Python 3.13

[ericpre]

Progress of the PR

• Add python 3.13 to CI,
• fix some numpy deprecation,
• fix warning in the test suite,
• [n/a] update docstring (if appropriate),
• [n/a] update user guide (if appropriate),
• add a changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting of the changelog entry (and eventual user guide changes) in the docs/readthedocs.org:rosettasciio build of this PR (link in github checks)
• [n/a] add tests,
• ready for review.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 87.84%. Comparing base (332412f) to head (160807e).
Report is 21 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #339      +/-   ##
==========================================
- Coverage   87.88%   87.84%   -0.05%     
==========================================
  Files          85       85              
  Lines       11241    11242       +1     
  Branches     2294     2082     -212     
==========================================
- Hits         9879     9875       -4     
- Misses        863      868       +5     
  Partials      499      499              

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[CSSFrancis]

Looks like some good updates. LGTM