Editing a {sandpaper} lesson

Last updated on 2024-11-12 | Edit this page

Overview

Questions

What is the folder structure of a lesson?
How do you download an existing {sandpaper} lesson?

Objectives

Understand how to clone an existing lesson from GitHub
Use sandpaper::build_lesson() to preview a lesson
Update the configuration for a lesson
Rearrange the order of episodes

If you want to edit and preview a full lesson using {sandpaper}, this is the episode for you. If you want to create a new lesson, head back to the episode for Creating a New Lesson. I believe it’s beneficial to experience editing a fully functional lesson, so you will edit THIS lesson. The first step is to fork and clone it from GitHub:

Fork and Clone a Lesson

If you are familiar with the process of forking and cloning, then you may fork and clone as you normally do. If you would like a reminder, here are the steps:

Think about a place on your computer where you want to work on your fork of the lesson (e.g. ~/Documents/Lessons/) and make sure that folder exists.
Go to https://github.com/carpentries/sandpaper-docs/fork/ to fork the repository to your account
(recommended) When creating your fork, you should uncheck “Copy the main branch only” checkbox.
In the shell and use this command to clone this repository to your working directory, replacing <USERNAME> with your username
BASH
```
cd ~/Documents/Lessons/
git clone git@github.com:<USERNAME>/sandpaper-docs.git
cd sandpaper-docs
```

One-step fork with R

If you use R and you also use an HTTPS protocol, you might be interested to know that the above three steps can be done in a single step with the {usethis} package via the GitHub API:

R

usethis::create_from_github("carpentries/sandpaper-docs", "~/Documents/Lessons/")

In the next section, we will explore the folder structure of a lesson.

Preview the Lesson

Open the lesson in RStudio (or whatever you use for R)
Use the keyboard shortcut ctrl + shift + b (cmd + shift + b on macOS) to build and preview this lesson (or type sandpaper::build_lesson() in the console if you are not using RStudio)
Open THIS file (episodes/editing.md) and add step 4: preview the lesson again.

What do you notice?

Show me the solution

What you should notice is that the only file updated when you re-render the lesson is the file you changed (episodes/editing.Rmd).

Folder Structure

🚧 This May Change 🚧

The exact folder structure still has the possibility to change based on user testing for the front-end of the lesson website.

The template folder structure will contain markdown files arranged so that they match what we expect the menubar for the lesson should be. All folders and files with an arrow <- are places in the lesson template you will be modifying:

|-- .gitignore         #  | Ignore everything in the site/ folder
|-- .github/           #  | Configuration for deployment
|-- episodes/          # <- PUT YOUR EPISODE MARKDOWN FILES IN THIS FOLDER
|-- instructors/       # <- Information for Instructors (e.g. guide.md)
|-- learners/          # <- Information for Learners (e.g. reference.md and setup.md)
|-- profiles/          # <- Learner and/or Instructor Profiles
|-- site/              #  | This is a "scratch" folder ignored by git and is where the rendered markdown files and static site will live
|-- config.yaml        # <- Use this to configure lesson metadata
|-- index.md           # <- The landing page of your site
|-- CONTRIBUTING.md    #  | Carpentries Rules for Contributions (REQUIRED)
|-- CODE_OF_CONDUCT.md #  | Carpentries Code of Conduct (REQUIRED)
|-- LICENSE.md         #  | Carpentries Licenses (REQUIRED)
`-- README.md          # <- Introduces folks how to use this lesson and where they can find more information.

This folder structure is heavily opinionated towards achieving our goals of creating a lesson infrastructure that is fit for the purpose of delivering lesson content for not only Carpentries instructors, but also for learners and educators who are browsing the content after a workshop. It is not designed to be a blog or commerce website. Read the following sections to understand the files and folders you will interact with most.

All source files in {sandpaper} are written in pandoc-flavored markdown and all require yaml header called title. Beyond that, you can put anything in these markdown files.

`config.yaml`

This configuration file contains global information about the lesson. It is purposefully designed to only include information that is editable and relevant to the lesson itself and can be divided into two sections: information and organization

Information

These fields will be simple key-pair values of information used throughout the episode

carpentry: The code for the specific carpentry that the lesson belongs to (swc, dc, lc, cp, incubator, lab)
carpentry_description: (Optional) Full organisation name. Not needed when carpentry is swc, dc, lc, cp, incubator, or lab.

