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

[editorialbot]

Submitting author: !--author-handle-->@bluegenes<!--end-author-handle-- (N. Tessa Pierce-Ward) Repository: https://github.com/sourmash-bio/sourmash Branch with paper.md (empty if default branch): Version: v4.8.9 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: !--reviewers-list-->@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

[editorialbot]

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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1101/029827 is OK
- 10.21105/joss.00027 is OK
- 10.12688/f1000research.19675.1 is OK
- 10.1101/2022.01.11.475838 is OK
- 10.1101/2022.11.02.514947 is OK
- 10.1016/j.amc.2019.02.018 is OK
- 10.1101/gr.277651.123 is OK
- 10.1101/2023.11.06.565843 is OK
- 10.1186/s12859-022-05103-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.94 s (493.5 files/s, 199723.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Standard ML                     97              0              0          57302
Python                         151          16321           7734          55735
SVG                              1              5              0          12420
Rust                            49           2294            858          11536
Markdown                        50           2606              0           7994
CSV                             56             11              0           5733
YAML                            15            123             20            775
TOML                             6             45              8            379
C/C++ Header                     1            163             46            275
Jupyter Notebook                 5              0           3572            271
make                             2             49              6            242
INI                              1             20              0            224
HTML                             1             45              3            146
Nix                              3             30             10            130
TeX                              1              8              0             88
JSON                            19              1              0             50
reStructuredText                 1              6              0             28
Rmd                              1             16             23             17
CSS                              1              2              0              8
Bourne Shell                     2              0              0              6
-------------------------------------------------------------------------------
SUM:                           463          21745          12280         153359
-------------------------------------------------------------------------------

Commit count by author:

   995  C. Titus Brown
   301  dependabot[bot]
   251  Luiz Irber
    65  Tessa Pierce Ward
    28  Laurent Gautier
    22  Keya Barve
    12  Tim Head
    10  Mohamed Abuelanin
     8  Olga Botvinnik
     7  Erik Young
     7  Taylor Reiter
     5  Pranathi Vemuri
     4  Connor Tiffany
     4  Tessa Pierce
     4  dependabot-preview[bot]
     3  Hannah Eve Houts
     3  S. Joshua Swamidass
     3  brooksph
     2  Camille Scott
     2  Daniel Standage
     2  David Koslicki
     2  Harriet Alexander
     2  Jason Stajich
     2  Peter Cock
     2  Titus Brown
     2  ccbaumler
     1  Abhishek Anant
     1  Andreas Sjödin
     1  Arfon Smith
     1  Brad Nelson
     1  Colton Baumler
     1  Connor T. Skennerton
     1  Daniel Dsouza
     1  Fabian Klötzl
     1  Francesco Beghini
     1  Ivan Ogasawara
     1  Katrin Leinweber
     1  Marisa Lim
     1  NapsterInBlue
     1  Phillip Brooks
     1  Ria Lodh
     1  Ricky Lim
     1  jgardner78
     1  ljcohen
     1  pyup.io bot

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 821

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

[bluegenes]

Thanks all! Note pyopensci review (accepted) here: https://github.com/pyOpenSci/software-submission/issues/129

[lwasser]

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.

@LilyAnderssonLee @elais

@arfon can also answer any questions if you have them! 🙌🏻

[majensen]

Thanks all. So this the horse of a different color I've heard tell about. I will follow the SOP and move this along!

[lwasser]

@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!!

[majensen]

@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.

[lwasser]

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.

[bluegenes]

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!

[majensen]

@bede, @amoeba - thanks for being willing to review this paper. It looks like it has already been reviewed and is being routed to JOSS for final publication. I will remove you as reviewers, but the gratitude will remain!

[majensen]

@editorialbot remove @bede as reviewer

[editorialbot]

@bede removed from the reviewers list!

[majensen]

@editorialbot remove @amoeba as reviewer

[editorialbot]

@amoeba removed from the reviewers list!

[majensen]

@editorialbot add @LilyAnderssonLee as reviewer

[editorialbot]

@LilyAnderssonLee added to the reviewers list!

[majensen]

@editorialbot add @elais as reviewer

[editorialbot]

@elais added to the reviewers list!

[majensen]

@editorialbot set 10.5281/zenodo.10951577 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10951577

[majensen]

@editorialbot set v4.8.8 as version

[editorialbot]

Done! version is now v4.8.8

[majensen]

Hi @bluegenes - you are a generous and warm hearted primary author - for which you will be penalized slightly. Can the Zenodo archive be updated with the full author list, and its title be brought in line with the title of the submitted paper? This is a JOSS editorial preference (which I can fight with with associate editor in chief about if you like).

