Bids Matlab Versions Save

MATLAB / Octave tools for BIDS datasets

v0.2.0

6 months ago

What's Changed

Note some changes are missing from these release notes, but should be listed in the pull request that merged the dev branch in the main branch.

[FIX] do not create empty json when copying to derivatives by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/322
[DOC] add orcid numbers to CITATION.CFF by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/337
[INFRA] only run update schema on upstream repo by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/343
[FIX] change download of moae demo dataset by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/351
[FIX] Skip missing suffix subgroup by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/365
[FIX] add test to catch error for invalid entities by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/367
[FIX] add warning when indexing folder with invalid MATLAB structure name by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/366
[DOC & ENH] update doc query and allow to query any BIDS entity by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/368
[REF] Use JSON version of the schema by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/415
[ENH] add NIRS support by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/433
[FIX] query with empty subject should return empty and not fail by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/455
[FIX] fix spelling with codespell by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/457
[FIX] make bids.copy strict by default by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/468
[FIX] add try catch for rare errors on invalid bids datasets by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/471
[FIX] cleaner handling of missing dependency by @nbeliy in https://github.com/bids-standard/bids-matlab/pull/473
[FIX] do not index files that start with certain string by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/479
[FIX] remove byte order mark from tsv file by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/556
[FIX] handle nan and and datetimes when printing tables by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/605
[MAINT] change to MIT license by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/653
[MAINT] Drop dev branch by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/654

Full Changelog: https://github.com/bids-standard/bids-matlab/compare/v0.1.0...v0.2.0

