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[PRE REVIEW]: sourmash v4: a multitool to quickly search, compare, and analyze genomic and metagenomic data sets #6783

Closed editorialbot closed 4 months ago

editorialbot commented 5 months ago

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: v4.8.8 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: !--reviewers-list-->@Kevin-Mattheus-Moerman<!--end-reviewers-list-- Managing EiC: Kevin M. Moerman

Status

status

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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 commented 5 months ago

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 commented 5 months ago 
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 commented 5 months ago

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 commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 821

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

editorialbot commented 5 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 5 months ago

@editorialbot invite @majensen as editor

editorialbot commented 5 months ago

Invitation to edit this submission sent!

majensen commented 5 months ago

@editorialbot assign me as editor

editorialbot commented 5 months ago

Assigned! @majensen is now the editor

majensen commented 5 months ago

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

majensen commented 5 months ago

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

bede commented 5 months ago

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 https://github.com/openjournals/joss-reviews/issues/6783#issuecomment-2141110759, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHWAAG6TQ7JPSF4OPSG37LZE7LCTAVCNFSM6AAAAABIJC7GA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBRGEYTANZVHE . You are receiving this because you were mentioned.Message ID: @.***>

majensen commented 5 months ago

@editorialbot add @bede as reviewer

editorialbot commented 5 months ago

@bede added to the reviewers list!

amoeba commented 4 months ago

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

majensen commented 4 months ago

That is awesome @amoeba - thank you

majensen commented 4 months ago

@editorialbot add @amoeba as reviewer

editorialbot commented 4 months ago

@amoeba added to the reviewers list!

majensen commented 4 months ago

@editorialbot start review

editorialbot commented 4 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6830.

Kevin-Mattheus-Moerman commented 4 months ago

@editorialbot remove @majensen as editor

editorialbot commented 4 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 4 months ago

@editorialbot assign me as editor

editorialbot commented 4 months ago

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

Kevin-Mattheus-Moerman commented 4 months ago

@editorialbot add me as reviewer

editorialbot commented 4 months ago

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

Kevin-Mattheus-Moerman commented 4 months ago

@editorialbot remove @bede as reviewer

editorialbot commented 4 months ago

@bede removed from the reviewers list!

Kevin-Mattheus-Moerman commented 4 months ago

@editorialbot remove @amoeba as reviewer

editorialbot commented 4 months ago

@amoeba removed from the reviewers list!

Kevin-Mattheus-Moerman commented 4 months ago

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

Kevin-Mattheus-Moerman commented 4 months ago

This was reviewed here; https://github.com/pyOpenSci/software-submission/issues/129