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               libSBML NEWS -- History of user-visible changes

    ====================================================================
    5.20.4
    ====================================================================

    This is mostly a bug fix release enhancing stability and improving
    performance when validating models. Main points:

    * support compilation when using libxml 2.12.0 and later
    * improved performance when testing for assignment cycles
    * cmake build system honors the BUILD_SHARED_LIB flag if defined

    ====================================================================
    5.20.2
    ====================================================================

    This is mostly a bug fix release enhancing stability when validating
    and converting models.

    * New features / improvements

      - Access to error logs from the C API

      - Attributes of the ModelHistory can now be accessed from
        const objects.

      - The FBC V3 package has been updated to reflect the latest
        specification. There are now optional attributes `fbc:reaction2`
        on the FluxObjective and `fbc:variable2` on the
        UserDefinedConstraintComponent.

    * Bug fixes

      - A bug converting / validating models with the 'comp' package
        has been fixed.

      - A crash when inferring units has been resolved.

      - A fix to the CMake Build system ensures that check for dependencies
        is more robust. Thanks to first time contributor @adelhpour

      - The type of the FBC V3 `coefficient` attribute on the
        UserDefinedConstraintComponent has been corrected, it was mistakenly
        a double before, now it has been corrected to be a SIdRef as
        described in the specification.

    ====================================================================
    5.20.0 (2023-04-03)
    ====================================================================

    Given the length of time since our last release the list of changes
    and acknowledgements of contributions is incomplete. We apologise and
    offer thanks to anyone who has been involved and those people who have
    contributed their spare time to continuing maintenance and development.

    * Addition of support for the SBML Spatial package

      - Now that the first official version of the specification for the
        SBML Level 3 Spatial package is available, the libSBML API for
        'spatial' is now included in the stable release of libSBML.
        Thus a CMake build using '-WITH_STABLE_PACKAGES' will now include
        the spatial package code.

    * New features

      - There is a new converter SBMLRateRuleConverter which will take
        a model with RateRules and infer the corresponding reaction network.
        This is still considered under development and we would really
        appreciate any feedback.

    * Bug fixes

      - A large number of code 'smells' have been cleaned up. Thanks to
        Jamie Quinn for undertaking this laborious task.

      - The python examples have been updated for Python 3.8 changes.
        Thanks to Akira Funahashi for committing these fixes.

      - The python code used for creating documentation has been
        updated for Python 3.10 changes. Thanks to
        Zbigniew Jędrzejewski-Szmek for submitting the changes.

    * Configuration/build system changes

      - Extensive continuous integration testing has been added to
        the GitHub repository.

    * Miscellaneous

      - Note there is now a Julia interface to libSBML available
        at https://lcsb-biocore.github.io/SBML.jl/stable/

    ====================================================================
    5.19.0 (2020-11-27)
    ====================================================================

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

            The libSBML source code has moved to GitHub.
                (https://github.com/sbmlteam/libsbml).

    The stable branch reflects the latest released code. The development
    branch is the main branch and we encourage users to create and
    submit pull requests against this branch. We are no longer
    maintaining a separate repository for experimental code for as yet
    unfinished packages.

    Please use the GitHub issue tracker to file any reports or submit a
    fix and do a Pull Request.

    We will gradually move away from SourceForge, but for this release
    code will be available from both SourceForge and GitHub.

    * Addition of support for the SBML Distributions package

      - Now that the first official version of the specification for the
        SBML Level 3 Distributions package is available, the libSBML API for
        'distrib' is now included in the stable release of libSBML.  This
        means that all prebuilt binaries for the stable release will
        include the 'distrib' package code. The src archive containing
        libSBML core code will continue to be available, with additional
        archives of the individual package code.

        NOTE: The libSBML GNU make-based build system has not been updated
              for packages. Thus, to build from src, it is necessary to
              use the CMake build system.

    * New features

      - Functions get/set/isSetMath have been added to the SBase class.
        These do not allow interacting with a non-existant <math> element
        but may facilitate using more generic functions.

    * Bug fixes

      - There was a memory leak introduced in the SWIG wrapper. Thanks to
        Fabian Fröhlich for spotting and fixing this.

      - The SBMLNamespaces class was being leaked in a number of places,
        these have now been plugged.

      - The MathML to infix parser was also leaking memory. Thanks to
        Liam Keegan for spotting and fixing these.

      - The validation code detecting assignment cycles was incorrectly
        including local parameters within its search. These have now
        been removed from the relevant code.

      - Conversion code was failing to detect when a local parameter used
        the 'id' of a speciesReference which is allowed in SBML Level 3.
        These can be converted to SBML Level 2 and the code has now been
        corrected so this conversion will take place.

      - The L3 infix parser has been improved to recognize the use of a
        name without parentheses as a misused function name or a csymbol,
        if appropriate.

      - There was an anomaly when using the addCVTerm() and
        appendAnnotation() functions which meant that if used in a certain
        order information could be lost. This has been corrected.  Thanks
        to Colin Halupczok for the detailed report.

      - Converting a <localParameter> to a global <parameter> object was
        failing if the metaid attribute was set. This has been changed to
        produce the correct behavior.

    * Configuration/build system changes

     - Import of the python library has been sorted in line with recent Linux
       changes to the location of the shared file.

     - Code has been fixed to be MingGW compliant.

     - The build configuration was updated to work with the latest version of R.

    * Miscellaneous

     - A number of memory leaks and possible access violations have been solved.

    STABLE PACKAGES

      - 'distrib' package-specific updates:

        - A new converter, AnnotationToDistribConverter, has been added
          to allow conversion from the existing annotation format used
          with <functionDefinitions> to the new 'distrib' format. This
          complements the existing DistribToAnnotationConverter that converts
          'distrib' to annotations.

    * Bug fixes

      - 'comp' package-specific bug fixes:

        - Comp flattening dropped conversion factors for particular
          instances of assignment rules. This has been corrected.
          Thanks to Matthias König for reporting this.

      - 'distrib' package-specific bug fixes:

        - There was unfortunately an infinite loop in the code using
          the <uncertainty> element. This has been removed.

      - 'render' package-specific bug fixes:

        - Some render classes were not handled correctly by language
          bindings. This has been fixed.

    EXPERIMENTAL PACKAGES

    * New features

      - 'spatial' package-specific updates:

        - Compression in the 'spatial' package is now based on strings.
          The code has been changed to reflect this.

        - Support for int and uint as DataKinds has been added to the
          spatial code in line with changes in the specification.

        - A range of validation tests have been added to the spatial
          code. As this is an experimental passage package still in
          development, we cannot guarantee that all validation has been
          implemented.

     * Bug fixes

      - 'spatial' package-specific bug fixes:

        - There were some memory leaks in the spatial code.
          Thanks to Liam Keegan for spotting these and congratulations
          for being our first GitHub user to address problems using a
          Pull Request.

    ====================================================================
    5.18.0 (2019-04-18)
    ====================================================================

    STABLE RELEASE

    * New features

      - LibSBML now defines a DefinitionURLRegistry to allow a user to log
        their own values of the 'definitionURL' attribute on a math <csymbol>
        element. Once logged these definitionURL values will not trigger the
        unknown csymbol error when reading a model that uses them.

      - LibSBML now defines a CallbackRegistry which allows a user to register
        a callback to interrupt a long running read operation. Examples for C++
        and Python are included. In future it would be anticipated that would
        have callbacks to interrupt long running validation or conversion
        processes.

    * Bug fixes

      - Validation was incorrectly stating that the id of a <localParameter>
        that mirrorred the id of a <species> should be listed as a
        <modifierSpeciesReference> in the enclosing <reaction>. It no longer
        issue an incorrect error.

      - The string to MathML parser was failing to identify known constants
        as arguments to a lambda function. lambda(pi, pi*2) should treat 'pi'
        as an unknown argument not the constant pi. This has been fixed.

      - The MathML parser adds logbase and degree to log and root elements
        respectively. These are dimensionless integers and but unit
        validation was failing.  This has been corrected.  Note this means
        that for L3 models libSBML will write out the dimensionless units
        on the relevant <cn> element explicitly.  This may cause an
        apparent difference in models if reading and then writing.

      - In MathML a <bvar> element within a <lambda> can only contain a
        <ci> child element. Validation was failing to spot when this was
        not the case. This has been corrected.

      - MathML within a <semantics> element was not being properly validated.
        This has been improved.

      - 'layout' package-specific bug fixes:

        - Code was failing to roundtrip glyphs that contained both a <curve>
          and a <boundingBox> element. This has been fixed.

    * Configuration/build system changes

      - The cmake files that enable using the check library on
        a Linux OS have been updated to make this easier.

      - Python 3.7 is now supported.

    * Miscellaneous

      - Several obscure memory leaks have been plugged.

    EXPERIMENTAL RELEASE

    * New features

      - 'distrib' package-specific updates:

         - The code has been updated to reflect the specification
           agreed during HARMONY 2019 version 0.24.

      - 'spatial' package-specific updates:

        - The code has been updated to reflect the specification
          version 0.93.

        - Attributes 'id' and 'name' have been added to the SpatialPoints
          class in anticipation of these being added to the specification.

        - Plugin code has changed so that child element class members are
          initialised to NULL.  This saves memory but may cause existing
          code to hit an issue when using a getAbc function; which may now
          return a NULL object when previously it did not.

    ====================================================================
    5.17.2-experimental (2018-12-06)
    ====================================================================

    ***                 Experimental only release                    ***

    This is an experimental only release, that is, a release of those
    files provided in the experimental folder of a full release.

    This includes updates to all the SBML L3 packages that are not yet
    accepted and undergoing development.

    NOTE: An experimental release is not as rigorously tested as a
    full release.  Any changes/fixes listed as either referring to
    stable or experimental code may change before the next full release.

    STABLE RELEASE

    * New features

      - The math code has been refactored to use the more efficient
        math-legacy code in combination with a math plugin system.
        This code has been optimized and we welcome feedback on any
        performance issues.  This means there is no longer a math-legacy
        build option.

      - The new math constructs introduced in SBML L3V2 have been refactored
        as a math extension; which facilitates the use of these math functions
        in an SBML L3V1 document.

      - 'comp' package-specific updates:

        - The 'comp' specification states that an external model must be
          an L3V1 document. Since this specification predates SBML L3V2
          we have relaxed the restriction to allow an L3V2 model using
          Model Composition to use an L3V2 external model.

        - The converter that 'flattens' a comp model has been optimized
          for speed with significant improvement for larger models.

      - Python interface specific updates:

        - In libSBML the set/add/unset methods return a code to indicate
          success or failure of the operation. The Python interface has
          been improved to produce a warning when a function fails. This
          behaviour can be enabled by setting a CMAKE configure option
          or an environment variable.

        - Sourceforge Tracker item #456: The Python interface has
          been changed to return an empty List of CVTerms rather
          than a None object.

        - Users have raised issued about Model objects retrieved from within an
          SBMLDocument object going out of scope when the document object
          is removed from scope. We have adjusted the code to allow a Model
          to remain in scope without it's parent document. Feedback would
          be apprceiated about whether this is sufficient or whether all child
          objects should be available regardless of whether their parent is
          still available.

        - Sourceforge Tracker item #468:  Functions deprecated in Python 3.6
          have been replaced to avoid deprecation warning messages.

    * Bug fixes

      - The function SBMLTypeCode_toString was not retuning the correct
        string for a ListOf element originating in a package. This
        has been corrected.

      - Using an SBML L3 package in an L2 document could cause a crash.
        This has been fixed. Thanks to Thomas Hamm for reporting it.

      - The code that checked for use of an L3V2 package with an L3V1
        document could cause a crash. This has been fixed.

      - Writing out a document without a model and no level and version
        was using level = version = 0; which is not valid. This has been
        changed to write a L3V2 document with no model.

      - There was an issue with newer architectures when casting a
        NaN to an integer - this has been now been avoided.

      - MATLAB interface specific bug fixes:

        - The matlab binding was failing to distinguish between a
          functionDefinition where the id ended with a logical operator,
          e.g. 'myor' and the actual logical function. This has been corrected.

      - 'comp' package-specific bug fixes:

        - There was an issue with flattening 'comp' models using conversion
          factors. This has been tracked down and fixed. Thanks to Matthias
          Konig for reporting it and providing examples.

      - 'render' package-specific bug fixes:

        - Historical render code did not create a NULL BoundingBox.
          Current code has been brought in line with this.

    * Configuration/build system changes

      - Python 3.7 is now supported and included in the builds.

      - The USE_LEGACY_MATH option has been removed as code has been
        reverted to use this math implementation (see above).

    EXPERIMENTAL RELEASE

    * New features

      - 'distrib' package-specific updates:

        - The distrib package code has been updated to include the use
          of csymbols to reference distributions. This is in line with
          the latest distrib specification.

    ====================================================================
    5.17.0 (2018-05-21)
    ====================================================================

    STABLE RELEASE

    * Addition of support for the SBML Render package

      - Now that the first official version of the specification for the
        SBML Level 3 Rendering package is available, the libSBML API for
        'render' is now included in the stable release of libSBML.  This
        means that all prebuilt binaries for the stable release will
        include the 'render' package code. The src archive containing
        libSBML core code will continue to be available, with additional
        src archives available in the stable branch: one containing
        libSBML core plus all stable packages and additional archives of
        the individual package code.

        NOTE: The libSBML GNU make-based build system has not been updated
              for packages. Thus, to build from src, it is necessary to
              use the CMake build system.

    * New features

      - The MATLAB language interface function TranslateSBML has been
        optimized for speed.

      - The MATLAB interface function OutputSBML can now be called with an
        output argument and no inputs; doing so will return information
        about the libSBML version and enabled packages used to build the
        binary files.

      - A new function getDefaultSBMLStruct has been added to the MATLAB
        interface. This function takes a string name of the element with
        level and version information and returns the relevant MATLAB-SBML
        structure for the element. Many thanks go to Thomas Pfau for
        supplying this function.

      - On occasion, the function getDerivedUnitDefinition that returns
        calculated units would report incorrect units without flagging any
        issues. This has been made less ambiguous and a derived
        UnitDefinition will not contain any units if it cannot be
        correctly determined.

      - Unit validation has been optimized and significantly speeded up for
        larger models.

      - 'comp' package-specific updates:

        - The C API for comp has been completed.

      - 'fbc' package-specific updates:

        - SourceForge Tracker item #455: Error messages have been improved.

      - 'multi' package-specific updates:

        - The C API for multi has been completed.

      - 'qual' package-specific updates:

        - SourceForge Tracker item #455: Error messages have been improved.

      - 'render' package-specific updates:

        - A full C API for the render package has been added.

    * Bug fixes

      - SourceForge Tracker item #459: An error in the function that
        converts libSBML infix notation to MATLAB infix notation failed
        when log functions failed. This is fixed. Thanks to Sven Thiele
        for reporting the issue.

      - The validation check for duplicate values of the 'metaid'
        attribute was not being extended to all packages. This has
        been fixed.

      - Python examples have been updated to work with Python v3.

      - 'qual' package-specific bug fixes:

        - SourceForge Tracker item #457: Validation of rule qual-20311
          was producing an error when it should have been a warning.
          Thanks to Justin McManus for reporting the problem.

    EXPERIMENTAL RELEASE

    * New features

      - 'distrib' package-specific updates:

        - The 'distrib' package has undergone significant changes.
          The code has been fully updated to match this. We have also
          used a Distrib prefix on all classes to prevent clashes with
          other packages or even other libraries. We welcome feedback
          on this approach.

    ====================================================================
    5.16.0 (2017-12-07)
    ====================================================================

    STABLE RELEASE

    * Note

      The L3 Render Package has been approved by the SBML Editors, but
      approval came too late in the libSBML release cycle to include it
      in this stable release of libSBML.

