Myokit

- Added `parse_model()` etc methods to parser.
- Made sure protocol is cloned in all simulations.
Protocols are not immutable and changes made after setting the protocol should not affect the simulation (or vice versa).
- Added a simulation that calculates the derivative of a state w.r.t. a parameter.
- Working on `MarkovModel` class.
- Added method to convert monodomain parameters to conductances to opencl simulation.
- Various small bugfixes.

- Various small bugfixes.

- Added `ATF` support.
- Added a Python-based `PacingSystem` to evaluate protocols over time in Python.
- Added `Protocol` to `SimulationLog` conversion.
- Improvements to GUI classes.
- Added protocol preview to GUI.
- Various small bugfixes.

- Fixed memory use and halting issue in `lib.fit`.
- Fixed bug in `aux.run()`.
APDs are now returned in SimulationLogs instead of plain dicts.
This allows saving as csv and is more consistent with what users would expect the simulation to return.

- Bugfix in PSO code: Initial positions weren't set properly, could end up out of bounds.

- Made threaded `run()` an option in `settings.py`.