def testOptimizerMethod(self):
if IGNORE_TEST:
return
METHOD_NAME = 'differential_evolution'
optimizerMethod = ModelFitter.OptimizerMethod(
method=METHOD_NAME,
kwargs={ "popsize": 100, "atol": 0.001})
fitter1 = self._makeMikeModel(fitterMethods=[METHOD_NAME])
fitter2 = self._makeMikeModel(fitterMethods=[optimizerMethod])
self.assertTrue(True) # Smoke test
@author: hsauro
@author: joseph-hellerstein
"""
import SBstoat
from SBstoat.modelFitter import ModelFitter
from tests import _testHelpers as th
import matplotlib
import os
import unittest
IGNORE_TEST = False
IS_PLOT = False
TIMESERIES = th.getTimeseries()
optimizerMethod = ModelFitter.OptimizerMethod(SBstoat.METHOD_LEASTSQ,
kwargs={"max_nfev": 100})
FITTER = th.getFitter(
cls=ModelFitter,
isPlot=IS_PLOT,
fitterMethods=[optimizerMethod],
bootstrapMethods=[optimizerMethod],
)
FITTER.fitModel()
FITTER.bootstrap(numIteration=10)
ANTIMONY_MODEL_BENCHMARK = """
# Reactions
J1: S1 -> S2; k1*S1
J2: S2 -> S3; k2*S2
# Species initializations
S1 = 10; S2 = 0;
k1 = 1; k2 = 2