Sorted-last-shapely-2-deprecation-warnings

[mattijn]

This PR makes reduces the number of warnings from 184 to 0.

It was especially the np.vstack which access the array interface under the hood. Like in the following:

import numpy as np
from shapely import geometry

a = {"type": "LineString", "coordinates": [[0, 0], [1, 0], [2, 0]]}
b = {"type": "LineString", "coordinates": [[0, 0], [1, 0], [2, 0]]}
arr = [geometry.shape(a), geometry.shape(b)]

np.vstack(arr)

<__array_function__ internals>:5: ShapelyDeprecationWarning: The array interface is deprecated and will no longer work in Shapely 2.0. Convert the '.coords' to a numpy array instead.
[1]:
array([[0., 0.],
       [1., 0.],
       [2., 0.],
       [0., 0.],
       [1., 0.],
       [2., 0.]])

Changing to np.vstack([a.coords for a in arr])