Configure pre-commit to do the static analysis

[peterfpeterson]

The main purpose of this is to move static analysis checks to pre-commit and make it happy. The main files to look at are .pre-commit-config.yaml and pyproject.toml. Almost everything else is a formatting change, fixing a static analysis warning, or suppressing a warning. Most warnings were suppressed rather than changed because they involved naming conventions and ignored arguments.

Check list for the pull request

• I have read the [CONTRIBUTING]
• I have read the [CODE_OF_CONDUCT]
• I have added tests for my changes
• I have updated the documentation accordingly

Check list for the reviewer

• I have read the [CONTRIBUTING]
• I have verified the proposed changes
• best software practices
  • all internal functions have an underbar, as is python standard
  • clearly named variables (better to be verbose in variable names)
  • code comments explaining the intent of code blocks
• All the tests are passing
• The documentation is up to date
• code comments added when explaining intent

Manual test for the reviewer

References