Move diagram generation, transition rates setting etc. to KineticModel

[dburov190]

Currently (i.e. after #136), ContactNetwork accepts transition rates for KineticModel; however, transition rates for MasterEquationEnsemble are set separately. This creates confusion, so it's better to either

• set transition rates inside KineticModel without ever touching ContactNetwork (through a factory method), or
• set true transition rates on ContactNetwork, and then let the ensemble read those that are needed, and pass distributions for those that have to be inferred via EAKF.

Besides, generate_diagram_indep and generate_diagram_neigh methods are inside ContactNetwork simply because of the names of weight labels; they don't really belong there. This can be fixed via a Glossary class which would hold all parameter names.