Refactor commands.py

[ibevers]

Ensures that only CLI specific code is in commands.py and all general-purpose code is in reusable modules.

[satra]

@ibevers - can you describe what this is for? also does pre-commit not handle some of the stylistic components for this?

[ibevers]

@ibevers - can you describe what this is for? also does pre-commit not handle some of the stylistic components for this?

There is general purpose logic in commands.py that should be refactored into reusable modules. I feel that commands.py should have only code that is specific to the CLI interface, and everything else should be imported from general-purpose modules.

b2aiprep/src/b2aiprep/commands.py

Line 333 in 4ca121b

def create_derived_dataset(bids_path, outdir):