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Looks great! Yeah, flashing an arduino can be a hassle depending on how it is connected indeed. In my case it is close to the Pi which has Arduino IDE installed, but still you need to unassign the serial connection in order to make the serial port accessible for the flash. It would be great to have some kind of a webservice available that could do it, but I guess that would be a lot of development work because you need the capabilities of Arduino IDE in a webapp. The upside however would be that maybe you can link the github repository so the download of motor.ino is not manual anymore. Just a thought.
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I manage with "make upload" and apply power to the arduino just as avrdude is run. This will upload even through isolation.
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Yes. If you hit reset button or just apply power exactly when running avrdude it uploads through tx/rx and optical isolation because it can't reset normally using usb serial hardware control line.
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Another update, first I thought the sound was due to the fact I had a new motor controller. However, now that I have experimented with another motor controller of another type it seems that my linear actuator was the cause. When using an "official" one from Raymarine there is no sound, when using any other motor it may give a sound. Some motors seem to be more "sensitive" to acoustics than others.
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Did you try putting an inductor in series with the noisy linear actuator?