      There are now two implementations of support for SBML Level 3
      Version 2 Core.  The libSBML code for L3V2 can now be considered
      stable and will only change for bug fixes.

    * New features

      - The MATLAB interface now supports both the 'qual' and 'groups'
        packages, in addition to 'fbc'.

      - Unit checking has been expanded to include checking the <math>
        of <trigger>, <constraint> and <stoichiometryMath> to at least
        allow detection of values with undeclared units.

      - Writing out an XMLNode that represented XHTML with multiple
        nested text elements could distrupt indentation (see bug fixes).
        A new function XMLNode::writeToStream(XMLOutputStream&) checks
        the indentation is correctly recovered after writing out the
        XMLNode.

      - 'comp' package-specific updates:

        - There has been some improvements made to the reporting of line
          numbers for errors and warnings.

    * Bug fixes

      - SF Tracker #450: Code validating the shadowing of localParameter
        was checking both 'id' and 'species' attributes. This rule should
        only check the species attribute.

      - SBML validation failed to distinguish between LocalParameters and
        Parameters in L3V1 when reporting errors. This is fixed.

      - libSBML had incorrectly reported that the 'fast' attribute was a
        required attribute of L3V2 <reaction> elements. This is fixed.

      - The libSBML C API does not work with default arguments. There were
        previously a few stray ones left in the API code. These have been
        removed.

      - The SBMLTransforms::evaluateASTNode function previously failed to
        check that model values had been evaluated prior to trying to
        evaluate an ASTNode. The relevant function now checks whether the
        map of values is present and populates it, if necessary.

      - Code that checked the syntax for attributes of type ID and IDREF
        did not always use the appropriate function. These cases have been
        fixed.

      - The use of an invalid syntax as the sbml:units attribute on a math
        <cn> element was not being detected. This has been fixed. Thanks
        to Nicolas Rodriguez for the report.

      - The SBMLTransforms::evaluateASTNode function missed the fact that
        in SBML Level 2, stoichiometry defaulted to '1'. This has been
        corrected.

      - The use of certain combinations of text elements in a <notes> element
        could derail the entire indentation of the document. This has been
        reported by several people. Hopefully this time we have fixed the
        situation for all cases where it may occur.

      - The interactive help text stored with the functions and classes in
        the Python bindings had many formatting problems and outright
        omissions due to bugs in our "rewrite_pydoc.py" code. Many of
        these problems should be fixed now.

      - 'fbc' package-specific bug fixes:

        - Validation incorrectly reported an empty <listOfFluxObjectives>
          even when a model was being created and did in fact have a
          <fluxObjective> element. This has been fixed. Thanks to Arthur
          Goldberg for reporting it.

        - An empty <geneProductAssociation> caused the reading of model
          files to crash libSBML. This no longer happens.

      - 'layout' package-specific bug fixes:

        - Conversion between Level 2 annotations using both layout and render
          and Level 3 packages has been corrected.

      - 'qual' package-specific bug fixes:

         - Functions to get math on a <functionTerm> element were missing
           from the C API. They have been added.

    * Configuration/build system changes

      - SourceForge Tracker item #447: Configuration no longer defines
        HAVE_IEEEFP_H when using MSVC compilers as it is not needed
        and not always present. Thanks to Alan Garny for spotting this.

      - SourceForge Tracker item #443 & separate unreported problems:
        Build failures with Java 9 should be fixed now.  Thanks to Chris
        West for reporting the issue related to building the docs.

    * Miscellaneous

      - SWIG only supports Javascript node 6x. Thus we cannot currently
        support later versions of node.

      - Documentation for the C API has been extensively improved.

      - Support has been added for Python 2 unicode input.

      - Currently we supply lib files built with MSVC2010 as part of the
        windows installers. These will be removed from future releases.
        Please let us know if this is an issue for you.

    EXPERIMENTAL RELEASE

    * New features

      - 'render' package-specific updates:

        - At the request of the SBMLEditors the attribute 'name' has been
          added to render elements.

     * Bug fixes

      - 'render' package-specific bug fixes:

        - Conversion between Level 2 annotations using both layout and
          render and Level 3 packages has been corrected.

      - 'spatial' package-specific bug fixes:

        - There was a mismatch in the SetOperation enumeration in the
          specification.  This has been agreed as 'union', 'intersection'
          and 'difference' and libSBML code has changed to reflect this.

        - Corrected the output of a <csGeometry> element to correctly use
          an upper case G.

    ====================================================================
    5.15.2 (2017-07-27)
    ====================================================================

    ***                 Experimental only release                    ***

    This is an experimental only release, that is, a release of those
    files provided in the experimental folder of a full release.

    This includes updates to all the SBML L3 packages that are not yet
    accepted and undergoing development.

    NOTE: An experimental release is not as rigorously tested as a
    full release.  Any changes/fixes listed as either referring to
    stable or experimental code may change before the next full release.

    STABLE RELEASE

    * New features

      There are no features in the stable branch; although there has
      been some optimization of code. We have also included testing
      of examples code in our test protocol.

    * Bug fixes

      - Infix parsing of lambda functions was failing to consider
        variable names as variables, when they might overlap with
        other names for MathML constructs or csymbols e.g. 'time'
        or 'pi'. This has been corrected so that a lambda function
        will correctly produce the necessary <bvar> elements.

      - Conversion of interchangeable booleans and numbers was not
        reporting consistent information. This has been improved.

      - Conversion between SBML levels and versions was failing to
        correctly identify a speciesReference identifier. This is
        now sorted.

      - Sourceforge Tracker #8: The MATLAB bindings were failing to
        correctly convert logical functions. This has been fixed. Thanks
        to Fabian Froehlich for the report.

      - The check that reports <localParameters> shadowing other identifiers
        was not noticing when it shadowed a speciesReference.  This has
        been corrected.

      - The evaluateAST function was not correctly dealing with a
        missing math element.

      - 'comp' package-specific bug fixes:

        - Reading in externally referenced documents during 'comp'
          validation and/or flattening was consuming large amounts of memory.
          This has now been optimized.

        - There were some slight discrepancies with writing out the id
          attribute in an L3V2 document using 'comp' L3V1V1. These have
          been sorted out.

        - There was a very obscure endless loop in validation that
          Chris Myers managed to find. This is now closed. Thanks Chris.

      - 'groups' package-specific bug fixes:

        - Sourceforge libSBML Tracker #438: The C API for the plugin
          objects was missing. This has been corrected. Thanks to CJF for
          the report.

    EXPERIMENTAL RELEASE

    * New features

      - 'arrays' package-specific updates:

        - A basic ArraysFlatteningConverter has been added. As yet, this does
          not deal with arrays of submodels from the 'comp' package.

      - 'distrib' package-specific updates:

        - NOTE: the code has not been updated to the latest proposed version
          of the 'distrib' specification as this is currently under major
          review.

     * Bug fixes

      - 'arrays' package-specific bug fixes:

        - The 'arrays' code was not always correctly reading and writing the
          namespace. This has been fixed.

    ====================================================================
    5.15.0 (2017-04-06)
    ====================================================================

    NOTE: This release includes support for the SBML L3V2(RC1)
    Release Candidate specifications.  This specification is not yet
    official and thus it, and the supporting code, may change.

    STABLE RELEASE

    * Multistate and Multicomponent Species

      - The first official version of the specification of the Multistate
        and Multicomponent Species package is now available, and thus the
        libSBML code for 'multi' is now included in the stable release of
        libSBML.  This means that all prebuilt binaries for the stable
        release will include the 'multi' package code. The src archive
        containing libSBML core code will continue to be available, with
        additional src archives available in the stable branch: one
        containing libSBML core plus all stable packages and additional
        archives of the individual package code.

        NOTE: The libSBML GNU make-based build system has not been updated
              for packages. Thus, to build from src, it is necessary to
              use the CMake build system.

    * New features

      - A new option has been added to the L3ParserSettings to allow
        users to turn off the parsing of the new L3 math elements. If
        enabled the parser will treat the new functions as generic
        user defined functions.

      - The L3Parser has been updated to parse '%' as rem.

      - The MATLAB binding has been updated to support SBML L3V2(RC 1).

      - Additional options are available for the TranslateSBML/OutputSBML
        functions for the MATLAB binding allowing users to add their own
        validation and customize the input/output of some fbc elements.
        (See documentation for more details.)

      - A new structure field 'cvterms' has been added to the MATLAB_SBML
        structure.  This supports annotations as a set of fields relating
        to qualifiers and resources rather than relying on annotation
        in the string format.

      - A new function setCharacters has been added to the XMLToken class.

      - The SBMLDocument object resulting from an invalid read will now
        report level and version as '0'. This facilitates distinguishing
        between an invalid read and a Level 3 Version 2 document that
        does not contain a <model> element.

    * Bug fixes

      - Code was failing to recognize the math elements <pi/> and
        <exponentiale/> as returning numeric values. This has been
        corrected.

      - A <stoichiometryMath> element with no child <math> was causing
        code to crash. This has been sorted.

      - Validation of MathML was failing to report when a <math> element
        contained two top-level elements. This is now caught and correctly
        reported.

      - A speciesReference id which has been declared 'constant' cannot be
        changed by an event. Validation was failing to catch this situation.
        This is now fixed.

      - Several fixes have been made to the conversion of SBML documents
        to lower levels and versions. These include: loss of compartment
        size; evaluation of functionDefinitions and initialAssignments;
        conversion of fast reactions; evaluation of stoichiometry using
        initialAssignment and rules and expanding functionDefinitions with
        no bvar elements.

      - The export of the Avagadro constant as an exponential number was
        losing precision. This has been fixed.

      - Unit checking was failing to correctly associate the model 'timeUnits'
        with the use of the csymbol for time. This has been corrected. Thanks
        to Matthias König for reporting it.

      - 'comp' package-specific bug fixes:

        - Validation of a model that indirectly referenced a replacedBy element
          was causing a problem. This has been resolved.

        - The flattening routine was failing to correctly adjust the metaid
          referenced by annotation where necessary.  This has been fixed.
          Thanks to Matthias König for reporting it.

      - 'fbc' package-specific bug fixes:

        - Validation was incorrectly reporting that a lower fluxBound could
          not have a value of -INF. This has been corrected.

        - The 'unsetActiveObjective' function now returns an OperationReturnValue
          in line with other set/unset functions.

    * Configuration/build system changes

      - The minizip library used for compression supported has been updated.
        There are no backwards compatability issues.

      - The CMake build has been extended to enable export of the configuration
        used in building. This will facilitate users who use libsbml and/or its
        dependencies as dependencies in other projects.

    * Miscellaneous

     - Beware that Doxygen 1.8.12 and later changed something in the HTML
       it creates, and as a result, the libSBML documentation-generation
       currently does not work for Doxygen versions after 1.8.11.  This will
       be fixed in a later release.  For the time being, use Doxygen 1.8.11.

     - We are aware that the released MATLAB binaries do not appear to work
       with MATLAB 2017a on Mac OSX. At present we are unable to address this
       issue but will resolve it and issue new binaries as soon as possible.

     - We are aware that the octave binding is not functioning as expected.
       We would be very interested to know of any users of the libsbml
       octave interface that are affected by this.

    EXPERIMENTAL RELEASE

    * New features

      - 'spatial' package-specific updates:

        - The spatial code has been adjusted for minor changes in the
          specification and now reflects rel0.91 of the specification.
          Some, but not all, validation has been added to the code.

    ====================================================================
    5.14.0 (2016-09-15)
    ====================================================================

    ***                 Experimental only release                    ***

    This is an experimental only release, that is, a release of those
    files provided in the experimental folder of a full release.

    This includes updates to all the SBML L3 packages that are not yet
    accepted and undergoing development.

    NOTE: An experimental release is not as rigorously tested as a
    full release.  Any changes/fixes listed as either referring to
    stable or experimental code may change before the next full release.

    This release includes support for the SBML L3V1R2(RC1) and L3V2(RC1)
    Release Candidate specifications.

    STABLE RELEASE

    * New features

      - An Iterator class has been added to the List utility.

    * Bug fixes

      - Validation was not being correctly invoked on <localParameter>
        objects. This has been fixed.

      - The functions for parsing a string to an ASTNode would cause a
        crash if passed a NULL pointer.  This has been fixed.  Thanks to
        Matthias König for reporting it.

      - The L3Parser has been improved to catch a case when a NULL input
        has been provided and return an error to the user.

    EXPERIMENTAL RELEASE

    * New features

      - 'multi' package-specific updates:

        - Code has been updated to reflect the latest v 1.0.7 specification.

    ====================================================================
    5.13.0 (2016-04-14)
    ====================================================================

    STABLE RELEASE

    * Groups

      - The first official version of the specification of Groups
        is now available, and thus the libSBML code for
        'groups' is now included in the stable release of libSBML.  This
        means that all prebuilt binaries for the stable release will
        include the 'groups' package code. The src archive containing
        libSBML core code will continue to be available, but there will be
        additional src archives available in the stable branch: one
        containing libSBML core plus all stable packages and additional
        archives of the individual package code.

        NOTE: The libSBML GNU make-based build system has not been updated
              for packages. Thus, to build from src, it is necessary to
              use the CMake build system.

    * New features

      - New functions have been added to the XMLOutputStream to allow the
        optional XML comment to be further customized.

      - The Python binding now includes a __version__ field.

      - 'comp' package-specific updates:

        - The SBMLResolver interface has been exposed within language bindings.

      - 'fbc' package-specific updates:

        - The MATLAB interface has been expanded to include a dedicated
          FBC V2 structure.  Thanks to the COBRA Toolbox team for their
          feedback and testing.

        - There was an issue with round-tripping geneProductAssociations
          between the expression and the infix representation.  This has
          been sorted.

      - 'groups' package-specific updates:

        - A function named 'copyInformationToNestedLists' has been
          added to facilitate keeping information consistent when multiple
          <group> objects refer to the same thing.

    * Bug fixes

      - Validation was failing to catch when the <piece> element of a
        <piecewise> had an incorrect number of children.  This has been
        fixed. Thanks to Jason Zwolak for the report.

      - Unit consistency checking was failing to interpret the units of
        <cn> elements when passed to a <functionDefinition>. This has been fixed.

      - The getListOfElements code was not being correctly ported to
        language bindings. This has been corrected.

      - Unit consistency checking was failing to correctly handle non-integer
        power expressions. This has been corrected. Thanks to Matthias König
        for reporting this.

      - The StrictUnitConsistencyValidator has been corrected to identify
        matching base SI units. Thus, 1000 litre will be correctly equated
        with 1 metre cubed.

      - Sourceforge libSBML Tracker #421: The MATLAB binding was failing
        to round-trip multi-byte characters used in strings. This has
        been fixed. Thanks to Will Matern for the report.

      - Validation was failing to report that a 'variable' attribute is
        not permitted on an AlgebraicRule.  This has been corrected.

      - Sourceforge libSBML Tracker #418: Using the isnan() function can
        cause issues with some compilers. LibSBML has a util_isNaN() function
        which should be used when necessary.  Thanks to Alan Garny for
        reporting this issue.

      - The functions that convert an enumeration value to a string had
        not been ported to language bindings.  This has now been sorted.
        Thanks to Matthias König for letting us know.

      - The new ASTNode class instances were failing to deal correctly with
        semantic annotations.  This has been fixed.

      - 'comp' package-specific bug fixes:

        - Failing to access an external model could cause an endless
          loop while attempting validation.  This has been corrected.
          Thanks to Chris Myers for the report.

      - 'fbc' package-specific bug fixes:

        - Sourceforge libSBML Tracker #419: The converters provided for
          converting from COBRA style SBML models to SBML+fbc style models
          were losing a charge of '0' if explicitly set. This has been
          corrected. Thanks to Ali Ebrahim for reporting the problem.

      - 'layout' package-specific bug fixes:

        - In some cases the value of the 'id' attribute was being written out
          as the 'name'.  This has been fixed.

