Refactor python module

Refactor python module

Author: jlubken

.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

@@ -9,5 +9,5 @@ COPY defaults defaults
 COPY src src
 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

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"

src/app.py

@@ -8,7 +8,7 @@
 from typing import TypeVar
 
 from dash import Dash
-from penn_chime.parameters import Parameters
+from penn_chime.model.parameters import Parameters
 
 from chime_dash.app.config import from_object
 from chime_dash.app.pages.root import Root

src/chime_dash/__init__.py

@@ -11,7 +11,7 @@
 from dash.development.base_component import ComponentMeta
 from dash_html_components import Div
 
-from penn_chime.parameters import Parameters
+from penn_chime.model.parameters import Parameters
 
 from chime_dash.app.utils.templates import read_localization_yml, read_localization_markdown
 

src/chime_dash/app/components/base.py

@@ -10,7 +10,7 @@
 from chime_dash.app.components.base import Component
 from chime_dash.app.components.menu import Menu
 
-from penn_chime.parameters import Parameters
+from penn_chime.model.parameters import Parameters
 
 
 class Navbar(Component):

src/chime_dash/app/components/navbar.py

@@ -12,8 +12,8 @@
     prepare_visualization_group
 )
 
-from penn_chime.models import SimSirModel
-from penn_chime.parameters import Parameters, Disposition
+from penn_chime.model.sir import Sir
+from penn_chime.model.parameters import Parameters, Disposition
 
 
 class ComponentCallbacks:
@@ -37,7 +37,7 @@ def handle_model_change(i, sidebar_data):
         viz_kwargs = {}
         if sidebar_data:
             pars = parameters_deserializer(sidebar_data["parameters"])
-            model = SimSirModel(pars)
+            model = Sir(pars)
             vis = i.components.get("visualizations", None) if i else None
             vis_content = vis.content if vis else None