fix all warnings shown in example notebooks

[atravitz]

a running list:

• cookbook/network_from_orion_fepp.ipynb
• cookbook/hand_write_ligand_network.ipynb: gufe warning about rdkit mol props

[jameseastwood]

• rbfe_tutorial/rbfe_python_turoial.ipynb "Creating the Transformation" produces DeprecationWarning: mapping input as a dict is deprecated; instead use either a single Mapping or list