Section Numbering Starts at 0 (e.g., 0.1, 0.1.1) in PDF Output with number-sections: true

[stevefatz95]

Description

Hi everyone,

When generating a PDF with Quarto, the section numbering starts with "0" (e.g., 0.1, 0.1.1) instead of beginning at "1". This appears to be caused by the inclusion of chapter numbering, which starts at zero. I want to remove chapter numbering entirely so that sections and subsections are numbered independently (e.g., 1, 1.1, 1.1.1) without any leading "0".

Here is a minimal reproducible example of the YAML configuration:

---  
title: "Sample Document"  
author: "Anonymous"  
date: 01-01-2025  
bibliography: references.bib  
biblio-style: authoryear  
format:  
  pdf:  
    latex_engine: xelatex  
    keep_tex: true  
    fontsize: 12pt  
    link-citations: true  
    colorlinks: true  
    toc: true  
    number-sections: true  
    fig-width: 5  
    fig-height: 5  
---

Expected Behavior:

Sections and subsections should be numbered independently, starting at "1" (e.g., 1, 1.1, 1.1.1).

Actual Behavior:

The numbering starts with a leading "0" (e.g., 0.1, 0.1.1), which corresponds to chapter numbering (I assume).

Attempted Fixes:

• Added \setcounter{chapter}{1} in the include-in-header option, but this did not resolve the issue.
• Added crossref: chapters: false to the YAML configuration, but chapter numbering still appears as "0".
• Switched to the article class, which does remove the chapter numbering but introduces other structural changes, and section numbering still does not behave as expected. This is neither functional nor ideal.

Desired Outcome:

A way to completely remove chapter numbering from the PDF output while retaining section numbering starting at "1" (e.g., 1, 1.1, 1.1.1).

Thanks for your help.

[mcanouil]

Unfortunately your example is not reproducible as it has no content, thus there is no way to see what you are reporting here.
Additionally, we don't have the bib file.

Please, use quarto render on your example and ensure it shows your issue and that it can be rendered by other.
Remove all options not required to actually make your example minimal, e.g., I don't believe setting colorlinks has anything to do with your issue.

The goal is to make it as easy as possible for us to recreate your problem so that we can fix it: please help us help you! Thanks.

Finally, you are using options that does not exist in Quarto such as keep_tex. Quarto uses - not _.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[Steinthal]

Add to your YAML:

shift-heading-level-by: -1

(see Numbering in the Quarto documentation)

[stevefatz95]

Yes, when I rendered several notebooks in September 2024, they were rendered properly.

I have just tried to render one of them which is like 1.3 and the output is correct but all new notebooks I create lead to same issue you also see.

[mcanouil]

Could you check the nbformat version of your notebooks?
It might be related to the version of nbformat being used but I doubt that since using R thus engine: knitr the result is the same.

...
  "nbformat": 4,
  "nbformat_minor": 5
...

[mcanouil]

If you use the following in 1.3, you have the correct numbering?

---
title: XXXX
format: pdf
number-sections: true
jupyter: python3
---

## Introduction

```{python}
# Import libraries for loading the dataset

print("Hello World")
```

### Subsection

Lipsum text

[stevefatz95]

The nbformat is the following:

 },
 "nbformat": 4,
 "nbformat_minor": 5
}

which is the same one you shared.

And yes, using the following in 1.3 gives me the correct numbering when rendering.

Additionally the YAML is the following:

---
title: "xxxx"
author: "xxxxx"
date: 06-30-2024
date-format: long
bibliography: references.bib
biblio-style: authoryear
format:
  pdf:
    fig-width: 5
    fig-height: 5
    latex_engine: xelatex
    keep_tex: true
    number-sections: true
    fontsize: 12pt
    colorlinks: true
    cite-method: biblatex
    toc: true
---

Which again, is basically the same one previously shared with you.

[mcanouil]

Note that latex_engine: xelatex and keep_tex: true are not valid options.

I cannot reproduce your claim it works on 1.3.450.