Supporting file are cleanup to soon when using multiformat

[Sciemon]

Bug description

An mwe can be found in the github repo
https://github.com/Sciemon/issue_figures_folder

Somehow latex assumes the figures are in a 'mediabag' folder that does not exist.

Steps to reproduce

It is only possible to render (with quarto render ...) the file 'model_requirements.qmd' if 'docx: default' is deleted from the yaml.

Expected behavior

if 'docx: default' is deleted, the pdf is rendered

Actual behavior

Otherwise latex throws the following error:

ERROR:
compilation failed- error
Unable to load picture or PDF file 'model_requirements_files/mediabag/figs/SVS_droop.pdf'.

}
l.373 ...ements_files/mediabag/figs/SVS_droop.pdf}###

Your environment

• IDE: VSCode 1.85.2
• OS: Windows 10

Quarto check output

Quarto 1.4.545
[>] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.69.5: OK
Deno version 1.37.2: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
Version: 1.4.545
Path: C:\Program Files\Quarto\bin
CodePage: 1252

[>] Checking tools....................OK
TinyTeX: v2024.01
Chromium: (not installed)

[>] Checking LaTeX....................OK
Using: TinyTex
Path: C:\Users\seberlein\AppData\Roaming\TinyTeX\bin\windows
Version: 2023

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

[>] Checking Python 3 installation....OK
Version: 3.11.7
Path: C:/Users/seberlein/AppData/Local/Programs/Python/Python311/python.exe
Jupyter: 5.7.1
Kernels: python3

(-) Checking Jupyter engine render....Traceback (most recent call last):
File "C:\Program Files\Quarto\share\jupyter\jupyter.py", line 21, in
from notebook import notebook_execute, RestartKernel
File "C:\Program Files\Quarto\share\jupyter\notebook.py", line 14, in
from yaml import safe_load
ModuleNotFoundError: No module named 'yaml'
[>] Checking Jupyter engine render....OK

[cderv]

Some context about the issue.

This is similar to this one

• gfm output gets overwritten if other formats are also generated #6705

but happens with mediabag supporting files and with output file name conflict.

Overall issue is order of cleanup for supporting files

I am putting back what I shared there at #6705 (comment) by adapting to this use case.

• Cleanup code is in renderCleanup()
  

  quarto-cli/src/command/render/cleanup.ts

  Lines 48 to 55 in 248a3a4

  	// if we aren't keeping the markdown or text and we are instructed to
  	// clean supporting files then do it
  	if (
  	!format.execute[kKeepMd] &&
  	!format.render[kKeepTex] &&
  	!format.render[kKeepTyp] &&
  	supporting
  	) {

  
  we are cleanup supporting file in some situations and this happens with docx format.

• We cleanup the whole directory and not just the file associated to the format
  

  quarto-cli/src/command/render/cleanup.ts

  Lines 83 to 88 in 248a3a4

  	// ammend supporting with mediabag if it exists
  	// (we can always delete the mediabag because it is generated by filters)
  	const mediabagDir = join(dirname(input), filesDirMediabagDir(input));
  	if (existsSync(mediabagDir)) {
  	supporting.push(mediabagDir);
  	}

• When rendering to --to all we pass through this 3 times, and not in the order I though.

  • Last format is called first. So docx cleanup will happen before PDF rendering.
  • Meaning that when PDF rendering happens, the shared resources is already deleted.

  quarto-cli/src/command/render/render-files.ts

  Lines 717 to 724 in e831190

  	onPostProcess: async (renderedFormats: RenderedFormat[]) => {
  	let completion = renderCompletions.pop();
  	while (completion) {
  	renderedFiles.push(await completion.complete(renderedFormats));
  	completion = renderCompletions.pop();
  	}
  	renderedFiles.reverse();
  	},

• If docx is called first, the cleaning step happens last. So PDF rendering can work ok.

Try just putting docx first as a workaround

diff --git a/model_requirements.qmd b/model_requirements.qmd
index 522edb4..3f12bf1 100644
--- a/model_requirements.qmd
+++ b/model_requirements.qmd
@@ -8,6 +8,7 @@ toc: true
 number-sections: true
 highlight-style: pygments
 format:
+  docx: default
   pdf:
     geometry:
       - top=30mm
@@ -17,7 +18,6 @@ format:
     html-math-method: katex
     default-image-extension: svg
     css: style.css
-  docx: default
 ---

Setting keep-md: true in the YAML as global, or just under docx format will also prevent the cleaning before PDF Rendering and should avoid the issue

This is a topic we can deal with

• Epic: Execution Planner #6518

It will happen with any combination of formats mixing

• Format that needs cleaning always (like docx)
• And other that may or may not (like HTML and embed-resources) or PDF that needs supporting file for tex rendering.

This would probably be the better options. @cscheid do you agree ?