sbmlteam/python-libsbml: Release 5.20.0

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/

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

• @tom91136 made their first contribution in https://github.com/sbmlteam/libsbml/pull/273
• @avandecreme made their first contribution in https://github.com/sbmlteam/libsbml/pull/284
• @harveymannering made their first contribution in https://github.com/sbmlteam/libsbml/pull/312

Full Changelog: https://github.com/sbmlteam/python-libsbml/compare/v5.19.7...v5.20.0