quarto-dev / quarto-dev/quarto-cli

Jupyter Execution is Confusing And Possibly Has A Bug

Open
#5,376 9 comments 0 reactions 1 assignee View on GitHub

Nobody has claimed this yet.

documentation early-in-release engines-jupyter
Dominant language
JavaScript
Stars
6k
Forks
458
Avg merge
1d 9h
Merged PRs (30d)
41

Description

Currently you must do the following to execute cells with Quarto. You either have to:

  1. pass the --execute flag to quarto preview or quarto render
  2. Set the enabled: true flag as specified here

However, this is confusing for many reasons

  1. enabled is not documented here under execution options https://quarto.org/docs/reference/formats/ipynb.html#execution
  2. The documentation suggests that setting eval: true should make quarto execute that cell (or notebook, if placed in the front matter). However, this is not the case. You have to additionally take the steps in number 1.
  3. If you have a project where some notebooks are executed but others are not, this leads to Quarto deleting all cell outputs in notebooks where eval: false on cells (or for the whole notebook if in front matter). However, I don't think this is desirable for notebooks, because you may have long-running computations that generate some output that you don't want get clobbered by Quarto - and it looks like there isn't a way to "protect" those cells or notebooks?

cc: @jjallaire @seem @cderv @mcanouil

BTW I'm on 1.3.333

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.