def make_dummy_activity_manager(world):
timer = Timer(
total_days=10,
weekday_step_duration=[8, 8, 8],
weekend_step_duration=[8, 8, 8],
weekday_activities=[
["primary_activity", "residence"],
["primary_activity", "residence"],
],
weekend_activities=[
["primary_activity", "residence"],
["primary_activity", "residence"],
],
)
activity_manager = CampActivityManager(
world=world,
policies=Policies.from_file(),
timer=timer,
all_activities=["primary_activity", "residence"],
activity_to_super_groups={
"primary_activity": ["learning_centers"],
"residence": ["households"],
},
)
return activity_manager
def test_time_reset():
timer = Timer(initial_day="2020-03-10", total_days=10)
start_time = timer.initial_date
next(timer)
next(timer)
next(timer)
next(timer)
assert timer.day == 2
timer.reset()
assert timer.day == 0
assert timer.shift == 0
assert timer.previous_date == start_time
next(timer)
next(timer)
next(timer)
next(timer)
assert timer.day == 2
def test_time_is_passing():
timer = Timer(initial_day="2020-03-10", total_days=10)
assert timer.now == 0
next(timer)
assert timer.now == 0.5
assert timer.previous_date == timer.initial_date
next(timer)
assert timer.now == 1.0
def test_weekend_transition():
timer = Timer(initial_day="2020-03-10", total_days=10)
for _ in range(0, 8): # 5 days for 3 time steps per day
next(timer)
assert timer.is_weekend is True
assert timer.activities == ["residence"]
next(timer)
assert timer.is_weekend is True
assert timer.activities == ["residence"]
next(timer)
assert timer.is_weekend is False
assert timer.activities == ["primary_activity", "residence"]
def test__seed_strength(selector, ):
geography = Geography.from_file(
filter_key={"super_area": [
"E02004940",
"E02004935",
"E02004936",
]})
demography = Demography.for_geography(geography)
for area in geography.areas:
area.populate(demography)
n_cases_region = pd.DataFrame({
'East of England':
np.array([100, 200, 300, 400]).astype(np.int),
'date': [
'2020-03-01',
'2020-03-02',
'2020-03-03',
'2020-03-04',
]
})
n_cases_region.set_index('date', inplace=True)
n_cases_region.index = pd.to_datetime(n_cases_region.index)
seed = InfectionSeed.from_file(super_areas=geography.super_areas,
selector=selector,
n_cases_region=n_cases_region,
seed_strength=0.2)
timer = Timer(
initial_day='2020-02-29',
total_days=7,
)
while timer.date <= timer.final_date:
time = timer.date
if (time >= seed.min_date) and (time <= seed.max_date):
seed.unleash_virus_per_region(time)
next(timer)
n_infected = 0
for super_area in geography.super_areas:
for person in super_area.people:
if person.infected:
n_infected += 1
n_cases = (seed.n_cases_region["East of England"].sum())
np.testing.assert_allclose(0.2 * n_cases, n_infected, rtol=0.05)
def test_initial_parameters():
timer = Timer(initial_day="2020-03-10", total_days=10)
assert timer.shift == 0
assert timer.is_weekend is False
assert timer.day_of_week == "Tuesday"
def from_file(
cls,
world: World,
interaction: Interaction,
infection_selector=None,
policies: Optional[Policies] = None,
infection_seed: Optional[InfectionSeed] = None,
leisure: Optional[Leisure] = None,
config_filename: str = default_config_filename,
save_path: str = "results",
) -> "Simulator":
"""
Load config for simulator from world.yaml
Parameters
----------
save_path
leisure
infection_seed
policies
interaction
world
config_filename
The path to the world yaml configuration
Returns
-------
A Simulator
"""
with open(config_filename) as f:
config = yaml.load(f, Loader=yaml.FullLoader)
if world.box_mode:
activity_to_groups = None
else:
activity_to_groups = config["activity_to_groups"]
time_config = config["time"]
if "checkpoint_dates" in config:
if isinstance(config["checkpoint_dates"], datetime.date):
checkpoint_dates = [config["checkpoint_dates"]]
else:
checkpoint_dates = []
for date_str in config["checkpoint_dates"].split():
checkpoint_dates.append(
datetime.datetime.strptime(date_str,
"%Y-%m-%d").date())
else:
checkpoint_dates = None
weekday_activities = [
activity
for activity in time_config["step_activities"]["weekday"].values()
]
weekend_activities = [
activity
for activity in time_config["step_activities"]["weekend"].values()
]
all_activities = set(
chain.from_iterable(weekday_activities + weekend_activities))
cls.check_inputs(time_config)
timer = Timer(
initial_day=time_config["initial_day"],
total_days=time_config["total_days"],
weekday_step_duration=time_config["step_duration"]["weekday"],
weekend_step_duration=time_config["step_duration"]["weekend"],
weekday_activities=time_config["step_activities"]["weekday"],
weekend_activities=time_config["step_activities"]["weekend"],
)
activity_manager = cls.ActivityManager(
world=world,
all_activities=all_activities,
activity_to_groups=activity_to_groups,
leisure=leisure,
policies=policies,
timer=timer,
)
return cls(
world=world,
activity_manager=activity_manager,
timer=timer,
infection_selector=infection_selector,
infection_seed=infection_seed,
save_path=save_path,
interaction=interaction,
checkpoint_dates=checkpoint_dates,
)