quarto render fails with relative path and knitr-based notebook.

[gordonwoodhull]

Bug description

When producing multiple outputs for side-by-side comparison, I prefer to run my utils/render-all-formats.ts script from a parent directory.

However, I'm currently unable to run a knitr-based notebook using a relative path.

The error is

Error in rmarkdown:::abs_path(input) : 
  The file 'baz/foo.qmd' does not exist.

but the file does exist, and running rmarkdown:::abs_path('baz/foo.qmd') directly in R is okay.

I only somewhat regret bisecting this over a slow internet connection. I think it will be no surprise that the bad commit seems to be "create ProjectContext in single-file mode to guarantee engine and target caching" a28ac25. Two big steps forward and a baby step back!

Steps to reproduce

Minimal repro: put any knitr-based notebook in a subdirectory, e.g. this baz/foo.qmd

---
title: "relative path"
---

```{r}
print(1+1)
```

Then run

quarto render baz/foo.qmd

I'm not sure how to write a regression test for this, since it's about invocation rather than the content of the example.

Expected behavior

It should render the qmd inside the directory.

Actual behavior

Error in rmarkdown:::abs_path(input) : 
  The file 'baz/foo.qmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/gordon/src/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/gordon/src/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/gordon/src/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/gordon/src/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/gordon/src/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/gordon/src/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/gordon/src/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/gordon/src/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/gordon/src/quarto-cli/src/quarto.ts:160:3

Your environment

MacOS Sonoma 14.4.1

Quarto check output

Quarto 99.9.9
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.13: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
fatal: not a git repository (or any of the parent directories): .git
      Path: /Users/gordon/src/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.04
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/gordon/Library/TinyTeX/bin/universal-darwin
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: 5.7.1
      Kernels: python3

(|) Checking Jupyter engine render..../Users/gordon/Library/Python/3.9/lib/python/site-packages/urllib3/__init__.py:35: NotOpenSSLWarning: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: https://github.com/urllib3/urllib3/issues/3020
  warnings.warn(
[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.3.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
      knitr: 1.45
      rmarkdown: 2.25

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

[cscheid]

This is a really bad one 😬.

[cscheid]

More information

Adding an empty _quarto.yml file to the same directory is a workaround.

[gordonwoodhull]

If only I had remembered this hint before my demo!

Yes, adding empty _quarto.yml to the root works great as a workaround to get quarto run to work with relative paths.

[mine-cetinkaya-rundel]

I just ran into this as well. Using the Render button in RStudio worked but quarto_render() or quarto render didn't and required adding the empty _quarto.yml file.

In my case I was also trying to run these in a different directory in a withr::with_dir() call, which wasn't helped by adding an empty _quarto.yml file in the root of the project.