Added an SIR Bio-PEPA model, which will not currently work since it uses the floor and H functions (possibly for other reasons as well), but it gives us a goal to aim for
Added a test for the Bio-PEPA command-line which currently fails as the pepapot script does not actually accept Bio-PEPA models yet.
Added the solving of BioPEPA files to the command-line interface. A little clean-up to do certainly, in particular there is no output currently.
Fixed some parsing errors in the sample SIR_RIBE.biopepa model. Just realised I do not allow comments, and so should add that now.
Added double slash comments to Bio-PEPA parsing. It seems to take a long time to parse the SIR_RIBE.biopepa example but not the other (non-comment containing) examples. I'll stick with this for now and see how it works once the rest of the model actually parsess.
Added an optimisation line for the parser which allows much speedier parsing in some cases.
Added a bit more information on the use of enablePackrat for the parser.
The command-line test for PEPA was failing because of a previous refactor. It is now fixed. I should not really have continued with the Bio-PEPA parsing stuff until I had fixed this but I had not noticed it.
Allow expression in Bio-PEPA population initialisations. Currently that also means that they are allowed to be non-integers and even negatives. We could check for these properties.
Silly error in Bio-PEPA command-line method.
Added the floor, exp and H functions to expression evaluation.
Updated the SIR_RIBE.biopepa test model to use ** for power function, simply because that is what we have defined. If there is demand for it I might also include ^ as a synonym.