feat(external): add velovi to external

[martinkim0]

closes feature request #2610

[adamgayoso]

cc @WeilerP

[codecov]

Codecov Report

Attention: Patch coverage is 76.36632% with 160 lines in your changes are missing coverage. Please review.

Project coverage is 88.71%. Comparing base (6062656) to head (9b11417).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2611      +/-   ##
==========================================
- Coverage   89.90%   88.71%   -1.20%     
==========================================
  Files         154      159       +5     
  Lines       12629    13306     +677     
==========================================
+ Hits        11354    11804     +450     
- Misses       1275     1502     +227     

Files	Coverage Δ
scvi/external/__init__.py	100.00% <100.00%> (ø)
scvi/external/velovi/__init__.py	100.00% <100.00%> (ø)
scvi/external/velovi/_constants.py	100.00% <100.00%> (ø)
scvi/external/velovi/_utils.py	27.58% <27.58%> (ø)
scvi/external/velovi/_module.py	82.40% <82.40%> (ø)
scvi/external/velovi/_model.py	76.06% <76.06%> (ø)

... and 2 files with indirect coverage changes

[WeilerP]

@martinkim0, the idea was to have velovi as part of the scvelo package. Either way is fine for me, we should just only have one option, IMO. What do you think, @adamgayoso?

[adamgayoso]

So I'm mostly indifferent, I had forgotten about this. But a few thoughts:

1. I think it will be easier to maintain if it's in scvi-tools because then it's easier to integrate any API changes (so that @martinkim0 doesn't have to make PRs into scvelo).
2. In that scenario, scvelo would export the model here, special utilities could be removed from here and kept only in scvelo, and the docs here can point to the scvelo docs for complete usage.

But really I think either is fine. @martinkim0 perhaps you should revert this as we make a decision.

[WeilerP]

I think that's totally reasonable and the better option! Let's keep it here and I'll remove it from scvelo.

[martinkim0]

Great! So I'm going to keep this commit then but remove the utility functions (get_permutation_scores and preprocess_data) and open a PR to add them to scvelo. Does that sound good?

[WeilerP]

Great! So I'm going to keep this commit then but remove the utility functions (get_permutation_scores and preprocess_data) and open a PR to add them to scvelo. Does that sound good?

Sounds good to me! Let's discuss everything else in the corresponding PR. Thanks in advance!