document without executable code reported as containing executable code

[aronatkins]

Bug description

Using Quarto 1.3.340 on macOS.

Given the following Markdown file named index.md, Quarto reports that the file must be named *.qmd because it contains executable code. There is no executable code in this document.

# Simple Markdown

This is a simple Markdown document containing an embedded R Markdown document.

````markdown
---
title: "embedded"
---

This is an embedded R Markdown document contained within a simple Markdown
document.

```{r setup, echo = FALSE, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

The resulting error:

quarto render index.md
#> ERROR: You must use the .qmd extension for documents with executable code.
#> 
#> Error: You must use the .qmd extension for documents with executable code.
#>     at Object.execute (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:55533:23)
#>     at renderExecute (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:86465:48)
#>     at renderFiles (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:86588:57)
#>     at async render (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:90675:21)
#>     at async Command.fn (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:90850:32)
#>     at async Command.execute (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:8437:13)
#>     at async quarto (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:127535:5)
#>     at async file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:127553:9

Encountered when trying to adapt a mkdocs site to use Quarto without performing a bunch of file renaming.

Checklist

• [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
• [x] Please format your issue so it is easier for us to read the bug report.
• [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
• [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
• [x] Please provide the output of quarto check so we know which version of quarto and its dependencies you're running.

[aronatkins]

Workaround: Rename index.md to index.qmd.

[aronatkins]

[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.1: OK
      Dart Sass version 1.55.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.3.340
      Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 3.6.3
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/3.6/Resources/library
      knitr: 1.42.8
      rmarkdown: 2.20

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

[aronatkins]

Workaround: Rename the file to index.qmd (which causes https://github.com/quarto-dev/quarto-cli/issues/5603), then add the YAML preamble:

---
execute:
  eval: false
---

[dragonstyle]

Since the cell identification / execution is being done using a text based approach, the context of being nested within the markdown cell isn't really being respected (as you discovered). The easiest way to display the syntax for executable code blocks within a markdown document like this is to escape the cell with double braces like:

# Simple Markdown

This is a simple Markdown document containing an embedded R Markdown document.

````markdown
---
title: "embedded"
---

This is an embedded R Markdown document contained within a simple Markdown
document.

```{{r setup, echo = FALSE, include=FALSE}}
knitr::opts_chunk$set(echo = TRUE)

which should resolve into the proper form and not be treated as executable...

[aronatkins]

Thanks @dragonstyle. Confirmed that by escaping each embedded executable chunk, the document is no longer seen as executable. The real example had quite a few more (scattered across a number of documents).

[cscheid]

(Apropos of our discussion of eventually using Pandoc commonmark_x AST instead of text for things like breakquartomd, this would be one of the use cases.)