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Recent Releases of babs

babs - 0.5.2

What's Changed

Other Changes

  • Fix babs sync-code by @smeisler in https://github.com/PennLINC/babs/pull/299
  • Fix jinja space rendering issue for participant_job.sh by @tientong98 in https://github.com/PennLINC/babs/pull/301

Full Changelog: https://github.com/PennLINC/babs/compare/0.5.1...0.5.2

- Python
Published by tientong98 about 1 year ago

babs - 0.5.1

What's Changed

Other Changes

  • Fix sync-code by @smeisler in https://github.com/PennLINC/babs/pull/297

Full Changelog: https://github.com/PennLINC/babs/compare/0.5.0...0.5.1

- Python
Published by mattcieslak about 1 year ago

babs - 0.5.0

This version got test coverage over 80% and adds the update-input-data action. It adds back the sync-code function too.

What's Changed

Other Changes

  • Add more CI tests by @mattcieslak in https://github.com/PennLINC/babs/pull/292
  • add back sync-code by @mattcieslak in https://github.com/PennLINC/babs/pull/293
  • add babs update-input-data by @mattcieslak in https://github.com/PennLINC/babs/pull/294
  • remove --datasets from docs by @mattcieslak in https://github.com/PennLINC/babs/pull/296

Full Changelog: https://github.com/PennLINC/babs/compare/0.4.0...0.5.0

- Python
Published by mattcieslak about 1 year ago

babs - 0.4.0

Version 0.4.0

Arguments and default behavior for babs submit and babs status have changed. The specification of input datasets all happens in the config yaml file now (the --datasets option is removed). See the walkthrough example for an up-to-date example of BABS in action.

What's Changed

🛠 Breaking Changes

  • Fix walkthrough test by @mattcieslak in https://github.com/PennLINC/babs/pull/286 ### 🎉 Exciting New Features
  • Add codecov again by @mattcieslak in https://github.com/PennLINC/babs/pull/289 ### 🐛 Bug Fixes
  • update e2e to use new CLIs by @mattcieslak in https://github.com/PennLINC/babs/pull/288 ### Other Changes
  • Make InputDataset handle individual input dataset checking/querying by @mattcieslak in https://github.com/PennLINC/babs/pull/277
  • Refactor babs init to use the InputDataset class by @mattcieslak in https://github.com/PennLINC/babs/pull/284
  • RF the slurm-interacting code by @mattcieslak in https://github.com/PennLINC/babs/pull/287
  • Test BABS on upenn cluster + update docs with simbids examples by @mattcieslak in https://github.com/PennLINC/babs/pull/290
  • Subclass BABS for different interactions by @mattcieslak in https://github.com/PennLINC/babs/pull/291

Full Changelog: https://github.com/PennLINC/babs/compare/0.3.0...0.4.0

- Python
Published by mattcieslak about 1 year ago

babs - 0.3.2

What's Changed

🐛 Bug Fixes

  • Fix distribution on PyPi by @tsalo in https://github.com/PennLINC/babs/pull/270
  • Fix babs submit --job by @singlesp in https://github.com/PennLINC/babs/pull/279 ### Other Changes
  • Pythonicize the variable names and loop structure by @mattcieslak in https://github.com/PennLINC/babs/pull/269
  • Add taskid to git branches by @singlesp in https://github.com/PennLINC/babs/pull/275

Full Changelog: https://github.com/PennLINC/babs/compare/0.3.0...0.3.2

- Python
Published by singlesp about 1 year ago

babs - 0.3.1rc1

What's Changed

🐛 Bug Fixes

  • Fix distribution on PyPi by @tsalo in https://github.com/PennLINC/babs/pull/270

Full Changelog: https://github.com/PennLINC/babs/compare/0.3.0...0.3.1rc1

- Python
Published by tsalo about 1 year ago

babs - 0.3.0

What's Changed

Critical bugfix for 0.2.0 and adds the ability to add small files to the BABS project so they can be tracked by git and accessed during the BIDS app run.

