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Recent Releases of MNE-BIDS

MNE-BIDS - v0.16.0

What's Changed

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

New Contributors

  • @AmaiaBA made their first contribution in https://github.com/mne-tools/mne-bids/pull/1222
  • @thht made their first contribution in https://github.com/mne-tools/mne-bids/pull/1285
  • @Aaronearlerichardson made their first contribution in https://github.com/mne-tools/mne-bids/pull/1291
  • @bootstrapbill made their first contribution in https://github.com/mne-tools/mne-bids/pull/1316

Full Changelog: https://github.com/mne-tools/mne-bids/compare/v0.15.0...v0.16.0

Scientific Software - Peer-reviewed - Python
Published by sappelhoff over 1 year ago

MNE-BIDS - v0.15.0

What's Changed

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

New Contributors

  • @marakw made their first contribution in https://github.com/mne-tools/mne-bids/pull/1230
  • @JuliusWelzel made their first contribution in https://github.com/mne-tools/mne-bids/pull/1255

Full Changelog: https://github.com/mne-tools/mne-bids/compare/v0.14...v0.15.0

Scientific Software - Peer-reviewed - Python
Published by sappelhoff almost 2 years ago

MNE-BIDS - v0.14

What's Changed

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

New Contributors

  • @pre-commit-ci made their first contribution in https://github.com/mne-tools/mne-bids/pull/1175

Full Changelog: https://github.com/mne-tools/mne-bids/compare/v0.13...v0.14

Scientific Software - Peer-reviewed - Python
Published by sappelhoff over 2 years ago

MNE-BIDS - v0.13

What's Changed

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

New Contributors

  • @laemtl made their first contribution in https://github.com/mne-tools/mne-bids/pull/1126
  • @JonathanVHoecke made their first contribution in https://github.com/mne-tools/mne-bids/pull/1137
  • @PierreGtch made their first contribution in https://github.com/mne-tools/mne-bids/pull/1149
  • @fordmcdonald made their first contribution in https://github.com/mne-tools/mne-bids/pull/1147

Full Changelog: https://github.com/mne-tools/mne-bids/compare/v0.12...v0.13

Scientific Software - Peer-reviewed - Python
Published by sappelhoff almost 3 years ago

MNE-BIDS - v0.12

What's Changed

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

New Contributors

  • @moritz-gerster made their first contribution in https://github.com/mne-tools/mne-bids/pull/1103

Full Changelog: https://github.com/mne-tools/mne-bids/compare/v0.11...v0.12

Scientific Software - Peer-reviewed - Python
Published by sappelhoff over 3 years ago

MNE-BIDS - v0.11.1

This is a patch release only.

Scientific Software - Peer-reviewed - Python
Published by sappelhoff over 3 years ago

MNE-BIDS - v0.11

What's Changed

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

New Contributors

  • @dependabot made their first contribution in https://github.com/mne-tools/mne-bids/pull/1016
  • @scott-huberty made their first contribution in https://github.com/mne-tools/mne-bids/pull/1023
  • @mscheltienne made their first contribution in https://github.com/mne-tools/mne-bids/pull/1032
  • @anandsaini024 made their first contribution in https://github.com/mne-tools/mne-bids/pull/1006
  • @bhvieira made their first contribution in https://github.com/mne-tools/mne-bids/pull/1026
  • @dengemann made their first contribution in https://github.com/mne-tools/mne-bids/pull/1072

Full Changelog: https://github.com/mne-tools/mne-bids/compare/v0.10...v0.11

Scientific Software - Peer-reviewed - Python
Published by sappelhoff over 3 years ago

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

New Contributors

  • @skjerns made their first contribution in https://github.com/mne-tools/mne-bids/pull/912
  • @yjmantilla made their first contribution in https://github.com/mne-tools/mne-bids/pull/924
  • @Swastyy made their first contribution in https://github.com/mne-tools/mne-bids/pull/971

Full Changelog: https://github.com/mne-tools/mne-bids/compare/v0.9...v0.10

Scientific Software - Peer-reviewed - Python
Published by hoechenberger about 4 years ago

MNE-BIDS - 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!

