Use numpy 2 in CI testing. Drop python 3.9, add python 3.13 to testing.

[chrisjonesBSU]

PR Summary:

Similar to mosdef-hub/mbuild#1252

PR Checklist

---

• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.08%. Comparing base (10858fa) to head (59be879).
⚠️ Report is 83 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #901   +/-   ##
=======================================
  Coverage   94.08%   94.08%           
=======================================
  Files          67       67           
  Lines        7238     7324   +86     
=======================================
+ Hits         6810     6891   +81     
- Misses        428      433    +5     

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