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tho I googled it alot, I could not figire it out what the best practice for working with RP GPIO is. I am making a device to monitor/control my home stuffs and I am sure I will want to upgrade my RP if a new baords come in the future. Also I am thinking to do something to be able to upgrade my codes online. So, could you please advise me the best practice to choose the GPIO mode to minimize the hassle of changing the boards and updating the existing codes in the future.

Thanks

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Your question is very general. But let me make a comment: Very frequently, when a program is written for a new task, a lot is learned in the process, and major portions of the program are re-written. So don't worry about the future at this time. This is a learning experience. Pick a small task and make it work. Turn on an LED when a door is opened, or report the temperature, or something. By the time you've finished, you should have a much better idea of what the lay of the land is, and be able to ask more directed questions.

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i set the gpio mode in the config.txt file now. https://www.raspberrypi.org/documentation/configuration/config-txt/gpio.md

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