Upgrade the dependencies to be consistent with the current engine dependencies

[micheles]

This is a HUGE project which is much larger than you could imagine. Things to do:

• make sure that the tests pass with the old libraries
• switch from nosests to pytest and fix the breaking tests
• see what libraries can be upgraded without breaking the tests
• work on the problematic libraries by fixing the broken tests.
• remove all the usages of basemap which is abandonware (there are plenty)

Specially problematic libraries are gdal, rtree, pyproj, geopandas.