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Is it possible to configure TeXshop to automatically run a script on a document at the beginning of the typesetting process? I am interested in having the application run a python script on the document to perform a number of regular expression substitutions, and send the result to TeXShop to typeset.

Slightly more complicated, is it possible to configure TeXShop to do this after expanding any input or include files into the document?

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The closest solution I can suggest is adding an engine to the "typesetting" engine menu. This lets you run your application if you click on "it." The TeXShop documentation explains how to add an engine to the menu. – Marc van Dongen Jan 1 at 8:57
For your second question: as it is not texshop but the (la)tex compiler that reads and expands the input and includes you cannot configure this in texshop. But it shouldn't be too complicated to imitate the behaviour of input and include within your python script or to make your script recognize and follow the input links. – Benedikt Bauer Jan 1 at 19:50

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