Linking to ancillary material formatted as Jupyter nb? I'm in the process of preparing a manuscript which provides ancillary material in the form of a Jupyter Notebook (*.ipynb) explaining how we implemented some key parts of our results. I'd like to link to the nbviewer rendering of our ancillary material, especially since some readers may not be familiar with how to read a *.ipynb file. For instance, 1511.08044 provides several appendices in this way, each of which can be viewed with a link of the form http://nbviewer.jupyter.org/urls/arxiv.org/src/1511.08044v1/anc/1.energies_vs_vgate.ipynb.
This naively seems to depend on knowing the paper identifier that arXiv will assign the manuscript once published, however, such that there doesn't seem to be a way to provide a link that works on initial submission. Is there a best practice known for providing Jupyter Notebooks that doesn't introduce this circularity?
I think you're asking the wrong question here.

For the sake of persistent archiving you should put all ancillary material at a sustainably archived website specifically designed to preserve scholarly communications material e.g. Zenodo https://zenodo.org/ or Dryad  http://datadryad.org/ or Figshare https://figshare.com/

Refer-to or cite the ancillary material archived on Zenodo with the Zenodo DOI that is generated upon archival of the material. From within that ancillary material which is archived, you can link to an nbviewer prettified instance of your Jupyter nb.

Direct-linking to nbviewer from within your article is a really bad idea. In five or ten years time it's very likely that the link will be broken. Always refer to ancillary material with persistent identifiers e.g. DOIs.