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Clean up posterior predictive sample methods #2377

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merged 9 commits into from Jan 4, 2024
Merged

Clean up posterior predictive sample methods #2377

merged 9 commits into from Jan 4, 2024

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martinkim0
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@martinkim0 martinkim0 commented Jan 4, 2024

  • Remove unused library_size argument (could add this back later once it is implemented) in VAE.sample
  • Add typing and additional documentation in VAE.sample
  • Clean up tensor shape annotations in VAE.sample and RNASeqMixin.posterior_predictive_sample
  • Use Python 3.9+ annotations in scvi.model.base._rnamixin
  • Clean up code in RNASeqMixin.posterior_predictive_sample

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codecov bot commented Jan 4, 2024

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (7523a30) 89.18% compared to head (4ca3f35) 89.18%.

Files Patch % Lines
scvi/model/base/_rnamixin.py 91.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2377      +/-   ##
==========================================
- Coverage   89.18%   89.18%   -0.01%     
==========================================
  Files         152      152              
  Lines       12487    12477      -10     
==========================================
- Hits        11137    11127      -10     
  Misses       1350     1350              

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@martinkim0 martinkim0 changed the title Clean up scvi.module.VAE.sample Clean up posterior predictive sample methods Jan 4, 2024
@martinkim0 martinkim0 merged commit 989cdcc into main Jan 4, 2024
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@martinkim0 martinkim0 deleted the ppd-sample branch January 4, 2024 21:56
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meeseeksdev backport to 1.1.x

meeseeksmachine pushed a commit to meeseeksmachine/scvi-tools that referenced this pull request Jan 9, 2024
martinkim0 added a commit that referenced this pull request Jan 9, 2024
Co-authored-by: Martin Kim <46072231+martinkim0@users.noreply.github.com>
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