Added `Shapely` to the requirements.txt

[cavriends]

There is no restriction on which version of Shapely will be installed (it is the latest, as per pip default). The deprecation warning that is thrown is (see the Shapely documentation on the migration)

ShapelyDeprecationWarning: Setting the 'coords' to mutate a Geometry
in place is deprecated, and will not be possible any more in Shapely 2.0

This is a placeholder as the underlying code has to be refactored to accommodate the changes.