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Recent Releases of cubids

cubids - 1.2.0

What's Changed

🛠 Breaking Changes

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

🎉 Exciting New Features

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

🐛 Bug Fixes

  • Remove unnecessary arguments from cubids apply by @tsalo in https://github.com/PennLINC/CuBIDS/pull/317
  • logger not printing metadata so use print instead by @tientong98 in https://github.com/PennLINC/CuBIDS/pull/333
  • Support BIDS URIs in CuBIDS apply by @tsalo in https://github.com/PennLINC/CuBIDS/pull/367
  • Stop adding leading zero to run entity when renaming files by @tsalo in https://github.com/PennLINC/CuBIDS/pull/382
  • Use forceunlock in copyexemplars Python workflow by @tsalo in https://github.com/PennLINC/CuBIDS/pull/396
  • Block autocompletion of arguments in CLI by @gabridele in https://github.com/PennLINC/CuBIDS/pull/393
  • Fixing bug to allow filenames in cubids apply and cubids copy-exemplars by @gabridele in https://github.com/PennLINC/CuBIDS/pull/404
  • cubids print-metadata-fields exits if no dataset_desciption.json by @singlesp in https://github.com/PennLINC/CuBIDS/pull/409
  • Fix: Update CuBIDS to allow both longitudinal and cross-sectional structure by adding is_longitudinal attribute to CUBIDS class by @tientong98 in https://github.com/PennLINC/CuBIDS/pull/406
  • Variant renaming suggestions are ignoring tolerances by @mattcieslak in https://github.com/PennLINC/CuBIDS/pull/417
  • addniftiinfo ImageOrientation 'None' in tuple fix by @ashleychari in https://github.com/PennLINC/CuBIDS/pull/428
  • Pass schema along to workflows by @tsalo in https://github.com/PennLINC/CuBIDS/pull/430
  • Remove non-alphanumeric characters from variant values by @tsalo in https://github.com/PennLINC/CuBIDS/pull/443
  • Strip p0 from all values by @tsalo in https://github.com/PennLINC/CuBIDS/pull/447 ### Other Changes
  • Fix test data path by @tsalo in https://github.com/PennLINC/CuBIDS/pull/319
  • Add specification to use relative path for files listed in scans.txt used in cubids purge by @tientong98 in https://github.com/PennLINC/CuBIDS/pull/345
  • Add --force-unlock to copy-exemplars and fix path to script in apply by @gabridele in https://github.com/PennLINC/CuBIDS/pull/346
  • Delete notebooks from sidebar by @B-Sevchik in https://github.com/PennLINC/CuBIDS/pull/371
  • remove links.rst from docs + add hyperlink by @shivaram-k in https://github.com/PennLINC/CuBIDS/pull/373
  • Updated python versions in testing matrix by @gabridele in https://github.com/PennLINC/CuBIDS/pull/374
  • Switch from using pkg_resources to importlib.resources by @singlesp in https://github.com/PennLINC/CuBIDS/pull/369
  • Test CLI utils by @tsalo in https://github.com/PennLINC/CuBIDS/pull/349
  • Update usage.rst to change from key group to entity set by @tientong98 in https://github.com/PennLINC/CuBIDS/pull/381
  • Fill in docstrings for functions in config.py and tests/utils.py by @singlesp in https://github.com/PennLINC/CuBIDS/pull/377
  • Cleanup notebooks by @smeisler in https://github.com/PennLINC/CuBIDS/pull/366
  • Add module docstrings for about.py, init.py, constants.py, and utils.py by @singlesp in https://github.com/PennLINC/CuBIDS/pull/398
  • Add docstrings for cubids/cli.py by @singlesp in https://github.com/PennLINC/CuBIDS/pull/391
  • Update docstrings for files in cubids/tests by @shivaram-k in https://github.com/PennLINC/CuBIDS/pull/397
  • Avoid copying shell prompt $ when copying example commands from docs by @gabridele in https://github.com/PennLINC/CuBIDS/pull/402
  • Updated docs explaining the installation for internetless use cases by @gabridele in https://github.com/PennLINC/CuBIDS/pull/401
  • add/edit docstrings for metadata_merge.py and validator.py by @singlesp in https://github.com/PennLINC/CuBIDS/pull/408
  • Update installation instructions to use miniforge by @B-Sevchik in https://github.com/PennLINC/CuBIDS/pull/375
  • Add FAQ page by @tsalo in https://github.com/PennLINC/CuBIDS/pull/388
  • Make Tien the development lead and add code sprint participants to contributor list by @tsalo in https://github.com/PennLINC/CuBIDS/pull/361
  • Switch from conda to mamba in CircleCI tests by @tsalo in https://github.com/PennLINC/CuBIDS/pull/416
  • Add/edit cubids.py docstrings by @singlesp in https://github.com/PennLINC/CuBIDS/pull/411
  • Split out non-class methods into utils module by @tsalo in https://github.com/PennLINC/CuBIDS/pull/419
  • Clarify handling of non-BIDS entities in entity sets (e.g., fmap-epi) by @tsalo in https://github.com/PennLINC/CuBIDS/pull/435
  • Fix NaN Handling during Clustering by @tientong98 in https://github.com/PennLINC/CuBIDS/pull/439
  • Improve testing of command-line interfaces by @tsalo in https://github.com/PennLINC/CuBIDS/pull/431

