[SOSlib-devel] changed to libSBML 3.0.1

[Rainer M. <ra...@tb...>]

Hi All,

SOSlib has switched to libSBML 3.0.1, new code is in CVS now.

Some minor bugs had to be fixed in libSBML. To avoid potential problems, 
you should thus preferably use the current CVS version of libSBML, but 
3.0.1 should in principle also work. However, in the latter case DON'T 
use SBML Version 1 models, as these are not correctly translated (imho) 
in the 3.0.1 release of libSBML. I have not tested the 3.0.0 release.

Also a well-hidden but potentially harmful bug of the compiled r.h.s 
functions for the sensitivity and adjoint solvers has been removed. Some 
equations where misinterpreted.
The bug could have lead to wrong sensitivities for species with 
hasOnlySubstanceUnits=true, or for predefined rateRules.

Feedback welcome.

ToDos before release:

* libSBML has a completely reworked handling of SBML parse and 
validation errors. These should be accomodated, in parallel to generally 
stream-lining and refactor SOSlib error handling.

* make objective function related structures independent of odeModel_t 
structure

* implement new features of SBML L2V3:
constraints, initialAssignments etc.

* implement variable Compartment sizes

Rainer