- fix for Bug1873: turn around the direction of the initial assignment. That way no invalid / duplicated assignments to a variable can exist. It also allows to modify the original element, rather than the newly created quantity representing the 'initial value'.
- first version for issue 1875: when exporting initial assignments, tag the new values with a custom annotation. Then upon import locate that annotation, and if present, skip importing that model quantity and initial assignment, and instead refer to the original element
- Bug1874: missed during the last commit: a modification to CReaction::setFunctionFromExpressionTree to override the function name (in case the user defined function is not yet in the function database)
- to make the function compatible with 'older' versions of libSBML (older = pre november), make getOriginalSBMLId take a non-const parameter
- removed unused function
- Language bindings don't expose annotations on CFunctions
- fix for issue 1881: found print to stdout, that was active outside of COPASI_DEBUG
- ensure COPASI_DEBUG is only defined when enabled
- fix compilation on linux x64 with *default* clapack sources
- add support for custom annotations to CReaction bindings
- ensure that LAPACK f2c does not interfere with the one supplied by clapack on linux 64
- add the option to go directly to the used kinetic law
- fix for bug 1882: mark products of irreversible reactions as modifier if they are also marked as modifier
Fixed Bug 1876. The standard deviation and RMS are now calculated ignoring missing
data points.
Fixed Bugs 1877 and 1879. The Fisher information matrix is now calculated
based on the residuals instead of the simulated values directly. Since the
residuals take into account missing data and scaling factors both issues
are resolved.