    * Configuration/build system changes

      - The Python bindings can now be configured to install using setup.py.

    * Miscellaneous

      - The Python version of libSBML available via PyPi now includes binary
        wheels for Windows and Mac OSX operating systems.

      - The Python version of libSBML available via PyPi now includes all
        dependencies.

      - We conducted a review of the mathml-infix parsing code and compared
        inputs and outputs with those of JSBML. This has produced a more
        synchronized approach between the two APIs.

      - There is a known bug in GCC versions 5.1 and 5.2 which results in the
        problem that calling the copy constructor of a base class in the
        constructor of derived classes produces crashing code.  The problem
        manifests itself in libSBML when using a language binding such as the
        Python interface. Workarounds have been added to the libSBML
        'Known Issues' documentation.

      - Sourceforge libSBML Tracker #417: Documentation was failing to write
        using Python 3.5.  This has been fixed.  Thanks to  Antonio Trande for
        reporting this.

    EXPERIMENTAL RELEASE

    * New features

      - 'multi' package-specific updates:

        - The code has been updated to reflect v 1.0.6 of the specification.

    ====================================================================
    5.12.0 (2015-11-12)
    ====================================================================

    STABLE RELEASE

    * New features

      - In SBML Level 2, some units were defined by default and did not
        need to be explicitly included in a model. The
        SBMLLevelVersionConverter adds these units explicitly when
        converting to SBML Level 3. We have an added an option to
        disable this functionality and return Level 3 models without
        the units implied by Level 2.

      - Sourceforge libSBML Tracker #242: 'addProduct etc using a species'
        We have added functions addProduct/addReactant/addModifier that
        take a Species as argument, along with a number of other optional
        values to completely specify the SpeciesReference object being
        created. This is a slight divergence from the direction libSBML
        usually takes and we would be grateful for any feedback
        on these functions.

      - Validation speed has been dramatically improved for models that
        make use of FunctionDefinitions and in particular nested
        FunctionDefinitions.

      - 'comp' package-specific updates:

        - The 'flattening' routines have been expanded to correctly deal
        with FBC V2.

      - 'fbc' package-specific updates:

        - The FBC Version 2 package has been accepted by the SBML Editors.
          The code supporting this is now available as part of the stable
          release.

    * Bug fixes

      - There was a very subtle bug in unit checking that incorrectly
        applied a multiplication factor. Thanks to Mike Cooling for
        the detailed example and anaylysis that revealed this. It
        has now been fixed.

      - In the new math code using the children of an ASTNode could result
        in the math namespace declaration being unecessarily written out
        in many places. This has been sorted out.

      - Sourceforge libSBML Tracker #414: "A missing break statement" was
        added.

    * Configuration/build system changes

      - The CMake files have added an option to dynamically link to a
        python version on Mac OSX systems rather than automatically link.
        Thanks to Kyle Medley for supplying the initial patch for this.

      - The test code has been tweaked to build and run with MSVC 2015.
        Fortunately the main code base worked with no issues.

    * Miscellaneous

      - Further documentation improvements have been added, especially for
        the FBC package.

    EXPERIMENTAL RELEASE

    * New features

      - 'multi' package-specific updates:

        - Full validation has been added to the multi package code.
          Thanks to Fengkai Zhang for his continued efforts on this.

    ====================================================================
    5.11.6-experimental (2015-07-16)
    ====================================================================

    ***                 Experimental only release                    ***

    This is an experimental only release, that is, a release of those
    files provided in the experimental folder of a full release.

    This includes updates to all the SBML L3 packages that are not yet
    accepted and undergoing development.

    NOTE: An experimental release is not as rigorously tested as a
    full release.  Any changes/fixes listed as either referring to
    stable or experimental code may change before the next full release.

    STABLE RELEASE

    * New features

      - There is a new function on SBMLDocument, checkConsistencyWithStrictUnits(),
        which applies the same validation as the checkConsistency() function with
      one difference being that it will always apply unit validation using
      exact identity comparison between units and it logs all unit
      violations as Error regardless of the SBML Level and Version.

      - There is a new converter that will convert to SBML L1V1. The 'regular'
        SBMLLevelVersionConverter does not support this level and version
        as we generally discourage the use of it. However users have requested
        the facility and thus we have included a separate converter to meet
        that need.

      - 'const' versions of the getElementBySId() and getElementByMetaId()
        functions have been added.

      - 'fbc' package-specific updates:

        -  Code has been updated to use support the FBC V2 format that is currently
         available as a Release Candidate document. Full validation for this
         format has been included.

    * Bug fixes

      - The static function UnitDefinition::reorder failed to correctly deal
        with situations where the same unit kind appeared multiple times. This
        has been fixed. Thanks to Matthias König for reporting the problem.

      - There were some discrepancies between math and math-legacy code reporting
        the incorrect use of the MathML <apply> tag. This has been standardized
      and more rigorously tested.

    * Miscellaneous

      - Several functions in libSBML checked for a NULL reference; something
        that it is considered a well-formed program should not be able to
        create. As more and more compilers are complaining about this code,
        on the grounds it should not be possible to create the NULL reference,
        we made the decision to remove this code. Please let us know if this
        is an issue for you.

    EXPERIMENTAL RELEASE

    * New features

      - L2V5 specific updates:

        - A new validation rule was identified during the review of the SBML
        Level 2 Version 5 specification. Support for this has been added.

      - 'arrays' package-specific updates:

        - The MathML elements included in the 'arrays' package has been
        reduced. The code now reflects this.

      - 'multi' package-specific updates:

        - The code has been updated to reflect v 1.0.4 of the specification.
        This includes full validation. Thanks to Fengkai Zhang for
        contributing the code.

    ====================================================================
    5.11.4 (2015-04-09)
    ====================================================================

    STABLE RELEASE

    * New features

      - The ASTNode class has a new function double getValue() that
        returns the numerical value of the ASTNode as a double.  This
        includes returning values for constants such as AST_CONSTANT_PI,
        AST_CONSTANT_E, and AST_NAME_AVOGADRO, or '1' for an ASTNode of type
        AST_CONSTANT_TRUE and '0' for AST_CONSTANT_FALSE.  Note, it does
        not attempt to evaluate the node and thus will return NaN for a
        function or node representing a named variable, and AST_NAME_TIME.

      - There has been a complete review of validation messages.  These
        have been unified in terms of spacing and line returns.  In
        addition many have been enhanced with additional model specific
        information designed to assist in locating and fixing the issues.

      - There is now an interface to PHP.  This has been tested on all
        platforms.

      - Historically libSBML did not provide unsetFoo functions where
        the attribute was a required attribute with a default value.
        At user request we have changed this so every attribute has a
        corresponding unset function.  Note that where the attribute
        has a default value it is still considered 'set' but not
        considered to have been explicitly set and will therefore not
        appear in the written output.

      - The L3Parser will now correctly parse a unary plus.

      - The L3Parser will now parse chains of relational operators.
        Identical operators become ASTNodes with relational type and
        each argument as a direct child.  Thus 'x < y < z' becomes
        an ASTNode of type AST_RELATIONAL_LT with three children
        representing x, y and z.  Non identical operators use a logical
        'and' function to combine the arguments. Thus 'x < y > z'
        becomes an ASTNode of type AST_LOGICAL_AND with two children
        each representing the relational operator; that is
        and(lt(x,y), gt(y,z))

      - The ability to index lists in the python bindings has been improved.

      - A new value 'LIBSBML_MISSING_METAID' has been added to the
        OperationReturnValues_t enumeration.  This value will be returned
        when a user attempts to set an annotation on an object that has
        no metaid attribute set.  Note this is a change in behaviour as
        previously the value returned would have been
        'LIBSBML_UNEXPECTED_ATTRIBUTE'.  We hope this change makes the
        issue clearer to users.

      - The package extension mechanism has been expanded to allow the
        extension of individual ListOfFoo classes.

    * Bug fixes

      - Conversion from SBML Level 3 to Level 2 was losing some
        LocalParameters. This has been sorted.  Thanks to Matthias
        König for spotting and reporting the problem.

      - Fixed a bug where using the expat parser failed to correctly
        report the presence of invalid XML namespaces.

      - Sourceforge libSBML Tracker #393: LibSBML was failing when
        built on an ARM processor running Fedora.  This has been
        sorted out.  Thanks to Zbigniew Jedrzejewski-Szmek for
        reporting the issue and testing solutions.

      - The formulaParser was incorrectly parsing particular syntax
        involving exponential, plus/minus signs and no spacing i.e.
        '2e3-3' was failing to parse.  This has been corrected.
        Thanks to Kieran Smallbone for reporting this and apologies
        for the length of time it took to fix.

      - Sourceforge libSBML Tracker #402: The functions that deal with
        user data on both ASTNode and SBase objects have been made
        to work with const versions of objects where appropriate.
        Thanks to Takeshi Abe for the request and the patch.

      - 'comp' package-specific bug fixes:

        - The code for determining whether an external file is available
          has been further tightened up.

      - 'fbc' package-specific bug fixes:

        - A bug in the code that reads GeneAssociations as an annotation
          meant information was being lost.  This has been corrected.
          Thanks to Matthias König for reporting the problem.

      - 'layout' package-specific bug fixes:

        - The names of some functions meant they were failing to
          correctly port to the Python bindings.  The binding mechanism
          has been fixed to correct this.  Thanks to Kieran Smallbone
          for reporting this.

        - The SpeciesReferenceGlyph attribute 'role' can take the value
          'undefined' but this was not written out. This has been
          changed.

    * Configuration/build system changes

      - This release includes pre-built binaries for the MATLAB
        bindings that should work for many Linux and MacOSX
        platforms.  Please advise us it you find a combination
        of platform and MATLAB version for which these fail.

    * Miscellaneous

      - The names of some arguments to functions have
        been modified to convey the fact that the object
        is not owned by the collection object to which it
        has been added.

    EXPERIMENTAL RELEASE

    * New features

      - 'distrib' package-specific updates:

        - There are new example programs that will create the
          examples given in the current specification.

      - 'multi' package-specific updates:

        - The multi code has been updated in line with the specification
          Release 1.0.2 dated November 2014. This code has been contributed
          by Fengkai Zhang. Many thanks, Fengkai.

      - 'spatial' package-specific updates:

        - The spatial code has been updated in line with the specification
          Release 0.90 dated March 2015.

    * Bug fixes

      - 'multi' package-specific bug fixes:

        - The multi attributes that can be added to a math <ci> element
          where being lost when written out.  This has been fixed.

    ====================================================================
    5.11.2-experimental (2015-01-15)
    ====================================================================

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

    ***                 Experimental only release                    ***

    This is an experimental only release, that is, a release of those
    files provided in the experimental folder of a full release.

    This includes updates to all the SBML L3 packages that are not yet
    accepted and undergoing development.

    NOTE: An experimental release is not as rigorously tested as a
    full release.  Any changes/fixes listed as either referring to
    stable or experimental code may change before the next full release.

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

    STABLE RELEASE

    * New features

      - Functions have been added to allow users to determine the
        number of SBML L3 packages within a document that the build
        of libSBML does not support.

      - The StripPackageConverter has a new option
        'stripAllUnrecognized' which if set to true will strip all SBML
        L3 packages that are not supported by the build of libSBML
        being used.

      - The XMLErrorLog::remove(unsigned int errorId) function only
        removes the first instance of the error with the matching
        identifier. A new function removeAll(unsigned int errorId)
        has been added that will remove all instances of the error
        with the given id.

    * Bug fixes

      - A stack overflow could occur when libSBML was built with certain
        compilers on certain platforms. We have eliminated this problem
        from the situations in which we can replicate it. The issue
        occurred when performing intensive validation.

      - The math-legacy code was being caught in an endless loop when
        trying to read a nested piecewise function.
        This has been fixed.

      - Validation was failing to recognize some cases when the
        conditional part of a piecewise function returned a boolean and
        incorrectly indicated that such a model was incorrect.  We have
        fixed this as robustly as possible but encourage reports of
        situations where we have missed something.

      - 'layout' package-specific bug fixes:

        - Validation of layout was not correctly reporting line
          and column numbers. This has been corrected.

    * Configuration/build system changes

      - The CMake configuration has been improved to clearly
        report failure to find files necessary to work with
        particular language bindings.

      - Sourceforge libSBML Tracker #394: The '\n' symbol
        was not being correctly expanded on some systems. This
        has been made more robust.  Thanks to Antonio Trande
        for reporting this.

    EXPERIMENTAL RELEASE

    * New features

     - Support for the SBML Level 2 Version 5 Release 1
       (Release Candidate) specification has been added.
       Additions to libSBML include:
         - new API for adding Nested Annotations used on
           the existing CVTerm object:
             int addNestedCVTerm(const CVTerm* term)
             CVTerm* removeNestedCVTerm(unsigned int n)
             unsigned int getNumNestedCVTerms()
             CVTerm* getNestedCVTerm(unsigned int n)
             List* getListNestdCVTerms()
         - new and changed validation rules as in the specification
         - the ability to convert core SBML to and from L2V5

      - 'multi' package-specific updates:

        - The multi code has been updated in line with the specification
          Release 1.02 dated November 2014.

      - 'spatial' package-specific updates:

        - The spatial code has been updated in line with the specification
          Release 0.89 dated November 2014.

     * Bug fixes

      - 'spatial' package-specific bug fixes:

        - Sourceforge libsbml Tracker #387: The C# bindings for spatial
          were not working as expected. These have been fixed. Thanks to
          Harold Gómez for reporting this.

    ====================================================================
    5.11.0 (2014-11-27)
    ====================================================================

    STABLE RELEASE

    * New features

      - There is now an interface for JavaScript.  This has been tested
        on all platforms.  Building requires SWIG version 3.0.2 or greater
        and depends on node-gyp.  Feedback on this would be greatly
        appreciated.

      - We have made a source package for the libSBML R interface
        available for Linux and OSX users.

      - The facility of using the data members of objects as attributes
        in python has been extended to work with Python version 3.

      - The SBMLDocument class now has an 'isSetModel()' function.

      - There is a new writSBMLToStdString() function that returns a
        std::string rather than a char * that has to be freed by the caller.
        This facilitates cleaner memory management. Similarly there is
        a writeMathMLToStdString() function.

      - The errors reported by OutputSBML in the MATLAB binding have been
        extended to provide more information about the specific field
        causing a problem.  Thanks to Thomas Pfau for providing a template
        for adding this information.

      - Support for the MIRIAM qualifiers hasTaxon, isInstanceOf and
        hasInstance has been added.

      - More information has been added to error messages.

      - There are new functions to allow users to retrieve and print errors
        from the ErrorLog based on the severity of the error.  These are
        SBMLError* getErrorWithSeverity(unsigned int n, unsigned int severity)
        and printErrors(std::ostream& stream, unsigned int severity).

      - 'comp' package-specific updates:

        - A new flag has been added to the CompFlatteningConverter to
          allow a user to specify a comment separated list of packages
          that should be stripped before flattening is attempted.

        - The CompFlatteningConverter has been made more rigorous
          when it comes to specifying users options on models declared
          as ExternalModelDefinitions.

    * Bug fixes

      - There was an issue with using the libsbml namespace and the
        ReactionConverter.  This has been fixed.  Thanks to Andy Somogyi
        for reporting it.

      - The facility to use data members of objects as attributes
        was broken.  This has now been fixed.

      - Code checking the values of units attributes was incorrectly
        allowing the default Level 2 units, such as substance, to
        be used in Level 3.  This has been corrected.

      - Using unicode filenames with MATLAB on a Windows system proves to
        be very problematic. We have solved the problem but only for the
        case where filenames are entered directly via the dialogs that
        OutputSBML / TranslateSBML open up. There appears to be an issue
        with MATLAB using such filenames directly from the workspace.
        This has been added to the known issues documentation.

