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

begin{equation}

a^2 + b^2 = c^2

end{equation}

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.

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}

[@eq:label]

and compiling with

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

for more 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"} } });

</script>

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 

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.)

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

@eq:description

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.

If you use css styling you can add the following in your css file:

/*create an equation counter variable */



body {

   counter-reset:  EQU_COUNT 0 ;

}

and:

.MathJax_Display:after {

      content: "      (" counter(EQU_COUNT) ")";    

      counter-increment: EQU_COUNT;           

    }

This will automatically add a an incremented counter value after each equation.

If ConTeXt is used as the engine to produce the PDF output,
then one can simply precede the LaTeX display formula with a placeformula ConTeXt command in the Pandoc Markdown input:

placeformula

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

When multiple output formats are desired, it is better to use a GNU makefile containing a sed command:

SHELL := /usr/bin/env bash

NAME := $(basename $(wildcard *.md))



all: $(NAME).pdf $(NAME).docx



$(NAME).pdf: $(NAME).md

    pandoc 

    <(sed 's/^$$$$.*/\placeformulan&/' $<) 

    --smart --output=$(NAME).tex --to=context

    context $(NAME).tex



$(NAME).docx: $(NAME).md

    pandoc $< --smart --output=$(NAME).docx