vivarium-cell 0.1.5

A collection of models for simulating cells with Vivarium.

vivarium-cell

WARNING: This library has been deprecated. Please see https://vivarium-collective.github.io for alternatives.

vivarium-cell is a library of configurable cell process and composites for vivarium projects.

Installation

vivarium-cell can be used as a python library. To install:

$ pip install vivarium-cell

Setup in local repository

Clone the repository, make a python environment, and install dependencies.

First install numpy:

$ pip install numpy

Then the remaining requirements:

$ pip install -r requirements.txt

Run individual processes and composites

Each process file under cell/processes can run on its own. Some of these have their own command line options. For example, call the convenience_kinetics process with:

$ python vivarium_cell/processes/convenience_kinetics.py

Composites with multiple integrated processes can also be executed on their own:

$ python vivarium_cell/composites/gene_expression.py

Experiments

TODO

Tests

Tests are performed with pytest. Simply call the following to ensure everything is working properly:

$ pytest

To run only the fast tests:

$ pytest -m 'not slow'

Logging

Logging is done with python logging. To print out logging information, run a simulation with:

$ LOGLEVEL=INFO python vivarium_cell/..