[REVIEW]: sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets #6830
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type: For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type: |
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Thanks all! Note pyopensci review (accepted) here: pyOpenSci/software-submission#129 |
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hey @majensen 👋🏻 just to add to @bluegenes comment above, this package has already been reviewed by pyOpenSci. as such you will only need to review the paper / scope etc. The code should not be reviewed again. I am adding this note because i see two reviewers have been assigned. in the past, credit has been given to the reviewers on the pyOpenSci side of things who in this case are. @arfon can also answer any questions if you have them! 🙌🏻 |
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Thanks all. So this the horse of a different color I've heard tell about. I will follow the SOP and move this along! |
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@majensen 😆 i believe it is. i'm just curious - from your perspective as an editor - what could we (pyopensci / joss) do differently that would help make it more clear that is it a pyopensci fast track when such a package enters into your review process? and also - thank you!! |
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@lwasser well unless I missed it in the autogenerated material (very possible), I think it was @bluegenes herself who informed me in the thread. I wonder @openjournals/dev if there is a natural way to interconnect between the journals (one of the paper metadata files?), so that maybe a tag is autoadded or some other info is provided to give the editor a heads-up. I admit this my first time handling one of these over almost 5yr. |
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ahhhh good to know. and so good that @bluegenes posted here (and i was tagged in our slack as well!) . an auto label would be really nice and would make things easier. a check box in the review submission that triggers the bot to create a pyOpenSci approved label? that is a great idea. |
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hi all! Just fyi - I believe I included the info in the note to editor during submission, so I'm not sure if that got over to you or not. Thanks @lwasser for your help getting the reviews linked! |
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@editorialbot remove @bede as reviewer |
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@bede removed from the reviewers list! |
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@editorialbot add @LilyAnderssonLee as reviewer |
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@LilyAnderssonLee added to the reviewers list! |
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@editorialbot set 10.5281/zenodo.10951577 as archive |
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@editorialbot remove @majensen as editor |
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I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@editorialbot assign me as editor |
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Assigned! @Kevin-Mattheus-Moerman is now the editor |
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@editorialbot add @Kevin-Mattheus-Moerman as reviewer |
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@Kevin-Mattheus-Moerman added to the reviewers list! |
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@bluegenes apologies for the kinks in the cable with this review as I initially missed this was a pyOpenSci related submission. All is good/cleared up now and we are good to proceed. As AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked the pyOpenSci review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention: On the archive:
On the paper:
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I changed the LICENSE just now - good catch, we'll have to edit the .zenodo.json to fix that more permanently! In re the authors, we do not have that level of affiliation for many of them, and would need to put in a lot of work to get it - with no guarantee of success, since this is now a 9 year old package. We do have their ORCIDs, of course, but not all (most?) of the ORCIDs have public affiliation information. Could you confirm this is necessary for publication? Last but not least - if we do need to update the information on that scale, we will probably do so via .zenodo.json and then would release a new version, v4.8.10. So that would be the version to list then. thanks! |
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@ctb thanks for fixing the license listed on ZENODO. On the affiliations, this was relating to the paper, not the ZENODO archive. Also I am not asking for a major change. I only ask that for the 9 affiliations listed in the paper, that you check if you know and can add the city, state, country where possible. This would be to conform to our guidelines better but is no strict required for publication in that sense. So for instance in the case of Since this is only an affiliation rendering update as a minor change in Once completed as a minor paper change I think we can stick with |
thank you so much! that makes a lot of sense :). I'm traveling and it may take us a day or three to make these changes, but will do! |
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@ctb that is no problem, you can ping me here once you are ready. |
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Addresses fixed (by @bluegenes) in |
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@editorialbot generate pdf |
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@ctb thanks for making those changes. I have checked the review over at pyOpenSci/software-submission#129, and I have also checked your repository, the archive link, and the paper. All is now in order, so I will now proceed to accept this submission. |
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@editorialbot accept |
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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘 |
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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨 Here's what you must now do:
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@bluegenes congratulations on this JOSS publication! |
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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets: This is how it will look in your documentation: We need your help! The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
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Thank you @Kevin-Mattheus-Moerman! |
Submitting author: @bluegenes (N. Tessa Pierce-Ward)
Repository: https://github.com/sourmash-bio/sourmash
Branch with paper.md (empty if default branch):
Version: v4.8.9
Editor: @Kevin-Mattheus-Moerman
Reviewers: @Kevin-Mattheus-Moerman
Archive: 10.5281/zenodo.11557883
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