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[REVIEW]: qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations #1435

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @fboehm (Frederick Boehm) Repository: https://github.com/fboehm/qtl2pleio Version: v1.0.3 Editor: @csoneson Reviewer: @vjcitn, @rcorty Archive: 10.5281/zenodo.3263924

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Markdown: [![status](http://joss.theoj.org/papers/66bca5dc3d2e72b6259159bad07aafaf/status.svg)](http://joss.theoj.org/papers/66bca5dc3d2e72b6259159bad07aafaf)

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

@vjcitn & @rcorty, 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 @csoneson know.

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

Review checklist for @vjcitn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rcorty

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

csoneson commented 5 years ago

Yes - see e.g. https://texfaq.org/FAQ-capbibtex. For the DOIs for the articles from 1995, I also can't find them (neither on PubMed nor on https://www.crossref.org/guestquery/). @openjournals/joss-eics - do you have additional suggestions where to look, or is it ok to leave it like this?

fboehm commented 5 years ago

Thanks, @csoneson! Are there additional changes that I should make to complete the review process?

kyleniemeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

kyleniemeyer commented 5 years ago

Hi @fboehm, I made a few fixes to the bib file in https://github.com/fboehm/qtl2pleio/pull/20 (DOIs should not include the full URL in the bibtex file, just the DOI itself).

csoneson commented 5 years ago

Hi @fboehm - I have sent another email to @rcorty to get his feedback on the revised submission. If he doesn't reply, we'll find another way forward. @vjcitn - could you take one more look to see if your remaining issues have now been satisfactorily addressed (and if so, complete the final items in the checklist). Thanks!

csoneson commented 5 years ago

@kyleniemeyer Thanks for your input! Do you have a suggestion for where to possibly find DOIs for old articles, or is it ok to leave it without?

For the DOIs for the articles from 1995, I also can't find them (neither on PubMed nor on https://www.crossref.org/guestquery/). @openjournals/joss-eics - do you have additional suggestions where to look, or is it ok to leave it like this?

kyleniemeyer commented 5 years ago

@csoneson I went to the publisher's page for those articles, and they don't have one listed, so I don't think they have DOIs. Some publishers went back and generated DOIs for articles that were published prior to the adoption of DOIs, but apparently this one didn't. So I think it's fine—they just don't have DOIs.

kyleniemeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

rcorty commented 5 years ago

I believe this article and package are passing all requirements and I've updated my check boxes to reflect this.

vjcitn commented 5 years ago

I have updated check boxes. Package/paper passes.

csoneson commented 5 years ago

@rcorty, @vjcitn - thank you for your reviews!

csoneson commented 5 years ago

@fboehm - I'll make another pass through the paper and make sure that nothing is missing, and then we're ready to go. To prepare for acceptance, could you please make a Zenodo archive, and report the DOI in this thread. Make sure that the title and authors of the Zenodo archive match those of the paper.

csoneson commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

csoneson commented 5 years ago

@fboehm - one more small thing to fix in the references:

I'm not quite sure why the Bates & Eddelbuettel reference shows up as "D. Bates & Eddelbuettel" in the text - if I compile the paper locally this doesn't happen, and the bib file looks fine.

fboehm commented 5 years ago

@csoneson - Thanks so much! I’ve fixed the bib file by making the first S a capital letter.

fboehm commented 5 years ago

Zenodo assigned this DOI: 10.5281/zenodo.3263924

fboehm commented 5 years ago

Thank you, @vjcitn and @rcorty for your very helpful & constructive reviews!

csoneson commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

csoneson commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago 

OK DOIs

- 10.1214/aos/1176344552 is OK
- 10.1534/genetics.115.183624 is OK
- 10.1038/nmeth.2848 is OK
- 10.1534/genetics.107.080101 is OK
- 10.1534/g3.119.400098 is OK
- 10.32614/rj-2011-002 is OK
- 10.18637/jss.v040.i08 is OK
- 10.18637/jss.v052.i05 is OK

MISSING DOIs

- None

INVALID DOIs

- None
csoneson commented 5 years ago

@whedon set 10.5281/zenodo.3263924 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3263924 is the archive.

csoneson commented 5 years ago

@whedon set v1.0.3 as version

whedon commented 5 years ago

OK. v1.0.3 is the version.

csoneson commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago 

OK DOIs

- 10.1214/aos/1176344552 is OK
- 10.1534/genetics.115.183624 is OK
- 10.1038/nmeth.2848 is OK
- 10.1534/genetics.107.080101 is OK
- 10.1534/g3.119.400098 is OK
- 10.32614/rj-2011-002 is OK
- 10.18637/jss.v040.i08 is OK
- 10.18637/jss.v052.i05 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/802

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/802, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
csoneson commented 5 years ago

@openjournals/joss-eics - we are ready for acceptance here! The only weird thing is that the Bates & Eddelbuettel reference in the paper shows up as "D. Bates & Eddelbuettel" - however, the "D." is not included if I build the markdown locally.

kyleniemeyer commented 5 years ago

@csoneson yeah, that's strange. Not sure why it's happening. Unless that's a major issue, I think we should just proceed.

kyleniemeyer commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 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/803
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01435
  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...

kyleniemeyer commented 5 years ago

@fboehm congrats on your submission's publication in JOSS! Thanks to @vjcitn and @rcorty for reviewing, and @csoneson for editing.

whedon commented 5 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:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01435/status.svg)](https://doi.org/10.21105/joss.01435)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01435">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01435/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01435/status.svg
   :target: https://doi.org/10.21105/joss.01435

This is how it will look in your documentation:

DOI

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