Hydrogen kernel not detected

Question

When starting hydrogen in atom to execute python code, I usually get asked which kernel I want to use. I have three kernels. The one I use on my current project is the standard python3 kernel, where I have all the required libraries installed.

Today, when I tried to run some code, this kernel was not in the list. The two other environments (created with conda, I think) were still detected by Hydrogen.

I ran $ jupyter kernelspec list in my terminal (on macOS), and I got this :

  env1    /Users/me/Library/Jupyter/kernels/env1
  env2    /Users/me/Library/Jupyter/kernels/env2
  python3      /Applications/anaconda3/share/jupyter/kernels/python3

I have no idea what caused Hydrogen to stop detecting the python3 kernel.

Restarting atom did not solve this.

How can I make Hydrogen detect the python3 kernel? Any idea of what could have happened?

Answer 1

My hypothesis was that the problem had something to do with the python3 kernel no being in the same directory as the two still-detected kernels.

I created a symbolic link to python3 in the directory of env1 and env2 in Terminal:

cd /Users/me/Library/Jupyter/kernels
ln -s /Applications/anaconda3/share/jupyter/kernels/python3

I then restarted atom, and it now works as previously.

However, I don't know what caused the problem, and I'm not even entirely sure it is this symbolic link that solved it.

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Note : when doing jupyter kernelspec list, the python3 kernel is now listed under the /Users/me/Library/Jupyter/kernels directory.