This release adds multiple CLI commands that:
1) allow reproducing results from the article and seeing the effect of adding your own datasets:
- Adds `lionheart cross_validate` command. Perform nested leave-one-dataset-out cross-validation on your dataset(s) and/or the included features.
- Adds `lionheart validate` command. Validate a model on the included external dataset or a custom dataset.
- Adds `lionheart evaluate_univariates` command. Evaluate each feature (cell-type) separately on your dataset(s) and/or the included features.
2) expands what you can do with your own data:
- Adds `lionheart customize_thresholds` command. Calculate the ROC curve and probability densities (for deciding probability thresholds) on your data and/or the included features for a custom model or an included model. Allows using probability thresholds suited to your own data when using `lionheart predict_sample` and `lionheart validate`.
- Adds `--custom_threshold_dirs` argument in `lionheart predict_sample`. Allows passing the ROC curves and probability densities extracted with `lionheart customize_thresholds`.
Also:
- Adds `matplotlib` as dependency.
- Bumps `generalize` dependency requirement to `0.2.1`.
- Bumps `utipy` dependency requirement to `1.0.3`.