Fix all the warnings in Cython extensions

[sserita]

Describe the bug
We have many errors of the form

/opt/homebrew/Caskroom/miniconda/base/envs/pygsti/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^

when compiling Cython instructions. We should fix these, along with the several other unrelated (but probably should still be fixed) warnings, including this one:

C:\hostedtoolcache\windows\Python\3.12.8\x64\Lib\site-packages\setuptools\__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************
!!

To Reproduce
Run python setup.py build_ext --inplace to rebuild the extensions.

Expected behavior
Cython extensions build cleanly with no warnings.