Set simulator appropriately in gst.run(...) when checkpointing is used

[rileyjmurray]

If checkpointing is used in GST then we read the initial model at this code block:

pyGSTi/pygsti/protocols/gst.py

Lines 1380 to 1395 in c74fcb2

	elif isinstance(checkpoint, GateSetTomographyCheckpoint):
	# if the checkpoint's last completed iteration is non-negative
	# (i.e. the checkpoint actually has data in it)
	if checkpoint.last_completed_iter >= 0:
	seed_model = checkpoint.mdl_list[-1]
	# otherwise seed with target
	else:
	seed_model = mdl_start.copy()
	mdl_lsgst_list = checkpoint.mdl_list
	final_objfn = checkpoint.final_objfn
	# final_objfn initialized to None in the GateSetTomographyCheckpoint and will be overwritten
	# during the loop below unless the last completed iteration is the final iteration
	# in which case the loop should be skipped. If so I think it is ok that this gets
	# left set to None. There looks to be some logic for handling this and it looks
	# like the serialization routines effectively do this already, as the value
	# of this is lost between writing and reading.

At no point in this block do we set seed_model.sim according to the "simulator" keyword argument. We should update to add

                if simulator is not None:
                    seed_model.sim = simulator

after seed_model is defined.