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I would like to run python code within jupyter notebook running bash shell. I can do it other way around (bash code from python notebook) by using cell magic, but % operant is not working in bash shell. Is there a way to do it?

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Cell magic is implemented independently for each kernel (http://jupyter.cs.brynmawr.edu/hub/dblank/public/Jupyter%20Notebooks.ipynb). The Bash Kernel (assuming you're referring to this: https://github.com/takluyver/bash_kernel) is still quite limited in scope, so I don't expect that it will work any time soon.

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