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NMEA to pypilot
well, once pypilot detects a port it remembers so that is probably what happened and it is a hint for the future

it seems the initial autodetection without this knowledge may not have worked the first time you tried which is unfortunate. To recreate this you can delete the file ~/.pypilot/nmea0device assuming you have just 1 nmea device, and then reboot and see if it's detected or not. It may be that the serial driver for ftdi delays loading or maybe that it is registered as a gps device.

If you re-image the sd card it would also reset the state. It would be useful to know if you really had to manually restart pypilot or not.
I will try this and let you know. But since I didn't do anything else then checking stuff, rebooting pypilot should be what solved the problem.
I though you used ssh to restart pypilot without restarting the pi zero?

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