It’ll be some time before computational notebooks replace PDFs in scientific journals, because that would mean changing the incentive structure of science itself. Until journals require scientists to submit notebooks, and until sharing your work and your data becomes the way to earn prestige, or funding, people will likely just keep doing what they’re doing.
It is incredibly depressing that we live in a world where scientific knowledge is still shared mostly by means of PDF documents, but the title of this article is misleading at best. The future of science communication will not be built on yet another proprietary document format. On the other hand, the Web platform has all the technical capabilities needed to create any sort of “computational” papers, but it still lacks appropriate authoring tools to empower scientists to do it by themselves.
The reports of the scientific paper’s death have been (unfortunately) greatly exaggerated.