def shared_network():
from metawards import Network, Parameters
params = Parameters()
params.set_input_files("2011Data")
params.set_disease("ncov")
network = Network.build(params, profiler=None)
return network
def test_not_infected():
# create a disease where it will finish with everyone in the V state
lurgy = Disease("lurgy")
lurgy.add("E", beta=0.0, progress=1.0)
lurgy.add("I1", beta=0.4, progress=0.2)
lurgy.add("I2", beta=0.5, progress=0.5, too_ill_to_move=0.5)
lurgy.add("I3", beta=0.5, progress=0.8, too_ill_to_move=0.8)
lurgy.add("V", beta=0.0, progress=0.0, is_infected=False)
lurgy.add("R")
params = Parameters()
params.set_input_files("single")
params.add_seeds("5")
params.set_disease(lurgy)
network = Network.build(params=params, population=Population(1000))
outdir = os.path.join(script_dir, "test_not_infected")
with OutputFiles(outdir, force_empty=True, prompt=None) as output_dir:
trajectory = network.copy().run(population=Population(),
output_dir=output_dir,
nsteps=1000,
nthreads=1)
# should finish at about 60 days and not run to 1000
p = trajectory[-1]
assert p.day < 900
# there should be no recovereds, as all who were ill went to 'others'
assert p.recovereds == 0
assert p.others == p.population - p.susceptibles
# Now repeat with more threads
with OutputFiles(outdir, force_empty=True, prompt=None) as output_dir:
trajectory = network.copy().run(population=Population(),
output_dir=output_dir,
nsteps=1000,
nthreads=8)
# should finish at about 60 days and not run to 1000
p = trajectory[-1]
assert p.day < 900
# there should be no recovereds, as all who were ill went to 'others'
assert p.recovereds == 0
assert p.others == p.population - p.susceptibles
# now repeat with demographics
demographics = Demographics.load(redblue_json)
network.params.add_seeds("demographic,number\\n1,10")
network = network.specialise(demographics)
with OutputFiles(outdir, force_empty=True, prompt=None) as output_dir:
trajectory = network.copy().run(population=Population(),
output_dir=output_dir,
nsteps=1000)
# should finish at about 60 days and not run to 1000
p = trajectory[-1]
assert p.day < 900
assert p.recovereds == 0
assert p.others > 0
assert p.others == p.population - p.susceptibles
p_red = p.subpops[0]
p_blue = p.subpops[1]
assert p_red.day < 900
assert p_red.recovereds == 0
assert p_red.others > 0
assert p_red.others == p_red.population - p_red.susceptibles
assert p_blue.day < 900
assert p_blue.recovereds == 0
assert p_blue.others > 0
assert p_blue.others == p_blue.population - p_blue.susceptibles
OutputFiles.remove(outdir, prompt=None)