Output from Julia chunk broken into two parts

[sje30]

I've found a problem using 'quarto' when trying to render some simple
Julia code.

A full example of the quarto problem was reported here and
in turn, it was suggested this is a bug in Jupyter.

Example f.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8c784318",
   "metadata": {},
   "outputs": [],
   "source": [
    "println(typeof(ones(3,2)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8ed83174",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Julia 1.8.2",
   "language": "julia",
   "name": "julia-1.8"
  },
  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
   "name": "julia",
   "version": "1.8.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}

The output from the Julia chunk should be:

Matrix{Float64}

but that is broken over two output chunks as

Matrix{


Float64}

This was generated using:

% jupyter nbconvert f.ipynb --execute --to markdown
[NbConvertApp] Converting notebook f.ipynb to markdown
Starting kernel event loops.
[NbConvertApp] Writing 78 bytes to f.md
stephen@blur ~ % quarto render f.ipynb --execute --to markdown    

Starting julia-1.8 kernel...Done

Executing 'f.ipynb'
  Cell 1/2...Done
  Cell 2/2...Done

pandoc 
  to: markdown
  output-file: f.md
  standalone: true
  default-image-extension: png
  
Output created: f.md

f.md

---
pagetitle: f
toc-title: Table of contents
---

::: {.cell execution_count="1"}
``` {.julia .cell-code}
println(typeof(ones(3,2)))
```

::: {.cell-output .cell-output-stdout}
    Matrix{
:::

::: {.cell-output .cell-output-stdout}
    Float64}
:::
:::

System information

:::

% jupyter kernelspec list
Available kernels:
  ir           /Users/stephen/Library/Jupyter/kernels/ir
  julia-1.8    /Users/stephen/Library/Jupyter/kernels/julia-1.8
  python3      /Users/stephen/.pyenv/versions/3.10.6/share/jupyter/kernels/python3

% jupyter --version
Selected Jupyter core packages...
IPython          : 8.4.0
ipykernel        : 6.15.1
ipywidgets       : not installed
jupyter_client   : 7.3.4
jupyter_core     : 4.11.1
jupyter_server   : 1.18.1
jupyterlab       : 3.4.5
nbclient         : 0.6.6
nbconvert        : 6.5.3
nbformat         : 5.4.0
notebook         : 6.4.12
qtconsole        : not installed
traitlets        : 5.3.0


% uname -a
Darwin blur.lan 21.6.0 Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64

% quarto --version
1.1.251

[RRosio]

Hi @sje30, thank you for submitting this issue. We will keep this open in hopes that someone who uses the iJulia kernel can also verify that this is a jupyter issue but we recommend taking a look at this issue filed in the iJulia repo:JuliaLang/IJulia.jl#1047

[afshin]

Hi @sje30, I tried running your notebook with Julia 1.8.2 using both JupyterLab (3.5.0) and Jupyter Notebook (6.4.12) and in both cases, the output of my cell was correct:

I wonder if there's a minimum viable script we can follow to reproduce the error. Do you have any suggestions about your environment that might help isolate where the issue is arising?

[sje30]

thanks for investigating.

In quarto-dev/quarto-cli#3093 @cscheid noted that he could reproduce the error, but that he had to run the script a couple of times to get the broken output, so maybe it is stochastic?

For me, I got it every time I ran this code (rather than using the web-interface):

jupyter nbconvert f.ipynb --execute --to markdown

so does it make a difference when you run it in batch?

I also though @RRosio had a helpful point, that it seems to occur in other contexts too: JuliaLang/IJulia.jl#1047

[RRosio]

Hi @sje30, thank you again for opening this issue. As of now, we don't have a way to reliably reproduce this issue that indicates it is an issue coming from any part of the Jupyter stack. If new information comes up and it indicates that this is a problem with Jupyter we can go ahead and reopen this issue. Thank you!