Merge branch 'develop' into develop

Author: quinn-dougherty

docs/CONTRIBUTING.md

@@ -30,6 +30,7 @@ As of March 21, help is especially wanted from contributors with experience in K
 - Request review from the relevant maintainer(s).
 - Check your pull request periodically to see if any changes have been requested or any merge conflicts have arisen.
 - If a merge conflict arises, rebase against the latest `develop` branch and force-push the new branch as early as you can. You may need to do this more than once before your changes get merged. Do your best to keep your branch in a mergeable state until it is finished being reviewed and accepted.
+- If your change affects the results calculated or presented, update `change_date` in `src/penn_chime/parameters.py` when the pull request is ready for merge, so users can see when results have last changed
 - Note: Frequent contributors with write access can submit pull requests from a new branch in the `CodeforPhilly/chime` repository.
 
 ## Review & Release

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

@@ -8,7 +8,9 @@ context('Actions', () => {
   it('All + elements are clickable', () => {
     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.
     cy.get('input.st-al')
-      .should('has.value', '7')
+      .should('has.value', '70')
   })
 })

src/app.py

@@ -4,10 +4,8 @@
 import streamlit as st  # type: ignore
 
 from penn_chime.presentation import (
-    # additional_projections_chart,
     display_header,
     display_sidebar,
-    display_n_days_slider,
     draw_census_table,
     draw_projected_admissions_table,
     draw_raw_sir_simulation_table,
@@ -19,11 +17,10 @@
 )
 from penn_chime.settings import DEFAULTS
 from penn_chime.models import sim_sir_df, build_admissions_df, build_census_df
-from penn_chime.charts import (
-    additional_projections_chart,
-    admitted_patients_chart,
-    new_admissions_chart,
-)
+from penn_chime.charts import (additional_projections_chart,
+                               admitted_patients_chart,
+                               new_admissions_chart,
+                               chart_descriptions)
 
 # This is somewhat dangerous:
 # Hide the main menu with "Rerun", "run on Save", "clear cache", and "record a screencast"
@@ -39,10 +36,6 @@
     notes = "The total size of the susceptible population will be the entire catchment area for Penn Medicine entities (HUP, PAH, PMC, CCH)"
     show_more_info_about_this_tool(st=st, parameters=p, inputs=DEFAULTS, notes=notes)
 
-# PRESENTATION
-# Two more combination variable initialization / input element creation
-as_date = st.checkbox(label="Present result as dates instead of days", value=False)
-display_n_days_slider(st, p, DEFAULTS)
 
 # begin format data
 admissions_df = build_admissions_df(p=p)  # p.n_days, *p.dispositions)
@@ -51,30 +44,34 @@
 
 st.subheader("New Admissions")
 st.markdown("Projected number of **daily** COVID-19 admissions at Penn hospitals")
+new_admit_chart = new_admissions_chart(alt, admissions_df, parameters=p)
 st.altair_chart(
-    new_admissions_chart(alt, admissions_df, parameters=p, as_date=as_date),
-    use_container_width=True,
+    new_admit_chart, use_container_width=True
 )
+
+st.markdown(chart_descriptions(new_admit_chart))
+
 if st.checkbox("Show Projected Admissions in tabular form"):
-    draw_projected_admissions_table(st, admissions_df, as_date=as_date)
+    draw_projected_admissions_table(st, admissions_df, as_date=p.as_date)
 st.subheader("Admitted Patients (Census)")
 st.markdown(
     "Projected **census** of COVID-19 patients, accounting for arrivals and discharges at Penn hospitals"
 )
+census_chart = admitted_patients_chart(alt=alt, census=census_df, parameters=p)
 st.altair_chart(
-    admitted_patients_chart(alt=alt, census=census_df, parameters=p, as_date=as_date),
-    use_container_width=True,
+    census_chart, use_container_width=True
 )
+st.markdown(chart_descriptions(census_chart, suffix=" Census"))
 if st.checkbox("Show Projected Census in tabular form"):
-    draw_census_table(st, census_df, as_date=as_date)
+    draw_census_table(st, census_df, as_date=p.as_date)
 st.markdown(
     """**Click the checkbox below to view additional data generated by this simulation**"""
 )
 if st.checkbox("Show Additional Projections"):
     show_additional_projections(
-        st, alt, additional_projections_chart, parameters=p, as_date=as_date
+        st, alt, additional_projections_chart, parameters=p
     )
     if st.checkbox("Show Raw SIR Simulation Data"):
-        draw_raw_sir_simulation_table(st, parameters=p, as_date=as_date)
+        draw_raw_sir_simulation_table(st, parameters=p)
 write_definitions(st)
 write_footer(st)

