Header gets promoted to title on jupyter kernel, when code block appears first.

[wklimowicz]

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

The typst format "promotes" the first subheading to a title, even when I specify no title in a document, but only if a code block comes first. If the code block comes second, it behaves as expected.

Steps to reproduce

---
format:
  typst:
    keep-typ: true
---

<!-- #### First Header here -->

```{python}
#| echo: false
#| output: false
print("Hello")
```

#### First Header

Text.

If #### First Header is placed after the python code block, it becomes a title. If it's placed before the code block, it remains a header. This is the diff of the typst:

331d330
<   title: [First Header],
336a336,337
> = First Header
> <first-header>

Actual behavior

The first subsection header becomes the title.

Expected behavior

There should be no title, the subsection header should remain a subsection header.

Your environment

• IDE: Neovim
• Fedora 42

Quarto check output

Quarto 99.9.9
[✓] Checking environment information...
      Quarto cache location: /home/wojtek/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.8.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.4.5: OK
      Typst version 0.14.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: a7d8b6a794780a80df3728c94b4aaaa8299adb85
      Path: /home/wojtek/bin/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/wojtek/.TinyTeX/bin/x86_64-linux
      Version: 2025

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /usr/bin/google-chrome
      Source: PATH

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

[✓] Checking R installation...........OK
      Version: 4.5.0
      Path: /opt/R/4.5.0/lib64/R
      LibPaths:
        - /home/wojtek/.local/share/R/x86_64-pc-linux-gnu-library/4.5
        - /opt/R/4.5.0/lib64/R/library
      knitr: 1.50
      rmarkdown: 2.30

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

[✓] Checking Python 3 installation....OK
      Version: 3.13.11
      Path: /usr/bin/python3
      Jupyter: 5.7.2
      Kernels: python3, julia-1.11

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

[✓] Checking Julia installation...

[wklimowicz]

Looks like this only happens with jupyter engine with python (or matlab in my case): R/Julia are fine.

It also reproduces across formats other than typst, same thing with pdf/html.

---
format:
  pdf:
    keep-tex: true
---

```{python}
#| echo: false
#| output: false
print("Hello")
```

#### First Header

Text.

[wklimowicz]

The workaround I've found is to set title: "" within the pdf: section of the YAML: interestingly it doesn't work if you set it at the root level of the config:

---
format:
  pdf:
    title: ""
    keep-tex: true
---

[wklimowicz]

Actually, this still doesn't get around the bug: one header just disappears. This is probably the cleanest repro, works across all formats as long as it goes via jupyter.

---
format:
  typst:
    title: ""
    keep-typ: true
---

```{python}
```

#### First Header

Text.

### Second Header

Test.

[wklimowicz]

Leaving this Gemini patch here: it does fix my bug, but I don't understand the iteration that's happening to know if this won't break other stuff

gemini-cli diff + explanation

diff --git i/src/core/jupyter/jupyter-fixups.ts w/src/core/jupyter/jupyter-fixups.ts
index de0bbe325..ad979fa24 100644
--- i/src/core/jupyter/jupyter-fixups.ts
+++ w/src/core/jupyter/jupyter-fixups.ts
@@ -184,10 +184,11 @@ export function fixupFrontMatter(nb: JupyterNotebook): JupyterNotebook {
         title = headingText;
         cell.source = nbLines(lines);
         break;
-      } else if (currentCellIdx !== frontMatterCellIndex) {
-        break;
       }
     }
+    if (currentCellIdx !== frontMatterCellIndex) {
+      break;
+    }
     currentCellIdx++;
   }
 

The bug was located in src/core/jupyter/jupyter-fixups.ts within the
fixupFrontMatter function. This function iterates through the cells of a
Jupyter notebook to find a heading that can be promoted to the document title
when no title is explicitly provided in the YAML front matter.

The original logic failed to stop looking for a title heading if it
encountered non-markdown cells (like code blocks) before a markdown heading.
It only stopped if it encountered a markdown cell that didn't contain a
heading at its start. This allowed headings appearing after code blocks to be
incorrectly promoted to the document title, removing them from the body and
shifting the heading levels of the rest of the document (due to Pandoc's
shift-heading-level-by: -1).

The fix ensures that the title search terminates if it encounters any cell that
is not the YAML front matter cell and either:
 1. Is not a markdown cell.
 2. Is a markdown cell but does not have a heading at the very beginning.

This restricts heading promotion to only the very first content cell of the
notebook (optionally preceded by a single YAML front matter cell), which is
consistent with how Quarto handles title inference in other formats.

1 // src/core/jupyter/jupyter-fixups.ts
2
3   for (const cell of nb.cells) {
4     if (cell.cell_type === "markdown") {
5       const { lines, headingText, contentBeforeHeading } =
6         markdownWithExtractedHeading(
7           nbLines(jupyterCellSrcAsLines(cell)).join(""),
8         );
9       if (headingText && !contentBeforeHeading) {
10         title = headingText;
11         cell.source = nbLines(lines);
12         break;
13       }
14       // The old logic had the 'else if' here, which only triggered for markdown cells.
15     }
16
17     // The new logic correctly breaks for ANY cell that isn't the front matter cell 
18     // and didn't provide a title.
19     if (currentCellIdx !== frontMatterCellIndex) {
20       break;
21     }
22     currentCellIdx++;
23   }

I have verified this fix using a test script that covers:
 - Code block preceding a header (no promotion, fixed).
 - Header at the very start (promotion works).
 - Front matter followed by a header (promotion works).
 - Front matter followed by a code block then a header (no promotion, fixed).
 - Empty markdown cell at the start (no promotion).