test: run lint/format/type checks on entire repo

[ajbozarth]

Misc PR

Type of PR

• Bug Fix
• New Feature
• Documentation
• Other

Description

• Link to Issue: Fixes tests: pre-commit does not run linting and mypy on tests and examples #370

This updates the pre-commit to run linting, formatting, and mypy on the entire repo instead of just certain directories>

This is to bring it in line with the update dev docs in #369

Two future TODOs were added in the config where certain files or error were temporarily ignored

Testing

• Tests added to the respective file if code was changed
• New code has 100% coverage if code as added
• Ensure existing tests and github automation passes (a maintainer will kick off the github automation when the rest of the PR is populated)

[github-actions]

The PR description has been updated. Please fill out the template for your PR to be reviewed.

[mergify]

Merge Protections

Your pull request matches the following merge protections and will not be merged until they are valid.

🟢 Enforce conventional commit

Wonderful, this rule succeeded.

Make sure that we follow https://www.conventionalcommits.org/en/v1.0.0/

• title ~= ^(fix|feat|docs|style|refactor|perf|test|build|ci|chore|revert|release)(?:\(.+\))?:

[psschwei]

let's do issues rather than todo comments ?

[ajbozarth]

let's do issues rather than todo comments ?

I always open Issues for each TODO I add in code when working on projects. Personally I like having TODO comments in code for stubbed features and ignored warnings/errors as long as they are mirrored in issues to address them. In jupyterlab they even add the issue url to the TODO to cross reference, I'm open to that, I just was unsure if we'd merge this before addressing them or not

[ajbozarth]

I ended up just taking a shot at fixing the mypy errors in docs/ in e70c319

It will need a detailed look to make sure I didn't change any examples in a way that changes their intent.

[psschwei]

I don't have strong opinions on linting the whole repo (I could be persuaded either way), would be good for other @generative-computing/mellea-contributors to weigh in