From 4aa0d398b3ef34cea67cb91d83617a693a963f01 Mon Sep 17 00:00:00 2001 From: Ben Best Date: Fri, 6 Sep 2024 00:27:30 +0200 Subject: [PATCH] migrate to Quarto qmd #266 --- .Rhistory | 0 .github/workflows/deploy_bookdown.yml | 130 - .github/workflows/render_book.yml | 73 + .gitignore | 8 +- bio-data-guide/.nojekyll => .nojekyll | 0 DESCRIPTION | 24 +- README.md | 14 +- _quarto.yml | 65 + apps.qmd | 6 + bio-data-guide/02-application.Rmd | 11 - bio-data-guide/06-references.Rmd | 5 - bio-data-guide/README.md | 13 - bio-data-guide/_bookdown.yml | 7 - .../figure-epub3/unnamed-chunk-3-1.png | Bin 28808 -> 0 bytes .../figure-html/unnamed-chunk-3-1.png | Bin 97144 -> 0 bytes .../figure-latex/unnamed-chunk-3-1.pdf | Bin 276211 -> 0 bytes .../figure-html/nice-fig-1.png | Bin 71465 -> 0 bytes .../figure-latex/nice-fig-1.pdf | Bin 5848 -> 0 bytes bio-data-guide/_output.yml | 23 - bio-data-guide/packages.bib | 261 - building-the-guide.md | 4 + ...SENV.md => TPWD_HARC_BagSeine_OBISENV.qmd} | 0 ...=> 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index.qmd | 20 +- bio-data-guide/01-intro.Rmd => intro.qmd | 1 + lib/pre-render.R | 18 + {bio-data-guide => lib}/preamble.tex | 1 + {bio-data-guide => lib}/style.css | 0 references.qmd | 7 + .../ESIP Data Citation Guidelines v2.pdf | Bin .../OBIS_data_examples.bib | 0 .../OBIS_data_tiers}/README.md | 0 {bio-data-guide => refs}/book.bib | 0 refs/packages.bib | 84 + {bio-data-guide => refs}/tree.html | 0 bio-data-guide/04-tools.Rmd => tools.qmd | 0 56 files changed, 4152 insertions(+), 4186 deletions(-) delete mode 100644 .Rhistory delete mode 100644 .github/workflows/deploy_bookdown.yml create mode 100644 .github/workflows/render_book.yml rename bio-data-guide/.nojekyll => .nojekyll (100%) create mode 100644 _quarto.yml create mode 100644 apps.qmd delete mode 100644 bio-data-guide/02-application.Rmd delete mode 100644 bio-data-guide/06-references.Rmd delete mode 100644 bio-data-guide/README.md delete mode 100644 bio-data-guide/_bookdown.yml delete mode 100644 bio-data-guide/_bookdown_files/03-application_files/figure-epub3/unnamed-chunk-3-1.png delete mode 100644 bio-data-guide/_bookdown_files/03-application_files/figure-html/unnamed-chunk-3-1.png delete mode 100644 bio-data-guide/_bookdown_files/03-application_files/figure-latex/unnamed-chunk-3-1.pdf delete mode 100644 bio-data-guide/_bookdown_files/Standardizing-Marine-Biological-Data_files/figure-html/nice-fig-1.png delete mode 100644 bio-data-guide/_bookdown_files/Standardizing-Marine-Biological-Data_files/figure-latex/nice-fig-1.pdf delete mode 100644 bio-data-guide/_output.yml delete mode 100644 bio-data-guide/packages.bib rename datasets/TPWD_HARC_BagSeine/{TPWD_HARC_BagSeine_OBISENV.md => TPWD_HARC_BagSeine_OBISENV.qmd} (100%) rename datasets/atn_satellite_telemetry/{atn_satellite_telemetry_netCDF2DwC.Rmd => atn_satellite_telemetry_netCDF2DwC.qmd} (95%) rename datasets/atn_satellite_telemetry/data/src/{ atn_45866_great-white-shark_trajectory_20090923-20091123.nc => atn_45866_great-white-shark_trajectory_20090923-20091123.nc} (100%) rename datasets/hakai_salmon_data/{salmon-darwin-core-remap.Rmd => salmon-darwin-core-remap.qmd} (98%) rename datasets/hakai_seagrass_data/{hakaiSeagrassToDWC.Rmd => hakaiSeagrassToDWC.qmd} (93%) rename datasets/trawl_catch_data/{trawl-catch-data.Rmd => trawl-catch-data.qmd} (99%) rename bio-data-guide/05-extras.Rmd => extras.qmd (98%) rename bio-data-guide/03-faq.Rmd => faq.qmd (98%) rename {bio-data-guide/figs => figs}/PR_77.png (100%) rename {bio-data-guide/figs => figs}/PR_82.png (100%) rename {bio-data-guide/figs => figs}/basic_map.png (100%) rename {bio-data-guide/figs => figs}/code_change1.png (100%) rename {bio-data-guide/figs => figs}/code_change2.png (100%) rename {bio-data-guide/figs => figs}/code_change3.png (100%) rename {bio-data-guide/figs => figs}/code_snippet.png (100%) rename {bio-data-guide/figs => figs}/commit_a0919e.png (100%) rename {bio-data-guide/figs => figs}/commit_ef17f89.png (100%) create mode 100644 figs/contrib.rocks.svg rename {bio-data-guide/figs => figs}/issue_78.png (100%) create mode 100644 figs/mybinder.org_badge_logo.svg rename {bio-data-guide/figs => figs}/obis_dataset.png (100%) rename bio-data-guide/index.Rmd => index.qmd (52%) rename bio-data-guide/01-intro.Rmd => intro.qmd (99%) create mode 100644 lib/pre-render.R rename {bio-data-guide => lib}/preamble.tex (52%) rename {bio-data-guide => lib}/style.css (100%) create mode 100644 references.qmd rename ESIP Data Citation Guidelines v2.pdf => refs/ESIP Data Citation Guidelines v2.pdf (100%) rename {bio-data-guide => refs}/OBIS_data_examples.bib (100%) rename {OBIS_data_tiers => refs/OBIS_data_tiers}/README.md (100%) rename {bio-data-guide => refs}/book.bib (100%) create mode 100644 refs/packages.bib rename {bio-data-guide => refs}/tree.html (100%) rename bio-data-guide/04-tools.Rmd => tools.qmd (100%) diff --git a/.Rhistory b/.Rhistory deleted file mode 100644 index e69de29..0000000 diff --git a/.github/workflows/deploy_bookdown.yml b/.github/workflows/deploy_bookdown.yml deleted file mode 100644 index 7378e32..0000000 --- a/.github/workflows/deploy_bookdown.yml +++ /dev/null @@ -1,130 +0,0 @@ -name: renderbook - -on: - push: - branches: - - main - paths: - - '.github/workflows/deploy_bookdown.yml' - - 'bio-data-guide/**' - - workflow_dispatch: - -jobs: - bookdown: - name: Render-Book - runs-on: macOS-latest - steps: - - name: Check out repository - uses: actions/checkout@v4 - with: - submodules: 'recursive' - - - name: Install R - uses: r-lib/actions/setup-r@v2 - with: - r-version: '4.4.1' # 2024-09-04 - - - name: Install pandoc - uses: r-lib/actions/setup-pandoc@v2 - with: - pandoc-version: '3.3' # 2024-09-04 - - - name: Install Quarto - uses: quarto-dev/quarto-actions/setup@v2 - with: - tinytex: true # for pdf (sometimes bonks) - - - name: Install TinyTeX - uses: r-lib/actions/setup-tinytex@v2 - - # - uses: r-lib/actions/setup-r-dependencies@v2 - # with: - # extra-packages: any::bookdown - # needs: book - - name: Install R Dependencies - uses: r-lib/actions/setup-r-dependencies@v2 - with: - cache-version: 2 - # usethis::use_description(check_name = F) - # usethis::use_package("bookdown") - - # - name: Install packages - # run: Rscript -e ' - # install.packages("bookdown");' - # env: - # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - # - name: Install packages - # run: Rscript -e ' - # install.packages(c("librarian", "rgdal", "rmarkdown", "vroom", "xfun", "tidync"), type = "binary"); - # librarian::shelf(bookdown, dm, here, lubridate, , rmarkdown, tidyverse, worms); - # remotes::install_github("iobis/obistools", upgrade="never"); - # env: - # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - - name: Move headers one level down in edna example - run: | - sed -i'' -e 's/# /## /g' datasets/dataset-edna/README.md - - - name: Render Html Book - run: Rscript -e ' - setwd("bio-data-guide/"); - options(knitr.duplicate.label = "allow"); - bookdown::render_book("index.Rmd");' - - - name: Render epub book - run: Rscript -e ' - setwd("bio-data-guide/"); - options(knitr.duplicate.label = "allow"); - bookdown::render_book("index.Rmd", "bookdown::epub_book")' - - - name: remove binder image line from edna example for pdf - run: | - sed -i'' -e '/Binder/d' datasets/dataset-edna/README.md; - sed -i'' -e 's,!