You don't need the python-markdown-mathjax extension

[rmcgibbo]

Just put the javascript that grabs mathjax from the cdn right in the jinja template, base.html.

  <!-- MathJax support  -->
  <script type="text/javascript"
   src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
  <script type="text/x-mathjax-config">
  MathJax.Hub.Config({
    tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}
  });
  </script>