diff --git a/docs/source/changelog.md b/docs/source/changelog.md index 3917b43e..91e778e0 100644 --- a/docs/source/changelog.md +++ b/docs/source/changelog.md @@ -6,6 +6,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unreleased] +## [v0.3.0] - 2024-09-11 ### Added * [ENH] Add zero padding when numbers are passed for indices to `bids.File` or `bids.File.rename` #680 by @Remi-Gau - -### Changed - -### Deprecated - -### Removed +* [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 -### Security - +**Full Changelog**: https://github.com/bids-standard/bids-matlab/compare/v0.2.0...v0.3.0 ## [v0.2.0] -### Changed - -### Deprecated - -### Removed - -### Fixed - -### Security +## 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](https://github.com/bids-standard/bids-matlab/pull/647). + +* [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] -### Changed - -### Deprecated - -### Removed - -### Fixed - -### Security +* 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 +* 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 +* [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 +* 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 +* [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 +* docs: add CPernet as a contributor for code, ideas by @allcontributors in https://github.com/bids-standard/bids-matlab/pull/251 +* [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 +* 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 +* [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 +* @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