Merge remote-tracking branch 'upstream/develop' into develop

Author: mangala915

.gitattributes

@@ -0,0 +1 @@
+* text=auto

.github/workflows/pythonapp.yml

@@ -43,7 +43,7 @@ jobs:
         python -m pytest
     - name: Run App
       run: |
-        PARAMETERS=./defaults/cypress.cfg streamlit run src/app.py &
+        PARAMETERS=./defaults/cypress.cfg streamlit run st_app.py &
     - name: Cypress
       uses: cypress-io/github-action@v1
       with:

Dockerfile

@@ -7,7 +7,8 @@ COPY setup.py .
 COPY .streamlit .streamlit
 COPY defaults defaults
 COPY src src
+COPY st_app.py st_app.py
 RUN pip install -q .
 
-CMD ["streamlit", "run", "src/app.py"]
+CMD ["streamlit", "run", "st_app.py"]
 

Procfile

@@ -1 +1 @@
-web: PARAMETERS=defaults/webapp.cfg STREAMLIT_SERVER_PORT=$PORT streamlit run src/app.py
+web: PARAMETERS=defaults/webapp.cfg STREAMLIT_SERVER_PORT=$PORT streamlit run st_app.py

date_first_hospitalized.cfg defaults/date_first_hospitalized.cfgdate_first_hospitalized.cfg renamed to defaults/date_first_hospitalized.cfg

@@ -1,14 +1,16 @@
+--current-date 2020-04-28
 --current-hospitalized 14
 --date-first-hospitalized 2020-03-07
---hospitalized-los 7
+--hospitalized-days 7
 --hospitalized-rate 0.025
---icu-los 9
+--icu-days 9
 --icu-rate 0.0075
 --infectious-days 14
---known-infected 510
---market_share 0.15
+--mitigation-date 2020-04-28
+--market-share 0.15
 --n-days 60
 --population 4119405
+--recovered 0
 --relative-contact-rate 0.3
---ventilated-los 10
+--ventilated-days 10
 --ventilated-rate 0.005

doubling_time.cfg defaults/doubling_time.cfgdoubling_time.cfg renamed to defaults/doubling_time.cfg

@@ -1,14 +1,16 @@
+--current-date 2020-04-28
 --current-hospitalized 14
 --doubling-time 4.0
---hospitalized-los 7
+--hospitalized-days 7
 --hospitalized-rate 0.025
---icu-los 9
+--icu-days 9
 --icu-rate 0.0075
 --infectious-days 14
---known-infected 510
---market_share 0.15
+--market-share 0.15
+--mitigation-date 2020-04-28
 --n-days 60
 --population 4119405
+--recovered 0
 --relative-contact-rate 0.3
---ventilated-los 10
+--ventilated-days 10
 --ventilated-rate 0.005

docs/SUMMARY.md

@@ -9,8 +9,8 @@
   - [Data Analysis](contributing/data-analysis.md)
   - [Operations Support](contributing/operations-support.md)
 - Operations
-  - [Preparing a new release](./operations/prepare-new-chime-release.md)
-  - [Release Process](./operations/release=process.md)
+  - [Release Process](./operations/release-process.md)
+  - [Release Automation](./operations/release-automation.md)
   - [The `chime-live` Cluster](./operations/chime-live-cluster.md)
   - [Deploy to Heroku](./operations/heroku.md)
   - [Deploy with Chef Habitat](./operations/habitat.md)

docs/contributing/app-dev.md

@@ -12,19 +12,27 @@
 
 The application is built with [Streamlit](https://www.streamlit.io/), Streamlit requires:
 
-- Python 2.7.0 or later / Python 3.6.x or later
+- Python 3.6.x or later
 - PIP
 
 See [Streamlit's Getting Started guide](https://docs.streamlit.io/getting_started.html) for detailed information on prerequisites and setup
 
 ## Running CHIME Locally
 
+
+### With `venv`
+
+```bash
+python3 -m venv ~.venv
+. ~.venv/bin/activate
+pip install -e .
+```
+
 ### With `pipenv`
 
 ```bash
 pipenv shell
 pipenv sync --dev
-PARAMETERS=defaults/webapp.cfg streamlit run src/app.py
 ```
 
 ### With `conda`
@@ -33,32 +41,60 @@ PARAMETERS=defaults/webapp.cfg streamlit run src/app.py
 conda env create -f environment.yml
 source activate chime
 pip install streamlit
-PARAMETERS=defaults/webapp.cfg streamlit run src/app.py
 ```
 
+## Run the Streamlit Web App
+
+```bash
+PARAMETERS=-./defaults/webapp.cfg streamlit run st_app.py
+```
+
+## Run the Command Line Interface
+
+```bash
+PARAMETERS=./defaults/cli.cfg penn_chime
+```
+
+## Help with the Command Line Interface
+
+```bash
+penn_chime --help
+```
+
+### Choosing a Different Set of Parameters
+
+If you want a different set of default parameters, you may use your own configuration file.
+
+```bash
+PARAMETERS=./defaults/yours.cfg streamlit run st_app.py
+```
+
+Be sure to include `--current-date` in the file, if your `--current-hospitalized` is not today's value.
+Be sure to include `--mitigation-date` in the file if social distancing was implemented before today.
+
 ### Choosing a Different Port
 
-If you need to run the application on a different port than the default (8000), you can export a variable in your shell session to override it with any port number of your choice before running:
+If you need to run the application on a different port than the default (8000), you can set an environment variable.
 
 ```bash
-STREAMLIT_SERVER_PORT=1234 PARAMETERS=defaults/webapp.cfg streamlit run src/app.py
+STREAMLIT_SERVER_PORT=1234 PARAMETERS=./defaults/webapp.cfg streamlit run st_app.py
 ```
 
 ## Project Layout
 
 ### Application files
 
-- `src/app.py`: Main source for the application
-- `src/test_app.py`: [pytest](https://docs.pytest.org/en/latest/) tests for `app.py`
+- `st_app.py`: Startup script for the streamlit web application.
+- `src`: Source code for the `penn_chime` module.
+- `tests/`: [pytest](https://docs.pytest.org/en/latest/) tests for the `penn_chime` module.
 - `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
-- `pytest.ini`: Configuration for [pytest](https://docs.pytest.org/en/latest/)
+- `environment.yml`
 - `Pipfile`
 - `Pipfile.lock`
-- `environment.yml`
-- `requirements.txt`
 - `setup.py`
+- `setup.cfg`: Configuration for flake8, mypy, [pytest](https://docs.pytest.org/en/latest/)
 
 ### Documentation
 
@@ -85,6 +121,11 @@ pip install pytest
 pytest
 ```
 
+The test code runs from the local `tests` directory. Updating code in `tests` modifies the tests.
+Use `pip install -e .` so that your local changes to `src` are also the module under test.
+For CI, use `pip install .` to test the module installed in site-packages to ensure that the installed module is packaged correctly with all of its dependencies.
+Do not import from src in your tests or your python code as this will appear to work locally, but break the python module.
+
 ## Validating CHIME
 
 *No validation routine is available yet. If you have thoughts on how to add one, please contribute!*

setup.py

@@ -31,7 +31,6 @@
         "pandas",
         "pytest",
         "pyyaml",
-        "selenium",
         "streamlit",
         "gspread",
         "oauth2client"