You can force the use of a specific port; from the documentation
board = Arduino("115200", port="COM3") #Windows example
I've uploaded prototype.ino to a Nano and used serial monitor (you can use any terminal program) to read an analog input. The command is
@ar%1!
You can try the same to make sure that your sketch behaves as expected.
As this has nothing to do with Installation and Troubleshooting (IDE is working and you can upload code; see About the Installation & Troubleshooting category), I've moved your topic to Interfacing w/ Software on the Computer - Arduino Forum.
Note:
I'm not a Python person so might not be able to help further.