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/..
3 maintainers
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