I changed the python script to now generate new HTML files for every R or Matlab script in the CSV.  The HTML files are just wrappers that include the google-code-prettify script.  The rest of the python script uses these files, and should cause the site to link to them.
I fixed some typos in my edits to include google-code-prettify.  It now correctly generates all the HTML files I need.  Only issue is my own laptop isn't serving the script or accessing it from google correctly.  Not a huge problem. Wifi isn't good here, but I think it should run later today.