quarto-dev / quarto-dev/quarto-cli
qmd -> ipynb retains code lines only up to the first cell output
Open
@cscheid is already working on this.
Since Apr 7, 2025.
bug
ipynb-format
lua
- Dominant language
- JavaScript
- Stars
- 6k
- Forks
- 458
- Avg merge
- 1d 9h
- Merged PRs (30d)
- 41
Description
Bug description
The output of code into "source" field is only capturing up to the first emitted line of the code cell under engine: knitr.
For instance, if we have:
```{r}
x <- 1 + 1
x
print("Hello R world!")
sapply(1:10, function(x) x^2)
```
In the output.ipynb JSON have:
"source": [
"x <- 1 + 1\n",
"x"
],
with
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"[1] 2"
]
},
{
"output_type": "stream",
"name": "stdout",
"text": [
"[1] \"Hello R world!\""
]
},
{
"output_type": "stream",
"name": "stdout",
"text": [
" [1] 1 4 9 16 25 36 49 64 81 100"
]
}
],
Looking at the the native format, the results have been evaluated:
, Div
( "" , [ "cell" ] , [] )
[ CodeBlock
( "" , [ "r" , "cell-code" ] , [] ) "x <- 1 + 1\nx"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock ( "" , [] , [] ) "[1] 2" ]
, CodeBlock
( "" , [ "r" , "cell-code" ] , [] )
"print(\"Hello R world!\")"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock ( "" , [] , [] ) "[1] \"Hello R world!\"" ]
, CodeBlock
( "" , [ "r" , "cell-code" ] , [] )
"sapply(1:10, function(x) x^2)"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock
( "" , [] , [] )
" [1] 1 4 9 16 25 36 49 64 81 100"
]
]
So, I think what's happening is only the first CodeBlock is being sent to "source" while the others are being correctly condensed and, then, sent to "output". This is similar for Python code as well.
On a side note, is there a way to have engine: jupyter evaluate code from a Qmd? The evaluate: false doesn't seem to be able to be overridden and the authoring within qmd doesn't seem to retain cell results in the output.
https://quarto.org/docs/computations/r.html#disabling-execution
Steps to reproduce
qmd -> ipynb
---
title: "Quarto Conversion"
format: jupyter
engine: knitr
---
# Overview
Testing a Quarto an R + Python notebook
## Active cells
```{r}
x <- 1 + 1
x
print("Hello R world!")
sapply(1:10, function(x) x^2)
```
```{python}
y = 1 + 6
print(y)
print("Hello Python world!")
[x**2 for x in range(10)]
```
## Inactive cells
```r
print("Goodbye R world!")
2 + 2
sapply(1:10, function(x) x^4)
```
```python
print("Hello Python world!")
print([x**2 for x in range(10)])
8 + 5
```
ipynb format full JSON output
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Quarto Conversion\n",
"\n",
"# Overview\n",
"\n",
"Testing a Quarto an R + Python notebook\n",
"\n",
"## Active cells"
],
"id": "4f5a8b04-1046-41f8-9837-604ebaa0db0a"
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"[1] 2"
]
},
{
"output_type": "stream",
"name": "stdout",
"text": [
"[1] \"Hello R world!\""
]
},
{
"output_type": "stream",
"name": "stdout",
"text": [
" [1] 1 4 9 16 25 36 49 64 81 100"
]
}
],
"source": [
"x <- 1 + 1\n",
"x"
],
"id": "da39a8ca-a365-49e1-8e18-e465c57b33d7"
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"7"
]
},
{
"output_type": "stream",
"name": "stdout",
"text": [
"Hello Python world!"
]
},
{
"output_type": "stream",
"name": "stdout",
"text": [
"[0, 1, 4, 9, 16, 25, 36, 49, 64, 81]"
]
}
],
"source": [
"y = 1 + 6\n",
"print(y)"
],
"id": "f2d24e33-fbe5-48e1-a4b6-18d181937c61"
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Inactive cells\n",
"\n",
"``` r\n",
"print(\"Goodbye R world!\")\n",
"2 + 2\n",
"\n",
"sapply(1:10, function(x) x^4)\n",
"```\n",
"\n",
"``` python\n",
"print(\"Hello Python world!\")\n",
"print([x**2 for x in range(10)])\n",
"8 + 5\n",
"```"
],
"id": "d346e134-b945-4ad8-beea-cbf09a0b8340"
}
],
"nbformat": 4,
"nbformat_minor": 5,
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
}
}
}
qmd -> native
---
title: "Quarto Conversion"
format: native
engine: knitr
---
# Overview
Testing a Quarto an R + Python notebook
## Active cells
```{r}
x <- 1 + 1
x
print("Hello R world!")
sapply(1:10, function(x) x^2)
```
```{python}
y = 1 + 6
print(y)
print("Hello Python world!")
