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Oh yeah, basically the easiest way to do it would to pump water out of each basin, through a heat exchanger, and then back into the basin. That way you could have your whole temp control aparatus located outside of the terrarium. Plus that would also easily enable automatic water level management to keep the water levels identical. For your heat exchanger you could just use a CPU water block and a peltier device. You regulate the power going to the peltier device by monitoring a temp sensor in your water return pipe and just pulsing the peltier device on and off at different rates to control the heating or cooling rate. Plus with the peltier device you can just reverse the polarity to switch from heating to cooling to enable the shuffling of the basins. All of this would be controlled and charted in a csv file by a raspberry pi. Additionally you could connect a simple motion sensor so the pi could flag the times the snake was using one of the basins to make it easier to read the data.
Rather than monitoring ambient temp or humidity you would probably be better off just keeping them tightly controlled and constant via other systems. That would further reduce variables for the initial test.
Very true on the second part I mean you have to do that anyway for the reptile .