There are several breaking changes here so it is advised that you avoid updating until most issues are resolved.

Major Changes

• Add lattice-based simulations. See the documentation.
• Simulating a Network directly builds several dependency graphs. To help with multiple runs, use state, model = parse_model(network) to build the graphs outside a simulation then run simulate(state, model).
• Temporarily emoved the trials keyword. For now, use [simulate(state, model, ...) _ for 1:100].
• Simulation algorithm internals have changed drastically. The OptimizedDirect() and tau-leaping methods have been affected. Will restore functionality and expose interface for tau-leaping in future update.
• Petri nets are temporarily removed.
• Simulation data handling has been improved. Use save_points to specify when to save system state.
• Added SortingDirect() method.
• Simulation data is stored using RecursiveArrayTools.jl to provide SamplePath and Ensemble types. Types implement IterableTables.jl, which should provide good functionality with I/O and DataFrames.jl.