Build checks: Add more rules to Ruff and fix any issues that it finds

[cflynn3]

Currently in the tool.ruff section of the pyproject.toml file we have a number of rule codes that are currently excluded, but marked as 'to add later' or 'to fix later'. The objective of this task is to add those rules back in, and fix any issues with the existing code that are uncovered by those rules. We are particularly keen on re-enabling the docstring rules, as this will help us ensure that our readthedocs documentation remains in a good format.