      - The C API function ConversionProperties_removeOption now returns
        a pointer to the option being removed.  This is in line with other
        remove functions.

      - Validation failed to report an error when more than one model
        element was encountered and merely returned a document with the
        last model read.  This has now been corrected.

      - The getDerivedUnitDefinition function returns a pointer to an
        existing unitDefinition object maintained by the model.  However
        in the case of a Parameter a new unitDefinition object was being
        created, thus causing an inconsistency when it comes to freeing
        memory. This has now been corrected and
        Parameter::getDerivedUnitDefinition now returns an existing pointer.

      - 'comp' package-specific bug fixes:

        - Validation was failing to report when a portRef attribute
          had been used on a Port object and indeed this situation caused
          validation to crash in some cases.  This has now been sorted.

    * Configuration/build system changes

      - When javac fails to compile a class no error was reported
        and a useless jar file was created.  The build has been
        changed to highlight the issue.

      - Sourceforge libsbml Tracker #380: The use of #include Windows.h
        has been changed to lowercase to facilitate building using
        MinGW.  Thanks to Takeshi Abi for reporting the problem.

    * Miscellaneous

      - We have continued our review of code and many more memory leaks
        have been plugged.  Thanks to people, in particular Andy Somogyi,
        for reporting these.  Stable code has been rigorously tested using
        both Valgrind (http://valgrind.org/) and Visual Leak Detector for
        Visual C++ (https://vld.codeplex.com/). Experimental code is
        currently being reviewed.

      - Sourceforge libsbml Tracker #372: Documentation has been corrected.
        Thanks to Gerard Weatherby for reporting the issues.

      - The sample Java programs and configuration/importing instructions
        for Java now use a shortened and simplified static loading block
        (i.e., the part that explains how to use System.loadLibrary() to
        load libSBML).

      - We've made efforts to simplify the instructions for downloading,
        configuring and accessing libSBML.  Among the changes are that the
        API language manuals for Java, Python and C# now focus their
        instructions more on just those languages, rather than giving long
        generic instructions for all possible languages.

      - The SBML package extension mechanisms are now more thoroughly
        documented.

    EXPERIMENTAL RELEASE

    * New features

      Code for the Dynamic Structures ('dyn') package has been added.
      This reflects the draft specification Release 0.1 dated
      October 1 2014.

      - 'distrib' package-specific updates:

        - The UncertMLNode now uses a std::vector to save child members
          rather than the List class.

      - 'spatial' package-specific updates:

        - The spatial code has been updated in line with the specification
          Release 0.88 dated September 2014.

     * Bug fixes

      - 'distrib' package-specific bug fixes:

        - A number of memory leaks have been plugged.
          Thanks to Andy Somogyi for reporting them.

      - 'groups' package-specific bug fixes:

        - The values of the enumeration of SBMLGroupsTypeCode_t clashed
          with the values used by the comp enumeration.  The ones in
          the groups package have been changed.

      - 'req' package-specific bug fixes:

        - Sourceforge libsbml Tracker #373: The code was not keeping
          proper track of parent-child relationships which could
          lead to incorrect namespaces being used.  This is now sorted.
          Thanks to Gerard Weatherby for reporting it.

    ====================================================================
    5.10.2 (2014-07-17)
    ====================================================================

    STABLE RELEASE

    * New features

      - The static functions implemented by the SBMLTransforms class
        that are used by the converters that in-line FunctionDefinitions
        or expand InitialAssignments has been made available to all language
        bindings.  These are: replaceFD, expandInitialAssignments
        and evaluateASTNode.  Examples of using these functions
        are also provided.

      - The L3ParserSettings object can now be configured to compare
        built-in functions and constants caselessly (as it did in the
        past; the default), or to only accept the lower-case forms.

      - 'layout' package-specific updates:

        - The C API has been improved and appropriate argument checking
          has been implemented.

    * Bug fixes

      - There was an issue with detecting NULL elements with the
        R bindings.  This turns out to be a consequence of SWIG. A
        bug report has been filed with the SWIG development team,
        in the meantime, a revised SWIG file is included with the
        libSBML source and is used by the libSBML build when
        creating the R bindings.

      - The unit consistency checking code was ignoring numerical
        factors when checking the units of a KineticLaw matched the
        model wide units of extent per time (substance per time in
        SBML L1/L2). This has been changed.  Thanks to Daniel Palm
        for the report that exposed this.

      - Unit checking code determines whether a math expression contains
        parameters or numbers with undefined units. However, depending
        on where these occurred within the expression, libSBML was
        not always correctly establishing this.  This has been fixed.
        Thanks to Daniel Palm for reporting this.

      - The unit consistency checking code was losing numerical factors
        that were left after cancelling out units.  This could affect
        the overall definition of the remaining unit and thus impact code
        that looked for exact identity between units.  This has been fixed.
        Thanks to Daniel Palm for providing an example of a case where this
        was happening.

      - There was a bug in writing out MathML that manifested itself
        using the in-lining functionDefinition converter for a narrow
        set of functions.  This has been fixed.

      - Validation has been improved so as to no longer warn a user that
        a variable has no initial value if there exists an initialAssignment
        or assignmentRule that would set the value.

      - The SBMLError reporting an over-determined model was being logged
        with the incorrect category of error. This has been changed.

      - LibSBML incorrectly reported the units of 'pi' as radians. This
        has been corrected to report 'dimensionless'.  Thanks to Matthias
        König for reporting this.

      - The L3 parser did not recognize 'arcsinh' or 'asinh' as valid
        built-in functions.  This has been fixed.

      - 'comp' package-specific bug fixes:

        - When libSBML detects an SBML L3 package that it does not support
          validation of 'comp' references can report that a reference may
          be to an identifier within the unknown package. However, the code
          was failing to check whether the reference could be located within
          the xml relating to supported packages before issuing this warning.
          This has been fixed.  Thanks to Chris Myers for reporting it.

    * Configuration/build system changes

      - The CMake build system will now produce an uninstall target.

    * Miscellaneous

      - Continue our review of code a number of potential problems were
        highlighted during static analysis. These have been fixed.

      - Code review has also eliminated a number of compiler warnings
        raised by various different compilers on various different
        systems.

      - Various memory leaks have been plugged.  Thanks to people,
        in particular Andy Somogyi, for reporting these.

      - The short error messages for the following error codes in
        SBMLErrorTable.h had trailing periods, which was inconsistent with
        most of the other messages; the periods have been removed: 20109,
        99109, 99401, 99402, 99403, 99404, 99405, 99406.

      - In the API documentation, the instructions for setting PYTHONPATH
        was not correct for the installation produced by using CMake
        instead of GNU configure.  Further, the PYTHONPATH instructions
        for Ubuntu were actually for other Linux/Unix variants and vice
        versa.  This has been fixed by making the instructions use a
        single, more general approach that should work everywhere.

      - The API documentation lacked information about using PyPI for
        Python, and about how to install the R interface.  Fixed.

      - Various issues in the Python documentation have been fixed.  For
        example, in the table of member methods for each class in the API
        documentation for Python, the brief descriptions were missing --
        all the short member descriptions had the same text, "Python
        method signature(s)".  This was caused by a bug in our custom
        libSBML documentation generation tools.

      - The error code table in the documentation for SBMLError has been
        updated.

    EXPERIMENTAL RELEASE

    * New features

      - 'arrays' package-specific updates:

        - The arrays code has been updated in line with the specification
          dated June 19 2014. Changes include a change in attribute names
          and a revised set of supported math constructs.

        - Support for parsing from infix to ASTNodes and vice versa has
          been added for the majority of the math constructs currently
          listed within the arrays specification.

      - 'req' package-specific updates:

        - The req code has been updated in line with the specification
          Release 0.5 dated 30 May 2013.  Users should be aware that
          this update represents a significant change in code to reflect
          the change in structure of the package.

      - 'spatial' package-specific updates:

        - The spatial code has been updated in line with the specification
          Release 0.87 dated June 2014.  Users should be aware that
          this update represents a significant change in code to reflect
          the change in structure of the package.

     * Bug fixes

      - There was a potential stack-overflow issue with packages that
        extend SBase directly.  This has been fixed where appropriate.
        Thanks to Chris Myers for reporting it.

    ====================================================================
    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.

      - The Python API documentation lacked all the class constructors,
        due to a bug in the libSBML documentation production pipeline.
        This is now fixed.

    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.

    ====================================================================
    5.9.2-experimental (2014-01-31)
    ====================================================================

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

    ***                 Experimental only release                    ***

    This is an experimental only release, that is, a release of those
    files provided in the experimental folder of a full release.

    This includes updates to all the SBML L3 packages that are not yet
    accepted and undergoing development.

    NOTE: An experimental release is not as rigorously tested as a
    full release.  Any changes/fixes listed as either referring to
    stable or experimental code may change before the next full release.

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

    STABLE RELEASE

    * New features

      - The error messages relating to invalid SId syntax have been
        improved to report the attribute causing the problem.

      - The SBMLLevelVersionConverter has an option to ignore
        unrequired L3 packages. However there was no way to access
        this option when using the helper 'setLevelAndVersion'
        function.  This function has no been given a default argument
        to allow users to specify the ignore packages option.

      - A new version of the SBMLTransforms::evaluateASTNode function
        is available; allowing the user to pass a map of ids and values
      to the function rather than needing a whole model.

      - Two new functions are available to allow users to determine
        the compiled dependencies for the given instance of libSBML.
      int isLibSBMLCompiledWith(const char* option) will take the name
      of a dependency library e.g. 'expat' as argument and return a
      positive integer this library was used to compile libSBML, 0
      otherwise.
      const char* getLibSBMLDependencyVersionOf(const char* option)
      takes the name of the library and returns the version number
      of this library.

    * Bug fixes

      - Some of the perl examples had syntax errors - these have been fixed.
        Thanks to Joern Behre for reporting them.

      - Some subtle bugs in the ASTNode class have been fixed. These
        include returning 'bad allocation' as the name of a node;
        failing to replace the definitionURL of a csymbol node;
        not removing the units member when a node represents a function
        and incorrectly reporting failure when setting user data to NULL.
        Many additional tests have been added.

      - The Borland compiler does not handle implicit casts and
        unfortunately there was one such cast in the new code introduced
        for 5.9.0. This has now been fixed. Thanks to Totte Karlsson for
        reporting it.

      - A memory leak in SBasePluginCreator has been plugged. Thanks to
        Andy Somogyi for reporting it.

      - The instances of the extensions loaded into the ExtensionRegistry
        to facilitate plugins were not being correctly deleted. This
      has been corrected.

      - 'fbc' package-specific updates:

        - The CobraToFbcConverter was losing the charge and the
          capitalization of the formula when parsing the notes element.
          This has been fixed.

    * Configuration/build system changes

      - Any necessary fixes to facilitate the use of the new version
        of Mac OSX - Mac OSX 10.9 Mavericks - have been made.

    EXPERIMENTAL RELEASE

    * New features

      - 'req' package-specific updates:

      - The attributes in the req package are mandatory on all
        elements.  This caused huge numbers of errors when reading
        files which used the req package but did not actually
        need to attributes on many elements.  Thus the error has been
        suppressed.

      - 'spatial' package-specific updates:

        - The API for accessing compressed data has been improved
          to allow access to this data using language bindings.
          ImageData is now uncompressed during the first call to
          this and saved for subsequent access. Previously the data
          was uncompressed each time it was accessed.

        - Functions to determine whether an attribute has been set;
          i.e. the isSetFoo functions, have been provided where these
          were missing. Boolean attributes that have not been set are
          no longer written out.

    * Bug fixes

      - 'req' package-specific updates:

        - The csharp binding for this package was not complete.
          This has been corrected.

      - 'spatial' package-specific updates:

        - Errors relating to missing attributes have been sorted
          to correctly relate to attributes required by the specification.

    ====================================================================
    Version 5.9.0 (2013-11-14)
    ====================================================================

    STABLE RELEASE

    * Qualitative Models

      - The first official version of the specification of the Qualitative
        Models package is now available and thus the libSBML code for
        'qual' is now included in the stable release of libSBML.  This
        means that all prebuilt binaries for the stable release will
        include the 'qual' package code. The src archive containing
        libSBML core code will continue to be available but there will be
        additional src archives available in the stable branch: one
        containing libSBML core plus all stable packages and additional
        archives of the individual package code.

        NOTE: The libSBML GNU make-based build system has not been updated
              for packages. Thus, to build from src, it is necessary to
              use the CMake build system.

    * Layout

      - The layout specification for SBML Level 3 has been accepted and
        thus layout is now considered an official L3 package.  Since
        layout code has been included with libSBML for many years, this
        has no impact on the code included within the stable release.

    * New features

      - There are two new function SBML_formulaToL3String(ASTNode_t*) and
        SBML_formulaToL3StringWithSettings(ASTNode_t* L3ParserSettings_t*)
        that provide reciprocal AST to infix functionality based on the
        previously released L3Parser code.

      - Within an SBML file it may be possible to infer units for
        parameters based on their use within mathematical expressions.  A
        limited version of this functionality is now available using the
        SBMLInferUnitsConverter which will return a document with units
        attached to any parameters where it is possible to infer the
        units.

      - The SyntaxChecker class has a new function named
        isValidXMLanyURI(std::string) that can check whether a given
        string has the valid syntax for an XML anyURI datatype
        http://www.w3.org/TR/xmlschema-2/#anyURI.

      - There is a new base class ElementFilter that can be passed as an
        optional argument to the getAllElements function.  When
        implemented this allows the elements to be filtered in whatever
        fashion before being added to the List returned by the
        getAllElements() function. The example getAllElementsWithNotes
        illustrates this functionality.

      - There is new functionality to facilitate replacing the id
        attribute and all references to that id within a model. There is a
        new base class IdentifierTransformer that when passed to the
        function renameAllIds on the Model object will perform the
        transformation specified by the IdentifierTransformer class on all
        id attributes within the model. Users should derive their own
        IdentifierTransformer class to perform the transformation they
        require.  The example setIdFromName illustrates this
        functionality.

      - The class IdList which allows users to create and manipulate lists
        of 'id' strings has been made publically available.  Previously
        this class has been used internally by validation and conversion
        code.  It is now available in the sbml/util directory.

      - There is a new converter, the SBMLIdConverter, that will allow a
        user to replace several ids within a model. The converter requires
        a comma seperated list of existing ids and another of the
        replacement ids and will perform the necessary replacements.

      - There is a new converter, the SBMLLocalParameterConverter, that
        will allow a user to replace any localParameters with global
        parameters.  The promoteParameters example illustrates the use of
        this converter.

      - Following the results of the user survey the L3Parser has changed
        the precedence of the '^' operator to be greater than a unary '-'
        operator and the precedence of the '!' operator to be higher than
        algebraic operators (and equal to the unary '-' operator). The
        precedence of '&&' remains the same as the precedence of '||'.

      - It is now possible to override the severity of errors logged or to
        disable error logging completely. Any override is applied to the
        errorLog until such time as the status is reset.  This facilitates
        the use of functions, that may on occasion log errors, in a
        situiation were error logging is not required.

      - There is a new function XMLErrorLog::changeErrorSeverity
        (XMLErrorSeverity_t , XMLErrorSeverity_t, std::string package)
        that will change the severity of errors within the errorLog based
        on the package name supplied.

      - The XMLErrorLog and SBMLErrorLog classes now have explicit
        implementations for the copy and assignment constructors.

      - The SBase functions getURI() and getPrefix() that return
        information relating to the namespace of the object have been
        made public. Formerly these functions were protected.

      - The function removeTopLevelAnnotationElement(const std::string
        elementName, const std::string elementURI = "") allows users to
        remove a single top level element from the annotation node. If,
        having removed the specified annotation, the overall annotation
        node had no child elements the entire node was being deleted.
        There is now an additional optional argument to this function,
        bool removeEmpty, that allows the user to specify that they do not
        wish the annotation to be deleted.

