Update the Deep Review with latest Manubot

[dhimmel]

Closes #680

[dhimmel]

The original work for this PR begins in ea92847

You can browse what the repo will look like if this PR is merged at this tree.

Here's the PDF from a local build: manuscript.pdf.

• Before merging remember to create output branch to replace references branch.

@agitter ready for review

[agitter]

@dhimmel I should have time to review this weekend

[dhimmel]

I should have time to review this weekend

@agitter if okay with you, I recommend we merge now, since I anticipate people may begin making revisions this weekend and I don't want them to start off of the old repository.

I could then address any issues you identify in subsequent commits.

[agitter]

@dhimmel I can go through quickly now

[agitter]

I didn't inspect everything, but I didn't find any showstoppers in the parts I reviewed. There are two things I recommend changing now and others we can clean up post-merge. You can merge when you're ready.

Pre-merge suggestions:

• Keep authors/author-order.ipynb in the repository, that is our public record of how the author ordering was done and may have been referenced externally
• Fix the broken templating in the Author contributions section

Post-merge:

• Inspect pdf formatting and references in detail
• Customize the front matter and maybe the back matter. In the expanded format we lead with three pages of authors, which is too long
• Add back footnotes for corresponding authors and about the author order
• Clarify what is no longer templated (contributions and funding are not?)
• Perhaps rename manuscript.pdf back to deep-review.pdf along with the other outputs
• Add back the example tag in USAGE.md
• Double check that all author info transferred correctly
• Check the build warnings arXiv article 1702.05747 published in"None" at https://doi.org/10.1016/j.media.2017.07.005, etc.
• Make a note to all authors about the changes such as the ; between multiple references and prohibited characters in citations

[agitter]

@dhimmel should I create a new issue to track the items above that need to be fixed or double-checked?

[dhimmel]

should I create a new issue to track the items above that need to be fixed or double-checked?

Yep, and you can assign me the ones you want me to do!

Some quick notes:

Add back the example tag in USAGE.md

This seems like it should be an upstream manubot-rootstock change?

Perhaps rename manuscript.pdf back to deep-review.pdf along with the other outputs

We could create a symlink pointing to manuscript.pdf. I'd only do this if we think there are public links (outside of this repo) to deep-review.pdf.

The arXiv build warnings are because those studies have now been published with DOIs. We can fix these at the end or sooner?

Make a note to all authors about the changes such as the ; between multiple references and prohibited characters in citations

This should be partly done in the updated README.

[agitter]

Add back the example tag in USAGE.md

We had a Deep Review-specific example, [@tag:Zhou2015_deep_sea], that I had in mind. Any example from citation-tags.tsv would be fine, in which case it wouldn't be in the upstream manubot-rootstock.

Perhaps rename manuscript.pdf back to deep-review.pdf along with the other outputs

We can leave this alone. It was only my very minor personal preference.

The arXiv build warnings are because those studies have now been published with DOIs.

We could fix them now or immediately before resubmitting. I expect other preprints could be published. I just don't want to forget to do it.

This should be partly done in the updated README.

Your README update took care of the semi-colon. I'll use my #696 for the forbidden tags.