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[REVIEW]: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver #1757

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whedon opened this issue Sep 23, 2019 · 55 comments
Closed
38 tasks done

[REVIEW]: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver #1757

whedon opened this issue Sep 23, 2019 · 55 comments
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@arfon @tukss @pgrete
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AAS Papers being published together with a AAS submission accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Sep 23, 2019 •
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Submitting author: @doreenfan (Duoming Fan)
Repository: https://github.com/AMReX-Astro/MAESTROeX
Version: 19.09
Editor: @arfon
Reviewer: @tukss, @pgrete
Archive: 10.5281/zenodo.3549070

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cc6e46383ed1d2bd2886ab29ff3cd4e4"><img src="https://joss.theoj.org/papers/cc6e46383ed1d2bd2886ab29ff3cd4e4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cc6e46383ed1d2bd2886ab29ff3cd4e4/status.svg)](https://joss.theoj.org/papers/cc6e46383ed1d2bd2886ab29ff3cd4e4)

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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

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

Review checklist for @tukss

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

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?
  • Contribution and authorship: Has the submitting author (@doreenfan) 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 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: Do the authors clearly state 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?

Review checklist for @pgrete

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

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?
  • Contribution and authorship: Has the submitting author (@doreenfan) 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 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: Do the authors clearly state 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?
@whedon whedon added the review label Sep 23, 2019
@whedon whedon mentioned this issue Sep 23, 2019
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@whedon
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whedon commented Sep 23, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tukss, @pgrete it looks like you're currently assigned to review this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

@whedon
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whedon commented Sep 23, 2019 

Attempting PDF compilation. Reticulating splines etc...

@arfon
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arfon commented Sep 23, 2019

@tukss, @pgrete - thanks again for agreeing to review this submission. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

@whedon
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whedon commented Sep 23, 2019

👉 Check article proof 📄 👈

This was referenced Oct 7, 2019
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@tukss
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tukss commented Oct 11, 2019

I finished my review. Once the two outstanding issues are resolved, I am happy to accept this paper.

@arfon
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arfon commented Oct 11, 2019

I finished my review. Once the two outstanding issues are resolved, I am happy to accept this paper.

Excellent, thanks @tukss!

@pgrete - how are you getting long with your review?

@pgrete
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pgrete commented Oct 13, 2019

I've been on the road for the past weeks but back in the office now and reserved time next week to finish the review.

@arfon
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arfon commented Oct 13, 2019

I've been on the road for the past weeks but back in the office now and reserved time next week to finish the review.

Excellent, thanks for the update!

@crawfordsm
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Do we have the JOSS DOI for this yet?

@tukss
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tukss commented Oct 17, 2019

The proof PDF contains 10.21105/joss.01757, but it doesn't work yet. @arfon, can you comment if the DOI will change after acceptance?

@arfon
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arfon commented Oct 17, 2019

10.21105/joss.01757

@crawfordsm ☝️ this will be the DOI.

@pgrete
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pgrete commented Oct 17, 2019

I'm trying to understand the contribution of @XinlongSBU specifically this commit bbbc157984b9c2
Is the changeset that large because of the different parent or is this a significant contribution to the code (I'm asking as @XinlongSBU is not listed as author on the paper as far as I can tell).

@XinlongSBU
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XinlongSBU commented Oct 17, 2019 via email

This was referenced Oct 21, 2019
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@pgrete
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pgrete commented Oct 21, 2019

I'm done with my first pass of the review and opened issues for all things I spotted.

@arfon
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arfon commented Oct 22, 2019

Great, thanks @pgrete. @doreenfan - looks like you've got a collection of feedback here to work through. Please let us know here when you've had a chance to make your updates.

@whedon
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whedon commented Nov 20, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 20, 2019

👉 Check article proof 📄 👈

@arfon
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arfon commented Nov 20, 2019

@doreenfan @zingale - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

@zingale
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zingale commented Nov 21, 2019

Here's the Zenodo link: https://zenodo.org/record/3549070
DOI: http://doi.org/10.5281/zenodo.3549070

@arfon
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arfon commented Nov 21, 2019

@whedon set 10.5281/zenodo.3549070 as archive

@whedon
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whedon commented Nov 21, 2019

OK. 10.5281/zenodo.3549070 is the archive.

@arfon
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arfon commented Nov 21, 2019

@whedon accept

@whedon
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whedon commented Nov 21, 2019 

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Nov 21, 2019 


OK DOIs

- 10.1088/0067-0049/188/2/358 is OK
- 10.21105/joss.01370 is OK
- 10.5281/zenodo.2656476 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Nov 21, 2019

Check final proof 👉 openjournals/joss-papers#1112

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1112, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@arfon
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arfon commented Nov 21, 2019

@whedon accept deposit=true

@whedon
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whedon commented Nov 21, 2019 

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

@whedon
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whedon commented Nov 21, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented Nov 21, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01757 joss-papers#1113
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01757
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

@arfon arfon added the AAS Papers being published together with a AAS submission label Nov 21, 2019
@arfon
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arfon commented Nov 21, 2019

@tukss, @pgrete - many thanks for your reviews here ✨

@zingale - I forgot to ask for the AAS DOI before accepting this so while the JOSS paper is accepted and published we'll need to add the AAS metadata to the submission too when we have it.

@crawfordsm - is the AAS paper accepted yet? If so, do we know what the DOI is?

@doreenfan
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The AAS paper has been accepted, but I'm not sure what the DOI is.

@arfon
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arfon commented Dec 19, 2019

@doreenfan - can you merge this PR for me please? AMReX-Astro/MAESTROeX#128

@arfon
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arfon commented Dec 19, 2019

@whedon accept

@whedon
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whedon commented Dec 19, 2019 

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Dec 19, 2019 


OK DOIs

- 10.1088/0067-0049/188/2/358 is OK
- 10.21105/joss.01370 is OK
- 10.5281/zenodo.2656476 is OK

MISSING DOIs

- https://doi.org/10.21105/joss.01757 may be missing for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver

INVALID DOIs

- None

@arfon
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arfon commented Dec 19, 2019

OK, the paper is now updated with the AAS DOI information. Thanks again @tukss & @pgrete !

@arfon arfon closed this as completed Dec 19, 2019
@whedon
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whedon commented Dec 19, 2019

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01757/status.svg)](https://doi.org/10.21105/joss.01757)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01757">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01757/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01757/status.svg
   :target: https://doi.org/10.21105/joss.01757

This is how it will look in your documentation:

DOI

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