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libSBML-4.1.0-b2
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We are pleased to announce the release of libSBML-4.1.0-b2
which is available for download from

https://sourceforge.net/projects/sbml/files/

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This is a second beta version which adds further support for SBML
Level 3 as defined in the Level 3 specification Release 1 (Candidate)
published 2009-12-31.

* L3 Features introduced in this version:

- setFoo(xxx) functions for all new attributes in Level 3 Core

- unsetFoo() functions for all new optional attributes

- The "sbml:units" attribute on the MathML <cn> element is now
supported. This includes reading and writing and getUnits,
isSetUnits, setUnits and unsetUnits functions for manipulating the
attribute on an ASTNode.

- Support for the <csymbol> "avogadro"

- The ModelHistory element is now permissible on any SBML object

- Conversion to SBML Level 3 from Levels 1 & 2.


* The following Level 3 Features are not yet implemented:

- Validation of SBML Level 3 models

- Conversion from Level 3 to other Levels/Versions of SBML


* Here is an important note about default values of attributes: SBML
L3 does not specify default values, and libSBML-4.1.0-b1 followed
this principle. Users reported that this on occasion caused
problems. Although we are working on a more robust solution, the
current libSBML version constructs objects WITHOUT default values
but provides the initDefaults() functions to apply the L2 default
values, regardless of SBML Level. In other words,

Unit * unit = new Unit(3,1);
unit->initDefaults();

will assign values to the relevant attributes.


* Additional new features in this release:

- There are two new functions that allow within SBML transformations,
removing components that software may be unable to interpret and
replacing them with appropriate attributes etc. The first
'expandFunctionDefinitions' replaces any call to a function with
the appropriate math. The second 'expandInitialAssignments'
replaces the appropriate value attribute with the value calculated
by applying the InitialAssignment.

- The functions that look up SpeciesReference objects from the
ListOfs within a Reaction, will now search both the 'species' and
the 'id' attribute for a match.


* Bug fixes new in this beta release:

- [Tracker issue #2856390]
FunctionDefinition elements and Event elements were not written
when writing an SBML Level 2 file/string. This has been fixed.
Thanks to Lucian for reporting this problem.

- SpeciesReference::isSetStoichiometry() function wrongly returned
false when a stoichiometry attribute is absent in an input SBML
Level 2. This has been fixed. Thanks to Frank Bergmann for
spotting this.

- Macros in SBMLDocument.h contained unnecessary ';'. This has been
fixed. Thanks to Lucian Smith for reporting this problem.

- Compartment::setSpatialDimensions(unsigned int) function didn't
update a corresponding internal double value of spatialDimensions
attribute. This has been fixed. Thanks to Frank Bergmann for
reporting this.


* All the bug fixes that were also included in libSBML-4.0.1

******************************************************************************************

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

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

Thanks

Sarah, Akiya & Mike
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