Update the Deep Review with latest Manubot#681
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Related to comment at greenelab#2 (comment)
Provide 8/25 status update
Add in stub files so that we can start writing.
reality has struck!
…nto cgreene-patch-1
Start to stub in categorize section
2016-10-26 status report
Update 02_intro.md
* Enable tag citations See greenelab#2 (comment). * Reflow text to satisfy codeclimate
URL citation guidelines
Outline the Study section
Fill in more of the introduction
…and-scaling Hardware Limitations and Scaling
Pandoc upgraded to v2.0.0.1 Swap anaconda packages to conda-forge Update build.sh for pandoc 2.0 WeasyPrint was not renderring MathJax, so use --webtex to convert equations to SVGs for PDF output. See Kozea/WeasyPrint#59
Merge manubot-rootstock into the Deep Review at https://github.com/greenelab/manubot-rootstock/tree/46824e6b5e3e84cdab22beb5ce2fd656124c96ef Have not reconciled: * sections → content * authors.tsv → metadata.yaml
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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:
@agitter ready for review |
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@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. |
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@dhimmel I can go through quickly now |
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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.ipynbin 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 contributionssection
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
This build is based on 8eb858a. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/deep-review/builds/297004423 https://travis-ci.org/greenelab/deep-review/jobs/297004424 [ci skip] The full commit message that triggered this build is copied below: Merge PR #681 to update Manubot Update the Deep Review with latest Manubot
This build is based on 8eb858a. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/deep-review/builds/297004423 https://travis-ci.org/greenelab/deep-review/jobs/297004424 [ci skip] The full commit message that triggered this build is copied below: Merge PR #681 to update Manubot Update the Deep Review with latest Manubot
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@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:
This seems like it should be an upstream manubot-rootstock change?
We could create a symlink pointing to The arXiv build warnings are because those studies have now been published with DOIs. We can fix these at the end or sooner?
This should be partly done in the updated README. |
We had a Deep Review-specific example,
We can leave this alone. It was only my very minor personal preference.
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.
Your README update took care of the semi-colon. I'll use my #696 for the forbidden tags. |
Closes #680