Metadata-Version: 2.1
Name: bionetgen
Version: 0.2.7
Summary: A simple CLI for BioNetGen 
Home-page: https://github.com/ASinanSaglam/BNG_cli
Author: Ali Sinan Saglam
Author-email: als251@pitt.edu
License: unlicensed
Description: # A simple CLI for BioNetGen 
        
        [![BNG CLI build status](https://github.com/ASinanSaglam/BNG_cli/workflows/bng-cli-tests/badge.svg)](https://github.com/ASinanSaglam/BNG_cli/actions)
        
        ## 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](https://packaging.python.org/tutorials/packaging-projects/) for more information. 
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Description-Content-Type: text/markdown
