Replace Jupyter Notebook With Emacs Org Mode: Unleash the Power of Literate Programming

27 February 2023

Categories: Guides Tags: Emacs Programming


The popularity of Jupyter Notebook has surged in recent years as a powerful tool for interactive data analysis and visualization. However, there is an alternative that has been around for a longer time and is proving to be a valuable resource for many programmers: Emacs Org Mode. In this blog post, we will explore how you can replace Jupyter Notebook with Emacs Org Mode for a seamless and efficient literate programming experience.

What is Emacs Org Mode?

Emacs Org Mode is an extension of the versatile Emacs text editor, offering a powerful platform for note-taking, project management, and literate programming. Literate programming is an approach in which code and documentation are intertwined, allowing you to create executable documents that can be easily understood by others. Org Mode excels at this by providing a simple and intuitive markup language that supports rich text formatting, embedded code, and exporting to various formats, such as HTML, PDF, and more.

Why Replace Jupyter Notebook with Emacs Org Mode?

Getting Started with Emacs Org Mode for Literate Programming

Installing Emacs

  1. Choose your platform:

    • Linux: Use your distribution’s package manager to install Emacs (e.g., sudo apt-get install emacs for Ubuntu)
    • macOS: Install Emacs using Homebrew ( with the command: brew install --cask emacs
    • Windows: Download the installer from the official GNU Emacs website (
  2. Launch Emacs and familiarize yourself with the interface.

Configuring Org Mode

  1. Ensure Org Mode is installed and up-to-date by checking your Emacs package list (M-x list-packages) or manually updating it.

  2. Add Org Mode configuration settings to your Emacs init file (usually .emacs or init.el). For example:

    (require 'org)
    (setq org-src-fontify-natively t)
    (setq org-confirm-babel-evaluate nil)

Installing essential packages for data science

Install the following packages using the built-in Emacs package manager (M-x list-packages):

Configure the installed packages by adding appropriate settings to your Emacs init file.

Setting up a Python environment in Emacs

  1. Ensure Python is installed on your system and available in your PATH.

  2. Install the ipython packages using pip:

    pip install ipython
  3. Configure Emacs to use IPython as the default Python interpreter by adding the following to your Emacs init file:

    (setq python-shell-interpreter "ipython"
        python-shell-interpreter-args "-i --simple-prompt")

Creating and organizing Org files for literate programming

  1. Create a new Org file with the extension .org (e.g.,

  2. Learn the basics of Org Mode markup, such as headings, lists, and links.

  3. Write and execute code blocks within your Org file:

    • Inline code execution: Use src_<language>{<code>} to insert inline code (e.g., src_python{2 + 3}).

    • Code block execution: Use the following syntax to create a code block:

      #+BEGIN_SRC <language>

For example:

#+BEGIN_SRC python
print("Hello, Emacs Org Mode!")

Advanced Features of Emacs Org Mode for Data Science

Working with multiple languages in a single Org file

Org Mode’s support for various programming languages allows you to work with multiple languages in a single document.

Configure additional languages in your Emacs init file by adding the appropriate org-babel settings, such as:

 '((python . t)
   (R . t)
   (shell . t)
   ;; Add other languages here

Integrating with external tools and libraries

Use Org Mode’s #+CALL syntax to integrate external tools or libraries into your Org document.

Example: Integrating Pandoc for document conversion:

#+NAME: pandoc
#+BEGIN_SRC sh :results output :var input="" output="output.pdf"
pandoc $input -o $output

#+CALL: pandoc(input="", output="my_converted_file.pdf")

Debugging and profiling code within Org Mode

Leverage the debugging and profiling capabilities of your programming language within Org Mode.

Example: Debugging Python code with pdb:

#+BEGIN_SRC python :results output
import pdb

def my_function(a, b):
    return a + b

my_function(3, 5)

Customizing code block execution and display options

Customize code block execution with header arguments.

Example: Exporting code block results as a separate file:

#+BEGIN_SRC python :results file :file output.png
import matplotlib.pyplot as plt

x = [1, 2, 3, 4]
y = [2, 4, 6, 8]

plt.plot(x, y)

Utilizing Org Mode for project management and collaboration

Tips and Tricks for Optimizing Your Emacs Org Mode Workflow

Keyboard shortcuts for Org Mode

Learn and utilize Org Mode’s keyboard shortcuts to improve your productivity:

Customize your own keyboard shortcuts in your Emacs init file, if needed.

Customizing your Emacs theme

Choose from various built-in and community-provided Emacs themes to personalize your workspace.

Install a new theme using the Emacs package manager (M-x list-packages), and activate it by adding the following to your Emacs init file:

(load-theme 'theme-name t)

Adjust the appearance of Org Mode elements (e.g., headings, links, and code blocks) by customizing their faces.

Integrating with other Emacs packages for productivity

Enhance your Org Mode experience by integrating it with other Emacs packages:

Install and configure these packages according to their respective documentation.

Using Org Mode for note-taking and knowledge management

Use Org Mode as a powerful note-taking tool to complement your data science projects.

Organize and search your notes using Org Mode’s hierarchical structure and built-in search capabilities.

Example: Organizing notes in Org Mode:

* Data Science Concepts
** Supervised Learning
*** Regression
- Linear Regression
- Polynomial Regression
*** Classification
- Logistic Regression
- Decision Trees
** Unsupervised Learning
*** Clustering
- K-means Clustering
- Hierarchical Clustering

Transitioning from Jupyter Notebook to Emacs Org Mode

Importing existing Jupyter Notebooks into Org Mode

Use jupytext to convert Jupyter Notebooks to Org Mode files:

-Review the converted Org Mode file to ensure proper formatting and correct any issues.

Exporting Org files to Jupyter Notebook format

Overcoming common challenges during the transition


Recap of the benefits of using Emacs Org Mode for data science

Emphasizing the flexibility and customizability of Emacs Org Mode

Encouragement for readers to give Emacs Org Mode a try

Invitation to join the Emacs Org Mode community and share experiences