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Corrected typing types and fixed tests

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This commit is contained in:
Luis Aleixo 2022-01-24 15:01:16 +01:00
parent ad0f55acf1
commit 722278b154
11 changed files with 60 additions and 23 deletions
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14
cara/apps/calculator/model_generator.py
View file

@ -78,7 +78,7 @@ class FormData:
window_width: float
windows_number: int
window_opening_regime: str
short_range_option: str
short_range_option: bool
short_range_interactions: list
#: The default values for undefined fields. Note that the defaults here
@ -132,7 +132,7 @@ class FormData:
'windows_number': 0,
'window_opening_regime': 'windows_open_permanently',
'short_range_option': False,
'short_range_interactions': [],
'short_range_interactions': '[]',
}
@classmethod
@ -422,12 +422,12 @@ class FormData:
number=infected_occupants,
virus=virus,
presence=self.infected_present_interval(),
short_range_presence=self.short_range_intervals(),
short_range_activities=self.short_range_activities(),
mask=self.mask(),
activity=activity,
expiration=expiration,
host_immunity=0.,
short_range_presence=self.short_range_intervals(),
short_range_activities=self.short_range_activities(),
)
return infected
@ -456,7 +456,6 @@ class FormData:
exposed = mc.Population(
number=exposed_occupants,
presence=self.exposed_present_interval(),
short_range_presence=self.short_range_interactions,
activity=activity,
mask=self.mask(),
host_immunity=0.,
@ -632,14 +631,13 @@ class FormData:
breaks=self.infected_lunch_break_times() + self.infected_coffee_break_times(),
)
def short_range_intervals(self) -> models.Interval:
def short_range_intervals(self) -> typing.List[models.SpecificInterval]:
if (self.short_range_interactions):
short_range_intervals = []
for interaction in self.short_range_interactions:
start_time = time_string_to_minutes(interaction['start_time'])
duration = float(interaction['duration'])
short_range_intervals.append(models.SpecificInterval((start_time/60, (start_time + duration)/60)))
return short_range_intervals
else:
return []
@ -650,7 +648,7 @@ class FormData:
breaks=self.exposed_lunch_break_times() + self.exposed_coffee_break_times(),
)
def short_range_activities(self):
def short_range_activities(self) -> typing.List[str]:
if (self.short_range_interactions):
return [interaction['activity'] for interaction in self.short_range_interactions]
else:

8
cara/apps/calculator/report_generator.py
View file

@ -98,14 +98,14 @@ def interesting_times(model: models.ExposureModel, approx_n_pts=100) -> typing.L
def short_range_interesting_times(model: models.ExposureModel, times: typing.List[float]) -> typing.List[float]:
short_range_times = []
short_range_times : typing.List[float] = []
for period in model.concentration_model.infected.short_range_presence:
start, finish = period.boundaries()
start, finish = tuple(period.boundaries())
short_range_times = short_range_times + [time for time in times if time > start and time < finish]
return short_range_times
def jet_origin_concentrations(model: models.ExposureModel) -> models._ExpirationBase:
def jet_origin_concentrations(model: models.ExposureModel) -> typing.List[float]:
return [initial_concentrations_mouth[activity] for activity in model.concentration_model.infected.short_range_activities]
@ -113,7 +113,7 @@ def short_range_initial_concentrations(model: models.ExposureModel, time: float)
dilution = dilution_factor(np.linspace(0.1, 2., 1000))
jet_origin_initial_concentrations = jet_origin_concentrations(model)
for index, interaction in enumerate(model.concentration_model.infected.short_range_presence):
start, finish = interaction.boundaries()
start, finish = tuple(interaction.boundaries())
if start <= time <= finish:
expiration = build_expiration(model.concentration_model.infected.short_range_activities[index])
single_exposure_model = dataclass_utils.nested_replace(

5
cara/apps/expert.py
View file

@ -496,19 +496,18 @@ baseline_model = models.ExposureModel(
number=1,
virus=models.Virus.types['SARS_CoV_2'],
presence=models.SpecificInterval(((8., 12.), (13., 17.))),
short_range_presence=[],
short_range_activities=[],
mask=models.Mask.types['No mask'],
activity=models.Activity.types['Seated'],
expiration=models.Expiration.types['Speaking'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
),
exposed=models.Population(
number=10,
presence=models.SpecificInterval(((8., 12.), (13., 17.))),
short_range_presence=[],
activity=models.Activity.types['Seated'],
mask=models.Mask.types['No mask'],
host_immunity=0.,

