as discussed on the user list, we should incorporate/expose MathJax equation numbering functionality when it available in the stable version of mathjax. This looks like the relevant issue to keep track of the status of that functionality: mathjax/MathJax#71
It also appears that MathJax 2 is completely broken in the notebook. I am getting [Math Processing Error] instead of nice math. You can get MathJax 2 by doing:
from IPython.external import mathjax
mathjax.install_mathjax('v2.0')
But you will have to reload your browser a few times to make sure you are not getting the v1.1 version.
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