LibSBML news

           libSBML NEWS -- History of user-visible changes

====================================================================
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 
    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 
    that mirrorred the id of a  should be listed as a 
     in the enclosing . 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  element explicitly.  This may cause an 
    apparent difference in models if reading and then writing. 

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

  - MathML within a  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 
      and a  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 
 tag and set the  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
    .  Fixed.
    
  - If the units of an object referred to a UnitDefinition that had no
    , 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  to a  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  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
    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 /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  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 

LibSBML 5.18.0, an application programming interface (API) library for SBML.

SBML Team http://www.sbml.org/ sbml-team@googlegroups.com