Uploading sketch to DUE with Raspberry Pi

I've got a project that uses a Raspberry Pi to connect to an Arduino DUE via USB. I then remote into the Raspberry Pi to read any Serial outputs that are read into a python script.

It all works fine, but to upload a new version of the sketch I have to dismantle the setup to plug my laptop in.

I haven't been able to find any details about uploading sketches using Raspberry Pi. From what I can see the old Arduino IDE works on Pi but doesn't work with the DUE, whereas the new IDE works with the DUE but not with the Pi.

All the posts I see asking this seem to be a few months old, is there any way currently to do this?

Thanks

A search for "bossa raspberry pi" doesn't seem to reveal too much, alas...