When I run xelatex on the output from the pretext build, I get the output in the attached file. XeLaTex then appears to go into an infinite loop; I left it running for 20 minutes and it did not complete, with CPU at 100% the entire time.
There are several messages of the form:
LaTeX Warning: Hyper reference `section-simple-python-data_variables' on page 7
undefined on input line 1246.
The links do exist, however, and they build correctly for the web.