bids-matlab

• 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

• @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