moved Expiration types to the conftest file

cara/apps/expert.py

@@ -11,6 +11,7 @@ import matplotlib.figure
 from cara import models
 from cara import state
 from cara import data
+from cara.tests.conftest import expiration_types
 
 
 def collapsible(widgets_to_collapse: typing.List, title: str, start_collapsed=False):
@@ -405,13 +406,13 @@ class ModelWidgets(View):
 
     def _build_expiration(self, node):
         expiration = node.dcs_instance()
-        for name, expiration_ in models.Expiration.types.items():
+        for name, expiration_ in expiration_types.items():
             if expiration == expiration_:
                 break
-        expiration_choice = widgets.Select(options=list(models.Expiration.types.keys()), value=name)
+        expiration_choice = widgets.Select(options=list(expiration_types.keys()), value=name)
 
         def on_expiration_change(change):
-            expiration = models.Expiration.types[change['new']]
+            expiration = expiration_types[change['new']]
             node.dcs_update_from(expiration)
         expiration_choice.observe(on_expiration_change, names=['value'])
 
@@ -498,7 +499,7 @@ baseline_model = models.ExposureModel(
             presence=models.SpecificInterval(((8., 12.), (13., 17.))),
             mask=models.Mask.types['No mask'],
             activity=models.Activity.types['Seated'],
-            expiration=models.Expiration.types['Speaking'],
+            expiration=expiration_types['Speaking'],
             host_immunity=0.,
         ),
         evaporation_factor=0.3,

cara/models.py

@@ -695,19 +695,6 @@ class MultipleExpiration(_ExpirationBase):
         ]).sum(axis=0)
 
 
-# Typical expirations. The aerosol diameter given is an equivalent
-# diameter, chosen in such a way that the aerosol volume is
-# the same as the total aerosol volume given by the full BLO model
-# (integrated between 0.1 and 30 microns)
-# The correspondence with the BLO coefficients is given.
-_ExpirationBase.types = {
-    'Breathing': Expiration(1.3844), # corresponds to B/L/O coefficients of (1, 0, 0)
-    'Speaking': Expiration(5.8925),   # corresponds to B/L/O coefficients of (1, 1, 1)
-    'Shouting': Expiration(10.0411), # corresponds to B/L/O coefficients of (1, 5, 5)
-    'Singing': Expiration(10.0411),  # corresponds to B/L/O coefficients of (1, 5, 5)
-}
-
-
 @dataclass(frozen=True)
 class Activity:
     #: Inhalation rate in m^3/h

cara/tests/conftest.py

@@ -5,6 +5,19 @@ import cara.dataclass_utils
 import pytest
 
 
+# Typical expirations. The aerosol diameter given is an equivalent
+# diameter, chosen in such a way that the aerosol volume is
+# the same as the total aerosol volume given by the full BLO model
+# (integrated between 0.1 and 30 microns)
+# The correspondence with the BLO coefficients is given.
+expiration_types = {
+    'Breathing': models.Expiration(1.3844), # corresponds to B/L/O coefficients of (1, 0, 0)
+    'Speaking': models.Expiration(5.8925),   # corresponds to B/L/O coefficients of (1, 1, 1)
+    'Shouting': models.Expiration(10.0411), # corresponds to B/L/O coefficients of (1, 5, 5)
+    'Singing': models.Expiration(10.0411),  # corresponds to B/L/O coefficients of (1, 5, 5)
+}
+
+
 @pytest.fixture
 def baseline_model():
     model = models.ConcentrationModel(

