Refactor DataPreprocessor to steps-based pipeline, add CounterDiffTransformer and PreDist notebook#16

Merged

roelofsc merged 26 commits intomainfrom

Jan 14, 2026

Commits on Nov 11, 2025

Bugfix `plot_score_with_threshold`
roelofsc
committed

Commits on Dec 16, 2025

Add CounterDiffTransformer
roelofsc
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Update the DataPreprocessor so we can specify the pipeline easier through the configuration file, by providing a steps specification instead of a long list of arguments. Extend DataPreprocessor tes…
roelofsc
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Add steps at the same level as params for the DataPreprocessor.
roelofsc
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Allow for an unspecified data_preprocessor in the configuration file and update tests and test_data (test configuration files) accordingly
roelofsc
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Add `features_to_clip` parameter to the DataClipper (data_clipper.py) to complement `features_to_exclude`.
roelofsc
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Improve ColumnSelector missing column error message

teehari79
authored and
roelofsc
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Added the option features_to_select to ColumnSelector (similar to DataClipper features_to_exclude and features_to_clip)
roelofsc
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Update the docs.
roelofsc
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Update the CARE2Compare Notebooks and configurations. Fix a bug and clear up the Hyperopt notebook.
roelofsc
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Update configuration docs.
roelofsc
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Fix bug in and add tests for data_preprocessor.py
roelofsc
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Update the configuration docs and README.md and a utility function to generate a configuration file.
roelofsc
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Fix docstring issues for sphinx
roelofsc
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Fixed typo

chr39552
authored and
roelofsc
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Add plot_reconstruction_with_model which plots the reconstruction of counter diffs/rates if they are present in the reconstruction
roelofsc
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Commits on Jan 13, 2026