Devops cleanup

[gwaybio]

I made several quality of life changes (e.g., one sentence per line, cleaning up docs) without adding functionality (erring on the side of subtraction [e.g., dropping just])

What kind of change(s) are included?

• Documentation (changes docs or other related content)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

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• I have read and followed the CONTRIBUTING.md guidelines.
• I have searched for existing content to ensure this is not a duplicate.
• I have performed a self-review of these additions (including spelling, grammar, and related).
• These changes pass all pre-commit checks.
• I have added comments to my code to help provide understanding
• I have added a test which covers the code changes found within this PR
• I have deleted all non-relevant text in this pull request template.

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📚 Documentation preview 📚: https://zedprofiler--44.org.readthedocs.build/en/44/

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✅ All modified and coverable lines are covered by tests.
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Additional details and impacted files

@@           Coverage Diff           @@
##             main      #44   +/-   ##
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  Coverage        ?   92.48%           
=======================================
  Files           ?       15           
  Lines           ?     1344           
  Branches        ?        0           
=======================================
  Hits            ?     1243           
  Misses          ?      101           
  Partials        ?        0           

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[gwaybio]

One thing I didn't touch in this PR is the partial CLI functionality - we can probably skip this for now

[d33bs]

This seems like a helpful DevEx file we might want to keep. If you don't think the justfile is helpful as a format, maybe we port to a Makefile or poethepoet configuration?

[gwaybio]

as it was, the justfile setup was incompletely documented - unclear how/when to use, especially in the context of uv. My thought in this PR was to err toward subtraction, and that you would introduce any specific devex/ops cleanly, in the future (with a bias toward making decisions that expedite processing)

[d33bs]

Consider making the import here absolute to the package rather than relative. Generally, this is a practice that makes the import order more explicit and harder to ignore/forget about.

[gwaybio]

thanks! good point. I was matching conventions in this project, updated to absolute imports everywhere in e06341f