multi-line fig-cap in .qmd notebook still broken

[rmnldwg]

Bug description

First, I think this is the same issue as #6521. But it not only affects the rendering of .qmd files to .ipynb, but also the notebooks of manuscript projects. I hope it was ok to open a new issue, I did not know if a comment under the old one would have been enough or not.

When using the "manuscript" project, long fig-caps cause comically wide HTML previews. Trying to use a multi-line fig-cap does not work at all: It gets wrongly transformed and no figure output is displayed.

Steps to reproduce

First, the _quarto.yml file:

project:
  type: manuscript

manuscript:
  article: index.qmd
  notebooks: 
    - notebook: figures.qmd

format:
  html: default

Then the main manuscript index.qmd:

---
title: Manuscript
authors:
  - name: Roman Ludwig
---

## Section
This is a simple placeholder for the manuscript's main document.

{{< embed figures.qmd#fig-some-lines >}}

The notebook figures.qmd, once with one long fig-cap line:

---
title: Plotting Figures
---
```{python}
#| label: fig-some-lines
#| fig-cap: Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Donec ultrices tincidunt arcu non. Nulla aliquet porttitor lacus luctus accumsan tortor posuere ac. Dui accumsan sit amet nulla facilisi. Et tortor at risus viverra.
import matplotlib.pyplot as plt
import numpy as np

x = np.linspace(0., 1., 10)
data = np.random.uniform(size=10)
plt.plot(x, data)

plt.show()
```

And then lastly, the figures.qmd notebook with a multi-line fig-cap:

---
title: Plotting Figures
---
```{python}
#| label: fig-some-lines
#| fig-cap: >-
#|   Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
#|   incididunt ut labore et dolore magna aliqua. Donec ultrices tincidunt arcu non.
#|   Nulla aliquet porttitor lacus luctus accumsan tortor posuere ac. Dui accumsan sit
#|   amet nulla facilisi. Et tortor at risus viverra.
import matplotlib.pyplot as plt
import numpy as np

x = np.linspace(0., 1., 10)
data = np.random.uniform(size=10)
plt.plot(x, data)

plt.show()
```

Expected behavior

A single long line on a notebook's code cell should not cause the entire document to get rendered as wide as that cell, I guess?

But more importantly, multi-line fig-caps should work as one would expect YAML to work.

Actual behavior

In the first case, when using one long line in the fig-cap, the resulting notebook gets rendered way too wide:

While in the second case, it does not get rendered at all, because the figure caption is wrongly formatted (I presume):

Somehow it transforms the fig-cap: >- line to fig-cap: |- and inserts a blank line afterwards.

Note that in the main article, it looks fine when using the single long line, since there the code cell is not displayed.

Also, I looked at the code that was merged in #7893 and it seems that the YAML in the cell tags is correctly parsed. I.e., if I run nb_cell_yaml_options("python", cell) from here with the multi-line fig-cap, the returned dictionary contains a "fig-cap" key and its value has no newline characters \n in it.

I am not sure this helps, but I think the issue is not at the parsing step 😅

Your environment

• IDE: VS Code
• OS: Ubuntu 22.04 inside WSL2 on Widnows 11

I installed numpy, matplotlib, and jupyter to create this minimal plot.

Quarto check output

Quarto 1.5.30
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.13: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.30
      Path: /opt/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.04
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/rmnldwg/.TinyTeX/bin/x86_64-linux
      Version: 2024

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.10.12
      Path: /home/rmnldwg/repos/quarto-test/.venv/bin/python3
      Jupyter: 5.7.2
      Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........(None)

[mcanouil]

Sorry, but is all of that needed to reproduce?
Manuscript, the embed and the first figures.qmd does not seem to be useful.

