feat(all): add ruff as default linter and additional clean up

[spencer-tb]

🗒️ Description

Adds ruff as our default lint/format/import checker replacing flake8, black & isort.
Extra clean-up items are mentioned below.

From this point onwards we should strictly make sure our code adheres to the best Python standards.

🧑‍💻 .vscode

The settings.recommended.json has be split into 2 files:

• settings.json: locked config that users of the repo MUST use.
• .settings.local.recommended.json: settings that users can change, for example python testing extension related.

💥 Removal of tf

It seems relevant for us to deperate tf now. Most repo users are familiar with the uv fill etc approach now.

📜 Ruff Related Docstring Changes

A large portion of the diff comes from changes to the python docstrings, via:

One-line docstring should fit on one lineRuff D200
First line of docstring should be in imperative mood: "Handles all fill CLI flag pre-processing."Ruff D401
First line should end with a periodRuff D400

With a new linter its seems logical to enforce python docstring standards from now on. Note the warnings appear within VSCode and additionally when running tox. This required a lot of manual intervention to update our docstrings to use imperative mood.

🔑 Key Notes & Checks

• Filling for Cancun with EELS returns the same index.json root hash as upstream/main.
• Tox passes locally & in CI for tests, framework and docs.
• Nothing else has been checked by me.

🔗 Related Issues

• chore: replace flake8, flake8-spellcheck, isort and black with ruff and codespell

☑️ Remaining Todos

• Investigate all new mypy errors when running uv run mypy src/tests locally.
  • Note these don't exist when running mypy within a tox run, its a similar behaviour to main just with more errors.
• Update src/cli/gentest/source_code_generator.py to use ruff instead of black.
  • Tagging: (gentest): Update source code formatter #942
• Add codespell for spell checking. Note this PR removes fname8.
• Remove all the noqa: and type: ignore adding appropriate solutions.

✅ Checklist

• All: Set appropriate labels for the changes.
• All: Considered squashing commits to improve commit history.
• All: Added an entry to CHANGELOG.md.
• All: Considered updating the online docs in the ./docs/ directory.

[marioevz]

@spencer-tb could we rebase this to main please? I think it would make it easier to spot issues in the CI if we include the fixes from #905

[spencer-tb]

Some comments:

1. I have only tested out filling. We get the same index root hash as main. It would be nice for others to test out consume, execute and other clis.
2. Tox passes tests/framework/docs for me locally and in the CI with the new changes. 😄
3. I noticed that running mypy locally outside of tox gave me a lot of errors. These errors are not flagged during tox runs. This is a similar behaviour to main, however with the ruff changes there are substantially more. I think this is okay but its worth looking into.

Quoting the remaining todo's here:

• Investigate all the new mypy error when running uv run mypy src/tests locally.
  • Not these don't exist when running tox locally but its a similar behaviour to main just more errors.
• Update src/cli/gentest/source_code_generator.py to use ruff instead of black.
  • Tagging: (gentest): Update source code formatter #942
• Add codespell for spell checking.
• Remove all the noqa: and type: ignore adding an appropriate solution.

[marioevz]

Amazing job!

I will rebase, and double-check on the --fix/--no-fix parameters, then merge.