How to manage working directory in interactive development environments like Jupyter Notebook?

I'm having trouble with managing the working directory in Jupyter Notebook. For example, I have a .py script that requires me to change the working directory to its directory to run it properly. I've tried two approaches, but both have drawbacks: Using !cd: This executes in a subshell, so the IPython session's working directory doesn't change. But then I can't debug the script with breakpoints. Using %cd or os.chdir(): This allows debugging. But it changes the IPython session's working directory, which affects all subsequent cells. This often leads to errors when later cells execute in an unexpected working directory. How should I manage the working directory in a Jupyter Notebook workflow? Should I keep it fixed (e.g., as the notebook's directory) and avoid changes, or check and adjust it before running each cell? Some might argue that scripts shouldn't rely on the working directory, but refactoring third-party code with great efforts to avoid this is impractical. Are there any recommended practices that deal effectively with this scenario, while also applying to similar situations?

Apr 6, 2025 - 13:06

I'm having trouble with managing the working directory in Jupyter Notebook. For example, I have a .py script that requires me to change the working directory to its directory to run it properly. I've tried two approaches, but both have drawbacks:

Using !cd: This executes in a subshell, so the IPython session's working directory doesn't change. But then I can't debug the script with breakpoints.
Using %cd or os.chdir(): This allows debugging. But it changes the IPython session's working directory, which affects all subsequent cells. This often leads to errors when later cells execute in an unexpected working directory.

How should I manage the working directory in a Jupyter Notebook workflow? Should I keep it fixed (e.g., as the notebook's directory) and avoid changes, or check and adjust it before running each cell?

Some might argue that scripts shouldn't rely on the working directory, but refactoring third-party code with great efforts to avoid this is impractical. Are there any recommended practices that deal effectively with this scenario, while also applying to similar situations?