April 16, 2023
4 min
Diego García

7 Tips for Writing Better Python Notebooks

Python notebooks are critical tools for a variety of professionals, providing an interactive environment for writing, testing, and visualizing code. Improving the quality of these notebooks is essential for effective collaboration and productivity. This article provides valuable tips to help you create well-organized and easy-to-understand Python notebooks.

Python notebooks have become indispensable tools for data scientists, developers, and researchers. They provide an interactive environment for writing, testing, and visualising code while integrating text, images, and other multimedia. To help you get the most out of these powerful tools, we've put together seven tips for writing better Python notebooks 📓.

1. Start with a clear structure and outline

Organising your notebook with a clear structure and outline can greatly improve its readability and maintainability. Divide your work into sections using headings and subheadings in markdown blocks, and provide a brief overview of each section at the beginning. This will make it easier for others (and yourself) to follow your thought process and understand the flow of your work.

A well-structured data science notebook can greatly improve the readability and maintainability of your work, making it easier for others to understand and build upon. An example structure for a data science notebook might include the following sections:

  1. Introduction
  2. Data import and exploration
  3. Preprocess data
  4. Model selection and training
  5. Model evaluation and validation
  6. Hyperparameter tuning and model optimisation
  7. Results and Interpretation
  8. Conclusion and future work

By following this sample structure, you can create a well-organised and comprehensive data science notebook that effectively communicates your analysis process and findings.

2. Use markdown cells for documentation and explanation

Use markdown cells to provide context and explanation for your code. Write clear and concise explanations and include relevant images, tables or links where appropriate. Remember that a well-documented notebook serves not only as a record of your work, but also as a valuable resource for others who may use it in the future.

Remember that LaTeX is vastly supported directly so if you need to write formulas or mathematical expressions do not hesitate to use it.

Notebook with inlined markdown documentation

3. Keep your code clean and readable

Adopt a consistent coding style and follow best practices to ensure your code is clean and readable. This includes using meaningful variable names, following PEP 8 guidelines, and breaking complex functions into smaller, more manageable pieces. In addition, make sure you include comments where necessary to explain the purpose of specific code snippets.

4. Use functions and modules to encapsulate reusable code.

If you find yourself writing the same code several times, consider encapsulating it in a function or module. Not only does this make your notebook cleaner and more organised, but it also promotes code reusability and modularity. It will also make your code easier to debug and maintain in the long run.

Creating a module in Python is an excellent way to split your functions into different files, which helps with code organisation, reusability and maintainability. To create a module, simply write your Python functions in a separate file with a '.py' extension, such as 'my_module.py'. This file serves as your module, and you can define any number of functions or classes within it. To use the functions from your module in another Python script or notebook, you need to import the module using the 'import' statement followed by the name of the module (without the .py extension). For example, to import the functions from 'my_module.py', you would write import my_module in your script or notebook. Once the module is imported, you can access its functions using the module name as a prefix, such as 'my_module.my_function()'. By splitting your functions into separate modules, you can keep your code well structured and easily share functionality between different projects or notebooks.

Example or organizing your code in modules.

5. Perform incremental testing and debugging

Test and debug your code incrementally as you work on your notebook. This will help you catch errors early and minimise the time you spend debugging. It also ensures that your final notebook is more reliable and less prone to unexpected problems.

A good way to measure performance is to use magic commands, which are special commands in Python notebooks that help you perform various tasks more efficiently. Some magic commands are particularly useful for measuring the performance of your code. For example, the '%time' and '%timeit' magics allow you to measure the execution time of a single statement or expression. '%time' provides a single measurement, while '%timeit' runs the code multiple times and returns an average, making it more accurate for assessing performance. Another useful magic command is '%prun', which provides a more detailed performance analysis by profiling your code and showing the time spent on each function call. By using these magic commands, you can identify performance bottlenecks and optimise your code more effectively.

6. Keep secrets out of the code

Keeping sensitive information such as passwords and tokens secure is crucial when working with Python notebooks. One way to increase security is to store secrets outside your code and use environment variables to access them. Environment variables are global variables that exist outside the context of your notebook, allowing you to store and retrieve information without exposing it in your code.

Defining environment variables

By using environment variables to store sensitive information, you can keep secrets out of your code and increase the security of your notebook. In addition, this approach simplifies sharing and version control because you can distribute your notebooks without exposing sensitive data or having to manually remove it before sharing.

7. Review and refactor regularly

Review and refactor your notebook regularly to ensure it remains up-to-date and efficient. This may involve reviewing your code to optimise performance, improve readability, or update documentation. By continually refining your work, you can create a more polished and valuable end product.


Writing better Python notebooks is essential for effective collaboration, communication, and reproducibility in data science and programming projects. By following these seven tips, you can create notebooks that are clean, well-structured, and easy to understand, allowing you and your collaborators to work more efficiently and produce better results.

Happy coding!

Further reading

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