Global retention time alignment

[lazear]

This PR introduces improvements to retention time prediction, and increase stability of the linear equations solver

RT Retention times are now globally aligned across files:

• Normalize RTs within a file to unit scale (0.0 - 1.0)
• Align each file following https://pubmed.ncbi.nlm.nih.gov/31260443/

RT prediction is then performed on all files at once (on aligned RTs), rather than one file at a time - previously, there were many instances where some files in a search could not have RTs predicted, decreasing the effectiveness of delta_rt as a feature for LDA.

Sequence Deduplication Peptide sequences within a protein are now deduplicated - previously, repeated peptides would be called multiple times for the same protein (e.g. num_proteins > 1 even if the peptide was unique)

Gaussian solver

• Add small eps to diagonals of covariance matrix (need to look more into shrinking to determine the best route)

[lazear]

Passes idempotency/determinism check for b1906 file with:

• report_psms=2
• -100 to +500 Da precursor
• -10 to +10 fragment
• predict_rt on

Some non-deterministic behavior on larger sets, seems to be arising from RT alignment

[lazear]

Using SeqCst atomic ordering restores deterministic behavior on RT alignment, final results for searches with multiple runs