Release of libSBML-5.3.0
23 Dec '11 11:21
We are pleased to announce the release of libSBML-5.3.0 which is
available for download from
Version 5.3.0 (2011-12-23)
* New features
- Errors reported by the matlab binding function 'OutputSBML'
have been improved to provide information about why the
structure is invalid.
- There is a new virtual function on an SBase object 'setElementText'.
This enables a user to store text that the read functions encounter
within an XML element. Previously such text was ignored as no such
text existed as a part of an SBML Core element. Some L3 packages
may use this XML feature and can thus utilize this function.
- There is a new function on an ASTNode 'returnsBoolean' that returns
a predicate indicating that the math of the ASTNode will return a
boolean result or not. The function has an argument of type Model
with a default value of NULL. Where necessary, that is, when the
ASTNode involves a call to a user defined function, the check is
done in the context of the supplied argument Model or the parent
Model of the particular ASTNode if no argument is supplied.
- There are new functions to facilitate the use of packages. The
SBMLExtensionRegistry has a 'disableUnusedPackages' function which
disables registered packages that are not being used by the target
SBMLDocument. The base SBMLExtension class has a function 'isInUse'
that will establish whether a package is being used by the target
* Bug fixes
- The conversion code incorrectly converted an L3 model where the
stoichiometry was changed by a RateRule. This has been fixed.
- Conversion from L3 to L2 was failing to write out the
attribute of a Compartment regardless of the value. It now
correctly writes out a non default value.
- The RegisterConverters class was not included in the
LIBSBML_CPP_NAMESPACE. This has been corrected. Thanks to
Christoph Flamm for letting us know.
- There was a slight discrepancy in how the assignment operator
for the SBMLExtensionNamespaces was behaving depending on OS.
This has been sorted so that behaviour is the same for all.
- Tracker issue #3438777
The XercesParser was failing to find the line and column number
definitions with some compilers. This is now fixed. Thanks to
David Fange for reporting it.
- Tracker issue #3441615
There was an issue with SWIG, C# and MSVC compilers caused by
conflict with MS MFC and GDI classes. This has been fixed by
explicilty excluding these classes. Thanks to Totte Karlsson
for reporting this.
- Tracker issue #3461400
Writing out an L2 model with Layout annotation caused duplicate
annotations to be written out. This has been fixed. Thanks to
Raimund Rönn for reporting the problem.
- Tracker issue #3462055
A couple of typos have been corrected. Thanks to Raimund Rönn
for taking the time to report these.
- The documentation for Python did not omit internal libSBML
methods. This is now fixed, and the docs more properly reflect
the public libSBML API.
- We have fixed a number of errors in the Python API documentation,
such as return values being reported as "char" when in fact they
were strings, and have filled out more of the missing
- We have fixed many other small documentation bugs and filled out
more of the missing documentation.
- The matlab binding contains a function 'isSBML_Model' that checks
that the structure contains all the fields that are expected
in an SBML model. This function is used by OutputSBML to determine
if the model can be written out. Previously this function would
only report that a model was valid if each of the substructures had
the expected fields and no additional fields. This behaviour has
changed to allow users to include extra information within the
structure. Thus a model is considered invalid if it does not have
all the expected fields; additional fields are ignored.
- The libSBML examples code has been ported to all language bindings;
so all examples exist in each language.
- The API manuals for languages besides Java now feature a more
modern and attractive appearance.
* Configuration/build system changes
- Using CMake to link against the static runtime libraries on windows
when using libxml2 it was necessary to manually add links to other
libraries. The build system now takes care of these.
* New features
- There is now code to support the L3 render package.
Please report any problems you encounter using libSBML either to the
mailing list email@example.com or using the issue tracker
for libSBML at
Frank, Sarah & Mike
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