migrate to Quarto qmd #266

.github/workflows/render_book.yml

@@ -0,0 +1,73 @@
+name: Render Quarto book
+
+on:
+  push:
+     branches: 
+       - main
+  workflow_dispatch:
+
+jobs:
+  bookdown:
+    name: Render & publish Quarto book
+    runs-on: macOS-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+
+      - name: Install Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          tinytex: true  # for pdf
+
+      - name: Install librsvg (svg for pdf)
+        run: brew install librsvg
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.4.1'     # 2024-09-04
+
+      - name: Install R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+
+      - name: Render and Publish
+        # TODO: `quarto publish gh-pages` https://quarto.org/docs/publishing/github-pages.html#publishing
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+
+
+# Need to first create an empty gh-pages branch
+# see https://pkgdown.r-lib.org/reference/deploy_site_github.html
+# and also add secrets for a GH_PAT and EMAIL to the repository
+# gh-action from Cecilapp/GitHub-Pages-deploy
+
+  checkout-and-deploy:
+    runs-on: ubuntu-latest
+    needs: bookdown
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+
+      - name: Download artifact
+        uses: actions/download-artifact@v4
+        with:
+          # Artifact name
+          name: _book # optional
+          # Destination path
+          path: 'bio-data-guide/docs' # see _bookdown.yml: output_dir
+
+

.gitignore

@@ -1,3 +1,5 @@
-/bio-data-guide/docs
-/bio-data-guide/bio-data-guide.rds
-.Rproj.user
+/_book
+.Rproj.user
+/.quarto/
+.DS_Store
+.Rhistory

DESCRIPTION

@@ -11,4 +11,26 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Imports: 
-    bookdown
+    bookdown,
+    dm,
+    glue,
+    here,
+    httr,
+    leaflet,
+    librarian,
+    lubridate,
+    mapdata,
+    obistools (>= 0.1.0),
+    rmarkdown,
+    rnoaa (>= 1.4.0),
+    sf,
+    stringr,
+    terra,
+    tidync,
+    vroom,
+    worms,
+    worrms,
+    xfun
+Remotes: 
+    ropensci/rnoaa,
+    iobis/obistools

README.md

@@ -1,3 +1,15 @@
+# BioDataGuide
+
+Hello and welcome to the Darwin Core Marine Example Compendium! (We're calling it the BioDataGuide for short.) Here, we document relevant resources and standards 
+which apply to various marine biological data types. This is a growing guide that is put together by scientists and 
+data managers responsible for transforming their data to meet international standards.
+
+This guide is meant for  data managers, scientists, or technicians new to transforming/publishing/mobilizing data. 
+There is a general introduction to the world of international data integration, followed by some specific examples of 
+data transformations.
+
+To contribute to this guide see (CONTRIBUTING.md)[https://github.com/ioos/bio_data_guide/blob/master/Standardizing%20Marine%20Biological%20Data/CONTRIBUTING.md]
+
 # Standardizing Marine Biological Data Working Group (SMBD)
 
 ## Purpose
@@ -96,7 +108,7 @@ This is a work in progress, a growing guide that is being put together by scient
 The Guide is exported into multiple formats, including a [pdf](https://github.com/ioos/bio_data_guide/raw/gh-pages/darwin-core-guide.pdf) and an [epub](https://github.com/ioos/bio_data_guide/raw/gh-pages/darwin-core-guide.epub) document. 
 Chapters are written in R Markdown files; [contributions are welcome!](https://github.com/ioos/bio_data_guide/blob/main/CONTRIBUTING.md)
 
-Technical details of how to work with the book can be found in [`/building-the-data-guide.md`](https://github.com/ioos/bio_data_guide/blob/main/building-the-guide.md).
+Technical details of how to work with the book can be found in [`/refs/building-the-data-guide.md`](https://github.com/ioos/bio_data_guide/blob/main/refs/building-the-guide.md).
 
 <!--
 

_quarto.yml

@@ -0,0 +1,65 @@
+project:
+  type: book
+  pre-render: lib/pre-render.R
+  output-dir: _book
+  resources:
+  - "/.nojekyll"
+
+book:
+  title: "BioDataGuide"
+  subtitle: "Darwin Core Marine Example Compendium"
+  description: "Scaling multiple dimensions of diversity in biological data"
+  author: 
+    - "By: [Standardizing Marine Biological Data Working Group](https://github.com/ioos/bio_data_guide/graphs/contributors)"
+    - "![](figs/contrib.rocks.svg)"
+  date: today
+  date-format: "YYYY-MM-DD"
+  site-url: https://ioos.github.io/bio_data_guide/
+  repo-url: https://github.com/ioos/bio_data_guide/
+  repo-actions: [edit]
+  downloads: [pdf, docx, epub]
+  sharing: [twitter, facebook, linkedin]
+  # google-analytics: "G-V3HZN14Z8G" # TODO: add Google Analytics
+  search: true
+  page-navigation: true
+  chapters:
+    - index.qmd
+    - intro.qmd
+    - part: apps.qmd
+      chapters:
+        - datasets/TPWD_HARC_BagSeine/TPWD_HARC_BagSeine_OBISENV.qmd
+        - datasets/hakai_salmon_data/salmon-darwin-core-remap.qmd
+        - datasets/hakai_seagrass_data/hakaiSeagrassToDWC.qmd
+        - datasets/trawl_catch_data/trawl-catch-data.qmd
+        - datasets/dataset-edna/README.md
+        - datasets/atn_satellite_telemetry/atn_satellite_telemetry_netCDF2DwC.qmd
+  appendices:
+    - faq.qmd
+    - tools.qmd
+    - extras.qmd
+    - references.qmd
+
+bibliography: ["lib/book.bib", "lib/packages.bib", "lib/OBIS_data_examples.bib"]
+bibliographystyle: apa
+link-citations: true
+
+format:
+  html:
+    theme: cosmo
+    css: lib/style.css
+    toc: true
+    number-sections: true
+  pdf:
+    documentclass: scrreprt
+    # keep-tex: true  # for debugging
+    include-in-header: lib/preamble.tex
+    nocite: |
+      @*
+  docx:
+    toc: true
+    number-sections: true
+    highlight-style: github
+  epub: default
+
+
+

apps.qmd

@@ -0,0 +1,6 @@
+# Applications
+
+This chapter contains a series of example applications to convert source data to the Darwin Core standard. You can find
+these examples (and more!) in the GitHub repository under the [`datasets/`](https://github.com/ioos/bio_data_guide/tree/main/datasets)
+directory.
+