What's New

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

Version 0.3.0

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.

What's Changed

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

Version 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 #230

  • Convert --project-root to a positional argument by @tsalo in #235

  • Change --container-config-yaml-file to --container-config by @tsalo in #243

  • Change --type-system parameter to --queue by @tsalo in #234

  • Remove --job-account argument by @tsalo in #251

  • Change --type-session parameter to --processing-level by @tsalo in #233

Exciting New Features

  • Convert CLIs to subcommands by @tsalo in #210

  • Add a yml file for creating a mamba environment on an hpc by @mattcieslak in #217

  • Use jinja templates for creating scripts/yamls by @mattcieslak in #231

  • Add babs sync-code by @tientong98 in #236

  • Add section for adding singularity args by @mattcieslak in #250

Bug Fixes

  • [FIX] Output RIA path not found error by @tientong98 in #178

  • Replace pkg_resources with importlib.metadata by @tientong98 in #211

Other Changes

  • add backoff strategy for job polling by @asmacdo in #165

  • Introducing e2e slurm tests by @asmacdo in #169

  • [DOCS] Add examples of --list_sub_file/--list-sub-file by @tientong98 in #181

  • [DOCS] Add examples of --list_sub_file/--list-sub-file - Fixed rendering issues by @tientong98 in #183

  • update installation instructions with method to provide OSF credentials by @B-Sevchik in #186

  • Add participant selection flag to babs-init config yaml file by @tientong98 in #187

  • Support SLURM array jobs in babs-submit by @tientong98 in #188

  • Add a new docker build and fix CI tests by @mattcieslak in #189

  • Restyle with ruff by @mattcieslak in #190

  • Add back containerized slurm to the CI by @mattcieslak in #191

  • Fix shellcheck by @mattcieslak in #198

  • More e2e fixes by @mattcieslak in #201

  • Add default value for project_root by @smeisler in #194

  • containall, writable-tmpfs, absolute paths by @smeisler in #197

  • Adding --participant-label as the default subject selection flag if $SUBJECT_SELECTION_FLAG wasn't specified in YAML by @tientong98 in #202

  • Do shellcheck all the shell scripts by @yarikoptic in #203

  • Fix RTD build by @mattcieslak in #216

  • Fix style issues in documentation by @tsalo in #214

  • Make temporary directory in babs-submit by @smeisler in #207

  • change how subject ID and session ID are parsed from the jobs CSV by @mattcieslak in #227

  • Add ${TEMPLATEFLOW_HOME} in singularity run cmd by @tientong98 in #225

  • Add user and developer argument groups to babs merge arg parser by @singlesp in #239

  • Update example config yamls by @singlesp in #232

  • Add customized text to aslprep yaml by @singlesp in #246

  • don't shellcheck jinja templates by @mattcieslak in #245

  • Pass CI tests with jinja templates by @mattcieslak in #249

  • Add CITATION.cff and update citations in README by @tsalo in #252

  • Remove commented-out code by @tsalo in #253

  • Make a separate system module by @singlesp in #256

  • Move InputDatasets class into dataset module by @tsalo in #258

  • Move Container and InputDatasets into new files by @mattcieslak in #259

  • Remove unused functions and variables flagged by vulture by @tsalo in #260

  • RF: Add easily-testable script creation by @mattcieslak in #262

  • Add tests for function in utils module by @tsalo in #261

New Contributors

  • @tientong98 made their first contribution in #178

  • @B-Sevchik made their first contribution in #186

  • @smeisler made their first contribution in #194

  • @singlesp made their first contribution in #239

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

Version 0.1.0

What's Changed

Exciting New Features

  • Convert CLIs to subcommands by @tsalo in #210

  • Add a yml file for creating a mamba environment on an hpc by @mattcieslak in #217

Bug Fixes

  • [FIX] Output RIA path not found error by @tientong98 in #178

  • Replace pkg_resources with importlib.metadata by @tientong98 in #211

Other Changes

  • add backoff strategy for job polling by @asmacdo in #165

  • Introducing e2e slurm tests by @asmacdo in #169

  • [DOCS] Add examples of --list_sub_file/--list-sub-file by @tientong98 in #181

  • [DOCS] Add examples of --list_sub_file/--list-sub-file - Fixed rendering issues by @tientong98 in #183

  • update installation instructions with method to provide OSF credentials by @B-Sevchik in #186

  • Add participant selection flag to babs-init config yaml file by @tientong98 in #187

  • Support SLURM array jobs in babs-submit by @tientong98 in #188

  • Add a new docker build and fix CI tests by @mattcieslak in #189

  • Restyle with ruff by @mattcieslak in #190

  • Add back containerized slurm to the CI by @mattcieslak in #191

  • Fix shellcheck by @mattcieslak in #198

  • More e2e fixes by @mattcieslak in #201

  • Add default value for project_root by @smeisler in #194

  • containall, writable-tmpfs, absolute paths by @smeisler in #197

  • Adding --participant-label as the default subject selection flag if $SUBJECT_SELECTION_FLAG wasn't specified in YAML by @tientong98 in #202

  • Do shellcheck all the shell scripts by @yarikoptic in #203

  • Fix RTD build by @mattcieslak in #216

  • Fix style issues in documentation by @tsalo in #214

  • Make temporary directory in babs-submit by @smeisler in #207

  • change how subject ID and session ID are parsed from the jobs CSV by @mattcieslak in #227

  • Add ${TEMPLATEFLOW_HOME} in singularity run cmd by @tientong98 in #225

New Contributors

  • @tientong98 made their first contribution in #178

  • @B-Sevchik made their first contribution in #186

  • @mattcieslak made their first contribution in #189

  • @smeisler made their first contribution in #194

Full Changelog: https://github.com/PennLINC/babs/compare/0.0.8...0.1.0