This release fixes an issue with the python bindings in the pip package python-libsbml on linux machines.

This release further improves the ODE to Reaction converter,
improves the ASTNode::derivative function to support all allowed
math constructs, and resolves a number of build and stability
issues.

What's Changed

• Update html2md. by @luciansmith in #441
• Better testing of reaction to raterule by @skeating in #442
• • new groups / curves need to be added to the list of drawables by @fbergmann in #445
• Sk/test rate rule converter rigorously by @skeating in #450
• Added missing include in html2md by @vincent-noel in #440
• Test whether big/little endian using newer constructs. by @luciansmith in #437
• #453: check for NULL, ensure boundary condition is reset by @fbergmann in #454
• Add functions to translate gene product associations to and from ASTNodes by @luciansmith in #449
• #455: ensure we dont crash on no children by @fbergmann in #456
• Sk/log converter errors by @skeating in #457
• Sort multiple compartments by @skeating in #464
• Adds all the derivative values by @skeating in #463
• Bump version in preparation of new release by @fbergmann in #466
• Allow to bypass suitability tests in raterule connverter by @fbergmann in #465
• current release updated to list 5.21 by @fbergmann in #467
• #438: mark writeMathMLWithNamespaceToString as newobject by @fbergmann in #468

Full Changelog: v5.20.5...v5.21.0

This release adds support for retrieving / setting notes via Markdown (using the 3rdParty libraries html2md and maddy). Additionally, a number of stability and build issues were resolved.

What's Changed

• Sk/distrib units by @skeating in #384
• Detect ZLIB using find module by @fbergmann in #382
• Remove the check for zlib.h. by @luciansmith in #388
• #386: fix compilation of java when using gnumake by @fbergmann in #387
• #390: add hasPrefix to xmlnode / xmlattributes by @fbergmann in #391
• RateRuleConverter crashes on unsupported math by @fbergmann in #394
• Issue 385: flexibility with running strict unit validation by @fbergmann in #393
• Update GitHub Actions where needed by @fbergmann in #404
• Add basic converter for inferring reactions by @fbergmann in #405
• fix nightly build by @fbergmann in #406
• Fixing nightlies by @fbergmann in #407
• Fix nightly manylinux build by @fbergmann in #410
• A hack fix for issue 320, but it works. by @luciansmith in #413
• Fix curve child listOfElements by @luciansmith in #412
• Fix behavior of render getAllElements and memory leaks from there and elsewhere. by @luciansmith in #399
• At attempt to fix #398 by @luciansmith in #400
• Fix error message 21110. by @luciansmith in #419
• Test target compile features by @luciansmith in #422
• Revert header changes for cleaner merge. by @luciansmith in #423
• #417 : when reading L3 document with l2 layout ignore required flag by @fbergmann in #418
• Add html/markdown translators. by @luciansmith in #421
• Revert including util in the bindings. by @luciansmith in #425
• Revert including util in the bindings. by @luciansmith in #424
• Use latest C++ compilers. by @luciansmith in #426
• Maddy updated to handle links better. by @luciansmith in #427
• Fix leak on fail: xmlstr_c now freed. by @luciansmith in #430
• Allow uncerml annotations by @fbergmann in #432
• Making MISC_PREFIX user-settable by @vincent-noel in #428
• Sk/small fixes by @skeating in #392
• #429 : ensure that annotations / notes of kvps are written by @fbergmann in #433
• Update Maddy to not convert internal single underscores. by @luciansmith in #435

New Contributors

• @vincent-noel made their first contribution in #428

Full Changelog: v5.20.4...v5.20.5

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

New Contributors

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

Full Changelog: v5.20.2...v5.20.4

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.

FILES

Source

libSBML src archive zip
libSBML src archive tar.gz

Documentation

C++ API Documentation

MATLAB bindings for all OS

libSBML-5.20.2-matlab-binaries.tar.gz
libSBML-5.20.2-matlab-binaries.zip

Python bindings

Available as python-libsbml from PyPi.

R bindings

libSBML-5.20.2 src archive

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

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

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/

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

What's Changed

• FbcModelPlugin C API for createObjective and createGeneProduct by @exaexa in #252
• Remove the three 'Robin' boundary conditions. by @luciansmith in #263
• Relax annot by @skeating in #265
• Fbc v3 fixes by @skeating in #264
• As Mattias noticed, diffusion and advection can apply to parameters. by @luciansmith in #267
• #268 provide detailed error message on failure by @fbergmann in #269
• • bump to 5.19.7 by @fbergmann in #270

Full Changelog: v5.19.6...v5.19.7

This release solves a number of issues:

What's Changed

• User lowercase name for Windows library by @giordano in #225
• Fix typo in docstring of ASTNode_isLogical by @giordano in #230
• improve thread safety of UnitFormulaFormatter, PowerUnitsCheck by @lkeegan in #233
• Fix signature of SBase_getNumPlugins in prototype by @giordano in #237
• Ensure Translate/OutputSBML work on Octave and Matlab by @fbergmann in #175
• • add whitespace by @fbergmann in #239
• add FbcReactionPlugin_createGeneProductAssociation to C API by @exaexa in #247
• Cmake libxml fix by @fbergmann in #250
• Add SBMLNamespaces_addPackageNamespace{,s} functions to C API by @giordano in #235
• #241:issues with fbc v3 by @fbergmann in #243

New Contributors

• @exaexa made their first contribution in #247

Full Changelog: v5.19.5...v5.19.6

This prerelease, updates the build process to use cmake import libraries throughout. It ensures compatibility with latest version of expat, libxml and xerces-c to mitigate denial of service attacks.

Spatial is updated to solve an issue with validation.