microscopy-novice

This is the lesson repository for microscopy-novice

Development

This course is developed using the Carpentries Workbench. The sandpaper R package is the main driver used to configure and build the website (see installation instructions below).

For a comprehensive guide on how to use sandpaper, check out the documentation.

When making changes, please create a new branch and open a Pull Request. Don't push directly to main.

## Create new branch
git checkout main
git pull origin main
git switch -c <username>/<my_awesome_edits>

The basic workflow looks something like this (it's recommended, though not necessary, to run this in RStudio):

## Add new episode in plain Markdown format (use `create_episode_Rmd` for RMarkdown)
sandpaper::create_episode_md("Episode name")
## ...... Edit new episode md contents ......

## Preview site
sandpaper::serve()

## ...... Make further changes, the website preview should update automatically ......
## ...... Rinse and repeat ......

When you're happy, commit, push and open a PR on GitHub. This will trigger the sandpaper PR validation and preview workflows to validate and preview the new content. Once the PR gets approved, merge it into main and wait for the Build and Deploy action to complete, after which the updates should be visible on the website

Building the lesson locally

The sandpaper package is used to build the lesson website. We created forks of sandpaper and varnish to style the lesson website with IDEAS branding.

To install these forks locally, run the following from within an R session:

## Install devtools
install.packages("remotes")

## Install sandpaper and varnish from the IDEAS forks
## HealthBioscienceIDEAS/varnish is listed as a dependency of sandpaper, so will be installed as well
remotes::install_github("HealthBioscienceIDEAS/sandpaper", dependencies = TRUE)

Then to build the lesson locally, from within the microscopy-novice directory, run

sandpaper::build_lesson()

That should open the built home page in a browser window automatically, but if not, you can find the built HTML files in the site/ directory.