How to render pd.DataFrame table in pdf with nbconvert+pandoc

Question

I am generating a pdf from a set of Jupyter notebooks. For each .ipynb file, I'm running

$ jupyter-nbconvert --to markdown Untitled1.ipynb

and then merging them together with:

$ pandoc Untitled1.md [Untitled2.md ...] -f gfm --pdf-engine=pdflatex -o all_notebooks.pdf

(I am mostly following the example here.) One thing I noticed is that the pandas DataFrames, e.g.

import pandas as pd
df = pd.DataFrame({'a':[1,2,3]})
df.head()

are rendered in the pdf as

rather than

Any idea how to fix this issue, please? I am using $ jupyter-nbconvert --version 5.6.1 and $ pandoc --version 2.9.2.1. In the md file the table turns into the html block below. I suspect pandoc does not interpret it correctly. I tried the from-markdown-strict option suggested here, without any luck.

Thank you!

<div>
<style scoped>
    .dataframe tbody tr th:only-of-type {
        vertical-align: middle;
    }

    .dataframe tbody tr th {
        vertical-align: top;
    }

    .dataframe thead th {
        text-align: right;
    }
</style>
<table border="1" class="dataframe">
  <thead>
    <tr style="text-align: right;">
      <th></th>
      <th>a</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <th>0</th>
      <td>1</td>
    </tr>
    <tr>
      <th>1</th>
      <td>2</td>
    </tr>
    <tr>
      <th>2</th>
      <td>3</td>
    </tr>
  </tbody>
</table>
</div>

Answer 1

The problem seems to be in the connection between Jupyter and Pandoc. Jupyter didn't output formatted markdown and hence pandoc doesn't format it in the PDF.

Answer 2

For me the best way is using ipypublish (https://ipypublish.readthedocs.io/en/latest/)

Install

conda install -c conda-forge ipypublish

Setup pandas

from ipypublish import nb_setup
pd = nb_setup.setup_pandas(escape_latex = False)
...
pd.DataFrame(mydata)

Profit

jupyter nbconvert notebook.ipynb --no-input --no-prompt --to pdf

Make sure you run the notebook again before converting it, such that all the tables are rendered with ipypublish. Then they look cool in the notebook as well as in the PDF.