Replace setup.py with pyproject.toml, update actions to latest versions

[chrisjonesBSU]

PR Summary:

This replaces setup.py with a pyproject.toml file.

I've been noticing these deprecation messages recently when running pip install . from source. I think it's recommended to use pyproject.toml instead of setup.py

DEPRECATION: Legacy editable install of mbuild==1.0.0 from file:///home/chris/repos/mbuild (setup.py develop) is deprecated. pip 25.0 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at https://github.com/pypa/pip/issues/11457

It's not clear to me where setup.cfg fits into this now. Do we still need it for bumpversion?

This also updates a couple actions to their latest versions.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.85%. Comparing base (b5d76c3) to head (62b3b1a).
Report is 9 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1217      +/-   ##
==========================================
- Coverage   85.89%   84.85%   -1.05%     
==========================================
  Files          53       53              
  Lines        4799     4799              
==========================================
- Hits         4122     4072      -50     
- Misses        677      727      +50     

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[CalCraven]

| It's not clear to me where setup.cfg fits into this now. Do we still need it for bumpversion?
I think bump2version is no longer maintained, so probably time to move away from it. Based on the old thread here, it seemed like the introduction of more standard and flexible maintenance packages such as pyproject.toml replaced it.

Looks like our two options moving forwards are:

1. https://github.com/callowayproject/bump-my-version
2. 2. https://github.com/bulv1ne/poetry-bumpversion
      Thoughts?

[CalCraven]

While we're doing this maintenance, is there anything we would want to add to a ruff.toml such as what HOOMD-blue is using https://github.com/glotzerlab/hoomd-blue/blob/trunk-patch/ruff.toml?

[chrisjonesBSU]

We could use https://github.com/callowayproject/bump-my-version, it seems more actively maintained.

As far as the ruff.toml, we could definitely add one! Is there anything specific you have in mind, though? By not having one, the default options are listed out here