fix: does not require README.qmd for Quarto website

[eitsupi]

Fix #292

I don't know if ideally we should render README.Rmd / qmd, but we should be able to fix the error for now anyway.

[vincentarelbundock]

I believe that Quarto requires a index.qmd file, otherwise it will not build the website.

Currently, we enforce README.qmd and copy that over as index.qmd. If you want to make that change, my guess is that you'll have to convert README.md to index.qmd and ensure that it contains valid Quarto code.

[eitsupi]

I believe that Quarto requires a index.qmd file, otherwise it will not build the website.

No, Quarto CLI does not require any qmd file; if an index.html file is required, the source file can be index.md, index.Rmd, index.ipynb, or whatever.

[vincentarelbundock]

No, Quarto CLI does not require any qmd file; if an index.html file is required, the source file can be index.md, index.Rmd, index.ipynb, or whatever.

Could this possibly depend on the output format? Here, we output to a "website" format.

If you're very confident and add a test for a toy repo without README.md that builds properly, we should of course move forward.

I'm just surprised because I think I remember adding this check because we got bug reports from users who had README.md but not README.qmd.

[eitsupi]

Could this possibly depend on the output format? Here, we output to a "website" format.

I am sure Quarto will not require qmd files in any output format (otherwise it would be very difficult to use for users who only want to use ipynb, right?)
For example, there is not a qmd file in this repository (website source), but it has been around since before the Quarto CLI reached version 1.
https://github.com/rocker-org/website

[vincentarelbundock]

good example, thanks.

[eitsupi]

I believe the test project is now rendering correctly.

[vincentarelbundock]

@etiennebacher This seems like a clear improvement to me. Do you want to check before merging?

[etiennebacher]

Thanks both, I'll take a quick look later today

[vincentarelbundock]

I can't seem to build the marginaleffects website with this branch. It's a rather complicated website which requires a reticulate virtual environment with some packages. So not sure either of you will want to try it, but I'll post the error message here.

At first glance, it seems related to the index.md change.

[56/57] index.md
ERROR: You must use the .qmd extension for documents with executable code.

Stack trace:
    at Object.execute (file:///Applications/quarto/bin/quarto.js:40980:23)
    at renderExecute (file:///Applications/quarto/bin/quarto.js:78226:48)
    at renderFileInternal (file:///Applications/quarto/bin/quarto.js:78394:49)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async renderFiles (file:///Applications/quarto/bin/quarto.js:78262:17)
    at async renderProject (file:///Applications/quarto/bin/quarto.js:78672:25)
    at async Command.actionHandler (file:///Applications/quarto/bin/quarto.js:83271:32)
    at async Command.execute (file:///Applications/quarto/bin/quarto.js:8018:13)
    at async Command.parseCommand (file:///Applications/quarto/bin/quarto.js:7908:20)
    at async quarto (file:///Applications/quarto/bin/quarto.js:118497:9)
Error in `quarto::quarto_render()`:
✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Backtrace:
     ▆
  1. └─altdoc::render_docs(verbose = TRUE, freeze = TRUE)
  2.   └─altdoc:::.import_settings(...)
  3.     └─altdoc (local) finalize(settings, path, verbose, freeze)
  4.       └─quarto::quarto_render(...)
  5.         └─quarto:::quarto_run(args, echo = TRUE, quarto_bin = quarto_bin)
  6.           └─base::tryCatch(...)
  7.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.                 └─value[[3L]](cond)
 10.                   └─cli::cli_abort(msg, call = .call, parent = e)
 11.                     └─rlang::abort(...)
Execution halted
make: *** [website] Error 1

[eitsupi]

I can't seem to build the marginaleffects website with this branch.

My guess is that this is where this comes from.
https://github.com/vincentarelbundock/marginaleffects/blob/64b946a6443ad143bb4d25bcc24357ec1e501bad/README.md?plain=1#L94-L101

``` {latex}

I have never seen this notation before, what is the need for it?
If I understand correctly, this is not actually an executable code block, so I think this needs to be fixed.

[eitsupi]

Maybe you want to something like ```{=latex}?
https://pandoc.org/MANUAL.html#extension-raw_attribute
https://bookdown.org/yihui/rmarkdown-cookbook/raw-latex.html

[vincentarelbundock]

Wow @eitsupi you're very good at this. Solves it. Thanks. I'll stop bugging you now.

[eitsupi]

Never mind, I am glad you were able to resolve the issue! (I know nothing about latex......)

[etiennebacher]

Thanks, LGTM, especially if it doesn't break the docs of other packages. I'll merge but any idea about the windows failure?

[eitsupi]

any idea about the windows failure?

I have no idea.

Where does Rplots.pdf come from?