Adding a custom logo

The “carpentry” variable works with the {varnish} package to control the logo displayed on your lesson. You can display your own logo by

Adding the logo file as SVG (e.g. ‘ice-cream-logo.svg’) to your fork of {varnish} in the inst/pkgdown/assets/assets/images folder.
Setting “carpentry” to match the beginning of the name of your logo file. E.g. to use the ice-cream-logo.svg file given above, “carpentry” should be set to ‘ice-cream’.
Adding ‘varnish: [YOUR-GITHUB-USERNAME]/varnish’ to the Customization section of your lessons config.yaml file.

The rendered lesson will display your logo file with alternative text that matches the value of “carpentry”. For more informative alternative text, you can set “carpentry_description” to your organisation’s full name. E.g. “Ice Cream Carpentry” instead of “ice-cream”.

title: The main title of the lesson
life_cycle: What life cycle is the lesson in? (pre-alpha, alpha, beta, stable)
license: The license the lesson is registered under (defaults to CC-BY 4.0)
source: The github source of the lesson
branch: The default branch
contact: Who should be contacted if there is a problem with the lesson

Organization

These fields match the folder names in the repository and the values are a list of file names in the order they should be displayed. By default, each of these fields is blank, indicating that the default alphabetical order is used. To list items, add a new line with a hyphen and a space preceding the item name (-). For example, if I wanted to have the episodes called “one.md”, “two.Rmd”, “three.md”, and “four.md” in numerical order, I would use:

YAML

episodes:
- one.md
- two.Rmd
- three.md
- four.md

Below are the four possible fields {sandpaper} will recognize:

episodes: The names of the episodes (main content)
instructors: Instructor-specific resources (e.g. outline, etc)
learners: Resources for learners (e.g. Glossary terms)
profiles: Learner profile pages

Configuring Episode Order

Open config.yaml and change the order of the episodes. Preview the lesson after you save the file. How did the schedule change?

Show me the solution

The episodes appear in the same order as the configuration file and the timings have rearranged themselves to reflect that.

`episodes/`

This is the folder where all the action is. It contains all of the episodes, figures, and data files needed for the lesson. By default, it will contain an episode called introduction.Rmd. You can edit this file to use as your introduction. To create a new Markdown episode, use the folowing function:

R

sandpaper::create_episode_md("Episode Name")

This will create a Markdown episode called episode-name.md in the episodes/ directory of your lesson, pre-populated with objectives, questions, and keypoints. The episode will be added to the end of the episodes: list in config.yaml, which serves as the table of contents.

If you want to create an episode, but are not yet ready to render or publish it, you can create a draft using the draft_episode family of functions:

R

sandpaper::draft_episode_rmd("Visualising Data")

This will create an R Markdown episode called visualising-data.Rmd in the episodes/ directory of your lesson, but it will NOT be added to config.yaml, allowing you to work on it at your own pace without the need to publish it.

When you are ready to publish an episode or want to move an existing episode to a new place, you can use move_episode() to pull up an interactive menu for moving the episode.

R

sandpaper::move_episode("visualising-data.Rmd")

OUTPUT

ℹ Select a number to insert your episode
(if an episode already occupies that position, it will be shifted down)

1. introduction.md
2. episode-name.md
3. [insert at end]

Choice:

Should I use R Markdown or Markdown Episodes?

All {sandpaper} lessons can be built using Markdown, R Markdown, or a mix of both. If you want to dynamically render the output of your code via R (other languages will be supported in the future), then you should use R Markdown, but if you do not need to dynamically render output, you should stick with Markdown.

Sandpaper offers four functions that will help with episode creation depending on your usage:

R Markdown	Markdown
`create_episode_rmd()`	`create_episode_md()`
`draft_episode_rmd()`	`draft_episode_md()`

`instructors/`

This folder contains information used for instructors only. Downloads of code outlines, aggregated figures, and slides would live in this folder.

`learners/`

All the extras the learner would need, mostly a setup guide and glossary live here.

The glossary page is populated from the reference.md file in this folder. The format of the glossary section of the reference.md file is a heading title ## Glossary followed by a definition list. Definition lists are formatted as two lines for each term, the first includes the term to be defined and then the second line starts with a “:” and a space then the definition. i.e.

MARKDOWN

term
: definition

term: definition

`profiles/`

Learner profiles would live in this folder and target learners, instructors, and maintainers alike to give a focus on the lesson.

`index.md`

This is the landing page for the lesson. The schedule is appended at the bottom of this page and this will be the first page that anyone sees.

`README.md`

This page gives information to maintainers about what to expect inside of th repository and how to contribute.

