Adding model with cycle consistency and VampPrior

[Hrovatin]

Closes #2383

[codecov]

Codecov Report

Attention: Patch coverage is 90.25735% with 53 lines in your changes are missing coverage. Please review.

Project coverage is 89.40%. Comparing base (6062656) to head (8c25dba).
Report is 1 commits behind head on main.

❗ Current head 8c25dba differs from pull request most recent head 54f5734. Consider uploading reports for the commit 54f5734 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2421      +/-   ##
==========================================
- Coverage   89.90%   89.40%   -0.50%     
==========================================
  Files         154      161       +7     
  Lines       12629    13172     +543     
==========================================
+ Hits        11354    11777     +423     
- Misses       1275     1395     +120     

Files	Coverage Δ
scvi/external/__init__.py	100.00% <100.00%> (ø)
scvi/external/sysvi/__init__.py	100.00% <100.00%> (ø)
scvi/external/sysvi/_module.py	97.67% <97.67%> (ø)
scvi/external/sysvi/_priors.py	93.18% <93.18%> (ø)
scvi/external/sysvi/_utils.py	93.75% <93.75%> (ø)
scvi/external/sysvi/_trainingplans.py	91.39% <91.39%> (ø)
scvi/external/sysvi/_model.py	92.68% <92.68%> (ø)
scvi/external/sysvi/_base_components.py	73.52% <73.52%> (ø)

... and 4 files with indirect coverage changes

[martinkim0]

Hey, thanks for putting in this PR! A couple of high-level comments for now.

Could you restructure the files as follows?

• csi/model/_model.py -> csi/_model.py
• csi/model/_utils.py -> csi/_utils.py
• csi/module/_module.py -> csi/_module.py
• csi/module/_priors.py -> csi/_priors.py
• csi/nn/_base_components.py -> csi/_components.py
• csi/train/_trainingplans.py -> csi/_trainingplans.py
• Refactor csi/module/_module.py to use scvi.module.base.LossOutput instead of our previous LossRecorder and remove csi/module/_loss_recoder.py
• If the plan is to directly inherit from UnsupervisedTrainingMixin without any major changes except setting _training_plan_cls, this can be done within _model.py by directly subclassing UnsupervisedTrainingMixin and setting _training_plan_cls there instead, so I would recommend doing that and deleting csi/model/_training.py

I can take a look at compatibility with scArches in the next round.

We're also slowly migrating to newer typing annotations in Python. Could you add a from __future__ import annotations to the top of every file (except __init__.pys) and migrate typing from:

• Optional[x] -> x | None
• Union[x, y] -> x | y
• List[x] -> list[x]
• Tuple[x] -> tuple[x]
• Callable -> callable
• There's more, I don't remember all of them. The pre-commit hooks will warn about missing ones.

[Hrovatin]

I added changes and adapted tutorial accrordingly

[martinkim0]

Thanks for addressing the comments! I'll take another pass at it soon.

[martinkim0]

Some minor typing/style comments as well as implementation ones. I still don't understand all parts of the implementation so I will take another pass at this

[Hrovatin]

@martinkim0 thank you for looking at it again - I added the changes as requested

[martinkim0]

Sorry for the delay in reviewing this - hopefully taking a last pass this week and we get this merged!