Fix Pycytominer spelling in docs

[gwaybio]

Description

I fixed spelling of "Pycytominer" in a few prominent places. I also rearranged overview.md to introduce the concept of "presets" after describing the tool.

We probably should include an entirely new section on presets (or at least point to where presets are located for someone to actually view what is there)

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

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• 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.
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Summary by CodeRabbit

• Documentation

  • Corrected terminology and attribution references across docs
  • Added "Presets and Manual Overrides" section to the overview
  • Improved diagram formatting for readability
  • Fixed a module docstring typo

• Chores

  • Updated pre-commit hook versions (maintenance updates)

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📝 Walkthrough

Walkthrough

This PR fixes a misspelled reference to "pycytominer" in a module docstring and documentation, updates a mermaid diagram to use HTML line breaks, and adds a "Presets and Manual Overrides" section pointing to convert().

Changes

Documentation and Spelling Corrections

Layer / File(s)	Summary
Pycytominer spelling corrections cytotable/convert.py, docs/source/architecture.md, docs/source/contributing.md	Fixes misspelled references to "pycytominer" in the module-level docstring, architecture documentation introduction, and contributing guide upstream attribution link.
Overview documentation enhancements docs/source/overview.md	Changes mermaid flowchart node labels to use HTML <br/> line breaks and adds a new "Presets and Manual Overrides" section describing presets and how to use manual overrides via convert().
Pre-commit hooks .pre-commit-config.yaml	Bumps psf/black from 26.3.1 to 26.5.1 and jsh9/pydoclint from 0.8.3 to 0.8.4.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Poem

🐇 I hopped through docs at break of dawn,
Fixed a name that wandered on,
Br tags tidy the diagram’s view,
Presets and overrides point to you,
Happy code, and a carrot too!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title directly addresses the primary change: correcting Pycytominer spelling errors across multiple documentation files.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@docs/source/overview.md`:
- Around line 311-319: The file ends without a final newline which breaks the
end-of-file-fixer hook; open the docs/source/overview.md file (look for the "##
Presets and Manual Overrides" section or the closing code block) and add a
single newline character at the end of the file so the file ends with a trailing
newline, then save and commit.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 9a8f7a9b-6d0e-4bfc-ac5f-224a145e397c

📥 Commits

Reviewing files that changed from the base of the PR and between 5b8baf3 and a268883.

📒 Files selected for processing (4)

• cytotable/convert.py
• docs/source/architecture.md
• docs/source/contributing.md
• docs/source/overview.md

[gwaybio]

Looks like #452 has the same mypy version precommit issue I'm trying to address in 3bb59dc

[d33bs]

Thanks @gwaybio ! Sorry about the merge conflict caused by an earlier PR merge.

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@docs/source/overview.md`:
- Around line 366-374: The duplicate section heading "## Presets and Manual
Overrides" repeats an existing top-level anchor and causes MD024; remove or
rename this duplicated heading in the shown eval-rst block and keep the content
(or convert it to a paragraph/list) so anchors are unique; if you rename the
heading choose a distinct title (e.g., "Presets Overview" or "Using Presets")
and ensure references to presets.config and convert() (:data:`presets.config
<cytotable.presets.config>`, :mod:`convert() <cytotable.convert.convert>`) still
make sense after the change.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 43306717-3ea6-4dec-a1e8-efe66bb062b4

📥 Commits

Reviewing files that changed from the base of the PR and between 3bb59dc and 06a74bb.

📒 Files selected for processing (2)

• cytotable/convert.py
• docs/source/overview.md

✅ Files skipped from review due to trivial changes (1)

• cytotable/convert.py

[gwaybio]

merging this in @d33bs ! I reverted to changes you made in #427 (including keeping the section at the top). Tests pass, going to merge this in!