[REVIEW]: GNS: A generalizable Graph Neural Network-based simulator for particulate and fluid modeling

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@kks32@osorensen<!--end-editor-- Reviewers: @WPettersson, @archermarx Archive: 10.5281/zenodo.8249813

Status

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Markdown: [![status](https://joss.theoj.org/papers/d5d6ee3247e52ec932107d87ab7a9549/status.svg)](https://joss.theoj.org/papers/d5d6ee3247e52ec932107d87ab7a9549)

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

@WPettersson & @archermarx, 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 @osorensen 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 @WPettersson

📝 Checklist for @archermarx

editorialbot commented 1 year ago

Hello humans, 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:

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editorialbot commented 1 year ago

Software report:

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Language                     files          blank        comment           code
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Bourne Shell                     8             57             91            118
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JavaScript                       1              8             38             37
Dockerfile                       1              0              0             10
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SUM:                            48            457            762          11776
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gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1373

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/zenodo.6658322 is OK
- 10.17603/ds2-0phb-dg64 is OK

MISSING DOIs

- 10.1016/j.cma.2022.115704 may be a valid DOI for title: Model-Free Data-Driven Inference in Computational Mechanics

INVALID DOIs

- None

editorialbot commented 1 year ago

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

osorensen commented 1 year ago

@editorialbot add @karanprime as reviewer

editorialbot commented 1 year ago

@karanprime added to the reviewers list!

osorensen commented 1 year ago

@karanprime, thanks for agreeing to review. In order to generate your checklist, please write the following comment: @editorialbot generate my checklist

olgadoronina commented 1 year ago

Review checklist for @olgadoronina

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/geoelements/gns?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kks32) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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

[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

olgadoronina commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @olgadoronina, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

WPettersson commented 1 year ago

Review checklist for @WPettersson

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/geoelements/gns?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kks32) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[X] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[X] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[X] Installation: Does installation proceed as outlined in the documentation?
[X] Functionality: Have the functional claims of the software been confirmed?
[X] 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

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

[X] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[X] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[X] 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?

osorensen commented 1 year ago

👋 @TranzWu @karanprime, could you please update us on how it's going with your reviews?

osorensen commented 1 year ago

@olgadoronina, I notive there are a number of unchecked boxes in your checklists. Are these issues which should be fixed by the authors? If so, could you please elaborate here or by opening issues in the source repository?

WPettersson commented 1 year ago

Just so I can track what I'm waiting on (didn't want to add chatter around the official review checklist)

https://github.com/geoelements/gns/issues/34
- [X] Installation: Does installation proceed as outlined in the documentation?
- [X] Functionality: Have the functional claims of the software been confirmed?
- [X] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
- [X] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
https://github.com/geoelements/gns/issues/41
- [X] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
https://github.com/geoelements/gns/issues/40
- [X] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
https://github.com/geoelements/gns/issues/35
- [X] 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
- [X] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [X] 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?

osorensen commented 1 year ago

Thanks @WPettersson this is really useful.

osorensen commented 1 year ago

👋 @TranzWu @karanprime, could you please update us on how it's going with your reviews?

TranzWu commented 1 year ago

Review checklist for @TranzWu

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/geoelements/gns?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kks32) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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

[x] 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?
[x] 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, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

karanprime commented 1 year ago

Review checklist for @karanprime

Conflict of interest

[x] 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

[x] 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/geoelements/gns?
[ ] 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 (@kks32) 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
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[ ] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[ ] 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?

osorensen commented 1 year ago

@karanprime and @TranzWu, thanks for starting your reviews! If there are issues you think should be addressed, please report it either here or by opening issues in the source repository.

osorensen commented 1 year ago

@karanprime and @TranzWu, thanks for starting your reviews! If there are issues you think should be addressed, please report it either here or by opening issues in the source repository.

osorensen commented 1 year ago

👋 @TranzWu, @olgadoronina, @WPettersson, @karanprime, could you please update us on how it's going with your reviews?

