[r] add automatic website building

[immanuelazn]

Creates a PR to html-docs whenever something is pushed to main, and performs the website building workflow indicated in Wiki/Tool Development Workflows Title of PR is Update docs for commit: <most_recent_commit_message>

Message of PR is the git log of the most recent commit. I am open to changing this to something that better describes the changes to documentation. Example of how this would look can be found here. This PR was created as a result of pushing this commit into my personal BPCells main branch.

We can also make it perform an automatic push to html-docs, if that is preferred. We can also set this up to be a manually triggered workflow.

[immanuelazn]

Getting selective changes for vignettes was much more involved than anticipated. Apparently, we can't use pkgdown::build_articles() with the approach of renaming the non-changed files' extensions, as this breaks the linking to index. Additionally, using lazy=TRUE doesn't work with resetting git modification times off the box, as we use worktrees to build our website.

I decided to build the selective article rendering with using pkgdown::build_article(), and that seems to work! I also created a script that can manually be run, and redo's website building.

[immanuelazn]

Demo of the new build process:

• I prd the workflow into my fork's main branch. This auto triggered this PR.
• I then manually ran the workflow for full website build in this PR. We can see that it replaces old images in vignettes with the exact same image, and reflects pkgdown versioning differences in a bunch of files. However the content itself looks reasonable. Surprisingly, the action only took 10 minutes!
• I did a trial commit with only small syntactic changes in two vignettes. This triggered this PR, and reflects that changes were only made to two vignettes

[immanuelazn]

Some comments:

• I ended up just sticking to the current infrastructure route, instead of taking the github mtime changing option.
• I tested with the following workflow:
  • PRd the changes to my main branch (PR looks like this , but this is what it looks like when I don't squash commits). Both look acceptable. Action reflecting the build found here
  • I commited a change where I added the word "test" to the benchmarking Rmd, and added a new Rmd (PR looks like this). Action for this change found here We can see the git diff reflects the articles being updated accordingly, when compared to the previous steps PR. I also added this to personal website, and the articles are updated correctly (Found here).
  • I also manually rebuilt the docs to confirm that its still works. The non-deterministic nature is still an issue. Action reflecting the change found here. PR found here
  • I then tested when I added non-linked png files, and can confirm that these do not create a PR. I had to add a change to handle breaking early. GH actions still perceives it as a failure (Action found here). People are not happy that breaking early is not conventionally supported in GHA (as shown here). There are ways around it, but I don't think it's worth the additional complexitiy in the workflow. In the end the workflow still does its job

[bnprks]

This looks great! Should be very useful to help keep the docs site updated. Ready to merge from my perspective

For my own curiosity (we can discuss offline at some point)

• I noticed that you left some bioc:: and github:: packages off the DESCRIPTION Config/Needs/website section. I kind of expected those prefixes to just work since the github action ends up calling pak to do the install (supported prefixes). You mentioned some added complexity if trying to use those -- what was it that came up?

[immanuelazn]

Ah so that is my bad, I read that you need to have all external packages in a seperate header in your DESCRIPTION file. I looked through a few public repos and I couldn't find any that actually imported bioc packages through the same website header. This thought process was incorrect, and manual testing shows that it does indeed work. Good catch! PR with full rebuild shown here