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@mattcieslak mattcieslak released this 26 Mar 16:04
· 74 commits to main since this release
0.2.0
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Learn about vigilant mode.

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

🐛 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
  • RF: generate participant_job.sh in an easy-to-test way by @mattcieslak in #263
  • add What's new page, prepare for 0.2.0 release by @mattcieslak in #264

New Contributors

Full Changelog: 0.0.8...0.2.0

Contributors

yarikoptic, mattcieslak, and 6 other contributors
Assets 2
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