[REVIEW]: PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model. #4207

editorialbot · 2022-02-25T14:07:20Z

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

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.
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@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

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-02-25T14:07:21Z

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editorialbot · 2022-02-25T14:07:49Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (643.0 files/s, 92586.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           74           2112            653           9565
Markdown                        13            224              0            739
TOML                             5             86              1            357
TeX                              1             11              0            129
YAML                             4              6              0             84
-------------------------------------------------------------------------------
SUM:                            97           2439            654          10874
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-02-25T14:07:49Z

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 · 2022-02-25T14:07:50Z

Wordcount for paper.md is 827

editorialbot · 2022-02-25T14:09:21Z

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

elbeejay · 2022-02-25T14:12:20Z

@navidcy and @Datseris thanks again for agreeing to review this submission to JOSS. We've just switched over from whedon to the new editorialbot, and the review process has changed subtly. Instead of your checklist being at the top of this issue, you can generate your own checklist with the command @editorialbot generate my checklist. Otherwise the review process is functionally the same as it has been in the past -- please feel free to reach out to me with any questions. Remember to open issues in the PlanktonIndividuals.jl repository that are related to this JOSS review, and "link" them to this review issue by posting this URL (https://github.com/openjournals/joss-reviews/issues/4207) in the text of the issue you open.

We're starting this review before I've found a 3rd reviewer out of respect for @navidcy's availability in late March, so as a heads up to @zhenwu0728 and co-authors, I will still be reaching out to and hopefully adding another reviewer here.

Datseris · 2022-02-25T14:26:03Z

Review checklist for @Datseris

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/JuliaOcean/PlanktonIndividuals.jl?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@zhenwu0728) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

elbeejay · 2022-03-10T21:44:35Z

@editorialbot add @BrodiePearson as reviewer

editorialbot · 2022-03-10T21:44:37Z

@BrodiePearson added to the reviewers list!

BrodiePearson · 2022-03-10T21:55:16Z

Review checklist for @BrodiePearson

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/JuliaOcean/PlanktonIndividuals.jl?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@zhenwu0728) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Datseris · 2022-03-11T17:42:55Z

Hello @elbeejay , I would like to submit my review:

Summary

PlanktonIndividuals.jl is a Julia package that simulates the lifecycle and transport of plankton in oceanic currents. It has strong performance capabilities utilizing GPU infrastructure. The paper makes a clear case supporting the need for the package. The paper and authors satisfy the official checklist of JOSS. As far as I can tell, the documentation of the package is very good. It includes documentation strings, examples, and clearly states the actual physics used in the models via stating actual equations, something that (unfortunately) is missing from many packages. I was able to install the software and run their 0D example without problems. All in all, I would recommend publication, however, there are some points I would strongly recommend the authors to consider, and address satisfactorily.

Additions I would recommend

The first couple of sentences of either the Summary or the Statement of Need sections should introduce a general audience to the relevance of phytoplankton in general. The paper is written with the expectation that the reader already knows why this topic is useful, important, or relevant to do research on. As such, it is not written for a diverse, non-specialist audience as expected by JOSS guidelines. A couple of sentences can fix this. The paper furthermore does not define what "Eulerian" or "Lagrangian" means.
Julia has a general purpose software for individual based modelling, called Agents.jl, which the authors cite. The authors however do not discuss what features or functionalities are missing from Agents.jl that requires them to write a new package instead of extending the existing one. (Full disclosure to the editor: I am a developer of Agents.jl. Admittedly, for me it is actually clear why the authors could not use the existing Agents.jl infrastructure, but I do not believe it would be as clear for a general audience).
A discussion on the software design and extendability of the package is missing. For example, how does the software simulate ocean currents that transport phytoplantkon? Does it integrate with existing packages such as Oceanigans.jl? How much flexibility is there in the ocean+plankton interplay? Could it simulate other "particles" besides plankton? Could it simulate the tranport of non-alive chemicals, that nevertheless perform reactions with other chemicals? If not, why? is there something fundamentally special about planktons that separates them from other physical entities? It really is not clear to me why this package is named "PlanktonIndividuals" instead of something like "InvidualOceanTranport" or so. Given my experience in individual based modelling, I do not see a particularly reason of why the infastructure of this package would be limited only to Plankton.
The test suite of the package could definitely benefit from improvements. For example, the tests do not test individual atomic functions, as a unit test suite should, but rather entire simulation pipelines. The coverage also seems to be low at only 62%.
The documentation does not have installation instructions. Given that this is a registered package, it is easy to resolve this simply by adding "This package is registered, use Pkg.add("PlanktonIndividuals") to install it." in the homepage.
The package GitHub page does not have Community guidelines.

