Integrate TCRdist3 about scirpy HOT 5 CLOSED

@felixpetschko, since francesca mentioned you have been playing around with metrics as well, maybe this is something you would find interesting. The TCRdist metric is more relevant than levenshtein distance in practice. It's somewhat comparable to the alignment distance that Tobias has been working on, but might be even faster because it simplifies the alignment problem.

First step would be to get the code from nb_metrics.py to work inside scirpy. As a next step it would be interesting if this works on GPU using numba's GPU features (or any other framework - as you like).

I'll provide feedback on the clonotype clustering later -- which is also still the priority right now. If we can't speed that up, speeding up the distance metrics is in vain.

from scirpy.

Hi @grst Is anyone working on implementing this at the moment. If not, I would be interested in having a crack at it.

from scirpy.

I think @felixpetschko has this on his list -- Felix, is that still the plan?

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@grst @ShihanL Yes, I am working on this :)

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Closed in #502.

This is in the main branch and will be part of the next release.
@ShihanL, if you want to give it a try already, you can install the development version using

pip install git+https://github.com/scverse/scirpy.git@main

from scirpy.