cohenlabUNC/clpipe: clpipe 1.9.0

1.9.1 (Dec 7, 2023)

Enhancements

• convert2bids - This command will now detect whether dcm2bids or heudiconv is being used based on the extension type of the conversion config file. dcm2bids is used when a .json file is given, and heudiconv is used when .py. The -heudiconv
• clpipe - When creating a new project, a .clpipe folder is now created which houses a batch_config.json file. This allows users to easily update batch config defaults without having to create their own batch_config.json file. This file is referenced from the users standard clpipe_config.json file. The .clpipe folder will be used in the future to store any additional files that apply to an entire project.
• clpipe - Stack trace is now hidden again when -debug is not being used, like in older versions of clpipe (< v1.6)
• postprocess - Indexing / query time slightly improved through use of pattern-based indexing exceptions

Bug Fixes

• postprocess - Image scrubbing node now properly persists header information
• bids_validate - Fixed issue where SLURM logs did not save to log folder after 1.9
• preprocess - Fixed issue where SLURM logs did not save to log folder after 1.9

Development

• job_manager - Introduced JobManagerFactory for streamlined job manager selection and instantiation to replace the old BatchManager with BatchJobManager`` and LocalJobManager``, enhancing job submission flexibility and configuration options.
• job_manager - Upgraded job submission mechanism from os.system to subprocess.run for better process handling and output capture, especially when jobs are run locally.