Making your lesson citable

You can add information about how people should cite your lesson by adding a citation file to your lesson repository. If the root folder of your lesson project includes a file called CITATION or CITATION.cff, the ‘Cite’ page footer of your lesson site will link to this file.

We recommend that you add and maintain a CITATION.cff file for your lesson, in Citation File Format (CFF). CFF is a structured text file format that provides machine-readable citation information for projects. It is supported by a growing number of tools, including GitHub: if a project includes a CFF file in its default branch, GitHub will present citation information for the project under a ‘Cite this repository’ button in the About sidebar.

Creating a CFF for a lesson

You can use the cffinit webtool to create a new CFF for your lesson or update an existing file. When creating a CFF for a lesson, you should specify dataset as the type of work being described (This discussion includes explanation for why dataset is the appropriate type for a lesson.)

Example CFF for this lesson

cff-version: 1.2.0
title: Introduction to The Carpentries Workbench
message: >-
  Please cite this lesson using the information in this file
  when you refer to it in publications, and/or if you
  re-use, adapt, or expand on the content in your own
  training material. To cite the Workbench software itself,
  please refer to the websites for the individual
  components:
  https://carpentries.github.io/sandpaper/authors.html#citation,
  https://carpentries.github.io/pegboard/authors.html#citation,
  https://carpentries.github.io/varnish/authors.html#citation
type: dataset
authors:
  - given-names: Zhian
    family-names: Kamvar
    name-particle: N.
    orcid: 'https://orcid.org/0000-0003-1458-7108'
  - given-names: Toby
    family-names: Hodges
    email: tobyhodges@carpentries.org
    affiliation: The Carpentries
    orcid: 'https://orcid.org/0000-0003-1766-456X'
  - given-names: Erin
    family-names: Becker
    orcid: 'https://orcid.org/0000-0002-6832-0233'
  - orcid: 'https://orcid.org/0000-0002-7040-548X'
    given-names: Sarah
    family-names: Stevens
  - given-names: Michael
    family-names: Culshaw-Maurer
    orcid: 'https://orcid.org/0000-0003-2205-8679'
  - given-names: Maneesha
    family-names: Sane
  - given-names: Robert
    family-names: Davey
    orcid: 'https://orcid.org/0000-0002-5589-7754'
  - given-names: Amelia
    family-names: Bertozzi-Villa
  - given-names: Kaitlin
    family-names: Newson
    orcid: 'https://orcid.org/0000-0001-8739-5823'
  - given-names: Jennifer
    family-names: Stubbs
    orcid: 'https://orcid.org/0000-0002-6080-5703'
  - given-names: Belinda
    family-names: Weaver
  - given-names: François
    family-names: Michonneau
    orcid: 'https://orcid.org/0000-0002-9092-966X'
repository-code: 'https://github.com/carpentries/sandpaper-docs'
url: 'https://carpentries.github.io/sandpaper-docs/'
abstract: >-
  Documentation for The Carpentries Workbench, a set of
  tools that can be used to create accessible lesson
  websites.
keywords:
  - Carpentries
  - sandpaper
  - pegboard
  - varnish
  - R
  - pkgdown
license: CC-BY-4.0

Plain text CITATION file

As an alternative to Citation File Format, you can also use a plain text file, named CITATION (i.e. without the .cff extension), in which you add guidance for people wanting to cite your lesson in their publications/projects.

Example plain text CITATION file

Please cite this lesson as:

Zhian N. Kamvar et al,
Introduction to The Carpentries Workbench.
https://github.com/carpentries/sandpaper-docs

Key Points

sandpaper::build_lesson() renders the site and rebuilds any sources that have changed.
RStudio shortcuts are cmd + shift + B and cmd + shift + K
To edit a lesson, you only need to know Markdown and/or R Markdown
The folder structure is designed with maintainers in mind
New episodes can be added with sandpaper::create_episode()

Editing a {sandpaper} lesson

Overview

Questions

Objectives

Fork and Clone a Lesson

BASH

One-step fork with R

R

Preview the Lesson

Show me the solution

Folder Structure

🚧 This May Change 🚧

config.yaml

Information

Adding a custom logo

Organization

YAML

Configuring Episode Order

Show me the solution

episodes/

R

R

R

OUTPUT

Should I use R Markdown or Markdown Episodes?

instructors/

learners/

MARKDOWN

profiles/

index.md

README.md

Making your lesson citable

Creating a CFF for a lesson

Example CFF for this lesson

Plain text CITATION file

Example plain text CITATION file

Key Points

`config.yaml`

`episodes/`

`instructors/`

`learners/`

`profiles/`

`index.md`

`README.md`