Linting does not work properly and missing from CI/CD

[mjdemilliano]

Currently there are a number of problems with linting:

• Need to install the linter manually before it can be run
• flake8 shows many errors
• Linting is missing from tox
• Linting is not enabled in the Gitlab workflow

Linting is an important part of maintaining a good quality codebase so I recommend fixing this.

[roberthdevries]

Linting using ruff is added in GH-133