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I wonder if this is because the notebook changes the working directory of the process?

I thought so as well, however I'm passing the current os working dir (which is where the pulumi yaml files are located)

Can you try doing a normal python subprocess call from within the notebook to something like

pulumi config list

and see if that finds the config ok?

Yes, that works.

But automation doesn't how odd.... can you raise a bug at github.com/pulumi/pulumi about this. We can take a look, sounds like it might be something non-trival