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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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Manuscript diff for reviewers #798

Closed agitter closed 6 years ago

agitter commented 6 years ago

@dhimmel there are several options in greenelab/manubot-rootstock#54 for creating a manuscript diff to submit to the journal along with the revised manuscript. Do you have a recommendation for deep review?

agitter commented 6 years ago

I tried draftable with our current PDF and https://github.com/greenelab/deep-review/blob/55e779bc418f18e565b3598cc324fa15eeef383b/deep-review.pdf, which is approximately the version we submitted originally.

The results: https://draftable.com/compare/rtWcYEXlwupA

It does great for some sections, but others are marked as entirely new.

dhimmel commented 6 years ago

In the past, I've used the Word of Microsoft to compare and track changes between the two DOCX files. I think all of the methods will struggle with translocations. We could also try latexdiff. @agitter what do you think?

agitter commented 6 years ago

Will we be able to build a DOCX version of the original submission? I wasn't sure whether we'd have to modify the pre-manubot build system to do that.

If it is easy to compare two DOCX versions, let's try that to see how it compares to draftable. If that takes a lot of effort, I'm okay using draftable as a backup plan.

agitter commented 6 years ago

Word's diff is better than draftable's. gh-pages commit 005cc002765cb85a9441b57c5f87bd7960508c62 is based on version fb6f113a21059f342fb1f571713d7e3cd01cbeb2, which we tagged as version v0.9-preprint. I used htmlpreview to view that version of the HTML manuscript then copy/pasted it into a DOCX file: deep-review-v0.9-preprint.docx

I then copy/pasted the current HTML version into another DOCX and compared versions. The diff looks good to me: deep-review-diff.docx

@cgreene once we finalize the manuscript, I'll do this once more so we can submit the DOCX with tracked changes along with the new PDF.

agitter commented 6 years ago

Here is the diff between version v0.9-preprint and b3b57d37c4accabc2e15fd1d3f320a52ce25ed8b: deep-review-diff.docx

agitter commented 6 years ago

Closed per journal resubmission