Should _freeze directory be removed?

[TomSmithCGAT]

Summarising a meeting with @tavareshugo on 17th May 2024 in my own words..

The _freeze directory contains quarto cache to avoid re-rendering where code has not been updated. This saves time in the github action to update the website, but risks bloating the repo with old _freeze cache files and unwanted history due to change in the code block order.

For now, the plan is to leave it as it is and come back to this but we thought it would be good to summarise so we don't need to rediscuss

Solutions would be:

• Name all the code blocks. This would avoid issues where changing code makes a cache file change content since the naming is derived from the code block name.
• Remove the _freeze directory entirely. The downside is that this is expected to increase the github action run time. However, @tavareshugo's concern was in relation to the installation of R packages. The repo's publish_site github action uses an action for dependencies that should handle caching by default:

  course_expression_proteomics/.github/workflows/publish_site.yml

  Line 31 in 4c3458e

  uses: r-lib/actions/setup-r-dependencies@v2

  https://github.com/r-lib/actions/tree/v2/setup-r-dependencies
  However, I can't pretend to understand the action fully, especially since it appears to rely upon a DESCRIPTION file, which we don't have, so I'm not sure how the dependencies are even determined! Testing would be required to check the impact of removing _freeze entirely when it comes to the website rendering.