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theislab / scib

Benchmarking analysis of data integration tools
MIT License
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Function documentation #278

Closed lazappi closed 2 years ago

lazappi commented 2 years ago

It's awesome that the package is now available from PyPI but there's not a lot of documentation on how to use it. One basic thing would be to have full function docstrings with description of arguments. This is missing from a lot of places at the moment and where it does exist it's sometimes out of date, for example:

https://github.com/theislab/scib/blob/985d8155391fdfbddec024de428308b5a57ee280/scib/metrics/lisi.py#L25-L42

LuckyMD commented 2 years ago

I think the docstrings are there for all metrics functions that are actually being used. the lisi function is legacy code. @mumichae recently did a large overhaul that added a lot of this documentation. Any comment @mumichae ?

lazappi commented 2 years ago

I first place I noticed was actually in the functions for running all the metrics. I wasn't sure what all the arguments were and how the AnnData objects should be structured. I think in general there are some assumed places that various information needs to be stored but I couldn't see that documented anywhere.

LuckyMD commented 2 years ago

Thanks for bringing that up. We didn't look at the joint metrics functions in as much detail. But yes, that should be added.

mumichae commented 2 years ago

I agree, docstrings are far from complete. I included some more comprehensive function documentations #279