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/.
libsbgnTypes.pySBGN type definitions (GlyphClasses, ArcClasses, Languages)
utils.pySBGN utility function like writing & reading of files
validation/validation of SBGN files
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
To report bugs, request features or asking questions please file an issue.
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)
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.
- 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
- New documentation: http://libsbgn-python.readthedocs.io/en/latest/index.html
- Some python 3 bugfixes
- Additional examples
- Additional tests, coverage & switch to py-test
- pep8 fixes
- tox support and tox testing
- py3 support bugfixes
- SBGN validation with XSD schema
- update of bindings from latest schema
- bug fix in writing some attributes
- support for py2.6, 2.7, 3.4, 3.5
- continuous integration with travis
- unittests added
- x, y, w, d handled as float instead int according to specification
- initial release
© 2016-2020 Matthias König