Focusing on speeding up find_close_polygons instead of realizing that you're matching many points against the same set of polygons is also unfortunate, since th

Focusing on speeding up find_close_polygons instead of realizing that you're matching many points against the same set of polygons is also unfortunate, since that function being slow is a red herring. You can create a scipy.spatial.KDTree for example and just query all the points against that.