Software Open Access

libSBML-5.19.0

Keating, Sarah M; Bergmann, Frank T; Olivier, Brett G; Smith, Lucian P; Hucka, Michael

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5.19.0 (2020-11-27)
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        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. 
  

      

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