      - There are two new function on the SBase class that allow an
        element to be read from and written to an XMLNode.  The XMLNode is
        the underlying class used by the XML parsing layer of libSBML.
        The function XMLNode* SBase::toXMLNode() returns a pointer to an
        XMLNode that represents the SBase object; which will facilitate
        the ability to look up attributes of an object by name. The
        function void SBase::read(XMLNode& node,
        XMLErrorSeverityOverride_t) invokes the read functionality on a
        given XMLNode. This facilitates reading blocks of annotation that
        may represent SBML in some way.  It should be noted that these
        functions are computational expensive in that they serialise to a
        string. This drawback will be addressed in future libSBML
        architecture but cannot be overcome with the current libSBML-5
        implementation.

      - All set or add functions in libSBML return a value from the
        enumeration OperationReturnValue_t. There is now a function
        OperationReturnValue_toString that will return a string
        representation of the reason for the failure.

      - 'layout' package-specific updates:

        - The example code for layout has been moved to subdirectories
          named 'layout' beneath the appropriate language subdirectories
          in the examples directory.  This reflects the structure used for
          example code from all packages.

        - The code reading and writing layout as an annotation has been
          adapted to use the new read/write to/from XMLNode functions.
          This greatly reduces the complexity and repetition of code
          previously needed to perform these functions.

      - 'comp' package-specific updates:

        - All the validation rules have been fully implemented, up through
          release 3 of the specification.

        - Validation is now incorporated into the flattening process.  If
          there are no errors (or only warnings), the flattening process
          will proceed to produce a flattened version of the model.  If
          there are errors, the flattening process will halt and return an
          unchanged version of the model, with the errors noted in the
          model's error log.  This provides the user with detailed
          information regarding why a document has failed to flatten as
          well as detailing any warnings related to the document returned
          on success.

        - There is an additional option for the CompFlatteningConverter to
          allow the users to request that the document not be validated
          before or after flattening. This allows the user to produce a
          flattened model irrespective of the validity of the original
          model.  Errors produced during flattening will still stop the
          flattening process, as they make it impossible to flatten the
          model.

        - There is a further additional option for the
          CompFlatteningConverter to allow the users to specify how the
          required status of any unflattenable package should influence
          whether flattening is attempted or not. By default this option
          has a value of 'requiredOnly' which indicates that flattening
          will abort if it encounters an unflattenable package that has a
          'required' attribute of 'true'. Other options are 'all' or
          'none'.

        - The flattening routine has been extended to include all packages
          available within the stable release: layout, qual and fbc.
          NOTE: This means that the behavior of the flattening converter
          will be different than it used to be: in the past, the converter
          would either refuse to flatten a model with information from any
          of these packages, or would leave unmodified package information
          from the main model only.  Now, all information from all
          submodels will be properly integrated into the flattened model.

    * Bug fixes

      - The converter that expanded functionDefinitions was failing to
        correctly deal with any csymbols it encountered in the math.  This
        has been fixed.

      - Conversion between SBML Levels was not correctly handling the
        units attributes that appear on the Model object in an Level 3
        model. This has been fixed. Thanks to Pratham Shah for the report.

      - The UnitDefinition::printUnits function had a mismatch between
        integer and double values for the exponent; causing incorrect
        values to be used on occasion. This has been fixed. Thanks
        to Pratham Shah for reporting this.

      - An annotation on a package element is permitted to use the SBML
        namespace.  However, this situation was logging an error.  This
        has been corrected.

      - A memory leak in the TranslateSBML function has been plugged.
        Thanks to Neil Swainston for reporting the issue and testing the
        fix.

      - 'comp' package-specific bug fixes:

        - It is possible to construct a model which tries to delete an
          object more than once.  This was not being detected correctly.
          This has been addressed and flattening code will report this
          issue as an error.

        - Similarly replacing both an object and independently replacing
          a child of that object could also cause problems. These have
          been sorted.

    * Miscellaneous

      - The API manuals for Java, Python and C# now include information
        about the SBML Level 3 package extensions.  In addition, many
        content errors have been fixed, many formatting errors have been
        resolved, new sections have been added, and finally, the overall
        look and feel of the documentation has been updated (and hopefully
        improved).

      - The copyrights and license statements in LICENSE.txt/LICENSE.html
        have been updated to reflect the inclusion of code from Ralph
        Gauges (EML, Heidelberg, Germany), a small program from Sun
        Microsystems used in generating documentation, and the PrettyTable
        and Google Code Prettify utilities mentioned below.

      - To help produce better documentation, the libSBML sources now use
        (and incorporate) two utilities, PrettyTable 0.7.2 (in
        src/bindings/python/doc-converter) and Google Code Prettify (in
        docs/src).  Both are redistributable under terms compatible with
        the LGPL terms used for libSBML as a whole.  Please see the file
        LICENSE.txt or LICENSE.html for specific information about the
        authors and license terms of these packages.

      - A new, simple tutorial example of creating a model using the
        Python language interface is now available in the Python
        documentation.  The example was kindly provided by Martins Mednis
        (in 2012!).

    EXPERIMENTAL RELEASE

    * New features

    * Distributions

      - There is now a stabilized version of the specification for the
        Distributions package and the experimental release now includes
        code for this 'distrib' package.  As is the case with all packages
        included in the Experimental Release the binaries are built with
        'distrib' enabled and the libSBML source archive includes the
        source code.

    * Multistate, Multicomponent and Multicompartment Species

      - There is now a stabilized version of the specification for the
        Multistate, Multicomponent and Multicompartment Species Package
        and the experimental release now includes code for this 'multi'
        package.  As is the case with all packages included in the
        Experimental Release the binaries are built with 'multi' enabled
        and the libSBML source archive includes the source code.  It
        should be noted that it is not yet possible to extend the math
        <ci> element; which the 'multi' proposal does; however the
        definitionURL attribute can be used on the <ci> element to convey
        the necessary information until libSBML provides the ability to
        extend the math.

    * Groups

      - The 'groups' package code has been updated to include revisions
        made to the latest specification.

    ====================================================================
    Version 5.8.0 (2013-02-28)
    ====================================================================

    STABLE RELEASE

    * Flux Balance Constraints

      - The first official version of the specification of Flux Balance
        Constraints is now available and thus the libSBML code for
        'fbc' is now included in the stable release of libSBML.  This
        means that all prebuilt binaries for the stable release will
        include the 'fbc' package code. The src archive containing
        libSBML core code will continue to be available but there will be
        additional src archives available in the stable branch: one
        containing libSBML core plus all stable packages and additional
        archives of the individual package code.

        NOTE: The libSBML GNU make-based build system has not been updated
              for packages. Thus, to build from src, it is necessary to
              use the CMake build system.

    * New features

      - The converter that expands SBML FunctionDefinition constructs has
        been extended with an additional option that allows the user to
        specify particular <functionDefinition> objects that should not be
        expanded.

      - We have changed the behavior of the converter that converts
        between core Levels and Versions of SBML.  This converter has a
        boolean option, 'strict', that determines whether an invalid model
        can be converted or produced.  The code originally assumed that
        'strict = false' refers to syntactic validity only, and so even
        when the flag was set to false, the converter could fail to
        convert a model if semantic validity was not preserved.  This
        interpretation has been changed because people felt it was not
        useful; now, setting 'strict' to 'false' will always convert a
        model, and if there are errors related to altered semantics, the
        errors will be logged in the usual error log.

      - Documentation for the 'comp' and 'fbc' C++ API is now available.

      - 'comp' package updates:

        - The C API for comp is now available with an example of
          creating a model using this API.

        - The majority of 'comp' package validation rules have now been
          implemented and will be reported.  Validation has also been
          expanded to apply validation from core and other packages
          (where appropriate) to any ModelDefinitions contained within a
          comp model.

    * Bug fixes

      - LibSBML was still writing out the deprecated, and in some cases
        removed, attribute 'charge' on a <species>. This is no longer the
        case.

      - Some files caused the SBML Level and Version converter to enter an
        endless loop. This has been fixed.  Thanks to the good folks at
        Persistent Systems Ltd. for reporting this.

      - Reading an attribute with a value of type 'double' was failing
        to report when a different type was encountered for the value.
        This has now been sorted and will be correctly logged as an
        error by the readSBML functions.

      - The Level and Version converter was in some cases running unit
        validation even if the user had specified that they did not
        require strict unit validation.  This was in fact done by libSBML
        to allow an error to be logged; however, it has become clear that
        the large computational overhead of running unit validation is
        unecessary to merely log an error.  Thus, if the user has declared
        that they do not require unit validity, the checks will no longer
        be applied.

      - 'layout' package-specific bug fixes:

        - The extension namespaces were not being correctly set. This
          has been fixed.

      - 'comp' package-specific bug fixes:

        - The function 'renameSIdRefs' now functions properly for
          SBaseRef-derived classes.

    * Configuration/build system changes

      - 'fbc' package-specific build system changes:

        + The GNUMake build system has not been implemented for
          packages. Thus, to build from src, it is necessary to use CMake.

    * Miscellaneous

      - The structure of the API documentation has been slightly
        overhauled to provide clearer access to relevant information.

    EXPERIMENTAL RELEASE

    * New features

      - 'qual' package-specific new features:

        - New functions getInputBySpecies(std::string) and
          getOutputBySpecies(std::string) have been added to the
          Tranisition class. These will return the first Input/Output
          in the relevant list that matches the qualitativeSpecies
          attribute value supplied as argument.

    * Bug fixes

      - 'qual' package-specific bug fixes:

        - As validation of packages is starting to be introduced the
          situation whereby a ListOfFunctionTerms can contain no
          FunctionTerm elements but only a DefaultTerm caused issue
          with the code that reports an empty ListOf object. This
          has been fixed.

      - 'render' package-specific bug fixes:

        - Conversion between L3 and L2 annotation was not working as
          expected. This has been fixed.

        - The interaction between layout GraphicalObjects and the
          render 'objectRole' attribute was removing the attribute
          on occasion. This has been fixed and more fully tested.

    ====================================================================
    Version 5.7.0 (2013-01-14)
    ====================================================================

    STABLE RELEASE

    * Hierarchical Model Composition

      - The first official version of the specification of Hierarchical
        Model Composition is now available and thus the libSBML code for
        'comp' is now included in the stable release of libSBML.  This
        means that all prebuilt binaries for the stable release will
        include the 'comp' package code. The src archive containing
        libSBML core code will continue to be available but there will be
        additional src archives available in the stable branch: one
        containing libSBML core plus all stable packages and additional
        archives of the individual package code.

        NOTE: The libSBML GNU make-based build system has not been updated
              for packages. Thus, to build from src, it is necessary to
              use the CMake build system.

        Known limitations of the 'comp' code:

          + Documentation has not yet been integrated into the libSBML
            documentation.

          + Whilst the majority of validation rules have been implemented,
            some will report the schema error id rather than the specific
            comp validation rule id.  The more involved rules involving
            circular dependencies and in-depth referencing have not been
            implemented.  Validation of ModelDefinitions is implemented
            with respect to comp validation, but not with respect to core
            validation.

          + There is no C API for interacting directly with comp
            objects. However the C API for reading and validation will
            apply to the 'comp' package and flattening can be accessed via
            the converter C API to call the CompFlatteningConverter.

    * New features

      - Convenience functions have been added to the SBMLExtensionRegistry
        class to facilitate enabling/disabling packages using just the
        package name. For example: disablePackage(const std::string&
        package); enablePackage(const std::string& package);

      - Previously the setNotes function accepting a string as argument
        expected the string to contain the appropriate XHTML tags and
        would not set the value of the <notes> element to a string that
        did not meet this requirement.  The functionality of the
        setNotes(const std::string&) function has been extended to allow a
        user to add an optional boolean argument addXHTMLMarkup. When the
        value of this argument is 'true' the function will accept a
        string; wrap it with the XHTML <p> tag and set the <notes> element
        to this.

      - A C API for use with the converters has been added. Examples of
        using the converter API are available in all supported languages.

      - 'comp' package

        - Access to the flattening routines has been restricted to the
          CompFlatteningConverter.  This allows options to be specified by
          the user regarding ignoring other packages and whether to
          produce a document with no comp namespace or a document with the
          comp namespace but the required attribute set to 'false'.

        - Validation has been implemented (see note above). This is called
          via the checkConsistency function within core libSBML; which now
          accesses a checkConsistency function in the comp plugin.
          There are two categories of validation:
          LIBSBML_CAT_GENERAL_CONSISTENCY and LIBSBML_CAT_IDENTIFIER_CONSISTENCY
          which are enables or disable via the setConsistencyChecks()
          function on the SBMLDocument (in libSBML core).

        - The API for resolving external models has been updated to use a
          registry of resolvers. This facilitates the addition of user
          specific resolvers.

    * Bug fixes

      - The number of arguments expected by a piecewise function
        was incorrectly assumed to be two. However, a piecewise
        function can have a single argument. This has been corrected.

      - Validation of SBML Level 3 was issuing a general warning about
        missing required attributes but failing to identify which
        attribute had caused the error to be reported.  This has been
        corrected. Thanks to Nicolas Rodriguez for pointing this out.

      - Validation was failing to report the incorrect use of a function
        call if the lambda function usesd expected no arguments. This
        has been fixed.

      - The L3Parser was not dealing with the sqrt function correctly.
        This has been sorted.

      - 'comp' package-specific bug fixes:

        + SBOTerms were not being correctly dealt with when they
          occured on a Port element. This has been corrected. Thanks
          to Chris Myers for reporting this.

    * Configuration/build system changes

      - Building the MATLAB binding for libSBML can be problematic due to
        the need to identify and use the MATLAB mex compiler.  When MATLAB
        is being accessed over a network this can result in misleading
        error messages.  The build system has been improved to halt
        compilation if the mex compiler is not available and to give a
        clearer error message as to how to proceed.

      - The build system has been updated to facilitate use with the
        Mac OS X 10.8 operating system (Mountain Lion).

      - 'comp' package-specific build system changes:

        + The GNUMake build system has not been implemented for
          packages. Thus, to build from src, it is necessary to use CMake.

    * Miscellaneous

      - It was reported that gcc 4.7 found the various definitions of
        isnan used within some parts of libSBML to be problematic.  This
        problem has been addressed and there are now functions util_isNaN
        and util_isFinite in the util file that are used throughout
        libSBML.  Thanks to Totte Karlsson for reporting this.

      - Where test files compare double values the comparisons have
        been unified to use the util_isEqual(double, double) function
        and thus avoid inaccurate results that can be machine dependent.

      - This NEWS.txt file has reduced in size with NEWS dating from
        prior to libSBML-5 now saved as an OLD_NEWS.txt file.

    EXPERIMENTAL RELEASE

    * New features

      - 'Qual' package:

        - The package specification redefined whether some attributes or
          elements were required; the code has been updated appropriately.

      - 'Fbc' package:

        - The package specification added some optional attributes
          and deprecated the use of strict less than or greater than;
          the code has been updated appropriately.

    * Bug fixes

      - 'Render' package:

        - In some cases the code was failing to add expected attributes
          to particular elements.  This has been corrected.

    ====================================================================
    Version 5.6.0 (2012-08-03)
    ====================================================================

    A note on the use of SWIG:

    All aspects of libSBML-5.6.0 requiring SWIG are known to work with
    SWIG version 2.0.4.  Issues with later versions have been found
    with respect to some areas of a libSBML build.  These will be
    addressed in future releases but for libSBML-5.6.0 we recommend
    the use of SWIG 2.0.4.

    STABLE RELEASE

    * New features

      - LibSBML now includes a binding to R (The R Project for Statistical
        Computing). The binding is generated using SWIG and thus can be
        built by users. Alternatively, the libSBML-5.6.0 release provides
        R packages that can be installed directly into R.

