LibSBML 5.20.4

This is mostly a bug fix release enhancing stability and improving
performance when validating models. Main points:

• support compilation when using libxml 2.12.0 and later
• improved performance when testing for assignment cycles
• cmake build system honors the BUILD_SHARED_LIB flag if defined

What's Changed

• FIX: support compilation with libxml2 2.12.0 by @mtasaka in sbmlteam/libsbml#358
• • ensure expat can be found when crosscompiling by @fbergmann in sbmlteam/libsbml#368
• Replace deprecated unittest.makeSuite() by @penguinpee in sbmlteam/libsbml#370
• Disable csharp build on nightly macOS runs by @fbergmann in sbmlteam/libsbml#371
• add printf style formatting to Rf_error calls by @spotaws in sbmlteam/libsbml#375
• Assignment cycle optimization by @fbergmann in sbmlteam/libsbml#377
• Allow FBC objects to be used in both L3v1 and L3v2 core documents. by @luciansmith in sbmlteam/libsbml#362
• Change model failures to slightly more likely mistake. by @luciansmith in sbmlteam/libsbml#373
• Enable CMake user option BUILD_SHARED_LIB by @Waschina in sbmlteam/libsbml#366
• Remove all checks for SBML core version when adding package elements. by @luciansmith in sbmlteam/libsbml#380
• Prepare 5.20.4 release by @fbergmann in sbmlteam/libsbml#381

New Contributors

• @mtasaka made their first contribution in sbmlteam/libsbml#358
• @penguinpee made their first contribution in sbmlteam/libsbml#370
• @spotaws made their first contribution in sbmlteam/libsbml#375
• @Waschina made their first contribution in sbmlteam/libsbml#366

Full Changelog: sbmlteam/libsbml@v5.20.2...v5.20.4

Release 5.20.2

This is mostly a bug fix release enhancing stability when validating
and converting models.

• New features / improvements

  • Access to error logs from the C API

  • Attributes of the ModelHistory can now be accessed from
    const objects.

  • The FBC V3 package has been updated to reflect the latest
    specification. There are now optional attributes fbc:reaction2
    on the FluxObjective and fbc:variable2 on the
    UserDefinedConstraintComponent.

• Bug fixes

  • A bug converting / validating models with the 'comp' package
    has been fixed.

  • A crash when inferring units has been resolved.

  • A fix to the CMake Build system ensures that check for dependencies
    is more robust. Thanks to first time contributor @adelhpour

  • The type of the FBC V3 coefficient attribute on the
    UserDefinedConstraintComponent has been corrected, it was mistakenly
    a double before, now it has been corrected to be a SIdRef as
    described in the specification.

Release 5.20.1

This release fixes minor issues within libsbml. More information on the libSBML Release page.

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/

What's Changed

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

New Contributors

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

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

Release 5.19.7

Further fixes for Fbc V3, among minor other improvements. For details see:

https://github.com/sbmlteam/libsbml/releases/tag/v5.19.7

libSBML 5.19.6

This release fixes a number of issues related to the FBC v3 Package. A full list of changes is on the libSBML notes

https://github.com/sbmlteam/libsbml/releases/tag/v5.19.6

libSBML 5.19.5

This release of python-libsbml contains updates to the build system, that makes it compatible with latest versions of expat and libxml. The released binaries are compiled against the latest expat version (2.4.8) solving the issue of previous binaries being vulnerable to a denial of service attack due to entity expansion.

The experimental binaries fix an issue with the spatial validation.

Release 5.19.3

This release is essentially the same as 5.19.2, the main difference is that the distrib package is now enabled by default for python-libsbml. Thanks to Matthias for pointing this out.

LibSBML 5.19.2

Release 5.19.2 fixes an issue that prevented libsbml to build with python 3.10 (and 3.11). This release hosts the source only archive for the conda build.

Python LibSBML 5.19.0

New version of the python packages for libSBML 5.19. This also included the source archive. This now uses the official libSBML 5.19 sources.