Fix observed variable detection

[vitkl]

Create a separate method to detect observed sites and apply it everywhere necessary to automatically exclude observed sites.

Fixes #1801

[codecov[bot]]

Codecov Report

Base: 90.65% // Head: 90.43% // Decreases project coverage by -0.22% :warning:

Coverage data is based on head (df52036) compared to base (3b687c0). Patch coverage: 100.00% of modified lines in pull request are covered.

:exclamation: Current head df52036 differs from pull request most recent head a81cd39. Consider uploading reports for the commit a81cd39 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1805      +/-   ##
==========================================
- Coverage   90.65%   90.43%   -0.23%     
==========================================
  Files         138      123      -15     
  Lines       10918    10283     -635     
==========================================
- Hits         9898     9299     -599     
+ Misses       1020      984      -36     

Impacted Files	Coverage Δ
scvi/model/base/_pyromixin.py	94.44% <100.00%> (-0.91%)	:arrow_down:
scvi/dataloaders/_ann_dataloader.py	89.39% <0.00%> (-4.55%)	:arrow_down:
scvi/data/_preprocessing.py	74.80% <0.00%> (-1.71%)	:arrow_down:
scvi/dataloaders/_anntorchdataset.py	91.17% <0.00%> (-1.48%)	:arrow_down:
scvi/train/_trainingplans.py	93.76% <0.00%> (-0.70%)	:arrow_down:
scvi/autotune/_manager.py	77.77% <0.00%> (-0.30%)	:arrow_down:
scvi/data/_manager.py	98.25% <0.00%> (-0.23%)	:arrow_down:
scvi/model/_scvi.py	95.94% <0.00%> (-0.11%)	:arrow_down:
scvi/model/base/_base_model.py	93.22% <0.00%> (-0.09%)	:arrow_down:
... and 58 more

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[vitkl]

Still a work in progress, unfortunately, the solution I added doesn't seem to exclude observed variables. I will do a deeper dive some time this year.

[vitkl]

I think this should be addressable by removing different procedures for different AutoGuide classes (https://github.com/scverse/scvi-tools/pull/2695).