Improve tutorial preset documentation

[d33bs]

Description

This PR seeks to improve tutorial preset documentation, especially when it comes to data and column management. It was inspired by comments from @kate-bowers-broad.

References #425

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 read the CONTRIBUTING.md guidelines.
• My code follows the style guidelines of this project.
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• I have made corresponding changes to the documentation.
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• I have added tests that prove my fix is effective or that my feature works.
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Summary by CodeRabbit

• Documentation
  • Expanded overview and tutorial docs with step‑by‑step guidance and examples for overriding preset join SQL to control which columns appear in final joined outputs, plus advice and checks for validating and adjusting exported files.
• Chores
  • Updated tooling configuration (pre‑commit hook) to a newer helper version.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 494c8957-2729-4bba-b13b-2e7ca4184639

📥 Commits

Reviewing files that changed from the base of the PR and between 9d3db1e and 9ca6504.

📒 Files selected for processing (2)

• docs/source/overview.md
• docs/source/tutorials/cellprofiler_to_parquet.md

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

• docs/source/overview.md

🚧 Files skipped from review as they are similar to previous changes (1)

• docs/source/tutorials/cellprofiler_to_parquet.md

---

📝 Walkthrough

Walkthrough

Updated documentation to explain that presets determine join SQL and how to override it via joins= in cytotable.convert() (with an example editing the SELECT list). Also bumped the vulture pre-commit hook from v2.15 to v2.16.

Changes

Cohort / File(s)	Summary
Documentation: preset join SQL & examples docs/source/overview.md, docs/source/tutorials/cellprofiler_to_parquet.md	Added explicit guidance that presets control the final join SQL and that users can override it by passing joins="SELECT ..." to cytotable.convert(). Included a concrete example showing how to derive custom_joins from cytotable.presets.config[PRESET]["CONFIG_JOINS"], modify the SELECT list (e.g., replace image.Metadata_ImageNumber, with image.*,), and pass it to convert(); expanded notes about related parameters (page_keys, chunk_size, compartment names) and fixed a Markdown code-fence.
Tooling: pre-commit hook version bump .pre-commit-config.yaml	Updated the vulture pre-commit hook version from v2.15 to v2.16 (no other changes).

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 I nibble rows and tweak the SELECT,
I swap a field with gentle inspect.
A custom JOIN, a tidy Parquet bed,
Columns pruned neat, no surprises ahead. 🥕

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately reflects the primary changes: documentation improvements focused on preset management in tutorials, covering override guidance and column control examples.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

docs/source/tutorials/cellprofiler_to_parquet.md (1)

131-136: Fix fenced block closures to avoid markdownlint/rendering issues.

The fence closers are inconsistent (Line 131 and Line 152 use four backticks for inner 3-backtick blocks), which is likely causing the MD040 warning on Line 136.

Suggested markdown fence cleanup

-````
+```
...
-````
+```

Also applies to: 152-152

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@docs/source/tutorials/cellprofiler_to_parquet.md` around lines 131 - 136, The
fenced code blocks that surround the paragraph "This is the main way to
customize which columns are included in the joined output while still reusing
the rest of the preset." use inconsistent closing fences (four backticks) and
should be changed to match the inner triple-backtick blocks; update the closing
fences around that block and the similar block later (the one around the inner
``` examples) so that all outer fences use three backticks to properly open and
close the inner 3-backtick code examples and resolve the MD040/rendering issue.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@docs/source/tutorials/cellprofiler_to_parquet.md`:
- Around line 118-121: Replace the hardcoded preset key in the example so it
uses the active preset variable instead of "cellprofiler_csv": update the
snippet that references config["cellprofiler_csv"] to use config[PRESET] (or the
actual preset variable name used elsewhere in the document) so that CUSTOM_JOINS
are pulled from the currently selected preset; ensure the PRESET (or preset)
identifier is the same symbol used earlier in the tutorial.

---

Nitpick comments:
In `@docs/source/tutorials/cellprofiler_to_parquet.md`:
- Around line 131-136: The fenced code blocks that surround the paragraph "This
is the main way to customize which columns are included in the joined output
while still reusing the rest of the preset." use inconsistent closing fences
(four backticks) and should be changed to match the inner triple-backtick
blocks; update the closing fences around that block and the similar block later
(the one around the inner ``` examples) so that all outer fences use three
backticks to properly open and close the inner 3-backtick code examples and
resolve the MD040/rendering issue.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: a5820013-01b1-45cb-88f7-dd9b977e168f

📥 Commits

Reviewing files that changed from the base of the PR and between 6a1aeb1 and 5ba5e54.

📒 Files selected for processing (2)

• docs/source/overview.md
• docs/source/tutorials/cellprofiler_to_parquet.md

[gwaybio]

LGTM!

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@docs/source/tutorials/cellprofiler_to_parquet.md`:
- Around line 135-144: The example output shown for print(custom_joins) is
inconsistent with the preceding code (missing COLUMNS(...), EXCLUDE(...), JOINs
and WHERE clauses); update the docs so the printed SQL either matches the actual
preset SQL (provide a faithful truncated excerpt from the real output) or
explicitly mark the block as abbreviated/pseudocode (e.g., prepend "Abbreviated
output:" or "Truncated for brevity:"); locate the mention of print(custom_joins)
in the tutorial and replace the current SQL block with the faithful truncated
output or a clear label indicating it is not the full SQL.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 94e08b38-58eb-4e81-b1e1-ee246165e1a2

📥 Commits

Reviewing files that changed from the base of the PR and between 4d7c6d3 and 9d3db1e.

📒 Files selected for processing (3)

• .pre-commit-config.yaml
• docs/source/overview.md
• docs/source/tutorials/cellprofiler_to_parquet.md

✅ Files skipped from review due to trivial changes (2)

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