3. Conclusions

In this paper we proposed a novel publication workflow built around Jupyter Book, Jupyter Notebook and reveal.js. Our exhibit demonstrates how to create narrative-driven documents (peppered with executable code examples), computational notebooks and interactive slides, all from a single markdown source. Furthermore, we outlined a strategy for hosting and disseminating such materials through version-controlled environments similar to code sharing repositories. Such a platform facilitates an intuitive review mechanism inspired by software engineering practice, thus endowing provenance and transparency to the scientific publication process. While our exhibit is currently a bare-bones proof-of-concept built from open-source tools, it shows the potential for transforming the current PDF workflow into an environment focused on content creators and reviewers. One can even imagine automating parts of this process with “bots” validating submissions based on predefined criteria, and partially pre-populating a review form to streamline the entire publication life-cycle (akin to continuous integration and deployment pipelines in software engineering).

While addressing some of the main issues with current publishing practice, the proposed workflow is not (yet) a silver bullet and the underlying technology needs further development to mature into reliable software. We envisage that engagement of the scientific community and open discussion are needed to steer the development and foster broader adoption of such tools, for example, workshops encouraging submission and review in such a format. Interactivity is a great advantage of Jupyter Book publications, but the compute resources employed to execute the underlying code have to be accounted for and provisioned since relying upon free code-execution environments (such as Google Colab and MyBinder) is not sustainable in the long term. Given that the main output of the proposed workflow is a collection of web pages, they either need to be accessed online or downloaded and browsed locally to take full advantage of their format; generating PDFs and EPUBs is also possible, however they lack interactivity and may not be visually appealing since they only play a secondary role. Notably, the proposed framework is not as powerful as LaTeX, which benefits from decades of development and a rich ecosystem of packages, therefore any customisation or automation will require a bespoke plugin that may be slow to create and buggy at first. Nonetheless, without making the first step – and addressing the disadvantages associated with it – the publishing process will not benefit from the technology that we developed to make our research possible in the first place.