Metadata-Version: 2.1
Name: vivarium-cell
Version: 0.1.5
Summary: A collection of models for simulating cells with Vivarium.
Home-page: https://github.com/vivarium-collective/vivarium-cell
Author: Eran Agmon, Ryan Spangler
Author-email: eagmon@stanford.edu, ryan.spangler@gmail.com
License: MIT
Description: # vivarium-cell
        
        **WARNING: This library has been deprecated. Please see https://vivarium-collective.github.io for alternatives.**
        
        [vivarium-cell](https://github.com/vivarium-collective/vivarium-cell) is a library of configurable
         cell process and composites for vivarium projects.
        
        ![vivarium](doc/_static/lacY_transport.png)
        
        # 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/..
        ```
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
