Test/cicd code quality and formatting

[444B]

Pull Request Template

TL;DR

Provide a brief summary of the changes made.

• added code quality checks
• used black, isort, flake8, mypy and bandit to clean up the code, resolving 3 security issues
• bumped minimum python version to 3.9 to resolve minimum import issues in numpy 1.26.4
• issues in code checking will continue on a failure when in a branch that begins with /test but will fail when being published to main and if the issues still exist
• lots of code cleanup and removal of whitespace
• introduction of tests/run_checks.sh in order to replicate code checks locally what would normally take place in a Github Action.
• slowly starting to write unit tests with pytest

Problem Solved

1. Describe the problem your changes address.
2. Please mention the issue number if relevant
   • code was not following a standard
   • this led to security issues in the code, such as making use of subprocces() where not necessary

Manual Testing

• [X] You have manually tested all changes to ensure they work as intended. Replace the [ ] with a [X] if True.

How was this tested? Describe the tests that you ran to verify your changes.

• run locally

Additional Notes

Include any additional information that might be relevant for reviewers.

[444B]

will merge with the failed build-upload-push since that was a failure in test env. I think