[MAINT] pre-release 0.2.0 #647
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…into transformers
[ENH] upgrade transformers
[FIX] fix bugs in setting modality and getting entity order from schema
…582) * add warning mentioning which json files could not be read * add file not found erro
* update doc * update example * fixes
* add electrodes and optodes as dependencies * inline function * fix
* index and query phenotype * do not load content and metadata
* do not add subject to layout if it is empty * subject is in structure if schemaless * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactor * get properties and not fields when dealing with bids.File instance * rerun * silence failing tests on windows --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * CI: Use PAT to submit pull requests (#534) This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions. * Bump peter-evans/create-pull-request from 4 to 5 (#536) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#548) * update schema * readd token$ * update ci (#558) * [FIX] remove byte order mark from tsv file (#556) * fix bom * add data * octave fix * Bump matlab-actions/run-command from 1.1.3 to 1.2.0 (#570) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.1.3 to 1.2.0. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.1.3...v1.2.0) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#577) * update schema * rm token * docs: add coxroy as a contributor for bug, ideas, and userTesting (#585) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * BIDS schema update (#587) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#592) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#594) Co-authored-by: Remi-Gau <[email protected]> * Bump matlab-actions/run-command from 1.2.0 to 1.2.1 (#602) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.0 to 1.2.1. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.2.0...v1.2.1) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [FIX] handle nan and and datetimes when printing tables (#605) * fix bugs in tables and datetimes * skip on windows * update schema --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Remi-Gau <[email protected]>
* use inheritance in get_meta_list * refactor
* improve API * add doc * skip octave for test
* better handle printting of paths in windows * fix more paths * more clean up * fix more paths
* First attempt to incorporate json into bids.File * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * lint * Added util function to update structures * Style and tests for util/update_struct.m * Using metadata field instead of json_struct * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed JSONFile subclass * Added tests for metadata for File class * Fixed spelling in doc * File: Added functions that act on individual fields * File: fixed style * Splitted File.metadada tests into smaller ones --------- Co-authored-by: Beliy Nikita <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Gau <[email protected]>
* update timing * try speed up test by not indexing dependencies * run on latest and oldest matlab * [DATALAD] Recorded changes * [DATALAD] Recorded changes * cancel previous runs * speed up some tests or functions * run slow and fast tests in parallel * windows env var fix * try using globals * fix * add more slow test * add doc
* update demo * doc changes
* rm atlas and update res and den metadata * fix
* fix tests after merge from main * fix test octave
* BIDS schema update (#628) Co-authored-by: Remi-Gau <[email protected]> * Bump actions/checkout from 3 to 4 (#629) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * BIDS schema update (#633) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#634) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#635) Co-authored-by: Remi-Gau <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#636) updates: - [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BIDS schema update (#637) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#639) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#640) Co-authored-by: Remi-Gau <[email protected]> * Bump matlab-actions/setup-matlab from 1.2.4 to 1.2.5 (#641) Bumps [matlab-actions/setup-matlab](https://github.com/matlab-actions/setup-matlab) from 1.2.4 to 1.2.5. - [Release notes](https://github.com/matlab-actions/setup-matlab/releases) - [Commits](matlab-actions/setup-matlab@v1.2.4...v1.2.5) --- updated-dependencies: - dependency-name: matlab-actions/setup-matlab dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump matlab-actions/run-command from 1.2.1 to 1.2.2 (#642) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.1 to 1.2.2. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.2.1...v1.2.2) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [FIX] update test after schema update (#643) * fix test after schema update * set os version for doc * update schema * fix typos * update tests --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Remi-Gau <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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