v0.17.0

What's Changed

• use better random seeds and tell others about it by @sappelhoff in #1340
• gh upload artifact: also hidden files by @sappelhoff in #1341
• [MRG] Adding eye tracking to ch map by @christian-oreilly in #1344
• reduce non-determinism in tests by @drammock in #1347
• optionally return event_id dict from read_raw_bids, and use value column from events file if present by @drammock in #1349
• fix eager dtype conversion of value column by @drammock in #1353
• FIX: Support UTF-8 encoding for JSON files by @scott-huberty in #1357
• FIX: Use "recording" for recording entity, not "rec" by @scott-huberty in #1359
• bump required mne version by @sappelhoff in #1361
• allow get_entity_vals to ignore sidecars by @drammock in #1362
• [MRG] Update empty-room matching to look for and prioritize same-session recordings with task "noise" (closes #1354) by @berkgercek in #1364
• maint: update comment in conf.py by @drammock in #1367
• WIP Rework mne bids path match by @waldie11 in #1355
• BUG: Fix bug with path search by @larsoner in #1379
• auto-gen a GeneratedBy dict by @drammock in #1384
• os.path to pathlib: part 1 / n by @sappelhoff in #1339
• Fix BIDSPath partially matching a value by @PierreGtch in #1388
• more op to path conversions by @sappelhoff in #1391
• Refactor _handle_events_reading to allow extracting annotation information stand-alone by @matthiasdold in #1389
• allow more linkcheck retries by @sappelhoff in #1394
• fix links for linkcheck by @sappelhoff in #1396
• Add python 3.13 by @sappelhoff in #1400
• Gracefully handle absence of bids-validator, and allow running it through npx by @hoechenberger in #1404
• counteract flaky test by @sappelhoff in #1409
• Pass extra columns in events.tsv to the Annotations by @PierreGtch in #1401
• [MRG] Ensure check is passed to update function by @teonbrooks in #1411
• Require root, subject, task attributes for read_raw_bids by @teonbrooks in #1414
• FIX, DOC: Dont pair recording parameter w/ rec BIDS entity by @scott-huberty in #1417
• add T2w to suffix allowlist by @harrisonritz in #1420
• Escape period in extension regex by @nathan-az in #1433
• MAINT: Prep for release by @larsoner in #1437
• MAINT: Fix dep for release by @larsoner in #1438

New Contributors

• @christian-oreilly made their first contribution in #1344
• @berkgercek made their first contribution in #1364
• @waldie11 made their first contribution in #1355
• @matthiasdold made their first contribution in #1389
• @harrisonritz made their first contribution in #1420
• @nathan-az made their first contribution in #1433

Full Changelog: v0.16.0...v0.17.0

v0.16.0

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1262
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1263
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1264
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1265
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1266
• Simplify authors and copyright in all .py files (and make consistent) by @sappelhoff in #1267
• misc minor fixes by @sappelhoff in #1272
• correctly track anonymization date of empty room recordings when written simultaneously with data by @drammock in #1270
• Maint: FIX CI failures (HED related) by @sappelhoff in #1273
• Update mne_bids_report.py by @drammock in #1275
• MAINT: Compat with MNE 1.8 birthday date by @larsoner in #1278
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1279
• minor test cleanup by @drammock in #1274
• try sphinx 7.4.7 by @sappelhoff in #1280
• suppress channel unit change warnings by @sappelhoff in #1282
• Add new lint rules, remove unneeded noqa calls, refine noqa calls by @sappelhoff in #1283
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1284
• include OPM channels as megmag under .pick/get_coil_types() by @AmaiaBA in #1222
• Expose ignore_json, add ignore_nosub to file match/search funcs by @sappelhoff in #1281
• add contributor guide link to welcome bot by @sappelhoff in #1286
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1287
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1289
• fix doc and logging mark_channels by @sappelhoff in #1293
• MAINT: Bump to 3.10 min req by @larsoner in #1297
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1296
• FIX: Workaround header dropdown rendering issue by @scott-huberty in #1298
• Add event metadata handling by @thht in #1285
• fixed string subID bug by @Aaronearlerichardson in #1291
• Misc maintenance by @sappelhoff in #1299
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1301
• MAINT: Update BIDS Validator infrastructure by @sappelhoff in #1303
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1304
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1305
• deprecate empty list as indicator for marking all channels by @drammock in #1307
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1308
• MAINT: Updates for latest MNE by @larsoner in #1312
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1313
• Fix participant tsv values when Info contains weight and height information as numpy arrays by @thht in #1310
• Add intersphinx_registry and toml-sort by @mscheltienne in #1314
• Fix broken links in examples by @bootstrapbill in #1316
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1317
• Fix handling of README files with extensions by @thht in #1318
• remove bids-validator pin by @sappelhoff in #1322
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1326
• Add chpi to known channel list by @skjerns in #1325
• Fix warning given if no events are written and task is resting state by @skjerns in #1327
• Add link to mne-bids-pipeline by @skjerns in #1328
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1330
• fix canonical ref by @drammock in #1333
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1331
• adapt bids-validator url by @sappelhoff in #1334
• Control example order via explicit list, not via sorting titles by @drammock in #1321
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1335
• REL: 0.16.0 by @sappelhoff in #1336

