Warnings - shapely deprecation warning and some user warning

There are some warnings from shapely lib and from pleque.io.tools. We have ignored them in the last update, but they should be considered in the future I think. It creates bit of a spam.

The warnings should be popping up in the tests, but here is also an example with pleque==0.0.6:

>>> from pleque.io.compass import cdb
>>> cdb(21673, 1150.0)

/compass/Shared/Common/IT/projects/solps/python-solps-environment/.venv/lib/python3.9/site-packages/pleque/io/tools.py:35: UserWarning: rename 'Rt' to 'R' does not create an index anymore. Try using swap_dims instead or use set_index after rename to create an indexed coordinate.
  ds = ds.rename({'Rt': 'R', 'Zt': 'Z'})
/compass/Shared/Common/IT/projects/solps/python-solps-environment/.venv/lib/python3.9/site-packages/pleque/io/tools.py:35: UserWarning: rename 'Zt' to 'Z' does not create an index anymore. Try using swap_dims instead or use set_index after rename to create an indexed coordinate.
  ds = ds.rename({'Rt': 'R', 'Zt': 'Z'})
<__array_function__ internals>:200: ShapelyDeprecationWarning: The array interface is deprecated and will no longer work in Shapely 2.0. Convert the '.coords' to a numpy array instead.