cara/tests/models/test_concentration_model.py

@@ -5,6 +5,7 @@ import numpy.testing as npt
 import pytest
 
 from cara import models
+from cara.tests.conftest import expiration_types
 
 
 @pytest.mark.parametrize(
@@ -45,7 +46,7 @@ def test_concentration_model_vectorisation(override_params):
                 viable_to_RNA_ratio = 0.5,
                 transmissibility_factor=1.0,
             ),
-            expiration=models._ExpirationBase.types['Breathing'],
+            expiration=expiration_types['Breathing'],
             host_immunity=0.,
         ),
         evaporation_factor=0.3,
@@ -67,7 +68,7 @@ def simple_conc_model():
             mask=models.Mask.types['Type I'],
             activity=models.Activity.types['Seated'],
             virus=models.Virus.types['SARS_CoV_2'],
-            expiration=models.Expiration.types['Breathing'],
+            expiration=expiration_types['Breathing'],
             host_immunity=0.,
         ),
         evaporation_factor=0.3,

cara/tests/models/test_exposure_model.py

@@ -8,6 +8,7 @@ from dataclasses import dataclass
 from cara import models
 from cara.models import ExposureModel
 from cara.dataclass_utils import replace
+from cara.tests.conftest import expiration_types
 
 
 @dataclass(frozen=True)
@@ -64,7 +65,7 @@ def known_concentrations(func):
         mask=models.Mask.types['Type I'],
         activity=models.Activity.types['Standing'],
         virus=models.Virus.types['SARS_CoV_2_ALPHA'],
-        expiration=models.Expiration.types['Speaking'],
+        expiration=expiration_types['Speaking'],
         host_immunity=0.,
     )
     normed_func = lambda x: func(x) / dummy_infected_population.emission_rate_when_present()
@@ -205,7 +206,7 @@ def test_infectious_dose_vectorisation():
             viable_to_RNA_ratio = 0.5,
             transmissibility_factor=1.0,
         ),
-        expiration=models.Expiration.types['Speaking'],
+        expiration=expiration_types['Speaking'],
         host_immunity=0.,
     )
     cm = known_concentrations(lambda t: 1.2)

cara/tests/test_expiration.py

@@ -6,6 +6,7 @@ import pytest
 
 from cara import models
 from cara.monte_carlo.data import expiration_distribution
+from cara.tests.conftest import expiration_types
 
 
 def test_multiple_wrong_weight_size():
@@ -34,8 +35,8 @@ def test_multiple_wrong_diameters():
 def test_multiple():
     weights = (1., 1.)
     mask = models.Mask.types['Type I']
-    e1 = models.Expiration.types['Breathing']
-    e2 = models.Expiration.types['Singing']
+    e1 = expiration_types['Breathing']
+    e2 = expiration_types['Singing']
     aerosol_expected = (e1.aerosols(mask) + e2.aerosols(mask))/2.
     e = models.MultipleExpiration([e1, e2], weights)
     npt.assert_almost_equal(aerosol_expected, e.aerosols(mask))

cara/tests/test_infected_population.py

@@ -2,6 +2,7 @@ import numpy as np
 import pytest
 
 import cara.models
+from cara.tests.conftest import expiration_types
 
 
 @pytest.mark.parametrize(
@@ -35,7 +36,7 @@ def test_infected_population_vectorisation(override_params):
                 viable_to_RNA_ratio = 0.5,
                 transmissibility_factor=1.0,
             ),
-            expiration=cara.models._ExpirationBase.types['Breathing'],
+            expiration=expiration_types['Breathing'],
             host_immunity=0.,
     )
     emission_rate = infected.emission_rate(10)

cara/tests/test_monte_carlo.py

@@ -6,6 +6,7 @@ import pytest
 import cara.models
 import cara.monte_carlo.models as mc_models
 import cara.monte_carlo.sampleable
+from cara.tests.conftest import expiration_types
 
 
 MODEL_CLASSES = [
@@ -53,7 +54,7 @@ def baseline_mc_model() -> cara.monte_carlo.ConcentrationModel:
             presence=cara.models.SpecificInterval(((0., 4.), (5., 8.))),
             mask=cara.models.Mask.types['No mask'],
             activity=cara.models.Activity.types['Light activity'],
-            expiration=cara.models.Expiration.types['Breathing'],
+            expiration=expiration_types['Breathing'],
             host_immunity=0.,
         ),
         evaporation_factor=0.3,