Add support for pre-commit with mypy and Ruff and start adding type hints

[valeriupredoi]

Description

OK @bnlawrence @davidhassell I have added full infrastructure for pre-commit with ruff and mypy (though I have turned off mypy temporarily, while we fix or exclude ruff barfs, then I can turn it back on and we'll have to fix the type hints). Because the code is a mix of (very) old code, code that's been written with functionality in mind, and decent standards code, we have Ruff complaining about a lot of things - some of them are already fixed via a pre-commit run -a, some need attention but are easy fixes, and some are really tricky to fix; how do you propose we do the work? For now pre-commit doesn't run on tests/ nor on doc/ - I'll have to turn on running on tests/ at some point in the future, but let's focus on the main source code for now.

To run pre-commit, check out this branch, make sure you have pre-commit installed (from conda-forge) then:

pre-commit install
pre-commit run -a

Before you get started

• ☝ Create an issue to discuss what you are going to do

Checklist

• This pull request has a descriptive title and labels
• This pull request has a minimal description (most was discussed in the issue, but a two-liner description is still desirable)
• Unit tests have been added (if codecov test fails)
• Any changed dependencies have been added or removed correctly (if need be)
• If you are working on the documentation, please ensure the current build passes
• All tests pass

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.83%. Comparing base (628f227) to head (367c5e9).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #173   +/-   ##
=======================================
  Coverage   76.83%   76.83%           
=======================================
  Files          15       15           
  Lines        2936     2936           
  Branches      467      467           
=======================================
  Hits         2256     2256           
  Misses        558      558           
  Partials      122      122           

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