chore: Move to using Ruff for pre-commit

[henryiii]

Description

This moves the flake8 & pyupgrade checks into a single Ruff check, and moves the config to pyproject.toml. There are a lot of checks that could be added (see https://scikit-hep.org/developer/style#ruff), I've just stuck to replicating the current config. The one loss is flake8-encodings, someone could request this added to Ruff.

I've skipped the failing checks for notebooks, might be worth checking to see if they are valid.

Checklist Before Requesting Reviewer

• Tests are passing
• "WIP" removed from the title of the pull request
• Selected an Assignee for the PR to be responsible for the log summary

Before Merging

For the PR Assignees:

• Summarize commit messages into a comprehensive review of the PR

* Drop flake8, yesqa, pyupgrade, and nbqa-pyupgrade pre-commit hooks in favor of Ruff.
   - Remove .flake8 config file as no longer used.
   - Remove nbqa config options for pyupgrade in pyproject.toml and add ruff config options.

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (49c116e) 98.30% compared to head (1d2d271) 98.30%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2124   +/-   ##
=======================================
  Coverage   98.30%   98.30%           
=======================================
  Files          69       69           
  Lines        4531     4531           
  Branches      645      645           
=======================================
  Hits         4454     4454           
  Misses         45       45           
  Partials       32       32           

Flag	Coverage Δ
contrib	97.88% <100.00%> (ø)
doctest	61.15% <0.00%> (ø)
unittests-3.10	96.31% <100.00%> (ø)
unittests-3.8	96.33% <100.00%> (ø)
unittests-3.9	96.35% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/pyhf/cli/spec.py	100.00% <100.00%> (ø)

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[henryiii]

I've opened an issue about flake8-encodings in astral-sh/ruff#3278.

[matthewfeickert]

Thanks for this PR @henryiii and sorry that I'm so slow in getting to it.

I've skipped the failing checks for notebooks, might be worth checking to see if they are valid.

Which checks are these? It looks like everything is passing. Or am I missing something that you are now skipping in the PR?

[matthewfeickert]

A note to self, the reason this is safe to remove is that the option was deprecated in v1.0.0. c.f. https://github.com/nbQA-dev/nbQA/blob/26f3ce04cd29bdfcda487fefdbae78925e80a5ff/nbqa/cmdline.py#L37