Can't render Python script

[mjkrasny]

Bug description

while following the guide from: https://quarto.org/docs/computations/render-scripts.html#syntax

The rendered document is not executing included python script.
The output looks like in the screenshot attached.

Steps to reproduce

Python Script file (script.py)

# %% [markdown]
# Test external script

# %%
#| echo: true
x = 35

print (x)
# %% [markdown]
"""
## Exploring the data
...
"""

Quarto document (document.qmd)

---
title: "Test-document"
author: "XX YY"
execute:
    enabled: true
    echo: true
    python: true
---


{{< include script.py >}}

I have fresh quarto install: 1.5.55

Expected behavior

Expected nice quarto document, with python code executed.

Actual behavior

Rendered document contains markdown and python syntax, python code is not executed.

Your environment

• IDE: VSCode (but I don't think it matters)
• Quarto version 1.5.55

Quarto check output

PS C:\Users---------------> quarto check
Quarto 1.5.55
[>] Checking versions of quarto binary dependencies...
Pandoc version 3.2.0: OK
Dart Sass version 1.70.0: OK
Deno version 1.41.0: OK
Typst version 0.11.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
Version: 1.5.55
Path: C:\Users----------------------------
CodePage: 1252

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

[>] Checking LaTeX....................OK
Tex: (not detected)

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

[>] Checking Python 3 installation....OK
Version: 3.11.9 (Conda)
Path: C:/Users/----------------------------
Jupyter: (None)

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

[>] Checking R installation...........(None)

  Unable to locate an installed version of R.
  Install R from https://cloud.r-project.org/

[cderv]

The Script rendering in Quarto means you can do quarto render script.py

If you want to include python code into a .qmd document, you need to use computation cell with the right syntax.
https://quarto.org/docs/computations/python.html

Here by using include shortcode, you are just "copy pasting" the content of the script.py as a text file into the .qmd body. It won't be executed because there is not python cell in the .qmd

Hope this helps understand.

[mjkrasny]

OK. all clear now. Thanks. Running the 'quarto render script.py' works fine.

But is there a way to combine/include more than one python scripts in the one *.qmd document?

Thanks.

[cderv]

But is there a way to combine/include more than one python scripts in the one *.qmd document?

You can use as many include shortcode as you need, but if you want execution, you need to insert in a computation cells.

Otherwise, you need to add some python code cells that source the python scripts.

Two ideas to try out.

i'll close this issue, but feel free to open a new discussion if you have questions or need more help.

[mjkrasny]

Ok, I found what I need/want. It is called embed: https://quarto.org/docs/authoring/notebook-embed.html

However it is only limited to other *.qmd files or Jupyter Notebooks. Is there any chance to embed python script file instead of jupyter notebook?

Just as general use case is that I'm working on a report where the main text is kept in the main.qmd file, but all computations and plotting is done in python scripts. Using Spyder IDE is much more convenient (to me) than any other tool to explore and play with data, but the final outcome from the scripts (i.e. plots) should go to the main document. I hope it makes sense?

[cderv]

Is there any chance to embed python script file instead of jupyter notebook?

embed feature works by rendering notebook and retrieving code cells output in there. So even if we make it possibly for a Jupyter percent script version, it will render top ipynb first.

I hope it makes sense?

I understand the usage. knitr engine allows such things by allowing storing code in script and loading them in cell specially
Either reading a sciprt as a cell content or reading code cells from a script content. But those are knitr engine specific, and Jupyter does not allow such use case.

For now, include and embed shortcode are the closest to this. Using .py in embed is not supported yet - as we can convert those to Jupyter notebook, I wonder if we could activate it. I'll open an issue to track this idea.

[mjkrasny]

Thanks for rising this to the new feature request.
For now, I'm trying to work around using jupyter notebooks rendered from scripts with the use of Jupytext.
The issue I'm facing is that after creation of script.ipynb file I must manually run cells in the noteboook before rendering my document.qmd file.

Is there a way to render the notebook each time at document render?
the "execute: enabled: true" in yaml doesn't work.

error:

PS C:\EXP_Quarto-Report_v1> quarto render main_document.qmd
ERROR: The notebook script.ipynb doesn't contain output to embed with the cell id, tag, or label 'print-data_2'. Please be sure to have executed any cells that you are embedding.

my working example:

document.qmd:

---
title: Test - embedded jupyter
author: XXX YYY
toc: true
execute: 
  enabled: true
  echo: false
format:
  html:
    code-fold: true
---

# Example Heading 1
Here is some text

more text

## Include full notebook
now include python script: script.py, which is translated to jupyter by jupytex

{{< embed script.ipynb >}}


## Embed specific cell
{{< embed script.ipynb#print-data_2 >}}

extra value = 
{{< embed script.ipynb#print-data_3 >}}

script.py:

# %% [markdown]
# This is a multiline
# Markdown cell

# %% [markdown]
# Another Markdown cell


#%% code cell #0
#| label: read-data
#| code-fold: true
x = 42

#%% code cell #1
#| label: print-data
#| code-fold: true
print(x)



#%% code cell #2
#| label: print-data_2
#| code-fold: true
print(x+58)



#%% code cell #3
#| label: print-data_3
#| code-fold: true
print(x**2)

output after manual execution of jupyter notebook:

[mcanouil]

use --execute flag.

[mjkrasny]

I tried, same error:

[cderv]

@mjkrasny you need to execute your embeded document. Quarto won't render .ipynb by default.
See our doc about workflow with Python engine : https://quarto.org/docs/computations/python.html#workflow and embed from ipynb https://quarto.org/docs/authoring/notebook-embed.html#jupyter-notebooks for more context.

The errors here is saying that your ipynb to embed does not have the expected cell-id, and tells you to check that it has been executed. Please follow the advices.

[mjkrasny]

ok, so the workflow at the moment is like this:

1. generate script.py file
2. convert to jupyter notebook using jupytext
3. open notebook, and run it all
4. render document.qmd

what is the point of "execute" command in YAML, and --execute flag then?

I think it would be great if they could run jupyter notebook in background, so step 3 would be obsolete.

But of course, the ideal case scenario is to work with percent .py script notation as already raised by @cderv (#10385)