def __call__(self, **kwargs):
"""
This function should perform some sanity checks, but right now it does nothing.
"""
cf = CommonFunctions(self)
cf.phycassert(not model.update_freqs_separately, 'update_freqs_separately is no longer allowed')
cf.phycassert(not model.update_relrates_separately, 'update_freqs_separately is no longer allowed')
def __call__(self, **kwargs):
cf = CommonFunctions(self)
cf.phycassert(not self.update_freqs_separately, 'update_freqs_separately is no longer allowed')
cf.phycassert(not self.update_relrates_separately, 'update_freqs_separately is no longer allowed')
self.set(**kwargs)
self.checkModelParameters(cf)
return self.saveas()
def checkSanity(self):
"""
Place asserts in this function that should be checked before anything substantive
is done during a call of a SS object.
"""
cf = CommonFunctions(self)
if self.refdist_is_prior and self.refdistfile is not None:
cf.phycassert(False, 'cannot specify ss.refdist_is_prior = True and also specify a reference distribution using ss.refdistfile')
if not self.refdist_is_prior and self.refdistfile is None:
cf.phycassert(False, 'ss.refdist_is_prior is False but you have not specified a reference distribution (i.e. ss.refdistfile is None)')
cf.phycassert(mcmc.ncycles > 0, 'mcmc.ncycles cannot be less than 1 for the stepping-stone method')
cf.phycassert(mcmc.allow_polytomies == False or self.ti == True, "mcmc.allow_polytomies must be False to use the generalized stepping-stone method (we're working on relaxing this requirement)")
#if not self.override_fixed_topology_restriction:
# cf.phycassert(mcmc.fix_topology == True, "mcmc.fix_topology must be True to use the stepping-stone method (we're working on relaxing this requirement)")
models = partition.getModels()
if len(models) > 0:
m = models[0]
else:
m = model
if m.edgelen_hyperprior:
cf.warning("the generalized stepping-stone method has only been tested on models in which model.edgelen_hyperprior = None (proceed at your own risk)")