New Contributors

• @AmaiaBA made their first contribution in #1222
• @thht made their first contribution in #1285
• @Aaronearlerichardson made their first contribution in #1291
• @bootstrapbill made their first contribution in #1316

Full Changelog: v0.15.0...v0.16.0

v0.15.0

What's Changed

• Update error messages to include EEGLAB format by @laemtl in #1198
• MAINT: bump versions by @sappelhoff in #1200
• Move project config to pyproject.toml, remove BINDER support by @sappelhoff in #1202
• Remove flake8, pydocstyle, black, etc. in favor of ruff by @sappelhoff in #1203
• MRG: Use hatchling as build backend by @hoechenberger in #1204
• [MRG] add CSS to truncate long version string by @drammock in #1206
• add NIRS citation by @sappelhoff in #1207
• MRG: Add defusedxml dependency to "full" variant by @hoechenberger in #1218
• [MRG] BUG: Fix dtype bug for counts by @larsoner in #1227
• fully prune 'events_data' from codebase by @sappelhoff in #1229
• Do not zero-pad indices in BIDSPath entities anymore; do not warn about prepending missing dots for extensions by @alexrockhill in #1215
• FIX: account for potential .{integer}_meg4 extensions in CTF format by @marakw in #1230
• MRG: Fix documentation build by @hoechenberger in #1233
• Bump ruff to v0.3.0 by @hoechenberger in #1232
• Run unit tests on Apple Silicon and bump Node version to LTS (currently 20) by @hoechenberger in #1231
• Fixup for #1231 by @hoechenberger in #1234
• bump cache for build CI by @sappelhoff in #1238
• account for optional Z in time strs by @sappelhoff in #1240
• Fix string format "blabla" "bla" by @mscheltienne in #1243
• Update pre-commit hooks, fix sphinx_gallery by @pre-commit-ci in #1245
• Remove ref-names from .git_archival.txt by @sappelhoff in #1249
• [MRG] MAINT: get test suite ready for pytest >= 8 by @sappelhoff in #1252
• MISC maintenance fixes by @sappelhoff in #1251
• [ADD] describing fields in event.json file by @JuliusWelzel in #1255
• [MRG] auto-add event_id key for BAD_ACQ_SKIP by @drammock in #1258
• MAINT: Setup new way of releasing by @sappelhoff in #1259
• REL: 0.15.0 by @sappelhoff in #1260

New Contributors

• @marakw made their first contribution in #1230
• @JuliusWelzel made their first contribution in #1255

Full Changelog: v0.14...v0.15.0

v0.14

What's Changed

• MRG: Use explicitly public namespaces by @larsoner in #1165
• Bump actions/checkout from 3 to 4 by @dependabot in #1166
• MRG: Correctly handle reading when BIDS channel order differs from Raw by @hoechenberger in #1171
• MEG: Add git pre-commit configuration by @hoechenberger in #1173
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1175
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1179
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1180
• BIDSPath no longer warns on missing file by @sappelhoff in #1181
• [MRG] Add recording entity to get_entity_vals by @sappelhoff in #1182
• Fix numpy 2.0 deprecation by @mscheltienne in #1184
• Bump actions/setup-node from 3 to 4 by @dependabot in #1185
• MRG: Fix bug with writing ctc/cal for emptyroom by @larsoner in #1189
• MAINT: Tweak test for latest MNE by @larsoner in #1191
• [MRG] Add support for eeglab export by @laemtl in #1187
• REL: 0.14 by @sappelhoff in #1193

