It really is just so sad, that I cannot get a publication-quality report from a jupyter notebook as of now. To me, the main isses are:
- no support for yaml headers (can be integrated as plain markdown, but look ugly in the notebook itself)
- no official way of hiding input cells (the extension also only allows hiding in html, not pdf)
- difficult (if not impossible?) to get automatically generated markdown tables (cf. Jupyter Notebook + R + nbconvert ... tables?)
In essence, I’d dream of using the notebook format for interactive development jointly with my non-coding collaborators and then just use nbconvert to get a .md file (which I can process using pandoc to whatever output format I need for submission). Cross-referencing would also be nice, but is not supported by pandoc, so probably not going to happen.