[d-morrison]

Completes the heading promotion started in #569, #570 and #571. number-sections: true numbers by heading level and the page title is not a numbered level, so a body that starts at ## numbers its sections 0.1, 0.2. Those three PRs promoted the pages and some fragments, which left the included section subfiles at ## and gave pages sections at two levels (the review of #569 found this).

This PR (1 of 3 for the subfiles) moves the algebra, calculus and indicator section headings up one level (## to #, ### to ##). Div titles stay at ####. It also sets the revealjs shift-heading-level-by to 1, so each # section is one slide as before; every mds page is promoted once this set of PRs lands.

Checked with a script that expands includes and reports any page that starts below level 1 or skips a level: it reports none for all pages with #569 to #571 and this set of PRs applied. Rendered algebra-basics.qmd to HTML (sections number 1 to 6) and to revealjs (6 h2 slides).

The set (#569, #570, #571, and the three subfile PRs) is one change and is meant to merge together. Each alone leaves mixed levels.

---

Generated by Claude Code

[github-actions]

Claude finished review — View run

---

Review of PR #582 at 7ee3696

This round covers the one new commit, 7ee3696 ("Move the indicator section out of this PR"). It reverts the ### to ## demotions in _subfiles/indicator-functions/_sec-indicator-functions.qmd. That diff against base is now empty, so my earlier blocking finding 2 is resolved.

I traced the heading levels by reading the files and did not render the site. The diff adds or changes no math, so the macro check does not apply.

Still open from the prior review (2026-11-02, commit 1d37f33):

1. Blocking: _quarto-website.yml:352. shift-heading-level-by: 1 still applies to every reveal.js page on the site.

   • Several pages this PR does not touch still start their sections at ##. They are functions.qmd:16, _functions.qmd:204, _sets.qmd:126, _sets.qmd:194, algebra.qmd and calculus.qmd.
   • In reveal.js those headings are shifted to level 3. With slide-level: 2 they no longer start a slide, so they fold into the previous slide.
   • Only the split-page subfiles were promoted to # to compensate.
   • Either scope the shift to the split pages, or promote the remaining pages in the same PR. Render a few unedited decks, such as functions-slides and sets-slides, to confirm.

2. Blocking: _algebra.qmd:9-13 and algebra.qmd:41. The headings in the combined pdf, docx and reveal.js output are now mixed.

   • _subfiles/_sec_algebra_basics.qmd, _sec_algebra_sums.qmd and _sec_algebra_exponentials.qmd are now #.
   • Their siblings in the same combined document stay ##: ## Cosine and sine and ## Complex numbers in _algebra.qmd, and ## Further reading in algebra.qmd.
   • In the PDF, "Equalities" and "Polynomials" become chapter-level while "Cosine and sine" and "Further reading" stay section-level.
   • In reveal.js, "Cosine and sine" and "Complex numbers" shift to level 3 and stop starting slides, while the algebra sections shift to level 2 and do start them.
   • The calculus page has the same split. _subfiles/_sec_calculus_*.qmd are #, but calculus.qmd:38 ## Further reading {#sec-additional-resources} stays ##.
   • Promote the leftover wrappers and Further reading to #, or demote the subfiles.

Suggestion

3. _calc-derivatives.qmd and _calc-integrals.qmd. These were demoted from ### to ##.
   • Their wrapper is now # Derivatives or # Integration, so the hierarchy is consistent.
   • The HTML section numbers (number-sections: true, number-depth: 2) change, for example from 1.1 to 1.
   • @sec- cross-reference text will render with the new numbers. The ids are unchanged, so URL anchors are safe.
   • The PR description should say this.

Verdict

Needs more work. The indicator-functions concern is resolved. The site-wide reveal.js shift and the mixed heading levels in the combined algebra and calculus outputs remain.

@claude address review comments in [this review](https://github.com/Morrison-Lab/mds/pull/582)

Structured Review Data (JSON)

{
  "schema_version": "1.1",
  "reviewer": "claude",
  "commit_sha": "7ee3696772f1b8a6dcb2ad8f63f21fccba5122ba",
  "verdict": "NOT_CLEAN",
  "findings": [
    {"file": "_quarto-website.yml", "line": 352, "category": "bug", "message": "shift-heading-level-by: 1 applies to every revealjs page; untouched pages with ## sections (functions, sets, algebra and calculus Further reading) drop to level 3 and stop starting slides under slide-level: 2."},
    {"file": "_algebra.qmd", "line": 9, "category": "bug", "message": "Subfiles promoted to # while sibling ## Cosine and sine, ## Complex numbers and ## Further reading stay ##, giving mixed levels in pdf, docx and revealjs combined output; same for calculus.qmd Further reading."}
  ],
  "detailed_assessment": "The indicator-functions subfile is now reverted to base, resolving the earlier flat-hierarchy finding, but the global revealjs shift still demotes untouched ## sections and _algebra.qmd mixes # and ## headings.",
  "holistic_assessment": "The promotion is applied unevenly across includers and the site-wide shift setting, so slide decks and combined algebra and calculus outputs risk regressions that need rendering to validate."
}

Reviewed commit: 7ee3696

[github-actions]

💰 Cost: $0.2680 (review) — run

[github-actions]

PR Preview Action v1.8.1
Preview removed because the pull request was closed.

_{2026-11-02 21:48 UTC}