So, I answer this question pretty quickly, but instead of deleting it, I will add text so that the next person can find it. The problem was not pygraphviz , but Textmate 2.x was a bit strange regarding PATH . It seems that textmate uses its own path, but you cannot find this variable in the variable editor. However, you can add to it using the usual syntax as shown below. This is fixed for me as well.

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