def add_standard_sampling_run(self):
"""
Add the <run> element (only) for a standard analysis, i.e. without
path sampling. The <state>, <init> etc. are added to whatever this
method names self.run.
"""
self.run = xml.run(
self.beast,
id="mcmc",
spec="MCMC",
chainLength=self.config.mcmc.chainlength,
numInitializationAttempts=1000,
sampleFromPrior=self.config.mcmc.sample_from_prior,
)
def add_path_sampling_run(self):
"""
Add the <run> element (only) for a path sampling analysis. We call
this self.ps_run and assign the nested <mcmc> element to self.run,
so that <state>, <init> etc. will be correctly added there.
"""
attribs = {
"id":
"ps",
"spec":
"beast.inference.PathSampler",
"chainLength":
self.config.mcmc.chainlength,
"nrOfSteps":
self.config.mcmc.steps,
"alpha":
self.config.mcmc.alpha,
"rootdir":
self.config.admin.basename + "_path_sampling",
"preBurnin":
int((self.config.mcmc.preburnin / 100) *
self.config.mcmc.chainlength),
"burnInPercentage":
self.config.mcmc.log_burnin,
"deleteOldLogs":
"true",
}
if self.config.mcmc.do_not_run:
attribs["doNotRun"] = "true"
self.ps_run = xml.run(self.beast, attrib=attribs)
self.ps_run.text = """cd $(dir)
java -cp $(java.class.path) beast.app.beastapp.BeastMain $(resume/overwrite) -java -seed $(seed) beast.xml"""
attribs = {}
attribs["id"] = "mcmc"
attribs["spec"] = "MCMC"
attribs["chainLength"] = str(self.config.mcmc.chainlength)
self.run = xml.mcmc(self.ps_run, attrib=attribs)
def test_nesting():
e = xml.beast()
xml.run(xml.beast())
for ee in e:
assert ee.tag == 'run'
def test_subelement(kw, assertion):
assert assertion(xml.run(None, **kw))