Merge branch 'develop' into split-ingress

Author: MooseQuest

.cache/v/cache/lastfailed

@@ -0,0 +1,3 @@
+{
+  "test_app.py": true
+}

.dockerignore

@@ -25,3 +25,4 @@ venv
 ENV
 env.bak
 venv.bak
+cypress

.github/ISSUE_TEMPLATE/dash-feature.md

@@ -0,0 +1,14 @@
+---
+name: Dash feature request
+about: Report something that's missing from the Dash version
+title: [dash]
+labels: 'dash'
+assignees: ''
+
+---
+
+### Description:
+
+
+
+[ ] This is something we can copy over from streamlit (screenshots if applicable)

.github/ISSUE_TEMPLATE/general-bug-report.md

@@ -0,0 +1,27 @@
+---
+name: General bug report
+about: Create an report to help us improve.
+title: [bug]
+labels: 'bug'
+assignees: ''
+
+---
+
+<!--
+Before you begin, please help us manage volume by checking if this could be submitted another way:
+- Usage questions? Ask in Slack [#chime-help](https://codeforphilly.org/chat?channel=chime-help).
+- Feature ideas? Propose in Slack for discussion.
+- Is this something you can debug and fix? Pull requests are very welcome.
+-->
+
+### Description:
+
+### Steps to reproduce:
+1.
+2.
+3.
+
+### Expected behavior:
+
+### What I got instead:
+(screenshots if applicable)

.github/ISSUE_TEMPLATE/model.md

@@ -0,0 +1,26 @@
+---
+name: Bug report for model
+about: Feedback or bug report for the epidemiological model and analysis.
+title: [model]
+labels: 'models'
+assignees: ''
+
+---
+
+<!--
+Please note: Any changes to the model have a huge impact on rapidly evolving hospital system & public health decisions. The current model has been in use for a while now, and it has been validated against other similar models, so any changes to the model must meet a very high bar.
+
+However, these 2 types of issue reports are very welcome:
+- Bugs causing this model to produce invalid results. In this case, please include details and a suggested fix.
+- If this model is producing a significantly different result than another well-known epidemiological model. In this case, please include proof of this difference and a suggested fix to our approach.
+
+For questions or early discussion, please join us in [#chime-analysis](https://codeforphilly.org/chat?channel=chime-analysis) in Slack instead.
+-->
+
+### Summary
+
+
+### Additional details
+
+
+### Suggested fix

.github/workflows/heroku.yml

@@ -0,0 +1,28 @@
+name: Deploy working development app to Heroku staging project
+
+on:
+  push:
+    branches:
+      - 'develop'
+
+env:
+  HEROKU_USER: 32dd7c8d-eb68-4420-bfe2-9ed047ef8fb0
+  HEROKU_SECRET: ${{ secrets.heroku_secret_key }}
+  HEROKU_APP: cfp-ci-chime
+  HEROKU_EMAIL: [email protected]
+
+jobs:
+  deploy-heroku-stg:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Deploy app
+        id: deploy_stg_job
+        uses: akhileshns/[email protected]
+        with:
+          heroku_api_key: ${HEROKU_SECRET}
+          heroku_app_name: ${HEROKU_APP}
+          heroku_email: ${HEROKU_EMAIL}
+      - name: Return app URL
+        run: |
+          echo "Deployed to: https://${HEROKU_APP}.herokuapp.com/"

.github/workflows/pythonapp.yml

@@ -37,3 +37,11 @@ jobs:
       run: |
         pip install pytest
         python -m pytest
+    - name: Run App
+      run: |
+        streamlit run src/app.py &
+    - name: Cypress
+      uses: cypress-io/[email protected]
+      with:
+        working-directory: e2e
+

Dockerfile

@@ -1,13 +1,11 @@
 FROM python:3.7.7-slim-buster
-
-COPY .streamlit ~/
-
-COPY ./requirements.txt /app/requirements.txt
-
+RUN mkdir /app
 WORKDIR /app
-
-RUN pip install -q -r requirements.txt
-
-COPY . ./
-
-CMD ["streamlit", "run", "app.py"]
+COPY .streamlit .streamlit
+COPY README.md .
+COPY setup.py .
+COPY settings.cfg .
+COPY src src
+RUN pip install -q .
+
+CMD ["streamlit", "run", "src/app.py"]

Procfile

@@ -1 +1 @@
-web: STREAMLIT_SERVER_PORT=$PORT streamlit run app.py
+web: STREAMLIT_SERVER_PORT=$PORT streamlit run src/app.py

README.md

@@ -1,21 +1,24 @@
 # CHIME
 
-The **C**OVID-19 **H**ospital **I**mpact **M**odel for **E**pidemics
+The **C**OVID-19 **H**ospital **I**mpact **M**odel for **E**pidemics ([penn-chime.phl.io](http://penn-chime.phl.io/))
 
 [![CHIME](https://user-images.githubusercontent.com/1069047/76693244-5e07e980-6638-11ea-9e02-1c265c86fd2b.gif)](http://predictivehealthcare.pennmedicine.org/chime)
 
-Try it out online at [penn-chime.phl.io](http://penn-chime.phl.io/)
+## Background
+The [CHIME](https://penn-chime.phl.io/) (COVID-19 Hospital Impact Model for Epidemics) Application is designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily (i.e. new) and running totals of (i.e. census) inpatient hospitalizations, ICU admissions, and patients requiring ventilation. These estimates are generated using a [SIR (Susceptible, Infected, Recovered)](https://mathworld.wolfram.com/SIRModel.html) model, a standard epidemiological modeling technique. Our model has been validated by several epidemiologists including [Michael Z. Levy, PhD](https://www.dbei.med.upenn.edu/bio/michael-z-levy-phd), Associate Professor of Epidemiology, Department of Biostatistics, Epidemiology and Informatics at the Perelman School of Medicine.
 
-Interested in [contributing](https://codeforphilly.github.io/chime/CONTRIBUTING.html)?
+Originally developed in `github.com/pennsignals/chime`, active development is now at `github.com/CodeForPhilly/chime`.
 
-Join our [Code For Philly](https://codeforphilly.org/projects/chime) project or our [Slack workspace](https://codeforphilly.org/chat) in the [#covid19-chime-penn](https://codeforphilly.org/chat/covid19-chime-penn) channel if you'd like to chat with us. We'd appreciate your [feedback](http://predictivehealthcare.pennmedicine.org/contact/).
+### Documentation
+
+- [User Documentation](https://code-for-philly.gitbook.io/chime/)
+- [Developer Documentation](https://codeforphilly.github.io/chime/)
 
-## Documentation
+## Contributing
 
-- [Getting Started: Try Online](https://codeforphilly.github.io/chime/getting-started/try-online.html)
-- [Getting Started: Run Locally](https://codeforphilly.github.io/chime/getting-started/run-locally.html)
 - [Contributing: Overview](https://codeforphilly.github.io/chime/CONTRIBUTING.html)
-- [Contributing: Application Development](https://codeforphilly.github.io/chime/contributing/app-dev.html)
+
+Join our [Code For Philly](https://codeforphilly.org/projects/chime) project or our [Slack workspace](https://codeforphilly.org/chat) in the [#covid19-chime-penn](https://codeforphilly.org/chat/covid19-chime-penn) channel if you'd like to chat with us. We'd appreciate your [feedback](http://predictivehealthcare.pennmedicine.org/contact/).
 
 ## Thanks