Arduino communication protocol with python - beyond pyserial and Arduino example
Ok, after quite some time looking for something that would allow me to easily control an arduino with the raspberry pi, I found the FIRMATA protocol which allows one to communicate with the arduino through many languages. (a snippet from the github page for SEO purposes is shown at the end of this message).

From there I looked for through the python frameworks, and had a long chat with MrYsLab who helped me integrate the arduino Due to his pymata and pymataExpress frameworks. They work quite well and enable you to have a script that quickly and efficiently communicates with the arduino. I'm sure proper frameworks from ros.org or gobot are better. But pymata worked for me hence my answer to my own question.


processing 


https://github.com/firmata/processing   
http://funnel.cc 

python 


https://github.com/firmata/pyduino 
https://github.com/lupeke/python-firmata 
https://github.com/tino/pyFirmata 
https://github.com/MrYsLab/PyMata 
https://github.com/MrYsLab/pymata-aio  

perl


https://github.com/ntruchsess/perl-firmata 
https://github.com/rcaputo/rx-firmata  

ruby


https://github.com/hardbap/firmata 
https://github.com/PlasticLizard/rufinol  
http://funnel.cc  

clojure


https://github.com/nakkaya/clodiuno 
https://github.com/peterschwarz/clj-firmata  

javascript


https://github.com/jgautier/firmata  
http://breakoutjs.com 
https://github.com/rwldrn/johnny-five  

java


https://github.com/4ntoine/Firmata 
https://github.com/kurbatov/firmata4j 
https://github.com/reapzor/FiloFirmata  

.NET


https://github.com/SolidSoils/Arduino 
http://www.imagitronics.org/projects/firmatanet/ 
https://github.com/wbadry/FirmataCSharpClientClass  

Flash/AS3


http://funnel.cc  
http://code.google.com/p/as3glue/  

PHP


https://bitbucket.org/ThomasWeinert/carica-firmata 
https://github.com/oasynnoum/phpmake_firmata

Haskell


http://hackage.haskell.org/package/hArduino

iOS


https://github.com/jacobrosenthal/iosfirmata

Dart


https://github.com/nfrancois/firmata

Max/MSP


http://www.maxuino.org/

Elixir 


https://github.com/kfatehi/firmata

Modelica


https://www.wolfram.com/system-modeler/libraries/model-plug/  

golang


https://github.com/kraman/go-firmata

Qt/QML


https://github.com/callaa/qfirmata 

Android/Kotlin


https://github.com/xujiaao/android-firmata

Smalltalk 


https://github.com/pharo-iot/Firmata