def run_sim(self,
params_dict=None,
write_results_json=False,
population_type=None):
if not self.simulation_parameters or params_dict: # If we need one, or have one here
self.set_simulation_parameters(params_dict=params_dict)
pass
self.simulation_parameters['interventions'] = self.interventions
self.sim = Sim(pars=self.simulation_parameters, datafile=None)
if not self.simulation_prognoses:
self.simulation_prognoses = parameters.get_prognoses(
self.simulation_parameters[
TestProperties.ParameterKeys.ProgressionKeys.
ProbabilityKeys.progression_by_age])
pass
self.sim['prognoses'] = self.simulation_prognoses
if population_type:
self.sim.update_pars(pop_type=population_type)
self.sim.run(verbose=0)
self.simulation_result = self.sim.to_json(tostring=False)
if write_results_json or self.is_debugging:
with open(self.expected_result_filename, 'w') as outfile:
json.dump(self.simulation_result,
outfile,
indent=4,
sort_keys=True)
pass
def run_sim(self, params_dict=None, write_results_json=True):
if not self.simulation_parameters or params_dict: # If we need one, or have one here
self.set_simulation_parameters(params_dict=params_dict)
pass
self.sim = Sim(pars=self.simulation_parameters,
datafile=None)
self.sim.run(verbose=0)
self.simulation_result = self.sim.to_json(tostring=False)
if write_results_json:
with open(self.expected_result_filename, 'w') as outfile:
json.dump(self.simulation_result, outfile, indent=4, sort_keys=True)
pass
def test_basic_contact_trace():
tweaking = {
'n_days': 60,
'pop_size': 2000,
'pop_type': 'hybrid'
}
start_days = []
interventions = []
test_prob_start_day = 35
prob_test_perfect_symptomatic = test_prob(symp_prob=1.0, symp_quar_prob=1.0, asymp_quar_prob=1.0,
test_sensitivity=1.0, test_delay=1, start_day=test_prob_start_day)
start_days.append(test_prob_start_day)
interventions.append(prob_test_perfect_symptomatic)
contact_trace_start_day = 35
all_contacts = {
'h': 1.0,
'w': 1.0,
's': 1.0,
'c': 1.0
}
single_day_delays = {
'h': 1,
'w': 1,
's': 1,
'c': 1
}
brutal_contact_trace = contact_tracing(trace_probs=all_contacts,
trace_time=single_day_delays,
start_day=contact_trace_start_day)
start_days.append(contact_trace_start_day)
interventions.append(brutal_contact_trace)
tweaking['interventions'] = interventions
test_stuff_simulation = Sim(pars=tweaking)
test_stuff_simulation.run()
test_stuff_results = test_stuff_simulation.to_json(tostring=False)
with open("DEBUG_test_intervention_list_simulation.json","w") as outfile:
json.dump(test_stuff_results, outfile, indent=4, sort_keys=True)
pass
assert test_stuff_results["results"]["n_symptomatic"][test_prob_start_day] > 0 # If there are symptomatics
assert sum(test_stuff_results["results"]["new_tests"][test_prob_start_day:test_prob_start_day + 5]) > 0 # then there should be tests
assert sum(test_stuff_results["results"]["new_diagnoses"][test_prob_start_day + 1:test_prob_start_day + 6]) > 0 # and some diagnoses
assert sum(test_stuff_results["results"]["new_diagnoses"][test_prob_start_day + 2:test_prob_start_day + 7]) > 0 # and therefore some quarantined
pass
def setUp(self):
super().setUp()
self.sim = Sim()
self.pars = parameters.make_pars()
self.is_debugging = False