src/cli.py

@@ -9,8 +9,8 @@
 from pandas import DataFrame
 
 from penn_chime.parameters import Parameters
-from penn_chime.utils import build_admissions_df, build_census_df, RateLos
-
+from penn_chime.utils import RateLos
+from penn_chime.models import build_admissions_df, build_census_df
 
 class FromFile(Action):
     """From File."""
@@ -123,8 +123,9 @@ def main():
             "Recovered": p.recovered_v,
         }
     )
-    admits_df = build_admissions_df(p.n_days, *p.dispositions)
-    census_df = build_census_df(admits_df, *p.lengths_of_stay)
+
+    admits_df = build_admissions_df(p)
+    census_df = build_census_df(admits_df, p)
 
     prefix = a.prefix
     for df, name in (

src/penn_chime/charts.py

@@ -1,3 +1,6 @@
+
+from math import ceil
+import datetime
 from altair import Chart  # type: ignore
 import pandas as pd  # type: ignore
 import numpy as np  # type: ignore
@@ -7,11 +10,12 @@
 
 
 def new_admissions_chart(
-    alt, projection_admits: pd.DataFrame, parameters: Parameters, as_date: bool = False,
+    alt, projection_admits: pd.DataFrame, parameters: Parameters
 ) -> Chart:
     """docstring"""
     plot_projection_days = parameters.n_days - 10
     max_y_axis = parameters.max_y_axis
+    as_date = parameters.as_date
 
     y_scale = alt.Scale()
 
@@ -45,12 +49,13 @@ def new_admissions_chart(
 
 
 def admitted_patients_chart(
-    alt, census: pd.DataFrame, parameters: Parameters, as_date: bool = False
+    alt, census: pd.DataFrame, parameters: Parameters
 ) -> Chart:
     """docstring"""
 
     plot_projection_days = parameters.n_days - 10
     max_y_axis = parameters.max_y_axis
+    as_date = parameters.as_date
     if as_date:
         census = add_date_column(census)
         x_kwargs = {"shorthand": "date:T", "title": "Date"}
@@ -84,10 +89,16 @@ def admitted_patients_chart(
 
 
 def additional_projections_chart(
-    alt, i: np.ndarray, r: np.ndarray, as_date: bool = False, max_y_axis: int = None
+    alt, parameters: Parameters
 ) -> Chart:
+    i = parameters.infected_v
+    r = parameters.recovered_v
     dat = pd.DataFrame({"Infected": i, "Recovered": r})
     dat["day"] = dat.index
+
+    as_date = parameters.as_date
+    max_y_axis = parameters.max_y_axis
+
     if as_date:
         dat = add_date_column(dat)
         x_kwargs = {"shorthand": "date:T", "title": "Date"}
@@ -112,3 +123,43 @@ def additional_projections_chart(
         )
         .interactive()
     )
+
+
+def chart_descriptions(chart: Chart, suffix: str = ""):
+    """
+
+    :param chart: Chart: The alt chart to be used in finding max points
+    :param suffix: str: The assumption is that the charts have similar column names.
+                   The census chart adds " Census" to the column names.
+                   Make sure to include a space or underscore as appropriate
+    :return: str: Returns a multi-line string description of the results
+    """
+    messages = []
+
+    cols = ["Hospitalized", "ICU", "Ventilated"]
+    asterisk = False
+    day = "date" if "date" in chart.data.columns else "day"
+
+    for col in cols:
+        if chart.data[col].idxmax() + 1 == len(chart.data):
+            asterisk = True
+
+        on = chart.data[day][chart.data[col].idxmax()]
+        if day == "date":
+            on = datetime.datetime.strftime(on, "%b %d")  # todo: bring this to an optional arg / i18n
+        else:
+            on += 1  # 0 index issue
+
+        messages.append(
+            "{}{} peaks at {:,} on day {}{}".format(
+                col,
+                suffix,
+                ceil(chart.data[col].max()),
+                on,
+                "*" if asterisk else "",
+            )
+        )
+
+    if asterisk:
+        messages.append("_* The max is at the upper bound of the data, and therefore may not be the actual max_")
+    return "\n\n".join(messages)

