Upgrade pybind11 to 2.13.2

[tigercosmos]

Pybind11 just released a new version, which has better support for Python 3.13.

[tigercosmos]

Related Numpy issue:

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.0.dev0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

[yungyuc]

Is this issue for updating github actions?

[tigercosmos]

Not sure, need to do more experiments, but I guess we will need to update CI to support NumPy 2.