CalCOFI Docs

This repository is rendered as a Quarto book.

Rendering the book on your local machine (optional)

A Github Action will build the book automatically when you push changes to the repository. However, you can also build the book locally on your machine, which is especially helpful for testing output and for debugging any issues.

Setup software (R, Rstudio, Quarto, TinyTex) and download the repository

• Make sure you have the most recent version of R and R Studio

• Check that Quarto is installed and functioning on your machine. Check the version of Quarto installed in the R Console:

  quarto::quarto_version()

• Install TinyTex (used for rendering to PDF) in the bash Terminal:

  quarto install tinytex

• In R Studio, File > New Project... > Version Control > Git.

• Fork or clone the GitHub repository from this Repository URL:

  https://github.com/ioos/bio_data_guide.git

• Install all the required packages listed in the DESCRIPTION from the R Console:

  remotes::install_deps()

Render the Quarto book

• Render all Quarto output formats (i.e., html, pdf, epub) from source files (*.qmd) listed in the _quarto.yaml (starting with chapters:) into the output-dir (i.e.,_book) from the bash Terminal:

  quarto render

• If you have any problems, be sure to show versions of quarto and tinytex in the bash Terminal:

  quarto check

• Inspect results (index.html, CalCOFI.io-Docs.pdf|docx|epub) in the output directory _book/.

• Commit and push changes to all modified files via the Git pane in R Studio. Note that the _book directory is ignored by git (per the .gitignore file), since the book is rendered and published by the Github Action (.github/workflows/render_book.yml) into the gh-pages Github branch.

Adding R package dependencies to DESCRIPTION

Depending on the type of R package:

• CRAN

  usethis::use_package("dplyr")

• Github (and not CRAN)

  usethis::use_dev_package("obistools", remote = "iobis/obistools")

• CRAN meta-package

  usethis::use_package("tidyverse", type = "depends")