Use upstream pybind11 instead of old pybind11 2.3.dev0 #30
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pydnp3 is using an old version of pybind11 that is using some deprecated pthread features it seems, and causes segfaults. Using the most recent pybind11 fixes this. I don't think there's any reason pybind11 should be a submodule, it can just be a dependency instead, as the latest version 2.9.1 is available from pip.
cmake is deleted because it does not compile, and does not seem to be needed as a python module. You just need your system's cmake.