Hi Leigh
Did you manage to solve the problem?
I have the same and I don't know what can I do. My margin admonitions don't 
appear correctly, and my figures aren't centered.

I also have this message when I build my book: 

*building [html]: *targets for 13 source files that are out of date

My jupyter-book version:

(base) geomicrobio@geomicrobio-mac --- % jupyter-book --version

Jupyter Book      : 0.11.2

External ToC      : 0.2.3

MyST-Parser       : 0.13.7

MyST-NB           : 0.12.3

Sphinx Book Theme : 0.1.2

Jupyter-Cache     : 0.4.3

NbClient          : 0.5.3


and this is my yaml: 

title: Genómica computacional. Manual de bioinformática.

author: Nayeli Luis y Marisol Navarro

logo: images/bioinformatics3.png


execute:

  execute_notebooks: force


latex:

  latex_documents:

    targetname: book.tex


bibtex_bibfiles:

  - references.bib


html:

  use_issues_button: true

  use_repository_button: true


parse:

  myst_enable_extensions:

    - html_image

    - colon_fence

    - html_admonition

    - deflist


El sábado, 9 de octubre de 2021 a las 5:11:35 UTC-5, leigh.f...@gmail.com 
escribió:

> Hello All,
>
> I'm using Sphinx v4.1.2 with Jupyter-Book v0.11.2 to generate a book, with 
> a config.yml file included below.  I'm receiving the following warning, 
> which is preventing a compilation of the book using the xelatex engine.  I 
> wondered if anyone has a workaround?
>
> *WARNING: cannot override config setting 'html_add_permalinks' with 
> unsupported type, ignoring*
>
> Suggestions are very welcome!
>
>
> Contents of config.yml:
>
> # Force re-execution of notebooks on each build.
>
> # See https://jupyterbook.org/content/execute.html
>
> execute:
>
>   execute_notebooks: force
>
> only_build_toc_files: true
>
> # HTML-specific settings
>
> html:
>
>   home_page_in_navbar: false
>
>   use_issues_button: false
>
>   use_repository_button: false
>
> # Interact link settings
>
> notebook_interface            : "notebook"
>
> # Launch button settings
>
> repository:
>
>   url: https://github.com/executablebooks/jupyter-book  # Online location 
> of your book
>
>   branch: master  # Which branch of the repository should be used when 
> creating links (optional)
>
> binder:
>
>   binderhub_url               : "https://mybinder.org";
>
>   text                        : "Launch binder"
>
> latex:
>
>   latex_engine                : "xelatex"
>
>   latex_documents:
>
>     targetname: book.tex
>
> # Add a bibtex file so that we can create citations
>
> #bibtex_bibfiles:
>
> #  - references.bib
>
> parse:
>
>   myst_enable_extensions:
>
>     # don't forget to list any other extensions you want enabled,
>
>     # including those that are enabled by default!
>
>     - amsmath
>
>     - dollarmath
>
>     - html_image
>
> myst_dmath_double_inline: True
>
> number_equations: true
>
> sphinx:
>
>   config:
>
>     mathjax_path: 
> https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
>
>
>
>

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