def test_stopstart(workdir):
"""Run the test_stopstart setting."""
with chdir_context(workdir):
configs = sim.read_config("cfg_check1")
sim.run_disease_simulation(configs, write_epi=True)
configs = sim.read_config("cfg_check2")
sim.run_disease_simulation(configs, write_epi=True)
configs = sim.read_config("cfg_check3")
sim.run_disease_simulation(configs, write_epi=True)
assert_equal_files("test1.out", "test1_stopstart.out.expected")
assert_equal_files("test2.out", "test2_stopstart.out.expected")
assert_equal_files("test3.out", "test3_stopstart.out.expected")
def test_det(workdir):
"""Run the test_det setting."""
with chdir_context(workdir):
configs = sim.read_config("cfg_test_det")
sim.run_disease_simulation(configs, write_epi=True)
assert_equal_files("test_det.out", "test_det.out.expected")
import patchsim as sim
class MyIntervention:
def __init__(self):
self.original_beta = None
self.reduced_beta = None
def __call__(self, configs, patch_df, params, Theta, seeds, vaxs, t):
if self.original_beta is None:
self.original_beta = params["beta"]
self.reduced_beta = params["beta"] * 0.9
# For first 10 step do nothing to beta
if t < 10:
params["beta"] = self.original_beta
# Next 10 steps keep it low
elif 10 <= t < 20:
params["beta"] = self.reduced_beta
# After that restore
else:
params["beta"] = self.original_beta
configs = sim.read_config('cfg_test_foi')
my_intervention = MyIntervention()
sim.run_disease_simulation(configs,
write_epi=True,
intervene_step=my_intervention)
import sys
sys.path.append('../')
import patchsim as sim
configs = sim.read_config('cfg_test_stoc')
sim.run_disease_simulation(configs,write_epi=True)
import sys
sys.path.append('../')
import patchsim as sim
configs = sim.read_config('cfg_test_det')
sim.run_disease_simulation(configs, write_epi=True)
import sys
sys.path.append('../')
import patchsim as sim
configs = sim.read_config('cfg_paramfile')
sim.run_disease_simulation(configs, write_epi=True)
import sys
sys.path.append('../')
import patchsim as sim
configs = sim.read_config('cfg_check1')
sim.run_disease_simulation(configs, write_epi=True)
configs = sim.read_config('cfg_check2')
sim.run_disease_simulation(configs, write_epi=True)
configs = sim.read_config('cfg_check3')
sim.run_disease_simulation(configs, write_epi=True)