Convert psw from a Quarto book to a qwt-template website

[d-morrison]

Converts Principles of Scientific Writing from a Quarto book into a Quarto website modeled on the d-morrison/qwt template. psw's content already used definition/example/theorem div environments; this brings in the qwt extensions that render them as styled callouts, plus multi-format output and the qwt CI suite.

Highlights

• Config: book _quarto.yml → website profile pair (_quarto.yml base + _quarto-website.yml), output to _site/. Navbar: Home · Chapters dropdown · References · GitHub.
• Structure: content pages moved into chapters/; each page gets multi-format front matter (HTML site + RevealJS slides + PDF handout + DOCX). index.qmd (Preface) and references.qmd stay at root.
• Theorem rendering: ports qwt's _extensions/ (callouty-theorem, custom-callout, div-anchors, equation-anchors, slidebreak), the reveal lua filters, styles.css/styles-reveal.scss, and the reveal light/dark toggle.
• Workflows: publish.yml/preview.yml now deploy _site/ (with R setup + freeze cache); added check-non-standard-chars, lint-changed-files, and the qwt-derived @claude agent + review workflows (these supersede the basic ones added by /install-github-app).
• Metadata: DESCRIPTION, .gitignore, .Rbuildignore, lychee.toml, .lintr.R, .gitattributes, and a psw-adapted CLAUDE.md.
• Merged main: the new paper-organization chapter is integrated into chapters/ with front matter and a navbar entry.

Verified locally (Quarto 1.9.36 / R 4.6.0)

• Full quarto render builds all 7 chapters + index/references into _site/.
• defining-terms renders #def-/#exm-/#thm- blocks as colored theorem callouts.
• A sample chapter produced all four formats (HTML, -slides.html, .docx, -handout.pdf).
• All 12 workflow YAMLs parse; publish/preview target _site/.

Notes

• The @claude bots require the CLAUDE_CODE_OAUTH_TOKEN secret — already present in this repo.
• No macros git submodule added (psw uses none).

🤖 Generated with Claude Code

[d-morrison]

@claude review

[claude]

Claude finished @d-morrison's task in 3m 42s —— View job

---

Code Review

• Gather context
• Read CLAUDE.md and repo guidelines
• Review configuration changes (_quarto.yml, _quarto-website.yml)
• Review workflow changes
• Review extensions and Lua filters
• Review content structure changes
• Post final review

---

Overall, this is a well-structured and thorough conversion. The config profile split, extension porting, multi-format front matter, and qwt workflow suite are all implemented cleanly. A few issues need attention before merging, most critically a CI check that will fail on existing content.

---

Blocking issues

1. check-non-standard-chars CI will fail immediately on existing content

chapters/citations-evidence.qmd already uses em-dashes (—) at lines 73 and 202:

provide a citation—over-citing is preferable to under-citing.
...is not optional—it is essential to scientific communication.

The new .github/workflows/check-non-standard-chars.yaml runs on pull_request targeting main, which means it will fail on this PR itself. Em-dashes are standard typographic characters in academic/scientific prose and should not be treated as errors in .qmd content.

Options:

• Remove – (en dash) and — (em dash) from NON_STANDARD_CHARS in .github/scripts/check-non-standard-chars.py — curly quotes are the real issue in .qmd/.R files, not dashes.
• Or apply the em/en-dash check only to .R files, where they'd actually break parsing.

Fix this →

---

Non-blocking issues

2. publish.yml uses quarto-dev/quarto-actions/setup@HEAD (unpinned)

Every other use of quarto-actions in this repo uses @v2 (including the render step in the same workflow and preview.yml). @HEAD means the action resolves to whatever is on the default branch of quarto-actions at run time, which could pick up breaking changes silently.

publish.yml:21:

uses: quarto-dev/quarto-actions/setup@HEAD   # ← unstable

Should match:

uses: quarto-dev/quarto-actions/setup@v2

Fix this →

3. Timezone set twice in both publish.yml and preview.yml

Both workflows set TZ: America/Los_Angeles at the job level via env: AND again in a dedicated step (echo "TZ=..." >> $GITHUB_ENV). The step is redundant when a job-level env: already sets the variable for every step. Pick one approach and remove the other.

publish.yml:13-14 and publish.yml:39-41:

env:
  TZ: America/Los_Angeles    # ← job-level
...
- name: Set timezone to Pacific Time
  run: echo "TZ=America/Los_Angeles" >> $GITHUB_ENV  # ← redundant

4. execute: and knitr: blocks duplicated across _quarto.yml and _quarto-website.yml

Both files contain identical:

execute:
  warning: false
  message: false
  cache: false
  freeze: auto
knitr:
  opts_chunk:
    collapse: true
    comment: "#>"

Since _quarto.yml is the base and _quarto-website.yml is the profile overlay, the values in _quarto.yml are already inherited unless overridden. The duplication in _quarto-website.yml is harmless but creates a maintenance hazard — updating one but not the other would cause a silent mismatch. Consider removing the duplicate block from _quarto-website.yml unless you intentionally want the profile to win.

