refactor: update ruff to 0.3.4

[kenibrewer]

Description

This updates ruff to the latest version and applies the formatting to pycytominer repo. This set of changes are formatting/whitespace only.

What is the nature of your change?

• [ ] Bug fix (fixes an issue).
• [ ] Enhancement (adds functionality).
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected).
• [ ] This change requires a documentation update.

Checklist

Please ensure that all boxes are checked before indicating that a pull request is ready for review.

• [x] I have read the CONTRIBUTING.md guidelines.
• [x] My code follows the style guidelines of this project.
• [x] I have performed a self-review of my own code.
• [x] I have commented my code, particularly in hard-to-understand areas.
• [x] I have made corresponding changes to the documentation.
• [x] My changes generate no new warnings.
• [x] New and existing unit tests pass locally with my changes.
• [x] I have added tests that prove my fix is effective or that my feature works.
• [x] I have deleted all non-relevant text in this pull request template.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 94.96%. Comparing base (af5a4ef) to head (3c5eafd). Report is 2 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #386 +/- ## ======================================= Coverage 94.96% 94.96% ======================================= Files 56 56 Lines 3137 3137 ======================================= Hits 2979 2979 Misses 158 158 ``` | [Flag](https://app.codecov.io/gh/cytomining/pycytominer/pull/386/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/cytomining/pycytominer/pull/386/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining) | `94.96% <100.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining#carryforward-flags-in-the-pull-request-comment) to find out more.

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