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Quarto Manuscripts

Overview

Quarto manuscript projects provide a framework for writing and publishing scholarly articles. A Quarto manuscript lets you:

  • Use one or more notebooks or .qmd documents as the source of content and computations, and then publish these computations alongside the manuscript, allowing readers to dive into your code.

  • Produce manuscripts in multiple formats (including LaTeX or MS Word formats required by journals), and give readers easy access to all of the formats through a manuscript website.

The output of a Quarto manuscript is a website (live example). The article itself appears as the content of the website, and can include all the elements common to scholarly writing like figures, tables, equations, cross references and citations. The website also makes available other formats (e.g. PDF, Docx) as well as links to all of the computations used to create the article.

A screenshot of the content area on the manuscript webpage. Content shows a title block including the article title, authors, and abstract, body text, and an image with a caption.

Article Content

A screenshot of the menu on the right hand side of the manuscript webpage. The menu has headings: Table of contents, Other Formats, Notebooks and Other Links.

Navigation

On the right, you’ll see navigation: a table of contents for the article itself followed by links to Other Formats, Notebooks and Other Links.

Other Formats

These links allow a reader to download alternative formats of your article. In this example, there is an MS Word version that may be useful for a reviewer to provide feedback and a PDF version that uses the American Geophysical Union’s (AGU) template. Additionally, there is a MECA archive, a zip file that is designed to capture your article and its supporting documents into a single file suitable for sending to a publisher.

Notebooks

These are links to notebooks included in the manuscript. The “Article Notebook” is the notebook version of the article itself. In this example, “Data Screening” is a notebook from which a single cell is embedded in the article. Any other notebooks that are included in the project, even if they are not directly used in the article will also appear here.

When a reader visits any of these notebook links, they are served an HTML version of the notebook, allowing them to view the code and output without leaving their browser. In addition, a link to download the source code of the notebook is also provided.

Screenshot of the notebook view of data-screening.ipynb. The top of the page has a link Back to the Article and a button to Download Notebook. The content of the page includes some text and a cell displaying code.

HTML view of the Data Screening notebook

Get Started

Install Quarto

Manuscripts are a feature in the 1.4 release of Quarto. Before you get started, make sure you install the latest release version of Quarto.

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Highlights

Quarto 1.11 includes a security update and improvements to accessibility, Typst documents, and Julia notebooks.

The bundled Deno runtime is updated to 2.9.8, which rejects certificates from the compromised eMudhra / emSign certificate authorities. Earlier versions trusted these certificates, allowing an attacker on the network to impersonate HTTPS sites to commands such as quarto publish, quarto add, and quarto use template, and to TypeScript scripts run by Quarto. See quarto-dev/quarto-cli#15152 for details.

Accessibility improvements include:

  • Keyboard navigation: Bootstrap-themed HTML output adds a Skip to main content link, keyboard-operable website sidebar sections, and keyboard scrolling for overflowing code and cell output. A two-tone focus ring makes keyboard focus easier to follow.
  • Figures and diagrams: fig-alt is now honored for Mermaid and Graphviz diagrams in html, revealjs, docx, and typst output, and for images and computational figures in docx. Alternative text and visible captions remain separate.
  • Presentations: In normal slide view, keyboard focus stays on the current slide of a revealjs presentation. Screen readers no longer announce incremental content before it is revealed, and switching back to the presentation’s browser tab preserves keyboard focus.

Authoring improvements include:

  • Typst: Add lists of figures and tables with lof: true and lot: true. Proof, remark, and solution blocks now use theorem styling, and labeled blocks can be cross-referenced.
  • Definition lists: Write definition lists as a .definition-list div containing a nested bullet list, the definition-list syntax used by Quarto 2.
  • Julia notebooks: The julia engine supports keep-ipynb: true to save the executed notebook alongside its source. It also includes fixes for notebook execution hangs and metadata changes not invalidating cached cell outputs.

When upgrading:

  • On macOS, the bundled Deno 2.9.8 runtime requires macOS 12 or later. Update older macOS systems before upgrading to Quarto 1.11; rendering engines and formats may have additional requirements.
  • Shared metadata now reaches Pandoc templates and Lua filters as merged values. Inherited lists such as keywords combine with document values; a document list no longer replaces an inherited list in that metadata.
  • Custom HTML themes should use the Quarto focus-ring variables. Quarto no longer uses Bootstrap’s $focus-ring-color, $focus-ring-box-shadow, $btn-focus-width, or $btn-focus-box-shadow for its focus styling.
  • Page-level open-graph and twitter-card options are now validated. Unknown keys within these options in document front matter or _metadata.yml produce an error instead of being silently ignored.

Release Notes

You can find release notes and installers for all platforms in the download page.

Choose Your Tool

You can author Quarto manuscripts in any tool or notebook editor. The tutorials below walk you through authoring Quarto manuscripts with a few common tools.

Choose your tool to start learning:

Jupyter

VS Code

RStudio