5. index.qmd still says "This book"

index.qmd:18:

"This book will present my perspective on scientific writing..."

After the conversion to a website, this should read "This website will present..." (or "This guide will present..." for format-neutral language).

Fix this →

6. chapters/intro.qmd is an empty placeholder

The file has only a YAML front matter block and no body content. It will render as a blank page in the navbar. Either add stub content or mark it draft: true in the front matter until it's filled in.

7. styles.css contains large commented-out template boilerplate

styles.css lines 1–38 are commented-out template examples (heading colors, paragraph margins, code blocks, callouts). These appear to be copy-paste artifacts from a starter template. They add ~40 lines of noise with no functional value. Fine to keep if there's intent to uncomment them, but otherwise worth trimming.

---

Minor observations

• _quarto-website.yml render exclusion "!README.md": There is currently no README.md at the repo root, so this exclusion is a no-op. It's a forward-looking guard (fine), but could mislead someone checking why a file isn't rendering.

• appendix-document-metadata.qmd: Has 4–5 trailing blank lines after the closing ::: (lines 39–43). Not a build issue but minor.

• _quarto-website.yml global filters include RevealJS-specific Lua: revealjs-level1-slide-breaks.lua and revealjs-html-links.lua run for all formats via the base filters: list in _quarto.yml. As long as those filters guard on FORMAT == "revealjs" internally, this is fine — worth a quick sanity check if PDF/DOCX output ever behaves unexpectedly.

• DESCRIPTION: RoxygenNote: 7.3.3 is present — this is typically auto-updated by devtools::document(). Fine to leave; just make sure roxygen2 >= 7.3.3 is available in the CI where devtools::document() runs.

---

Suggested follow-up @claude prompt

@claude address review comments in [this review](https://github.com/d-morrison/psw/pull/28)

[d-morrison]

Claude Code CLI (local session) is working on this — paws off until I'm done.

[d-morrison]

Addressed the review (commit ff7f5d7).

Blocking

• avoid vague and metaphorical language #1 em-dash CI failure — removed the en-dash (U+2013) and em-dash (U+2014) entries from NON_STANDARD_CHARS in .github/scripts/check-non-standard-chars.py (plus docstring/report text). They're valid prose characters; curly quotes are still flagged. Verified the checker now passes (exit 0) on the existing content, including the em-dashes in chapters/citations-evidence.qmd.

Non-blocking — all fixed

• #2 publish.yml: pinned quarto-actions/setup @HEAD → @v2.
• read, summarize, and link #3 removed the redundant Set timezone step in both publish.yml and preview.yml (job-level env: TZ already covers all steps).
• citation(s) are needed for every claim, unless you provide direct evidence #4 removed the duplicated execute:/knitr: blocks from _quarto-website.yml (inherited from base _quarto.yml).
• copy-paste with caution #5 index.qmd: "This book" → "This website".
• incorporate "On Writing" #6 chapters/intro.qmd: marked draft: true (empty placeholder).
• incorporate Elements of Style #7 styles.css: trimmed commented-out starter-template boilerplate.

Minor observations

• Trailing blank lines trimmed in appendix-document-metadata.qmd.
• !README.md render exclusion: left as a forward-looking guard (your note).
• RevealJS Lua filters: confirmed both revealjs-level1-slide-breaks.lua and revealjs-html-links.lua guard on FORMAT == "revealjs" and early-return otherwise — safe for PDF/DOCX.
• DESCRIPTION RoxygenNote: left as-is per your note.

@claude review

[claude]

Claude finished @d-morrison's task in 1m 8s —— View job

---

Code Review (follow-up)

• Gather context
• Read CLAUDE.md and repo guidelines
• Review commit ff7f5d7 (review feedback addressed)
• Verify each blocking/non-blocking issue from previous review
• Post final review

---

All items from the previous review are correctly addressed in commit ff7f5d7. Verified each fix against the current branch state:

#	Issue	Fix	Verified
1 (blocking)	check-non-standard-chars CI failure on em-dashes	En/em dashes removed from NON_STANDARD_CHARS; docstring updated to explain the intentional exclusion	✅
2	publish.yml unpinned @HEAD	Changed to @v2	✅
3	Redundant timezone step in both workflows	Step removed from publish.yml and preview.yml; job-level env: TZ remains	✅
4	Duplicate execute:/knitr: in _quarto-website.yml	Blocks removed; replaced with a comment noting they're inherited from base	✅
5	index.qmd still said "This book"	Changed to "This website"	✅
6	chapters/intro.qmd empty placeholder	draft: true added to front matter	✅
7	styles.css commented-out boilerplate	Trimmed to a single descriptive header comment	✅
(minor)	Trailing blank lines in appendix-document-metadata.qmd	Cleaned; file now ends cleanly after the closing :::	✅

No new issues introduced by ff7f5d7. The commit is clean — surgical changes only, no unrelated modifications.

This PR is ready to merge.

[github-actions]

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