A simple CLI for BioNetGen
Project description
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.
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