Merge branch 'develop' into dash_urls_and_callbacks

Author: Eric Smyth

Dockerfile.dash

@@ -6,7 +6,7 @@ ARG PORT
 ENV PORT $PORT
 
 COPY requirements.txt requirements.txt
-RUN pip install -q -r requirements.txt
+RUN pip install -r requirements.txt
 
 COPY src src 
 

Pipfile.lock

@@ -6,7 +6,7 @@ context('Increment steppers', () => {
   });
 
   it('Increment regional population', () => {
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
 
     cy.get('input.st-al').eq(0)
       .should('has.value', '3600000');
@@ -16,11 +16,11 @@ context('Increment steppers', () => {
     cy.get('input.st-al').eq(0)
       .should('has.value', '3600001');
 
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
   });
 
   it('Increment hospital market share', () => {
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
 
     cy.get('input.st-al').eq(1)
       .should('has.value', '15');
@@ -30,11 +30,11 @@ context('Increment steppers', () => {
     cy.get('input.st-al').eq(1)
       .should('has.value', '15.1');
 
-    cy.contains('Hospitalized Admissions peaks at 303');
+    cy.contains('Hospitalized Admissions peaks at 302');
   });
 
   it('Increment doubling time', () => {
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
 
     cy.get('input.st-al').eq(3)
       .should('has.value', '4');
@@ -44,6 +44,6 @@ context('Increment steppers', () => {
     cy.get('input.st-al').eq(3)
       .should('has.value', '4.25');
 
-    cy.contains('Hospitalized Admissions peaks at 273');
+    cy.contains('Hospitalized Admissions peaks at 272');
   });
 });

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

@@ -25,7 +25,7 @@ spec:
         app: chime
     spec:
       containers:
-      - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.1.0
+      - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.1.2
         name: chime
         ports:
         - containerPort: 8000

k8s/app.yaml

@@ -1,10 +1 @@
-streamlit
-pandas
-numpy
-pytest
-altair
-dash
-dash_bootstrap_components
-pyyaml
-gunicorn
-selenium
+-e .

requirements.txt

@@ -1,45 +1,48 @@
-# -*- coding: utf-8 -*-
 """Setup file for chime
 """
-__version__ = "1.1.0"
+__version__ = "1.1.2"
 __author__ = "Predictive Healthcare @ Penn Medicine"
 
 from os import path
+from setuptools import setup, find_packages, find_namespace_packages
 
-from setuptools import setup, find_namespace_packages
-
-CWD = path.abspath(path.dirname(__file__))
-
-with open(path.join(CWD, "README.md"), encoding="utf-8") as inp:
-    LONG_DESCRIPTION = inp.read()
-
-with open(path.join(CWD, "requirements.txt"), encoding="utf-8") as inp:
-    REQUIREMENTS = [el.strip() for el in inp.read().split(",")]
 
 setup(
     name="penn_chime",
-    python_requires=">=3.7",
     version=__version__,
-    description="COVID-19 Hospital Impact Model for Epidemics",
-    long_description=LONG_DESCRIPTION,
-    long_description_content_type="text/markdown",
     author=__author__,
     author_email="",
+    description="COVID-19 Hospital Impact Model for Epidemics",
     url="https://github.com/CodeForPhilly/chime",
     project_urls={
         "Bug Reports": "https://github.com/CodeForPhilly/chime/issues",
         "Source": "https://github.com/CodeForPhilly/chime",
         "Documentation": "https://codeforphilly.github.io/chime/",
     },
-    package_dir={"": "src"},
-    packages=find_namespace_packages(where="src", exclude=("tests")),
-    install_requires=REQUIREMENTS,
+    package_dir={'': 'src'},
+    packages=find_namespace_packages(where='src', exclude=('tests')),
+    install_requires=[
+        "streamlit",
+        "pandas",
+        "numpy",
+        "altair",
+        "pytest",
+        "dash",
+        "dash_bootstrap_components",
+        "pyyaml",
+        "gunicorn", 
+        "selenium"
+    ],
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    entry_points={"console_scripts": ["penn_chime=penn_chime.cli:main"]},
+    python_requires='>=3.7',
+    entry_points = {
+        'console_scripts': ['penn_chime=penn_chime.cli:main'],
+    },
     keywords=[],
     include_package_data=True,
 )
+

setup.py

@@ -12,7 +12,7 @@
     write_definitions,
     write_footer,
 )
-from penn_chime.settings import DEFAULTS
+from penn_chime.settings import get_defaults
 from penn_chime.models import SimSirModel
 from penn_chime.charts import (
     build_admits_chart,
@@ -28,18 +28,19 @@
 # In dev, this should be shown
 st.markdown(hide_menu_style, unsafe_allow_html=True)
 
