Upgrade flake8 and other dependancies

[ramereth]

We need to do this in a single PR due to them depending on each other.

• Bump flake8 from 6.0.0 to 6.1.0
• Bump pycodestyle from 2.10.0 to 2.11.0
• Bump pyflakes from 3.0.1 to 3.1.0