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To make a numbered equation in Pandoc, I defer to using pure LaTeX:

a^2 + b^2 = c^2

In PDF form, it gives a nice numbered equation, however, this equation doesn't show up at all in the HTML output because the equation is within the \begin environment and is ignored. I would like to keep the numbering in the PDF, but would like the equation to show up in the HTML, with or without the numbering.

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In pandoc you can do:

(@foo)  $a^2 + b^2 = c^2$

As (@foo) says, ...

(@bar)  $e = x + y$

This will give you running equation numbers in both PDF and HTML. However, the equations will not be centered or display-formatted. (You can use $$ for display math, but then the numbers probably won't be lined up right -- though maybe this can be fixed with CSS.)

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Doing it this way, the equation ends up being placed on the left and slightly above the equation itself. Is there a way to have the equation number on the right just like in the regular latex format? – user1027169 May 3 '13 at 20:11
No, there's no way to get the number on the right. You could probably fix alignment issues with display math using CSS. – John MacFarlane May 4 '13 at 2:06
I meant in the PDF output, the equation number gets moved to the left. As you mentioned, the HTML shouldn't be an issue with some CSS. – user1027169 May 4 '13 at 16:25
@JohnMacFarlane just wondering if this (displaymath, right-aligned eqs) is something that might be addressed in later pandoc releases, or if explicit LaTeX environment remains the way to go for pdf output? – cboettig Jun 23 '14 at 18:20
Mathjax supports \ref and \eqref in plain HTML: cdn.mathjax.org/mathjax/latest/test/sample-eqrefs.html --- can Pandoc users get access to this functionality? (I'm converting multimarkdown to html.) – Ahmed Fasih Jun 29 '14 at 4:26

An extension exists on github: pandoc-crossref

install it with:

cabal update
cabal install pandoc-crossref

or in archlinux using ArchHaskell

pacman -Sy pandoc-crossref

you can use it by doing:

$$ math $$ {#eq:label}

and compiling with

pandoc file.md --filter pandoc-crossref -o file.pdf

for mor information see the documentation

Alternatively, as described in https://github.com/jgm/pandoc/issues/1938#issuecomment-74011358 you can use --mathjax for HTML rendering

if your equations are in math.txt

$$ a^2 + b^2 = c^2 $$

create a file header

<script type="text/x-mathjax-config">
  MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "all"} } });

and compile with

pandoc math.txt -t html -s -o test.html --mathjax=https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML -H header 
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Welcome to TeX.SX! You can have a look at our starter guide to familiarize yourself further with our format. – Symbol 1 Apr 1 '15 at 9:27

Another option for equation numbers and references is the pandoc-eqnos filter.

Install pandoc-eqnos as root using the bash command

pip install pandoc-eqnos 

To tag an equation with the label eq:description, use

$$ y = mx + b $$ {#eq:description}

The prefix #eq: is required whereas description can be replaced with any combination of letters, numbers, dashes, slashes and underscores.

To reference the equation, use


To apply the filter, use the following option with pandoc:

--filter pandoc-eqnos

Full details and demos are given on the pandoc-eqnos Web page at github.

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