A quick search of Digikey brings up the cheapest pogo pins at $0.59 each. At this price, it would cost $23.60 per board to break out all 40 GPIO pins using pogo pins. It's unlikely that anything other than the initial prototyping boards, or a dedicated development board would need all 40 GPIO. A typical PiCart board may need 10 pins, costing $5.90 per board in pogo pins. There may be cheaper off brand pins available, but I refuse to sacrifice quality on such a vital component. A bad electrical connection caused by a faulty pogo Pin would likely render the entire board useless and impossible to troubleshoot for the intended users. If my initial testing goes well, I may place a very large order to get a bulk discount on the pins. I may also be able to get them through the PCB fab house directly at a better price, with assembly.
Though the price of these pins is off putting, I still plan to use them unless I can find a better solution. Edge connectors do come to mind though.
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