OpenProblems.bio

This repository is used to build openproblems.bio.

Installation

• Install quarto v1.4.527, R >= 4.3 and Python >= 3.10.

• Clone this repo with git clone --recursive git@github.com:openproblems-bio/website.git

• Run Rscript -e 'install.packages("renv")' if you don't have {renv} installed.

• Run Rscript -e 'renv::restore()' to install R and Python packages recorded in the renv lockfile (renv.lock) and Python requirements (requirements.txt). This might take a while.

If contributing to the documentation, install Java, Docker and Viash (See Requirements).

Preview

Run quarto preview to render a preview version of the site.

To reduce the time it takes to render the site, quarto is set to not execute runnable code by default. As such, some content may be missing -- mostly the output of code blocks. Use quarto preview --profile evaluate_code to evaluate runnable code blocks.

Tip: When you already did a render or preview with or without the profile argument, you need to remove the _site and _freeze directories to see a change by executing rm -r _site _freeze

Build

Run quarto render --profile evaluate_code to render the site.

License

This repository contains a Quarto website with different types of content:

• Markdown content and JSON data files are licensed under the Creative Commons Attribution 4.0 International License (CC-BY). See LICENSE-CC-BY for details.

• All other source files (e.g. R, Python, CSS, SCSS, and EJS) are licensed under the MIT License. See LICENSE-MIT for details.