v5.20.0

The SBML Team with the addition of new members from ARC at UCL is pleased to announce the 5.20.0 release of libSBML.

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FILES

Source

libSBML src archive zip
libSBML src archive tar.gz

Documentation

C++ API Documentation

MATLAB bindings for all OS

libSBML-5.20.0-matlab-binaries.tar.gz
libSBML-5.20.0-matlab-binaries.zip

Python bindings

Available as python-libsbml from PyPi.

R bindings

libSBML-5.20.0 src archive

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NEWS

Given the length of time since our last release the list of changes
and acknowledgements of contributions is incomplete. We apologise and
offer thanks to anyone who has been involved and those people who have
contributed their spare time to continuing maintenance and development.

• Addition of support for the SBML Spatial package

  • Now that the first official version of the specification for the
    SBML Level 3 Spatial package is available, the libSBML API for
    'spatial' is now included in the stable release of libSBML.
    Thus a CMake build using '-WITH_STABLE_PACKAGES' will now include
    the spatial package code.

• New features

  • There is a new converter SBMLRateRuleConverter which will take
    a model with RateRules and infer the corresponding reaction network.
    This is still considered under development and we would really
    appreciate any feedback.

• Bug fixes

  • A large number of code 'smells' have been cleaned up. Thanks to
    Jamie Quinn for undertaking this laborious task.

  • The python examples have been updated for Python 3.8 changes.
    Thanks to Akira Funahashi for committing these fixes.

  • The python code used for creating documentation has been
    updated for Python 3.10 changes. Thanks to
    Zbigniew Jędrzejewski-Szmek for submitting the changes.

• Configuration/build system changes

  • Extensive continuous integration testing has been added to
    the GitHub repository.

• Miscellaneous

  • Note there is now a Julia interface to libSBML available
    at https://lcsb-biocore.github.io/SBML.jl/stable/

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What's Changed

• use . to access convertStringToXMLNode by @fbergmann in #272
• Infer reactions by @skeating in #266
• Update autotools config for better platform detection by @tom91136 in #273
• #275: check that spatial dimensions match before running test by @fbergmann in #276
• Fix crash when infering units by @avandecreme in #284
• Accept timezones really far from UTC by @avandecreme in #291
• fix Java Testrunner by @fbergmann in #292
• • ubuntu 18.04 no longer supported by @fbergmann in #285
• Update the spec URLs. by @luciansmith in #294
• Fbc v3 matlab by @skeating in #277
• Cmake documentation by @fbergmann in #298
• C modelhistory by @skeating in #295
• Add test case for replaceFD issue #299 by @lkeegan in #300
• • add compile option for mxArrayToString by @fbergmann in #301
• Fix bug in SBMLTransforms::replaceFD by @lkeegan in #303
• #232: allow to store maps for each model by @fbergmann in #302
• Improve IdList support in bindings by @fbergmann in #308
• Issue 296 setannotation by @fbergmann in #305
• Xml from file by @skeating in #311
• Xmlns in math by @skeating in #310
• Update version by @fbergmann in #309
• converted setNamesFromIds.cpp example into a python file by @harveymannering in #312
• allow model history without creator by @skeating in #313
• Docs by @skeating in #304

New Contributors

• @tom91136 made their first contribution in #273
• @avandecreme made their first contribution in #284
• @harveymannering made their first contribution in #312

Full Changelog: v5.19.7...v5.20.0