sibyl-team / covasim-experiments

Scripts for running sibyl-team interventions in covasim

Testing covasim

This repository contains the notebook used for the testing

Install first covasim -> https://github.com/sibyl-team/covasim

Then install additional modules -> https://github.com/sibyl-team/covasibyl

Python environments

Since covasim requires packages with are not available in the Conda repositories, you should create a new virtual environment to mantain a clear separation.

Instructions for dummies

1. Activate your conda environment

2. Go to the folder in which you want to make the new virtual environment ("folder"). Type

   python -m venv "folder"/covasim
   

   and it will create a new environment in folder/covasim (replace placeholders!)

3. Activate the new environment (you don't really need to activate conda environment first now)

   source "folder"/covasim/bin/activate
   

4. Navigate to the folder containing the codes, and run pip install . to install the package in the new environment, or pip install -e . if you want to be able to change the source on the run and make new functionality

5. You should install also ipykernel and install the new kernel if you want to use the Jupyter notebook:

   • Install ipykernel by pip
   • Run python -m ipykernel install --user --name covasim --display-name "Python (<Add some details here>)"

6. Now you're ready to go!