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I'm trying to compile Blender as a python module on my windows machine so I can use an external IDE. In the tutorial on the blender site. I've tried to follow it, however, the instructions are pretty confusing. The first step says to copy bin\bpy.pyd C:\Python36\Lib\site-packages\. I can't find the bpy.pyd in the blender directory or the blender source. How can I do this?

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You missed the build step in this tutorial. The install part refers to the bpy.pyd you have just built, and can be found in the "blender-git/build" directory. There is a tutorial on building blender on windows. Just don't forget the cmake options: WITH_PYTHON_INSTALL=OFF, WITH_PLAYER=OFF, WITH_PYTHON_MODULE=ON

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