Other Changes

  • Fix SLURM JOB_ID bug by @mattcieslak in https://github.com/PennLINC/babs/pull/267
  • Add imported_files section to config files by @mattcieslak in https://github.com/PennLINC/babs/pull/266
  • Update docs to reflect changes in 0.3 by @mattcieslak in https://github.com/PennLINC/babs/pull/268

Full Changelog: https://github.com/PennLINC/babs/compare/0.2.0...0.3.0

- Python
Published by mattcieslak about 1 year ago

babs - 0.2.0

What's Changed

This release is the result of a major refactor of the codebase. The most important changes are that babs is a standalone command and the babs-* commands are now subcommands of babs. Please switch and scripts that use babs-<command> to use babs <command> instead. There are also a number of arguments that have been renamed and/or removed. Please refer to the --help output for the latest information.

The config yaml format has also changed. See examples of valid configurations in the notebooks directory.

🛠 Breaking Changes

  • Change babs init parameter --input to --datasets by @tsalo in https://github.com/PennLINC/babs/pull/230
  • Convert --project-root to a positional argument by @tsalo in https://github.com/PennLINC/babs/pull/235
  • Change --container-config-yaml-file to --container-config by @tsalo in https://github.com/PennLINC/babs/pull/243
  • Change --type-system parameter to --queue by @tsalo in https://github.com/PennLINC/babs/pull/234
  • Remove --job-account argument by @tsalo in https://github.com/PennLINC/babs/pull/251
  • Change --type-session parameter to --processing-level by @tsalo in https://github.com/PennLINC/babs/pull/233 ### 🎉 Exciting New Features
  • Convert CLIs to subcommands by @tsalo in https://github.com/PennLINC/babs/pull/210
  • Add a yml file for creating a mamba environment on an hpc by @mattcieslak in https://github.com/PennLINC/babs/pull/217
  • Use jinja templates for creating scripts/yamls by @mattcieslak in https://github.com/PennLINC/babs/pull/231
  • Add babs sync-code by @tientong98 in https://github.com/PennLINC/babs/pull/236
  • Add section for adding singularity args by @mattcieslak in https://github.com/PennLINC/babs/pull/250 ### 🐛 Bug Fixes
  • [FIX] Output RIA path not found error by @tientong98 in https://github.com/PennLINC/babs/pull/178
  • Replace pkg_resources with importlib.metadata by @tientong98 in https://github.com/PennLINC/babs/pull/211 ### Other Changes
  • add backoff strategy for job polling by @asmacdo in https://github.com/PennLINC/babs/pull/165
  • Introducing e2e slurm tests by @asmacdo in https://github.com/PennLINC/babs/pull/169
  • [DOCS] Add examples of --listsubfile/--list-sub-file by @tientong98 in https://github.com/PennLINC/babs/pull/181
  • [DOCS] Add examples of --listsubfile/--list-sub-file - Fixed rendering issues by @tientong98 in https://github.com/PennLINC/babs/pull/183
  • update installation instructions with method to provide OSF credentials by @B-Sevchik in https://github.com/PennLINC/babs/pull/186
  • Add participant selection flag to babs-init config yaml file by @tientong98 in https://github.com/PennLINC/babs/pull/187
  • Support SLURM array jobs in babs-submit by @tientong98 in https://github.com/PennLINC/babs/pull/188
  • Add a new docker build and fix CI tests by @mattcieslak in https://github.com/PennLINC/babs/pull/189
  • Restyle with ruff by @mattcieslak in https://github.com/PennLINC/babs/pull/190
  • Add back containerized slurm to the CI by @mattcieslak in https://github.com/PennLINC/babs/pull/191
  • Fix shellcheck by @mattcieslak in https://github.com/PennLINC/babs/pull/198
  • More e2e fixes by @mattcieslak in https://github.com/PennLINC/babs/pull/201
  • Add default value for project_root by @smeisler in https://github.com/PennLINC/babs/pull/194
  • containall, writable-tmpfs, absolute paths by @smeisler in https://github.com/PennLINC/babs/pull/197
  • Adding --participant-label as the default subject selection flag if $SUBJECTSELECTIONFLAG wasn't specified in YAML by @tientong98 in https://github.com/PennLINC/babs/pull/202
  • Do shellcheck all the shell scripts by @yarikoptic in https://github.com/PennLINC/babs/pull/203
  • Fix RTD build by @mattcieslak in https://github.com/PennLINC/babs/pull/216
  • Fix style issues in documentation by @tsalo in https://github.com/PennLINC/babs/pull/214
  • Make temporary directory in babs-submit by @smeisler in https://github.com/PennLINC/babs/pull/207
  • change how subject ID and session ID are parsed from the jobs CSV by @mattcieslak in https://github.com/PennLINC/babs/pull/227
  • Add ${TEMPLATEFLOW_HOME} in singularity run cmd by @tientong98 in https://github.com/PennLINC/babs/pull/225
  • Add user and developer argument groups to babs merge arg parser by @singlesp in https://github.com/PennLINC/babs/pull/239
  • Update example config yamls by @singlesp in https://github.com/PennLINC/babs/pull/232
  • Add customized text to aslprep yaml by @singlesp in https://github.com/PennLINC/babs/pull/246
  • don't shellcheck jinja templates by @mattcieslak in https://github.com/PennLINC/babs/pull/245
  • Pass CI tests with jinja templates by @mattcieslak in https://github.com/PennLINC/babs/pull/249
  • Add CITATION.cff and update citations in README by @tsalo in https://github.com/PennLINC/babs/pull/252
  • Remove commented-out code by @tsalo in https://github.com/PennLINC/babs/pull/253
  • Make a separate system module by @singlesp in https://github.com/PennLINC/babs/pull/256
  • Move InputDatasets class into dataset module by @tsalo in https://github.com/PennLINC/babs/pull/258
  • Move Container and InputDatasets into new files by @mattcieslak in https://github.com/PennLINC/babs/pull/259
  • Remove unused functions and variables flagged by vulture by @tsalo in https://github.com/PennLINC/babs/pull/260
  • RF: Add easily-testable script creation by @mattcieslak in https://github.com/PennLINC/babs/pull/262
  • Add tests for function in utils module by @tsalo in https://github.com/PennLINC/babs/pull/261
  • RF: generate participant_job.sh in an easy-to-test way by @mattcieslak in https://github.com/PennLINC/babs/pull/263
  • add What's new page, prepare for 0.2.0 release by @mattcieslak in https://github.com/PennLINC/babs/pull/264

