def test__infection_is_isolated(selector):
geography = Geography.from_file({"area": ["E00002559"]})
world = generate_world_from_geography(geography, include_households=True)
interaction = Interaction.from_file()
infection_seed = InfectionSeed(world.super_areas, selector)
n_cases = 5
infection_seed.unleash_virus(
n_cases) # play around with the initial number of cases
policies = Policies([])
simulator = Simulator.from_file(
world=world,
interaction=interaction,
infection_selector=selector,
config_filename=pathlib.Path(__file__).parent.absolute() /
"interaction_test_config.yaml",
leisure=None,
policies=policies,
save_path=None,
)
infected_people = [person for person in world.people if person.infected]
assert len(infected_people) == 5
infected_households = []
for household in world.households:
infected = False
for person in household.people:
if person.infected:
infected = True
break
if infected:
infected_households.append(household)
assert len(infected_households) <= 5
simulator.run()
for person in world.people:
if not (person.residence.group in infected_households):
assert not person.infected and person.susceptible
def test__generate_leisure_from_world():
geography = Geography.from_file({"super_area": ["E02002135"]})
world = generate_world_from_geography(geography,
include_households=True,
include_commute=False)
world.pubs = Pubs.for_geography(geography)
world.cinemas = Cinemas.for_geography(geography)
world.groceries = Groceries.for_geography(geography)
person = Person.from_attributes(sex="m", age=27)
household = Household()
household.area = world.areas[0]
household.add(person)
person.area = geography.areas[0]
leisure = generate_leisure_for_world(
list_of_leisure_groups=["pubs", "cinemas", "groceries"], world=world)
leisure.distribute_social_venues_to_households([household])
leisure.generate_leisure_probabilities_for_timestep(0.1, False)
n_pubs = 0
n_cinemas = 0
n_groceries = 0
for _ in range(0, 1000):
subgroup = leisure.get_subgroup_for_person_and_housemates(person)
if subgroup is not None:
if subgroup.group.spec == "pub":
n_pubs += 1
elif subgroup.group.spec == "cinema":
n_cinemas += 1
elif subgroup.group.spec == "grocery":
n_groceries += 1
assert 0 < n_pubs < 100
assert 0 < n_cinemas < 100
assert 0 < n_groceries < 107
def test__teacher_distribution(geography_school):
geography_school.schools = Schools.for_geography(geography_school)
world = generate_world_from_geography(geography_school, include_households=False)
for school in world.schools:
students = len(school.students)
teachers = len(school.teachers.people)
ratio = students / teachers
assert ratio < 40
def create_world(geography):
geography.hospitals = Hospitals.for_geography(geography)
geography.companies = Companies.for_geography(geography)
geography.schools = Schools.for_geography(geography)
geography.care_homes = CareHomes.for_geography(geography)
geography.cemeteries = Cemeteries()
geography.companies = Companies.for_geography(geography)
world = generate_world_from_geography(geography, include_households=True)
return world
def test__onearea_world(geography):
geography = Geography.from_file(filter_key={"area": ["E00088544"]})
world = generate_world_from_geography(geography)
assert hasattr(world, "households")
assert isinstance(world.households, Households)
assert len(world.areas) == 1
assert len(world.super_areas) == 1
assert world.super_areas.members[0].name == "E02003616"
assert len(world.areas.members[0].people) == 362
assert len(world.households) <= 148
def make_world(geography):
geography.hospitals = Hospitals.for_geography(geography)
geography.schools = Schools.for_geography(geography)
geography.companies = Companies.for_geography(geography)
geography.care_homes = CareHomes.for_geography(geography)
geography.universities = Universities.for_super_areas(
geography.super_areas)
world = generate_world_from_geography(geography,
include_households=False,
include_commute=False)
return world
def create_world_nc(self, geography_commute_nc):
world = generate_world_from_geography(
geography_commute_nc, include_commute=False, include_households=False
)
worker_distr = WorkerDistributor.for_geography(geography_commute_nc)
worker_distr.distribute(geography_commute_nc.areas, geography_commute_nc.super_areas, world.people)
commute_generator = CommuteGenerator.from_file()
for area in world.areas:
commute_gen = commute_generator.regional_gen_from_msoarea(area.name)
for person in area.people:
person.mode_of_transport = commute_gen.weighted_random_choice()
return world
def create_world():
geography = Geography.from_file({"area": ["E00003282"]})
demography = Demography.for_geography(geography)
geography.hospitals = Hospitals(
[
Hospital(
n_beds=1000,
n_icu_beds=1000,
super_area=geography.super_areas[0],
coordinates=geography.areas[0].coordinates,
)
]
)
world = generate_world_from_geography(
geography=geography, include_households=True, include_commute=False
)
return world
def create_world(geography_h5):
with h5py.File("test.hdf5", "w"):
pass # reset file
geography = geography_h5
geography.hospitals = Hospitals.for_geography(geography)
geography.schools = Schools.for_geography(geography)
geography.companies = Companies.for_geography(geography)
geography.care_homes = CareHomes.for_geography(geography)
geography.universities = Universities.for_super_areas(geography.super_areas)
world = generate_world_from_geography(
geography=geography, include_households=True, include_commute=True
)
world.pubs = Pubs.for_geography(geography)
world.cinemas = Cinemas.for_geography(geography)
world.groceries = Groceries.for_geography(geography)
leisure = generate_leisure_for_world(
["pubs", "cinemas", "groceries", "household_visits", "care_home_vists"], world
)
leisure.distribute_social_venues_to_households(world.households)
return world
"super_area": [
"E02003282",
"E02001720",
"E00088544",
"E02002560",
"E02002559",
"E02004314",
]
})
geography.hospitals = Hospitals.for_geography(geography)
geography.schools = Schools.for_geography(geography)
geography.companies = Companies.for_geography(geography)
geography.care_homes = CareHomes.for_geography(geography)
geography.universities = Universities.for_super_areas(geography.super_areas)
world = generate_world_from_geography(geography,
include_households=True,
include_commute=True)
print("World length", len(world.people))
world.to_hdf5("world.hdf5")
world = generate_world_from_hdf5("world.hdf5")
# leisure
geography = load_geography_from_hdf5("world.hdf5")
world.cinemas = Cinemas.for_geography(geography)
world.pubs = Pubs.for_geography(geography)
world.groceries = Groceries.for_super_areas(world.super_areas,
venues_per_capita=1 / 500)
world.cemeteries = Cemeteries()
selector = InfectionSelector.from_file()
def create_area():
g = Geography.from_file(filter_key={"super_area": ["E02003353"]}, )
world = generate_world_from_geography(g)
return world
def make_super_areas():
geo = Geography.from_file({"super_area": ["E02003353"]})
geo.care_homes = CareHomes.for_geography(geo)
world = generate_world_from_geography(geo, include_households=True)
return world
def create_box_world():
geography = Geography.from_file({"area": ["E00000697"]})
return generate_world_from_geography(geography, box_mode=True)
def create_world_nc(self, geography_commute_nc):
world = generate_world_from_geography(geography_commute_nc,
include_households=False,
include_commute=False)
return world