Merge branch 'develop' into issues/66

Author: quinn-dougherty

.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/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

@@ -10,4 +10,4 @@ RUN pip install -q -r requirements.txt
 
 COPY . ./
 
-CMD ["streamlit", "run", "app.py"]
+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/pennsignals/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
 

app.py

@@ -4,30 +4,30 @@ Welcome, grab a cup of coffee, and let's roll our sleeves up! By participating i
 
 ## What should I work on?
 
-As of March 19, help is especially wanted in these areas:
-
-- **Python wizards** for application development ([#chime-app](https://codeforphilly.org/chat?channel=chime-app))
-  - Hardening the code
-  - Making it more flexible
-  - Unit tests!
-- **DevOps heroes** for application hosting ([#chime-ops](https://codeforphilly.org/chat?channel=chime-ops))
-  - Maintaining Penn's instance
-  - Ensuring easy redeploys
-- **Math and stats friends** for model improvements ([#chime-analysis](https://codeforphilly.org/chat?channel=chime-analysis))
-- **Consulting DevOps champs** to help other public agencies set up their own instances ([#chime-help](https://codeforphilly.org/chat?channel=chime-help)
+Our project work is organized by 4 main areas:
+
+| Area        | What type of help wanted? | Project Board                                         | Slack channel           | Maintainers |
+| --- | --- | --- | --- | --- |
+| App Platform        | Python wizards to work on application development, hardening the code, making it more flexible, and unit testing | [Board](https://github.com/CodeForPhilly/chime/projects/3) | [#chime-app](https://codeforphilly.org/chat?channel=chime-app) | @quinndougherty                      |
+| Analysis            | Epidemiologists and other math and stats friends, for model improvements | [Board](https://github.com/CodeForPhilly/chime/projects/5) | [#chime-analysis](https://codeforphilly.org/chat?channel=chime-analysis) | @sam-qordoba, @cjbayesian                   |
+| DevOps              | DevOps heroes (especially if you have Kubernetes experience) for hosting, maintenance, and ensuring easy redeploys. | [Board](https://github.com/CodeForPhilly/chime/projects/2) | [#chime-ops](https://codeforphilly.org/chat?channel=chime-ops) | @moosequest, @themightychris, @lottspot |
+| General Project Ops | Writing, documentation, and project and product management | [Board](https://github.com/CodeForPhilly/chime/projects/6) |  | @mariekers                           |
+
+As of March 21, help is especially wanted from contributors with experience in Kubernetes and Python.
 
 ## Before You Begin
 
-- Join the [#covid19-chime-penn](https://codeforphilly.org/chat?channel=covid19-chime-penn) channel, and [request write access](https://codeforphilly.slack.com/archives/CV4NGQYMP/p1584665484368300) to the `CodeforPhilly/chime` Github repository.
-- Our highest-priority work is organized in the [Github Project Management board](https://github.com/CodeForPhilly/chime/projects/2). Look for an issue matching your interests & skills in one of the "Ready" columns.
-- Assign yourself to the issue and add a comment to briefly describe your plan.
-- For new ideas, please first discuss the change(s) you wish to make via [issue](https://github.com/codeforphilly/chime/issues) or appropriate Slack channel (platform/app - #chime-app, devops - #chime-ops, modeling - #chime-analysis). 
+- Join the [#covid19-chime-penn](https://codeforphilly.org/chat?channel=covid19-chime-penn) channel for project-wide announcements.
+- Our highest-priority work is organized in [Github Project Boards](https://github.com/CodeForPhilly/chime/projects). Look for an issue matching your interests & skills in the "Ready" columns.
+- Comment on the issue to let us know you're picking it up, briefly describe your plan, and go forth!
+- For new ideas, please first discuss the change(s) you wish to make via [issue](https://github.com/codeforphilly/chime/issues) or the appropriate Slack channel (see table above).
 
 ## Making and Submitting Changes
 
 - [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.
+- 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.
 - Note: Frequent contributors with write access can submit pull requests from a new branch in the `CodeforPhilly/chime` repository.
@@ -39,8 +39,8 @@ As of March 19, help is especially wanted in these areas:
 - Maintainers will review pull requests, asking for changes as needed.
 - Once a PR has 1 approval and passes automated tests, maintainers will merge to release branches.
   - Exception: Documentation or infrastructure support PRs can be merged directly to master.
-- Deploys to production must be signed off on by @beckerfluffle or @cchivers.
+- Deploys to production must be signed off by @beckerfluffle or @cchivers.
 
 ## Requesting Functionality
 
-**Stakeholders/Users**: Check the [#covid19-chime-penn](https://codeforphilly.org/chat/covid19-chime-penn) channel on [Slack](https://codeforphilly.org/chat) to see if your need is already being addressed.
+**Stakeholders/Users**: Check the [#chime-users](https://codeforphilly.org/chat/chime-users) channel on [Slack](https://codeforphilly.org/chat) to see if your need is already being addressed.

docs/CONTRIBUTING.md

@@ -1,6 +1,6 @@
-# CHIME Documentation
+# CHIME Developer Documentation
 
-This book is the living documentation for developers and operators working on [the CHIME project](https://github.com/CodeForPhilly/chime) or running instances of it.
+This book is the living documentation for developers and operators working on [the CHIME project](https://github.com/CodeForPhilly/chime) or running instances of it. Hospitals and public officials, please see [User Documentaiton](https://code-for-philly.gitbook.io/chime/).
 
 It is maintained in the [GitBook format](https://gitbookio.gitbooks.io/docs-toolchain/structure.html) within [the `docs/` directory](https://github.com/CodeForPhilly/chime/tree/develop/docs) of the project's main Git repository, and new versions are published automatically upon merge to the `develop` branch to: [codeforphilly.github.io/chime](https://codeforphilly.github.io/chime)
 

docs/README.md

@@ -24,7 +24,7 @@ See [Streamlit's Getting Started guide](https://docs.streamlit.io/getting_starte
 ```bash
 pipenv shell
 pipenv install
-streamlit run app.py
+streamlit run src/app.py
 ```
 
 ### With `conda`
@@ -33,7 +33,7 @@ streamlit run app.py
 conda env create -f environment.yml
 source activate chime
 pip install streamlit
-streamlit run app.py
+streamlit run src/app.py
 ```
 
 ### Choosing a Different Port
@@ -42,15 +42,15 @@ If you need to run the application on a different port than the default (8000),
 
 ```bash
 export STREAMLIT_SERVER_PORT=1234
-streamlit run app.py
+streamlit run src/app.py
 ```
 
 ## Project Layout
 
 ### Application files
 
-- `app.py`: Main source for the application
-- `test_app.py`: [pytest](https://docs.pytest.org/en/latest/) tests for `app.py`
+- `src/app.py`: Main source for the application
+- `src/test_app.py`: [pytest](https://docs.pytest.org/en/latest/) tests for `app.py`
 - `script/`: Developer workflow scripts following [GitHub's Scripts To Rule Them All](https://github.com/github/scripts-to-rule-them-all) pattern.
 - `.streamlit/`: [Streamlit config options](https://docs.streamlit.io/cli.html)
 - `.env`: Local environment variables to use when running application, this file is copied from `.env.example` to start you out and then ignored by git