Snakebids App Extras

[pvandyken]

There's a couple ideas floating around that are somewhat challenging to incorporate into the snakemake core. These include logging (#184), bids validation (#222), dataset_description.json manipulation (#154), and possibly others, plus a few utility functions I've thought of but haven't raised yet.

I'd like to propose that, for these types of problems, we conceive of a sort of snakebids extra (or some more catchy name) that is not directly handled by SnakebidsApp but is intended to be manually invoked by the developer within the run.py. The implementation of these "extras" would be extremely flexible (functions, classes, etc), although some may benefit from "plugging" into SnakebidsApp. These extras could be packaged in with snakebids or distributed as 3rd party libaries. The main defining feature is that they are used within run.py (so calling snakemake directly would skip the extras).

Obviously this is not really an "actionable" idea leading to a specific new feature. I more wanted to create a conceptual category we can start sorting feature ideas into. It might even be worth creating some Issue tags to this end.

[pvandyken]

I've thought about this some more: one thing extra modules may need ready access to is the key arguments parsed from the CLI (input/ouput dir, participant_label, derivatives, etc). SnakeBidsApp doesn't make this readily available right now (arg parsing only happens after run_snakemake() is called). We should be able to make this information accessible by moving a lot more of the logic into the class initialization. I'll raise an issue on this when I get a chance.