I have replaced the normal sequential run of the top level roots_for_degree and heatmap functions with making them tasks and running them in the ruffus.pipeline_run.
Still no parallelization. That's next. This just simulates exactly how the script ran before.
Interesting thing to note, that my previous runs of 16 degree, size 200 fractals, took approx. 33-36 seconds. Now replaced to run in the pipeline they take 45 seconds. Seems like a good bit of overhead, but perhaps it isn't linear, and will more than make up for running roots in parallel.