Closed editorialbot closed 2 years ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.15 s (643.0 files/s, 92586.9 lines/s)
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Language files blank comment code
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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
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SUM: 97 2439 654 10874
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gitinspector failed to run statistical information for the repository
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
Wordcount for paper.md
is 827
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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.
@editorialbot add @BrodiePearson as reviewer
@BrodiePearson added to the reviewers list!
Hello @elbeejay , I would like to submit my review:
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.
Pkg.add("PlanktonIndividuals")
to install it." in the homepage.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.
@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!
Thank you for your comments and suggestions @Datseris! @gaelforget and I are working on it.
@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.
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
Reminder set for @navidcy in one week
@editorialbot remind @BrodiePearson in two weeks
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@editorialbot remind @navidcy in seven days
Reminder set for @navidcy in seven days
:wave: @navidcy, please update us on how your review is going (this is an automated reminder).
:wave: @navidcy, please update us on how your review is going (this is an automated reminder).
I’m really sorry. I’m down with covid… :(
@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
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:
@navidcy I wish you all the best in your recovery. I'll remove you from the reviewer list here in a moment.
@BrodiePearson thanks for completing your review :+1: your comments appear to be fairly straightforward for @zhenwu0728 and co-authors to address.
@editorialbot remove @navidcy from reviewers
@navidcy removed from the reviewers list!
:wave: @BrodiePearson, please update us on how your review is going (this is an automated reminder).
@zhenwu0728 I think you've gotten a nice set of reviews that are overall quite supportive of the package, and constructive in terms of their feedback and suggestions. When do you anticipate making changes and having revisions complete by? Some rough timeline will be helpful so that @BrodiePearson, @Datseris, and I know when we can expect to have to take another look at this. Thanks!
Thanks for the reminder, @elbeejay. And thanks for all the insightful and constructive comments from @Datseris and @BrodiePearson. We've already started the revision of the paper and the package (e.g. add unit tests) and hopefully finish in one week or so. I'll upload a point-to-point response once finished. Thanks again!
Hi @elbeejay, @Datseris, and @BrodiePearson, Thanks for all your comments and suggestions. With the help of @gaelforget, we would like to submit our responses: Please note that the revised package and paper are tagged v0.5.0.
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.
Reply: Thank you for the positive evaluation of our package and paper.
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.
Reply: Thanks for pointing it out. We have added two sentences at the beginning of Summary. Also, "Eulerian" or "Lagrangian" are explained at the end of the second paragraph of Summary.
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).
Reply: Thanks for the comment. We are sorry that we did not state clearly in the paper about the purpose of our package and how it compares with other individual based models. Now we have added some text in the fourth and fifth paragraph in Statement of Need for clarification.
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.
Reply: Thank you for the comment. Individual-based modeling and the transport of Lagrangian particles are part of the framework of our package. However, its defining component is the phytoplankton physiological equations and biogeochemical equations embeded in this framework. The possibility to simplify equations in the model to simulate simple passive tracers and particles is shown in Fig 3. Yet, representing all types of material interactions within the Ocean is beyond the scope of our package.
The discussion of the package design has been extended in the last two paragraphs of the summary. Possible extensions to the model are provided in the final paragraph of the paper. Others can be envisioned but those listed are viewed as rather high priority.
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%.
Reply: Thank you for the suggestion. We have now added unit tests and brought up the coverage to 80%.
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.
Reply: It has been added in Readme.
The package GitHub page does not have Community guidelines.
Reply: Thanks for pointing it out. We have added a CONTRIBUTING.md in the package.
The author affiliation is just "MIT, EAPS".
Reply: These have been revised in the paper.
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
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?
Reply: Thanks for the comment. A sentence about the modifiable parameters is added in the third paragraph of Summary.
Quality of Writing & References: Some minor typos:
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?
Reply: These have been revised in the paper.
@editorialbot generate pdf
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Hi @zhenwu0728, thanks for addressing the comments and providing us with a thorough set of responses. At this time, I'd like to ask @Datseris and @BrodiePearson to take a look at your responses when they get a chance. I'll update the version number for JOSS, thanks for pointing that out!
@editorialbot set v0.5.0 as version
Done! version is now v0.5.0
@elbeejay @zhenwu0728 Thanks for making the modifications. This looks good to me now. (note, there is a minor typo in the new Figure 3 caption: "liens" to "lines")
@zhenwu0728 Thanks for your reply! @elbeejay I recommend publication as is!
Fantastic, thanks @BrodiePearson and @Datseris for taking a look at the revisions. @Datseris if you don't mind checking off the remaining boxes in your reviewer checklist just for the sake of completeness that'd be appreciated.
@zhenwu0728 I'll have a closer look at everything later today or tomorrow to hopefully catch any remaining typos and the like, then I'll give you a list of the final steps we'll need you to take before publication.
Thanks all!
@editorialbot generate pdf
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Thanks @Datseris and @BrodiePearson for the very helpful reviews.
@zhenwu0728 and @gaelforget I have some minor suggestions for edits I think you should make to the paper.
[e.g., lakes, ..., @citeA; @citeB]
Minor comments aside this seems like it's about ready to go. Once the the above changes to the paper are made (and I would suggest you both do a final read through yourselves to ensure it reads the way you'd like), there are a few final archival steps I need you to do:
Please let me know when these steps are complete, they allow us to finalize the metadata that will be associated with the JOSS publication. Once that is done I can recommend that we accept and publish this paper.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@elbeejay Thanks for these comments! I've incorporated them into the paper. The version tag is v0.5.1. The DOI of the archived version is 10.5281/zenodo.6507001. Please let me know if you have any questions.
Hi @zhenwu0728,
Thanks for making those revisions. One minor thing, and I apologize if I was unclear above, please revise the citation in the Statement of need to be: [e.g. lakes, coastal waters, and open ocean, @follows2007emergent; @geider1997dynamic]
, in the paper.md
file, which I believe should end up getting typeset as: (e.g. lakes, coastal waters, and open ocean, Follows et al., 2007; Geider et al. 1997) in the compiled PDF. Let me know if this doesn't work, my intent is for the paper to no longer have the nested parentheses there.
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
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