[eljost]

I'm a computational/theoretical chemist and use python extensivly.

To me te question seems a bit poorly phrased. What is the goal of the course? Are they supposed to learn how to program? Then it's of course fundamentals first, especially the stuff you cited (variables, functions, scoping). You can't solve any problem without knowing this stuff.

If they are supposed to learn a specific library/tool then, in my opinion, it depends on the libs/tools you want to teach them. Maybe this libary is not that relevant for comp. biologists, but take scikit-learn. You still have to know how to program when you wan't to use this library properly. On the other hand if they shall learn some GUI-tools then I guess they don't have to know how to program. You can ask yourself: Can you anticipate what tools/libraries your students will be using in a few years? If you can answer yes to this, then teach them a bit about these tools. If your field is constantly evolving/changing then it would be better to invest in the basics, so your students can adapt easier.

Considering the fact that you are (hopefully) and have to be constantly learning as a practicing scientist it is of great importance to get the basics right.