New Contributors

• @pre-commit-ci made their first contribution in #1175

Full Changelog: v0.13...v0.14

v0.13

What's Changed

• MRG: Fix amending a dataset when new columns are being added to participants.tsv by @hoechenberger in #1113
• pin sphinx < 6.0 by @sappelhoff in #1115
• update for new version of google analytics by @agramfort in #1119
• MAINT: Use git by @larsoner in #1121
• [MRG] Fix copyfile_eeglab type conflicts by @laemtl in #1126
• [MRG] FIX: Convert line_freq and overwrite to proper types in CLI by @sappelhoff in #1125
• MAINT: Work around MNE change by @larsoner in #1128
• MRG: Silence warnings about missing events.tsv when reading empty-room or resting-state data by @hoechenberger in #1133
• MRG: Write events.json with "sample", "value", and "trial_type" entries by @hoechenberger in #1132
• add new intersphinx by @sappelhoff in #1135
• MRG: Add sessions as official suffix by @JonathanVHoecke in #1137
• MRG: Don't create directories when accessing BIDSPath.fpath by @hoechenberger in #1139
• MRG: Drop support for MNE-Python <1.3, add new CI job to cover "previous stable" MNE version by @hoechenberger in #1140
• fix version dropdown + misc maintenance by @sappelhoff in #1142
• MAINT: Use Black for formatting by @sappelhoff in #1144
• Fix name and add affiliation and orcid by @richardkoehler in #1146
• filter h5py triggered numpy deprecation warning by @sappelhoff in #1148
• Add ability to delete files from a BIDS dataset by @PierreGtch in #1149
• require testing data for test by @sappelhoff in #1150
• [MRG] fix(write.py): throw warning instead of error on conflicting bids versions by @fordmcdonald in #1147
• misc maint prior to release by @sappelhoff in #1154
• only copy BTI headshape file if present by @sappelhoff in #1158
• test minimal vs full mne-bids install by @sappelhoff in #1161
• Fix BTi handling in mne-bids by @sappelhoff in #1160
• REL: v0.13 by @sappelhoff in #1156

New Contributors

• @laemtl made their first contribution in #1126
• @JonathanVHoecke made their first contribution in #1137
• @PierreGtch made their first contribution in #1149
• @fordmcdonald made their first contribution in #1147

Full Changelog: v0.12...v0.13

v0.12

What's Changed

• Start developing 0.12 by @sappelhoff in #1078
• avoid creating many Annotations objects in for loop by @agramfort in #1079
• ENH: Better error message by @larsoner in #1080
• ENH: Improve error message by @larsoner in #1081
• ENH: Allow returning candidate BIDSPaths by @larsoner in #1083
• ENH: Make suggestion by @larsoner in #1087
• MRG: Enforce specification of all annotation descriptions in event_id if event_id is passed to write_raw_bids() by @hoechenberger in #1086
• DOC: Fix doc build by @larsoner in #1091
• fix: nirs convert only auto accepted by @sappelhoff in #1092
• BUG: Fix API for candidates by @larsoner in #1093
• more specific import to maybe avoid issue by @sappelhoff in #1095
• ENH: Better error message on fpath by @larsoner in #1097
• ENH: Auto warning stacklevel by @larsoner in #1099
• MRG: Fix writing preloaded data of a non-BIDS format with automated format conversion by @hoechenberger in #1102
• [ENH] Add function to enable smart path search #1098 by @moritz-gerster in #1103
• Fix CI via catching a warning by @sappelhoff in #1106
• MAINT: Update CIs and bump minimum to 3.8 by @larsoner in #1108
• Add support for writing neuromag122 data to BIDS by @agramfort in #1110
• [MRG] fix links, remove ubuntu 20.04 from CI by @sappelhoff in #1111
• rel: v0.12 by @sappelhoff in #1112

New Contributors

• @moritz-gerster made their first contribution in #1103

Full Changelog: v0.11...v0.12

v0.11.1

This is a patch release only.

