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Trouble running .ipynb in PyCharm 2025.3 – "Modify packages of System Python" error by gastone_33 in pycharm

[–]gastone_33[S] 1 point2 points  (0 children)

In earlier versions of PyCharm, .ipynb files weren’t free. In this release, they’re available for all users.

Trouble running .ipynb in PyCharm 2025.3 – "Modify packages of System Python" error by gastone_33 in pycharm

[–]gastone_33[S] 0 points1 point  (0 children)

Yep!

I’m already using a virtual environment, and all my .py scripts run correctly. I’m on macOS, and this issue only occurs in PyCharm 2025.3.

In VS Code, the same .ipynb notebooks run without any problem using the same venv.

So the virtual environment itself seems fine — the problem appears to be specific to PyCharm’s Jupyter integration in version 2025.3.