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D1 could be used for rotary as well as D7 (both have interrupt)
I don't think we need memory. Even with only the atmega32u4 we could still store 40 events in the internal EEPROM and the goal is to extract the data to the bioreactor. Except if we think about another application
I/O 3 and I/O 4 are not mandatory I think so could be removed if required. But they could also be present if there is no memory.
Following the hierarchy of the bioreactor add a 'making' folder and the pinMapping for the pHmeter
https://github.com/Hackuarium/bioreactor/blob/master/docs/making/pinMapping.md
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