Interrupts for Engine

[eagmon]

Currently Engine.front tracks all processes next updates, with a dict that has the next update times and the updates that will be applied: {'time': 14.0, 'update': {update-to-be-applied}}. The process's next update time is determined by the global time plus the timestep given by its Process.calculate_timestep().

Having interrupts would allow other processes to change a given process's next update time to be earlier. This might be necessary if, for example, an event such as chromosome replication needs to reset transcription at a given time. If the interrupt time is before the previously-determined next update time, the transcription process would need to be rerun from its previous initial state, and would return a new update dict: {'time': 13.0, 'update': {new}}.

To add this feature requires that we save the initial state provided for the process, so it could be re-run from that state at a shorter interval. Something like: {'time': 14.0, 'update': {update-to-be-applied}, 'state': {saved-view}}. It would also require the interrupt times to be received and handled by Engine.run_for.

[U8NWXD]

Would a saved "view" of the state be enough? Currently the views we give to processes aren't copies. If we used a similar view here, any changes to the state would also affect the saved view. To prevent this, I think we'd need to deepcopy the view

[eagmon]

Agree -- a "view" would not be enough, it would need to be a deepcopy. This would clearly add overhead, so maybe it should be optional? Processes can opt in for interruption, in which case the deepcopy of the view is applied.