[REVIEW]: AMReX: a framework for block-structured adaptive mesh refinement

[whedon]

Submitting author: @asalmgren (Ann Almgren)
Repository: https://github.com/AMReX-Codes/amrex
Version: current master branch on github
Editor: @kyleniemeyer
Reviewer: @matthewturk, @RemiLehe , @cmsquared
Archive: 10.5281/zenodo.2754709

Status

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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) 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

@matthewturk & @RemiLehe & @cmsquared, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @kyleniemeyer know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @matthewturk

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (current master branch on github)?
• Authorship: Has the submitting author (@asalmgren) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @RemiLehe

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (current master branch on github)?
• Authorship: Has the submitting author (@asalmgren) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @cmsquared

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (current master branch on github)?
• Authorship: Has the submitting author (@asalmgren) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @matthewturk, it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[kyleniemeyer]

👋 @asalmgren @matthewturk @RemiLehe @cmsquared

The actual review will take place in this issue; you can find the individual reviewer checklists above. Thanks!

[whedon]

👉 Check article proof 📄 👈

[asalmgren]

Looks good.

…

On Mon, Apr 8, 2019 at 9:51 AM whedon ***@***.***> wrote: 👉 Check article proof 📄 👈 <https://github.com/openjournals/joss-papers/blob/joss.01370/joss.01370/10.21105.joss.01370.pdf> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1370 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKJPYrBJpsovrMFDtnI3cYmyGF2J_sb-ks5ve3OEgaJpZM4cipG5> .

[cmsquared]

Just to disclose a possible perceived COI: In the last 4 years, I have been on published papers or meeting abstracts with Zhang, Almgren, Beckner, Bell, Friesen, Katz, Nonaka, and Zingale from the author list. Most of this was for work we had done together either on astrophysics or utilizing/writing tools that were based on the predecessor of AMReX: BoxLib. I do not feel this is an actual COI given that I have not worked on AMReX, nor any of the updated modifications to codes that once used BoxLib and now use AMReX.

[cmsquared]

The team has addressed the points outlined in the Issue raised above via a series of commits. I am happy to recommend this article for publication.

[kyleniemeyer]

Thanks @cmsquared!

@RemiLehe @matthewturk just wanted to check in on the status of your reviews

[RemiLehe]

Thanks for the reminder! I'll try to send my review comments today.

[RemiLehe]

I have completed the review ; here are a few comments regarding the checklist itself:

• Regarding possible perceived COI: As mentioned off-line to @kyleniemeyer, I am currently working and collaborating with the AMReX team for the WarpX project. I am not developing the AMReX source code, though.

• Regarding the license: AMReX uses a modified 3-clause BSD license, which has been adapted for UC Berkeley/LBNL. (Open-source software from LBNL usually use this license.) Strictly speaking, it is not in the OSI approved list. (or I missed it)