simfection 0.1.0

A stochastic, interaction-based infectious disease model

Simfection

Simfection is an open-source, stochastic, interactions-based infectious disease model.

Getting Started

Requirements

simfection has only been tested with Python 3.7.

Installing from PyPI

It is recommended that you install simfection in a virtual environment. A great place to keep your virtual environments is in a $HOME/.venv/ directory. If you do not already have such a directory, (1) navigate to your home directory, (2) create it, and (3) enter into the directory.

cd $HOME # $HOME may not be a defined variable for you. If not, navigate home.
mkdir .venv
cd .venv

First, (1) create the a virtual environment called simfection using the venv module. Next (2) activate the virtual environment and (3) install simfection. Finally, (4) copy the command line executable to your main environment and (5) deactivate the birtual environment. (Note: you may need to change the final path /usr/local/bin if you are running Windows.)

python3 -m venv simfection
source simfection/bin/activate
pip3 install simfection
cp simfection/bin/simfection /usr/local/bin/
deactivate

Installing simfection into a virtual environment and then making it accessible from within your main environment avoids any version conflicts with simfection's dependencies.

Confirm Installation

To confirm that simfection was successfully installed, execute simfection -h at command line. You should see a list of available parameters.

To execute a model run, (1) change our of the .venv directory and (2) execute simfection.

cd $HOME
simfection