v0.1.0

2 years ago

What's Changed

Bids report by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/1
small fix in a filter that skipped json files when they were in the root folder by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/8
Readme update: Add converter and viewer by @tanguyduval in https://github.com/bids-standard/bids-matlab/pull/13
[WIP] Unit tests - read metadata by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/10
Query by @tanguyduval in https://github.com/bids-standard/bids-matlab/pull/12
multi file datasets (such as BrainVision) should be represented as a single dataset, not multiple by @robertoostenveld in https://github.com/bids-standard/bids-matlab/pull/14
Add some extra comments to better explain each function by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/21
More detailed error messages by @apjanke in https://github.com/bids-standard/bids-matlab/pull/30
gitignore: ignore local copy of bids-examples by @apjanke in https://github.com/bids-standard/bids-matlab/pull/31
util.tsvread: Make it a recursive call to self by @apjanke in https://github.com/bids-standard/bids-matlab/pull/33
util: Support jsonencode/jsondecode as regular functions by @apjanke in https://github.com/bids-standard/bids-matlab/pull/24
Include QUERY in the H1 line for query's helptext by @apjanke in https://github.com/bids-standard/bids-matlab/pull/29
Make function helptext more concise with a +bids/Contents.m by @apjanke in https://github.com/bids-standard/bids-matlab/pull/32
README: Document requirements by @apjanke in https://github.com/bids-standard/bids-matlab/pull/36
Handle non-standard-format metadata JSON files by @apjanke in https://github.com/bids-standard/bids-matlab/pull/37
Doc: Typo fixes in comments and helptext by @apjanke in https://github.com/bids-standard/bids-matlab/pull/38
Refactoring and renaming by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/41
Create a tsvwrite function by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/40
Tolerant option for bids.layout by @tanguyduval in https://github.com/bids-standard/bids-matlab/pull/11
docs: add gllmflndn as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/52
docs: add Remi-Gau as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/53
docs: add apjanke as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/54
docs: add tanguyduval as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/55
docs: add robertoostenveld as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/56
Fix or suppress M-lint code inspection warnings by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/57
Move +bids/private stuff to +bids/+internal? by @apjanke in https://github.com/bids-standard/bids-matlab/pull/25
[INFRA] Use Ubuntu Focal 20.04 in Travis tests by @gllmflndn in https://github.com/bids-standard/bids-matlab/pull/72
[FIX] Filter subjects and sessions when querying modalities (issue #65) by @gllmflndn in https://github.com/bids-standard/bids-matlab/pull/71
[FIX] fix writing nan issues when dealing with arrays by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/74
Add Brainstorm to README by @cMadan in https://github.com/bids-standard/bids-matlab/pull/62
add code of conduct from bids-specs by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/80
[INFRA] set up miss_hit linter config and github action by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/58
Add tsvwrite to documentation by @gllmflndn in https://github.com/bids-standard/bids-matlab/pull/85
miss_hit.cfg: define project_root by @apjanke in https://github.com/bids-standard/bids-matlab/pull/87
docs: add apjanke as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/88
README: fix MISS_HIT name styling by @apjanke in https://github.com/bids-standard/bids-matlab/pull/89
Add .editorconfig? by @apjanke in https://github.com/bids-standard/bids-matlab/pull/86
docs: add apjanke as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/90
docs: add cMadan as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/91
docs: add guiomar as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/93
Skip datasets when labelled as non-conformant by @gllmflndn in https://github.com/bids-standard/bids-matlab/pull/94
[DOC] Describe what bids-matlab can and cannot do by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/84
apply MISS_HIT linter across the board by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/95
Decision making & contributing by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/81
[FIX] add "dir" to the list of func entities by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/99
[INFRA] Customize code suggestions & completions by adding a functionSignatures file by @mslw in https://github.com/bids-standard/bids-matlab/pull/42
docs: add mslw as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/106
[INFRA] conversion BIDS schema to json by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/101
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/110
[INFRA] run tests with github action by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/100
[INFRA] switch to moxunit for tests by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/108
refactoring and linting by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/109
[ENH] update schema - changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/119
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/120
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/125
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/128
Feature #asl bids by @HenkMutsaerts in https://github.com/bids-standard/bids-matlab/pull/127
[MISC] refactor and add tests for layout asl by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/132
docs: add HenkMutsaerts as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/135
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/136
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/138
docs: add nbeliy as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/139
[ENH] implement bids-schema - part 1 by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/124
[ENH] schemaless layout indexes json files by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/147
[ENH] add possibility to query for (and filter queries with) extensions by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/150
[ENH] improve management of "intended_for" by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/151
[ENH] update fieldname m0 scan estimate by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/149
docs: add mnoergaard as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/158
docs: add nbeliy as a contributor by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/159
Bug in file_utils by @nbeliy in https://github.com/bids-standard/bids-matlab/pull/166
[HOT FIX] fixed bug in file_utils by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/168
[HOT FIX] implement hot fix for tsv write by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/170
[ENH] schema-less indexing collects files prefix that can be returned / filtered by query by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/154
[HOT FIX] implement hot fix for tsv write by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/173
[INFRA] BIDS schema update by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/180
[INFRA] remove obsolete schema files by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/181
[FIX] lower priority to use SPM function to deal with json files by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/178
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/188
[DOC] update instructions to run the tests by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/183
[ENH] index sessions.tsv and scans.tsv by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/182
[FIX] default pattern of get_metada expects suffixes to be preceded by underscore by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/179
[FIX] default pattern of get_metada expects suffixes to be preceded by underscore by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/189
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/191
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/193
[FIX] ensures that metadata file have the same prefix as the queried file by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/195
