Merge branch 'develop' into pip_installation_scripts

Author: quinn-dougherty

e2e/cypress/integration/tests/actions.spec.js

@@ -3,14 +3,14 @@
 context('Actions', () => {
   beforeEach(() => {
     cy.visit('http://localhost:8000')
-  })
+  });
 
   it('All + elements are clickable', () => {
-    cy.get('.step-up').click( { multiple: true } )
+    cy.get('.step-up').click( { multiple: true } );
 
     // This gets the "first" input from the sidebar. From clicking step up,
-    // the number of days to project should increase from default 60 to 70.
+    // the Regional Population should increase from default 4119405 to 4219405.
     cy.get('input.st-al')
-      .should('has.value', '70')
+      .should('has.value', '4219405')
   })
-})
+});

src/penn_chime/presentation.py

@@ -11,7 +11,7 @@
 from .parameters import Parameters
 
 DATE_FORMAT = "%b, %d"  # see https://strftime.org
-
+DOCS_URL = "https://code-for-philly.gitbook.io/chime"
 
 hide_menu_style = """
         <style>
@@ -63,7 +63,12 @@ def display_header(st, m, p):
         """**IMPORTANT NOTICE**: Admissions and Census calculations were previously **undercounting**. Please update your reports generated before """ + p.change_date() + """. See more about changes [here](https://github.com/CodeForPhilly/chime/labels/models)."""
     )
     st.markdown(
-        """*This tool was developed by the [Predictive Healthcare team](http://predictivehealthcare.pennmedicine.org/) at [Penn Medicine](https://www.pennmedicine.org) to assist hospitals and public health officials with hospital capacity planning, but can be used anywhere in the world. Customize it for your region by modifying data inputs in the left pane, or read the [User Documentation](https://code-for-philly.gitbook.io/chime/) to learn more.*"""
+        """*This tool was developed by the [Predictive Healthcare team](http://predictivehealthcare.pennmedicine.org/) at
+    Penn Medicine to assist hospitals and public health officials with hospital capacity planning, 
+    but can be used anywhere in the world. 
+    Customize it for your region by modifying data inputs in the left panel.
+    For questions on how to use this tool see the [User docs]({docs_url}). Code can be found on [Github](https://github.com/CodeForPhilly/chime)*.
+    """.format(docs_url=DOCS_URL)
     )
 
     st.markdown(
@@ -95,6 +100,7 @@ def display_header(st, m, p):
             r_t=m.r_t,
             doubling_time_t=abs(m.doubling_time_t),
             impact_statement=("halves the infections every" if m.r_t < 1 else "reduces the doubling time to"),
+            docs_url=DOCS_URL,
             infection_warning_str=infection_warning_str,
             infected_population_warning_str=infected_population_warning_str
         )
@@ -103,6 +109,30 @@ def display_header(st, m, p):
     return None
 
 
+class InputWrapper:
+    """Helper to separate Streamlit input definition from creation/rendering"""
+    def __init__(self, st_obj, label, value, kwargs):
+        self.st_obj = st_obj
+        self.label = label
+        self.value = value
+        self.kwargs = kwargs
+
+    def build(self):
+        return self.st_obj(self.label, value=self.value, **self.kwargs)
+
+
+class NumberInputWrapper(InputWrapper):
+    def __init__(self, st_obj, label, min_value=None, max_value=None, value=None, step=None, format=None, key=None):
+        kwargs = dict(min_value=min_value, max_value=max_value, step=step, format=format, key=key)
+        super().__init__(st_obj.number_input, label, value, kwargs)
+
+
+class CheckboxWrapper(InputWrapper):
+    def __init__(self, st_obj, label, value=None, key=None):
+        kwargs = dict(key=key)
+        super().__init__(st_obj.checkbox, label, value, kwargs)
+
+
 def display_sidebar(st, d: Constants) -> Parameters:
     # Initialize variables
     # these functions create input elements and bind the values they are set to
@@ -111,149 +141,163 @@ def display_sidebar(st, d: Constants) -> Parameters:
 
