Feature/add precommit hooks

[laurejt]

Associated Issue(s): resolves #17

Changes in this PR

• Adds the following pre-commit hooks:
  • ruff linter and formatter
  • yamlfmt: YAML formatter
  • codespell
  • some out-of-the-box file checks
  • check uv.lock
  • validate GitHub Actions workflow files
• Adds ruff and pre-commit to dev dependencies
• Add yamlfmt.yml config file to retain linebreaks but only keep a single line in groups of many blank lines
• Add ruff rule set excluding type annotations and documentation
• Temporarily fixed pyproject.toml's pytest configuration to support Python 3.9 (intend to update when 3.9 support is dropped)
• Fixed unit test TestViafEntity.test_rdf within test_api
• Fixed broken GitHub Actions workflow unit_tests.yml
• Fixed broken GitHub Actions workflow python-publish.yml
• Otherwise updated files according to pre-commit hooks

Notes

Include any additional notes that will help in the reviewing of this pull request

• I removed the option for running the python-publish.yml manually since there is no way to restrict to a specific branch.

Reviewer Checklist

• Verify that pytest can be run locally successfully
• Confirm the file style changes look reasonable

[rlskoeser]

Revisions look good to me.

[rlskoeser]

These versions look old. I assume you are holding off on updating, and this PR is solely reformatting? (Want to make sure we're tracking that work somewhere)

[laurejt]

Yes, but I'll make a new issue on updating this workflow.