What Python distribution and Jupyter version are you using? (Is it
possible you have multiple versions installed on your system and it is
picking the wrong one? You can force IJulia to build with a particular
Jupyter program by setting the JUPYTER environment variable to the path of
your jupyter executable and then re-running Pkg.build().)
Did you try Pkg.update() to make sure you are using the latest version of
IJulia etc?
You can also look at the file Pkg.dir("IJulia", "deps", "deps.jl") to see
what version of Jupyter IJulia thinks it is using.