This might be a feature request for the GitHub page, but I figured I'd post 
here first. It's a handful of related issues involving LaTeX to HTML 
transforms via MathJax.

First, there doesn't seem to be any native way to turn on equation 
numbering for MathJax. This seems like a pretty easy add, as its just 
another code snipped included before the MathJax <script> call.

Second, equation environments are getting transformed into basic display 
math. Since traditional equation numbering in LaTeX (e.g. \label{eq:1}) 
doesn't work outside of the equation environment, this isn't ideal.

Alternatively, using the MathJax option {autonumber:"all"} (instead of the 
default "AMS") would number all display math and would require users to 
include "\notag" or "\nonumber" in any display math they don't want to be 
numbered. It's a decent quick workaround, but would require some extra work 
for users as they're more likely to be using the equation environment when 
writing in LaTeX.

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