def test_mcmc(self):
self.mcfitter.sample(steps=50, nthin=1, verbose=False)
assert_equal(self.mcfitter.nvary, 2)
# smoke test for corner plot
self.mcfitter.objective.corner()
# we're not doing Parallel Tempering here.
assert_(self.mcfitter._ntemps == -1)
assert_(isinstance(self.mcfitter.sampler, emcee.EnsembleSampler))
# should be able to multithread
mcfitter = CurveFitter(self.objective, nwalkers=50)
res = mcfitter.sample(steps=33, nthin=2, verbose=False, pool=2)
# check that the autocorrelation function at least runs
acfs = mcfitter.acf(nburn=10)
assert_equal(acfs.shape[-1], mcfitter.nvary)
# check chain shape
assert_equal(mcfitter.chain.shape, (33, 50, 2))
# assert_equal(mcfitter._lastpos, mcfitter.chain[:, -1, :])
assert_equal(res[0].chain.shape, (33, 50))
# if the number of parameters changes there should be an Exception
# raised
from pytest import raises
with raises(RuntimeError):
self.p[0].vary = False
self.mcfitter.sample(1)
# can fix by making the sampler again
self.mcfitter.make_sampler()
self.mcfitter.sample(1)
def test_mcmc(self):
self.mcfitter.sample(steps=50, nthin=1, verbose=False)
# we're not doing Parallel Tempering here.
assert_(self.mcfitter._ntemps == -1)
assert_(isinstance(self.mcfitter.sampler, emcee.EnsembleSampler))
# should be able to multithread
mcfitter = CurveFitter(self.objective, nwalkers=50)
res = mcfitter.sample(steps=33, nthin=2, verbose=False, pool=2)
# check that the autocorrelation function at least runs
acfs = mcfitter.acf(nburn=10)
assert_equal(acfs.shape[-1], mcfitter.nvary)
# check chain shape
assert_equal(mcfitter.chain.shape, (33, 50, 2))
# assert_equal(mcfitter._lastpos, mcfitter.chain[:, -1, :])
assert_equal(res[0].chain.shape, (33, 50))
