[REVIEW]: sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@bluegenes@Kevin-Mattheus-Moerman@Kevin-Mattheus-Moerman<!--end-reviewers-list-- Archive: 10.5281/zenodo.11557883

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/11313337f8dcd9183cf24d4624062971"><img src="https://joss.theoj.org/papers/11313337f8dcd9183cf24d4624062971/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/11313337f8dcd9183cf24d4624062971/status.svg)](https://joss.theoj.org/papers/11313337f8dcd9183cf24d4624062971)

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

@bede & @amoeba, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

@bede, please create your checklist typing: @editorialbot generate my checklist

@amoeba, please create your checklist typing: @editorialbot generate my checklist

ctb commented 4 months ago

Proof looks good to me!

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot set 10.5281/zenodo.11557883 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.11557883

Kevin-Mattheus-Moerman commented 3 months ago

@lwasser on this:

@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!!

My apologies. I should have caught this when the submission came in and should have fast tracked it myself.

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot remove @LilyAnderssonLee as reviewer

editorialbot commented 3 months ago

@LilyAnderssonLee removed from the reviewers list!

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot remove @elais as reviewer

editorialbot commented 3 months ago

@elais removed from the reviewers list!

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot remove @majensen as editor

editorialbot commented 3 months ago

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

@editorialbot commands

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot assign me as editor

editorialbot commented 3 months ago

Assigned! @Kevin-Mattheus-Moerman is now the editor

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot add @Kevin-Mattheus-Moerman as reviewer

editorialbot commented 3 months ago

@Kevin-Mattheus-Moerman added to the reviewers list!

Kevin-Mattheus-Moerman commented 3 months ago

Added pyOpenSci label, as this was already reviewed here: https://github.com/pyOpenSci/software-submission/issues/129

Kevin-Mattheus-Moerman commented 3 months ago

@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:

[ ] I updated the archive as the one listed was for the wrong version. Please can you confirm this is correct, i.e. this review is for tagged release version v4.8.9 which is archived here 10.5281/zenodo.11557883.
[x] Please edit the ZENODO listed license to match your software license. It currently lists this: But it should refer to you actual BSD-3-Clause license. You need to process this change by manually editing your archive entry.

On the paper:

[ ] Please add city, state, country to all affiliations, and please spell out country names, so use United States of America in full.

ctb commented 3 months ago

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!

Kevin-Mattheus-Moerman commented 3 months ago

@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 1. University of California, Davis you could use e.g. 1 University of California Davis, Davis, CA, United States of America, and for 2 Woods Hole Oceanic Institution you could use e.g. 2 Woods Hole Oceanic Institution, Woods Hole, MA, Unites States of America.

Since this is only an affiliation rendering update as a minor change in paper.md there is no need to mint a new version etc. Hope this helps. Hope you can make this minor change where possible.

Once completed as a minor paper change I think we can stick with v4.8.9 but you can decide on that, please let me know.

ctb commented 3 months ago

Since this is only an affiliation rendering update as a minor change in paper.md there is no need to mint a new version etc. Hope this helps. Hope you can make this minor change where possible.

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!

Kevin-Mattheus-Moerman commented 3 months ago

@ctb that is no problem, you can ping me here once you are ready.

ctb commented 3 months ago

Addresses fixed (by @bluegenes) in latest branch on github! @Kevin-Mattheus-Moerman

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 3 months ago

@ctb thanks for making those changes. I have checked the review over at https://github.com/pyOpenSci/software-submission/issues/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.

