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Thursday, April 10, 2014

libSBML 5.10.0 Released

As of now libSBML 5.10.0 is available for download:

as well as the python source packages in pypi:

and additional linux python packages from the OBS:


The full release announcement is as always on sbml-discuss. Here I would just like to call out a number of changes in this release:

  • We were able to fix a number of memory leaks within libSBML, and would recommend everyone to upgrade.
  • There is now an extensible ASTNode layer implemented, that can be used to add additional math to the set understood by libsbml. This is primarily of importance for SBML Level 3 packages like ‘arrays’ and ‘multi’ that extend math. If your software tool does not use these packages, and is not extending math, then you can use the ‘old’ implementation by specifying  the cmake option ‘LIBSBML_USE_LEGACY_MATH’.
  • The CMake build no longer modifies any files within the source directory, and so it is finally possible to have differently configured build directories side-by-side.
  • It is possible to influence precisely how comp-flattening influences each element in the flattening process. This is made possible by passing along a custom transformer class that will be called on each element by libSBML.
  • The CMake files have also been updated, so that it is possible for others to include the libSBML sources anywhere within their cmake projects and simply add libSBML as subdirectory to their project. All that needs to be done to make this work, is to set CMake variables to the root of the libSBML sources and the root of the libSBML build directory.
  • We have solved several issues with respect to compatibility with OSX Mavericks. The only remaining issue, is that when you install the standalone python packages, you will get an error as the python distutils are pretty much broken with Apples switch to Clang. For now you will have to define the ARCHFLAGS environment variable to include: ‘ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future’.



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