Update DevOps configs

[tomvothecoder]

Description

• Update conda env dependencies
• Add dev-nompi.yml which includes the nompi version of esmf to avoid the yaksa leak error that breaks VS Code testing API
• Update pre-commit dependency versions and fix new issues for black, flake8, and mypy
• Move most of setup.cfg to pyproject.toml
• Add Makefile with convenient developer commands
• Update test_diags.py and test_allsets.py to use pytest

Checklist

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

If applicable:

• New and existing unit tests pass with my changes (locally and CI/CD build)
• I have added tests that prove my fix is effective or that my feature works
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have noted that this is a breaking change for a major release (fix or feature that would cause existing functionality to not work as expected)