psm_utils integration and code refactoring

compomics / DeepLC

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

https://iomics.ugent.be/deeplc

Apache License 2.0

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Closed RalfG closed 1 year ago

RalfG commented 1 year ago

psm_utils integration:

Accepts PSM utils object that gets converted to peprec, accepted on level:
1. make_preds
2. calibrate_preds

Cherry picked from branch that started from testing commits (#45)