Best Beginner friendly Python & Jupyter IDE Comparison 2025

JupyterLab Desktop is no longer being developed, and we need to find alternatives that actually work for teaching Python and scientific computing.

Why Not Online Interpreters?

You might think: “Just use Google Colab or another online interpreter – no installation needed!”

Here’s why that doesn’t work: Everyone who comes to my Python courses, whether from universities or companies, would rather spend hours fixing local installation problems than work online. The reason is data policy.

Universities and companies can’t upload their data to online platforms that use it to train AI models. It violates institutional policies. While online interpreters are easy to set up for absolute beginners, you’ll need a local IDE eventually anyway.

What About Regular JupyterLab?

JupyterLab has the same interface as JupyterLab Desktop, but without the built-in browser. This creates problems:

Browser Compatibility Issues:
When teaching 12 people, someone uses Firefox, someone uses Chrome, someone uses Safari. All these browsers have different cache sizes and RAM requirements. There’s usually always a problem with at least one person’s setup.

No Double-Click Support:
You can’t just double-click a Jupyter Notebook file to open it. You have to open a terminal in the folder where the file is, type “jupyter lab”, and then open the file from there. For beginners, this means I have to teach command line basics before they can even open a file.

The Other Alternatives

Spyder

Spyder hasn’t really improved its Jupyter Notebook support since last year. It can open notebooks, but only with very basic functionality. It’s excellent for regular Python files and multi-file projects, but it’s just not made for Jupyter Notebooks.

Zed

Still in beta on Windows as of November 2024. Since most people in my courses use Windows, I can’t recommend it.

Wing IDE

Very professional Python IDE, but Jupyter Notebook support costs $179 per year. I can’t tell beginners to pay for something they can get for free, especially when they don’t need most of the pro features.

The Real Contenders: PyCharm vs VS Code

Last year I excluded PyCharm from the comparison because basic Jupyter Notebook functionality required a paid subscription. Now they’ve made it free. (You’re welcome.)

Both IDEs now have the same basic functionality:

– Double-click to open Jupyter Notebook files
– Built-in table of contents
– Ruler guides for line breaks
– Zoom into interactive matplotlib plots

The differences are in the details.

PyCharm: Python-Only Focus

PyCharm is made by JetBrains, who create different IDEs for different programming languages. This means PyCharm is specialized for Python only.

Advantages:
– Cleaner interface – you only see menu options and buttons relevant to Python
– Everything works out of the box – no extensions to install
– Zero configuration needed
– Compatible with Miniforge (my recommended package manager)

Limitations:
– Doesn’t work natively with micromamba, pixi (workarounds needed)
– Smaller extension ecosystem – JetBrains checks every extension
– No HDF5 file viewer plugin available

VS Code: General Purpose Powerhouse

VS Code is a general-purpose IDE. By default, it doesn’t have much functionality – you install extensions to add what you need.

Advantages:
– Open source with massive extension ecosystem
– Whatever functionality you need, there’s probably an extension
– HDF5 file viewer plugin available (important for scientists)
– Works with all package managers including micromamba and pixi
– More people use it, so better community support

Limitations:
– Interface can feel overloaded – shows options for JavaScript debugging even when you only do Python
– Requires installing extensions and some configuration
– More setup time needed

What About AI Coding Tools?

You might ask: “Why not just use Cursor or Windsurf? They have powerful AI tools built in!”

Here’s my take: For beginners, there’s value in learning programming first, then using AI tools.

It’s like using a calculator without learning basic math. If you know math and the calculator tells you 2+2=5, you know it’s wrong. But if you’ve never learned arithmetic and the calculator says 2+2=5, you have to believe it.

Same with AI coding. If the AI gives you buggy code and you don’t understand what’s happening, you can’t fix it. The AI can’t fix it either – otherwise it wouldn’t have made the error in the first place. Usually once they make a mistake and you try to fix it, it just gets worse. Then you’re stuck.

Plus, Cursor and Windsurf aren’t really made to work with Jupyter Notebooks yet, which are really useful for scientific computing.

What About Built-in AI?

PyCharm: Just released their Junie AI assistant, but reviews have been mixed so far.

VS Code: GitHub Copilot is built in. I reviewed it last year when it was terrible. But Microsoft made it open source a few months ago, so I expect it to improve quickly. Once things become open source, they usually get better fast because more people can contribute.

Right now, Cursor and Windsurf are better for pure AI-driven development. But I wouldn’t write off GitHub Copilot yet.

Complete IDE Comparison Tables

Here’s the detailed breakdown of all the IDEs I tested:

My Final Recommendation

For beginners starting with Python and Jupyter Notebooks, my recommendation is PyCharm Community Edition.

Choose PyCharm if:
– You’re a beginner learning Python
– You want something that works immediately after installation
– You prefer a cleaner interface with only relevant options
– You’re using Miniforge (my recommended package manager)

Choose VS Code if:
– Your team or colleagues already use it
– You need specific extensions (like HDF5 viewers)
– You work with multiple programming languages
– You’re comfortable spending time on setup and configuration
– You need to use micromamba or pixi

Avoid Cursor and Windsurf if:
– You’re learning programming for the first time
– You primarily work with Jupyter Notebooks
– You want to understand your code rather than just generate it

What’s Next?

This is part two of a three-part series on setting up your Python development environment in 2025:

Part 1: Package Managers (Anaconda alternatives – Miniforge)
Part 2: IDE Comparison (this post) – Watch Video
Part 3: Complete setup guide showing how to install and configure everything together (coming soon)

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This article is part of our comprehensive guide to Python development environments. Check out Training Scientists for more detailed insights and video tutorials.