Merge branch 'develop' into btr-pr-template

Author: BrianThomasRoss

defaults/cli.cfg

@@ -1,14 +1,14 @@
 --current-hospitalized 69
---doubling-time 4.0
+--doubling-time 5.0
 --hospitalized-days 7
 --hospitalized-rate 0.025
 --icu-days 9
 --icu-rate 0.0075
---infectious-days 14
+--infectious-days 10
 --market-share 0.15
 --n-days 100
 --population 3600000
 --recovered 0
---relative-contact-rate 0.3
+--relative-contact-rate 0.45
 --ventilated-days 10
 --ventilated-rate 0.005

defaults/webapp.cfg

@@ -1,15 +1,15 @@
 --current-hospitalized 69
 --date-first-hospitalized 2020-03-07
---doubling-time 4.0
+--doubling-time 5.0
 --hospitalized-days 7
 --hospitalized-rate 0.025
 --icu-days 9
 --icu-rate 0.0075
---infectious-days 14
+--infectious-days 10
 --market-share 0.15
 --n-days 100
 --population 3600000
 --recovered 0
---relative-contact-rate 0.3
+--relative-contact-rate 0.45
 --ventilated-days 10
 --ventilated-rate 0.005

docs/operations/README.md

@@ -1,6 +1,6 @@
 # Operations guide to resources
 
-This guide will show you where nodes, and k8s clusters are stored and their heirarchy.
+This guide will show you where nodes, and k8s clusters are stored and their hierarchy.
 
 ## Production
 
@@ -13,4 +13,4 @@ Production k8s cluster is available on linode datacenter.
 
 Pre Production k8s cluster is available on linode datacenter.
 
-`chime-bus`
+`chime-bus`

docs/operations/prepare-new-chime-release.md

@@ -37,4 +37,4 @@ At the end of following this process you will have deployed a new CHIME version
  the review of another DevOps admin whenever possible. Ensure to link
  to the PR in the deployment issue previously opened on GitHub.
 
-6. One approved you will need to [create a release to auto deploy](release-process.md)
+6. Once approved, you will need to [create a release to auto deploy](release-process.md)

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

@@ -6,7 +6,7 @@ context('Increment steppers', () => {
   });
 
   it('Increment regional population', () => {
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('Regional population (3600000)');
 
     cy.get('input[type=number]').eq(0)
       .should('has.value', '3600000');
@@ -16,11 +16,11 @@ context('Increment steppers', () => {
     cy.get('input[type=number]').eq(0)
       .should('has.value', '3600001');
 
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('Regional population (3600001)');
   });
 
   it('Increment hospital market share', () => {
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('The estimated number of currently infected individuals is 20128.');
 
     cy.get('input[type=number]').eq(1)
       .should('has.value', '15');
@@ -30,11 +30,11 @@ context('Increment steppers', () => {
     cy.get('input[type=number]').eq(1)
       .should('has.value', '15.1');
 
-    cy.contains('Hospitalized Admissions peaks at 302');
+    cy.contains('The estimated number of currently infected individuals is 19996.');
   });
 
   it('Increment doubling time', () => {
-    cy.contains('Hospitalized Admissions peaks at 300');
+    cy.contains('An initial doubling time of 4.0 days');
 
     cy.get('input[type=number]').eq(3)
       .should('has.value', '4');
@@ -44,6 +44,6 @@ context('Increment steppers', () => {
     cy.get('input[type=number]').eq(3)
       .should('has.value', '4.25');
 
-    cy.contains('Hospitalized Admissions peaks at 272');
+    cy.contains('An initial doubling time of 4.25 days');
   });
 });

src/app.py

@@ -17,9 +17,7 @@
 from penn_chime.charts import (
     build_admits_chart,
     build_census_chart,
-    build_descriptions,
     build_sim_sir_w_date_chart,
-    build_table,
 )
 
 # This is somewhat dangerous:
@@ -35,49 +33,25 @@
 display_header(st, m, p)
 
 st.subheader("New Admissions")
-st.markdown("Projected number of **daily** COVID-19 admissions. \n\n _NOTE: Now including estimates of prior admissions for comparison._")
+st.markdown("Projected number of **daily** COVID-19 admissions.")
 admits_chart = build_admits_chart(alt=alt, admits_floor_df=m.admits_floor_df, max_y_axis=p.max_y_axis)
 st.altair_chart(admits_chart, use_container_width=True)
-st.markdown(build_descriptions(chart=admits_chart, labels=p.labels, prefix="admits_", suffix=" Admissions"))
 display_download_link(
     st,
     filename=f"{p.current_date}_projected_admits.csv",
     df=m.admits_df,
 )
 
-if st.checkbox("Show Projected Admissions in tabular form"):
-    admits_modulo = 1
-    if not st.checkbox("Show Daily Counts"):
-        admits_modulo = 7
-    table_df = build_table(
-        df=m.admits_floor_df,
-        labels=p.labels,
-        modulo=admits_modulo)
-    st.table(table_df)
-
-
 st.subheader("Admitted Patients (Census)")
-st.markdown("Projected **census** of COVID-19 patients, accounting for arrivals and discharges \n\n _NOTE: Now including estimates of prior census for comparison._")
+st.markdown("Projected **census** of COVID-19 patients, accounting for arrivals and discharges.")
 census_chart = build_census_chart(alt=alt, census_floor_df=m.census_floor_df, max_y_axis=p.max_y_axis)
 st.altair_chart(census_chart, use_container_width=True)
-st.markdown(build_descriptions(chart=census_chart, labels=p.labels, prefix="census_", suffix=" Census"))
 display_download_link(
     st,
     filename=f"{p.current_date}_projected_census.csv",
     df=m.census_df,
 )
 
