Rename functions and variables to deprecate "bagel" and reflect non-imaging data

[alyssadai]

Input files to digest are now simply called digest files to minimize confusion with other files generated or used by Neurobagel or Nipoppy.

To help with code readability, we should rename instances of bagel to either digest, data, or something similar that is intuitive.

Also, now that digest accepts both phenotypic and imaging files as input, we should update the function and variable names to reflect this:

• utility.py:
  • extract_pipelines
  • get_pipelines_overview
    ...

[Ravish990]

Hi , I am Ravish . I am interested in maintaining it . Will you please assign it to me? I would love to fix it.