index.Rmd

--- 
title: "A Course Template"
author: "John Doe"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
description: |
  This is a template for a course material using bookdown and learnitdown.
  The HTML output format for this example is bookdown::gitbook,
  set in the _output.yml file.
cover-image: "images/front-cover.png"
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
github-repo: 'learnitr/bookdown'
url: 'https://learnitr.github.io/bookdown/'
---

# About {.unnumbered}

This is a _sample_ book written in **Markdown** with **[{learnitdown}](https://github.com/learnitr/learnitdown)** additions (see \@ref(learnitdown)).

`r learnitdown::clean_ex_toc()`

<!-- The following inline chunk displays a login diagnostic box. Uncomment it if you use this bookdown inside of a Wordpress site, see https://learnitr.github.io/learnitrdoc/wordpress.html.-->

<!-- `r learnitdown::clean_ex_toc()` `r learnitdown::diagnose_login(lang = "en")` -->

## Usage {.unnumbered}

Each **bookdown** chapter is an .Rmd file, and each .Rmd file can contain one (and only one) chapter. A chapter *must* start with a first-level heading: `# A good chapter`, and can contain one (and only one) first-level heading.

Use second-level and higher headings within chapters like: `## A short section` or `### An even shorter section`.

The `index.Rmd` file is required, and is also your first book chapter. It will be the homepage when you render the book.

## Render book {.unnumbered}

You can render the HTML version of this example book without changing anything:

1. Find the **Build** pane in the RStudio IDE, and

1. Click on **Build Book**, then select your output format, or select "All formats" if you'd like to use multiple formats from the same book source files.

Or build the book from the R console:

```{r, eval=FALSE}
bookdown::render_book()
```

To render this example to PDF as a `bookdown::pdf_book`, you'll need to install XeLaTeX. You are recommended to install TinyTeX (which includes XeLaTeX): <https://yihui.org/tinytex/>.

## Preview book {.unnumbered}

As you work, you may start a local server to live preview this HTML book. This preview will update as you edit the book when you save individual .Rmd files. You can start the server in a work session by using the RStudio add-in "Preview book", or from the R console:

```{r eval=FALSE}
bookdown::serve_book()
```


```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
  .packages(), 'bookdown', 'knitr', 'rmarkdown'
), 'packages.bib')
```

## Render with GitHub action {.unnumbered}

You can include the `docs` directory in git, but each time you will change something in a page of the book, you will get to commit a whole bunch of other files corresponding to the book rendering. Our advice is to use a GitHub action to build your book and to place the `docs` directory in the `.gitignore` file. That way, you will only commit the source files and the rendered book will be available at the URL of your repository.

To create the required GitHub action you enter the following code in R:

```r
usethis::use_github_action(url = "https://raw.githubusercontent.com/ropenscilabs/actions_sandbox/master/.github/workflows/deploy_bookdown.yml")
```

TODO: continue this (obviously, this file needs to be edited)!

See here: https://orchid00.github.io/actions_sandbox/websites-using-pkgdown-bookdown-and-blogdown.html#deploy-bookdown

There is also an action to deploy on Netlify here: https://github.com/EmilHvitfeldt/bookdown-github-actions-netlify/blob/master/.github/workflows/bookdown.yaml


### GitHub configuration to display the book {.unnumbered}

TODO...


<details>

<summary>System information</summary>

```{r, class.source='hidden-code'}
sessioninfo::session_info()
```

</details>