     if d.known_infected < 1:
         raise ValueError("Known cases must be larger than one to enable predictions.")
-
-    n_days = st.sidebar.number_input(
-        "Number of days to project",
-        min_value=30,
-        value=d.n_days,
-        step=10,
-        format="%i",
-    )
-
-    current_hospitalized = st.sidebar.number_input(
+    st_obj = st.sidebar
+    current_hospitalized = NumberInputWrapper(
+        st_obj,
         "Currently Hospitalized COVID-19 Patients",
         min_value=0,
         value=d.current_hospitalized,
         step=1,
         format="%i",
     )
-
-    doubling_time = st.sidebar.number_input(
+    n_days = NumberInputWrapper(
+        st_obj,
+        "Number of days to project",
+        min_value=30,
+        value=d.n_days,
+        step=10,
+        format="%i",
+    )
+    doubling_time = NumberInputWrapper(
+        st_obj,
         "Doubling time before social distancing (days)",
         min_value=0,
         value=d.doubling_time,
         step=1,
         format="%i",
     )
-
-    relative_contact_rate = (
-        st.sidebar.number_input(
-            "Social distancing (% reduction in social contact)",
-            min_value=0,
-            max_value=100,
-            value=int(d.relative_contact_rate * 100),
-            step=5,
-            format="%i",
-        )
-        / 100.0
-    )
-
-    hospitalized_rate = (
-        st.sidebar.number_input(
-            "Hospitalization %(total infections)",
-            min_value=0.001,
-            max_value=100.0,
-            value=d.hospitalized.rate * 100,
-            step=1.0,
-            format="%f",
-        )
-        / 100.0
-    )
-    icu_rate = (
-        st.sidebar.number_input(
-            "ICU %(total infections)",
-            min_value=0.0,
-            max_value=100.0,
-            value=d.icu.rate * 100,
-            step=1.0,
-            format="%f",
-        )
-        / 100.0
-    )
-    ventilated_rate = (
-        st.sidebar.number_input(
-            "Ventilated %(total infections)",
-            min_value=0.0,
-            max_value=100.0,
-            value=d.ventilated.rate * 100,
-            step=1.0,
-            format="%f",
-        )
-        / 100.0
+    relative_contact_rate = NumberInputWrapper(
+        st_obj,
+        "Social distancing (% reduction in social contact)",
+        min_value=0,
+        max_value=100,
+        value=int(d.relative_contact_rate * 100),
+        step=5,
+        format="%i",
     )
-
-    hospitalized_los = st.sidebar.number_input(
+    hospitalized_rate = NumberInputWrapper(
+        st_obj,
+        "Hospitalization %(total infections)",
+        min_value=0.001,
+        max_value=100.0,
+        value=d.hospitalized.rate * 100,
+        step=1.0,
+        format="%f",
+    )
+    icu_rate = NumberInputWrapper(
+        st_obj,
+        "ICU %(total infections)",
+        min_value=0.0,
+        max_value=100.0,
+        value=d.icu.rate * 100,
+        step=1.0,
+        format="%f",
+    )
+    ventilated_rate = NumberInputWrapper(
+        st_obj,
+        "Ventilated %(total infections)",
+        min_value=0.0,
+        max_value=100.0,
+        value=d.ventilated.rate * 100,
+        step=1.0,
+        format="%f",
+    )
+    hospitalized_los = NumberInputWrapper(
+        st_obj,
         "Hospital Length of Stay",
         min_value=0,
         value=d.hospitalized.length_of_stay,
         step=1,
         format="%i",
     )
-    icu_los = st.sidebar.number_input(
+    icu_los = NumberInputWrapper(
+        st_obj,
         "ICU Length of Stay",
         min_value=0,
         value=d.icu.length_of_stay,
         step=1,
         format="%i",
     )
-    ventilated_los = st.sidebar.number_input(
+    ventilated_los = NumberInputWrapper(
+        st_obj,
         "Vent Length of Stay",
         min_value=0,
         value=d.ventilated.length_of_stay,
         step=1,
         format="%i",
     )
-
-    market_share = (
-        st.sidebar.number_input(
-            "Hospital Market Share (%)",
-            min_value=0.001,
-            max_value=100.0,
-            value=d.market_share * 100,
-            step=1.0,
-            format="%f",
-        )
-        / 100.0
-    )
-    susceptible = st.sidebar.number_input(
+    market_share = NumberInputWrapper(
+        st_obj,
+        "Hospital Market Share (%)",
+        min_value=0.001,
+        max_value=100.0,
+        value=d.market_share * 100,
+        step=1.0,
+        format="%f",
+    )
+    susceptible = NumberInputWrapper(
+        st_obj,
         "Regional Population",
         min_value=1,
         value=d.region.susceptible,
         step=100000,
         format="%i",
     )
-
-    known_infected = st.sidebar.number_input(
+    known_infected = NumberInputWrapper(
+        st_obj,
         "Currently Known Regional Infections (only used to compute detection rate - does not change projections)",
         min_value=0,
         value=d.known_infected,
         step=10,
         format="%i",
     )
+    as_date = CheckboxWrapper(st_obj, "Present result as dates instead of days", value=False)
+    max_y_axis_set = CheckboxWrapper(st_obj, "Set the Y-axis on graphs to a static value")
 