New Contributors

  • @tientong98 made their first contribution in https://github.com/PennLINC/CuBIDS/pull/329
  • @gabridele made their first contribution in https://github.com/PennLINC/CuBIDS/pull/346
  • @B-Sevchik made their first contribution in https://github.com/PennLINC/CuBIDS/pull/371
  • @shivaram-k made their first contribution in https://github.com/PennLINC/CuBIDS/pull/373
  • @singlesp made their first contribution in https://github.com/PennLINC/CuBIDS/pull/369
  • @smeisler made their first contribution in https://github.com/PennLINC/CuBIDS/pull/366
  • @ashleychari made their first contribution in https://github.com/PennLINC/CuBIDS/pull/428

Full Changelog: https://github.com/PennLINC/CuBIDS/compare/1.1.0...1.2.0

- Python
Published by tsalo 12 months ago

cubids - 1.1.0

What's Changed

🎉 Exciting New Features

  • Make CLI commands available as cubids <command> by @tsalo in https://github.com/PennLINC/CuBIDS/pull/268
  • Add ASL fields to config by @tsalo in https://github.com/PennLINC/CuBIDS/pull/282 ### 🐛 Bug Fixes
  • Remove --ignore_subject_consistency param from cubids validate by @tsalo in https://github.com/PennLINC/CuBIDS/pull/276 ### Other Changes
  • Use black and isort to autoformat the main package by @tsalo in https://github.com/PennLINC/CuBIDS/pull/266
  • Reorganize packaging and hopefully fix tests by @tsalo in https://github.com/PennLINC/CuBIDS/pull/267
  • Move notebooks into example gallery by @tsalo in https://github.com/PennLINC/CuBIDS/pull/278
  • Drop jinja and wrapt from dependencies and pin other requirements by @tsalo in https://github.com/PennLINC/CuBIDS/pull/295
  • Run Pytests across all supported Python versions by @tsalo in https://github.com/PennLINC/CuBIDS/pull/279
  • Improve documentation by @tsalo in https://github.com/PennLINC/CuBIDS/pull/290
  • Prepare for 1.1.0 release by @tsalo in https://github.com/PennLINC/CuBIDS/pull/311

New Contributors

  • @tsalo made their first contribution in https://github.com/PennLINC/CuBIDS/pull/266
  • @dependabot made their first contribution in https://github.com/PennLINC/CuBIDS/pull/293

Full Changelog: https://github.com/PennLINC/CuBIDS/compare/1.0.2...1.1.0

- Python
Published by tsalo almost 2 years ago

cubids - Version 1.0.2

What's Changed

  • Add image orientation by @scovitz in https://github.com/PennLINC/CuBIDS/pull/205
  • review feedback milestone: adding code/CuBIDS option and converting CSVs to TSVs by @scovitz in https://github.com/PennLINC/CuBIDS/pull/217
  • Reviewer feedback incorporated into docs and pybids layout update by @scovitz in https://github.com/PennLINC/CuBIDS/pull/227
  • Data dictionaries by @scovitz in https://github.com/PennLINC/CuBIDS/pull/230
  • No index metadata by @scovitz in https://github.com/PennLINC/CuBIDS/pull/231
  • updated updatejson to no longer use pybids by @scovitz in https://github.com/PennLINC/CuBIDS/pull/232
  • Minor tune ups: codespell'ing (fixes + tox + CI (github actions)), remove of unintended to be committed 2 files by @yarikoptic in https://github.com/PennLINC/CuBIDS/pull/239
  • ENH: Make "NumVolumes" an integer for 3D images by @cookpa in https://github.com/PennLINC/CuBIDS/pull/211
  • adding note about fmap renamekeygroups by @megardn in https://github.com/PennLINC/CuBIDS/pull/140
  • Update usage.rst by @megardn in https://github.com/PennLINC/CuBIDS/pull/138
  • printing erroneous jsons and only rounding float parameters by @scovitz in https://github.com/PennLINC/CuBIDS/pull/257

New Contributors

  • @yarikoptic made their first contribution in https://github.com/PennLINC/CuBIDS/pull/239
  • @cookpa made their first contribution in https://github.com/PennLINC/CuBIDS/pull/211
  • @megardn made their first contribution in https://github.com/PennLINC/CuBIDS/pull/140

Full Changelog: https://github.com/PennLINC/CuBIDS/compare/v1.0.1...1.0.2

- Python
Published by mattcieslak over 2 years ago

cubids - CuBIDS Initial Release

Initial release of "Curation of BIDS on Disk" (CuBIDS).

- Python
Published by scovitz almost 5 years ago