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how to enable built-in pullups (or pull-downs) of GPIOs ?
There's currently no good way to enabled pull-ups or pull-downs, in a general (i.e. not Pi-specific) way. Other libraries poke /dev/mem (bad), or the custom /dev/gpiomem (only slightly less bad), but we're hoping to convince the kernel maintainers to add this functionality in a portable way, that will also work on future hardware.
Short version: it's a known omission currently. If this is something you want to be able to do earlier, you could try to extend the IO library to mess with /dev/gpiomem.