Merge branch 'develop' into chime-bus-preprod

Author: MooseQuest

Pipfile

@@ -4,6 +4,7 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
+pytest = "*"
 
 [packages]
 streamlit = "*"

Pipfile.lock

@@ -25,10 +25,12 @@ As of March 19, help is especially wanted in these areas:
 
 ## Making and Submitting Changes
 
-- Base your work on the `develop` branch in [Code for Philly's fork of the `chime` repository](https://github.com/CodeForPhilly/chime).
-- Submit a pull request, also against the `develop` branch.
+- [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [CodeforPhilly/chime](https://github.com/CodeForPhilly/chime) repo.
+- Base your work on the `develop` branch.
+- Submit pull requests from your fork, also against the `develop` branch of the `CodeforPhilly/chime` repo.
 - 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.
+- Note: Frequent contributors with write access can submit pull requests from a new branch in the `CodeforPhilly/chime` repository.
 
 ## Review & Release
 

docs/CONTRIBUTING.md

@@ -32,7 +32,7 @@
 
 ## Deploying a New CHIME Version
 
-1. [MaCreateke a new release](release-process.md)
+1. [Create a new release](release-process.md)
 2. Wait for the `Docker` GitHub Actions workflow to complete
 3. Verify the new version shows up at the top as "Latest version" here: https://github.com/CodeForPhilly/chime/packages/155340
 4. Run:

docs/operations/chime-live-cluster.md

@@ -1,9 +1,11 @@
 from typing import Tuple
 
 import numpy as np
+import streamlit as st
 
 
 # The SIR model, one time step
+@st.cache
 def sir(y, beta, gamma, N):
     S, I, R = y
     Sn = (-beta * S * I) + S
@@ -21,6 +23,7 @@ def sir(y, beta, gamma, N):
 
 
 # Run the SIR model forward in time
+@st.cache
 def sim_sir(
     S, I, R, beta, gamma, n_days, beta_decay=0
 ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
@@ -37,7 +40,7 @@ def sim_sir(
     s, i, r = np.array(s), np.array(i), np.array(r)
     return s, i, r
 
-
+@st.cache
 def get_hospitalizations(
     infected: np.ndarray, rates: Tuple[float, float, float], market_share: float
 ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:

penn_chime/models.py

@@ -46,7 +46,7 @@ def display_header(
     st.markdown(
         """*This tool was developed by the [Predictive Healthcare team](http://predictivehealthcare.pennmedicine.org/) at
     Penn Medicine. For questions and comments please see our
-    [contact page](http://predictivehealthcare.pennmedicine.org/contact/). Code can be found on [Github](https://github.com/pennsignals/chime).
+    [contact page](http://predictivehealthcare.pennmedicine.org/contact/). Code can be found on [Github](https://github.com/CodeForPhilly/chime).
     Join our [Slack channel](https://codeforphilly.org/chat?channel=covid19-chime-penn) if you would like to get involved!*"""
     )
 

penn_chime/presentation.py

@@ -1,7 +1,8 @@
 import numpy as np
 import pandas as pd
+import streamlit as st
 
-
+@st.cache
 def build_admissions_df(n_days, hosp, icu, vent) -> pd.DataFrame:
     days = np.array(range(0, n_days + 1))
     data_dict = dict(zip(["day", "hosp", "icu", "vent"], [days, hosp, icu, vent]))
@@ -12,7 +13,7 @@ def build_admissions_df(n_days, hosp, icu, vent) -> pd.DataFrame:
     projection_admits["day"] = range(projection_admits.shape[0])
     return projection_admits
 
-
+@st.cache
 def build_census_df(projection_admits, hosp_los, icu_los, vent_los) -> pd.DataFrame:
     """ALOS for each category of COVID-19 case (total guesses)"""
     n_days = np.shape(projection_admits)[0]