-p = display_sidebar(st, DEFAULTS)
+d = get_defaults()
+p = display_sidebar(st, d)
 m = SimSirModel(p)
 
 display_header(st, m, p)
 
 if st.checkbox("Show more info about this tool"):
     notes = "The total size of the susceptible population will be the entire catchment area for our hospitals."
-    display_more_info(st=st, model=m, parameters=p, defaults=DEFAULTS, notes=notes)
+    display_more_info(st=st, model=m, parameters=p, defaults=d, notes=notes)
 
 st.subheader("New Admissions")
 st.markdown("Projected number of **daily** COVID-19 admissions. \n\n _NOTE: Now including estimates of prior admissions for comparison._")
-admits_chart = build_admits_chart(alt=alt, admits_df=m.admits_df, max_y_axis=p.max_y_axis)
+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, suffix=" Admissions"))
 display_download_link(
@@ -53,15 +54,15 @@
     if not st.checkbox("Show Daily Counts"):
         admits_modulo = 7
     table_df = build_table(
-        df=m.admits_df,
+        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._")
-census_chart = build_census_chart(alt=alt, census_df=m.census_df, max_y_axis=p.max_y_axis)
+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, suffix=" Census"))
 display_download_link(
@@ -75,15 +76,15 @@
     if not st.checkbox("Show Daily Census Counts"):
         census_modulo = 7
     table_df = build_table(
-        df=m.census_df,
+        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_df=m.sim_sir_w_date_df)
+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)
 st.altair_chart(sim_sir_w_date_chart, use_container_width=True)
 display_download_link(
     st,
@@ -93,7 +94,7 @@
 
 if st.checkbox("Show SIR Simulation in tabular form"):
     table_df = build_table(
-        df=m.sim_sir_w_date_df,
+        df=m.sim_sir_w_date_floor_df,
         labels=p.labels)
     st.table(table_df)
 

src/app.py

@@ -2,7 +2,7 @@
 
 This directory provides the interface for the dash app.
 
-![Current interface](docs/assets/interface.png)
+![Current interface](docs/interface.png)
 
 ## Tree
 Structure of the app

src/chime_dash/README.md

@@ -1 +1,51 @@
-x = 1
+"""
+chime_dash/app
+
+dash instance defined here
+"""
+
+from dash import Dash
+from typing import TypeVar
+from chime_dash.app.config import from_object
+from penn_chime.settings import get_defaults
+from chime_dash.app.components import Body
+from chime_dash.app.utils.callbacks import wrap_callbacks
+
+DashAppInstance = TypeVar('DashAppInstance')
+DEFAULTS = get_defaults()
+
+
+def create_app(context: str = 'prod') -> DashAppInstance:
+    """
+    create_app initializes the app instance
+
+    Args:
+        context (str, optional): One of either 'prod', 'dev', 'testing.
+        Defaults to 'prod' where dash.Dash.run_server(debug=False).
+        Change to 'dev' or 'test' to set debug to true.
+
+    Returns:
+        Env: Config variables based on context argument received
+        DashAppInstance: Dash instance with appropriate configuration settings
+    """
+
+    Env = from_object(context)
+
+    LANGUAGE = Env.LANG
+    body = Body(LANGUAGE, DEFAULTS)
+
+
+    App = Dash(
+        __name__,
+        external_stylesheets=body.external_stylesheets,
+        external_scripts=body.external_scripts,
+    )
+
+    App.title = Env.CHIME_TITLE
+    App.layout = body.html
+    wrap_callbacks(App)
+
+
+
+    return Env, App
+

src/chime_dash/__init__.py

@@ -12,10 +12,12 @@
 from dash_html_components import Div
 
 from penn_chime.parameters import Parameters
-from penn_chime.settings import DEFAULTS
+from penn_chime.settings import get_defaults
 
 from chime_dash.app.utils.templates import read_localization_yml, read_localization_markdown
 
+DEFAULTS = get_defaults()
+
 
 class Component(ABC):
     """Base component for rendering dash html objects and registering callbacks