-if st.checkbox("Show Projected Census in tabular form"):
-    census_modulo = 1
-    if not st.checkbox("Show Daily Census Counts"):
-        census_modulo = 7
-    table_df = build_table(
-        df=m.census_floor_df,
-        labels=p.labels,
-        modulo=census_modulo)
-    st.table(table_df)
-
-
 st.subheader("Susceptible, Infected, and Recovered")
 st.markdown("The number of susceptible, infected, and recovered individuals in the hospital catchment region at any given moment")
 sim_sir_w_date_chart = build_sim_sir_w_date_chart(alt=alt, sim_sir_w_date_floor_df=m.sim_sir_w_date_floor_df)
@@ -88,10 +62,4 @@
     df=m.sim_sir_w_date_df,
 )
 
-if st.checkbox("Show SIR Simulation in tabular form"):
-    table_df = build_table(
-        df=m.sim_sir_w_date_floor_df,
-        labels=p.labels)
-    st.table(table_df)
-
 display_footer(st)

src/chime_dash/README.md

@@ -119,7 +119,7 @@ Install the chime base module
 ```
 and run
 ```bash
-> python src/dash_app.py
+> PARAMETERS=defaults/webapp.cfg python src/dash_app.py
 ```
 in the project root and visit the local url.
 

src/penn_chime/charts.py

@@ -127,51 +127,6 @@ def build_sim_sir_w_date_chart(
     )
 
 
-def build_descriptions(
-    *,
-    chart: Chart,
-    labels: Dict[str, str],
-    prefix: str = "",
-    suffix: str = ""
-) -> str:
-    """
-
-    :param chart: The alt chart to be used in finding max points
-    :param suffix: 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: 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[prefix+col].idxmax() + 1 == len(chart.data):
-            asterisk = True
-
-        # todo: bring this to an optional arg / i18n
-        on = datetime.strftime(chart.data[day][chart.data[prefix+col].idxmax()], "%b %d")
-
-        messages.append(
-            "{}{} peaks at {:,} on {}{}".format(
-                labels[col],
-                suffix,
-                ceil(chart.data[prefix+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)
-
-
 def build_table(
     *, df: pd.DataFrame, labels: Dict[str, str], modulo: int = 1
 ) -> pd.DataFrame:

src/penn_chime/models.py

@@ -287,18 +287,6 @@ def sir(
     s_n = (-beta * s * i) + s
     i_n = (beta * s * i - gamma * i) + i
     r_n = gamma * i + r
-
-    # TODO:
-    #   Post check dfs for negative values and
-    #   warn the user that their input data is bad.
-    #   JL: I suspect that these adjustments covered bugs.
-
-    #if s_n < 0.0:
-    #    s_n = 0.0
-    #if i_n < 0.0:
-    #    i_n = 0.0
-    #if r_n < 0.0:
-    #    r_n = 0.0
     scale = n / (s_n + i_n + r_n)
     return s_n * scale, i_n * scale, r_n * scale
 

tests/penn_chime/test_charts.py

@@ -1,18 +1,11 @@
-from math import ceil
-from datetime import datetime
-
 import altair as alt
 import pytest
 
 from penn_chime.charts import (
     build_admits_chart,
     build_census_chart,
-    build_descriptions,
 )
 
-# TODO add test for asterisk
-
-
 DISPOSITION_KEYS = ("hospitalized", "icu", "ventilated")
 
 
@@ -26,36 +19,6 @@ def test_admits_chart(admits_floor_df):
         build_admits_chart()
 
 
-def test_build_descriptions(admits_floor_df, param):
-    chart = build_admits_chart(alt=alt, admits_floor_df=admits_floor_df)
-    description = build_descriptions(chart=chart, labels=param.labels, prefix="admits_")
-
-    hosp, icu, vent = description.split("\n\n")  # break out the description into lines
-
-    max_hosp = chart.data["admits_hospitalized"].max()
-    assert str(ceil(max_hosp)) in hosp
-
-
-def test_no_asterisk(admits_floor_df, param):
-    param.n_days = 600
-
-    chart = build_admits_chart(alt=alt, admits_floor_df=admits_floor_df)
-    description = build_descriptions(chart=chart, labels=param.labels, prefix="admits_")
-    assert "*" not in description
-
-
-def test_census(census_floor_df, param):
-    chart = build_census_chart(alt=alt, census_floor_df=census_floor_df)
-    description = build_descriptions(chart=chart, labels=param.labels, prefix="census_")
-
-    assert str(ceil(chart.data["census_ventilated"].max())) in description
-    assert str(chart.data["census_icu"].idxmax()) not in description
-    assert (
-        datetime.strftime(chart.data.iloc[chart.data["census_icu"].idxmax()].date, "%b %d")
-        in description
-    )
-
-
 def test_census_chart(census_floor_df):
     chart = build_census_chart(alt=alt, census_floor_df=census_floor_df)
     assert isinstance(chart, (alt.Chart, alt.LayerChart))