Use numpy 2 in CI testing. Drop python 3.9, add python 3.13 to testing, remove openbabel from enviroment-dev.yml

[chrisjonesBSU]

PR Summary:

This pins the numpy version used in the environment.yml files to >=2.0 and <2.3.
There are breaking changes in some upstream packages in 2.3 (ParmEd/ParmEd#1406)

There were a couple syntax changes needed in some unit tests. Tests with numpy 2 are passing in gmso as well, so I'll start a PR there. I'll check in foyer and ffutils next.

PR Checklist

---

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

[CalCraven]

I don't think the RDKIT pin would be necessary, but something to keep an eye on. 'rdkit<2025.3.3'.
Seems like maybe a pypi issue.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.96%. Comparing base (6758a4f) to head (ea7a20d).
⚠️ Report is 54 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1252      +/-   ##
==========================================
- Coverage   85.98%   85.96%   -0.03%     
==========================================
  Files          53       53              
  Lines        4860     4860              
==========================================
- Hits         4179     4178       -1     
- Misses        681      682       +1     

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[chrisjonesBSU]

Openbabel's progress to supporting 3.13 seems to be stalled at the moment, so I think we can remove it from the environment-dev.yml file, as it is the only barrier to supporting python 3.13. openbabel isn't a dependency of mBuild's conda-forge package anyway. I added a task to the CI that installs openbabel for python versions != 3.13, so the relevant methods are still getting tested here. GMSO and foyer don't use openbabel.