[DOC] update install isntructions in README by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/197
[INFRA] update miss_hit version and add pre-commit hook by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/198
[WIP] Function to copy derivatives by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/171
[FIX] fix and refactor report by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/206
[Fix] fix issues when parsing prefix and ordering entities after parsing filename by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/210
[FIX] fix bugs in copy to derivatives by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/207
[FIX] return empty output of append to layout when failing to parse using schema by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/212
[INFRA] remove unnecessary tsv files in test folder by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/216
[INFRA] remove unnecessary tsv files in test folder by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/217
[INFRA] add copyright checks from miss_hit by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/218
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/220
[ENH] implement input parser for copy_to_derivatives by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/221
[ENH] copy participants, sessions, scans TSV to derivatives by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/222
[ENH] add basic function to generate and update dataset_description by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/184
[ENH] add basic filename, path and derivatives JSON creation by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/203
[ENH] add basic capabilities to initialize a dataset by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/224
[REF] refactor schema functions into a class by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/225
[INFRA] fix CI by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/227
[DOC] set up sphinx and read the docs by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/229
Refactor report and update doc, jupyter notebook, binder by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/230
Update binder and jupyter notebooks by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/231
Refactoring by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/232
[FIX] files with missing required entities, unknown entities or extensions are skipped when using layout with schema by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/237
Refactor error and warning handling by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/239
[ENH] Index nested derivatives by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/240
[FIX] copy to derivatives for windows by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/242
[FIX] typos in filename function by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/246
[FIX] fix bug in create filename when entities is missing by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/247
Speed up dependencies indexing by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/243
Dev - jsonwrite by default by @CPernet in https://github.com/bids-standard/bids-matlab/pull/249
docs: add CPernet as a contributor for code, ideas by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/251
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/253
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/254
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/255
[FIX] enforce valid fieldnames in schema content and skip schema metadata loading by default by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/256
[FIX] update bids init related functions to more BIDS compliant default output by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/257
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/260
[FIX] allows filtering with entities for query than "data" by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/259
[ENH] Index tsv and json files in root folder by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/261
add error message to parse_filename by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/264
Improve bids.init by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/263
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/266
[DOC] add matlab exchange badge in README by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/270
[DOC] General update of the sphinx doc by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/269
[ENH] improves constructors for schema and dataset description by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/271
Added treatment of bids-incomatible files in dataset by @nbeliy in https://github.com/bids-standard/bids-matlab/pull/268
[ENH] refactor create_filename and create_path into a bids.File class by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/273
[ENH] update Schema class to new schema structure by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/285
[INFRA] implement matlab github action by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/201
[INFRA] silence codecov by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/290
[ENH] Improve bids.query by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/286
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/291
[ENH] fix and improve bids.report by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/280
[TEST] add test for copying to derivatives with an exclude filter by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/292
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/296
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/297
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/299
Improvement of File.m interface by @nbeliy in https://github.com/bids-standard/bids-matlab/pull/289
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/301
[FIX] fix the regex when querying subjects by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/295
docs: add ChristophePhillips as a contributor for ideas by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/303
[INFRA] add CITATION.cff file by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/284
[ENH] update and standardize API by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/305
[ENH] do not index json with bids.layout by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/307
[ENH] make bids.query return list of availables labels for some common derivative entities by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/308
[ENH] validate entity keys provided when using BIDS schema to create filenames by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/309
[INFRA] test for matlab octave difference by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/310
[INFRA] fix failing tests on windows by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/311
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/312
[ENH] add support for microscoy by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/315
Changes by create-pull-request action by @github-actions in https://github.com/bids-standard/bids-matlab/pull/317
[REL] rc0.1.0 by @Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/287

New Contributors

@tanguyduval made their first contribution in https://github.com/bids-standard/bids-matlab/pull/13
@robertoostenveld made their first contribution in https://github.com/bids-standard/bids-matlab/pull/14
@apjanke made their first contribution in https://github.com/bids-standard/bids-matlab/pull/30
@allcontributors made their first contribution in https://github.com/bids-standard/bids-matlab/pull/52
@gllmflndn made their first contribution in https://github.com/bids-standard/bids-matlab/pull/72
@cMadan made their first contribution in https://github.com/bids-standard/bids-matlab/pull/62
@mslw made their first contribution in https://github.com/bids-standard/bids-matlab/pull/42
@github-actions made their first contribution in https://github.com/bids-standard/bids-matlab/pull/110
@HenkMutsaerts made their first contribution in https://github.com/bids-standard/bids-matlab/pull/127
@nbeliy made their first contribution in https://github.com/bids-standard/bids-matlab/pull/166
@CPernet made their first contribution in https://github.com/bids-standard/bids-matlab/pull/249

Full Changelog: https://github.com/bids-standard/bids-matlab/commits/v0.1.0