Is there any way to check if the robot has paused execution of the main thread due to a prompt or popup?
Obviously I can set a bool to true before the popup and low afterwards, but this gets really tedious when the program gets long.

There’s currently not a way to do this but you could create a function that does this and then when you want a pop up you would simply use that function instead of the pop up node in polyscope. 

You could do something like this:

Make an assignment in the Before Start section of the program and name the variable popupShowing and set it to False

Create a script file with the following code:

def my_popup(msg, title="Popup"):
  popupShowing = True
  popup(msg,title, False,False, True)
  popupShowing=False
end

my_popup("This will use the default title")
my_popup("This uses a custom title", "Custom Title")

You could do something like this:

def getBooleanFromOperator(msg):
  popupShowing = True
  local answer = request_boolean_from_primary_client(msg)
  popupShowing = False
  return answer
end

yesOrNo = getBooleanFromOperator("Do you want to continue operation") # The message would be what is displayed on the pendant

request_boolean_from_primary_client(msg)
request_integer_from_primary_client(msg)
request_float_from_primary_client(msg)
request_string_from_primary_client(msg)

Thank you!