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 3 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Irber given-names: Luiz orcid: "https://orcid.org/0000-0003-4371-9659" - family-names: Pierce-Ward given-names: N. Tessa orcid: "https://orcid.org/0000-0002-2942-5331" - family-names: Abuelanin given-names: Mohamed orcid: "https://orcid.org/0000-0002-3419-4785" - family-names: Alexander given-names: Harriet orcid: "https://orcid.org/0000-0003-1308-8008" - family-names: Anant given-names: Abhishek orcid: "https://orcid.org/0000-0002-5751-2010" - family-names: Barve given-names: Keya orcid: "https://orcid.org/0000-0003-3241-2117" - family-names: Baumler given-names: Colton orcid: "https://orcid.org/0000-0002-5926-7792" - family-names: Botvinnik given-names: Olga orcid: "https://orcid.org/0000-0003-4412-7970" - family-names: Brooks given-names: Phillip orcid: "https://orcid.org/0000-0003-3987-244X" - family-names: Dsouza given-names: Daniel orcid: "https://orcid.org/0000-0001-7843-8596" - family-names: Gautier given-names: Laurent orcid: "https://orcid.org/0000-0003-0638-3391" - family-names: Hera given-names: Mahmudur Rahman orcid: "https://orcid.org/0000-0002-5992-9012" - family-names: Houts given-names: Hannah Eve orcid: "https://orcid.org/0000-0002-7954-4793" - family-names: Johnson given-names: Lisa K. orcid: "https://orcid.org/0000-0002-3600-7218" - family-names: Klötzl given-names: Fabian orcid: "https://orcid.org/0000-0002-6930-0592" - family-names: Koslicki given-names: David orcid: "https://orcid.org/0000-0002-0640-954X" - family-names: Lim given-names: Marisa orcid: "https://orcid.org/0000-0003-2097-8818" - family-names: Lim given-names: Ricky orcid: "https://orcid.org/0000-0003-1313-7076" - family-names: Nelson given-names: Bradley orcid: "https://orcid.org/0009-0001-1553-932X" - family-names: Ogasawara given-names: Ivan orcid: "https://orcid.org/0000-0001-5049-4289" - family-names: Reiter given-names: Taylor orcid: "https://orcid.org/0000-0002-7388-421X" - family-names: Scott given-names: Camille orcid: "https://orcid.org/0000-0001-8822-8779" - family-names: Sjödin given-names: Andreas orcid: "https://orcid.org/0000-0001-5350-4219" - family-names: Standage given-names: Daniel orcid: "https://orcid.org/0000-0003-0342-8531" - family-names: Swamidass given-names: S. Joshua orcid: "https://orcid.org/0000-0003-2191-0778" - family-names: Tiffany given-names: Connor orcid: "https://orcid.org/0000-0001-8188-7720" - family-names: Vemuri given-names: Pranathi orcid: "https://orcid.org/0000-0002-5748-9594" - family-names: Young given-names: Erik orcid: "https://orcid.org/0000-0002-9195-9801" - family-names: Brown given-names: C. Titus orcid: "https://orcid.org/0000-0001-6001-2677" contact: - family-names: Brown given-names: C. Titus orcid: "https://orcid.org/0000-0001-6001-2677" doi: 10.5281/zenodo.11557883 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Irber given-names: Luiz orcid: "https://orcid.org/0000-0003-4371-9659" - family-names: Pierce-Ward given-names: N. Tessa orcid: "https://orcid.org/0000-0002-2942-5331" - family-names: Abuelanin given-names: Mohamed orcid: "https://orcid.org/0000-0002-3419-4785" - family-names: Alexander given-names: Harriet orcid: "https://orcid.org/0000-0003-1308-8008" - family-names: Anant given-names: Abhishek orcid: "https://orcid.org/0000-0002-5751-2010" - family-names: Barve given-names: Keya orcid: "https://orcid.org/0000-0003-3241-2117" - family-names: Baumler given-names: Colton orcid: "https://orcid.org/0000-0002-5926-7792" - family-names: Botvinnik given-names: Olga orcid: "https://orcid.org/0000-0003-4412-7970" - family-names: Brooks given-names: Phillip orcid: "https://orcid.org/0000-0003-3987-244X" - family-names: Dsouza given-names: Daniel orcid: "https://orcid.org/0000-0001-7843-8596" - family-names: Gautier given-names: Laurent orcid: "https://orcid.org/0000-0003-0638-3391" - family-names: Hera given-names: Mahmudur Rahman orcid: "https://orcid.org/0000-0002-5992-9012" - family-names: Houts given-names: Hannah Eve orcid: "https://orcid.org/0000-0002-7954-4793" - family-names: Johnson given-names: Lisa K. orcid: "https://orcid.org/0000-0002-3600-7218" - family-names: Klötzl given-names: Fabian orcid: "https://orcid.org/0000-0002-6930-0592" - family-names: Koslicki given-names: David orcid: "https://orcid.org/0000-0002-0640-954X" - family-names: Lim given-names: Marisa orcid: "https://orcid.org/0000-0003-2097-8818" - family-names: Lim given-names: Ricky orcid: "https://orcid.org/0000-0003-1313-7076" - family-names: Nelson given-names: Bradley orcid: "https://orcid.org/0009-0001-1553-932X" - family-names: Ogasawara given-names: Ivan orcid: "https://orcid.org/0000-0001-5049-4289" - family-names: Reiter given-names: Taylor orcid: "https://orcid.org/0000-0002-7388-421X" - family-names: Scott given-names: Camille orcid: "https://orcid.org/0000-0001-8822-8779" - family-names: Sjödin given-names: Andreas orcid: "https://orcid.org/0000-0001-5350-4219" - family-names: Standage given-names: Daniel orcid: "https://orcid.org/0000-0003-0342-8531" - family-names: Swamidass given-names: S. Joshua orcid: "https://orcid.org/0000-0003-2191-0778" - family-names: Tiffany given-names: Connor orcid: "https://orcid.org/0000-0001-8188-7720" - family-names: Vemuri given-names: Pranathi orcid: "https://orcid.org/0000-0002-5748-9594" - family-names: Young given-names: Erik orcid: "https://orcid.org/0000-0002-9195-9801" - family-names: Brown given-names: C. Titus orcid: "https://orcid.org/0000-0001-6001-2677" date-published: 2024-06-28 doi: 10.21105/joss.06830 issn: 2475-9066 issue: 98 journal: Journal of Open Source Software publisher: name: Open Journals start: 6830 title: "sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06830" volume: 9 title: "sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 3 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 3 months ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5547
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06830
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 3 months ago

@bluegenes congratulations on this JOSS publication!

editorialbot commented 3 months 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](https://joss.theoj.org/papers/10.21105/joss.06830/status.svg)](https://doi.org/10.21105/joss.06830)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06830">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06830/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06830/status.svg
   :target: https://doi.org/10.21105/joss.06830

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:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

bluegenes commented 3 months ago

Thank you @Kevin-Mattheus-Moerman!

openjournals / joss-reviews