Executing Rmarkdown in jupyter-book

[ozika]

Hi all,

I would like to build a book that's made mostly of python notebooks + one/two notebooks in Rmarkdown.
I came across about this bit on the docs about telling sphinx how to deal with Rmd, however, this doesn't actually run the cells. It treats the document as a md file with code blocks.

It might be a stretch, but is there a way to execute Rmd when building? Alternatively, could one run Rmd in RStudio and then add the generated html file?

Thanks! Ondrej

[chrisjsewell]

however, this doesn't actually run the cells

Heya, yep it does execute the cells: the page you point to is an rmd that has been read and executed by jupyter-book. Perhaps your configuration is incorrect for execution

[ozika]

maybe a better question would be - what is required for it to run. I have jupyter-book and jupytext on the most recent versions. I am not telling jupyter-book anything about what R kernel to use for example.

[chrisjsewell]

Well the juyter-book documentation itself is the working example, e.g. you can see it being read/executed in the CI here: https://github.com/executablebooks/jupyter-book/runs/4755786872?check_suite_focus=true

[chrisjsewell]

Is anything in your book executing, e.g. do you have a standard .ipynb notebook in there that correctly executes, and have you changed anything on the execution configuration: https://jupyterbook.org/content/execute.html#trigger-notebook-execution

[chrisjsewell]

what is the contents of your _config.yml?

[ozika]

Yes, there are a bunch of .ipynb ntbks that run fine. Here is the _config.yml file:

# Book settings
# Learn more at https://jupyterbook.org/customize/config.html

title: Longitudinal study on worries and COVID
author: Ondrej Zika

# Force re-execution of notebooks on each build.
# See https://jupyterbook.org/content/execute.html
execute:
  execute_notebooks: force

# Information about where the book exists on the web
repository:
  url: https://github.com/ozika/covid_public  # Online location of your book
  path_to_book: content  # Optional path to your book, relative to the repository root
  branch: gh-pages  # Which branch of the repository should be used when creating links (optional)

# Add GitHub buttons to your book
# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository

sphinx:
  config:
    nb_custom_formats:
        .Rmd:
            - jupytext.reads
            - fmt: Rmd

html:
  use_issues_button: true
  use_repository_button: true