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refactor(model): move base model utils to new files #2731

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merged 3 commits into from Apr 17, 2024
Merged

refactor(model): move base model utils to new files #2731

merged 3 commits into from Apr 17, 2024

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@martinkim0 martinkim0 commented Apr 17, 2024 •
edited

  • moves scvi.model.base._utils._load_legacy_saved_files to scvi.model.base._save_load._load_legacy_saved_files
  • moves scvi.model.base._utils._load_saved_files to scvi.model.base._save_load._load_saved_files
  • moves scvi.model.base._utils._initialize_model to scvi.model.base._save_load._initialize_model
  • moves scvi.model.base._utils._validate_var_names to scvi.model.base._save_load._validate_var_names
  • moves scvi.model.base._utils._prepare_obs to scvi.model.base._de_core._prepare_obs
  • moves scvi.model.base._utils._de_core to scvi.model.base._de_core._de_core
  • moves scvi.model.base._utils._fdr_de_prediction to scvi.model.base._de_core_._fdr_de_prediction
  • refactors imports accordingly

@martinkim0 martinkim0 added the on-merge: backport to 1.2.x on-merge: backport to 1.2.x label Apr 17, 2024
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codecov bot commented Apr 17, 2024 •
edited

Codecov Report

Attention: Patch coverage is 97.70115% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 88.87%. Comparing base (462a861) to head (3548e93).

Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #2731      +/-   ##
==========================================
- Coverage   89.38%   88.87%   -0.52%     
==========================================
  Files         159      160       +1     
  Lines       13294    13299       +5     
==========================================
- Hits        11883    11819      -64     
- Misses       1411     1480      +69
Files Coverage Δ
src/scvi/external/contrastivevi/_model.py 80.40% <100.00%> (ø)
src/scvi/external/poissonvi/_model.py 74.64% <100.00%> (ø)
src/scvi/hub/_metadata.py 93.47% <100.00%> (ø)
src/scvi/model/_multivi.py 73.52% <100.00%> (ø)
src/scvi/model/_peakvi.py 89.34% <100.00%> (ø)
src/scvi/model/_totalvi.py 87.99% <100.00%> (ø)
src/scvi/model/base/_archesmixin.py 93.93% <100.00%> (ø)
src/scvi/model/base/_base_model.py 93.40% <100.00%> (-0.02%) ⬇️
src/scvi/model/base/_rnamixin.py 95.61% <100.00%> (ø)
src/scvi/model/base/_save_load.py 83.11% <100.00%> (ø)
... and 2 more

... and 2 files with indirect coverage changes

@martinkim0 martinkim0 merged commit a80c315 into main Apr 17, 2024
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@martinkim0 martinkim0 deleted the refactor-1 branch April 17, 2024 20:00
meeseeksmachine pushed a commit to meeseeksmachine/scvi-tools that referenced this pull request Apr 17, 2024
@martinkim0 @meeseeksmachine
Backport PR scverse#2731: refactor(model): move base model utils to n…
82e7294 
…ew files
@meeseeksmachine meeseeksmachine mentioned this pull request Apr 17, 2024
Merged
martinkim0 added a commit that referenced this pull request Apr 17, 2024
@meeseeksmachine @martinkim0
Backport PR #2731 on branch 1.2.x (refactor(model): move base model u…
7d4c77a 
…tils to new files) (#2732)

Backport PR #2731: refactor(model): move base model utils to new files

Co-authored-by: Martin Kim <46072231+martinkim0@users.noreply.github.com>
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