For what it's worth, I did something similar for my master's dissertation, but couldn't be bothered to learn make, so I used a python library called pydoit: ht

For what it's worth, I did something similar for my master's dissertation, but couldn't be bothered to learn make, so I used a python library called pydoit: http://pydoit.org/ http://pydoit.org/ All my analysis code, plots, etc were already in python, so it fit in well. Lyx has a CLI from where I exported .tex and compiled to pdf.