epochs/10_epochs_overview.py	313	# To change the temporal extent of the :class:`~mne.Epochs`, you can use the	COMMENT
MEDIUM	tutorials/epochs/10_epochs_overview.py	386	# channel will appear in a separate column. Then you can use any of Pandas'	COMMENT
MEDIUM	tutorials/epochs/10_epochs_overview.py	454	# If you want to iterate over :class:`~mne.Epochs` objects, you can use an	COMMENT
MEDIUM	tutorials/preprocessing/60_maxwell_filtering_sss.py	347	# want to doublecheck, you can use :func:`mne.chpi.get_active_chpi` (currently	COMMENT
MEDIUM	tutorials/preprocessing/40_artifact_correction_ica.py	430	# you can use as a proxy for EOG. You can use a single channel, or create a	COMMENT
LOW	tutorials/preprocessing/40_artifact_correction_ica.py	45	# the artifacts in your data to make sure you choose the right repair tool.	COMMENT
MEDIUM	tutorials/preprocessing/45_projectors_background.py	315	# Python :class:`dict`, so you can use its ``.keys()`` method to see what	COMMENT
MEDIUM	tutorials/preprocessing/55_setting_eeg_reference.py	79	# earlobe or mastoid channels, so this is just for demonstration purposes:	COMMENT
MEDIUM	tutorials/preprocessing/55_setting_eeg_reference.py	97	# the signal at* ``Fp1``. In this situation, you can add back ``Fp1`` as a flat	COMMENT
MEDIUM	tutorials/preprocessing/55_setting_eeg_reference.py	132	# To set a "virtual reference" that is the average of all channels, you can use	COMMENT
MEDIUM	tutorials/preprocessing/55_setting_eeg_reference.py	220	# To create a bipolar reference, you can use :meth:`~mne.set_bipolar_reference`	COMMENT
MEDIUM⚡	tutorials/preprocessing/25_background_filtering.py	1056	# were used through the 'auto' setting, you can use	COMMENT
MEDIUM	tutorials/preprocessing/50_artifact_correction_ssp.py	251	# To compute SSP projectors for the heartbeat artifact, you can use	COMMENT
MEDIUM	tutorials/preprocessing/50_artifact_correction_ssp.py	268	# end of the list). If you don't want that, you can change that behavior with	COMMENT
LOW	tutorials/preprocessing/50_artifact_correction_ssp.py	40	# the artifacts in your data to make sure you choose the right repair tool.	COMMENT
MEDIUM	tutorials/raw/20_event_arrays.py	199	# you can change that with the ``id`` parameter. It is also possible to specify	COMMENT
MEDIUM	tutorials/raw/10_raw_overview.py	293	# inaccurate, you can change the type of any channel with the	COMMENT
MEDIUM	tutorials/raw/10_raw_overview.py	341	# or combine two or more separate :class:`~mne.io.Raw` objects — you can use	COMMENT
MEDIUM	tutorials/evoked/30_eeg_erp.py	108	# system, you can add sensor locations to the data with	COMMENT
MEDIUM	tutorials/evoked/30_eeg_erp.py	583	# measures. First, you can use an a priori time window based on prior	COMMENT
MEDIUM	tutorials/evoked/10_evoked_overview.py	128	# If you've already created the :class:`~mne.Evoked` object, you can use the	COMMENT
MEDIUM	tutorials/evoked/10_evoked_overview.py	281	# you can use :meth:`~mne.Epochs.equalize_event_counts` prior to averaging.	COMMENT
LOW	tutorials/forward/25_automated_coreg.py	103	# Don't forget to save the resulting ``trans`` matrix!	COMMENT
MEDIUM	tutorials/forward/80_fix_bem_in_blender.py	348	# :ref:`tut-fix-meshes-smoothing` does not work, you can try fixing the mesh	COMMENT
LOW	tutorials/forward/80_fix_bem_in_blender.py	257	# When editing BEM surfaces/meshes in Blender, make sure to use	COMMENT
MEDIUM	tutorials/forward/30_forward.py	151	# you can use the following code.	COMMENT
MEDIUM	tutorials/forward/30_forward.py	169	# dipoles inside the brain (requires the :term:`BEM` surfaces) you can use the	COMMENT
MEDIUM	tutorials/forward/30_forward.py	290	# To save to disk a forward solution you can use	COMMENT
MEDIUM	tutorials/forward/35_eeg_no_mri.py	98	# To use an infant head model for M/EEG data, you can use	COMMENT

