Fix PCA and Add Chain Diagnostic

[KSkwarczynski]

Exacutive Summary

• Fix PCA
• Make CovUtils to reduce amount of code in CovBase
• Make ReserveMemory to reduce amount of hardcoding
• Remove some GetXsecDetID as same thing was doing GetDetId.
• inline everywhere...
• Move parts related with yaml from covaraince xsec to base. This was neccessary to make PCA for flux work but also will be handy for yaml Cov Osc
• Tidy parts of covariance classes add MaCh3 log whnever I can
• lot's of fancy messages
• Move many T2K plotting scripts and validate them
• Adding legacy comments from former mebers
• Now save cov matrix into foutput of FitterBase
• Make new Monitor Class with usefull prinouts liek CPU/GPU info, progress bar etc.
• Sliglhy udpate cmake depednacies flow

First fancy messages CPU Only: With GPU: Covariance printing:

Boring Validations PCA: First plots that decomposition works: PCA_Flux.pdf Debug_PCA.pdf

Here are posteriors from PCA chain where I PCA-ed flux. Short chain, not full stat so complete garbage but it seems to wrok with trnaforming back and forth

Validating Diagnostic - Neccessary due to ROOT changes and fact that T2K uses toml not yaml and fact we load now yaml not root file Here are all plots I have produced, enjoy: PenaltyTerm.pdf Processor.pdf Corr.pdf Comparison.pdf

Here is updated stucutre of FitterBaseOuput:

Dependancy graph Last but not least udpate cmake to make dependancy graph MaCh3 Before MaCh3 Now:

MaCh3 Now GPU:

As a bonus MaCh3 T2K

MaCh3 T2K Updated:

Another Update: 2D LLH scan:

Sorry for another large PR...