Minor technical details

waterbodys -> water bodies
Citation Droop (1973) has title in all capitals
The author affiliation is just "MIT, EAPS".

elbeejay · 2022-03-12T20:24:19Z

Thank you for the thorough review @Datseris! I agree with your comments about the documentation being quite comprehensive and clear, and your suggestions to @zhenwu0728 and co-authors seem reasonable to me.

elbeejay · 2022-03-14T00:50:57Z

@navidcy I was going to ping you so that hopefully this review doesn't slip through the cracks before you are unavailable - the new JOSS procedure requires you to create your own reviewer checklist with the command @editorialbot generate my checklist

Thanks!

zhenwu0728 · 2022-03-14T14:50:49Z

Thank you for your comments and suggestions @Datseris! @gaelforget and I are working on it.

navidcy · 2022-03-17T03:43:32Z

@navidcy I was going to ping you so that hopefully this review doesn't slip through the cracks before you are unavailable - the new JOSS procedure requires you to create your own reviewer checklist with the command @editorialbot generate my checklist

Thanks!

Thanks. I haven't forgotten about this.

elbeejay · 2022-03-27T16:29:30Z

Hello all, I'm going to ask our editorial bot to send out reminders to @navidcy and @BrodiePearson over the next few weeks just to hopefully keep things moving along with this review. @zhenwu0728 please feel free to provide an update in this thread when you feel you have addressed @Datseris comments to ensure those outstanding review checklist items can be crossed off.

Thanks all,
Jay

editorialbot · 2022-03-27T16:29:42Z

Reminder set for @navidcy in one week

elbeejay · 2022-03-27T16:29:53Z

@editorialbot remind @BrodiePearson in two weeks

editorialbot · 2022-03-27T16:29:54Z

Reminder set for @BrodiePearson in two weeks

elbeejay · 2022-03-27T16:30:16Z

@editorialbot remind @navidcy in seven days

editorialbot · 2022-03-27T16:30:17Z

Reminder set for @navidcy in seven days

editorialbot · 2022-04-03T16:29:46Z

👋 @navidcy, please update us on how your review is going (this is an automated reminder).

editorialbot · 2022-04-03T16:30:22Z

👋 @navidcy, please update us on how your review is going (this is an automated reminder).

navidcy · 2022-04-04T21:59:30Z

I’m really sorry. I’m down with covid… :(

BrodiePearson · 2022-04-04T22:04:02Z

@elbeejay Here is my review:

Overall this looks like a useful package with good documentation. I particularly like that the package has both stand-alone utility (lab experiments) and an ability to integrate with other software packages used to simulate ocean flows (e.g., Oceananigans). I only have a few very small comments to add beyond the previous review

Review Comments

Functionality documentation: The paper does not mention whether the model parameters can be varied (i.e. whether the system can be used to simulate something other than the default biogeochemistry). It looks like this is easy to do, as some parameters are changed in the global example. Could you add a comment in the paper noting that the biogeochemistry can be modified and the possible extent of these modifiable parameters?
Quality of Writing & References: Some minor typos:
- Line 11: "cell density and stochiometry"
- Line 22: "The outputs of *PlanktonIndividuals.jl includes" (currently it sounds like it is referring to the dynamical models of the previous sentence)
- Line 34: "individual cells or plankton patches" (the comma implies cells==plankton patches, which I assume is not the case)
- Line 45: Remove "for"
- Figure 3: Is this showing maps of tracer concentration with overlaid individuals (dots) & their tracks up until that point (lines)? Could you add/expand on this description within the abstract?

