Cannot export notebook with images to PDF

[davidvandebunte]

What docker image(s) are you using?

datascience-notebook

Host OS system

Ubuntu 24.04

Host architecture

x86_64

What Docker command are you running?

docker run --rm \                                                                      
    -p "$JPORT":"$JPORT" \                                                             
    --env JUPYTER_ENABLE_LAB=yes \                                                     
    --env NB_USER="$USER" \                                                            
    --env NB_GID=1000 \                                                                
    --volume "$HOME":"$HOME" \                                                         
    --volume $(pwd):$(pwd) \                                                           
    --user root \                                                                      
    --workdir $(pwd) \                                                                 
    quay.io/jupyter/datascience-notebook \
    start.sh jupyter lab \                                                             
    --port "$JPORT" \                                                                  
    --notebook-dir $(pwd)

How to Reproduce the problem?

With a .md or .ipynb notebook that includes images open, select "File -> Save and Export Notebook As" and then the "PDF" option.

Command output

! Undefined control sequence.
l.450 \pandocbounded
{\includesvg[keepaspectratio]{KeychainLabels.svg}}

Expected behavior

A PDF file is produced.

Actual behavior

The JupyterLab server errors out.

Anything else?

See Pandoc 3.2.1 introduced new LaTex macro \pandocbounded · Issue #391 · Wandmalfarbe/pandoc-latex-template. It looks like the solution to this issue is to update to v2.5.0 of this package. It's possible that nbconvert needs an update first, see Incompatibility issue with latest version of pandoc · Issue #2173 · jupyter/nbconvert (which looks unresolved).

Latest Docker version

• I've updated my Docker version to the latest available, and the issue persists

[mathbunnyru]

Hi @davidvandebunte,

Could you make your example reproducible on any machine?
Remove docker command flags which are not needed, write a command which would work on any machine with docker installed, add a file example.
In general, it's a great idea to simplify an issue as much as possible and create an MRE

[davidvandebunte]

Hey @mathbunnyru,

You'll likely find the issue is reproducible already with whatever docker image you are using (it doesn't have to be the datascience-notebook) and whatever docker run command you're already using. Then create a notebook with an image in it; here's a Markdown cell:

Hello there! Here's an image:

![upload.wikimedia.org/wikipedia/commons/6/6b/Bitmap_VS_SVG.svg](https://upload.wikimedia.org/wikipedia/commons/6/6b/Bitmap_VS_SVG.svg)

Let me know if that doesn't work, though. I'll edit my docker run command above to make it shorter though, it's the longest part of the report.

[mathbunnyru]

Ok, I've been able to reproduce the problem.

This is purely a problem of jupyter nbconvert:

• SVG images in Markdown are not rendered in latex export nbconvert#244
• LaTeX and PDF export: Incorrect export of SVG images included via ![]() nbconvert#2192

There is a PR, which fixes it: jupyter/nbconvert#2190
There are some issues with shell escape, so it's unlikely that this will be merged as is.

Good news - I've been able to make it kind-of work in our images, but not in a good way at all.

1. Change an image like this:

FROM quay.io/jupyter/minimal-notebook

RUN wget 'https://patch-diff.githubusercontent.com/raw/jupyter/nbconvert/pull/2190.diff' -P /tmp/ && \
    sed -i 's/share\/templates\/latex\///g' /tmp/2190.diff && \
    cd /opt/conda/share/jupyter/nbconvert/templates/latex && \
    git apply /tmp/2190.diff

RUN cd /home/jovyan && \
    wget 'upload.wikimedia.org/wikipedia/commons/6/6b/Bitmap_VS_SVG.svg'

USER root

RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    inkscape && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

USER ${NB_UID}

2. Run this image
3. Create the markdown cell:

Hello there! Here's an image:

![upload.wikimedia.org/wikipedia/commons/6/6b/Bitmap_VS_SVG.svg](Bitmap_VS_SVG.svg)

4. Run inside the container (you may use terminal inside JupyterLab):

jupyter nbconvert --to latex Untitled.ipynb
xelatex --shell-escape Untitled.tex

[mathbunnyru]

A few key points:

• I applied the PR as a patch (had to rename some directories, though)
• downloaded Bitmap_VS_SVG.svg as a file and inserted from a file to the notebook (it gives an error for links)
• installed inkscape package
• had to run jupyter nbconvert manually and then xelatex with --shell-escape

I know it's not a proper solution.
It is 100% an upstream issue, so I don't think we can provide more help as part of this project.
Please, if you have any ideas and want to help the nbconvert project, it would be great if you worked on the issue I mentioned above - our images will automatically get a new version when it is released and it would be great for all users.
And you could also provide additional details there.

So, I am closing this issue. Hope this helps a little bit, or at least makes it clear where to look at.