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greenelab / deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine
https://greenelab.github.io/deep-review/
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Post-Manubot update cleanup #700

Closed agitter closed 6 years ago

agitter commented 6 years ago

We wanted to merge #681 quickly, so here are some lingering questions and confirmations from that merge:

@dhimmel if you are still willing to re-engineer the author template scripts, that will address most of these. I'll review the formatting and author info that I didn't scrutinize during the #681 review.

agitter commented 6 years ago

While reviewing the author information I noticed the unnecessary OTHER in Yifan Peng's funding information. I'll leave it until we decide what we're going with the templates.

https://doi.org/10.1371/journal.pbio.1001661 isn't working with the new CSL. The last author is not shown, perhaps because it is a consortium. The rest of the pdf formatting and reference list looked good.

agitter commented 6 years ago

@dhimmel do you still plan to work on the new templating that will replace the author table processing functions? We can at least decide which templates that were lost in #681 should be re-implemented.

dhimmel commented 6 years ago

do you still plan to work on the new templating that will replace the author table processing functions?

Yeah. It seems like that the author section is the only part that still needs reworking? I could make it like the format from preprint v1, if that's what you prefer. Let me know if there are any improvements on that format you'd like before I get started.

agitter commented 6 years ago

I believe daef821 is the last time I added templates. There I see templates in the front matter for listing authors, affiliations, and corresponding authors and the methods for funding. I thought I also had them for the contributions statement, but apparently I didn't implement that.

With so many authors, I do prefer having the front matter author list be more compact. It wouldn't need to be identical to preprint v1, but something that puts all authors in a single wrapped line followed by a list of affiliations will fit better on a single PDF page. We could make the affiliations smaller font to further save space. The notes about author order and corresponding authors could be hard coded because those don't change. We do have some repeated affiliations.

What do you think about the funding section? That will need to be updated after we add the new v2 authors. We can use the metadata.yaml support for initials to add those manually instead of deriving them from names like I did previously.

We also need to update the contributions statement, but I don't see a good way to template that with our current metadata.yaml fields.

dhimmel commented 6 years ago

What do you think about the funding section?

Let's do the funding section manually.

We also need to update the contributions statement

Let's also do this manually.

The automated section would be the author's list and affiliations.

agitter commented 6 years ago

@dhimmel do you agree we can close this per #769 and #771? The contributions and funding will be updated manually. I already have a reminder in #561.