[Bug]: chunk fails to run on context: setup

[jimjam-slam]

Bug description

This could potentially be related to #105 (although I'm not in a position to say for sure), but in the following reprex, running the second chunk fails with Error: object 'bad_mtcars' not found when the first chunk has context: setup.

If you remove context: setup from the first chunk and then run the two sequentially, the second runs as expected (printing the data frame).

---
title: "Test"
engine: knitr
filters:
  - webr
webr:
  packages: ["dplyr", "tibble", "crayon"]
format:
  html: default
---

This first chunk creates a dataset derived from `mtcars` for demonstration purposes:

```{webr-r}
#| label: spike-data
#| context: setup
mtcars |>
  tibble::rownames_to_column(var = "car") |>
  tibble::as_tibble() |>
  dplyr::select(car, cyl, disp, wt) |>
  dplyr::mutate(wt = dplyr::case_when(
    wt < 2 ~ -wt,
    TRUE ~ wt)) ->
bad_mtcars
```

Then we print it to see how it looks:

```{webr-r}
#| label: spike-data
bad_mtcars
```

Steps to reproduce

1. Render reprex doc as is and run chunk; note failure
2. Remove #| context: setup from first chunk
3. Re-render and run both chunks

Your environment

IDE: VSCode
OS: macOS 14.0

Here's the session info inside WebR (I was a little surprised that tibble and dplyr were loaded even if I didn't run either chunk—does putting them in the YAML load them too?)

R version 4.3.0 (2023-04-21)
Platform: wasm32-unknown-emscripten (32-bit)
Running under: emscripten

Matrix products: default
BLAS:   unknown 


locale:
[1] en_US.UTF-8 C           en_US.UTF-8 en_US.UTF-8 en_US.UTF-8 C          

time zone: Australia/Melbourne
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] crayon_1.5.2 tibble_3.2.1 dplyr_1.1.3 

loaded via a namespace (and not attached):
 [1] utf8_1.2.4       R6_2.5.1         tidyselect_1.2.0 webr_0.2.2      
 [5] magrittr_2.0.3   glue_1.6.2       pkgconfig_2.0.3  generics_0.1.3  
 [9] lifecycle_1.0.4  cli_3.6.1        fansi_1.0.5      vctrs_0.6.4.9000
[13] tools_4.3.0      pillar_1.9.0     rlang_1.1.2 

Quarto check output

Quarto 99.9.9
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.9: 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: 99.9.9
      Path: /Users/rensa/Code/quarto-cli/package/dist/bin

Check file:///Users/rensa/Code/quarto-cli/src/resources/vendor/deno-land/x/puppeteer@9-0-2/mod.ts
[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/rensa/Library/TinyTeX/bin/universal-darwin
      Version: 2021

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.7 (Conda)
      Path: /Users/rensa/miniforge3/bin/python
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with conda install jupyter

[✓] Checking R installation...........OK
      Version: 4.2.1
      Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources
      LibPaths:
        - /Users/rensa/Library/R/arm64/4.2/library
        - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
      knitr: 1.42
      rmarkdown: 2.21

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

[coatless]

This is a duplicate of #105 and #88 on the notion of the packages key not aligning nicely with the non-interactive cells.

(I was a little surprised that tibble and dplyr were loaded even if I didn't run either chunk—does putting them in the YAML load them too?)

From v0.3.8 onward, we added a new feature to autoload R packages specified in packages, e.g. library(packages[i]), prior to the document being modifiable.

https://quarto-webr.thecoatlessprofessor.com/qwebr-meta-options.html#autoload-packages

[coatless]

@jimjam-slam I reworked a bit on the non-interactive cells in #120. They should now respect the packages key completely.

Care to give it a go and let me know if something else is amiss?

quarto add coatless/quarto-webr@cell-state-manager

[jimjam-slam]

I'll give it a spin today!

[coatless]

@jimjam-slam thanks; please make sure to re-pull if you already grabbed a copy of dev as I pushed one more fix onto that branch.

[jimjam-slam]

Can confirm it's working great when I pull the cell-state-manager branch! Thanks very much—I'll be keen to see this hit main!

[coatless]

@jimjam-slam excellent; I appreciate it!

After I clean up how non-interactive cells are displayed visually, this branch will likely hit main in the next 24 hours.

Main changes for the visualization relate to state changes for non-interactives, e.g. loading webr ... , hidden cells executing, processing this cell, deleting status if setup.

Still have a few more tweaks related to introducing a new toolbar above interactive cells. c.f. #91 .

[jimjam-slam]

Nice! I wrote up a blog post while exploring the new quarto-webr functionality; I'll put it out once I get to test everything together!

[coatless]

Merged in.

The status visualization changes that were committed in can be seen here:

I'll probably regress showing a visual indicator for the setup context in the document.