migrate: Rmd bookdown -> Quarto book

.github/workflows/publish.yml

@@ -0,0 +1,44 @@
+on:
+  workflow_dispatch:
+  push:
+    branches: main
+
+name: Quarto Publish
+
+jobs:
+  build-deploy:
+    runs-on: macOS-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install librsvg (svg for pdf)
+        run: brew install librsvg
+
+      - name: Install Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install TinyTex (pdf)
+        uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install headless chromium (mmd -> img)
+        run: quarto install chromium
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.4.0'
+
+      - name: Install R Dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -5,3 +5,5 @@ _publish.R
 _book
 _bookdown_files
 rsconnect
+/.quarto/
+.DS_Store

DESCRIPTION

@@ -1,6 +1,20 @@
-Package: placeholder
-Type: Book
-Title: Does not matter.
-Version: 0.0.1
-Imports: bookdown
-Remotes: rstudio/bookdown
+Package: docs
+Title: Documentation for Marine Energy Toolkit
+Version: 0.0.0.9000
+Authors@R: 
+    person("Ben", "Best", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-2686-0784"))
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Imports: 
+    dplyr,
+    glue,
+    here,
+    knitr,
+    librarian,
+    quarto,
+    stringr,
+    yaml

_quarto.yml

@@ -0,0 +1,54 @@
+project:
+  type: book
+  # pre-render: lib/pre-render.R
+  output-dir: _book
+  resources:
+  - "/.nojekyll"
+
+book:
+  title: "MEtkit Help"
+  subtitle: "Marine Energy Toolkit Help"
+  description: "Help documentation to set up, maintain, and use the Marine Energy Toolkit"
+  author:
+  - name: Benjamin D. Best
+    orcid: 0000-0002-2686-0784
+    email: [email protected]
+    affiliations:
+      - name: EcoQuants LLC
+        state: CA
+  date: today
+  date-format: "YYYY-MM-DD"
+  site-url: https://marineenergy.github.io/help/
+  repo-url: https://github.com/marineenergy/help/
+  repo-actions: [edit]
+  downloads: [pdf, docx]
+  sharing: [twitter, facebook, linkedin]
+  # google-analytics: "G-V3HZN14Z8G" # TODO: add Google Analytics
+  search: true
+  page-navigation: true
+  chapters:
+    - index.qmd
+    - sysadmins.qmd
+    - rtech.qmd
+    - community.qmd
+    - application.qmd
+    - summary.qmd
+    #- references.qmd
+
+bibliography: ["refs/book.bib", "refs/packages.bib"]
+bibliographystyle: apa
+link-citations: true
+
+format:
+  html:
+    theme: cosmo
+    toc: true
+    number-sections: true
+  pdf:
+    documentclass: scrreprt
+    # keep-tex: true  # for debugging
+  docx: default
+
+
+
+

mhk-env_help.Rproj → help.Rproj

@@ -9,10 +9,8 @@ UseSpacesForTab: Yes
 NumSpacesForTab: 2
 Encoding: UTF-8
 
-RnwWeave: knitr
+RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
-
-BuildType: Website

index.Rmd → index.qmd

@@ -1,23 +1,11 @@
---- 
-title: "A Minimal Book Example"
-author: "Yihui Xie"
-date: "`r Sys.Date()`"
-site: bookdown::bookdown_site
-output: bookdown::gitbook
-documentclass: book
-bibliography: [book.bib, packages.bib]
-biblio-style: apalike
-link-citations: yes
-github-repo: rstudio/bookdown-demo
-description: "This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook."
----
-# How to use the help documentation:
+# Welcome
+
+## How to use the help documentation:
 This help documentation is organized by role, including System Administrators (sysadmins), RShiny Application developers (rtech), and community users (community). Information related to corresponding workflows are located in each section of the help documentation. 
 
 For information related to server setup and location please refer to the sysadmins section of the documentation. For application development methods and existing workflows to update the application please refer to the rtech section of the help. In order to understand how to contribute to the application as a part of the user community please refer to the community section of the documentation.
 
