It's been a while ago since last time I tried Jupyter with Mathematica, and things may have improved since then, so I will only focus on limitations that I believe cannot be addressed. While using Jupyter is much better than using the "naked" Mathematica kernel from the command line, and may be suitable for occasional use, it is not nearly comparable to using the full Mathematica notebook interface. The quality and usability of Jupyter with Mathematica is nowhere near that of the native notebook interface.
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