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libSBML-3.3.1
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We are pleased to announce the release of libSBML-3.3.1 which is
available for download from

https://sourceforge.net/project/showfiles.php?group_id=71971&package_id=71670

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This release contains the following:

* Changes

- Validation relating to attributes that have been removed from
later SBML Levels/Versions (e.g. 'offset' on <unit>) has changed
slightly. Reading in a model that contains such an invalid
attribute reports a schema error. This has not changed but
checking the consistency of a document that has been created using
an invalid attribute will now report an error stating that the
attribute has been removed e.g. Validation Rule 20411 in SBML
L2V2 specification.

- The code used to a convert an SBML L2V4 model was failing to
perform the conversion if the units in the L2V4 model would
produce a target model that had invalid units. Ralph Gauges
pointed out that this behaviour was inconsistent with existing
behaviour, which allows conversion of invalid models. The code
has been changed to merely log the invalid units as a warning,
whilst performing the conversion if it is otherwise possible.

- The RDFAnnotationParser class was not marked as external within
the Windows prebuilt dlls. This has been changed and the relevant
functions have been implemented within the C API.

- The helper function 'printUnits' on the UnitDefinition class was
only printing out the kind and exponent of any unit. Sven Sahle
requested that this be extended to include scale and multiplier.
The unit
<unit kind="mole" exponent="-1" multiplier="2" scale="1"/>
will now be output as
"mole (exponent = -1, multiplier 2, scale = 1)".
In addition, the function now has an optional argument,
defaulting to false, that if set to true will write the units out
in a more compact form e.g.
"(20 mole)^-1"


* Bug fixes:

- The makefile for the java examples directory required Java 1.5 not
versions greater than 1.5. This has been changed. Thanks to
Nicolas Rodriguez for reporting this.

- A problem in error logging whilst reading a file meant that files
with certain errors caused libSBML to crash. This has been fixed.

- 'configure' requested doxygen version 1.5.4, but actually some of
the latest documentation code requires 1.5.8.

- The parseCVTerms function was crashing if the qualifier used
within one of the CVTerms was unknown. This has been fixed.
Thanks to Allyson Lister for the effort involved in tracking this
down.

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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

Akiya, Mike & Sarah

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