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Experimental release notes

This page provides information about the libSBML experimental-only releases.

5.14.0-experimental (2016-09-16)

Release 5.14.0-experimental is available from our project's SourceForge download area.


Experimental only release

The main change in this release is that it supports the SBML L3V2(RC1) specification and has the relaxations that have been made to SBML L3V1 in the L3V1R2 (RC1) specification. There will be a presentation at COMBINE 2016 outlining the main changes and things that software developers need to consider. We will make this presentation available shortly after the meeting.

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
   - 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.

5.11.6-experimental (2015-07-16)

Release 5.11.6-experimental is available from our project's SourceForge download area.


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.

5.9.2-experimental (2014-01-30)

Release 5.9.2-experimental is available from our project's SourceForge download area.


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.

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This page was last modified 09:18, 16 September 2016.



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