Update libsbml

[cjmyers]

---

libSBML-5.17.2-experimental

We are pleased to announce the release of libSBML-5.17.2-experimental, which is available for download from

https://sourceforge.net/projects/sbml/files/libsbml/5.17.2-experimental/

and as python-libsbml-5.17.2-experimental

==================================================================== 5.17.2-experimental (2018-12-06)

Experimental only release

This is an experimental only release, that is, a release of those files provided in the experimental folder of a full release.

This includes updates to all the SBML L3 packages that are not yet accepted and undergoing development.

NOTE: An experimental release is not as rigorously tested as a full release. Any changes/fixes listed as either referring to stable or experimental code may change before the next full release.

STABLE RELEASE

• New features

  • The math code has been refactored to use the more efficient math-legacy code in combination with a math plugin system. This code has been optimized and we welcome feedback on any performance issues. This means there is no longer a math-legacy build option.

  • The new math constructs introduced in SBML L3V2 have been refactored as a math extension; which facilitates the use of these math functions in an SBML L3V1 document.

  • 'comp' package-specific updates:

    • The 'comp' specification states that an external model must be an L3V1 document. Since this specification predates SBML L3V2 we have relaxed the restriction to allow an L3V2 model using Model Composition to use an L3V2 external model.

    • The converter that 'flattens' a comp model has been optimized for speed with significant improvement for larger models.

  • Python interface specific updates:

    • In libSBML the set/add/unset methods return a code to indicate success or failure of the operation. The Python interface has been improved to produce a warning when a function fails. This behavior can be enabled by setting a CMAKE configure option or an environment variable.

    • Sourceforge Tracker item #456: The Python interface has been changed to return an empty List of CVTerms rather than a None object.

    • Users have raised issued about Model objects retrieved from within an SBMLDocument object going out of scope when the document object is removed from scope. We have adjusted the code to allow a Model to remain in scope without it's parent document. Feedback would be appreciated about whether this is sufficient or whether all child objects should be available regardless of whether their parent is still available.

    • Sourceforge Tracker item #468: Functions deprecated in Python 3.6 have been replaced to avoid deprecation warning messages.

• Bug fixes

  • The function SBMLTypeCode_toString was not retuning the correct string for a ListOf element originating in a package. This has been corrected.

  • Using an SBML L3 package in an L2 document could cause a crash. This has been fixed. Thanks to Thomas Hamm for reporting it.

  • The code that checked for use of an L3V2 package with an L3V1 document could cause a crash. This has been fixed.

  • Writing out a document without a model and no level and version was using level = version = 0; which is not valid. This has been changed to write a L3V2 document with no model.

  • There was an issue with newer architectures when casting a NaN to an integer - this has been now been avoided.

  • MATLAB interface specific bug fixes:

    • The matlab binding was failing to distinguish between a functionDefinition where the id ended with a logical operator, e.g. 'myor' and the actual logical function. This has been corrected.

  • 'comp' package-specific bug fixes:

    • There was an issue with flattening 'comp' models using conversion factors. This has been tracked down and fixed. Thanks to Matthias Konig for reporting it and providing examples.

  • 'render' package-specific bug fixes:

    • Historical render code did not create a NULL BoundingBox. Current code has been brought in line with this.

• Configuration/build system changes

  • Python 3.7 is now supported and included in the builds.

  • The USE_LEGACY_MATH option has been removed as code has been reverted to use this math implementation (see above).

EXPERIMENTAL RELEASE

• New features

  • 'distrib' package-specific updates:

    • The distrib package code has been updated to include the use of csymbols to reference distributions. This is in line with the latest distrib specification.

=====================================================

Please report any problems you encounter using libSBML either to the mailing list libsbml-team@googlegroups.com or using the issue tracker for libSBML at

https://sourceforge.net/tracker/?group_id=71971&atid=942737

Thanks,

the LibSBMLTeam

-- You received this message because you are subscribed to the Google Groups "sbml-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss+unsubscribe@googlegroups.com. To post to this group, send email to sbml-discuss@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/51a41392-4f0f-3f79-a8d6-4ac8f38f7300%40caltech.edu. For more options, visit https://groups.google.com/d/optout.

[LukasBuecherl]

Issue #579 is about updating libsbml to 5.18.0 making this issue obsolete.