What's New

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