Adding model with cycle consistency and VampPrior

[Hrovatin]

Closes #2383

[codecov]

Codecov Report

Attention: Patch coverage is 88.20375% with 44 lines in your changes missing coverage. Please review.

Project coverage is 84.40%. Comparing base (c53efe0) to head (df4b335).
Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
src/scvi/external/sysvi/_base_components.py	72.17%	32 Missing ⚠️
src/scvi/external/sysvi/_model.py	90.90%	7 Missing ⚠️
src/scvi/external/sysvi/_module.py	97.01%	4 Missing ⚠️
src/scvi/external/sysvi/_priors.py	97.67%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2421      +/-   ##
==========================================
- Coverage   84.81%   84.40%   -0.42%     
==========================================
  Files         173      178       +5     
  Lines       14793    15168     +375     
==========================================
+ Hits        12547    12802     +255     
- Misses       2246     2366     +120     

Files with missing lines	Coverage Δ
src/scvi/external/__init__.py	100.00% <100.00%> (ø)
src/scvi/external/sysvi/__init__.py	100.00% <100.00%> (ø)
src/scvi/external/sysvi/_priors.py	97.67% <97.67%> (ø)
src/scvi/external/sysvi/_module.py	97.01% <97.01%> (ø)
src/scvi/external/sysvi/_model.py	90.90% <90.90%> (ø)
src/scvi/external/sysvi/_base_components.py	72.17% <72.17%> (ø)

... and 5 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]

@canergen Sorry, I am no longer active there and overlooked that you responded. I sent you my personal email over zolip to arrange a meeting.

[ori-kron-wis]

@Hrovatin there are some fixes that need to be done regarding the pre-commit ruff rules (everything that involves linting the code, formatting it etc'..) to be compatible with the rest of our repo and package.
So those errors can be found under Details in the pre-commits.co-pr test below.
Once this is fixed we can continue.
LMK if you need help.

[Hrovatin]

The changes I pushed today are not yet ready for review. Missing docs, cleanup, and test on real data.

[Hrovatin]

@canergen @ori-kron-wis The PR is now ready for review.

@ori-kron-wis Can you help me fix the cuda test err? For some reason, it can not import SysVI, although for me, it works locally. I also was not able to test on GPU since I only have MacOS access and I get the err where mps is detected but not used. - If you have any solutions for that also please let me know.