CODEWITHSUNDEEP
python-3.xjupyter-notebooknbconvertpapermill
PKL
PKL

Reputation: 115

Hide code cells in Jupyter Notebook, execute with Papermill, transform to PDF with nbconvert

I want to run a python program (not command line) using papermill to execute a jupyter notebook and then transform it into a PDF. The idea is working, but I'm unable to hide the input cells.

For papermill report_mode = True is supposed to hide input cells, but there seems to be a problem with jupyter Classic (https://github.com/nteract/papermill/issues/130)

Other extension like hide_input or html scripts are also not sufficient. Maybe a nbconvert template for hide cells is a solution, but I didn't get that running.

My minimal Code:

pm.execute_notebook(
        "Input.ipynb",
        "Output.ipynb",
        parameters=dict(id=id),
        report_mode=True,
    )
notebook_filename = "Output.ipynb"

with open(notebook_filename) as f:
    nb = nbformat.read(f, as_version=4)
pdf_exporter = PDFExporter()
pdf_data, resources = pdf_exporter.from_notebook_node(nb)

So I'm looking for a way to execute the Notebook, hide the input cells and transform the Notebook to a PDF. I want to use nbconvert in Python and not as a command line tool, since the Script shall run daily.

Upvotes: 1

Views: 2394

Answers (2)

Eduardo
Eduardo

Reputation: 1413

You're missing one small detail in your code:

pm.execute_notebook(
        "Input.ipynb",
        "Output.ipynb",
        parameters=dict(id=id),
        report_mode=True,
    )
notebook_filename = "Output.ipynb"

with open(notebook_filename) as f:
    nb = nbformat.read(f, as_version=4)
pdf_exporter = PDFExporter()

# add this
pdf_exporter.exclude_input = True

pdf_data, resources = pdf_exporter.from_notebook_node(nb)

You can also use Ploomber for this; it has a few benefits, like running notebooks in parallel:

# convert.py

from pathlib import Path
from ploomber import DAG
from ploomber.tasks import NotebookRunner
from ploomber.products import File
from ploomber.executors import Parallel

dag = DAG(executor=Parallel())

# hide input and convert to PDF using the LaTeX converter
NotebookRunner(
    Path('input.ipynb'),
    File('output-latex.pdf'),
    dag=dag,
    # do not include input code (only cell's output)
    nbconvert_export_kwargs={'exclude_input': True},
    name='latex')

# hide input and convert to PDF using the web PDF converter (no need to install LaTeX!
NotebookRunner(
    Path('input.ipynb'),
    File('output-web.pdf'),
    dag=dag,
    # do not include input code (only cell's output)
    nbconvert_export_kwargs={'exclude_input': True},
    # use webpdf converter
    nbconvert_exporter_name='webpdf',
    name='web')

# generate both PDFs
if __name__ == '__main__':
    dag.build()

Note: as of Ploomber 0.20, notebooks must have a "parameters" cell (you can add an empty one). See instructions here.

To run it:

pip install ploomber
python convert.py

Upvotes: 0

cwalvoort
cwalvoort

Reputation: 1967

I know you said you "don't want to use command line", but how about having your python script execute a subprocess command after running papermill? Mixing with this answer:

import subprocess

subprocess.call('jupyter nbconvert --to pdf --TemplateExporter.exclude_input=True Output.ipynb')

Upvotes: 3

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