@kks32, FYI I'm also contacting the reviewers by e-mail, so hopefully we will have some progress in not too long.

osorensen commented 1 year ago

@kks32, I notice that @WPettersson has opened several issues in the source repo. Could you please update us on how it's going addressing these issues?

kks32 commented 1 year ago

Hi @osorensen I'm working on addressing all the issues. Will finalize the response and update by next week. Thank you!

osorensen commented 1 year ago

Thanks @kks32!

osorensen commented 1 year ago

👋 @kks32, any updates on how it's going addressing the issues?

kks32 commented 1 year ago

@osorensen Thank you. We had a major update to PyTorch 2.0 for our packages, that helps address the issue of installation. I will complete the other tasks listed in our repo shortly.

osorensen commented 1 year ago

:wave: @kks32, any updates on how it's going addressing the issues raised by the reviewers?

WPettersson commented 1 year ago

@osorensen Just wanted to point out that I think most of the issues have been addressed (possibly all). I just need to go through the new paper version and check that out and I might be ready to sign off.

osorensen commented 1 year ago

Thanks for pointing this out, @WPettersson. Looking forward to hearing back from you.

osorensen commented 1 year ago

👋 @TranzWu, @olgadoronina, @karanprime, could you please take another look at this submission, and see if some them missing boxes in your review checklists can now be checked? Please elaborate here or in the source repository if you have any further issues.

karanprime commented 1 year ago

@osorensen Thanks, I will go through the new version of the paper and update the review.

osorensen commented 1 year ago

@osorensen Just wanted to point out that I think most of the issues have been addressed (possibly all). I just need to go through the new paper version and check that out and I might be ready to sign off.

@WPettersson, have you had a chance yet to go through this submission once more to see if the items in your checklist can be checked off?

osorensen commented 1 year ago

@kks32, I notice that you haven't responded to this issue opened by @WPettersson. Could you please give us a timeline for when it will be fixed?

WPettersson commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

WPettersson commented 1 year ago

@osorensen Sorry for the delay, I've gone through it all now and am happy with this publication, with the one caveat that the paper itself is ~1300 words long.

osorensen commented 1 year ago

Thanks a lot for your work @WPettersson! I think the word count for the paper is fine, particularly since the number of references contributes to inflating it a bit.

osorensen commented 1 year ago

👋 @TranzWu, could you please take a new look at your checklist and see if further of the boxes can be checked? If you have any particular points about the submission, please mention them here or open an issue in the source repository.

osorensen commented 1 year ago

👋 @olgadoronina, could you please take a new look at your checklist and see if further of the boxes can be checked? If you have any particular points about the submission, please mention them here or open an issue in the source repository.

osorensen commented 1 year ago

👋 @karanprime, could you please take a new look at your checklist and see if further of the boxes can be checked? If you have any particular points about the submission, please mention them here or open an issue in the source repository.

osorensen commented 1 year ago

👋 @TranzWu, could you please take a new look at your checklist and see if further of the boxes can be checked? If you have any particular points about the submission, please mention them here or open an issue in the source repository.

osorensen commented 1 year ago

👋 @olgadoronina, could you please take a new look at your checklist and see if further of the boxes can be checked? If you have any particular points about the submission, please mention them here or open an issue in the source repository.

@olgadoronina, I also tried to reach out to you by e-mail. It would be much appreciated if you could please take a new look at the submission.

osorensen commented 1 year ago

👋 @karanprime, could you please take a new look at your checklist and see if further of the boxes can be checked? If you have any particular points about the submission, please mention them here or open an issue in the source repository.

@karanprime, I also tried to reach out to you by e-mail. It would be much appreciated if you could please take a new look at the submission.

osorensen commented 1 year ago

@kks32, sorry that this is taking so long, but I'm not able to get in touch with the reviewers, either by e-mail or GitHub. If I don't get any response by the end of this week, I will have to state looking for an additional reviewer. I'll keep you posted.

kks32 commented 1 year ago

Thank you @osorensen ! I understand.

osorensen commented 1 year ago

👋 @archermarx @ashwinvis, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

osorensen commented 1 year ago

:wave: @ipadjen, @ashwinvis, @OHildreth would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

archermarx commented 1 year ago

👋 @archermarx @ashwinvis, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Apologies for the delay on this. I was at a conference. I am happy to review this submission!

osorensen commented 1 year ago

Thanks a lot @archermarx!

openjournals / joss-reviews