Convert to Quarto website with multi-format support

[Copilot]

Converted from book to website template following ucdavis/win pattern. Added simultaneous HTML, DOCX, and RevealJS rendering to website profile.

Configuration

Profile-based architecture:

• _quarto.yml - profile selector (default: website)
• _quarto-website.yml - HTML + DOCX + RevealJS outputs
• _quarto-revealjs.yml - standalone slides profile
• _quarto-handout.yml - standalone PDF profile

Multi-format website rendering:

# _quarto-website.yml
format:
  html:
    # website configuration
  docx:
    # Word documents
  revealjs:
    output-file: "{stem}-slides.html"
    chalkboard: false

Per-file output specifications:
Each .qmd file includes YAML front matter to prevent filename conflicts:

---
title: "Chapter Title"
format:
  html: default
  revealjs:
    output-file: chapter-slides.html
  pdf:
    output-file: chapter-handout.pdf
  docx:
    output-file: chapter.docx
---

Single quarto render produces:

• _site/index.html - website page
• _site/index.docx - Word document
• _site/index-slides.html - presentation slides
• _site/index-handout.pdf - PDF handout

Structure Changes

• Project type: book → website
• Output directory: docs/ → _site/
• Navigation: book sidebar → navbar with dropdown menus
• Chapters: root → chapters/ subdirectory

Document Metadata

Added appendix-document-metadata.qmd included at end of all pages via {{< include >}}. Contains git commit metadata, visible only in DOCX format for version tracking.

Package Management

R packages (knitr, rmarkdown) managed by CI using setup-r-dependencies:

- uses: r-lib/actions/setup-r@v2
  with:
    use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
  with:
    packages: |
      any::knitr
      any::rmarkdown

License

Changed from CC0 to MIT License.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>convert this project to a quarto website</issue_title>
<issue_description>use https://github.com/ucdavis/win as an example</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes convert this project to a quarto website #1

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

[d-morrison]

also {{< include >}} a version of https://github.com/UCD-SERG/lab-manual/blob/main/appendix-document-metadata.qmd at the end of each website page

[Copilot]

also {{< include >}} a version of https://github.com/UCD-SERG/lab-manual/blob/main/appendix-document-metadata.qmd at the end of each website page

Added appendix-document-metadata.qmd and included it at the end of all website pages using {{< include >}} (commit 81e7aeb).

The metadata section is configured to only display in DOCX format and includes instructions for enabling automated git metadata retrieval with R/knitr.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• cloud.r-project.org
  • Triggering command: /opt/R/4.5.2/lib/R/bin/exec/R /opt/R/4.5.2/lib/R/bin/exec/R -e install.packages(c('knitr',~+~'rmarkdown'),~+~repos='REDACTED') (dns block)
  • Triggering command: /opt/R/4.5.2/lib/R/bin/exec/R /opt/R/4.5.2/lib/R/bin/exec/R -e source('renv/activate.R');~+~renv::restore(prompt~+~=~+~FALSE) 64.list ist defaults:amd64.list st rep fo/libcolord2:amquarto fo/grub-efi-amd6--version fo/crun.list fo/libharfbuzz-subset0:amd64.list fo/p�� fo/libdata-dpath-perl.list fo/libtext-wrapi18n-perl.list t-sass/src/dart e/jupyter/jupyterm fo/python3-pyasn-Rf fo/libc6-i386.li/tmp/RtmpmbCI4H t-sass/src/dart (dns block)
• packagemanager.posit.co
  • Triggering command: /opt/R/4.5.2/lib/R/bin/exec/R /opt/R/4.5.2/lib/R/bin/exec/R -e source('renv/activate.R');~+~renv::restore(prompt~+~=~+~FALSE) 64.list ist defaults:amd64.list st rep fo/libcolord2:amquarto fo/grub-efi-amd6--version fo/crun.list fo/libharfbuzz-subset0:amd64.list fo/p�� fo/libdata-dpath-perl.list fo/libtext-wrapi18n-perl.list t-sass/src/dart e/jupyter/jupyterm fo/python3-pyasn-Rf fo/libc6-i386.li/tmp/RtmpmbCI4H t-sass/src/dart (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

[d-morrison]

use https://github.com/r-lib/actions/tree/v2-branch/setup-r-dependencies in the github actions workflows instead of the setup-renv step.

to get revealjs output to work in the website profile, we'll need to add a specific output-file for each format in each chapter, like we did in https://github.com/ucdavis/win/blob/main/chapters/01-introduction.qmd for example. otherwise, the html and revealjs output files have the same names by default

[d-morrison]

add this back

[d-morrison]

use mit license