To add to what Luka said,
It depends on how you connect your Moteinos. The Moteinos with a 6 pin header, can communicate directly over serial GPIO (all Moteinos are currently 3.3v levels so no conflict with the 3.3v GPIO of the Pi).
You simply connect moteino-TX to Pi-RX (if you have 1 way communication) and vice versa (if you also want data from the Pi back).
Then you simply read data from the GPIO serial port (it is /dev/ttyAMA0 in linux, not sure in win but probably a COMxx port?). It is common to send a carriage return between messages from your Moteino, to know when to "stop" reading characters in 1 message, and continue reading another incoming message.
If you connect a Moteino through a FTDI-Adapter (or equivalent USB-serial converter) then you would connect to the USB and it would simply be another serial/COM port on your Pi, not the GPIO one. Also note that on Raspbian there are common issues enabling the GPIO serial port,
read about it here.
Also the
Gateway app I've developed is something to look into if you just want a secure mobile-friendly interface to control nodes and log data from them on your Pi. A moteino can serve as the "gateway" node to all your other nodes, a
sample sketch for it is here.
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