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Standalone libSBML Python module

This is used to create a standalone module for Python. The module consists of libSBML and libSBML extensions for accepted/released SBML Level 3 packages.

License Latest stable release

Main Authors: Frank T. Bergmann, Sarah Keating, Ben Bornstein, Lucian P. Smith, Akiya Jouraku, and Michael Hucka.

Repository: https://github.com/sbmlteam/python-libsbml

Developers' discussion group: https://groups.google.com/forum/#!forum/libsbml-development

License: For full license information, please refer to the file ../LICENSE.txt for details.

♥️ Please cite the libSBML paper and the version you use

Article citations are critical for us to be able to continue support for libSBML. If you use libSBML and you publish papers about your software, we ask that you please cite the libSBML paper:

Benjamin J. Bornstein, Sarah M. Keating, Akira Jouraku, and Michael Hucka (2008) LibSBML: An API Library for SBML. Bioinformatics, 24(6):880–881, doi:10.1093/bioinformatics/btn051.

☀ Background and introduction

libSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It's not an application itself, but rather a library you embed in your own applications. The library supports all Levels and Versions of SBML, up to Level 3 Version 1 Core.

This repository contains code to generate a standalone Python module wrapping libSBML with a Python API. The API is the standard Python API implemented with the help of SWIG and provided in the libSBML distribution.

Preparing the package build

First you will have a compiler compatible with your python version installed, as well as a recent version of:

  • cmake
  • swig

In order to to build the python package, you will have to check out the repository, including its submodules, from there on all dependencies, libsbml and the python bindings will be built:

git clone https://github.com/sbmlteam/python-libsbml
cd python-libsbml
git submodule update --init

By default, we track the latest release of the libSBML project via submodule in libsbml_source the version number is also read from the VERSION.txt file from the submodule. So if another version of libSBML should be built, the submodule has to updated. For example manually like so to follow the latest development:

cd libsbml_source
git checkout development
git pull origin development

Building the package

Once those steps are done, the library can be build using the setup.py script.

python setup.py build

to build the experimental package, all that needs to be done is to set the environment variable LIBSBML_EXPERIMENTAL=1 prior to building

⁇ Getting Help

The libSBML library, and associated utilities such as this Python module, under active development by a distributed team. If you have any questions, please feel free to post or email on the (https://groups.google.com/forum/#!forum/libsbml-development) forum, or contact the libSBML Team directly.

☮ Copyright and license

Please see the file ../LICENSE.txt for copyright and license details.

More information

Please visit SBML.org for more information about SBML (the Systems Biology Markup Language), as well as many resources for working with SBML.