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I have a shell script file that contains the necessary parameters to run the Python file. I can only run this script with the green button on the top right of pycharm, but when I select the debug option, it quickly goes out of debug mode. This script file contains the python 3 command.

How can I debug code with this script?

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You're asking PyCharm to debug two different programming languages at the same time. Instead, create a Debug configuration for your Python script with all the necessary parameters: https://www.jetbrains.com/help/pycharm/creating-and-editing-run-debug-configurations.html

This might take a moment to set up but you will then be able to set breakpoints and debug your Python script.

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Thank you for your answer. The problem was solved according to your instructions.
Glad to hear that! Feel free to upvote and/or mark the answer as accepted if it solved your problem.
@JanWilamowski , I have a .sh script which execute a python file main.py, I'd like to set breakpoints both in the .sh and in .py and Debug with a Shell Script configuration under PyCharm. Do you mean it is not possible and I have to debug separately ? Thank you:)
@RémyHosseinkhanBoucher I'm not sure if that's possible but you could ask a new question about that

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