Merge branch 'develop' into mishmosh/docs

Author: mariekers

__init__.py

@@ -1,7 +1,12 @@
 import pytest
+import pandas as pd
 
-from penn_chime.models import sir
-from penn_chime.presentation import display_header
+from app import (S_default, known_infections, known_cases, current_hosp, doubling_time, relative_contact_rate,
+                 hosp_rate, icu_rate, vent_rate, hosp_los, icu_los, vent_los, market_share, S, initial_infections,
+                 detection_prob, hospitalization_rates, I, R, beta, gamma, n_days, beta_decay,
+                 projection_admits, alt)
+from penn_chime.models import sir, sim_sir
+from penn_chime.presentation import display_header, new_admissions_chart
 
 
 # set up
@@ -75,3 +80,52 @@ def test_sir():
         0.20297029702970298,
         0.0049504950495049506,
     ), "This contrived example should work"
+
+
+def test_sim_sir():
+    """
+    Rounding to move fast past decimal place issues
+    """
+    s, i, r = sim_sir(S, I, R, beta, gamma, n_days, beta_decay=beta_decay)
+    assert round(s[0], 0) == 4119405
+    assert round(s[-1], 2) == 3421436.31
+    assert round(i[0], 2) == 533.33
+    assert round(i[-1], 2) == 418157.62
+    assert round(r[0], 0) == 0
+    assert round(r[-1], 2) == 280344.40
+
+
+def test_initial_conditions():
+    """
+    Note: For the rates (ie hosp_rate) - just change the value, leave the "100" alone.
+        Easier to change whole numbers than decimals.
+    """
+    assert current_hosp == known_cases
+    assert doubling_time == 6
+    assert relative_contact_rate == 0
+    assert hosp_rate == 5 / 100
+    assert icu_rate == 2 / 100
+    assert vent_rate == 1 / 100
+    assert hosp_los == 7
+    assert icu_los == 9
+    assert vent_los == 10
+    assert market_share == 15 / 100
+    assert S == S_default
+    assert initial_infections == known_infections
+
+
+def test_derived_variables():
+    assert hospitalization_rates == (hosp_rate, icu_rate, vent_rate)
+    assert detection_prob == initial_infections / (current_hosp / market_share / hosp_rate)
+
+
+def test_new_admissions_chart():
+    chart = new_admissions_chart(alt, projection_admits, n_days - 10)
+    assert type(chart) == alt.Chart
+    assert chart.data.iloc[1].Hospitalized < 1
+    assert round(chart.data.iloc[49].ICU, 0) == 43
+    with pytest.raises(TypeError):
+        new_admissions_chart()
+
+    empty_chart = new_admissions_chart(alt, pd.DataFrame(), -1)
+    assert empty_chart.data.empty