Update: I found a better way.

A few days ago I became interested in using Jupyter Notebooks to generate automatic reports to help me analyze and compare data between experimental conditions. I already use Jupyter’s nbconvert to generate html documentation with figures, based on python code. It is really nice. However, one thing was still missing: how to send parameters to jupyter-nbconvert so that I can fully automate my reports?

I found some interesting solutions on the web such as nbparameterise or nbrun, but for my very simple use case, the best is no external tool at all. Also, I may want to hide the parameters from the report, for example if one of the parameters is a password*.

Then I realized that what I need is really super simple. The trick is to write the parameters to a temporary module that will be imported by the Jupyter notebook. Here, for simplicity, we assume that all files are in a same folder.

Master script (the script that automates report generation)

import subprocess

def generate_arguments(dictionary):
    """Create a 'arguments.py' module to initialize a Jupyter notebook."""
    with open('arguments.py', 'w') as fid:
        for key in dictionary:
            fid.write(f'{key} = {repr(d[key])}\n')


# Prepare the arguments
generate_arguments({
    'variable1': 'value1',
    'variable2': 1234,
    'variable3': ['a', 'b', 'c'],
    'variable4': {'a': 1, 'b': 2},
})


# Run the notebook
subprocess.call(['jupyter-nbconvert',
                 '--execute',
                 '--to', 'html',
                 'NAME_OF_THE_NOTEBOOK.ipynb'])

In this example, the generate_arguments function creates a local python module named arguments with this contents:

variable1 = 'value1'
variable2 = 1234
variable3 = ['a', 'b', 'c']
variable4 = {'a': 1, 'b': 2}

Slave Notebook (the notebook that generates a report based on input arguments)

The only thing to do is to begin the Jupyter Notebook with this line:

import arguments

which will declare the variable needed by the report.

*Obviously, if the parameters contain sensitive information, caution has to be taken (ensure the file is local, not readable by others, not backed up, erase it afterward, etc.)