\[\](https://contrib.rocks/image?repo=ioos/bio_data_guide),,g' bio-data-guide/index.Rmd - - - name: Render pdf book - run: Rscript -e ' - setwd("bio-data-guide/"); - options(knitr.duplicate.label = "allow"); - bookdown::render_book("index.Rmd", "bookdown::pdf_book")' - - - uses: actions/upload-artifact@v3 - with: - name: _book - path: 'bio-data-guide/docs' # see _bookdown.yml: output_dir - -# 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 - - - name: Deploy to GitHub Pages - uses: actions/deploy-pages@v4 - with: - build_dir: 'bio-data-guide/docs' # see _bookdown.yml: output_dir - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - diff --git a/.github/workflows/render_book.yml b/.github/workflows/render_book.yml new file mode 100644 index 0000000..3b2dca7 --- /dev/null +++ b/.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 + + diff --git a/.gitignore b/.gitignore index cb22ace..4c8451a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ -/bio-data-guide/docs -/bio-data-guide/bio-data-guide.rds -.Rproj.user \ No newline at end of file +/_book +.Rproj.user +/.quarto/ +.DS_Store +.Rhistory diff --git a/bio-data-guide/.nojekyll b/.nojekyll similarity index 100% rename from bio-data-guide/.nojekyll rename to .nojekyll diff --git a/DESCRIPTION b/DESCRIPTION index fb9ef5d..8e10cce 100644 --- a/DESCRIPTION +++ b/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 diff --git a/README.md b/README.md index 4145729..7f191dc 100644 --- a/README.md +++ b/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). + +\nMathewBiddle + + + + + + + +\n7yl4r + + + + + + + +\nBr-Johnson + + + + + + + +\nDylan-Pugh + + + + + + + +\nzmonteith + + + + + + + +\nalbenson-usgs + + + + + + + +\nbbest + + + + + + + +\ntimvdstap + + + + + + + +\ngbaillie-onc + + + + + + + +\nlaurabrenskelle + + + + + + + +\nemiliom + + + + + + + +\nmlonneman + + + + + + + +\ndaltonkell + + + + + + + +\nmstoessel + + + + + + + + diff --git a/bio-data-guide/figs/issue_78.png b/figs/issue_78.png similarity index 100% rename from bio-data-guide/figs/issue_78.png rename to figs/issue_78.png diff --git a/figs/mybinder.org_badge_logo.svg b/figs/mybinder.org_badge_logo.svg new file mode 100644 index 0000000..af18a46 --- /dev/null +++ b/figs/mybinder.org_badge_logo.svg @@ -0,0 +1 @@ +launchlaunchbinderbinder \ No newline at end of file diff --git a/bio-data-guide/figs/obis_dataset.png b/figs/obis_dataset.png similarity index 100% rename from bio-data-guide/figs/obis_dataset.png rename to figs/obis_dataset.png diff --git a/bio-data-guide/index.Rmd b/index.qmd similarity index 52% rename from bio-data-guide/index.Rmd rename to index.qmd index c3d10b2..9d322fd 100644 --- a/bio-data-guide/index.Rmd +++ b/index.qmd @@ -1,19 +1,3 @@ ---- -title: "Darwin Core Marine Example Compendium" -author: "By: [Standardizing Marine Biological Data Working Group](https://github.com/ioos/bio_data_guide/graphs/contributors) ![](https://contrib.rocks/image?repo=ioos/bio_data_guide)" -date: "Updated: `r Sys.Date()`" -url: https://ioos.github.io/bio_data_guide/ -github-repo: ioos/bio_data_guide -site: bookdown::bookdown_site -documentclass: book -bibliography: ["book.bib", "packages.bib", "OBIS_data_examples.bib"] -biblio-style: apa -link-citations: yes -nocite: | - @* -description: "Scaling multiple dimensions of diversity in biological data" ---- - # Preface {-} This book contains a collection of examples and resources related to mobilizing marine biological data to the @@ -26,6 +10,6 @@ If you would like to join the SMBD or learn more, checkout this [README](https:/ ```{r include=FALSE} # automatically create a bib database for R packages knitr::write_bib(c( - .packages(), 'bookdown', 'knitr', 'rmarkdown' -), 'packages.bib') + .packages(), 'bookdown', 'knitr', 'rmarkdown'), + 'lib/packages.bib') ``` diff --git a/bio-data-guide/01-intro.Rmd b/intro.qmd similarity index 99% rename from bio-data-guide/01-intro.Rmd rename to intro.qmd index 8e521e1..32fe2da 100644 --- a/bio-data-guide/01-intro.Rmd +++ b/intro.qmd @@ -1,4 +1,5 @@ # Introduction {#intro} + The world of standardizing marine biological data can seem complex for the naive oceanographer, biologist, scientist, or programmer. This book intends to ease the burden of learning about the [Darwin Core standard](https://dwc.tdwg.org/) by compiling a list of example applications and tools for translating source data into Darwin Core. This collection of diff --git a/lib/pre-render.R b/lib/pre-render.R new file mode 100644 index 0000000..da2cb17 --- /dev/null +++ b/lib/pre-render.R @@ -0,0 +1,18 @@ +# load libraries +librarian::shelf( + glue, stringr, quiet = T) + +# update Github repo contributors image +download.file( + "https://contrib.rocks/image?repo=ioos/bio_data_guide", + "figs/contrib.rocks.svg") + +# update dataset-edna/README.md with downloaded Binder svg +file_md <- "datasets/dataset-edna/README.md" +url_svg <- "https://mybinder.org/badge_logo.svg" +fig_svg <- "figs/mybinder.org_badge_logo.svg" +if (!file.exists(fig_svg)) + download.file(url_svg, fig_svg) +readLines() |> + str_replace(url_svg, glue("/{fig_svg}")) |> + writeLines("datasets/dataset-edna/README.qmd") diff --git a/bio-data-guide/preamble.tex b/lib/preamble.tex similarity index 52% rename from bio-data-guide/preamble.tex rename to lib/preamble.tex index dfd2e14..25767b1 100644 --- a/bio-data-guide/preamble.tex +++ b/lib/preamble.tex @@ -1 +1,2 @@ \usepackage{booktabs} +\usepackage{authblk} \ No newline at end of file diff --git a/bio-data-guide/style.css b/lib/style.css similarity index 100% rename from bio-data-guide/style.css rename to lib/style.css diff --git a/references.qmd b/references.qmd new file mode 100644 index 0000000..664d7c3 --- /dev/null +++ b/references.qmd @@ -0,0 +1,7 @@ +--- +nocite: | + @* +--- + +# References {.unnumbered} + diff --git a/ESIP Data Citation Guidelines v2.pdf b/refs/ESIP Data Citation Guidelines v2.pdf similarity index 100% rename from ESIP Data Citation Guidelines v2.pdf rename to refs/ESIP Data Citation Guidelines v2.pdf diff --git a/bio-data-guide/OBIS_data_examples.bib b/refs/OBIS_data_examples.bib similarity index 100% rename from bio-data-guide/OBIS_data_examples.bib rename to refs/OBIS_data_examples.bib diff --git a/OBIS_data_tiers/README.md b/refs/OBIS_data_tiers/README.md similarity index 100% rename from OBIS_data_tiers/README.md rename to refs/OBIS_data_tiers/README.md diff --git a/bio-data-guide/book.bib b/refs/book.bib similarity index 100% rename from bio-data-guide/book.bib rename to refs/book.bib diff --git a/refs/packages.bib b/refs/packages.bib new file mode 100644 index 0000000..23943e4 --- /dev/null +++ b/refs/packages.bib @@ -0,0 +1,84 @@ +@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 = {2024}, + url = {https://www.R-project.org/}, +} + +@Manual{R-bookdown, + title = {bookdown: Authoring Books and Technical Documents with R Markdown}, + author = {Yihui Xie}, + 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 = {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 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, + title = {bookdown: Authoring Books and Technical Documents with {R} Markdown}, + author = {Yihui Xie}, + publisher = {Chapman and Hall/CRC}, + address = {Boca Raton, Florida}, + year = {2016}, + 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}, +} + +@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}, + 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}, + isbn = {9780367563837}, + url = {https://bookdown.org/yihui/rmarkdown-cookbook}, +} + diff --git a/bio-data-guide/tree.html b/refs/tree.html similarity index 100% rename from bio-data-guide/tree.html rename to refs/tree.html diff --git a/bio-data-guide/04-tools.Rmd b/tools.qmd similarity index 100% rename from bio-data-guide/04-tools.Rmd rename to tools.qmd