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I found a workaround by using the path from the package root folder to the "make_libraries.py"
rosrun rosserial_windows src\rosserial_windows\make_libraries.py my_library
The library has been build which was my original problem. I'm guessing that the package is looking in its root folder and not the folder pointed to in CMakeList.txt
The problem is that I don't know why and I realised this because a different package had the exact same error, but that is a different question. I did a search for "ros-for-windows not finding python files" and I found this question which gave me the workaround.
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