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Should I Use Jupyter Notebooks or Python Scripts for My Next ML Project?

Denis Vorotyntsev
7 min readDec 5, 2022

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In the world of machine learning and data science, two popular tools for working with code are Jupyter notebooks and Python scripts. But which one should you use for your next machine learning project? In this blog post, we will compare the advantages and disadvantages of Jupyter notebooks and Python scripts, and provide guidance on when to use each one. We will cover topics such as interactivity, portability, flexibility, and documentation, to help you make an informed decision about which tool is best suited for your project. Whether you are new to machine learning or an experienced practitioner, this post will provide valuable insights and practical advice for choosing the right tool for your next machine learning project.

Advantages of Jupyter notebooks

Jupyter notebooks are interactive

One of the key features of Jupyter notebooks is that they are interactive, which means that you can write, run, and view the output of your code all in one place. This is in contrast to traditional Python scripts, which require you to write your code in a separate file, and run it using the command line or IDE.

The interactivity of Jupyter notebooks is a major advantage, as it allows you to quickly test your ideas, experiment with different approaches, and explore your data in a flexible and responsive environment. You can write your code in small, modular blocks, and run each cell individually or all at once, to see the results. This makes it easy to iterate on your code, and try different things without having to start from scratch each time.

Example of Jupyter Notebook interactivity. Source — “Jupyter Superpower — Interactive Visualization Combo with Python

Additionally, the interactivity of Jupyter notebooks allows you to view the output of your code in a variety of formats, including text, images, and other media. This is particularly useful when working with machine learning algorithms, as you can easily visualize the results of your code, using built-in plotting libraries, such as Matplotlib and Seaborn. You can also display the output of your code as tables, lists, or other data structures, which can help you understand the behavior of your algorithms and the properties of your data.

In summary, the interactivity of Jupyter notebooks is a major advantage, as it allows you to quickly write, run, and view the output of your code in a single, flexible environment. This makes Jupyter notebooks a great choice for machine learning projects, where you need to iterate on your ideas, experiment with different approaches, and visualize the results of your code.

Support of text, images and other media

Another advantage of Jupyter notebooks is that they support rich text, images, and other media, which makes them a great choice for documenting your work and sharing your results with others. This is in contrast to Python scripts, which are plain text files that do not support any formatting or media.

Notebooks allow to create rich analyses and visualizations. Source — “A Jupyter notebook example for interactive mapping with Earth Engine, ipyleaflet, and ipywidgets”.

With Jupyter notebooks, you can include explanations, examples, and visualizations in your notebooks, which can help others understand your code and your findings. For example, you can use Markdown, a lightweight markup language, to add headings, bullet points, links, and other formatting to your notebooks. This can make your notebooks more readable and easier to navigate, and can help you organize your ideas and explanations in a clear and concise way.

Additionally, Jupyter notebooks support a wide range of media formats, including images, videos, audio files, and other types of data. This is particularly useful when working with machine learning algorithms, as you can easily include visualizations, charts, graphs, and other representations of your data in your notebooks. For example, you can use Matplotlib or Seaborn to create scatter plots, histograms, or other visualizations of your data, and include them in your notebooks, along with your code and explanations.

Jupyter notebook is a great learning tool

Jupyter notebooks are well-suited for teaching and learning, as they allow you to combine code, explanations, and examples in a single document. This makes it easy to create interactive tutorials, lectures, and exercises that can help others learn about machine learning and data science.

To use Jupyter notebooks for learning, you can start by creating a new notebook, and writing your explanations and examples in Markdown cells. You can then add code cells, where you can write and run your Python code, and view the output of your code in the same notebook. This allows you to create a narrative that combines code, explanations, and examples, which can help others understand the concepts and techniques you are teaching.

Most of the home tasks in the famous Andrew Ng’s Neural Networks and Deep Learning MOOC were present in notebooks. Source — “In-Depth Review: Andrew Ng’s Neural Networks and Deep Learning MOOC on Coursera

You can use the interactive features of Jupyter notebooks to create interactive exercises and challenges for your learners. For example, you can provide a code cell with a partially completed algorithm, and ask your learners to fill in the missing parts, or modify the code to solve a specific problem. This can help your learners apply what they have learned, and test their knowledge and skills in a hands-on, interactive environment.

Furthermore, you can use the rich media support of Jupyter notebooks to include visualizations, charts, graphs, and other representations of your data, which can help your learners understand the concepts and techniques you are teaching. For example, you can use Matplotlib or Seaborn to create scatter plots, histograms, or other visualizations of your data, and include them in your notebooks, along with your code and explanations. This can make your notebooks more

Advantages of Python scripts

Easy to build and integrate

With Python scripts, you can write your code in small, modular blocks, and combine them into a larger pipeline, by calling the relevant functions or modules from your scripts. This allows you to create reusable and composable components, that can be easily integrated into your pipeline, and run as part of a larger system or workflow.

One of the main advantages of using Python scripts for machine learning projects is that they are easy to integrate and maintain over time. This is in contrast to Jupyter notebooks, which are proprietary files that require the Jupyter environment to run, and may be more difficult to integrate with other tools and libraries.

Python scripts are easy to test

Suppose you are working on a machine learning project that involves training a neural network to classify images into different categories. You have written your training code in a Jupyter notebook, and you want to test the accuracy of your model on a validation set.

To test your model in a Jupyter notebook, you will need to run the cells containing your training code, and then run additional cells that load the validation set, feed it to your model, and evaluate the model’s performance. This can be time-consuming and error-prone, as you will need to make sure that all the relevant cells are executed in the correct order, and that the output of each cell is correct and consistent.

On the other hand, if you had written your training code in a Python script, you could simply run the script, passing the path to the validation set as an argument. This would automatically load the validation set, train your model, and evaluate its performance, without having to manually run multiple cells in a Jupyter notebook. Additionally, you could easily automate this process, by using a continuous integration system, such as Jenkins or Travis CI, to run your script on a regular basis, and get notified if the performance of your model changes or degrades over time.

Testing Python scripts can be easier and more efficient than testing Jupyter notebooks, as you can run the scripts directly, without having to manually execute multiple cells in a notebook. This can save you time and effort, and can make your testing process more reliable and consistent.

Code testing in scripts is much more easier and could be automated using CI/CD tools such as GitHub Actions. Source — “Using GitHub Actions to Run Automated Tests

Choosing the right tool

In conclusion, whether to use Jupyter notebooks or Python scripts for your next machine learning project depends on your specific requirements and preferences. Jupyter notebooks are ideal for data exploration and visualization, as they are interactive and support rich media. Python scripts are more suitable for automation, integration, and deployment, as they are portable, flexible, and easy to maintain.

If you want to quickly prototype and test your ideas, and visualize the results of your code, then Jupyter notebooks may be the right choice for you. If you want to build larger systems, automate tasks, or integrate with external tools and libraries, then Python scripts may be a better option.

Ultimately, the choice between Jupyter notebooks and Python scripts depends on the specific goals and constraints of your project. You may want to use both tools, depending on the needs of your project, and switch between them as your project evolves and grows. By understanding the advantages and disadvantages of each tool, and using them wisely, you can make the most of both Jupyter notebooks and Python scripts, and create effective and efficient machine learning solutions.

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