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

[editorialbot]

Submitting author: @bluegenes (N. Tessa Pierce-Ward)
Repository: https://github.com/sourmash-bio/sourmash
Branch with paper.md (empty if default branch):
Version: v4.8.8
Editor: @Kevin-Mattheus-Moerman
Reviewers: @Kevin-Mattheus-Moerman
Managing EiC: Kevin M. Moerman

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)

Author instructions

Thanks for submitting your paper to JOSS @bluegenes. Currently, there isn't a JOSS editor assigned to your paper.

@bluegenes if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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 (491.0 files/s, 198730.5 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:

   994	C. Titus Brown
   299	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]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[Kevin-Mattheus-Moerman]

@editorialbot invite @majensen as editor

[editorialbot]

Invitation to edit this submission sent!

[majensen]

@editorialbot assign me as editor

[editorialbot]

Assigned! @majensen is now the editor

[majensen]

@amoeba are you open to reviewing this work? Thanks for considering - @majensen

[majensen]

Hi @bede - would you be willing to review this work for JOSS? Thanks for your consideration -- @majensen

[bede]

Hi Mark, yes, certainly

…

On Fri, 31 May 2024 at 03:04, Mark Jensen ***@***.***> wrote: Hi @bede <https://github.com/bede> - would you be willing to review this work <#m_8882923951265368344_m_2110076668829038873_6783> for JOSS <https://joss.theoj.org>? Thanks for your consideration -- @majensen <https://github.com/majensen> — Reply to this email directly, view it on GitHub <#6783 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHWAAG6TQ7JPSF4OPSG37LZE7LCTAVCNFSM6AAAAABIJC7GA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBRGEYTANZVHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[majensen]

@editorialbot add @bede as reviewer

[editorialbot]

@bede added to the reviewers list!

[amoeba]

Hi @majensen: Yes I can review this and within the next two weeks.

[majensen]

That is awesome @amoeba - thank you

[majensen]

@editorialbot add @amoeba as reviewer

[editorialbot]

@amoeba added to the reviewers list!

[majensen]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6830.

[Kevin-Mattheus-Moerman]

@editorialbot remove @majensen as editor

[editorialbot]

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

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot assign me as editor

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot add me as reviewer

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot remove @bede as reviewer

[editorialbot]

@bede removed from the reviewers list!

[Kevin-Mattheus-Moerman]

@editorialbot remove @amoeba as reviewer

[editorialbot]

@amoeba removed from the reviewers list!

[Kevin-Mattheus-Moerman]

Apologies @bede @amoeba @majensen because this has been reviewed already here: pyOpenSci/software-submission#129 we follow a different procedure. Thanks anyway for being willing to help!

[Kevin-Mattheus-Moerman]

This was reviewed here; pyOpenSci/software-submission#129