v0.11

What's Changed

• Start 0.11 dev cycle by @hoechenberger in #985
• FIX: zenodo metadata by @sappelhoff in #986
• [MAINT, MRG] remove voxels from example by @alexrockhill in #988
• [BUG, MRG] Fix ACPC Coordinates in surface RAS when they should be in scanner RAS by @alexrockhill in #990
• [MRG] FIX: BrainProducts -> Brain Products by @sappelhoff in #993
• [MRG] bump BIDS_VERSION to 1.7.0 by @sappelhoff in #997
• [MRG] update make_dataset_description by @sappelhoff in #996
• MRG: Simplify storage of empty-room data by @hoechenberger in #998
• MRG: Suppress MaxShield warning in many places by @hoechenberger in #1000
• [MRG] Update installation documentation by @hoechenberger in #1001
• MRG: Make Inspector work even if mne-qt-browser is installed by @hoechenberger in #1007
• [MRG] allow copyfile_brainvision to work with .dat extension by @dominikwelke in #1008
• MRG: Remove deprecated mark_bad_channels() by @hoechenberger in #1009
• follow up: allow copyfile_brainvision to work with .dat extension by @dominikwelke in #1010
• [MRG] Bump to pybv 0.7.3 by @sappelhoff in #1011
• MRG: Make print_dir_tree expand ~ by @hoechenberger in #1013
• ci: add dependabot workflow to update github actions by @sappelhoff in #1015
• Bump actions/cache from 2 to 3 by @dependabot in #1016
• Bump actions/checkout from 2 to 3 by @dependabot in #1017
• Bump codecov/codecov-action from 2 to 3 by @dependabot in #1018
• Bump actions/setup-python from 2 to 4 by @dependabot in #1019
• DOC: Document make_dataset_description by @larsoner in #1029
• amended _write_electrodes_tsv to exclude writing stim channels to electrodes.tsv by @scott-huberty in #1023
• MRG: In BIDSPath, don't infer the datatype from the suffix by @hoechenberger in #1030
• [MRG, DOC] Fix whats_new.rst link by @mscheltienne in #1032
• MRG: Don't store invalid weight and height in info['subject_info']; write weight and height to participants.tsv by @hoechenberger in #1031
• Add EGI as manufacturer by @anandsaini024 in #1006
• [MRG] Complete .zenodo.json for contributor credit by @sappelhoff in #1028
• [MRG] FIX: Use os.replace instead of os.rename when copying CTF files (needed for windows) by @sappelhoff in #1035
• [MRG] migrate from .zenodo.json to CITATION.cff by @sappelhoff in #1037
• [MRG] Raise an error message when src==dest in write_raw_bids by @adam2392 in #889
• [MRG] handle empty TSVs robustly and warn by @sappelhoff in #1038
• Fixes for EEGLAB: do not 'simplify cells' when loading. by @sappelhoff in #1039
• [MRG] Improve check of scans.tsv for BrainVision files by @teonbrooks in #1034
• try fix for docs (nirs example) by @sappelhoff in #1050
• MRG: Set channel type to misc if we cannot perform a proper conversion from BIDS to MNE channel types by @hoechenberger in #1052
• MRG: Fix doc build for sphinx-gallery >=0.11.1 by @hoechenberger in #1055
• Deprecate write_raw_bids()'s events_data parameter in favor of "events" by @hoechenberger in #1054
• Doc Smallfix: Updated the BIDSPath in-place update method example by @bhvieira in #1026
• [MRG] MAINT: Use new GitHub issue forms (yml) by @sappelhoff in #1056
• Move emojis in issue templates to the titles by @hoechenberger in #1058
• MRG: Add "description" entity to BIDSPath by @hoechenberger in #1057
• MRG: Add support for GSR and temperature channels by @hoechenberger in #1059
• MRG: Deprecate silently adding a leading period to an extension in BIDSPath by @hoechenberger in #1061
• MRG: Remove special-casing for NIRS bids-validator by @hoechenberger in #1063
• Fix chpi write by @eort in #1067
• [MRG] Suggest alternatives when value not found in list by @larsoner in #1066
• Fix Inspector tests for Matplotlib 3.6 compatibility by @hoechenberger in #1069
• MAINT: Ensure we dont download without permission by @larsoner in #1073
• fix CI after upstream changes by @sappelhoff in #1071
• [MRG]: Add support for reading curry EEG files by @dengemann in #1072
• MAINT: Tolerate new MNE behavior by @larsoner in #1076
• Provide more helpful error messages when trying to write non-prelaoded concatenated data by @hoechenberger in #1075
• REL: v0.11 by @sappelhoff in #1077

