Build graph now copies to a new graph using size_t as the vertex descriptor. Might be able to make it cleaner code, though.
Can now make transitions and put them into the GSPN.
Can now make transitions and put them into the GSPN.
Tested whether the new graph is bipartite (yes) and whether the stochiometric coefficients copied (yes).
Some comments. This code works with the sequence of metapopulations made for Jason.
There was a problem compiling with two ways to print the marking. There is now one default way.
Forgot a const in the marking.
The ExplicitTransitions are now simplified to work only with the PetriGraphType.
The bvd builds with a much more compact builder for the gspn with explicit transitions.
Now building sirmixed with the new method. Brownion won't compile. Unsure whether firing is working correctly. Maybe the stochiometric coefficients are off.
Changed random number generators to std::random because they are sure to compile with clang 3.4 and boost 1.55. annoying that the two don't play well together. -Wno-deprecate-register is necessary too. Brownion now compiles.
The SIR example is fixed. Now has recovery and reads parameters from the command line. It's much clearer with the new GSPN construction method. Also adding install-sh because moved to a new machine and configure fails without it, so it must be one of the necessary temporaries in order not to have to do autoreconf.
ExplicitTransitions now rigorously hides its members once it is built. There are also comments and tidying before committing to the main repository. Need to check this on gcc before the rebase.