Metadata-Version: 2.1
Name: libsbgnpy
Version: 0.2.2
Summary: sbmlsim are utilities for simulation of SBML.
Home-page: https://github.com/matthiaskoenig/libsbgn-python
Author: Matthias Koenig
Author-email: konigmatt@googlemail.com
Maintainer: Matthias Koenig
Maintainer-email: konigmatt@googlemail.com
License: LGPL-3.0
Download-URL: https://pypi.org/project/libsbgnpy
Project-URL: Source Code, https://github.com/matthiaskoenig/libsbgn-python
Project-URL: Documentation, https://libsbgnpy.readthedocs.io
Project-URL: Bug Tracker, https://github.com/matthiaskoenig/libsbgn-python/issues
Keywords: modeling,standardization,SBGN,libsbgn
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Requires-Dist: lxml
Requires-Dist: requests
Provides-Extra: development
Requires-Dist: black ; extra == 'development'
Requires-Dist: bump2version ; extra == 'development'
Requires-Dist: isort ; extra == 'development'
Requires-Dist: tox ; extra == 'development'
Requires-Dist: pytest (>=6.1) ; extra == 'development'
Requires-Dist: pytest-cov (>=2.8.1) ; extra == 'development'

libsbgnpy : Python library for SBGN
====================================

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Python library to work with the Systems Biology Graphical Notation (`SBGN <http://sbgn.github.io/sbgn/>`__). This library is based on the SBGN XML schema and supports reading, 
writing and validation of SBGN files.

The initial library was generated using `generateDS <https://pypi.org/project/generateDS/>`__. Additional utility functions for reading, writing, and rendering SBGN documents are provided.

Documentation with examples is available at `https://libsbgn-python.readthedocs.io <https://libsbgn-python.readthedocs.io>`__.

* ``libsbgn.py`` python library
* ``libsbgnTypes.py`` SBGN type definitions (GlyphClasses, ArcClasses, Languages)
* ``utils.py`` SBGN utility function like writing & reading of files
* ``render.py`` SBGN rendering
* ``test/`` unittests
* ``examples/`` python examples
* ``validation/`` validation of SBGN files


How to cite
===========
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.597155.svg
   :target: https://doi.org/10.5281/zenodo.597155
   :alt: Zenodo DOI

Installation
============
``libsbgnpy`` is available from `pypi <https://pypi.python.org/pypi/libsbgnpy>`__ and
can be installed via::

    pip install libsbgnpy

Support
=======
To report bugs, request features or asking questions please file an `issue <https://github.com/matthiaskoenig/libsbgn-python/issues/new>`__.

License
=======

* Source Code: `LGPLv3 <http://opensource.org/licenses/LGPL-3.0>`__
* Documentation: `CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>`__

The libsbgnpy source is released under both the GPL and LGPL licenses version 2 or
later. You may choose which license to use the software under.

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License or the GNU Lesser General Public
License as published by the Free Software Foundation, either version 2 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding
=======
Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054).


Software using libsbgnpy
========================
* `Mimoza <http://mimoza.bordeaux.inria.fr/>`__ takes a model in SBML format and visualizes it in several formats (downloadable as a COMBINE archive).

Python Language Bindings
========================
The python language bindings were created from the XML schema using
generateDS and than adapted to include GlyphClasses and ArcClasses.::

    /usr/local/bin/generateDS.py -o "libsbgn.py" -s "libsbgnSubs.py" SBGN.xsd

The necessary constraints for GlyphClasses, ArcClasses and Languages were added and
some utility functions created.

© 2016-2020 Matthias König


