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libSBML 3.0.1
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We are pleased to announce the release of libSBML-3.0.1 which is now
available from the download area of the SBML project on

http://sf.net/project/showfiles.php?group_id=71971&package_id=71670

The main change in this version of libSBML is that the default XML
parser is now libxml2. The API itself is unchanged although there have
been a number of bug fixes and improvements to existing features.

In particular:

- Fixed a memory leak in XercesParser.cpp, reported (with the fix)
by Sebastian Bauer.

- There is a new file, common/lisbml-version.h, that provides
constants called LIBSBML_VERSION, LIBSBML_VERSION_STRING, and
LIBSBML_DOTTED_VERSION, so that applications can more easily find
out the version of a particular installation of libSBML.

- SBML_formulaToString was incorrectly limiting the length of the
buffer used to write a number and thus truncating the exponent on
numbers with 15 digits. This is now fixed.

- It appears there is a difference in the way gcc and MSVC deal with
the clean-up of strings following calls to the c_str() function. In
the case of MSVC this can on occasion result in a returned char *
being garbage. Since the unit tests for libSBML run using gcc this
has only recently come to light and should now be fixed.

- The MATLAB binding function has a second optional argument
that indicates whether the model is to be validated prior to import.
The default value is 0; indicating no validation. In the case of no
argument to the function; which opens a browse window to locate the
file to import; the user will be prompted to indicate whether
validation should be done. In the case of validation errors these
will be displayed to the user, who will be prompted as to whether to
import the model regardless.

- An additional 'ModelingPractice' validator has been added to the
set of validators available for consistency checking. This validator
reports
1) a compartment with no size assigned
2) a local parameter id that shadows an id in the global namespace

- A document with a missing XML declaration now correctly reports the
MissingXMLDecl error EXCEPT when using libxml2. The reason for this
inconsistency is that libxml2 assigns a default (1.0) xml version if
either the XML version or the entire XML declaration is missing.

- The error ids for a small number of consistency checks has changed.
These relate to validation rules that were never part of the written
specification of SBML and thus do not have published numbers.
These rules check that the timeUnits/substanceUnits and formula of a
KineticLaw are valid in versions of SBML prior to Level 2 Version 2.
The changes are as follows:
21127 changed to 99127
21128 changed to 99128
21129 changed to 99129

- The error id of the check on the general consistency of MathML has
changed from 10219 to 99219.

- Support for <annotation> and <annotation-xml> with a <semantics>
element in MathML has been added.

- The format of error, warning and other diagnostic messages has
been improved and made more regular, and the message strings of
validation rules been updated to match more closely those in the
Level 2 Version 3 specification. The formatting of messages
printed by SBMLDocument.printErrors() has changed as a result.

- A document with a missing XML encoding attribute should cause
XMLError::MissingXMLEncoding to be returned, not MissingXMLDecl,
as was mistakenly the case previously.


Please report any problems you encounter using libSBML
either to the mailing list libsbml-discuss, or using the
issue tracker for libSBML on SourceForge:

http://sbml.org/software/libsbml/issue-tracker



Thanks

Sarah and Mike
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