Misc updates to verification scripts

[nawtrey]

• Renames rms.py to rmsd.py

• Expands the scope of RMSD analysis

• Changes all sum calculations in calculations.py to use math.fsum() to minimize accuracy loss for complex diagrams

• Removes functionality from timing.py where each plot generated would save the plotted data as a .csv

• Adds function get_fit_string to timing.py

• Corrects misleading print statements in timing.py

• Changes timing.py and rmsd.py to take all_data.csv as input instead of entire data directory

• Adds in module consolidate_data.py which takes all .csv files in data and concatenates them into a single .csv

• Updates README in kda/scripts

• Changes check_transition_fluxes in verification.py to use general variable names

• Reorders .csv data stored by each run of verification.py such that the probability values are last

• Adds transition flux checks using SVD probabilities

• Adds checks that SVD and KDA probability sums are close to 1

• Fixes comments in svd.py so they are easier to read

Description

Provide a brief description of the PR's purpose here.

Todos

Notable points that this PR has either accomplished or will accomplish.

• [ ] TODO 1

Questions

• [ ] Question1

Status

• [x] Ready to go

[codecov[bot]]

Codecov Report

Merging #24 (d124153) into master (90d9407) will increase coverage by 0.01%. The diff coverage is 100.00%.

[nawtrey]

Lots of changes here. Not an ideal PR by any means, but I have to get these in master before I can move forward.

The only changes to the KDA package code are small. The shift to math.fsum() in calculations.py is tested pretty thoroughly in test_kda.py, and should be inconsequential compared to using the np.sum() function. The only other changes are to svd.py, and those are just moving comments.

The verification scripts aren't tested so they will have no affect on the test suite. These scripts are still in a fluid state, so I likely won't be adding them to the testing suite for some time.

[nawtrey]

Note to self: don't make a README until the scripts are in a stable state

[nawtrey]

All tests are passing and we have a groundbreaking code coverage increase of 0.1%. Merging.