16
cara/models.py
View file

@ -32,7 +32,7 @@ or length N arrays, where N is the number of parameterisations to run; N must be
the same for all parameters of a single model.
"""
from dataclasses import dataclass
from dataclasses import dataclass, field
import typing
import numpy as np
@ -678,9 +678,6 @@ class Population:
#: The times in which the people are in the room.
presence: Interval
#: Short range interactions
short_range_presence: list
#: The kind of mask being worn by the people.
mask: Mask
@ -701,6 +698,12 @@ class _PopulationWithVirus(Population):
#: The virus with which the population is infected.
virus: Virus
#: Short range interactions
short_range_presence: typing.List[SpecificInterval]
#: The type of expiractory activities in the short range interactions
short_range_activities: typing.List[str]
@method_cache
def fraction_of_infectious_virus(self) -> _VectorisedFloat:
"""
@ -751,10 +754,7 @@ class EmittingPopulation(_PopulationWithVirus):
@dataclass(frozen=True)
class InfectedPopulation(_PopulationWithVirus):
#: The type of expiration that is being emitted whilst doing the activity.
expiration: _ExpirationBase
#: The type of expiractory activities in the short range interactions
short_range_activities: list
expiration: _ExpirationBase
@method_cache
def fraction_of_infectious_virus(self) -> _VectorisedFloat:

2
cara/tests/conftest.py
View file

@ -23,6 +23,8 @@ def baseline_model():
host_immunity=0.,
# superspreading event, where ejection factor is fixed based
# on Miller et al. (2020) - 50 represents the infectious dose.
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)

4
cara/tests/models/test_concentration_model.py
View file

@ -47,6 +47,8 @@ def test_concentration_model_vectorisation(override_params):
),
expiration=models._ExpirationBase.types['Breathing'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -69,6 +71,8 @@ def simple_conc_model():
virus=models.Virus.types['SARS_CoV_2'],
expiration=models.Expiration.types['Breathing'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)

6
cara/tests/models/test_exposure_model.py
View file

@ -66,6 +66,8 @@ def known_concentrations(func):
virus=models.Virus.types['SARS_CoV_2_ALPHA'],
expiration=models.Expiration.types['Speaking'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
)
normed_func = lambda x: func(x) / dummy_infected_population.emission_rate_when_present()
return KnownNormedconcentration(dummy_room, dummy_ventilation,
@ -154,6 +156,8 @@ def conc_model():
# superspreading event, where ejection factor is fixed based
# on Miller et al. (2020) - 50 represents the infectious dose.
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -197,6 +201,8 @@ def test_infectious_dose_vectorisation():
),
expiration=models.Expiration.types['Speaking'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
)
cm = known_concentrations(lambda t: 1.2)
cm = replace(cm, infected=infected_population)

2
cara/tests/test_infected_population.py
View file

@ -37,6 +37,8 @@ def test_infected_population_vectorisation(override_params):
),
expiration=cara.models._ExpirationBase.types['Breathing'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
)
emission_rate = infected.emission_rate(10)
assert isinstance(emission_rate, np.ndarray)

8
cara/tests/test_known_quantities.py
View file

@ -76,6 +76,8 @@ def build_model(interval_duration):
host_immunity=0.,
# superspreading event, where ejection factor is fixed based
# on Miller et al. (2020) - 50 represents the infectious dose.
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -238,6 +240,8 @@ def build_hourly_dependent_model(
activity=models.Activity.types['Light activity'],
known_individual_emission_rate=970 * 50,
host_immunity=0,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -261,6 +265,8 @@ def build_constant_temp_model(outside_temp, intervals_open=((7.5, 8.5),)):
activity=models.Activity.types['Light activity'],
known_individual_emission_rate=970 * 50,
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -291,6 +297,8 @@ def build_hourly_dependent_model_multipleventilation(month, intervals_open=((7.5
activity=models.Activity.types['Light activity'],
known_individual_emission_rate=970 * 50,
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)

2
cara/tests/test_monte_carlo.py
View file

@ -55,6 +55,8 @@ def baseline_mc_model() -> cara.monte_carlo.ConcentrationModel:
activity=cara.models.Activity.types['Light activity'],
expiration=cara.models.Expiration.types['Breathing'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)

16
cara/tests/test_monte_carlo_full_models.py
View file

@ -42,6 +42,8 @@ def shared_office_mc():
activity=activity_distributions['Seated'],
expiration=build_expiration({'Speaking': 0.33, 'Breathing': 0.67}),
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -84,6 +86,8 @@ def classroom_mc():
activity=activity_distributions['Light activity'],
expiration=build_expiration('Speaking'),
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -117,6 +121,8 @@ def ski_cabin_mc():
activity=activity_distributions['Moderate activity'],
expiration=build_expiration('Speaking'),
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -156,6 +162,8 @@ def skagit_chorale_mc():
activity=activity_distributions['Moderate activity'],
expiration=build_expiration('Shouting'),
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -195,6 +203,8 @@ def bus_ride_mc():
activity=activity_distributions['Seated'],
expiration=build_expiration('Speaking'),
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -229,6 +239,8 @@ def gym_mc():
activity=activity_distributions['Heavy exercise'],
expiration=expiration_distributions['Breathing'],
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -263,6 +275,8 @@ def waiting_room_mc():
activity=activity_distributions['Seated'],
expiration=build_expiration({'Speaking': 0.3, 'Breathing': 0.7}),
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)
@ -340,6 +354,8 @@ def test_small_shared_office_Geneva(mask_type, month, expected_pi,
activity=activity_distributions['Seated'],
expiration=build_expiration({'Speaking': 0.33, 'Breathing': 0.67}),
host_immunity=0.,
short_range_presence=[],
short_range_activities=[],
),
evaporation_factor=0.3,
)