Quarto Website in RStudio vs Positron

[ajsmit]

Good morning,

I maintain a Quarto website, The Tangled Bank, originally developed in RStudio. It has ~190 pages with many code chunks. In RStudio, data files are referenced with relative paths (relative to each .qmd file). Both “Run Current Chunk” and rendering (page or full site) work as expected.

In Positron, rendering still works, but interactive execution does not. Clicking “Run Cell” fails to find files when using paths relative to the .qmd. If I switch to paths relative to the project root (where the .Rproj file is), the chunks run interactively—but then rendering breaks.

I know about approaches like here::here(), but rewriting 190 .qmd files is not feasible.

Is there a way to make interactive code execution in Positron respect the same relative path behaviour as RStudio?

Thanks,
AJ Smit

[juliasilge]

Thanks for this question! We have some discussion on this in #6449, and I'll especially highlight what I say in #6449 (comment):

OK, I am going to sum up the current situation:

• The defaults right now are similar to RStudio's behavior; we use the file's directory as the working directory when rendering, and there are no changes to the console's working directory for code coming from .Rmd or .qmd. All of this can be set/changed by the user, using here::here() or the knit_root_dir argument to rmarkdown::render() or by explicitly changing the working directory.
• Positron does not have inline output, which is I bet what the original discussion was getting at. Setting the working directory in inline output makes sense, but it doesn't really for send-to-console execution.
• We could address this use case in the future with a treatment similar to what we land on for Python cells are evaluated in the project or current working directory #3156, for example providing a way to spawn a new, quasi-notebook-like console session for .Rmd and .qmd files.

So I can understand better, in RStudio did you use inline output in your .qmd files (vs. send-to-console)?

You can update the working directory from the File Explorer pane if you right click:

[ajsmit]

Hi Julia,

Thank you for the reply. Currently, in RStudio, I send the output inline in my Quarto document. But I am also comfortable sending to the Console. I am happy to adopt any approach that gives me the same experience in Positron.

To replicate the experience I have in Positron (sending output to the Console), I would have to make the following adjustment to RStudio:

• Tools > Global Options > R Markdown, then untick "Show output inline for all R Markdown documents".

Doing this, all data files pointed to from the base of the RStudio Project (also the base working directory in Positron) load as expected, but rendering (pages or the website) breaks.

So:

• In both RStudio and Positron, to render (website or individual page), I have to use relative file paths (i.e., relative to the subdirectory the .qmd file is in).
• To render code chunks to the console, I have to use paths referenced from the root of the RStudio Project or the base working directory in Positron.

Therefore, at present, Positron does not (seem to?) have a facility where I can render the entire project and execute code chunks, as each requires a different path specification.

Apologies if this does not make sense. As I always tell my students, if I fail to explain clearly, it is possible that I don't fully understand the problem myself.

AJ

[ajsmit]

Just a quick follow-up. Your suggestion to "update the working directory from the File Explorer pane" works, but then each time I change to a different folder within my project, I would have to manually adjust the working directory in this way. I need a solution that "sticks" regardless of where I am.

[juliasilge]

I am sorry you are dealing with these differences in behavior when it comes to working directory! I know it's super frustrating 😩

You might consider sticking with RStudio for this project until you are ready to take on a big migration, because the approach you use now only works with RStudio's specific behavior for inline output. When you are ready to make some big changes (because, say, something else about Positron makes it worth it to you) then I think what I would do is to use here::here() to make more explicit the expectations about where files are relative to the base directory of the project; the project will still work in RStudio after you make these changes (read more here). If you just want to do a bit of work here and there with Positron, then I would use the manual updates to the working directory for the console, like you mentioned.