I recommend using the winscard/pcsc interface directly. winscard is a standard library on Windows, PCSC.framework is standard on Mac OS, and libpcsclite is available on Linux by installing pcscd/pcsc-lite.

I recently implemented a library (https://github.com/pyauth/exile) to use Yubikeys to sign AWS API requests, which required writing Python ctypes bindings to call these libraries. It turned out to be fairly easy once I threw away the idea that I should rely on any of the intermediary libraries, and just started talking via the winscard/PCSC protocol directly.