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[REVIEW]: A Framework to Quality Control Oceanographic Data #2063

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @castelao (Guilherme Castelao) Repository: https://github.com/castelao/CoTeDe Version: v0.21.3 Editor: @kthyng Reviewer: @jessicaaustin, @evanleeturner Archive: 10.5281/zenodo.3733959

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@jessicaaustin & @evanleeturner, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kthyng know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @jessicaaustin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @evanleeturner

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

castelao commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

castelao commented 4 years ago

@kthyng I'm sorry for my lack of attention on the bibliography records and thank you very much for your PR. I did a few other adjustments.

castelao commented 4 years ago

I just release a new version of CoTeDe and the new DOI is: 10.5281/zenodo.583710

Do I need to do anything else? Thank you

kthyng commented 4 years ago

@castelao I'm still seeing that the "note" section in your .bib file isn't coming through to be printed in your paper. For example, in the .bib file for Boyer et al, there is a note for the Technical Editor, but this doesn't come through to the reference in your paper. I can try to work on this at some point to see which entry type will carry through the note field, but it might be a few days before I have a chance.

castelao commented 4 years ago

@kthyng, you are already too generous with your time, I can do it myself. Thank you.

Yes, I noticed that, but my understanding is that the lack of the note field is the result of the reference type 'manual' combined with the bibliography style used by JOSS. Different journals adopt different styles, and since this is not my expertise, I always provide the fields and let each journal style to decide how to use those fields.

One alternative is to move back from manual to incollection, as it was originally, which would allow an editor field. But notice that Mishonov is a technical editor and not a regular editor, so it would not be fully correct. My opinion is that hacking it to force those changes would go against the principle of using BibTeX. I'm more inclined to provide the fields and let the style definition decides how to use those and what to show. The fields currently shown are enough to uniquely identify this reference, and it is normal to have fields that are not shown in the reference. For instance, most styles omit the fields 'keys' and 'URL'.

If you think that it is necessary to show the technical editor, I can figure this out.

kthyng commented 4 years ago

@castelao Sure, the combination of items results in what ultimately shows up in the references. The thing that is most in your control is what type of entry a given reference is entered as. I think it is a good goal to have the information about the references show up, and it doesn't taking Latex hacking so much as appropriate field/entry choice. When I looked up that reference online, it was requested to show the Technical Editor in the citation, so I would try to respect that. That wasn't the only entry that had information in the bibtex entry that wasn't showing up in the references list. Can you give it another small chunk of time to do your best to faithfully represent the references?

castelao commented 4 years ago

@kthyng certainly. I just did a test, and if I replace the note field by an editor field it shows up in the PDF. The problem is that the editor field is not standard for a manual type of entry. But editor field is standard for an 'incollection' entry.

Was intentional that you changed from 'incollection' to 'manual'? I could move it back to incollection, or I can exchange 'note' by 'editor' and keep the 'manual' type of entry. Let me know your preference.

kthyng commented 4 years ago

@castelao I changed from incollection to manual when I saw your other bib entries were manual and had note fields — I assumed that meant the note fields were coming through. And as I recall, the editor field wrote "Editor" but since the person is a technical editor, not just editor, I figured a less specific field would be more appropriate to use (then keeping the language "Technical Editor").

castelao commented 4 years ago

One alternative to force that output is to use:

... series = {(A. V. Mishonov, {T}echnical {E}ditor) {NOAA} {Atlas} {NESDIS} 87}, ...

Would you prefer that or incollection with editor (which would be 'Ed.' only instead of Technical Editor)?

On Mon, Mar 30, 2020 at 2:17 PM Kristen Thyng notifications@github.com wrote:

@castelao https://github.com/castelao I changed from incollection to manual when I saw your other bib entries were manual and had note fields — I assumed that meant the note fields were coming through. And as I recall, the editor field wrote "Editor" but since the person is a technical editor, not just editor, I figured a less specific field would be more appropriate to use (then keeping the language "Technical Editor").

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castelao commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

castelao commented 4 years ago

@kthyng I spoke with Tim Boyer today, the first author of that publication, and he said that on his side there is no problem with using 'Editor' instead of 'Technical Editor'.

kthyng commented 4 years ago

ok great, let's move ahead then.

kthyng commented 4 years ago

@whedon add 10.5281/zenodo.583710 as archive

whedon commented 4 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands
kthyng commented 4 years ago

@whedon set 10.5281/zenodo.583710 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.583710 is the archive.

kthyng commented 4 years ago

@castelao Can you edit the metadata at your Zenodo archive so that the title and authors on your paper exactly match there?

Also, what is the proper version number for your repository currently?

castelao commented 4 years ago

@kthyng I just updated the DOI record itself, thanks for noticing that.

The current version is 0.21.3

kthyng commented 4 years ago

@whedon set 10.5281/zenodo.3733959 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3733959 is the archive.

kthyng commented 4 years ago

Looks like the zenodo archive changed numbers too, so I updated that. Let me know if this is incorrect

kthyng commented 4 years ago

@whedon set v0.21.3 as version

whedon commented 4 years ago

OK. v0.21.3 is the version.

kthyng commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.13155/33951 is OK
- 10.1016/j.mio.2014.09.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1410

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1410, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
kthyng commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1411
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02063
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

kthyng commented 4 years ago

Congratulations to @castelao on your new publication! Many thanks to reviewers @jessicaaustin and @evanleeturner — we have relied on your time and expertise!

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

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reStructuredText:
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   :target: https://doi.org/10.21105/joss.02063

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