      - During HARMONY 2012, people discussed the issue of providing
        support for Level 3 Layout in other SBML Level 3 packages.  The
        conclusion was that additional GeneralGlyph elements should be
        added in order to support references to as-yet unknown types of
        objects to be defined in Level 3 packages. These additional
        elements have been included in the libSBML layout code.

      - Although libSBML GNU makefiles have technically supported Python 3
        for some time, there had been no feedback regarding the use of
        Python 3 until recently.  In response to the feedback, we have the
        updated the build system to facilitate the use of different
        versions of Python 3.  On Windows, the libSBML release also
        includes prebuilt installers for Python 3.2.

      - The libSBML 'configure' command now accepts the additional option
        --with-python-interpreter, which allows you to specify the Python
        interpreter that should be used.  This is useful when a system has
        multiple versions of Python installed in the same directories, and
        the version that should be used can be selected by explicitly
        invoking the desired version.  The option takes a full path, as in
        "--with-python-interpreter=/usr/bin/python2.7".

      - In order to facilitate the use of identifiers.org URLs, we added
        an additional function, getSBOTermAsURL, to the SBase class.  This
        function returns a string representation of the SBOTerm in its
        resolvable identifiers.org URL format; e.g.,
        "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN"

      - The use of libSBML get and set functions in Python; a by-product
        of the use of SWIG; is not particularly intuitive. LibSBML-5.6.0
        applies a patch that allows the use of indexing in the python
        environment i.e. model->getSpecies(0)->getId() can be replaced
        with model.species[0].id. This patch is limited to Python 2 versions
        at present. It does not adversely effact existing functions for
        either Python 2 or Python 3.  Many thanks to Gordon Ball
        (Computational Medicine, Karolinska Institute) for creating and
        sharing this patch.

    * Bug fixes

      - When using a copy of libSBML compiled with Level 3 package
        support, attributes from the "sbml" namespace were not given a
        namespace prefix when they should have been.  This has been fixed.

      - The L3Parser had some subtle bugs on some operating systems when
        dealing with very long numbers or exponentials. These have been
        tracked down and fixed.

      - Although libSBML explicitly prevented History or CVTerm objects
        from being added to the annotation of an object when that object
        had no metaid attribute value, it was still possible to add
        History and CVTerm directly to the annotation.  This could lead to
        invalid MIRIAM annotations because they lacked a metaid attribute
        value.  LibSBML now checks that an object to which any MIRIAM
        compliant annotation is being added has a metaid.

      - When returning a MIRIAM-compliant annotation, all CVTerms were
        lost if just one had an invalid qualifier.  This has been fixed.

      - The decompression code uses a macro OF that is not defined for all
        versions of linux.  A definition has been added to avoid problems.
        Thanks to Kai Wohlfahrt for reporting this.

      - There was a potential memory leak issue while registering
        SBMLConverters.  Thanks to Akira Funahashi and his team for spotting
        the problem and supplying a fix.

    * Configuration/build system changes

      - As SBML Level 3 packages and their code become available, there is
        a increasing number of possibilities in the matrix of what a
        particular instance of libSBML has included. In order to
        facilitate code that may rely on the presence of one or more
        packages, the CMake configuration process has been improved to
        include a set of flags that identify the packages included in a
        particular build.  The file convertLayout.cpp in the examples/c++
        directory illustrates the use of these #define's.

      - The MATLAB bindings failed to build on Mac OS X whenever an Xcode
        version was used that did not include the Mac OS 10.6 SDK.  This
        has been fixed.

      - The CMake build system has been made more resilient to finding
        include files from previous libSBML installations.

    EXPERIMENTAL RELEASE

    * New features

      - The Qualitative Modeling package "qual" is now supported.

      - The R binding is available for all packages.

      - 'Groups' package:

        - At HARMONY it was agreed that the 'group' element needed an
          additional attribute 'kind'. This has been added.

      - 'Spatial' package:

        - There was an issue with the encoding of image data for the
          spatial package. This has been solved by providing a function
          that will uncompress the data and return it to the user in a
          usable form.

      - 'Comp' package:

        - Instantiated Model objects in Submodels now are set to have that
          Submodel as their parent.  The SBMLDocument is still set to the
          document of the original Model, so that its own Submodel
          references can be properly tracked down.

    ====================================================================
    Version 5.5.0 (2012-05-11)
    ====================================================================

    STABLE RELEASE

    * Revision of annotation and SBML MIRIAM RDF

      Following discussions on the libsbml-development mailing list
      we have adjusted the way functions affecting annotations interact
      with the SBML MIRIAM RDF classes for History and CVTerms.

        - Previously any annotation was assessed and if it contained
          MIRIAM RDF the corresponding classes were created and the original
          annotation XMLNodes relating to these objects was removed from the
          annotation. When the annotation was retrieved the xml was reconstructed
          from the History and CVTerm classes.  This is no longer the case.
          In 5.5 we have changed the code so that the MIRIAM objects are
          created BUT the original annotation remains intact. It is only
          reconstructed if the code has directly altered the History or CVTerm
          classes via the class API, otherwise the original annotation
          is returned.

        - We reassessed the use of the appendAnnotation function. Previously
          any annotation was appended regardless of whether the existing
          annotation already contained a top level element with the same
          namespace.  We considered this to be a bug, since it would result
          in invalid SBML. Thus, the appendAnnotation function now checks
          whether there is an existing top-level element with the same
          namespace of any it is to append and does not append if it
          encounters a duplicate. It returns an OperationReturnValue of
          LIBSBML_DUPLICATE_ANNOTATION_NS to indicate this to the user.

        - In our reassessment of appendAnnotation we came to the conclusion
          that it was virtually impossible to correctly determine the intent
          of the user in cases where both the existing and appending annotation
          contained RDF that complied with the SBML MIRIAM RDF History or
          CVTerms. Thus the appendAnnotation function no longer treats RDF
          as a "special" case.  If there is existing RDF, no further RDF will
          be appended. Users wishing to alter existing History or CVTerms should
          use the API provided or construct their own annotation and use the
          setAnnotation function.

        - New functions removeTopLevelAnnotationElement(std::string name) and
          replaceTopLevelAnnotationElement(XMLNode* annotation) have been
          introduced to allow users to remove or replace a single top level
          annotation element whilst conserving any other annotation that may be
          present.

    * New features

      - There is now a version of the infix to MathML parser that is independent
        of L1 constructs. This parser is available as three functions:
        SBML_parseL3Formula(""), SBML_parseL3FormulaWithModel("", Model*) and
        SBML_parseL3FormulaWithSettings("", L3ParserSettings *). There is
        a new object L3ParserSettings that allows the user to tailor the
        results of the function, for example to parse "log" as natural log
        or log base 10; to allow users to enter units on numbers as "10m" or
        to disable this feature along with some other options.

      - The getLine() and getColumn() functions did on some occasions
        return a maximum int value when the correct lines and columns
        could not be determined. This produced inconsistent behaviour as
        some XML parsers return '0' as if they cannot determine location.
        This has been unified and libSBML's getLine()/getColumn() will now
        return '0' if the location is unknown.

      - There is a new class SBMLDocumentPluginNotRequired which allows a
        package code to derive from an object where the required attribute is
        considered 'false' until it has been set. Note this is not a "default"
        value it is just the value with which the boolean attribute is
        initialised.  The existing SBMLDocumentPlugin class assumes a value
        of 'true'.  This is in fact a change in behaviour but since users
        should set this value it should not cause a problem.

    * Bug fixes

      - Tracker issue#3509843
        The annotation element in SBML should contain only elements.  Schema
        validation reports this but libSBML was not. This has been corrected.
        Thanks to Camille Laibe for still running schema validation and reporting
        the issue.

      - There was a subtle bug involving accessing a NULL ModelHistory object.
        This has been fixed.

      - Area units were not being properly converted between SBML Levels. They
        are now.

      - An AST plus or times node that was created with more than two children
        was written out as only having two children; thus losing information.
        This behaviour has been corrected.

      - Functions used to add objects to other objects in libSBML check that
        the SBML Level/Version/Namespaces of the objects correspond. However
        these checks were imposing the condition that the number of namespaces
        on both objects be the same.  This is not a necessary condition and
        the code has been relaxed.  Thanks to Chris Myers for pointing it
        out.

      - In XML if the sbml element is not prefixed but the only declaration
        of the sbml namespace is, then technically the sbml element has not
        been placed into the sbml namespace. LibSBML was failing to report this.
        This has now been fixed.

      - There was a curious indentation issue that arose if notes used text as
        child elements of an element that also had another non-text child element.
        This could proliferate and cause models where the indentation ran into
        the thousands of spaces.  This has been sorted out and no longer
        happens.

    * Miscellaneous

      - The uninstallation instructions were out of date.  This is now
        updated, for example to mention that the Mac OS X installer does
        in fact provide an uninstall script.

    * Configuration/build system changes

      - Doxygen versions 1.7 and 1.8 are now supported, but due to
        differences in the new version, older versions of Doxygen are no
        longer supported.  The 'configure' script will now only accept
        version 1.7 at minimum.

      - Some changes have been made to facilitate building libSBML
        with the Borland compiler.  This included standardising the use
        of #ifdefined rather than using #if.  Thanks to Totte Karlsson for
        the effort of getting this to work.

      - The CMake build has been updated to facilitate the use of the Intel
        compiler.

    EXPERIMENTAL RELEASE

    * New features

      - New macros provided so that SBMLNamespaces objects may easily be created
        to allow package elements to be extended by other packages (for example:
        a comp:modelDefinition to have a layout:listOfLayouts).  These macros
        now used throughout package system when creating new package elements.

      - In 'comp':
        -  ExternalModelDefinitions have a new function, 'getReferencedModel'
           that tries to find the referenced document and model, if the reference
           URI is a 'file' type.  If the SBMLDocument has its fileURI set, this will
           use that to search for relative filenames.

        -  With the above in place, automated flattening now works with
           ExternalModelDefinitions that point to local files.

        -  May now use ModelDefinitions to create the main Model of an SBMLDocument.

    ======================================================================
    Version 5.4.1 (2012-02-24)
    ======================================================================

    STABLE RELEASE

    * Bug fixes

      - The MATLAB binding function isSBML_Model had a subtle bug
        that meant it could crash in certain circumstances.  This has
        been addressed.  Thanks to Ying Zhang for the report.

      - When determining units from rate rules unit checking failed
        to catch the case where time had been redefined as dimensionless.
        This is now fixed.  Thanks to Kieran Smallbone for reporting it.

      - Documentation files for MATLAB were missing from the dmg
        installers for MacOS.  This has been fixed.

      - 'getElementBySId' could potentially return initial assignments,
        event assignments, assignment rules, and rate rules that assigned
        *to* the SId in question, instead of returning the actual element
        with the SId.  This has been fixed.

    EXPERIMENTAL RELEASE

    * Bug fixes

      - LibSBML will now automatically register any packages that are
        enabled in code. Previously libSBML could be built including
        package code but users needed to perform an additional step
        to actually use it. This was causing some confusion.

    ======================================================================
    Version 5.4.0 (2012-02-16)
    ======================================================================

    STABLE RELEASE

    * New features

      - Basic validation of MIRIAM compliant RDF annotations that
        are parsed into ModelHistory or CVTerm objects has been
        added to facilitate the use of annotations that are not
        yet quite complete.  Warnings are now issued relating to
        whether or not the rdf:about attribute accurately points to
        the metaid of the containing object and whether the object
        that was created was consisdered a valid object in the
        attributes and subelements that are required.

      - It has been noted that unless the checkConsistency function is
        called immediately after reading an SBML document, it does not
        report all potential errors.  Since users may wish to apply the
        function to a model being constructed this seems to be a
        disadvantage of the function.  However, as this function has been
        in libSBML for many years it was decided not to alter the
        functionality but to add a new function 'validateSBML' which, when
        called from a document object, will force a write and read of the
        in memory object and report validation errors for the object as
        written.  Thus, all errors will be reported with line numbers that
        would correspond to the document if written out.

      - Conversion of a model containing FunctionDefinitions to L1
        is now supported.

      - Conversion of a model containing InitialAssignments to L2V1
        and L1 is now supported.

      - There is a new isSetBody() function for the FunctionDefinition
        class that returns true if the body of the lambda function
        has been set.

      - The MATLAB/Octave binding function OutputSBML now takes an
        additional optional flag (extensions_allowed defaulting to true)
        that allows a user to specify whether the MATLAB_SBML structure
        should be considered valid if it contains any additional fields.

      - Multiple namespaces using the same prefix are not allowed in XML.
        The function that added XMLNamespaces in libSBML checks for an
        existing namespace with the prefix of the namespace being added
        and overwrites the original if a duplicate is found.  This
        behaviour meant that it was possible to unintentionally remove
        the sbml namespace.  The behaviour of the function has been altered
        such that if the namespace being added has a prefix that duplicates
        that of the existing sbml namepace then the function returns failure
        and the new namespace is not added.  Should the sbml namespace need
        to be replaced it can be done by using the remove function before
        adding the new namespace.

      - SBase objects that occur in Level 3 package code need to keep
        track of the namespace of the package to which they belong. However,
        a conversion might alter the namespace; for example with layout
        where the level 2 layout annotation has its own namespace.
        The getURI function has been altered to adopt the approach used for
        tracking the core sbml namespace of any object i.e. the namespaces of
        the containing document take precedence and the namespace stored on
        an actual object is only considered if it does not belong to a document.
        An additional function getElementNamespace() can be used to obtain
        the namespace stored on the actual object.

    * Bug fixes

      - Tracker issue #3472034
        Line numbers were not being reported as accurately for L2 models
        as for L3 models. We have overviewed all the code relating
        to line numbers and improved the accuracy and consistency
        of line numbers reported. Thanks to Raimund Rönn for the report.

      - Tracker issue #3471902
        The documentation for the readSBMLFromString function claimed it
        prepend the xml encoding if it was not present. In fact, the
        function did not do this. This has been corrected. Thanks to
        Raimund Rönn for reporting it.

      - Tracker issue #3466104
        Fixed inaccuracies in the documentation. Thanks to Raimund Rönn
        for his careful reading and taking the time to report the errors.

      - Validation failed to notice that csymbol avogadro was not valid
        in Level 2. This is fixed.

      - Exceptions were not being correctly wrapped for language bindings
        causing potential code crashes.  This has been corrected.

      - A number of minor issues with regard to conversion between levels
        and versions have been fixed. These include conversion from L3 to
        L1 failing to include a compartment; stopping conversion of models
        with hasOnlySubstanceUnits = true to L1; correcting conversion of
        L3 models with localParameters and preventing conversion of L3
        models where Events had Priorities or where the csymbol avogadro
        had been used.

      - The internalConsistency validator was incorrectly reporting that
        the an Event must have a listOfEventAssignments in a level 3 model.
        This restriction was actually removed in SBML Level 3.

      - The MathML subset used by SBML has plus/times/and/or/xor.  In the
        MathML specification all these functions are nary functions i.e.
        they are permitted to have any number of arguments including zero.
        LibSBML had in fact restricted these functions to two or more
        arguments.  This inconsistency has been corrected.

      - Validation was failing to apply constraints to L3 LocalParameters.
        This has been corrected.

      - Using a value for a units attribute that was not a builtin unit or
        the identifier of a UnitDefinition is invalid.  However, the way in
        which this was reported varied according to which unit attribute
        caused the issue.  This has been standardized to produce an id
        warning about a dangling UnitSIdRef and (if selected) unit warnings
        relating to the impact of the actual attribute.

      - In certain situations libSBML would write out both the stoichiometry
        attribute and a stoichiometryMath element. Since these are mutually
        exclusive this should not happen.  It has been fixed.

      - The code that checked for consistent namespaces when adding one
        object to another was too restrictive.  This has been sorted.  Thanks
        to Chris Myers for reporting it.

