pg-sui 1.6.16a3__py3-none-any.whl → 1.7.0__py3-none-any.whl

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Files changed (33) hide show
  1. {pg_sui-1.6.16a3.dist-info → pg_sui-1.7.0.dist-info}/METADATA +26 -30
  2. {pg_sui-1.6.16a3.dist-info → pg_sui-1.7.0.dist-info}/RECORD +29 -33
  3. pgsui/__init__.py +0 -8
  4. pgsui/_version.py +2 -2
  5. pgsui/cli.py +577 -125
  6. pgsui/data_processing/config.py +1 -2
  7. pgsui/data_processing/containers.py +203 -530
  8. pgsui/data_processing/transformers.py +44 -20
  9. pgsui/impute/deterministic/imputers/mode.py +475 -182
  10. pgsui/impute/deterministic/imputers/ref_allele.py +454 -147
  11. pgsui/impute/supervised/imputers/hist_gradient_boosting.py +4 -3
  12. pgsui/impute/supervised/imputers/random_forest.py +3 -2
  13. pgsui/impute/unsupervised/base.py +1269 -534
  14. pgsui/impute/unsupervised/callbacks.py +28 -33
  15. pgsui/impute/unsupervised/imputers/autoencoder.py +870 -841
  16. pgsui/impute/unsupervised/imputers/vae.py +931 -787
  17. pgsui/impute/unsupervised/loss_functions.py +156 -202
  18. pgsui/impute/unsupervised/models/autoencoder_model.py +7 -49
  19. pgsui/impute/unsupervised/models/vae_model.py +40 -221
  20. pgsui/impute/unsupervised/nn_scorers.py +53 -13
  21. pgsui/utils/classification_viz.py +240 -97
  22. pgsui/utils/misc.py +201 -3
  23. pgsui/utils/plotting.py +73 -58
  24. pgsui/utils/pretty_metrics.py +2 -6
  25. pgsui/utils/scorers.py +39 -0
  26. pgsui/impute/unsupervised/imputers/nlpca.py +0 -1666
  27. pgsui/impute/unsupervised/imputers/ubp.py +0 -1660
  28. pgsui/impute/unsupervised/models/nlpca_model.py +0 -206
  29. pgsui/impute/unsupervised/models/ubp_model.py +0 -200
  30. {pg_sui-1.6.16a3.dist-info → pg_sui-1.7.0.dist-info}/WHEEL +0 -0
  31. {pg_sui-1.6.16a3.dist-info → pg_sui-1.7.0.dist-info}/entry_points.txt +0 -0
  32. {pg_sui-1.6.16a3.dist-info → pg_sui-1.7.0.dist-info}/licenses/LICENSE +0 -0
  33. {pg_sui-1.6.16a3.dist-info → pg_sui-1.7.0.dist-info}/top_level.txt +0 -0
pgsui/data_processing/config.py CHANGED
@@ -166,7 +166,7 @@ def load_yaml_to_dataclass(
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  Notes:
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  - `preset` is **CLI-only**. If the YAML contains `preset`, it will be ignored (default) or cause an error depending on `yaml_preset_behavior`.
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- - Pass a `base` instance that is already constructed from the CLI-selected preset (e.g., `NLPCAConfig.from_preset(args.preset)`), and this function will overlay the YAML on top of it. Any additional `overlays` (a nested dict) are applied last.
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+ - Pass a `base` instance that is already constructed from the CLI-selected preset (e.g., `VAEConfig.from_preset(args.preset)`), and this function will overlay the YAML on top of it. Any additional `overlays` (a nested dict) are applied last.
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  Args:
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  path (str): Path to the YAML file.
@@ -479,7 +479,6 @@ def apply_dot_overrides(
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  t.Any: The updated dataclass instance (same object identity is not guaranteed; a deep copy is made).
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  Notes:
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- - No hard-coding of NLPCAConfig. Pass `root_cls=NLPCAConfig` (or UBPConfig, etc.) when starting from a dict.
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  - Dict payloads encountered at intermediate nodes are merged into the expected dataclass type using schema introspection.
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  - Enforces unknown-key errors to keep configs honest.
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