Fix pre-commit file

[trevorb1]

Closes #268

Changes proposed in this Pull Request

In this PR I have finished setting up pre-commit to actually perform our formatting/linting! Fixes include:

• Fix file exclusions
• Get rid of default pyupgrade if favour of this pyupgrade
• Get rid of reorder-inputs and move to isort. This is due to a conflict between reorder-inputs and Black. See this issue thread on the Black repo. This does require the addition of an .isort.cfg file

Checklist

• [x] I tested my contribution locally and it seems to work fine.
• [x] Code and workflow changes are sufficiently documented.
• [x] Changed dependencies are added to envs/environment.yaml.
• [x] Changes in configuration options are added in all of config.default.yaml.
• [x] Changes in configuration options are also documented in doc/configtables/*.csv.

[trevorb1]

@ktehranchi; this update will change quite a few files, but mainly just the import statements. If you have a large PR you are working on, can you please check if this will slot in okay before I merge it? Just want to try to avoid merge conflicts! :)

Maybe the easiest way to do this will be (but this is def just a guess):

• Pull in the newest .pre-commit-config.yaml (and .isort.cfg) files
• Install pre-commit with pip install pre-commit
• Run all file with pre-commit run --all-files

Or the other options:

• I can wait to merge this until you have merged your changes in
• I can merge this if you feel confident the import changes will be easy to manage on your end. Then we can revert if necessary.