-    as_date = st.sidebar.checkbox(label="Present result as dates instead of days", value=False)
-
-    max_y_axis_set = st.sidebar.checkbox("Set the Y-axis on graphs to a static value")
     max_y_axis = None
     if max_y_axis_set:
-        max_y_axis = st.sidebar.number_input(
-            "Y-axis static value", value=500, format="%i", step=25,
-        )
+        max_y_axis = NumberInputWrapper(st_obj, "Y-axis static value", value=500, format="%i", step=25)
+
+    # Build in desired order
+    st.sidebar.markdown("### Regional Parameters [ℹ]({docs_url}/what-is-chime/parameters)".format(docs_url=DOCS_URL))
+    susceptible.build()
+    market_share.build()
+    known_infected.build()
+    current_hospitalized.build()
+
+    st.sidebar.markdown("### Spread and Contact Parameters [ℹ]({docs_url}/what-is-chime/parameters)"
+                        .format(docs_url=DOCS_URL))
+    doubling_time.build()
+    relative_contact_rate.build()
+
+    st.sidebar.markdown("### Severity Parameters [ℹ]({docs_url}/what-is-chime/parameters)".format(docs_url=DOCS_URL))
+    hospitalized_rate.build()
+    icu_rate.build()
+    ventilated_rate.build()
+    hospitalized_los.build()
+    icu_los.build()
+    ventilated_los.build()
+
+    st.sidebar.markdown("### Display Parameters [ℹ]({docs_url}/what-is-chime/parameters)".format(docs_url=DOCS_URL))
+    n_days.build()
+    max_y_axis.build()
+    as_date.build()
 
     return Parameters(
-        as_date=as_date,
-        current_hospitalized=current_hospitalized,
-        doubling_time=doubling_time,
-        known_infected=known_infected,
-        market_share=market_share,
-        max_y_axis=max_y_axis,
-        n_days=n_days,
-        relative_contact_rate=relative_contact_rate,
-        susceptible=susceptible,
+        as_date=as_date.value,
+        current_hospitalized=current_hospitalized.value,
+        market_share=market_share.value,
+        known_infected=known_infected.value,
+        doubling_time=doubling_time.value,
+
+        max_y_axis=max_y_axis.value,
+        n_days=n_days.value,
+        relative_contact_rate=relative_contact_rate.value / 100.0,
+        susceptible=susceptible.value,
 
-        hospitalized=RateLos(hospitalized_rate, hospitalized_los),
-        icu=RateLos(icu_rate, icu_los),
-        ventilated=RateLos(ventilated_rate, ventilated_los),
+        hospitalized=RateLos(hospitalized_rate.value / 100.0, hospitalized_los.value),
+        icu=RateLos(icu_rate.value / 100.0, icu_los.value),
+        ventilated=RateLos(ventilated_rate.value / 100.0, ventilated_los.value),
     )
 
 
@@ -362,7 +406,7 @@ def write_definitions(st):
     st.subheader("Guidance on Selecting Inputs")
     st.markdown(
         """**This information has been moved to the 
-[User Documentation](https://code-for-philly.gitbook.io/chime/what-is-chime/parameters#guidance-on-selecting-inputs)**"""
+[User Documentation]({docs_url}/what-is-chime/parameters#guidance-on-selecting-inputs)**""".format(docs_url=DOCS_URL)
     )