Use parametrisation to render many ipynb notebooks from a template

[danieltomasz]

Description

I have a problem with getting parametrisation right.
My use case is: I do neuroimaging study, I would like to use jupyter notebook to run the same pipeline for data from all participant but on one step the analysis involve manual intervention to remove components that might differ from one participants to another

My idea is is have an template.ipynb(ipynb, not qmd)

with following cells:

title: "Test"
format: ipynb
jupyter: python3
execute:
  enabled: true

# | tags: [parameters]

subject = 101

print(subject)

and then create notebook for every participant where I could later adjust thing manually.
But I have a problem that the parametrisation doesnt work
running

 quarto render notebooks/test/test.ipynb  -P subject:102

gives me a file test.out.ipynb where 101 is not changed as a parameter

I am on macOS 14.4 with quarto 1.5.23

[danieltomasz]

I am able to create a ipynb file from qmd, but not from .ipynb (after I install papermill to my jupyter env, which is not really documented here https://quarto.org/docs/computations/parameters.html)

---
title: "Test"
format: ipynb
jupyter: conda-paths-3.12
execute:
  enabled: true
---

```{python}
# | tags: [parameters]

subject = 101

```

```{python}
print(subject)
```

and running

quarto render notebooks/test/test.qmd -P subject:102 --to ipynb

In this setup in output file I have 2 cells where variable subject is defined

how can i make it only one cell? and how I can ensure that parameter will occur in the output filename?

[danieltomasz]

ipynb works when I add the tag, but not via comment tag, but to cell via jupyter interface - in that regards the documentation was confusing for me;

[mcanouil]

Would you mind elaborate on the confusing part of the documentation? What could be improved to avoid that for future users?
Thank for your feedback.

[danieltomasz]

For me most confusing was the part of tagging cell in Jupyter
according to the documentation https://quarto.org/docs/computations/parameters.html

designate a cell with the tag parameters

And in the cell below

#| tags: [parameters]

While what I actually needed to do was to install papermill and manually (through installing addition VSCode plugin Jupyter Cell Tags) add tag to the cell containing the parameter to substitute; just adding
#| tags: [parameters] didnt have any effect when I was running .ipynb template

I was not able to do make my template to work using what was explicitly in the documentation page (but mention of the papermill package set me on a good path)

[danieltomasz]

Also, the naming of the parametrized output — I would expect that quarto take control of it, but it created the same name of the output file for every parameter (I fixed it outside quarto by using an external make-like python package to run quarto for every parameter in a loop and substitute parameter in python fstring which I added as an output option);
If I specified output as ipynb while the template was ipynb (without adding the output option), quarto was overwriting the original file; I might create and issue with reproducible example, if this is a bug not a default behaviour

[cderv]

While what I actually needed to do was to install papermill and manually (through installing addition VSCode plugin Jupyter Cell Tags) add tag to the cell containing the parameter to substitute; just adding
#| tags: [parameters] didnt have any effect when I was running .ipynb template

When executing a render with params, we do error when parameters are passed and papermill is not available

Starting python3 kernel...ERROR: 

The papermill package is required for processing --execute-params

In the doc, we only say (https://quarto.org/docs/computations/parameters.html#jupyter)

For Jupyter, Quarto uses the same syntax for defining parameters as Papermill.

do you mean we should add a code cell for explicit installation step of papermill at this place in the doc ?

Also, the naming of the parametrized output — I would expect that quarto take control of it, but it created the same name of the output file for every parameter

This would be a feature request indeed. It is not something that quarto is doing right now.