Enable E741 ruff check

[robertapplin]

Description of work

This PR fixes any remaining ruff E741 errors, documented here:
https://docs.astral.sh/ruff/rules/ambiguous-variable-name/

It also enables this check to run on all pull requests.

To test:

Code review - check that all changes look reasonable

Run ruff locally on all files using the following terminal command

pre-commit run ruff --all-files

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[jclarkeSTFC]

Looks good, I just spotted some small things.

[jclarkeSTFC]

Thanks for making those changes.

[thomashampson]

I think we should check with more people before deciding whether to turn this rule on. It's quite common to e.g. loop over the indices h, k, and l, and maybe we shouldn't be restricting this.

[RichardWaiteSTFC]

I don't mind hugely, but it's a bit confusing to change just l to L and leave h,k lower case...personally I would prefer to supress the objection to h,k,l as these mean something in our domain and probably involves changing a lot of files (are we sure we have good test coverage for all of them, would it pick up if there was an existing L variable already?). Granted H,K,L is equally meaningful but in python you tend to use lower case to start a variable name. Just my opinion though!

[robertapplin]

It was decided that the l variable is meaningful and readable in a situation where the file is using h,k,l variables. In this case, l is preferrable to L. Therefore it was decided its best to suppress E741 at the top of files that are likely to use h,k,l , so that we can then keep the E741 check on by default for all other files

[peterfpeterson]

I merged without Tom's (in github) approval. The changes he requested were made.