      - Conversion between levels was inconsistent when it came to dealing
        with rational stoichiometry.  This has been fixed.

      - The tests for the Perl bindings use of BigInt caused ActivePerl
        to crash on a Windows system. A workaround to prevent this has
        been put in place.

      - LibSBML class constructors currently throw exceptions rather than
        create objects with invalid SBML namespace/level/version
        information.  This could potential result in code crashing
        when using one of the language bindings.  These have now been
        rigorously tested and measures put in place to prevent such
        crashes from happening.

      - The SBMLTransforms class now correctly evaluates piecewise
        expressions.

      - The MathML infix converter now deals correctly with unary plus
        and times.

      - The help text for classes and methods in the Python library were
        previously unformatted, marked-up Doxygen input text, making the
        help text unhelpful.  We wrote a new conversion program to process
        the marked-up text and produce plain-text documentation strings in
        the Python library.  Users can now use the standard Python 'help'
        function to obtain help as expected.

      - The StripPackageConverter was not working as expected. This has been
        fixed.

    * Miscellaneous

    * Configuration/build system changes

      - As libSBML has evolved over the years the header files
        included by a given code file have expanded. This makes it
        necessary to recompile many files when only a single header
        file has been altered.  In an attempt to eliminate unnecessary
        dependencies we have done an overview of the code. However,
        merely replacing existing include files with those that are
        actually required may cause build issues for other users. Thus we have
        introduced a LIBSBML_USE_STRICT_INCLUDES flag. This flag is
        not defined by default and thus no includes will change. Defining
        the flag means that code will only include the minimum number of
        necessary header files. We encourage people to consider using this
        flag as it may become the default behaviour in later versions of
        libSBML.  The flag is available via the CMake build interface.

    EXPERIMENTAL RELEASE

    * New features

     - Code for the 'render' extension is now available.

     - All package code has been updated to use the new line/column
       number reporting mechanism.

     - Package language bindings have been updated to properly wrap
       exceptions and use covariant return types.

     - There is a new example with the 'layout' package that demonstrates
       conversion between the layout and render L3 package representation
       and the L2 annotation representation.

    ======================================================================
    Version 5.3.0 (2011-12-23)
    ======================================================================

    STABLE RELEASE

    * 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
        document.

    * 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 spatialDimensions
        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
        documentation.

      - We have fixed many other small documentation bugs and filled out
        more of the missing documentation.

    * Miscellaneous

      - 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.

    EXPERIMENTAL RELEASE

    * New features

      - There is now code to support the L3 render package.

    ======================================================================
    Version 5.2.0 (2011-11-11)
    ======================================================================

    * Download directory structure

      - Prior to this release we have provided stable libSBML source
        code and associated binary installers, but only provided the
        source code of the L3 packages that are in beta development.
        In response to requests to provide binaries including the package
        code, we have slightly reorganised the directory structure of
        the 5.2.0 release.

        The top level directory remains as expected

        https://sourceforge.net/projects/sbml/files/libsbml/5.2.0

        This directory contains two sub-directories 'stable' and
        'experimental'.

        1) files/libsbml/5.2.0/stable

        This directory contains the source code and various binary
        installers arranged in a structure identical to that used
        in the  5.1.0-b0 and 5.0.0 releases.

        2) files/libsbml/5.2.0/experimental

        This directory also contains two subdirectories.

        a) files/libsbml/5.2.0/experimental/src

        This directory contains the archives of the beta source
        code for the L3 packages; similar to those previously contained
        in the separate top level directory /5.1-packages-beta/.

        b) files/libsbml/5.2.0/experimental/binaries

        This directory contains binaries that include the stable
        source code plus the beta code for ALL of the packages. It
        should be noted that these binaries may be untested and
        are provided 'as-is' to facilitate experimentation with L3 packages.

    * New features

      - There is a new method 'removeFromParentAndDelete()' that enables
        the complete removal of child objects from any SBase object.

      - There is a new method 'getAllElements()' that returns a List
        containing all the children, both direct and indirect, of the
        object on which it is invoked.

      - There are new methods that will rename any references to
        SId and UnitSId throughout the model.

      - A new converter has been added that will convert the units
        of a model to base SI units.

      - A new converter has been added that will order AssignmentRules
        and InitialAssignments in such a way that forward references
        are avoided.

      - The validation API has been refactored to facilitate the use of
        third-party validators. The existing API has been maintained; in
        addition, it is now possible to call any external validator,
        regardless of programming language, using the new validator API.

      - There is a new UserData object on the SBase class. This
        facilitates storing additional application-specific information
        that may be useful to particular software.

      - A new function, appendFrom(ListOf *), on the ListOf class allows
        the contents of one ListOf object to be appended to another.

      - There are new functions getNumRegisteredPackages() and
        getRegisteredPackageName(index) that allow the user to establish
        which Level 3 packages have been enabled in the instance of the
        libSBML library being used.

      - The C API for interacting with the package plugin mechanism
        has been expanded.

    * Bug fixes

      - The functions that add SBase objects were only checking that the
        object being added had the correct Level and Version of SBML.  It
        failed to check that any SBML namespaces used also matched.  This has
        been corrected.

      - Error checking failed to catch SBML L3 models with an empty
        <listOfEventAssignments>.  Fixed.

      - If the units of an object referred to a UnitDefinition that had no
        <lisOfUnits>, the warnings generated by the unit checking code
        were inconsistent.  These have now been standardized.

      - The UnitDefinition::isVariantOfMass() function did not check that
        the exponent of any unit was '1'.  This has been fixed.

      - The postal address for the Free Software Foundation was out of
        date in all files where it was mentioned.  Fixed.

      - It was (erroneously) possible to allow the SBML namespace to be
        replaced and lead to the production of a document with no SBML
        namespace.  Fixed.

      - Some of the older libSBML C code called the exit() function when a
        memory allocation error occurred. This is not an ideal way to
        handle a problem. Since the functionality has existed in libSBML
        for many years it has been removed from a standard build but can
        be reenabled using a configuration flag should any users wish to
        do so.

      - The point at which an MSVC call to the c_str() function tidies up its
        memory usage when running in debug mode is different to the point at
        which the memory is tidied up when running in release mode or with other
        C compilers.  This means that a C function that returns a char * which
        is created using c_str() will return an invalid pointer. Unit testing
        does not highlight this issue as it only occurs in an MSVC Debug build.
        Duplicating the string before returning it solves the problem.
        LibSBML-5.1.0-b0 had three new functions where the string duplication
        was missing.  This has now been fixed.

      - In the layout code, adding a <Point> to a <BoundingBox> produced
        an element with the wrong name. This has been fixed; a fix that
        revealed further issues with the constructors for packageNamespaces.
        This issue has also been fixed.  Thanks to Chris Myers for reporting
        the original problem.

    * Miscellaneous

      - There were inconsistencies arising from the naming of functions
        related to packages; some being named doPkgFoobar and others
        doPackageFoobar.  All of these functions now use the doPackageFoobar
        naming format.  Existing functions using the Pkg format will still
        work but should be considered deprecated.

      - The text of many SBML validation and consistency-checking error
        messages have been edited to hopefully improve readability,
        clarity and consistency.

      - All example files have been overhauled and new ones added.

      - Users reported that some of the SBML files in the "test-data"
        directories were invalid, not realizing that this was actually
        intentional because the files are used for testing libSBML.  In
        order to avoid confusion, the files containing invalid SBML have
        been renamed to append '-invalid' to their file names.

      - The files located in the validator/test-data directory, used for
        testing the SBML validation code, have been reorganised into
        smaller subdirectories.  The new subdirectories group the files
        according to the type of validation being tested.

    * Configuration/build system changes

    ======================================================================
    Version 5.1.0-b0 (2011-08-25)
    ======================================================================

    This release includes a provisional implementation of support for an
    SBML Level 3 package for "layout" based on code from Ralph Gauges of
    the COPASI group.  No other packages are included with this release;
    this applies to the "groups" package as well, which was in the beta
    release but is not in this release.  However, the SVN repository on
    SourceForge has a branch for packages where ongoing development is
    proceeding, and as specifications and code for SBML Level 3 packages
    are settled, future libSBML releases will include stable versions of
    packages as they become available.  Source code for beta versions of
    packages will also be made available from a separate download area,
    http://sf.net/projects/sbml/files/libsbml/5.1-packages-beta

    * New features

     - The inline formula code will now deal with a unary plus.

     - There is a new API for performing conversions between SBML Levels,
       Versions, and SBML Level 3 packages on an SBML Document.  Existing
       functions such as setLevelAndVersion() have been reimplemented
       using the new API and so will continue to work as expected.  The
       new API will facilitate the introduction of conversion routines
       that deal with Level 3 packages.

     - The MATLAB_SBML Structure produced using the MATLAB/Octave bindings
       now includes fields for the SBML Level and Version on all
       sub-structures.

     - There are new functions getElementBySId() and getElementByMetaId()
       that will traverse the entire document and return a pointer to an
       SBase object with the SId or MetaId supplied.

     - There are new functions on the SBO class to reflect the new top-level
       names introduced in the SBO ontology.

    * Bug fixes

     - There were a couple of places where the clone methods failed to
       create a proper copy.  These have been fixed.  Thanks to Nicolas
       Rodriguez for reporting this.

     - The introduction of the ability to place a units attribute from
       the SBML L3V1 core namespace into a <cn> MathML element meant that
       the code for reading and writing MathML needed to be fully aware
       of which SBML namespaces it was working with.  This has been done.

     - Tracker issue #3296228
       Importing a file with a large number of validation errors into
       MATLAB was causing memory issues within MATLAB.  The handling of
       errors has been improved to avoid this situation.

    * Miscellaneous

     - Necessary updates to support the latest version of swig.

    * Configuration/build system changes

     - The introduction of Mac OS X 10.7 Lion produced issues with both
       XCode 4.0 and MATLAB.  These have been addressed.

    ======================================================================
    Version 5.0.0 (2011-04-14)
    ======================================================================

    This is the first release of libSBML-5.0.0.

    There are three types of potential changes in this release compared to
    the beta 5.0.0 release: changes that relate to support for SBML Levels
    1, 2 and Level 3 Core; changes that relate to support for L3 packages,
    and changes that were introduced in libSBML-4.3.1. These are listed
    separately below for convenience.

    This release includes a provisional implementation of support for an
    SBML Level 3 package for "layout" based on code from Ralph Gauges of
    the COPASI group.  No other packages are included with this release;
    this applies to the "groups" package as well, which was in the beta
    release but is not in this release.  However, the SVN repository on
    SourceForge has a branch for packages where ongoing development is
    proceeding, and as specifications and code for SBML Level 3 packages
    are settled, future libSBML releases will include stable versions of
    packages as they become available.  Source code for beta versions of
    packages will also be made available from a separate download area,
    http://sf.net/projects/sbml/files/libsbml/5.0-packages-beta

    -------------------------
    Known limitations
    -------------------------

    At present, libSBML 5 will not attempt to convert a model between SBML
    Levels (e.g., from Level 3 to Level 2) if the model uses SBML Level 3
    packages.  This applies to SBML layout elements and annotations too.
    Our aim is to support conversion between L2 layout annotations and the
    L3 layout package, but this functionality will be introduced in a
    future release of libSBML.

    --------------------------------------
    SBML Level 3 Package extension changes
    --------------------------------------

    * New features

     - The extension mechanism for supporting SBML Level 3 packages now
       includes a full C API.

     - LibSBML now has greatly improved detection and error reporting of
       unimplemented/unknown SBML Level 3 packages.

    * Bug fixes

     - The "layout" extension now provides more seamless access to L2
       layout annotations in L2 models.

    * Additional documentation

     - There is now more detailed and integrated documentation describing
       the use of CMake as an alternative to GNU make for building and
       installing libSBML.

    -------------------------------
    General libsbml-core changes
    -------------------------------

    * New features

     - There are now functions will set the Qualifier on a CVTerm from a
       string; in addition to the existing functions that use values from
       the enumeration of QualifierTypes.

     - SBML L2 contains an number of attributes that have default values.
       LibSBML does not write these values out.  This behaviour has
       changed slightly for libSBML-5.  If a user explicitly sets the
       value of an attribute to be the default value; then it will be
       written out.  For example setting the spatialDimensions of an L2
       <compartment> to be '3' will result in a document where this is
       explicitly written.

     - In SBML L3, it is possible to have a compartment with no
       spatialDimensions attribute declared.  LibSBML-4 would not convert
       such a model to L2, since an L2 compartment has spatialDimensions
       '3' by default.  This behaviour has been altered for libSBML-5 and
       if the user opts for nonstrict units when applying the conversion
       function, a compartment with no spatialDimensions declared will be
       converted.

     - There are additional functions XMLNamespaces::getNumNamespaces and
       XMLAttributes::getNumAttributes.  These are aliases for the existing
       getLength functions but are more in keeping with the rest of the API.

    * Bug fixes

     - The conversion functions for converting an L2 model to L3 were
       failing to set the stoichiometry value.  This has been fixed.

     - The internalConsistencyCheck was failing to report when required
       attributes or elements were missing from an object.  This has been
       corrected.

     - The XMLConstructorException was not exposed.  It is now.

    * Configuration/build system changes

      - The header files libsbml-config-win and libsbml-config-unix have
        been replaced with a single libsbml-config-common file.

      - The organization of the source directories has been radically
        changed, moving the previous directories src/annotation, src/math,
        etc., to become subdirectories of src/sbml.  This allows us to
        entirely avoid a step that was previously to create a copy of all
        the header files into <libsbml>/include.  That copy operation lead
        to a lot of wasted time when debugging code and accidentally
        making changes to the wrong file.

      - The 'win' directory that previously containing MSVC project files
        has been removed.  The addition of packages made maintaining this
        directory problematic.  The CMake build system provides an easy
        alternative for generating any project files required.

    -------------------------------
    Libsbml-core changes from 4.3.x
    -------------------------------

    Also available in Version 4.3.1 (Released 2011-03-29)

    * New features

      - There is now API documentation for the MATLAB and Octave bindings.

    * Bug fixes

      - Certain versions of the libxml2 parser fail to catch a prefix
        being assigned to an empty namespace. Additional code has
        been included to catch this error if the version of libxml2 has
        not reported it.

      - The improved build of the MATLAB interface proved unsuccessful
        in cases where the user had a startup.m file that changed
        directory.  This has been corrected.

      - The SyntaxChecker::hasExpectedXHTMLSyntax(xhtml) function had not
        applied the relaxation on the XHTML restrictions for SBML
        Level 3.  This has been sorted out.

      - The SyntaxChecker::isValidSBMLSId(string) function was incorrectly
        reporting that an empty string was a valid id.  This has been corrected.

    * Miscellaneous changes

      - Choosing --enable-universal-binary on MacOS 10.5 now includes all
        three of the following architectures: i386, x86_64, ppc.  It
        previously only selected i386 and ppc.

    Also available in Version 4.3.0 (Released 2011-03-04)

    * New features

      - There was some disagreement about what libSBML when asked to write
        out a required attribute in Level 3 where the value of the attribute
        had not in fact been set. Following discussion within the libSBML
        team and subsequently the libsbml-development mailing list it was
        decided that the appropriate behaviour was to ignore the attribute
        when writing out the model and thus not inadvertently give the
        impression it has a value.

      - Conversion from Level 3 to Level 2 involving variable stoichiometry
        has now been implemented and this feature of L3 can now be converted
        to L2.

      - There is a getSupportedNamespaces function on the SBMLNamepaces
        class which returns a List of the SBMLNamespaces supported by
        this version of libSBML.

      - Tracker issue #2082682
        The unit checking of math involving the root function has been
        fully addressed. Previously unit checking was only applied to
        the expression root(n, x) if n was an integer. It can now handle
        any value of n including an expression.

