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Open Science Bootcamp 2023

This site

This page describes the technologies and tools we use for generating this site.

RStudio

Rick Gilmore drafted the site using the RStudio Integrated Development Environment (IDE) on his desktop computer. Penn State supports RStudio Server which allows users to run RStudio in a web browser (https://rstudio.tlt.psu.edu). However the versions of R seem out-of-date, and this service is only available to users whose computers are behind the PSU firewall (connected via GlobalProtect).

bookdown

The R package bookdown generates the site.

We use the Bootstrap format. To view specific parameters, see the src/_bookdown.yml, src/_output.yml, and src/index.Rmd files.

renv

We use the renv package to manage package dependencies. In most cases, to render the site anew, the user should do the following:

  1. Install renv via install.packages('renv').
  2. Execute renv::restore() from the R console to install local copies of the required packages.

R Markdown

Most of the content of the site is written in R Markdown, an extension of Markdown.

Image files are located in src/include/img; CSS style sheets are in src/include/css; and BibTex-formatted reference files are in src/include/bib.

Any “child” R Markdown files needed can be stored in src/include/rmd.

GitHub

We use git for version control and push changes to GitHub at https://github.com/penn-state-open-science/bootcamp-2023.

GitHub has a ‘pages’ feature that will automatically turn HTML and associated files into a hosted website with a convenient URL. In our case, the URL is https://penn-state-open-science.github.io/bootcamp-2023/.

File structure

  • All source documents are under src/.
  • The rendered website is in docs/.
  • Files related to package management are located in renv/

Editing and rendering

A typical editing and site rendering cycle goes like this:

  1. Edit the relevant *.Rmd files in src/.
  2. Save the changed files.
  3. Render the site via bookdown::render_book('src').
  4. View the site locally in a browser by opening docs/index.html.

TODO: Incorporate GitHub actions to generate the site. This would save a step.

Sending emails

TODO: Develop workflow for sending registered participants reminder emails.

Here is a tutorial for how to send email from Quarto/R Markdown using the blastula package:

https://www.youtube.com/watch?v=_QQGW_RUw_I