[python] Fix errors with latest versions of NumPy and Matplotlib

NEWS.txt

scripts/python3/data_manip/conversion/convert_gebco.py

scripts/python3/data_manip/conversion/convert_hycom.py

scripts/python3/data_manip/conversion/convert_jcope2.py

scripts/python3/data_manip/conversion/convert_to_ini.py

scripts/python3/data_manip/conversion/convert_to_spg.py

scripts/python3/data_manip/conversion/dat2vtu.py

scripts/python3/data_manip/extraction/parser_gmsh.py

scripts/python3/data_manip/extraction/parser_kenue.py

scripts/python3/data_manip/extraction/parser_selafin.py

scripts/python3/data_manip/extraction/telemac_file.py

scripts/python3/data_manip/formats/conlim.py

scripts/python3/data_manip/formats/ecmwf.py

scripts/python3/data_manip/formats/grib.py

scripts/python3/data_manip/formats/serafin_file.py

scripts/python3/postel/parser_output.py

scripts/python3/postel/plot2d.py

scripts/python3/postel/plot_vnv.py

scripts/python3/pretel/compute_weight.py

scripts/python3/pretel/convert_to_bnd.py