bionetgen 0.2.7

A simple CLI for BioNetGen

A simple CLI for BioNetGen

Installation

Currently this library is in testing so it's in test PyPI and not directly installable via pip from there. Use the following to get the library

$ pip install -i https://test.pypi.org/simple bionetgen

Features

PyBioNetGen comes with a command line interface (CLI) entrypoint as well as a functional library that can be imported. The CLI can be used to run BNGL models, generate Jupyter notebooks and do rudimentary plotting.

The library side provides a simple BNGL model runner as well as a model object that can be manipulated and used to get libRoadRunner simulators for the model.

The model object requires a system call to BioNetGen so the initialization can be relatively costly, in case you would like to use it for parallel applications, use the libRR simulator for those.

Environment Setup

The following demonstrates setting up and working with a development environment:

### create a virtualenv for development

$ make virtualenv

$ source env/bin/activate


### run bionetgen cli application

$ bionetgen --help


### run pytest / coverage

$ make test

Docker

Included is a basic Dockerfile for building and distributing BioNetGen CLI, and can be built with the included make helper:

$ make docker

$ docker run -it bionetgen --help

Publishing to PyPI

You can use make dist command to make the distribution and push to PyPI with

python -m twine upload dist/*

You'll need to have a PyPI API token created, see here for more information.