New Contributors

  • @tientong98 made their first contribution in https://github.com/PennLINC/babs/pull/178
  • @B-Sevchik made their first contribution in https://github.com/PennLINC/babs/pull/186
  • @mattcieslak made their first contribution in https://github.com/PennLINC/babs/pull/189
  • @smeisler made their first contribution in https://github.com/PennLINC/babs/pull/194
  • @singlesp made their first contribution in https://github.com/PennLINC/babs/pull/239

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.8...0.2.0

- Python
Published by mattcieslak about 1 year ago

babs - 0.0.8

What's Changed

:blue_book: Enhancements in Documentation

  • [DOCS] Example walkthrough: Step 0 does not affect the end result by @asmacdo in https://github.com/PennLINC/babs/pull/159
  • [DOCS] minor changes in eg walkthrough: explain when Step 0 is optional by @zhao-cy in https://github.com/PennLINC/babs/pull/164
  • [DOCS] update contact email and add BABS paper by @zhao-cy in https://github.com/PennLINC/babs/pull/162

New Contributors

  • @asmacdo made their first contribution in https://github.com/PennLINC/babs/pull/159

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.7...0.0.8

- Python
Published by zhao-cy over 2 years ago

babs - 0.0.7

What's Changed

🐛 Bug Fixes

  • [FIX] Fix validator for unzipped input datasets: considering folders not in patterns of sub-* by @zhao-cy in https://github.com/PennLINC/babs/pull/143 ### :blue_book: Enhancements in Documentation
  • [DOCS] update docs during paper revision by @zhao-cy in https://github.com/PennLINC/babs/pull/146
  • [DOCS] achieve checks in NMIND docs domain at silver level by @zhao-cy in https://github.com/PennLINC/babs/pull/148 ### Other changes
  • Add issue templates by @tsalo in https://github.com/PennLINC/babs/pull/130

New Contributors

  • @tsalo made their first contribution in https://github.com/PennLINC/babs/pull/130

