Vivarium

NOTE: This repository has been archived.

The vivarium package has been renamed and migrated into the vivarium-suite monorepo.

What changed

• PyPI distribution: vivarium -> vivarium-engine
• Import path: vivarium -> vivarium.engine
• Source: ihmeuw/vivarium (archived) -> ihmeuw/vivarium-suite (under libs/engine/)
• Docs: https://vivarium-engine.readthedocs.io/

What this last release (v4.2.0) is

A backward-compatibility shim; installing it pulls in:

• vivarium-engine>=5.0.0 - the real implementation under the new import path.
• vivarium-compat>=0.6.0 - an import hook that lets import vivarium continue to work, emitting a DeprecationWarning. Update your imports before the hook is removed.

If you depend on a specific pre-rename version (e.g. vivarium==4.1.5), pin to that version - those earlier releases still ship the original module and continue to install standalone.

To migrate fully to the new package

Install:

pip install vivarium-engine  # was: pip install vivarium

Import:

import vivarium.engine  # was: import vivarium

Original package overview

Vivarium is a simulation framework written using standard scientific Python tools.

Vivarium requires Python 3.10-3.12 to run

You can install vivarium from PyPI with pip:

> pip install vivarium

or build it from source with

> git clone https://github.com/ihmeuw/vivarium.git

> cd vivarium

> conda create -n ENVIRONMENT_NAME python=3.12

> pip install -e .[dev]

This will make the vivarium library available to python and install a command-line executable called simulate that you can use to verify your installation with

> simulate test

Check out the docs!