Add support for formatting `Rmd` files

[dereckmezquita]

Requesting support for Rmd documents and Qmd as well. Desired feature to support formatting only the R code blocks within the document.

PS: great formatter I especially enjoy the style and code layout it imposes - much better than other R formatters.

[juliasilge]

What kinds of problems are you having with using Air with .Rmd? For example, in Positron or VS Code, the Quarto extension does know about .Rmd and will provide formatting in the same way that it can for .qmd.

[dereckmezquita]

I'm having issues using air format from the command line on Rmd files. The formatter fails with "Failed to parse due to syntax errors" even though the file is valid and builds correctly with knitr.

After debugging, I found that Air appears to be parsing markdown prose as if it were R code. Specifically:

1. YAML arrays break parsing: tags: [statistics, mathematics] fails because Air interprets the brackets as R syntax. Changing to block format works:

tags:
  - statistics
  - mathematics

2. R keywords in prose break parsing: Any use of for, if, while, etc. in the markdown text causes Air to fail. For example, this prose fails:

This chapter establishes the framework for statistical thinking.

But this works:

This chapter establishes the framework of statistical thinking.

Minimal reproduction:

---
title: "Test"
tags:
  - statistics
  - mathematics
---

```{r setup}
x <- 1

This is a framework for analysis.

y <- 2

Running air format test.Rmd produces: ERROR Failed to format test.Rmd: Failed to parse due to syntax errors.

Remove the word "for" from the prose and it formats fine.

knitr works fine:

Air seems to be attempting to parse the entire file as R code rather than isolating the chunks.

Environment:

• Running via CLI: air format file.Rmd

Is Rmd/qmd support intended to work from the command line, or only within the IDE extensions? Happy to provide more details if helpful.

r$> sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Mexico_City
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.5.1

[DavisVaughan]

air format file.Rmd is not intended to work. You cannot format Rmd/Qmd from the command line using air right now. You can only format Rmd/Qmd via Positron while in Source Mode in a Rmd/Qmd.

[fh-mthomson]

The use case where I came across this was wanting to automate/enforce, via pre-commit hooks + CI (GitLab), that air was used.

Illustrative, simplistic example:

1. Currently: styler::style_dir() runs on all files (.R + .[R|q]md)
2. With air: air format . (only runs on .R files)

There are CI / pre-commit optimizations I can consider, but if air format file.Rmd doesn't work, I think it would be blocking.

PS air is amazing - so fast and so easy to use with Positron!

[etiennebacher]

If it's of interest, Ruff is now implementing formatting for Python code in markdown code blocks, and they also want to do this for Quarto documents: issue, PR (+ several other PRs for markdown support in general).