AI Response Leakage9 hits · 79 pts

Severity	File	Line	Snippet	Context
HIGH	examples/visualization/brain.py	21	# In this example we use the ``sample`` data which is data from a subject	COMMENT
HIGH⚡	examples/simulation/plot_stc_metrics.py	58	# In this example we simulate two types of cortical sources: a region and	COMMENT
HIGH	…simulation/simulated_raw_data_using_subject_anatomy.py	30	# In this example, raw data will be simulated for the sample subject, so its	COMMENT
HIGH	…simulation/simulated_raw_data_using_subject_anatomy.py	128	# Generate source time courses for each region. In this example, we want to	COMMENT
HIGH	examples/preprocessing/eeg_bridging.py	398	# In this example, we have shown a dataset where electrical bridging occurred	COMMENT
HIGH	tutorials/clinical/20_seeg.py	230	# In this example, it is simply the source with the largest raw signal value.	COMMENT
HIGH⚡	tutorials/preprocessing/70_fnirs_processing.py	106	# In this example the data is clean and the coupling is good for all	COMMENT
HIGH⚡	tutorials/preprocessing/70_fnirs_processing.py	116	# In this example we will mark all channels with a SCI less than 0.5 as bad	COMMENT
HIGH	…rials/stats-sensor-space/40_cluster_1samp_time_freq.py	185	# In this example, we wish to set the threshold for including data bins in	COMMENT

Redundant / Tautological Comments41 hits · 62 pts

Severity	File	Line	Snippet	Context
LOW	mne/epochs.py	296	# Check if we already have an entry for merged keys of duplicate	COMMENT
LOW	mne/epochs.py	1672	# Check if indices and reasons are of the same length	COMMENT
LOW	mne/epochs.py	4191	# Check if criterion is a function and apply it	COMMENT
LOW	mne/bem.py	1482	# Open the file, create directory	COMMENT
LOW	mne/chpi.py	1802	# Set bads to empty list here. In theory flux jumps etc. or even flat channels	COMMENT
LOW	mne/time_frequency/tests/test_csd.py	363	# Check if the CSD matrices are hermitian	COMMENT
LOW	mne/io/nirx/nirx.py	149	# Check if required files exist and store names for later use	COMMENT
LOW	mne/io/eeglab/eeglab.py	468	# Check if data is embedded in the same .set file	STRING
LOW	mne/io/eeglab/eeglab.py	515	# Check if data is embedded in .set file	COMMENT
LOW	mne/io/eeglab/eeglab.py	518	# Check if we have already loaded and cached the embedded data	COMMENT
LOW	mne/tests/test_epochs.py	589	# Check if callable returns a tuple with reasons	COMMENT
LOW	mne/tests/test_morph.py	519	# Check if not morphed, but voxel size not boolean, raise ValueError.	COMMENT
LOW	mne/utils/tests/test_config.py	77	# Check if get_config with key=None returns all config	COMMENT
LOW	mne/decoding/tests/test_ssd.py	316	# Check if the 5 first 5 components are the same for both	COMMENT
LOW⚡	mne/viz/tests/test_raw.py	928	# Check if single annotation toggle works	COMMENT
LOW⚡	mne/viz/tests/test_raw.py	933	# Check if annotation filtering works - All annotations	COMMENT
LOW⚡	mne/viz/tests/test_raw.py	942	# Check if annotation filtering works - filtering annotations	COMMENT
LOW	mne/viz/tests/test_ica.py	504	# Check if annotation filtering works - All annotations	COMMENT
LOW	mne/viz/tests/test_ica.py	512	# Check if annotation filtering works - filtering annotations	COMMENT
LOW	mne/viz/_brain/_brain.py	1605	# Check if limits have changed at all.	COMMENT
LOW	mne/_fiff/meas_info.py	2238	# Check if all elements are numbers - convert to numpy array	COMMENT
LOW	mne/_fiff/meas_info.py	2252	# Check if this is a tagged MNE type	COMMENT
LOW	mne/preprocessing/_peak_finder.py	150	# Check if we still need to add the last point	COMMENT
LOW	mne/preprocessing/_lof.py	80	# Check if there are different channel types	COMMENT
LOW	mne/preprocessing/eyetracking/tests/test_calibration.py	107	# Check if the copied object is an instance of Calibration	COMMENT
LOW	mne/preprocessing/eyetracking/tests/test_calibration.py	109	# Check if the an attribute of the copied object is equal to the original object	COMMENT
LOW	mne/minimum_norm/spatial_resolution.py	79	# Check if input options are valid	COMMENT
LOW	mne/minimum_norm/inverse.py	207	# Open the file, create directory	COMMENT
LOW	mne/minimum_norm/inverse.py	431	# Open the file, create directory	COMMENT
LOW	mne/forward/forward.py	462	# Check if a custom reference has been applied	COMMENT
LOW	mne/forward/forward.py	571	# Open the file, create directory	COMMENT
LOW	mne/channels/montage.py	1917	# Set device to head transform to identity (canonical positions)	STRING
LOW	mne/channels/channels.py	2116	# Check if channel indices are out of bounds	COMMENT
LOW	mne/channels/channels.py	2119	# Check if heterogeneous sensor type combinations	COMMENT
LOW	mne/channels/channels.py	2134	# Check if combining less than 2 channel	COMMENT
LOW	tutorials/inverse/35_dipole_orientations.py	254	# Set loose to 0.2, the default value	COMMENT
LOW	tutorials/evoked/30_eeg_erp.py	474	# Print output from the good time window that contains the peak	COMMENT
LOW	tutorials/evoked/30_eeg_erp.py	499	# Print output	COMMENT
LOW	tutorials/evoked/30_eeg_erp.py	541	# Print output	COMMENT
LOW	doc/sphinxext/directive_formatting.py	92	# Check if text resembling directives is present	COMMENT
LOW	doc/sphinxext/directive_formatting.py	140	# Check if previous line is part of another directive	COMMENT

