Fully integrate metrics module

andim / pyrepseq

Python library for immune repertoire analysis

MIT License

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Fully integrate metrics module #22

Closed yutanagano closed 8 months ago

yutanagano commented 8 months ago

The integration has been done, but as mentioned in #16 the code to which it should now be integrated is shaky as there does not seem to be tests. I am submitting a pull request as I think I have done everything on my end.

yutanagano commented 8 months ago

@andim integration seems more or less fully complete:

the module-wide pdist and cdist have been put back but with a deprecationwarning
the pcDelta and related functions have been refactored to fully integrate with the metric system
I discovered that actually pc and pcDelta are indeed minimally tested in test_coincidence.py. Apologies...
- But pcDelta on tuples/DataFrames and with maxseqs set is not tested

andim commented 8 months ago

Thanks Yuta!