Add pre-commit for code formatting

[johnwason]

I configured pre-commit and adjusted the GitHub Action to run instead of the shell scripts for code formatting. pre-commit offers many more checks so quite a few changes are suggested. I did not commit any of the suggested changes.

pre-commit can be run from the command line using:

python3 -m pre_commit run --all

See https://pre-commit.com/

The pre-commit action output will show the changes made by the formatters.