Calculating PEPs can be extremely slow due to numpy OMP multiprocessing

[MatthewThe]

On some systems (e.g. Ubuntu), calculating PEPs with getQvaluesFromScores is extremely slow (more than 1 minute instead of just a few seconds) when OMP multithreading is not disabled for numpy. This can be circumvented by prepending the call to Triqler/Qvality by OMP_NUM_THREADS=1. I'm not sure yet which of the numpy functions is causing this, but it's most likely one of the matrix functions used in the IRLS.

triqler/triqler/qvality.py

Line 28 in b433f7b

def getQvaluesFromScores(targetScores, decoyScores, includePEPs = False, includeDecoys = False, tdcInput = False, pi0 = 1.0, plotRegressionCurve = False, numBins = 500):

[wfondrie]

@MatthewThe - any idea on a timeline for a new release containing this PR?

[MatthewThe]

Sorry, updating the package is indeed long overdue. I will try to make a new release tomorrow.