Python 3.13 migration

[pmfurlong]

Motivation and context:
Added compatibility with python 3.13. Comes with added upgrade to python 2.0.4

How has this been tested?
I have run the unittests and they all pass.

How long should this take to review?

• Average (neither quick nor lengthy) A small number of lines changed, but distributed over multiple of files.

Types of changes:

• Breaking change (fix or feature that causes existing functionality to change)
  Changes some calls to numpy that are no longer backwards compatible.

Checklist:

• [ X ] I have read the CONTRIBUTING.rst document.
• [ X ] I have updated the documentation accordingly.
• [ X ] I have included a changelog entry.
• [ N/A ] I have added tests to cover my changes.
• [ X ] I have run the test suite locally and all tests passed.