[majensen]

I would also capitalize the article after the colon in the title: "sourmash v4: A multitool...".

[bluegenes]

Hi @bluegenes - you are a generous and warm hearted primary author - for which you will be penalized slightly. Can the Zenodo archive be updated with the full author list, and its title be brought in line with the title of the submitted paper? This is a JOSS editorial preference (which I can fight with with associate editor in chief about if you like).

Thank you, we wanted to make sure everyone gets credit for their contributions!

Looks like we could update the authorship by including a .zenodo.json file (much simpler given the number of authors we have!), but then I think this would be updated as part of a new release. We will need that anyway to update the title -- would that work? cc @ctb

[ctb]

OK, we verified that the .zenodo.json works to set the author list - see sourmash v4.8.9rc2 on zenodo. And the paper title was fixed in https://github.com/sourmash-bio/sourmash/pull/3203. So if we release sourmash v4.8.9 then it will be updated properly.

[ctb]

OK, we just went ahead and released sourmash v4.8.9 - see zenodo. If we need to update v4.8.8 we'll do that too!

[majensen]

Great - can we now entitle the Zenodo archive "sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets"? Again it's a JOSS policy, but we can argue for a exception if you like.

[majensen]

@editorialbot set v4.8.9 as version

[editorialbot]

Done! version is now v4.8.9

[ctb]

I think I did it!

https://zenodo.org/records/11557883

[majensen]

@editorialbot generate pdf

[editorialbot]

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

[majensen]

Ok team - can you consider the following minor updates (line numbers in PDF in previous post): l. 36 - (?) where ref should be l. 41 - “flexible set of programmatic functionality” -> “flexible set of programmatic tools” [?] l. 47 - PIG-PARADIGM gets gold medal for the farthest backed backronym. (or whatever) l. 51. - “with the DHS” -> “with the US Department of Homeland Security (DHS)” (I assume) l. 51. - “The US Government” -> “The US Government (USG)…” l. 51 - how about a comma after each “retains” in this sentence. I know it’s boilerplate. l. 65 - Why is this title italicized and not the others? (probable answer: there is no journal and bibtex thinks the title is the journal)

[bluegenes]

Hi @majensen,

Thanks for your review!

l. 47 - PIG-PARADIGM gets gold medal for the farthest backed backronym. (or whatever)

agreed! :joy:

I've fixed/updated the following:

l. 36 - (?) where ref should be l. 41 - “flexible set of programmatic functionality” -> “flexible set of programmatic tools” [?] l. 65 - Why is this title italicized and not the others? (probable answer: there is no journal and bibtex thinks the title is the journal)

However, line 51 was given to us verbatim by our DHS coauthor, and I believe the manuscript would need to go through another DHS review if we change it. Can we keep as is?

l. 51. - “with the DHS” -> “with the US Department of Homeland Security (DHS)” (I assume) l. 51. - “The US Government” -> “The US Government (USG)…” l. 51 - how about a comma after each “retains” in this sentence. I know it’s boilerplate.

Shall we do another release that includes these updates?

[majensen]

@bluegenes thanks! No, we're all good.

[majensen]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1101/029827 is OK
- 10.21105/joss.00027 is OK
- 10.12688/f1000research.19675.1 is OK
- 10.1101/2022.01.11.475838 is OK
- 10.1101/2022.11.02.514947 is OK
- 10.1016/j.amc.2019.02.018 is OK
- 10.1101/gr.277651.123 is OK
- 10.1186/s12859-022-05103-0 is OK

MISSING DOIs

- 10.1101/2023.11.06.565843 may be a valid DOI for title: Fast, lightweight, and accurate metagenomic functi...

INVALID DOIs

- None

[editorialbot]

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5519, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[majensen]

@bluegenes can you real quick look at the suggestion by editorialbot for the DOI ref above?

[ctb]

@bluegenes can you real quick look at the suggestion by editorialbot for the DOI ref above?

That is the correct reference, and it renders correctly in the PDF. Is there something we should do about it? (It's a valid DOI, it resolves correctly, etc - not sure why it's listed as MISSING?)

thanks!!

[danielskatz]

The entry in the bibtex file (line 81) doesn't list the DOI. It should be added in that entry: doi={10.1101/2023.11.06.565843},

[ctb]

🤦 thx ;)

[ctb]

@editorialbot generate pdf

edit: OK, may not have permissions for that 😆

[editorialbot]

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