Apply Ruff code formatting and linting to entire DEA Tools

[robbibt]

Proposed changes

This pull request does a major reformat of our DEA Tools code, aimed to standardise our code and clear up any major code isues. I've used Ruff (https://docs.astral.sh/ruff/) to do this, running the following code formatting and code linting commands to automatically update code:

ruff format
ruff check --fix

These commands make changes like:

• Reformatting code to follow PEP8 (e.g. consistent indentation, spacing, and standardising quotes)
• Removing unused imports and variables
• Sorting and grouping imports
• Replacing deprecated/overly complex syntax with simpler, more Pythonic equivelents

These commands are theoretically safe (e.g. designed to not break code), but it's a bit hard to tell as we don't have complete unit testing in DEA Tools. We're likely going to have to rely heavily on the Jupyter Notebooks integration tests to see if any notebooks break after the change.

[vnewey]

I haven't gone through all the changes.
Let's merge and see if the integration tests pass . :)