Shinylive apps are not isolated

[davidchall]

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

There is an issue with how Quarto locates auxiliary source files for Shiny apps, so these apps are not truly isolated (as implied by the standalone config field). This prevents me from using common file naming patterns across multiple Shiny apps in a single Quarto document.

For example, consider a directory structure:

• test.qmd
• app1/
  • app.py
  • helper.py (contains helper1)
• app2/
  • app.py
  • helper.py (contains helper2)

When I attempt to use helper1 and helper2 in their respective apps, then I encounter an ImportError because one of the apps looks at the helper.py source code of the other app. It appears to be a race condition which app is located, because the working app alternates randomly.

Steps to reproduce

Since this requires several files to demonstrate the issue, I've created a reprex repo here: https://github.com/davidchall/quarto-shinylive-bug

Here's the Quarto source file from this repo:

---
title: Test
format: html
filters:
  - shinylive
---

```{shinylive-python}
#| standalone: true

## file: app.py
{{< include "app1/app.py" >}}

## file: helper.py
{{< include "app1/helper.py" >}}
```

```{shinylive-python}
#| standalone: true

## file: app.py
{{< include "app2/app.py" >}}

## file: helper.py
{{< include "app2/helper.py" >}}
```

Actual behavior

Only one app loads successfully, because both apps attempt to load from app2/helper.py. The error message is:

  File "/home/pyodide/app_0wpouot7xx0ufdvibcl1/app.py", line 1, in <module>
    from helper import helper1
ImportError: cannot import name 'helper1' from 'helper' (/home/pyodide/app_uwgf7rt7kak5fn8bus6x/helper.py). Did you mean: 'helper2'?

Expected behavior

The first app should load helper1 from app1/helper.py and the second app should load helper2 from app2/helper.py. The apps should be isolated.

Your environment

• IDE: VSCode 1.104.1
• macOS 15.6.1

Quarto check output

Quarto 1.8.24
[✓] Checking environment information...
Quarto cache location: /Users/davidhall/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.6.3: OK
Dart Sass version 1.87.0: OK
Deno version 2.3.1: OK
Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.8.24
Path: /Applications/quarto/bin

[✓] Checking tools....................OK
TinyTeX: (external install)
Chromium: (not installed)

[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /Users/davidhall/Library/TinyTeX/bin/universal-darwin
Version: 2022

[✓] Checking Chrome Headless....................OK
Using: Chrome found on system
Path: /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
Source: MacOS known location

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

[✓] Checking Python 3 installation....OK
Version: 3.10.18
Path: /Users/davidhall/code/shiny-treeview/.venv/bin/python3
Jupyter: 5.8.1
Kernels: python3

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

[✓] Checking R installation...........OK
Version: 4.5.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
knitr: 1.50
rmarkdown: 2.29

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

[cscheid]

The first app should load helper1 from app1/helper.py and the second app should load helper2 from app2/helper.py. The apps should be isolated.

What makes you expect that? Include shortcodes behave like copy-and-pasting; we make this explicit in the docs.

[davidchall]

The first app should load helper1 from app1/helper.py and the second app should load helper2 from app2/helper.py. The apps should be isolated.

What makes you expect that? Include shortcodes behave like copy-and-pasting; we make this explicit in the docs.

See the .qmd source file under "Steps to reproduce". The 1st app includes app1/helper.py and the 2nd app includes app2/helper.py. In fact, if I look at the generated test.html file then I see that the source code is copied correctly. The problem lies downstream from the include statement.

[mcanouil]

If the include shortcode does properly copy the code as it should, the issue is not Quarto but the shinylive extension on the way it resolves the code in such context.

Does the issue persist if you copy the code without using the include shortcode?

[davidchall]

Yes, the issue persists. I've updated https://github.com/davidchall/quarto-shinylive-bug to simplify the MBE.

Should we transfer this issue to https://github.com/quarto-ext/shinylive? Or do I need to create a new issue there?

[mcanouil]

So, if there is an issue it is either at the Quarto extension or Pyodide level or shiny.

Carlos will decide to transfer or not.

[cscheid]

Ok, thanks for clarifying! Let's hear from the shinylive extension folks first, and we can reopen this issue if we learn that it's quarto-cli after all.