Release of libSBML-5.10.0

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Sarah Keating

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Jun 9, 2014, 3:24:54 PM6/9/14
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----------------------
libSBML-5.10.0
----------------------

We are pleased to announce the release of libSBML-5.10.0 which is
available for download from

https://sourceforge.net/projects/sbml/files/libsbml/5.10.0/

====================================================================
5.10.0 (2014-04-10)
====================================================================

STABLE RELEASE

* New features

    - New ASTNode infrastructure

      The code underlying the ASTNode class has been refactored to
      facilitate the extension of MathML by SBML L3 packages.  The
      API and behaviour has not changed except in places where
      invalid MathML was being incorrectly parsed or created. It is
      no longer possible to add a child to an ASTNode that represents
      a number, for example.

      Extensive testing has been done to ensure that the API and
      correct behaviour of the ASTNode class remains unchanged and
      unless you have derived your own classes from the ASTNode class
      this change should not affect your implementation in any way.

      ** Please inform us if this turns out to be incorrect. We have
      tried to anticipate and test use cases but we are aware that
      it is possible that we have missed some.

      In order to allow people to continue to use the original AST code
      if they choose, the source code archives provide this code within
      a 'math-legacy' directory and the libSBML configuration system
      provides an option to build libSBML using this legacy code.

    - General maintenance: we have done a number of sweeps of code to
      identify and add such things as missing virtual functions.  We
      have also investigated memory leaks reported by users and have
      done some extensive memory leak checking on the more intensive
      functionality such as validation/comp flattening etc.  However,
      this remains an ongoing task.

    - There is a new converter, the SBMLReactionConverter, which
      will replace any Reactions within a Model with the equivalent
      RateRules.  An example of the use of this converter can be
      found at examples/c++/convertReactions.cpp.

    - There are new functions available on the Model class:
      InitialAssignment* getInitialAssignmentBySymbol(const std::string&
symbol);
      Rule* getRuleByVariable(const std::string& variable);
      AssignmentRule* getAssignmentRuleByVariable(const std::string&
variable);
      RateRule* getRateRuleByVariable(const std::string& variable);
      These functions return the designated object using the 'symbol' or
      'variable' attribute.  This is duplicate functionality as the
      objects can be retrieved using getRule and getInitialAssignment.
      However the other similar functions on the Model class retrieve
      objects by the 'id' attribute. If future versions of SBML
      introduce the 'id' attribute on Rules and InitialAssignments we
      will need functions that act differently.


    - 'comp' package-specific updates:

      - The code that facilitates resolving files in relation to
        ExternalModelDefinitions has been reviewed and made as robust
        as possible.

      - The ability to customize the way SIds and SIdRefs are
        renamed during the flattening process has been added. A
        class of type PrefixTransformer can be created and assigned.
        This allows the user to add additional changes to the renaming
        process. An example that illustrates the use of this facility
        to also rename the 'name' attribute of objects originating in
        subModels has been included in the examples/c++/comp directory.

      - Unit tests have been added for the C API, and this exposed some
        missing functions. The missing functions have now been added.
        

* Bug fixes

    - There were issues with propagating the package-enabling
      functionality through the children of an element.  These issues
      have been resolved.
        
    - The converters that apply structural changes to the SBML document
      used a setDocument function that expected a const SBMLDocument
      object. Since the converters change the document, and in fact
      immediately re-cast the document object, this function was both
      confusing and inaccurate.  There is now a setDocument function
      that does not expect a const SBMLDocument object.

    - There were some inconsistencies in the behaviour of LocalParameter
      objects from SBML Level 3 in relation to the 'constant'
      attribute. These have been fixed.


    - 'layout' package-specific bug fixes:

      - There were some discrepancies between the naming of arguments
        to some constructors and the actual values being set using
        these arguments. These have been corrected without changing
        the resulting behaviour.

      - Sometimes when an SBML Level 2 document with 'layout' and
        'render' annotations was upgraded to SBML Level 3, the 'render'
        namespace went missed from the annotation in the Level 3
        document.  This has been fixed.

      - The 'render' package "objectRole" attribute was not being
        correctly handled by the 'layout' code when the 'render' package
        was disabled.  This has been corrected.


    - 'qual' package-specific bug fixes:

      - Certain validation errors were not being correctly reported,
        with either missing information or bad line numbers.  This
        problem has been fixed.  Thanks to Nicolas Rodriguez for
        reporting the problem.


* Configuration/build system changes

    - WARNING: There is a bug in the Microsoft Visual Studio 2013
      compiler that can cause strange output when doing repetitive file
      reading and writing.  We became aware of this when running our
      unit tests on the comp flattening routines.
      http://connect.microsoft.com/VisualStudio/feedback/details/
      808199/visual-c-2013-floating-point-broken-on-first-use We
      included a fix in our test files (libsbml/src/sbml/packages
      /comp/util/test/TestRunner.c) but users should be aware that this
      is an issue that may arise with this particular version of the
      MSVC compiler.

    - The CMake files have been updated to allow for the use when
      libSBML is merely being referenced within a CMake build, rather
      being specifically built.

    - Both the GNU make and CMake configuration systems generate certain
      header files that are specific to the libSBML build being
      requested.  Previously, libSBML source code included project
      definition files for MSVC.  These files were checked into SVN and
      included within the released src archive distribution.  Their
      inclusion could potentially cause problems for people who wanted
      to create different build configurations from the same source
      code.  Given that with CMake it is possible to generate MSVC
      project files directly, we no longer include them in the source
      archive distribution, and therefore, it is also not necessary to
      include the header files generated by the configuration process.
      Thus, these header files have been removed, and for CMake users
      they will be generated within the build directory to facilitate
      different builds using the same src tree.

    - There were issues with classes exported across the Windows dll
      interface.  These have been fixed, and we have added additional
      tests to catch these issues.  Thanks to Andy Somogyi for reporting
      the problem.


* Miscellaneous

    - Python installers for various Linux distributions are now
      available from the Open Build Service and via pypi. Links to the
      relevant release can be found in the documentation on SourceForge
      download pages for libSBML.

    - The copyright statement for all example programs that we produced
      ourselves has been changed to use a less restrictive license, so
      that users can use the examples in their software without
      limitation.  The new license is the MIT license.

    - The LICENSE.* files for libSBML now include a previously-missing
      3rd party software acknowledgement for the Python argparse library
      by Steven J. Bethard.  (The argparse.py module is included with
      libSBML distributions.)

    - A number of extraneous files have been removed from the
      documentation source directory (docs/src/); in addition, the
      directory has undergone some minor restructuring.


EXPERIMENTAL RELEASE

* New features

    - Support for the 'arrays' package according to the specification
      dated September 11, 2013 (0.1 alpha) has been added to the
      experimental release files. Note the extended MathML is accessible
      via the ASTNode class; however, the current version version does
      not yet include support for parsing to and from infix notation.


    - 'multi' package-specific updates:

      - The ability to extend ASTNodes and hence use extended MathML
        has been added and thus it is now possible to use the attributes
        on the <ci> elements of math as specified by the 'multi'
        package. The example relating to this has been updated accordingly.


   * Bug fixes

    - 'render' package-specific bug fixes:

      - On occasion when an L2 document with layout and render
        annotations was being upgraded to L3 the render namespace
        was missed from the annotation in the L3 document.


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

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

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

Thanks

the LibSBMLTeam


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