Adding model with cycle consistency and VampPrior

[Hrovatin]

Closes #2383

[codecov]

Codecov Report

Attention: Patch coverage is 88.26667% with 44 lines in your changes missing coverage. Please review.

Project coverage is 84.62%. Comparing base (c53efe0) to head (6a2e3eb).
Report is 10 commits behind head on main.

Files with missing lines	Patch %	Lines
src/scvi/external/sysvi/_base_components.py	72.64%	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%   84.62%   -0.20%     
==========================================
  Files         173      183      +10     
  Lines       14793    15436     +643     
==========================================
+ Hits        12547    13063     +516     
- Misses       2246     2373     +127     

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	72.64% <72.64%> (ø)

... and 14 files with indirect coverage changes

---- 🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[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]

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.

[canergen]

Do you still need nan_to_num if you use here a softplus activation? You should consider changing it. It's just for backward compatibility still exp in scvi.

[canergen]

Does it need it's own get_latent_representation or can it inherit from VAEMIXIN class?

[canergen]

First look, looks good. Two comments. Should we wait for FClayers to be compatible and then use FClayers? Or do you think it will anyhow not work?

[Hrovatin]

The FCLayers I use now are the a base for the suggestion that you are working of so it should work with minor modifications in how API is accessed in SysVI. If that is planned to be finished soon then lets wait, but otherwise I suggest merging so that we finally get it in main and then switching afterwards

Also @canergen can you please help with tests. I can not check code on GPU locally (don't have any) and the CI tests fail - I think not due to my side as I can make the below import

ImportError while importing test module '/__w/scvi-tools/scvi-tools/tests/external/sysvi/test_sysvi.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/external/sysvi/test_sysvi.py:10: in <module>
    from scvi.external import SysVI
E   ImportError: cannot import name 'SysVI' from 'scvi.external' (/usr/local/lib/python3.12/site-packages/scvi/external/__init__.py)```