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.6...0.0.7

- Python
Published by zhao-cy over 2 years ago

babs - 0.0.6

What's Changed

🐛 Bug Fixes

  • [FIX] add a function for deciding the command for job cancellation based on cluster system by @zhao-cy in https://github.com/PennLINC/babs/pull/134 ### :blue_book: Enhancements in Documentation
  • [DOCS] add DOI link to zenodo archive by @zhao-cy in https://github.com/PennLINC/babs/pull/125
  • [DOCS] minor changes in example walkthrough and docs for jobs by @zhao-cy in https://github.com/PennLINC/babs/pull/131
  • [DOCS] add guide on how to test BABS by @zhao-cy in https://github.com/PennLINC/babs/pull/129
  • [DOCS] clean example YAML files by @zhao-cy in https://github.com/PennLINC/babs/pull/132
  • [DOCS] minor fix in docs by @zhao-cy in https://github.com/PennLINC/babs/pull/135

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.5...0.0.6

- Python
Published by zhao-cy almost 3 years ago

babs - 0.0.5

What's Changed

🎉 Exciting New Features

  • [ENH] refactoring of babs_submit function and updator of job status table by @djarecka in https://github.com/PennLINC/babs/pull/99
  • [DOCS/ENH] Documentation enhancement and review by @zhao-cy in https://github.com/PennLINC/babs/pull/103
    • This also includes enhancements in CLI and printed messages of BABS functions.
  • [ENH] Add an option of creating a wrapper output folder of all derivatives by @zhao-cy in https://github.com/PennLINC/babs/pull/116
    • Now, BABS is compatible with latest version of fMRIPrep. ### :blue_book: Enhancements in Documentation
  • [DOCS] prepare example walkthrough by @zhao-cy in https://github.com/PennLINC/babs/pull/81
  • [DOCS] add instructions on how to add partitions for slurm in example walkthrough by @zhao-cy in https://github.com/PennLINC/babs/pull/108
  • [DOCS] Revisions in docs after testing on MIT slurm cluster by @djarecka in https://github.com/PennLINC/babs/pull/109
  • [DOCS] Update walkthrough.rst by @yibeichan in https://github.com/PennLINC/babs/pull/119
  • [DOCS] add guides in eg walkthrough: if there is no internet on compute nodes by @zhao-cy in https://github.com/PennLINC/babs/pull/121

New Contributors

  • @yibeichan made their first contribution in https://github.com/PennLINC/babs/pull/119

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.4...0.0.5

- Python
Published by zhao-cy almost 3 years ago

babs - 0.0.4

We're excited to release the first version of BABS that works on Slurm clusters! 🎉

What's Changed

🎉 Exciting New Features

  • [ENH] adding slurm as a system type by @djarecka in https://github.com/PennLINC/babs/pull/92
  • [ENH] test out BABS's Slurm version by @zhao-cy in https://github.com/PennLINC/babs/pull/96
  • [FIX/ENH] Fix directives and job accounting; enhance example container config YAML filenames by @zhao-cy in https://github.com/PennLINC/babs/pull/98
    • The docs about Slurm directives are also added in this PR

New Contributors

  • @djarecka made their first contribution in https://github.com/PennLINC/babs/pull/92

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.3...0.0.4

- Python
Published by zhao-cy about 3 years ago

babs - 0.0.3

What's Changed

🛠 Breaking Changes

  • [ENH] singularity run: handle FreeSurfer license and Templateflow home by @zhao-cy in https://github.com/PennLINC/babs/pull/83
  • [ENH] Improve section names in container config YAML file by @zhao-cy in https://github.com/PennLINC/babs/pull/88 ### :blue_book: Documentation and examples updates
  • [ENH] update toy BIDS App version used for CircleCI testing by @zhao-cy in https://github.com/PennLINC/babs/pull/90

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.2...0.0.3

- Python
Published by zhao-cy about 3 years ago

babs - 0.0.2: First release of BABS: for SGE clusters

We are excited to announce the first release of BABS! :tada:

It currently works on SGE clusters. This includes functions of babs-init, babs-check-setup, babs-submit, babs-status, and babs-merge. For how to use these functions, please refer to BABS's readthedocs.

BABS is also available on PyPI now. You can install it by running the command below:

pip install babs

- Python
Published by zhao-cy about 3 years ago