Run formatter on entire project

[alanking]

We have used Black formatter for the automated ingest repo: irods/irods_capability_automated_ingest@a4f4f51

Ruff looks promising: https://github.com/astral-sh/ruff

Other options are welcome for consideration.

[d-w-moore]

Let's keep this for v3.0.0 but make it the last commit applied broadly to the Python source.

[alanking]

Another data point for Ruff (linter) and Black (formatter): irods/irods_testing_environment#234

[alanking]

Done in #677