[x**2 for x in range(10)]
```
## Inactive cells
```r
print("Goodbye R world!")
2 + 2
sapply(1:10, function(x) x^4)
```
```python
print("Hello Python world!")
print([x**2 for x in range(10)])
8 + 5
```
Native output
Pandoc
Meta
{ unMeta =
fromList
[ ( "title"
, MetaInlines [ Str "Quarto" , Space , Str "Conversion" ]
)
]
}
[ Header 1 ( "overview" , [] , [] ) [ Str "Overview" ]
, Para
[ Str "Testing"
, Space
, Str "a"
, Space
, Str "Quarto"
, Space
, Str "an"
, Space
, Str "R"
, Space
, Str "+"
, Space
, Str "Python"
, Space
, Str "notebook"
]
, Header
2
( "active-cells" , [] , [] )
[ Str "Active" , Space , Str "cells" ]
, Div
( "" , [ "cell" ] , [] )
[ CodeBlock
( "" , [ "r" , "cell-code" ] , [] ) "x <- 1 + 1\nx"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock ( "" , [] , [] ) "[1] 2" ]
, CodeBlock
( "" , [ "r" , "cell-code" ] , [] )
"print(\"Hello R world!\")"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock ( "" , [] , [] ) "[1] \"Hello R world!\"" ]
, CodeBlock
( "" , [ "r" , "cell-code" ] , [] )
"sapply(1:10, function(x) x^2)"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock
( "" , [] , [] )
" [1] 1 4 9 16 25 36 49 64 81 100"
]
]
, Div
( "" , [ "cell" ] , [] )
[ CodeBlock
( "" , [ "python" , "cell-code" ] , [] )
"y = 1 + 6\nprint(y)"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock ( "" , [] , [] ) "7" ]
, CodeBlock
( "" , [ "python" , "cell-code" ] , [] )
"print(\"Hello Python world!\")"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock ( "" , [] , [] ) "Hello Python world!" ]
, CodeBlock
( "" , [ "python" , "cell-code" ] , [] )
"[x**2 for x in range(10)]"
, Div
( "" , [ "cell-output" , "cell-output-stdout" ] , [] )
[ CodeBlock
( "" , [] , [] ) "[0, 1, 4, 9, 16, 25, 36, 49, 64, 81]"
]
]
, Header
2
( "inactive-cells" , [] , [] )
[ Str "Inactive" , Space , Str "cells" ]
, CodeBlock
( "" , [ "r" ] , [] )
"print(\"Goodbye R world!\")\n2 + 2\n\nsapply(1:10, function(x) x^4)"
, CodeBlock
( "" , [ "python" ] , [] )
"print(\"Hello Python world!\")\nprint([x**2 for x in range(10)])\n8 + 5"
]
Expected behavior
The source portion of the ipynb should list all of the code; not just the first code blocks after a cell is evaluated.
Actual behavior
All output was retained; but source contained only the lines inside of the cell up to the first line of code that output.
Your environment
- IDE: VS Code 1.95.3
- OS: macOS 15.1.1 (24B91)
Quarto check output
Quarto 1.6.37
[✓] Checking environment information...
Quarto cache location: /Users/ronin/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.4.0: OK
Dart Sass version 1.70.0: OK
Deno version 1.46.3: OK
Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.6.37
Path: /Applications/quarto/bin
[✓] Checking tools....................OK
TinyTeX: (not installed)
Chromium: (not installed)
[✓] Checking LaTeX....................OK
Using: Installation From Path
Path: /opt/homebrew/bin
Version: undefined
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.12.7
Path: /Users/ronin/Documents/GitHub/quarto/colab/build/bin/python3
Jupyter: 5.7.2
Kernels: ir, python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........OK
Version: 4.4.2
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
knitr: 1.49
rmarkdown: 2.29
[✓] Checking Knitr engine render......OK
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.