Updates for Python 3.12

[d33bs]

Description

This PR focuses on adding updates which enable compatibility with Python 3.12. I found that we needed to update Numpy and Pandas, which in turn required updates for database querying through Pandas and SQLAlchemy, whose API has changed. This resulted in some changes to test_cells. Eventually I found that test_collate fails due to the database API shifts from cytominer-database (which would require outside updates we're unable to make directly).

It might be that we consider Python 3.12 support alongside dropping collate support. Otherwise we may need to update cytominer-database to provide compatibility. On a related note, I found there were various issues which might need to be solved but I've proposed sidestepping in #473 by relying on cytominer-database==v0.3.4.

What is the nature of your change?

• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

Checklist

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• I have read the CONTRIBUTING.md guidelines.
• My code follows the style guidelines of this project.
• I have performed a self-review of my own code.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• New and existing unit tests pass locally with my changes.
• I have added tests that prove my fix is effective or that my feature works.
• I have deleted all non-relevant text in this pull request template.

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📚 Documentation preview 📚: https://pycytominer--474.org.readthedocs.build/en/474/

[d33bs]

Closing this as I feel it might have been an incorrect attempt in the midst of the dependency changes.