Refactor DataPreprocessor to steps-based pipeline, add CounterDiffTransformer and quickstart config generator#15

Merged

roelofsc merged 15 commits intodevelopfrom

feature-counter-transformer

Dec 16, 2025

Commits on Nov 26, 2025

Add CounterDiffTransformer
roelofsc
committed

Commits on Nov 27, 2025

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
committed
Add steps at the same level as params for the DataPreprocessor.
roelofsc
committed
Allow for an unspecified data_preprocessor in the configuration file and update tests and test_data (test configuration files) accordingly
roelofsc
committed

Commits on Dec 3, 2025

Commits on Dec 4, 2025

Fix docstring issues for sphinx
roelofsc
committed

Commits on Dec 8, 2025

Fixed typo

chr39552
authored and
chr39552
committed

Commits on Dec 10, 2025

Add plot_reconstruction_with_model which plots the reconstruction of counter diffs/rates if they are present in the reconstruction
roelofsc
committed