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[REVIEW]: LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy #2006

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @uellue (Dieter Weber) Repository: https://github.com/LiberTEM/LiberTEM Version: 0.5.0 Editor: @majensen Reviewers: @alvarolopez, @fedorov Archive: 10.5281/zenodo.3763313

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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

@alvarolopez & @fedorov, 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 @majensen know.

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

Review checklist for @alvarolopez

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @fedorov

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

majensen commented 4 years ago

@uellue I see the following people not in the paper author list, but listed in the archive

Dey, Shankhadeep;
Levin, Barnaby D.A.;
Ophus, Colin;
Peter, Simon;
Schyndel van, Jay; Shin, Jaeweon; Sunku, Sai;

If these folks are not willing to be on the paper, let me know here. I can understand why they would remain on the archive, so I will want to have an EIC weigh in on the protocol in this situation.

uellue commented 4 years ago

@majensen In the archive we have everybody who contributed a commit or who contributed to LiberTEM in other ways that establish co-authorship of the software. One would have to actively opt out of being listed there since contributing commits to a software automatically establishes co-authorship. Furthermore, being a co-author of the software doesn't mean endorsement or responsibility for the entire content.

However, to be co-author of a paper means responsibility and endorsement for the entire manuscript. That's why we require co-authors to actively opt in per our authorship policy. Some people didn't respond, and some responded that they didn't want to be on the paper. All people with extensive contributions to LiberTEM are also co-authors of the paper.

majensen commented 4 years ago

@whedon check references

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.5281/zenodo.2450624 is OK
- 10.1145/1327452.1327492 is OK
- 10.1109/nuicone.2012.6493198 is OK
- 10.1109/mcse.2011.37 is OK
- 10.1145/2934664 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.5281/ZENODO.3396791 is OK
- 10.5281/ZENODO.2649351 is OK
- 10.1017/s1431927619000497 is OK
- 10.5281/ZENODO.3763313 is OK
- 10.1142/9789811204579_0005 is OK

MISSING DOIs

- None

INVALID DOIs

- None
majensen commented 4 years ago

@whedon set 10.5281/zenodo.3763313 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3763313 is the archive.

majensen commented 4 years ago

@whedon set 0.5.0 as version

whedon commented 4 years ago

OK. 0.5.0 is the version.

majensen commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
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/1484

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1484, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
majensen commented 4 years ago

@openjournals/joss-eics - Please note that LiberTEM is a significant and ongoing project that has its own policies for author and contributor credit. It also has its own Zenodo archive location, for which 0.5.0 is the latest version and incorporates the comments of the reviewers here.

The author list on this paper is a subset of the author list on the archive, because of the nature of the project's community guidelines. (See @uellue comment and prior.) I hope that there can be a variance allowed in the JOSS policy of requiring the author lists to be the same on both the paper and the archive in this instance. Thanks -- @majensen

uellue commented 4 years ago

@majensen The final proof looks good, I just verified the text, links and Orcids.

labarba commented 4 years ago

I can see in the comments above the rationale for the different author lists in the Zenodo archive and the JOSS paper. But is there any reason why the Zenodo archive title cannot be made to match the JOSS paper archive?

majensen commented 4 years ago

Well, the archives for the project LiberTEM have a history of consistent naming. If I were to give a reason as an advocate for the author, I would say that the JOSS paper is a unique event in its history as a project, associated with the latest version of LiberTEM. Independently of this event, there is an established LiberTEM developer community and user base which has come to expect a certain convention in the naming of the software package that they contribute to and depend on. IMO, JOSS is fortunate in having the opportunity to publish this mature work under its masthead, and the journal might reasonably grant flexibility in this situation.

uellue commented 4 years ago

@labarba Is this a requirement that there's a 1:1 match with the Zenodo title? It seems that I overlooked it.

The title of the Zenodo deposition is the default one if GitHub integration for releases is activated. We can also call the paper LiberTEM/LiberTEM: 0.5.0 if you prefer. A more descriptive title would just be more appealing, I figured.

As @majensen wrote, we already have quite a number of releases on Zenodo and it would seem a bit odd to rename it just to match a paper title about it.

labarba commented 4 years ago

We have a (soft) policy of asking authors to manually edit the metadata of the Zenodo deposit after the release has done its thing, so the titles and author list matches the paper. Of course we don't want you to change the title of the paper to match the repo name. Look, I'm not insisting. That's what we regularly do. If you have your reasons, do as you wish.

uellue commented 4 years ago

@labarba Thank you for the clarification! If possible, I'd like to leave it as it is. Since both paper title and archive contain the unique name "LiberTEM", I think that readers will understand that the two are referring to each other even if the titles don't match 100%. :-)

majensen commented 4 years ago

@labarba Sounds like we are ready to pull the trigger

danielskatz commented 4 years ago

@majensen - when a submission is ready to be accepted, please tag @openjournals/joss-eics to be sure you get the on-duty AEiC, which changes week to week...

majensen commented 4 years ago

@openjournals/joss-eics This work is recommended for publication.

danielskatz commented 4 years ago

👋 @uellue - if you can merge https://github.com/LiberTEM/LiberTEM/pull/823, we can finalize the publication

danielskatz 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

- 10.5281/zenodo.2450624 is OK
- 10.1145/1327452.1327492 is OK
- 10.1109/nuicone.2012.6493198 is OK
- 10.1109/mcse.2011.37 is OK
- 10.1145/2934664 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.5281/ZENODO.3396791 is OK
- 10.5281/ZENODO.2649351 is OK
- 10.1017/s1431927619000497 is OK
- 10.5281/ZENODO.3763313 is OK
- 10.1142/9789811204579_0005 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/1507

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1507, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
danielskatz commented 4 years ago

👋 @uellue - sorry, I missed one - can you also merge https://github.com/LiberTEM/LiberTEM/pull/824

danielskatz 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/1508
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02006
  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...

sk1p commented 4 years ago

@danielskatz Thank you! :partying_face: :tada:

danielskatz commented 4 years ago

Thanks to @alvarolopez & @fedorov for reviewing! And @majensen for editing!

And congratulations to @uellue (Dieter Weber) and co-authors!!

whedon commented 4 years ago

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

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uellue commented 4 years ago

Thank you @danielskatz @alvarolopez @fedorov @majensen for reviewing and managing the submission!

@sk1p @kruzaeva @woozey @anandbaburajan @twentyse7en @jan-car @irahulcse @sayandip18 @magnunor Knut @rafaldb Many thanks and congratulations!

uellue commented 4 years ago

As a general remark, open writing and open review in combination with GitHub worked really well IMO, and the whole process was a refreshing, pleasant and productive experience. I'll be sure to recommend JOSS for papers like this. 👍