libsbgnpy

libsbgn python bindings


Keywords
SBGN, libsbgn
License
LGPL-3.0
Install
pip install libsbgnpy==0.2.0

Documentation

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libsbgnpy : Python library for SBGN

Python library to work with SBGN. This library is based on the SBGN XML schema and supports reading, writing and validation of SBGN files. Python >=3.5 is supported. The initial library was generated using generateDS. Additional utility functions for reading, writing and rendering SBGN documents are provided.

Documentation with examples is available at http://libsbgn-python.readthedocs.io/en/latest/.

  • 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
  • tests unittests
  • examples/ python examples
  • validation/ validation of SBGN files

To cite libsbgnpy use DOI

Installation

The package is available from pypi

pip install libsbgnpy

The latest develop version can be installed via

pip install git+https://github.com/matthiaskoenig/libsbgn-python.git@develop

Support

To report bugs, request features or asking questions please file an issue.

Contributing

Contributions are very welcome. The easiest way to fix a typo/bug or implement a feature is by following the contribution guidelines.

Software using libsbgnpy

  • Mimoza takes a model in SBML format and visualizes it in several formats (downloadable as a COMBINE archive)

License

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.

ChangeLog

v0.2.0

  • dropping support of python 2.7, 3.4
  • adding support for python 3.7, 3.8
  • fixing render endpoints (#31, #32)
  • fixing documentation builder
  • removing py2 legacy code

v0.1.7 Support for notes and extensions

  • Extension and Notes reading and writing
  • Extension and Notes examples

v0.1.6 Improved testing and documentation

v0.1.5

  • py3 support bugfixes
  • SBGN validation with XSD schema
  • update of bindings from latest schema
  • bug fix in writing some attributes

v0.1.4

  • support for py2.6, 2.7, 3.4, 3.5
  • continuous integration with travis

v0.1.3

  • unittests added
  • x, y, w, d handled as float instead int according to specification

v0.1.2

  • initial release

© 2016-2020 Matthias König