[REVIEW]: Nyx: A Massively Parallel AMR Code for Computational Cosmology

whedon commented 3 years ago

Submitting author: @jmsexton03 (Jean M. Sexton) Repository: https://github.com/AMReX-Astro/Nyx Version: 21.07 Editor: @dfm Reviewers: @c-white, @teuben Archive: 10.5281/zenodo.5059767

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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

@c-white & @bwoshea, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @c-white

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 repository url?
[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 (@jmsexton03) 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

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: 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?
[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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @teuben

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 repository url?
[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 (@jmsexton03) 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

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: 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?
[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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

dfm commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1137/0705041 is OK
- 10.1093/mnras/stz984 is OK
- 10.1088/0004-637x/765/1/39 is OK
- 10.3847/1538-4357/ab4f75 is OK
- 10.21105/joss.01370 is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK
- 10.1016/j.jcp.2007.07.035 is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1086/317361 is OK
- 10.1051/0004-6361:20011817 is OK
- 10.1086/313015 is OK
- 10.1145/2929908.2929916 is OK
- 10.3847/1538-4365/ab908c is OK
- 10.1093/mnras/stx1643 is OK
- 10.1093/mnras/stv195 is OK
- 10.3847/1538-4357/abed5a is OK

MISSING DOIs

- 10.1093/mnras/stab1855 may be a valid DOI for title: Simulating cosmic structure formation with the GADGET-4 code

INVALID DOIs

- None

whedon commented 3 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/2436

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2436, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

dfm commented 3 years ago

@c-white, @teuben: Thanks for your constructive reviews!! I really appreciate the time you took.

@jmsexton03: This has now been passed off to the Editors-in-Chief for a final check and they might have some final edits for you and then they'll run the final publication step.

(P.S. I'm not quite sure why the previous run of check references missed that DOI, but I'll open a PR momentarily to fix that - sorry! Edit: it got published in the meantime...)

jmsexton03 commented 3 years ago

@dfm Thanks for editing and following up regularly!

@c-white, @teuben Thanks for reviewing!

P.S. merged GADGET-4 DOI update PR

Kevin-Mattheus-Moerman commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/2440
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03068
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 3 years ago

Congratulations @jmsexton03 on your accepted paper!

Thank you @dfm for editing this work!

And a special thanks to the reviewers @c-white and @teuben!!!

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.. image:: https://joss.theoj.org/papers/10.21105/joss.03068/status.svg
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