Upgrading to numpy 2

[micheles]

This is hard since it requires upgrading many dependencies and fixing many tests. We can start trying

numpy 2.2.5
numba 0.61.2
scipy 1.13.1
shapely 2.1.0
matplotlib 3.10.1
onnxruntime 1.21.1

Then we need to remake the GDAL wheel and possibly many others.

NB: the oq-mbtk will have to change. For instance the upgrade to shapely 2 will require a change cascaded_union -> unary_union``. The wheel for netCDF4 will have to be recompiled to use numpy 2.