Closed agitter closed 5 years ago
I've converted the DOCX to markdown pasted below, courtesy of:
pandoc --to=gfm --wrap=none pcbi.1007128.docx
Thanks for converting @dhimmel. I'll stop copying from the detailed instructions in the individual issues now that we have everything here.
I'm thinking about which issues potentially affect the manuscript on GitHub and which issues can be handled without any changes to this repo. Here are the issues that I think it may make sense to modify the git repository while addressing them:
Is it so that all changes we make at this point should be directly to the word document from our previous submission? Or should we export another DOCX and then create a diff later? I'm leaning towards the former. For some issues, like the references formating, we can regenerate the bibliography with Manubot and copy-and-paste the revised section into the existing DOCX with tracked changes?
Finally, we can make changes to the Manubot source, that we end up reverting after producing a suitable output. This would make sense for changes where the journal requirements are a downgrade from our current implementation, e.g. https://github.com/greenelab/meta-review/issues/231 and https://github.com/greenelab/meta-review/issues/233.
For the last submission, I only uploaded the manuscript and diff as PDFs. Because PLOS doesn't have a DOCX of our manuscript, I expect we could safely export another DOCX and create a diff later. They'll use the new DOCX as the master version of our manuscript.
Could we make any final commits that we want to keep in the HTML version, bundle those with the post-submission commits, and tag that? Then we make any other edits needed for the resubmission and revert back to the tagged version once we pass the proofing stage. Maybe that's what you are suggested by your comment above about reverting changes that are a downgrade.
Please feel free to tag me in the relevant sub-issues.
Let me know how I can help.
Maybe that's what you are suggested by your comment above about reverting changes that are a downgrade.
I think we can make changes that are just-for-submission and general changes, as long as they aren't intermixed in the same pull requests. Then we'll tag the version we use to derive the resubmission DOCX. Then if we want to undo some of the just-for-submission changes, we can do a git revert
and look through the commit history.
@dhimmel that sounds good to me. You can go ahead and merge the other PRs I approved.
@dhimmel it looks like we are getting pretty close to finishing the formatting changes. Once we resolve the remaining reference formatting issues in https://github.com/greenelab/meta-review/pull/241 (or rather those that we want to address), we should be able to quickly finish everything and resubmit.
I believe we are ready to resubmit after merging #242 and #243.
It's not clear to me whether we need to generate another diff for this submission. The submission system states
This will open a new window where you can upload your corrected file(s), including the tracked-changes version of your manuscript file.
But perhaps that assumes we already submitted a DOCX version previously? I plan to submit without a diff and generate one later if they need it. I will start with the final https://github.com/greenelab/meta-review/blob/output/manuscript.docx and make the manual changes from there. The manual changes are:
@agitter great. I'll be available for the next couple hours but then will go offline for 5 days. So hopefully you will be able to move forward with the resubmission!
@dhimmel I'm starting the submission process. If I need to make any minor changes at the last minute, I may self-approve the PR so that we don't have to wait for you to return.
If I need to make any minor changes at the last minute, I may self-approve the PR so that we don't have to wait for you to return.
Yes please do!
I resubmitted with the formatting changes: https://github.com/greenelab/meta-review/releases/tag/v4.0
The PLOS Computational Biology team emailed the following message about formatting. The attachment below contains the specific requests. I'll create individual issues for each request and use this as the meta issue, as during revision.
Should I contact them to ask about all of the links in our text? If they remove them during proofing without telling us, the text will suffer.
Instructions in the submission system:
Attachment: pcbi.1007128.docx