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Is there are a way to save the Ipython notebook as an ipynb file from a cell within that notebook?

I know I can save it at any time by manually pressing "CTRL-M S", but I would like to use a command in a cell to do so (python command or %magic). In this way I could "Run all cells" and be sure that the output (e.g. inline figures) is saved into the notebookfile when the execution is finished.

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No, because the kernel does not know it is accessed from a notebook. Dev version have auto-save feature though, and you could write a javascript extension that listen for cell execution event. But Python is not the way to do it. (or display(Javascript('js-code-to-save-notebook')) in the last cell, but I did not tell you)

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