figure does not appear on website

[robpetrosino]

Description

I finally managed to push my manuscript on GH pages, and everything is looking good except for the figures, which instead are not showing:

The two figures are two ggplot objects (e.g., here) that do compile in the pdf version, but not in the html one.

The link to the GH page is: https://robpetrosino.github.io/frequency-effects_masked-priming/#sec-intro
The link to the repo: https://github.com/robpetrosino/frequency-effects_masked-priming/tree/main
Does anyone know how to solve the issue?

[mcanouil]

As said your "example" is quite too big.
You need to go step by step to remove everything not related to the issue to get something small.
Then and only then, you'll be able to figure out by yourself the issue, or at least we would be able to help.

I am sorry but we don't have the time to debug thousands lines document.

Also, as said in the other thread you need to fix your code cells and use only one syntax, YAML is the recommended one in Quarto.
But anyway, in both Rmarkdown/Quarto, mixing syntaxes is wrong and can lead to unintended side effects.

[robpetrosino]

Fair, sorry! I am trying to figure what is going wrong.

[cderv]

How to do you publish to gh-pages exactly ?

Your gh-pages branch is missing the index_files/ folder where the image is. Locally when doing quarto render index.qmd --to html I see the folder in the _manuscript output directory.

[robpetrosino]

I ran into this other guide from the Quarto website, and tried to quarto publish gh-pages. Now the gh-pages branch has the index_files, and the figures show up on the website!

So, for the future the right flow to publish is:

1. commit everything on the main branch
2. push on the main branch to origin
3. quarto publish gh-pages

Right?

[mcanouil]

I am not sure what I did wrong. I just imported the template, worked on the qmd files, and pushed it to the remote repo as indicated in the guide. I definitely did not use the quarto publish gh-pages command.

Sorry, I am confused. What guide exactly are you referring to?

[robpetrosino]

This is the first guide I was following: https://quarto.org/docs/manuscripts/publishing.html, which assumes you clone the quarto template. Earlier this morning I found this other guide that instead tells you what to do in case you didn't clone the template and/or didn't close all branches from the template.

I followed the first guide, but only after executing the flow 1-3 above the index_files folder appeared on the gh-pages branch, and the figures show up on the website!

[mcanouil]

I see, the section is not accurate.

• https://quarto.org/docs/manuscripts/publishing.html#push-to-publish

1. quarto render is needed to update the _freeze directory with computation results (not very clear currently and could be improved)
2. quarto publish gh-pages is needed before the GitHub Action can take over the publishing part.

[robpetrosino]

The page you linked here says to "commit and push the changes to Github", which I interpreted as push in the main branch. But now you seem to say that it is not strictly necessary for the GH Page to get updated, and we actually need to quarto publish gh-pages after quarto render (rather than just push in the main/origin branch). Is that correct?

[mcanouil]

commit and push the changes to Github

"changes" refers to your source code (Quarto documents, _quarto.yml, etc.) AND _freeze directory.

quarto publish gh-pages is only needed once, the very first time you publish to GitHub Pages (it initialise almost everything on GitHub side).

The part just before https://quarto.org/docs/publishing/github-pages.html#ignoring-output is outdated and not needed anymore. quarto publish gh-pages does that for you.

[robpetrosino]

Got it. So just to be clear -- for future updates of the same page, I will just have to push in the main branch, and the new version should be deployed in the gh-pages branch too. Correct?

[mcanouil]

Yes, using the GitHub Actions workflow you should have if you cloned/forked the template repository.