Scientific Software - Peer-reviewed - Python
Published by hoechenberger over 4 years ago

MNE-BIDS - v0.8

Notable changes

  • You can now write preloaded and potentially modified data with mne_bids.write_raw_bids by passing allow_preload=True. This is a first step towards supporting derivative files.
  • mne_bids.BIDSPath now has property getters and setters for all BIDS entities. What this means is that you can now do things like bids_path.subject = '01' instead of bids_path.update(subject='01').
  • We now support Deep Brain Stimulation (DBS) data.
  • The way we handle anatomical landmarks was greatly revamped to ensure we're always using the correct coordinate systems. A new function, mne_bids.get_anat_landmarks, helps with extracting fiducial points from anatomical scans.
  • When creating a BIDS dataset from FIFF files on macOS and Linux, MNE-BIDS can now optionally generate symbolic links to the original files instead of copies. Simply pass symlink=True to mne_bids.write_raw_bids. This can massively reduce the storage space requirements.

Scientific Software - Peer-reviewed - Python
Published by sappelhoff almost 5 years ago

MNE-BIDS - v0.7

Notable changes

  • Channel names in *_channels.tsv and *_electrodes.tsv files now always take precedence over the names stored in the raw files.
  • When reading data where the same trial type refers to different trigger values, we will now automatically create hierarchical event names in the form of trial_type/value1, trial_type/value2` etc.
  • :func:mne_bids.write_raw_bids now allows users to specify a format conversion via the new format parameter.
  • Various improvements to data reading and :class:mne_bids.BIDSPath make working with real-life data easier.
  • Many bug fixes in :func:mne_bids.write_raw_bids and in the MNE-BIDS Inspector.

Scientific Software - Peer-reviewed - Python
Published by hoechenberger about 5 years ago

MNE-BIDS - v0.6 🎄

These are challenging days for many of us, and to make your lives ever so slightly easier, we've been working hard to deliver this early Christmas present 🎁 And even if you do not celebrate Christmas, we are quite certain you will like what we got for you! So – what are you waiting for? It's time to unwrap!

Notable changes

  • The new Inspector, which can be invoked via :func:mne_bids.inspect_dataset, allows you to interactively explore your raw data,
    change the bad channels selection, and edit :class:mne.Annotations. It also performs automated detection of flat data segments or channels, to assist you during visual inspection. The capabilities of the inspector will be further expanded in upcoming releases of MNE-BIDS.

  • To further assist you during data inspection, we have added a function to summarize all events present in a dataset, :func:mne_bids.stats.count_events.

  • Sidecar JSON files can now be updated using a template via :func:mne_bids.update_sidecar_json.

  • You can now read and write FLASH MRI images using :func:mne_bids.write_anat. We also fixed some issues with MRI defacing along the way.

  • Event durations are now preserved upon reading and writing data (we used to set all event durations to zero before).

Scientific Software - Peer-reviewed - Python
Published by hoechenberger over 5 years ago

MNE-BIDS - v0.5

This is a big release with lots of changes, many of them breaking existing code. But do not fear: migration is easy, and you will love what we have been cooking for you!

  • We introduce mne_bids.BIDSPath, a new class for all BIDS file and folder operations.
  • MNE-BIDS now requires MNE-Python 0.21.
  • The new function mnebids.makereport() can help you populate a paragraph of your next paper’s methods section!
  • You can now interactively mark channels as bad using mnebids.markbad_channels().
  • Elekta/Neuromag/MEGIN fine-calibration and crosstalk files can now be stored in your BIDS dataset via mnebids.writemegcalibration() and mnebids.writemegcrosstalk().
  • When writing a raw file that contains annotations, these will now be converted to and stored as events by mnebids.writeraw_bids().

Scientific Software - Peer-reviewed - Python
Published by hoechenberger over 5 years ago

MNE-BIDS - v0.4

v0.4

Scientific Software - Peer-reviewed - Python
Published by sappelhoff about 6 years ago

MNE-BIDS - v0.3.1

NOTE

  • This GitHub release was not mirrored by a PyPI or conda-forge release (GitHub-only).
  • It was done only to trigger a Zenodo release (https://zenodo.org/record/3580273) to be used by JOSS: https://joss.theoj.org/papers/10.21105/joss.01896
  • Best ignore it and move along :slightlysmilingface:

Scientific Software - Peer-reviewed - Python
Published by sappelhoff over 6 years ago

MNE-BIDS - v0.3

v0.3

Scientific Software - Peer-reviewed - Python
Published by sappelhoff almost 7 years ago

MNE-BIDS - v0.2

v0.2

Scientific Software - Peer-reviewed - Python
Published by sappelhoff about 7 years ago

MNE-BIDS - v0.1

v0.1

Scientific Software - Peer-reviewed - Python
Published by jasmainak over 7 years ago