Cross-File Repetition6 hits · 30 pts

Severity	File	Snippet	Context
HIGH	mne/epochs.py	%(plot_psd_doc)s. parameters ---------- %(fmin_fmax_psd)s %(tmin_tmax_psd)s %(picks_good_data_noref)s %(proj_psd)s %(rej	STRING
HIGH	mne/evoked.py	%(plot_psd_doc)s. parameters ---------- %(fmin_fmax_psd)s %(tmin_tmax_psd)s %(picks_good_data_noref)s %(proj_psd)s %(rej	STRING
HIGH	mne/time_frequency/spectrum.py	%(plot_psd_doc)s. parameters ---------- %(fmin_fmax_psd)s %(tmin_tmax_psd)s %(picks_good_data_noref)s %(proj_psd)s %(rej	STRING
HIGH	mne/io/tests/test_raw.py	tests resampling doesn't affect data if sfreq is identical.	STRING
HIGH	mne/tests/test_source_estimate.py	tests resampling doesn't affect data if sfreq is identical.	STRING
HIGH	mne/tests/test_evoked.py	tests resampling doesn't affect data if sfreq is identical.	STRING

Cross-Language Confusion4 hits · 24 pts

Severity	File	Line	Snippet	Context
HIGH	mne/conftest.py	1246	"execution_count": null,	STRING
HIGH	mne/annotations.py	2650	Annotations returned by this function will all have zero (null) duration.	STRING
HIGH	mne/stats/parametric.py	99	# If df is undefined, variances are zero (assumes n1 > 0 & n2 > 0).	COMMENT
HIGH⚡	tutorials/stats-sensor-space/10_background_stats.py	437	# the null, no further inference on the cluster (e.g., peak location) can be	COMMENT

Verbosity Indicators6 hits · 13 pts

Severity	File	Line	Snippet	Context
LOW⚡	mne/bem.py	2069	# Step 2 : Create the parameter maps	COMMENT
LOW⚡	mne/bem.py	2079	# Step 3 : Synthesize the flash 5 images	COMMENT
LOW	mne/bem.py	2183	# Step 4 : Register with MPRAGE	COMMENT
LOW⚡	mne/stats/cluster_level.py	886	# Step 1: Calculate t-stat for original data	COMMENT
LOW⚡	mne/stats/cluster_level.py	998	# Step 2: If we have some clusters, repeat process on permuted data	COMMENT
LOW⚡	mne/stats/cluster_level.py	1000	# Step 3: repeat permutations for step-down-in-jumps procedure	COMMENT

Structural Annotation Overuse6 hits · 13 pts

Severity	File	Line	Snippet	Context
LOW⚡	mne/bem.py	2069	# Step 2 : Create the parameter maps	COMMENT
LOW⚡	mne/bem.py	2079	# Step 3 : Synthesize the flash 5 images	COMMENT
LOW	mne/bem.py	2183	# Step 4 : Register with MPRAGE	COMMENT
LOW⚡	mne/stats/cluster_level.py	886	# Step 1: Calculate t-stat for original data	COMMENT
LOW⚡	mne/stats/cluster_level.py	998	# Step 2: If we have some clusters, repeat process on permuted data	COMMENT
LOW⚡	mne/stats/cluster_level.py	1000	# Step 3: repeat permutations for step-down-in-jumps procedure	COMMENT

Modern Structural Boilerplate4 hits · 4 pts

Severity	File	Line	Snippet	Context
LOW	mne/io/constants.py	7	__all__ = ["FIFF"]	CODE
LOW	mne/io/pick.py	12	__all__ = [	CODE
LOW	mne/utils/_typing.py	16	__all__ = ["Color", "FileLike", "Self"]	CODE
LOW	mne/viz/_brain/__init__.py	11	__all__ = ["Brain"]	CODE

Fake / Example Data4 hits · 4 pts

Severity	File	Line	Snippet	Context
LOW	mne/viz/backends/tests/test_abstract.py	31	text = backend._Text("test", "placeholder", callback)	CODE
LOW	mne/report/js_and_css/highlightjs/highlight.min.js	421	;const e=["a","abbr","address","article","aside","audio","b","blockquote","body","button","canvas","caption","cite","cod	CODE
LOW	mne/report/js_and_css/highlightjs/highlight.min.js	1035	;const e=["a","abbr","address","article","aside","audio","b","blockquote","body","button","canvas","caption","cite","cod	CODE
LOW	mne/report/js_and_css/highlightjs/highlight.min.js	1061	;const e=["a","abbr","address","article","aside","audio","b","blockquote","body","button","canvas","caption","cite","cod	CODE

Example Usage Blocks1 hit · 2 pts

Severity	File	Line	Snippet	Context
LOW	mne/preprocessing/nirs/_tddr.py	75	# Usage:	COMMENT

Analysis Overview

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