PandemicModel

Repository for Delineo Disease Modeling at the Johns Hopkins University.

Developer Notes

Choose one of the below, either a local dev environment or a Conda environment.

Setting up local dev environment

1. Ensure you have python3.6 installed and set up.
2. Clone this repository.
3. Initialize a virtual environment: python3.8 -m venv ~/.envs/PandemicModel. (Consider using virtualenvwrapper for steps 3-4)
4. Activate the virtual environment: source ~/.envs/PandemicModel/bin/activate.
5. Install dependencies: pip install -r requirements.txt.

Setting up Conda environment

1. In the Anaconda CMD.exe Prompt, create a new environment with conda create -n myenv python=3.9.1, where myenv is the name of the environment. Python version 3.9.1 is what's up and running on the covidmod server so it's a good choice to use for your conda environment.
2. Activate the conda environment with conda activate myenv.
3. Clone this repository.
4. Navigate into the PandemicModel folder and run pip install -r requirements.txt.

For both, the best way to verify everything is working by running python test_master.py (run in root directory). If you get a bunch of numbers spit out to your terminal, then you're all set.

Troubleshooting

• Most likely, you will run into issues due to some dependency not being installed in your conda environment/virtual env. Check ClickUp and/or Slack for a full list of working dependencies.

Misc.

• Please do not commit venv stuff.
• If you pip install anything, remember to pip freeze > requirements.txt before committing any changes.
• You cannot commit to the master branch, remember to commit all changes to a new branch and open a PR when you're ready to merge.
• Do you need the Baltimore pkl file? https://drive.google.com/file/d/1DWG04IsdxIqKWCGYxdshpljrJ9D0ZWSv/view?usp=sharing

Important Folders/Files

All important files for running are in the /simulation folder

src/simulation/data: contains comorbidity data
src/simulation/synthpops: DO NOT TOUCH unless you really know what you're doing
src/simulation: run test_master.py to run the simulation code

Package

If you wish to work with the package code, follow these steps:

1. In setup.py, change the version number to a greater number.
2. Run deploy.sh to deploy it to the test-PyPi website.
3. Wait a little bit (~30 seconds), and download the Delineo simulator from the website.
4. Test with test. These files are to test the package.

API

A lot of the information on how to update the endpoints are found in the Fullstack guide, but in this repo, use the api folder to update the Flask app.

Tips

If you're coding in VSC, ensure that this setting is checked: File --> Preferences --> Settings --> Search Settings --> python.terminal.executeInFileDir