src/penn_chime/models.py

@@ -1,4 +1,9 @@
-"""Models."""
+"""Models.
+
+Changes affecting results or their presentation should also update
+parameters.py `change_date`, so users can see when results have last
+changed
+"""
 
 from typing import Generator, Tuple
 

src/penn_chime/parameters.py

@@ -1,4 +1,8 @@
-"""Parameters."""
+"""Parameters.
+
+Changes affecting results or their presentation should also update
+`change_date`, so users can see when results have last changed
+"""
 
 from numpy import log2  # type: ignore
 
@@ -23,7 +27,8 @@ def __init__(
         icu: RateLos,
         ventilated: RateLos,
         max_y_axis: int = None,
-        n_days: int = None
+        n_days: int = None,
+        as_date: bool = False
     ):
         self.current_hospitalized = current_hospitalized
         self.doubling_time = doubling_time
@@ -38,6 +43,7 @@ def __init__(
         self.ventilated = ventilated
 
         self.max_y_axis = max_y_axis
+        self.as_date = as_date
 
         self.rates = tuple(each.rate for each in (hospitalized, icu, ventilated))
         self.lengths_of_stay = tuple(
@@ -128,3 +134,11 @@ def n_days(self, n_days: int):
             i_icu_v,
             i_ventilated_v,
         )
+
+    def change_date(self):
+        """
+        This reflects a date from which previously-run reports will no
+        longer match current results, indicating when users should
+        re-run their reports
+        """
+        return "March 23 2020"

src/penn_chime/presentation.py

@@ -45,7 +45,7 @@ def display_header(st, p):
         unsafe_allow_html=True,
     )
     st.markdown(
-        """**IMPORTANT NOTICE**: Admissions and Census calculations were previously **undercounting**. Please update your reports. See more about this issue [here](https://github.com/CodeForPhilly/chime/pull/190)."""
+        """**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
@@ -93,6 +93,14 @@ 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(
         "Currently Hospitalized COVID-19 Patients",
         min_value=0,
@@ -204,6 +212,8 @@ def display_sidebar(st, d: Constants) -> Parameters:
         format="%i",
     )
 
+    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:
@@ -212,6 +222,7 @@ def display_sidebar(st, d: Constants) -> Parameters:
         )
 
     return Parameters(
+        n_days=n_days,
         current_hospitalized=current_hospitalized,
         doubling_time=doubling_time,
         known_infected=known_infected,
@@ -222,18 +233,7 @@ def display_sidebar(st, d: Constants) -> Parameters:
         icu=RateLos(icu_rate, icu_los),
         ventilated=RateLos(ventilated_rate, ventilated_los),
         max_y_axis=max_y_axis,
-    )
-
-
-def display_n_days_slider(st, p: Parameters, d: Constants):
-    """Display n_days_slider."""
-    p.n_days = st.slider(
-        "Number of days to project",
-        min_value=30,
-        max_value=200,
-        value=d.n_days,
-        step=1,
-        format="%i",
+        as_date=as_date,
     )
 
 
@@ -368,7 +368,7 @@ def write_footer(st):
 
 
 def show_additional_projections(
-    st, alt, charting_func, parameters, as_date: bool = False,
+    st, alt, charting_func, parameters
 ):
     st.subheader(
         "The number of infected and recovered individuals in the hospital catchment region at any given moment"
@@ -377,10 +377,7 @@ def show_additional_projections(
     st.altair_chart(
         charting_func(
             alt,
-            parameters.infected_v,
-            parameters.recovered_v,
-            as_date=as_date,
-            max_y_axis=parameters.max_y_axis,
+            parameters=parameters
         ),
         use_container_width=True,
     )
@@ -403,7 +400,6 @@ def draw_projected_admissions_table(
         admits_table = add_date_column(
             admits_table, drop_day_column=True, date_format=DATE_FORMAT
         )
-
     st.table(admits_table)
     return None
 
@@ -423,7 +419,8 @@ def draw_census_table(st, census_df: pd.DataFrame, as_date: bool = False):
     return None
 
 
-def draw_raw_sir_simulation_table(st, parameters, as_date: bool = False):
+def draw_raw_sir_simulation_table(st, parameters):
+    as_date = parameters.as_date
     days = np.arange(0, parameters.n_days + 1)
     data_list = [
         days,