Reduce dependencies for simplifed builds.

[micahjohnson150]

Removal of scipy and shapely to improve downstream building processes that rely on study-lyte

• Scipy was being using to integrate, we replaced that with our own version here.
• Scipy was also being used for some analytics and filtering. Those have also been given the own versions here.
• Shapely Point was being used as a small step toward geopandas use, its been removed in favor of a local class with x and y attributes.