Refactor MSMS Hits Generation #858
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update to py311
reconcile main branch updates with feature branch
test: change expected score values for hits refactor
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This PR will implement major changes to the MSMS hits generation routine, with the objective of simplifying the codebase and improving efficiency. Custom spectral alignment and scoring code has been replaced with MatchMS and the hits generation routine has been restructured to avoid extensive iteration. With these changes, the average experiment should have a ~6X speed increase to hits generation. This will allow for the analysis of much larger experiments or the use of larger atlases.
Custom code is still present for aligning spectra used in plotting MSMS mirror plots. Extensive docstrings have been added to some of the more esoteric functions that accomplish this.