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In order to fix the problem, brew-python vs system-python, you can add the following options to catkin_make_isolated. This will tell CMake to link against brew-python.

-DPYTHON_INCLUDE_DIR="/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Headers"
-DPYTHON_LIBRARY="/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib"

Adjust the paths to match your version of python.

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