PYE (plasma-yeast-ecoli) module

[rodvrees]

This pull request introduces a new plasma quantification benchmarking module (PYE) to the codebase, The most important changes are summarized below.

Quantification Datapoint Enhancements:

• Introduced the QuantDatapointPYE class, a new data structure for plasma (PYE) quantification benchmarking, extending QuantDatapointHYE with plasma-specific metrics such as spike-in error, quantification depth, dynamic range, and accuracy for human plasma. This includes methods for generating datapoints and computing plasma-specific metrics at various observation thresholds.
• Refactored QuantDatapointHYE to make metric calculation more flexible, allowing the maximum number of observed precursors (max_nr_observed) to be specified and defaulting to 6 if not provided. [1] [2] [3]
• Added or updated static methods for metric calculation (get_epsilon_metrics, get_precision_metrics, get_cv_metrics, and get_metrics), improving modularity and making them easier to extend for new module types. [1] [2] [3]