-
-# Prerequisites
+## Prerequisites
 
 This is a _sample_ book written in **Markdown**. You can use anything that Pandoc's Markdown supports, e.g., a math equation $a^2 + b^2 = c^2$.
 

packages.bib

@@ -3,30 +3,32 @@ @Manual{R-base
   author = {{R Core Team}},
   organization = {R Foundation for Statistical Computing},
   address = {Vienna, Austria},
-  year = {2021},
+  year = {2024},
   url = {https://www.R-project.org/},
 }
 
 @Manual{R-bookdown,
   title = {bookdown: Authoring Books and Technical Documents with R Markdown},
   author = {Yihui Xie},
-  year = {2021},
-  note = {https://github.com/rstudio/bookdown},
+  year = {2024},
+  note = {R package version 0.40},
+  url = {https://github.com/rstudio/bookdown},
 }
 
 @Manual{R-knitr,
   title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
   author = {Yihui Xie},
-  year = {2021},
-  note = {R package version 1.36},
+  year = {2024},
+  note = {R package version 1.48},
   url = {https://yihui.org/knitr/},
 }
 
 @Manual{R-rmarkdown,
   title = {rmarkdown: Dynamic Documents for R},
-  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
-  year = {2021},
-  note = {https://github.com/rstudio/rmarkdown},
+  author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+  year = {2024},
+  note = {R package version 2.28},
+  url = {https://github.com/rstudio/rmarkdown},
 }
 
 @Book{bookdown2016,
@@ -35,7 +37,7 @@ @Book{bookdown2016
   publisher = {Chapman and Hall/CRC},
   address = {Boca Raton, Florida},
   year = {2016},
-  note = {ISBN 978-1138700109},
+  isbn = {978-1138700109},
   url = {https://bookdown.org/yihui/bookdown},
 }
 
@@ -58,7 +60,6 @@ @InCollection{knitr2014
   publisher = {Chapman and Hall/CRC},
   year = {2014},
   note = {ISBN 978-1466561595},
-  url = {http://www.crcpress.com/product/isbn/9781466561595},
 }
 
 @Book{rmarkdown2018,
@@ -67,7 +68,7 @@ @Book{rmarkdown2018
   publisher = {Chapman and Hall/CRC},
   address = {Boca Raton, Florida},
   year = {2018},
-  note = {ISBN 9781138359338},
+  isbn = {9781138359338},
   url = {https://bookdown.org/yihui/rmarkdown},
 }
 
@@ -77,7 +78,7 @@ @Book{rmarkdown2020
   publisher = {Chapman and Hall/CRC},
   address = {Boca Raton, Florida},
   year = {2020},
-  note = {ISBN 9780367563837},
+  isbn = {9780367563837},
   url = {https://bookdown.org/yihui/rmarkdown-cookbook},
 }
 

references.qmd

@@ -0,0 +1,4 @@
+# References {.unnumbered}
+
+::: {#refs}
+:::

refs/packages.bib

@@ -0,0 +1,83 @@
+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2021},
+  url = {https://www.R-project.org/},
+}
+
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  year = {2021},
+  note = {https://github.com/rstudio/bookdown},
+}
+
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
+  year = {2021},
+  note = {R package version 1.36},
+  url = {https://yihui.org/knitr/},
+}
+
+@Manual{R-rmarkdown,
+  title = {rmarkdown: Dynamic Documents for R},
+  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+  year = {2021},
+  note = {https://github.com/rstudio/rmarkdown},
+}
+
+@Book{bookdown2016,
+  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2016},
+  note = {ISBN 978-1138700109},
+  url = {https://bookdown.org/yihui/bookdown},
+}
+
+@Book{knitr2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {https://yihui.org/knitr/},
+}
+
+@InCollection{knitr2014,
+  booktitle = {Implementing Reproducible Computational Research},
+  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
+  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  year = {2014},
+  note = {ISBN 978-1466561595},
+  url = {http://www.crcpress.com/product/isbn/9781466561595},
+}
+
+@Book{rmarkdown2018,
+  title = {R Markdown: The Definitive Guide},
+  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2018},
+  note = {ISBN 9781138359338},
+  url = {https://bookdown.org/yihui/rmarkdown},
+}
+
+@Book{rmarkdown2020,
+  title = {R Markdown Cookbook},
+  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2020},
+  note = {ISBN 9780367563837},
+  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
+}
+

02-rtech.Rmd → rtech.qmd

@@ -2,9 +2,12 @@
 
 ## Updating dynamic content
 
-- [Interactions]: re-knit env.Rmd.
+TODO:
+
+- Interactions: re-knit env.Rmd.
 
 ### Shiny App Content Updates
+
 To render changes made to content in a Shiny app, navigate to the folder that contains the application files to run the app. Shiny apps are served from a standard folder where they are symbolically linked to source files. These folders contain the global.R, ui.R, server.R scripts that run the app.
 
 - global.R: functions used in ui.R and server.R can be defined here, sourced here from other files or in loaded libraries