The following seems quite enough:

---
title: Plotting Figures
---

```{python}
#| label: fig-some-lines
#| fig-cap: >-
#|   Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
#|   incididunt ut labore et dolore magna aliqua. Donec ultrices tincidunt arcu non.
#|   Nulla aliquet porttitor lacus luctus accumsan tortor posuere ac. Dui accumsan sit
#|   amet nulla facilisi. Et tortor at risus viverra.
import matplotlib.pyplot as plt
import numpy as np

x = np.linspace(0., 1., 10)
data = np.random.uniform(size=10)
plt.plot(x, data)

plt.show()
```

---

For some reasons, additional linebreaks are added which makes the parser fails to parse the image markup. Note the difference with what is emitted using knitr.

Quarto document	HTML
--- title: Plotting Figures keep-md: true --- ```{python} #| label: fig-some-lines #| fig-cap: >- #| Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor #| incididunt ut labore et dolore magna aliqua. Donec ultrices tincidunt arcu non. #| Nulla aliquet porttitor lacus luctus accumsan tortor posuere ac. Dui accumsan sit #| amet nulla facilisi. Et tortor at risus viverra. import matplotlib.pyplot as plt import numpy as np x = np.linspace(0., 1., 10) data = np.random.uniform(size=10) plt.plot(x, data) plt.show() ```	--- title: Plotting Figures keep-md: true --- ::: {#cell-fig-some-lines .cell execution_count=1} ``` {.python .cell-code} import matplotlib.pyplot as plt import numpy as np x = np.linspace(0., 1., 10) data = np.random.uniform(size=10) plt.plot(x, data) plt.show() ``` ::: {.cell-output .cell-output-display} {#fig-some-lines width=571 height=411} ::: :::
--- title: Plotting Figures keep-md: true --- ```{r} #| label: fig-some-lines #| fig-cap: >- #| Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor #| incididunt ut labore et dolore magna aliqua. Donec ultrices tincidunt arcu non. #| Nulla aliquet porttitor lacus luctus accumsan tortor posuere ac. Dui accumsan sit #| amet nulla facilisi. Et tortor at risus viverra. plot(1) ```	--- title: Plotting Figures keep-md: true --- ::: {.cell} ```{.r .cell-code} plot(1) ``` ::: {.cell-output-display} {#fig-some-lines width=672} ::: :::

[rmnldwg]

Thanks for the quick response and sorry for the convoluted example!

I only encountered this issue in the supporting notebooks of the manuscript project type. Because in a default project (or in the main article of the manuscript project)...

1. ... the cell tags are not rendered, thus the long fig-cap doesn't bother me.
2. ... the rendered HTML code cell has a horizontal scroll bar (see image below).

So, I guess I wanted to show that it's sort of two related problems:

1. the wrong handling of cell tag YAML
2. the way code cells are displayed in manuscript notebooks

Maybe I should have just opened two issues? Anyways, apart from this minor hiccup, I really do enjoy writing papers with Quarto. Much better than using LaTeX directly! 👍🏻

[mcanouil]

the rendered HTML code cell has a horizontal scroll bar (see image below).

This is expected and can be controlled, see https://quarto.org/docs/output-formats/html-code.html#code-overflow.

the cell tags are not rendered, thus the long fig-cap doesn't bother me.

Sorry, but I don't understand what you mean here.

Note that #9421 (comment) shows how to easily reproduce the issue which is unrelated to Manuscript.

[rmnldwg]

Sorry for the late response!

Ok, maybe I did a bad job at trying to convey my problem. The issue I was trying to raise only affects the notebooks supporting a manuscript article. Like the data-screening.ipynb in the La Palma Earthquakes example from your documentation.

This [code overflow] is expected and can be controlled, see https://quarto.org/docs/output-formats/html-code.html#code-overflow.

For some reason, in those supporting notebooks to a manuscript project, the setting code-overflow does not have any effect (neither in the front matter, nor as a cell tag). This is why my supporting notebooks all become comically wide.

So, basically my issue is purely cosmetical. And it would be solved by either of two things:

1. multi-line cell tag YAML gets parsed correctly
2. code-overflow adjustable in notebooks supporting a manuscript project

If the second point is intended, then I am happy to shorten my example above or close the issue completely in favour of reopening #6521.

Thanks for your patience with me!