-Introduced CUnit class (with CBaseUnit and CUnitComponent) . . .
// This class defines a unit, which might be considered
// an enhanced form of metadata, in COPASI. It can merely
// contain the name and symbol of the unit, but is intended
// to also contain a list of the SI units it is derived from.
// This is intended to facilitate unit analysis, user input parsing,
// and easy compatibility to the SBML units representation.
(Previous functionality is there. TODO stubs are in place for
advanced features to be added shortly.)
- mark importing spatial models as an error (as COPASI does not allow editing spatial features), however let the model be loaded so the non-spatial ones can be edited.
- adapt spelling SEDML -> SED-ML
- choose ".sedml" rather than ".xml" so as not to confuse our users as to which files to open / import
- added two examples of SED-ML files (with SBML files) to the testsuite/distribution folder
- fix import of SED-ML plots, so that phase plots can be imported, as well as log plots
Bug 2005. Unit enums are now defined in CUnit.
Bug 2005. I introduce a typedef of unit enumeration values for backwards
compatibility.
- allow import of SED-ML documents, that explicitly define what level / version of SBML they include
- do not overwrite models of other files without warning, rather use a non-existing filename for the exported model
- modify SED-ML export to allow export of phase plots
- modify SED-ML export to not default to model1.xml for SBML file names
- continued renaming CModel::<unit> to CUnit::<unit>
Bug 1981. Updated fix. The problem was in the calculation of the Link
matrix which did not correctly update all values if no species or no
reactions where present.
Bug 1902. The start values are now remembered at the beginning of an
optimization ore parameter estimation task and are correctly displayed and
saved in the GUI.
Added SED-ML examples to package.
Added export of the environment variable COPASIDIR to CopasiUI shell
script executed under Linux instead of the CopasiUI binary which has been
moved to a non standard location.
Added missing model files required for the SED-ML examples to the Windows
installer packages.
Fixed SED-ML example files.
- fix SED-ML import of plots: typo, that used the same display name on all curves.
-implemented CUnit::addComponent and
CUnit::isDimensionless (uses prime number enumerations of CBaseUnit::Kind)
The Eigen value and Eigen vector calculations of the Fisher Information
Matrix are now production ready.