def test_long_sequence_gst_raises_on_bad_profile_options(self):
#check invalid profile options
with self.assertRaises(ValueError):
ls.do_long_sequence_gst(self.ds,
self.model,
self.fiducials,
self.fiducials,
self.germs,
self.maxLens,
advancedOptions={'profile': 3})
def test_long_sequence_gst_raises_on_bad_badfit_options(self):
with self.assertRaises(ValueError):
ls.do_long_sequence_gst(self.ds,
self.model,
self.fiducials,
self.fiducials,
self.germs,
self.maxLens,
advancedOptions={
'badFitThreshold': -100,
'onBadFit': ["foobar"]
})
def test_long_sequence_gst(self):
result = ls.do_long_sequence_gst(self.ds,
self.model,
self.fiducials,
self.fiducials,
self.germs,
self.maxLens,
advancedOptions=self.options)
def test_long_sequence_gst_chi2(self):
self.options.update(objective='chi2')
result = ls.do_long_sequence_gst(self.ds,
self.model,
self.fiducials,
self.fiducials,
self.germs,
self.maxLens,
advancedOptions=self.options)
def test_long_sequence_gst_raises_on_bad_advanced_options(self):
with self.assertRaises(ValueError):
ls.do_long_sequence_gst(self.ds,
self.model,
self.fiducials,
None,
self.germs,
self.maxLens,
advancedOptions={'objective': "FooBar"
}) # bad objective
with self.assertRaises(ValueError):
ls.do_long_sequence_gst(
self.ds,
self.model,
self.fiducials,
None,
self.germs,
self.maxLens,
advancedOptions={'starting point':
"FooBar"}) # bad starting point
def test_long_sequence_gst_advanced_options(self):
# TODO what exactly is being tested?
self.options.update({
#'starting point': self.model, #this is deprecated now - need to use protocol objects
'depolarizeStart': 0.05,
'cptpPenaltyFactor': 1.0
})
result = ls.do_long_sequence_gst(self.ds,
self.model,
self.fiducials,
None,
self.germs,
self.maxLens,
advancedOptions=self.options)
def test_long_sequence_gst_with_file_args(self, ds_path, model_path,
fiducial_path, germ_path):
io.write_dataset(ds_path, self.ds, self.lsgstStrings[-1])
io.write_model(self.model, model_path)
io.write_circuit_list(fiducial_path, self.fiducials)
io.write_circuit_list(germ_path, self.germs)
self.options.update(randomizeStart=1e-6,
profile=2,
verbosity=10,
memoryLimitInBytes=2 * 1000**3)
result = ls.do_long_sequence_gst(ds_path,
model_path,
fiducial_path,
fiducial_path,
germ_path,
self.maxLens,
advancedOptions=self.options)