[WIP] Replace flake8 with ruff for linting

[asears]

Improves #138

• Removes .flake8
• Adds pyproject toml ruff with bandit security scan settings.
• Other rules available. https://docs.astral.sh/ruff/rules/
• Update the lint workflow and makefile

Requires some GitHub workflow tests and poetry lock generation, can a maintainer have a look at the PR? This may affect local dev experience and have existing scan warnings to address.

ruff . 
ruff . --fix
ruff . --fix-unsafe

ruff . --format not yet replacing black.

[gengliangwang]

@asears Thanks for working on this! I wonder why we have to remove flake8. Currently we can simply use make format to format the Python files. For linting errors from flake8, they are easy to address.