Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
[v0.3.0] - 2024-09-11
Added
[ENH] Add zero padding when numbers are passed for indices to
bids.Fileorbids.File.rename680 by Remi-Gau[ENH] remove checks for participants.tsv or samples.tsv in derivatives by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/666
[ENH] sanitize entities in rename spec by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/679
[ENH] Added modality retrieval from path by nbeliy in https://github.com/bids-standard/bids-matlab/pull/656
[ENH] add zero padding to entity labels / indices when passed as numbers by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/680
[ENH] add support for BIDS MRS by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/718
Fixed
[FIX] Create valid participants and sessions tsv during dataset init 688 by Remi-Gau
[FIX] create valid participants and sessions tsv during dataset init by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/688
[FIX] handle error for misshaped tsv by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/667
[FIX] index modality at same level as sessions by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/681
[FIX] set default empty modality for files with no entities by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/691
[FIX] ignore ‘na’ as trial types when creating default models by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/709
[FIX] Suppress warning when session is taken for modality when going schemaless by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/710
[FIX] fix validation of F contrasts by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/711
[FIX] handle rare case where intended for field is empty by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/716
Full Changelog: https://github.com/bids-standard/bids-matlab/compare/v0.2.0…v0.3.0
[v0.2.0]
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
devbranch 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]
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
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
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
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
[INFRA] conversion BIDS schema to json by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/101
[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 in https://github.com/bids-standard/bids-matlab/pull/119
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
[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
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
[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
[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
[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
[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
[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
[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
[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
Improvement of File.m interface by nbeliy in https://github.com/bids-standard/bids-matlab/pull/289
[FIX] fix the regex when querying subjects by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/295
[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
[ENH] add support for microscoy by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/315
[REL] rc0.1.0 by Remi-Gau in https://github.com/bids-standard/bids-matlab/pull/287
New Contributors
by tanguyduval made their first contribution in https://github.com/bids-standard/bids-matlab/pull/13
by robertoostenveld made their first contribution in https://github.com/bids-standard/bids-matlab/pull/14
by apjanke made their first contribution in https://github.com/bids-standard/bids-matlab/pull/30
by gllmflndn made their first contribution in https://github.com/bids-standard/bids-matlab/pull/72
by cMadan made their first contribution in https://github.com/bids-standard/bids-matlab/pull/62
by mslw made their first contribution in https://github.com/bids-standard/bids-matlab/pull/42
by HenkMutsaerts made their first contribution in https://github.com/bids-standard/bids-matlab/pull/127
by nbeliy made their first contribution in https://github.com/bids-standard/bids-matlab/pull/166
by 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