Closed nawtrey closed 3 years ago
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.
Note to self: don't make a README until the scripts are in a stable state
All tests are passing and we have a groundbreaking code coverage increase of 0.1%. Merging.
Renames
rms.py
tormsd.py
Expands the scope of RMSD analysis
Changes all sum calculations in
calculations.py
to usemath.fsum()
to minimize accuracy loss for complex diagramsRemoves functionality from
timing.py
where each plot generated would save the plotted data as a .csvAdds function
get_fit_string
totiming.py
Corrects misleading print statements in
timing.py
Changes
timing.py
andrmsd.py
to takeall_data.csv
as input instead of entire data directoryAdds in module
consolidate_data.py
which takes all .csv files in data and concatenates them into a single .csvUpdates README in
kda/scripts
Changes
check_transition_fluxes
inverification.py
to use general variable namesReorders .csv data stored by each run of
verification.py
such that the probability values are lastAdds 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 readDescription
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