Releases · PennLINC/CuBIDS

What's Changed

🛠 Breaking Changes

Fix issue #283: Rename Key Group to Entity Set by @tientong98 in #329
Replace legacy validator with schema validator by @tientong98 in #337
Uniformize CLI named arguments to dash-only syntax by @gabridele in #372
Remove --container argument from CLIs by @tsalo in #394

🎉 Exciting New Features

Provide option to run locally installed bids-validator by @gabridele in #380
Use BIDS schema in CuBIDS by @tsalo in #392
Use cluster number in non-dominant acquisition variant names by @singlesp in #432
Add "C" prefix to cluster values in variants by @tsalo in #438
Bookend entity sets with datatype and acquisition entities by @tsalo in #442

🐛 Bug Fixes

Remove unnecessary arguments from cubids apply by @tsalo in #317
logger not printing metadata so use print instead by @tientong98 in #333
Support BIDS URIs in CuBIDS apply by @tsalo in #367
Stop adding leading zero to run entity when renaming files by @tsalo in #382
Use force_unlock in copy_exemplars Python workflow by @tsalo in #396
Block autocompletion of arguments in CLI by @gabridele in #393
Fixing bug to allow filenames in cubids apply and cubids copy-exemplars by @gabridele in #404
cubids print-metadata-fields exits if no dataset_desciption.json by @singlesp in #409
Fix: Update CuBIDS to allow both longitudinal and cross-sectional structure by adding is_longitudinal attribute to CUBIDS class by @tientong98 in #406
Variant renaming suggestions are ignoring tolerances by @mattcieslak in #417
add_nifti_info ImageOrientation 'None' in tuple fix by @ashleychari in #428
Pass schema along to workflows by @tsalo in #430
Remove non-alphanumeric characters from variant values by @tsalo in #443
Strip p0 from all values by @tsalo in #447

Other Changes

Fix test data path by @tsalo in #319
Add specification to use relative path for files listed in scans.txt used in cubids purge by @tientong98 in #345
Add --force-unlock to copy-exemplars and fix path to script in apply by @gabridele in #346
Delete notebooks from sidebar by @B-Sevchik in #371
remove links.rst from docs + add hyperlink by @shivaram-k in #373
Updated python versions in testing matrix by @gabridele in #374
Switch from using pkg_resources to importlib.resources by @singlesp in #369
Test CLI utils by @tsalo in #349
Update usage.rst to change from key group to entity set by @tientong98 in #381
Fill in docstrings for functions in config.py and tests/utils.py by @singlesp in #377
Cleanup notebooks by @smeisler in #366
Add module docstrings for about.py, init.py, constants.py, and utils.py by @singlesp in #398
Add docstrings for cubids/cli.py by @singlesp in #391
Update docstrings for files in cubids/tests by @shivaram-k in #397
Avoid copying shell prompt $ when copying example commands from docs by @gabridele in #402
Updated docs explaining the installation for internetless use cases by @gabridele in #401
add/edit docstrings for metadata_merge.py and validator.py by @singlesp in #408
Update installation instructions to use miniforge by @B-Sevchik in #375
Add FAQ page by @tsalo in #388
Make Tien the development lead and add code sprint participants to contributor list by @tsalo in #361
Switch from conda to mamba in CircleCI tests by @tsalo in #416
Add/edit cubids.py docstrings by @singlesp in #411
Split out non-class methods into utils module by @tsalo in #419
Clarify handling of non-BIDS entities in entity sets (e.g., fmap-epi) by @tsalo in #435
Fix NaN Handling during Clustering by @tientong98 in #439
Improve testing of command-line interfaces by @tsalo in #431