To have reproducible prototypes, I use Make to wrap the whole workflow in docker. Then I push the code to gist and forget about it. Although GitHub gist doesn't allow binary file, images embedded in .ipynb (JSON), on the other hand works in gist. Here is an example.

https://gist.github.com/ontouchstart/854a3c280b81f530d3ae9cb...

The notebook generated by nbconvert (see the instruction in the Makefile) is too big to display in GitHub gist Web UI but works fine in nbviewer.

https://nbviewer.jupyter.org/gist/ontouchstart/854a3c280b81f...

This has been my solution as well. There’s little that feels as good as running `make -B report` and watching the whole thing be rebuilt from scratch.

How do you manage encapsulating each step, and passing data between them?

I don't do it well. See

https://github.com/4kbt/ReplicableAnalysis

and

https://github.com/4kbt/PlateWash

as examples. The former is smaller/less complicated. The latter was my thesis work -- more complicated and (unfortunately) abuses recursive calls to Make.

Would that be easier with rake than with make?