Closed whedon closed 1 year ago
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@whedon generate pdf
@whedon generate pdf
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My only comment from proof reading (note some mild dyslexia means that proof reading probably isn't my best skill) is that on line 48 of the paper (https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/blob/9e37bde609c11a2df932c63cc3be07e08deb2a44/paper/paper.md?plain=1#L48) you should use the possessive form of "Software Carpentery" (i.e. "Software Carpentry's").
Ok cool thank you! I am equally useless with these things. I'll ask my co-authors to read through the pdf again to see if they spot anything else.
@whedon generate pdf
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I think I have now fixed the pandas reference. Can you let me know if you are happy with this? I'll send out the current version for final proof reading comments from my co-authors.
For the pandas reference I think something like
author = {{The pandas development team}},
might remove the weird capital T (cause LaTeX thinks that "The" is someones first name.
I added a blank first name like this:
author = {The pandas development team, {}},
@whedon generate pdf
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Might be getting into a bit of a rabbit hole, but that now adds a full stop at the end of the author which shouldn't be there (the full stop in the other references is to indicate the abbreviation of the author's first names). I will have a look into the reference style that JOSE is using.
According to this issue (https://github.com/openjournals/joss/issues/230, for JOSS but JOSE uses the same bot) the format is author-year (https://www.overleaf.com/learn/latex/Biblatex_bibliography_styles) so there shouldn't be a full stop between the author name and the bracketed year (unless the author first name is abbreviated). Can you try wrapping everything in curlys and see if that fixes it?
@whedon generate pdf
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Looks like that didn't work. I will ask around the editorial team to see if someone has a fix. This should give your co-authors some time to proof read also.
Aren't there full stops after all the author names? To me it doesn't look different to other references, but happy to hear about an improved solution.
There are, but those full stops indicate the abbreviation of the name i.e. Andrew -> A., however I have since found out that for “group authors” there is a full stop after (https://apastyle.apa.org/style-grammar-guidelines/references/examples/webpage-website-references). So I guess it is good as is! Sorry for the faff (I am still learning!).
The next step is minting a DOI with Zenodo but we should wait until your coauthors have proof read before we go to that step.
Thank you! yes that makes sense. I should hear by Wednesday from everyone and will proceed then.
@whedon generate pdf
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@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.26434/chemrxiv.13656665.v1 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1039/C8RP00105G is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1021/bk-2021-1387.ch009 is OK
- 10.21105/jose.00032 is OK
- 10.1021/acs.jchemed.1c00142 is OK
- 10.1021/acs.jchemed.9b01131 is OK
- 10.21105/jose.00148 is OK
- 10.1021/bk-2020-1365.ch001 is OK
- 10.1021/acsinfocus.7e5030 is OK
- 10.5281/zenodo.7344967 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/jose.00139 is OK
- 10.1109/mcse.2006.122 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon generate pdf
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Hi @arm61, We have finalised the proofs.
I have bumped the version to 1.1.0 for the changes that have been made since the submission.
The DOI from Zenodo is: 10.5281/zenodo.7782433
Is there anything else that is needed?
@whedon set 10.5281/zenodo.7782433 as archive
OK. 10.5281/zenodo.7782433 is the archive.
@whedon set 1.1.0 as version
OK. 1.1.0 is the version.
@whedon recommend-accept
Attempting dry run of processing paper acceptance...
:wave: @openjournals/jose-eics, this paper is ready to be accepted and published.
Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/117
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/117, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.26434/chemrxiv.13656665.v1 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1039/C8RP00105G is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1021/bk-2021-1387.ch009 is OK
- 10.21105/jose.00032 is OK
- 10.1021/acs.jchemed.1c00142 is OK
- 10.1021/acs.jchemed.9b01131 is OK
- 10.21105/jose.00148 is OK
- 10.1021/bk-2020-1365.ch001 is OK
- 10.1021/acsinfocus.7e5030 is OK
- 10.5281/zenodo.7344967 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/jose.00139 is OK
- 10.1109/mcse.2006.122 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Amazing @ppxasjsm, now we just wait for the editor-in-chief to make sure everything is okay!
Fantastic @arm61!
Dear @labarba I think the paper is ready for your final oversight.
I messaged @labarba over Slack last week and she is aware that this is waiting but we very busy with grant applications. Hopefully, it will all be confirmed soon 🙂
No problem at all! I very much understand. I just wanted to check in! Thanks for letting me know.
Hi, I just wanted to check in on this again. Any rough idea when you may get a chance to look at this?
hi @ppxasjsm 👋 – I appreciate your patience with this. I'm on travel and have a huge backlog to deal with when I get back. Thank you.
Please merge my PR with minor edits to the paper: https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/pull/52 …and double check the figure caption, which isn't showing for me in the preview service, but should! (I'm not sure what is going on there.)
I checked everything else, and will publish as soon as you merge and fix the caption as needed.
Hi @labarba I have merged edits and have figured out the figure caption (it was a missing new line) and things are now displaying ok for me.
@whedon generate pdf
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I looked at the proof and it seems ok to me, or let me know if there is anything else I can fix.
One last thing! Can you check if adding curly brackets will fix the way "Project Jupyter" is appearing as an author in the nbgrader paper? It shows as "Jupyter, P." and that is not quite what we want...
Submitting author: @ppxasjsm (Antonia S J S Mey) Repository: https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry Version: 1.1.0 Editor: @arm61 Reviewer: @lucydot, @ghutchis Archive: 10.5281/zenodo.7782433
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Review checklist for @lucydot
Conflict of interest
Code of Conduct
General checks
Documentation
Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)
JOSE paper
paper.md
file include a list of authors with their affiliations?Review checklist for @ghutchis
Conflict of interest
Code of Conduct
General checks
Documentation
Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)
JOSE paper
paper.md
file include a list of authors with their affiliations?