ci: add pre-commit-update and related updates

[d33bs]

Description

While working on #506 I noticed that I needed to update actionlint in order to effectively pass checks by pre-commit. This made me wonder if there were other updates we could apply with pre-commit-update. I added that as a check to the pre-commit configuration, then applied the updates. Afterwards I applied changes which helped meet the new standards from the checks within the updated configuration.

Should be merged after #505

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.

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

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 95.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 94.44%. Comparing base (bf375ba) to head (a475d14).

Files with missing lines	Patch %	Lines
pycytominer/cyto_utils/cell_locations.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #507      +/-   ##
==========================================
- Coverage   94.44%   94.44%   -0.01%     
==========================================
  Files          57       57              
  Lines        3188     3186       -2     
==========================================
- Hits         3011     3009       -2     
  Misses        177      177              

Flag	Coverage Δ
unittests	94.44% <95.00%> (-0.01%)	⬇️

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

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[gwaybio]

Likely also should be merged after #506

[gwaybio]

Sometimes linting changes to .ipynb files are wonky and inappropriate. Just double-clicking here to see if these changes are intentional

[d33bs]

Thanks - this slightly changed some of the formatting but in general the notebook looked sound. I'll do a triple-check here to see if I can run the notebook.