      - Checking of the units of measurement in math expressions has been
        further improved to provide checking to a deeper level with the
        overall math of the model.  Thus, the units of the expression a^b
        can now be validated even if the value of b is assigned b = c and
        the model states elsewhere that c = 2.

      - SBML Level 3 has no default attribute values and thus a number of
        new isSetXYZ functions were introduced in libSBML-4.1.0.  Users
        pointed out it was inconsistent that these functions returned
        'false' for a Level 2 model in which the attribute concerned *did*
        have a default value.  Thus, any newly introduced isSetXYZ
        function that deals with an attribute that had a default value in
        Level 2 will now return 'true' regardless of whether the user has
        explicitly set the function or not.

      - The MATLAB and Octave bindings now include the function
        OutputSBML() for writing the structure used in these environments
        back to SBML.  This function has previously shipped as part of
        SBMLToolbox.

      - There is an additional constructor for an SBMLDocument object that
        takes an instance of SBMLNamespaces as its argument.  This is similar
        to the constructors for all SBML objects.

      - There is now a custom manifest file included in the Java JAR file.
        It contains the version number of the libSBML release.  An example
        program demonstrating how to access the information is included
        as the file examples/java/printLibSBMLVersion.java.

      - An API manual for the C# language bindings is now available.  It
        is not as complete as the C++ and Java versions, but it is quite
        close.

    * Bug fixes

      - The InternalConsistency validator was failing to report the absence
        of required attributes or elements within an in-memory model.
        This has been sorted out with a large number of tests added.

      - Tracker issue #2960646
        When writing out an SBML model containing the root function
        Octave was failing to convert the formula into the appropriate
        MathML.  This has been fixed.

      - The code that checks for allowed functions in a Level 1
        document was reporting an error if it encountered one of the
        predefined functions.  This has been corrected.

      - Checking for NULL references has been greatly improved
        throughout.

      - The appendNotes function was not correctly checking for the
        xhtml namespaces declared at the top level.  This has been
        fixed.

      - In some cases the facility to create new 'Bags' within CVTerms
        was not performing as expected.  This has been sorted out.

      - Validation previously failed to report an error if a lambda
        function contained only <bvar> arguments and no actual function
        body.  This has been fixed.

      - LibSBML checks that each element within a model being read has
        the correct default namespace.  However, if the namespace had been
        'declared' via a prefix this check was not being performed.
        This has been corrected.

      - The code that checked that the top-level elements of an annotation
        had unique namespaces was incorrectly comparing prefixes rather
        than actual XML namespaces.  This has been fixed.  Thanks to
        Waclaw Kusnierczyk for reporting this and supplying the fix.

      - The XML namespace for a <math> element may be declared on the
        <sbml> element.  In this case, the XML namespace declaration must
        use a prefix.  Code that checked that the MathML elements had a
        declared namespace failed to check whether a prefix was correctly
        used.  This is now fixed.  Thanks to the JSBML developers for
        spotting this.

      - The code that allows users to use LocalParameter and Parameter
        interchangeably had a small bug where it failed to spot a
        duplicate id for a Parameter but not a LocalParameter.  This has
        been fixed.

      - If a <kineticLaw> element is present, it must contain a <math>
        element.  Prior to SBML Level 3 Version 1 Core, this has never
        been explicitly stated as a validation rule but should have been
        reported as a schema error.  In some case this was not happening.
        This is now fixed.

      - The printUnits.java example in examples/java incorrectly used
        getId() on SBML objects that aren't defined to have id's in SBML.
        Talk about setting a bad example!  Fixed.

    * Configuration/build system changes

      - MATLAB 2010b introduced some inconsistencies in the build system
        on certain platforms.  This has been fixed.  In addition, the
        'configure' script for Linux and MacOS no longer attempts to
        divine various properties of the MATLAB installation and run mex
        itself, and instead, invokes MATLAB to compile TranslateSBML and
        OutputSBML.  This should lead to fewer problems building the
        bindings for MATLAB.

      - Beginning with this release, LibSBML requires SWIG version 2.0.0
        or higher.  This is to avoid a problem where the C# bindings will
        not work with .NET 4 with SWIG versions prior to 2.0.0.

    ======================================================================
    Version 5.0.0-b1 (2010-12-31)
    ======================================================================

    This is the first beta release of libSBML-5.0.0. There are two types
    of potential changes from the alpha release: those that relate to
    support for SBML L1, L2 and L3 core, and those that relate to support
    for L3 packages. These are listed separately for convenience.

    -------------------------
    Package extension changes
    -------------------------

    * New features

      - Language bindings can now be generated to include and use the
        package extension mechanisms.  Given the slightly different
        nature of the MATLAB/Octave bindings, support for packages
        has not yet been extended to these languages.

      - Unit tests have been added for the code that implements the
        package extension mechanisms within libSBML core.

      - The appendAndOwn() function (used to add items to ListOf elements)
        has been updated to check that the item being added is appropriate
        for the ListOf to which it is being added.  This makes use of the
        virtual function SBase::isValidTypeForList().  Package developers
        need to be aware that in cases where a ListOf element can contain
        items of different types, they will need to provide
        implementations for this function.  ListOfRules provides an
        example; it can contain any of AlgebraicRule, AssignmentRule or
        RateRule.

    * API changes

      - Originally, information relating to packages, e.g. PackageName,
        PackageVersion, etc., was stored in static variables.  This proved
        problematic with dynamic libraries on Windows, and therefore these
        variables have been replaced with static methods on the Extension
        classes.  Example: getPackageName().

      - The setEnable() and isEnable() functions have been renamed to
        setEnabled() and isEnabled().

      - The getExtension() function now returns a clone of the required
        extension.  This avoids a situation whereby a user could
        inadvertently delete an extension object.

      - The Check unit testing framework has been adapted to enable the
        tests to be run in a native Windows environment.  This has lead to
        some slight changes in the signature of some methods in the
        annotation classes.  C++ methods that previously return
        std::string now return a const std::string&.

    * Bug fixes

      - It is no longer possible to register the same extension on multiple
        occasions.

    * Configuration/build system changes

      - We anticipate moving from a GNU Make build system to a CMake
        system because this facilitates the inclusion of L3 packages.
        This libSBML release includes all the necessary files to use the
        CMake system in addition to the existing makefiles.  The latter
        have been updated where necessary.  Support for makefiles will be
        phased out in the near future as we move toward having package
        code developed by others outside of the libSBML Team.
        Documentation on using CMake has been included in the docs
        directory.

    * Additional documentation

      - README-Building_libsbml-5_with_CMake.pdf

      - README-Package_Integration.pdf
        Details how to create CMake files for package code that will enable
        one step integration with libsbml-5 source code or an existing
        libsbml-5 installation.

    -------------------------------
    General libsbml-core changes
    -------------------------------

    * New features

      - Checking of the units of measurement in math expressions has been
        further improved to provide checking to a deeper level with the
        overall math of the model.  Thus, the units of the expression a^b
        can now be validated even if the value of b is assigned b = c and
        the model states elsewhere that c = 2.

      - SBML Level 3 has no default attribute values and thus a number of
        new isSetXYZ functions were introduced in libSBML-4.1.0.  Users
        pointed out it was inconsistent that these functions returned
        'false' for a Level 2 model in which the attribute concerned *did*
        have a default value.  Thus, any newly introduced isSetXYZ
        function that deals with an attribute that had a default value in
        Level 2 will now return 'true' regardless of whever the user has
        explictily set the function or not.

      - The MATLAB and Octave bindings now include the function
        OutputSBML() for writing the structure used in these environments
        back to SBML.  This function has previously shipped as part of
        SBMLToolbox.

    * Bug fixes

      - Checking for NULL references has been greatly improved
        throughtout.

      - Validation previously failed to report an error if a lambda
        function contained only <bvar> arguments and no actual function
        body.  This has been fixed.

      - The documentation for a number of methods had fallen slightly out
        of date with respect to the possible operation return codes they
        could return.  We've updated those documentation strings now.  The
        methods affected are in the classes Compartment, KineticLaw,
        Model, Reaction, Rule, SBase, Species, Unit, UnitDefinition, and
        XMLToken.

      - A number of validation checks had an incorrect ErrorCategory
        labels; thus, though these were reported by the correct part of
        the libSBML validator, querying the category would produce an
        inconsistent value.  These have been updated.

      - There were some character encoding issues in a number of error
        messages. These have been corrected.

      - The code that checked that the top-level elements of an annotation
        had unique namespaces was incorrectly comparing namespace
        prefixes, not the actual namespaces.  This has been fixed.  Thanks
        to Waclaw Kusnierczyk for reporting this and supplying the fix.

      - The XML namespace for a <math> element may be declared on the
        <sbml> element.  In this case, the namespace must use a prefix.
        Code that checked that the MathML elements had a declared
        namespace failed to check whether any required prefix was
        correctly used.  Thanks to the JSBML developers for spotting this.

      - The code that allows users to use LocalParameter and Parameter
        interchangeably had a small bug where it failed to spot a
        duplicate id for a Parameter but not a LocalParameter.  This has
        been fixed.

      - If a <kineticLaw> element is present, it must contain a <math>
        element.  Prior to SBML Level 3 Version 1 Core, this has never
        been explicitly stated as a validation rule but should have been
        reported as a schema error.  In some case this was not happening.
        This is now fixed.

      - The 'configure' script help text incorrectly claimed that Xerces
        was the default XML parser; it now correctly states libxml2 is.

    * Configuration/build system changes

      - MATLAB 2010b introduced some inconsistencies in the build system
        on certain platforms.  This has been fixed.

      - The organization of the source directories has been radically
        changed, moving the previous directories src/annotation, src/math,
        etc., to become subdirectories of src/sbml.  This allows us to
        entirely avoid a step that was previously to create a copy of all
        the header files into <libsbml>/include.  That copy operation lead
        to a lot of wasted time when debugging code and accidentally
        making changes to the wrong file.

    ======================================================================
    Version 5.0.0-a1 (released 2010-10-05)
    ======================================================================

    This is the next alpha release of libSBML-5.

    This includes full support for SBML Level 3 Core; as found in
    libSBML-4.2.0.

    It also includes mechanisms for support of a 'layout' and a 'groups'
    extension.  This support extends to all language bindings with the
    exception of matlab/octave.  Note these are dummy packages based on
    proposals for the layout and groups packages.  They do not represent
    fully approved L3 packages.

    There have been no API changes from the pre-alpha release.

    It is anticipated that the next release (beta) will rearrange the
    directory structure for contributed package code and provide
    a new build system to facilitate the inclusion/exclusion of
    packages.

    * Changes to dependencies on 3rd-party libraries:

      - The language bindings now require SWIG 2.0.0 or later.

    * Known issues:

      - The C API is not yet implemented.

    ======================================================================
    Version 5.0.0-a0 (released 2010-01-18)
    ======================================================================

    This is a pre-alpha release of libSBML-5 which provides support for
    package extensions in SBML Level 3. Since libSBML-5 is currently in
    development stage the API may be changed in the future. Also, some
    features for package extensions (e.g. validation, language bindings
    and etc.) are not supported yet (please see "Known Issues" below).

    Currently, the code is based on the SVN trunk of Revision:10522
    (i.e. based on 4.1.0-beta), and thus validating/converting SBML
    Level 3 core has not been supported yet.

    Please see the following bundled README files for details:

       (1) docs/00README-HowToUsePackageExtension.txt

      (For package developers)

       (2) docs/00README-ExtensionSupportClasses.txt
       (3) docs/00README-HowToImplementPackageExtension.txt
       (4) docs/00README-ChangesInSBase.txt

    * New Features:

    - Added new classes for supporting package extensions in 'src/extension'.

    - Added a new directory 'src/packages' in which additional package
      extensions will be located.

    - Added new functions for supporting package extensions in existing
      classes. Most of the new functions are implemented in SBase and
      SBMLNamespaces classes.

    - Added a package of layout extension as an example package in
      'src/packages/layout'. The package is based on existing
      implementation of layout extension (implemented by Ralph Gauges)
      bundled with libSBML-4.
      "--enable-layout" option is required when running configure script to
      build the layout package. Example codes using the layout package are
      provided in "examples/layout/".
      Currently, the package is built as additional shared library files
      (e.g. libsbml-layout.a and libsbml-layout.so on Linux) that depend on
      the shared library of core libSBML (e.g. libsbml.a and libsbml.so on
      Linux) when built with make command.
      The package is built into existing libsbml.dll when built with MSVC
      on Windows. This build configuration may be changed in the future
      release.

    - Added a package of groups extension (based on the proposal on 2009-10)
      as another example package in 'src/packages/groups'.
      "--enable-groups" option is required when running configure script to
      build the groups package. Example codes using the groups package are
      provided in "examples/groups".
      Currently, the package is also built as additional shared library files
      (e.g.  libsbml-groups.a and libsbml-groups.so on Linux) when built with
      make command whereas the package is built into libsbml.dll when built
      with MSVC on Windows. This build configuration may also be changed in
      the future release.

    * Changes:

    - Moved source files of layout extension from 'src/sbml/layout' to
      'src/packages/layout'.

    - SBMLTypeCode_t (enum type) now contains only typecodes of SBase
      objects defined in the SBML core. Each package extension should
      define a similar enum type for typecodes of SBase objects defined
      in each package extension (e.g. SBMLLayoutTypeCode_t for "layout"
      extension (defined in LayoutExtension.h) , and SBMLGroupTypeCode_t
      for "groups" extension (defined in GroupExtension.h).)

    - Changed the type of return value of SBase::getTypeCode() and
      ListOf::getItemTypeCode() functions (SBMLTypeCode_t -> int).

    - Changed the usage of SBase::getTypeCode() and ListOf::getItemTypeCode()
      functions. Currently, the value of each typecode can be duplicated
      between those of different packages (this duplication problem doesn't
      happen with existing code which uses only SBase objects of the SBML
      core). To distinguish the typecodes of different packages, not only
      the return value of getTypeCode() but also that of getPackageName()
      should be checked as follows:

         void example (const SBase *sb)
         {
           const std::string pkgName = sb->getPackageName();

           if (pkgName == "core")
           {
             switch (sb->getTypeCode())
             {
               case SBML_MODEL:
                  ....
                  break;
               case SBML_REACTION:
                  ....
             }
           }
           else if (pkgName == "layout")
           {
             switch (sb->getTypeCode())
             {
               case SBML_LAYOUT_LAYOUT:
                  ....
                  break;
               case SBML_LAYOUT_REACTIONGLYPH:
                 ....
             }
           }
           ...
         }

    - API changes:

      (- : libSBML-4 API,  + : libSBML-5 API)

        - virtual SBMLTypeCode_t SBase::getTypeCode() const
        + virtual int            SBase::getTypeCode() const

        - virtual SBMLTypeCode_t ListOf::getItemTypeCode() const
        + virtual int            ListOf::getItemTypeCode() const

        - const char* SBMLTypeCode_toString (SBMLTypeCode_t typecode)
        + const char* SBMLTypeCode_toString (int typecode,
                                             const char* pkgName)

        - SBase* SBase::getAncestorOfType(SBMLTypeCode_t type)
        + SBase* SBase::getAncestorOfType(int type,
                                          const std::string pkgName="core")

        - virtual void SBase::readAttributes (const XMLAttributes& attributes)
        + virtual void SBase::readAttributes (const XMLAttributes& attributes,
                                              const ExpectedAttributes& expattr)

    * Known Issues:

    - Validating functions need to be extended for package extensions.

    - Converting functions need to be extended for package extensions.

    - Language bindings (SWIG configuration files and underlying support
      code such as local.cpp) need to be modified for supporting package
      extensions. Currently, language bindings of "layout" extension
      (Java, Python, Ruby, and C#) should work.

    - SBML Core and additional package extensions should be located in
      their own namespaces to avoid potential name conflictions.

    - C wrapper API needs to be added/updated.

    * Initial release, March 12, 2003.
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