New Contributors

• @dependabot made their first contribution in #1016
• @scott-huberty made their first contribution in #1023
• @mscheltienne made their first contribution in #1032
• @anandsaini024 made their first contribution in #1006
• @bhvieira made their first contribution in #1026
• @dengemann made their first contribution in #1072

Full Changelog: v0.10...v0.11

v0.10

Major enhancements

• We now have experimental support for fNIRS data (SNIRF format). This is still super fresh, and the respective BIDS enhancement proposal (BEP) has not yet been finalized & accepted into the standard. However, we’re excitied to be able to do this first step towards fNIRS support!
• Numerous improvements have been added to enhance our support for various coordinate frames, including those that are not yet supported by MNE-BIDS. These changes are mostly relevant to iEEG users. Please see the detailed list of changes below.
• We have added support for storing and reading multiple anatomical landmarks (“fiducials”) for the same participant. This makes it possible, for example, to store different sets of landmarks for each recording session.
  It’s now possible to store Neuroscan (CNT) files with MNE-BIDS.

What's Changed

• MRG: Start 0.10 dev cycle by @hoechenberger in #920
• doc: update dependencies by @sappelhoff in #921
• [BUG] Add overwrite to export_raw for EDF conversions by @adam2392 in #930
• [MRG] fix loading without age information / single-column .tsv by @skjerns in #912
• MRG: Rework CI test matrix by @hoechenberger in #934
• MRG: Don't store age, sex, handedness for empty-room in participants.tsv by @hoechenberger in #935
• MRG: Fix handling of n/a event values when auto-renaming events on read by @hoechenberger in #937
• Bump openneuro-py dep to 2022.1+ & Fix doc build for MNE-Python 1.0 by @hoechenberger in #942
• Neuroscan Support by @yjmantilla in #924
• MRG: Migrate report to Jinja2 by @hoechenberger in #944
• MAINT: Fix setup by @larsoner in #945
• bump cache, install with deps by @sappelhoff in #951
• FIX: make update unalter the path instance if check fails by @agramfort in #950
• [MRG] explicitly declare pymatreader an optional dep for EEGLAB by @sappelhoff in #952
• [MRG] add metadata to ZENODO core archive by @sappelhoff in #953
• ENH : add support for landmarks as dict in write_anat and kind param … by @agramfort in #955
• MRG: Add "kind" kwarg to update_anat_landmarks() by @hoechenberger in #957
• CI: Add concurrency by @larsoner in #959
• doc: remove sphinx gallery css (now handled upstream); fix: testing split file by @sappelhoff in #964
• DOC: fix author list rendering by @Swastyy in #971
• MAINT: Report all unit test coverage by @larsoner in #974
• MRG: Make get_head_mri_trans() respect datatype and suffix attributes of MEG BIDSPath by @hoechenberger in #969
• [BUG, ENH, MRG] Pixels by @alexrockhill in #976
• [ENH, MRG] Clarify intracranial narrative for why individual coordinates are preferred by @alexrockhill in #975
• MRG: Initial support for NIRS data by @rob-luke in #406
• MRG: Make update_anat_landmarks() accept fiducials file by @hoechenberger in #977
• [ENH, MRG] Simplify reading dig by @alexrockhill in #979
• [ENH, MRG] Allow template coordinate frame writing by @alexrockhill in #980
• [BUG, MRG] Fix coordinate frames by @alexrockhill in #982
• [ENH, MRG] Add BIDS Standard Template Transformations by @alexrockhill in #983
• Prepare 0.10 release by @hoechenberger in #984

New Contributors

• @skjerns made their first contribution in #912
• @yjmantilla made their first contribution in #924
• @Swastyy made their first contribution in #971

Full Changelog: v0.9...v0.10

v0.9

Notable changes

• 🧠 Compatibility with MNE-Python 0.24!
• 👻 Anonymize an entire BIDS dataset via mne_bids.anonymize_dataset!
• 🏝 Conveniently turn a path into a BIDSPath via
  get_bids_path_from_fname!
• 🏎 :func:mne_bids.stats.count_events and mne_bids.BIDSPath.match
  are operating much faster now!
• 🔍 write_raw_bids now stores the names of the input files in the
  source column of *_scans.tsv, making it easier for you to
  go back to the source should you ever need to!