elbeejay · 2022-05-01T23:52:46Z

@editorialbot set v0.5.1 as version

editorialbot · 2022-05-01T23:52:47Z

Done! version is now v0.5.1

elbeejay · 2022-05-01T23:53:01Z

@editorialbot set 10.5281/zenodo.6507001 as archive

editorialbot · 2022-05-01T23:53:03Z

Done! Archive is now 10.5281/zenodo.6507001

zhenwu0728 · 2022-05-02T01:04:53Z

@editorialbot generate pdf

editorialbot · 2022-05-02T01:06:42Z

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

zhenwu0728 · 2022-05-02T01:09:02Z

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

elbeejay · 2022-05-02T12:34:12Z

@editorialbot check references

editorialbot · 2022-05-02T12:34:44Z

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 · 2022-05-02T12:37:39Z

@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 · 2022-05-02T12:38:00Z

@editorialbot recommend-accept

editorialbot · 2022-05-02T12:38:01Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-05-02T12:38:31Z

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 · 2022-05-02T12:39:32Z

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

Check final proof 👉 openjournals/joss-papers#3184

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

kyleniemeyer · 2022-05-04T19:46:40Z

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 · 2022-05-04T20:04:12Z

@editorialbot generate pdf

editorialbot · 2022-05-04T20:07:13Z

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

zhenwu0728 · 2022-05-04T20:09:29Z

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

kyleniemeyer · 2022-05-04T20:18:45Z

@editorialbot accept

editorialbot · 2022-05-04T20:18:46Z

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

editorialbot · 2022-05-04T20:20:45Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-05-04T20:20:46Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.04207 joss-papers#3197
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04207
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

zhenwu0728 · 2022-05-04T20:42:36Z

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

kyleniemeyer · 2022-05-04T20:53:55Z

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

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

editorialbot · 2022-05-04T20:54:00Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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editorialbot added Julia review labels Feb 25, 2022

editorialbot assigned elbeejay Feb 25, 2022

editorialbot mentioned this issue Feb 25, 2022

[PRE REVIEW]: PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model. #4176

Closed

Datseris mentioned this issue Mar 29, 2022

[PRE REVIEW]: VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data #4222

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 2, 2022

gaelforget mentioned this issue May 4, 2022

Biogeoceananigans.jl CliMA/Oceananigans.jl#2512

Closed

editorialbot added accepted published Papers published in JOSS labels May 4, 2022

kyleniemeyer closed this as completed May 4, 2022

[REVIEW]: PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model. #4207

[REVIEW]: PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model. #4207

Comments

editorialbot commented Feb 25, 2022 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Feb 25, 2022

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elbeejay commented Feb 25, 2022

Datseris commented Feb 25, 2022 • edited Loading

Review checklist for @Datseris

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

elbeejay commented Mar 10, 2022

editorialbot commented Mar 10, 2022

BrodiePearson commented Mar 10, 2022 • edited Loading

Review checklist for @BrodiePearson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Datseris commented Mar 11, 2022 • edited Loading

Summary

Additions I would recommend

Minor technical details

elbeejay commented Mar 12, 2022

elbeejay commented Mar 14, 2022

zhenwu0728 commented Mar 14, 2022

navidcy commented Mar 17, 2022

elbeejay commented Mar 27, 2022

editorialbot commented Mar 27, 2022

elbeejay commented Mar 27, 2022

editorialbot commented Mar 27, 2022

elbeejay commented Mar 27, 2022

editorialbot commented Mar 27, 2022

editorialbot commented Apr 3, 2022

editorialbot commented Apr 3, 2022

navidcy commented Apr 4, 2022

BrodiePearson commented Apr 4, 2022

Review Comments

elbeejay commented May 1, 2022

editorialbot commented May 1, 2022

elbeejay commented May 1, 2022

editorialbot commented May 1, 2022

zhenwu0728 commented May 2, 2022

editorialbot commented May 2, 2022

zhenwu0728 commented May 2, 2022

elbeejay commented May 2, 2022

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elbeejay commented May 2, 2022

elbeejay commented May 2, 2022

editorialbot commented May 2, 2022

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kyleniemeyer commented May 4, 2022 • edited Loading

zhenwu0728 commented May 4, 2022

editorialbot commented May 4, 2022

zhenwu0728 commented May 4, 2022

kyleniemeyer commented May 4, 2022

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zhenwu0728 commented May 4, 2022

kyleniemeyer commented May 4, 2022

editorialbot commented May 4, 2022

editorialbot commented Feb 25, 2022 •

edited

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Datseris commented Feb 25, 2022 •

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BrodiePearson commented Mar 10, 2022 •

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Datseris commented Mar 11, 2022 •

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