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Reviews for the Journal of Open Source Software
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[REVIEW]: PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model. #4207

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@zhenwu0728<!--end-author-handle-- (Zhen Wu) Repository: https://github.com/JuliaOcean/PlanktonIndividuals.jl Branch with paper.md (empty if default branch): Version: v0.5.1 Editor: !--editor-->@elbeejay<!--end-editor-- Reviewers: @Datseris, @BrodiePearson Archive: 10.5281/zenodo.6507001

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/015da73a23acb9d114cb5c5578dd41aa"><img src="https://joss.theoj.org/papers/015da73a23acb9d114cb5c5578dd41aa/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/015da73a23acb9d114cb5c5578dd41aa/status.svg)](https://joss.theoj.org/papers/015da73a23acb9d114cb5c5578dd41aa)

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

@navidcy & @Datseris, 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 @elbeejay 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

📝 Checklist for @Datseris

📝 Checklist for @BrodiePearson

elbeejay commented 2 years ago

@editorialbot set v0.5.1 as version

editorialbot commented 2 years ago

Done! version is now v0.5.1

elbeejay commented 2 years ago

@editorialbot set 10.5281/zenodo.6507001 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6507001

zhenwu0728 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

zhenwu0728 commented 2 years ago

Hi @elbeejay, thanks for the clarification. Now the citation should be good, no more nested parentheses.

elbeejay commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.02813 is OK
- 10.5194/gmd-10-4175-2017 is OK
- 10.1111/j.1529-8817.1973.tb04092.x is OK
- 10.3354/meps148187 is OK
- 10.1029/2021gb006941 is OK
- 10.1177/00375497211068820 is OK
- 10.3389/fmicb.2020.00086 is OK
- 10.1038/nrmicro.2016.62 is OK
- 10.1126/science.1254421 is OK
- 10.1016/j.ecolmodel.2011.10.001 is OK
- 10.1126/science.1138544 is OK

MISSING DOIs

- None

INVALID DOIs

- None
elbeejay commented 2 years ago

@zhenwu0728 looks great. Thanks again to @Datseris and @BrodiePearson for providing constructive reviews. At this time I will be recommending we accept and publish this paper in JOSS.

elbeejay commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.02813 is OK
- 10.5194/gmd-10-4175-2017 is OK
- 10.1111/j.1529-8817.1973.tb04092.x is OK
- 10.3354/meps148187 is OK
- 10.1029/2021gb006941 is OK
- 10.1177/00375497211068820 is OK
- 10.3389/fmicb.2020.00086 is OK
- 10.1038/nrmicro.2016.62 is OK
- 10.1126/science.1254421 is OK
- 10.1016/j.ecolmodel.2011.10.001 is OK
- 10.1126/science.1138544 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3184

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3184, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer commented 2 years ago

Hi @zhenwu0728, I'm the AEIC on duty doing some final checks before publishing.

In your article, could you add commas after instances of "e.g.", and remove "etc." from parenthetical statements that start with "e.g."?

Also, It looks like there is actually a JOSS article on Agents.jl you should probably cite (https://doi.org/10.21105/joss.01611), perhaps in addition to the newer article you do cite.

zhenwu0728 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

zhenwu0728 commented 2 years ago

Thanks @kyleniemeyer! I've added the citation you mentioned and also changed the "e.g.,"

kyleniemeyer commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3197
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04207
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

zhenwu0728 commented 2 years ago

Thanks a lot! @elbeejay @Datseris @BrodiePearson @kyleniemeyer

kyleniemeyer commented 2 years ago

Congratulations @zhenwu0728 on your article's publication in JOSS!

Many thanks to @Datseris and @BrodiePearson for reviewing this, and @elbeejay for editing.

editorialbot commented 2 years 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.04207/status.svg)](https://doi.org/10.21105/joss.04207)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04207">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04207/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04207/status.svg
   :target: https://doi.org/10.21105/joss.04207

This is how it will look in your documentation:

DOI

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