I am also having the same problem now. Everything was working fine to me one month back but when I am trying the code again, Jupyter is not importing the pygmt. I have tried this after creating new pygmt environment but problem is still persisting. But when I am trying to use pygmt in the terminal, there is no issue. And jupyter is also running in the same env.
This is very strange.
pygmt.show_versions() shows that you’re running in the pygmt1 environment, but it’s unclear why it finds the GMT 6.4.0 in your pygmt environment. On the other hand, when running in Jupyter notebook, it finds the unsupported GMT 6.1.0.