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.
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Summary by CodeRabbit

• Documentation

  • Fixed misspellings and corrected upstream repository references for accuracy.
  • Reorganized sections and adjusted diagram placement for improved clarity and readability.
  • Corrected a module-level docstring naming typo.

• Chores

  • Updated development tooling configuration for the type-checking hook.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 54098eb6-0393-42e5-a5a6-431f72eb46f2

📥 Commits

Reviewing files that changed from the base of the PR and between 3bb59dc and ef6074d.

📒 Files selected for processing (3)

• .pre-commit-config.yaml
• cytotable/convert.py
• docs/source/overview.md

📝 Walkthrough

Walkthrough

Fixes several documentation typos referencing "pycytominer", reorganizes content in docs/source/overview.md by moving the "Presets and Manual Overrides" block and adjusting the "Data Sources" diagram formatting, and bumps the pre-commit mypy hook version.

Changes

Documentation and tooling updates

Layer / File(s)	Summary
Pycytominer spelling corrections cytotable/convert.py, docs/source/architecture.md, docs/source/contributing.md	Corrects misspelled project name from "pyctyominer" to "pycytominer" in the convert module docstring, architecture introduction, and contributing guide attribution URL.
Overview documentation reorganization docs/source/overview.md	Relocates the "Presets and Manual Overrides" section to after the "Pagination" section and updates the "Data Sources" mermaid diagram node label formatting to use an HTML line break (Image<br/>file(s)).
Pre-commit mypy hook bump .pre-commit-config.yaml	Updates pre-commit/mirrors-mypy hook rev from v1.16.1 to v2.1.0.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 I hopped through docs with careful paws,
I fixed a name and nudged some laws,
A diagram’s line now breaks with grace,
A section moved to find its place,
I bumped a hook and tidied the space!

🚥 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 accurately describes the primary change: fixing Pycytominer spelling errors in documentation files across multiple locations.
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.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

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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.