Joss-reviews: [REVIEW]: CASTRO: A Massively Parallel Compressible Astrophysics Simulation Code

Created on 23 Jul 2020  ·  115Comments  ·  Source: openjournals/joss-reviews

Submitting author: @zingale (M. Zingale)
Repository: https://github.com/amrex-astro/Castro
Version: JOSS_paper
Editor: @eloisabentivegna
Reviewers: @kegiljarhus, @bonh, @joshia5
Archive: 10.5281/zenodo.4085328

:warning: JOSS reduced service mode :warning:

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Status

status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1188914fa6fa17523f1537761dc95743/status.svg)](https://joss.theoj.org/papers/1188914fa6fa17523f1537761dc95743)

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

@kegiljarhus & @bonh & @joshia5, 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 @eloisabentivegna 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 ✨

Review checklist for @kegiljarhus

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

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 (@zingale) 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: 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: 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 @bonh

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

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 (@zingale) 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: 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: 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)?
  • [ ] 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 @joshia5

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

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 (@zingale) 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: 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: 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)?
  • [ ] 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?
C Gnuplot Python accepted published recommend-accept review
Source
picture whedon

All 115 comments

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

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whedon picture whedon on 23 Jul 2020

PDF failed to compile for issue #2513 with the following error:

pandoc-citeproc: reference ctu not found
pandoc-citeproc: reference ppm not found
Error producing PDF.
! Undefined control sequence.
l.437 ... research. The GPU development of \castro

Looks like we failed to compile the PDF

whedon picture whedon on 23 Jul 2020

can we tell whedon to build the PDF off of the development branch? That's where the review should happen, and the refs are fixed there.

zingale picture zingale on 23 Jul 2020

@whedon generate pdf from branch development

zingale picture zingale on 23 Jul 2020 
Attempting PDF compilation from custom branch development. Reticulating splines etc...
whedon picture whedon on 23 Jul 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 23 Jul 2020

that proof looks good

zingale picture zingale on 23 Jul 2020

@whedon generate pdf from branch development

This should do, @zingale.

eloisabentivegna picture eloisabentivegna on 24 Jul 2020 
Attempting PDF compilation from custom branch development
. Reticulating splines etc...
whedon picture whedon on 24 Jul 2020

PDF failed to compile for issue #2513 with the following error:

error: pathspec 'development
' did not match any file(s) known to git.
error: pathspec 'development
' did not match any file(s) known to git.
pandoc-citeproc: reference ctu not found
pandoc-citeproc: reference ppm not found
Error producing PDF.
! Undefined control sequence.
l.437 ... research. The GPU development of \castro

Looks like we failed to compile the PDF

whedon picture whedon on 24 Jul 2020

@whedon generate pdf from branch development

eloisabentivegna picture eloisabentivegna on 24 Jul 2020 
Attempting PDF compilation from custom branch development. Reticulating splines etc...
whedon picture whedon on 24 Jul 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 24 Jul 2020

OK, all good!

eloisabentivegna picture eloisabentivegna on 24 Jul 2020

Dear @eloisabentivegna and @zingale. This is my first review for JOSS, so please bear with me. I have gone through the review checklist. I had no problems installing the software, running a problem and visualizing the results. Castro is a highly advanced software package which solves relevant scientific problems using state-of-the-art numerical methods. The software seems well-designed and the documentation is also extensive and well-written.

I only have a few minor comments to be addressed:

  • Some developers listed as core developers in the preface of the documentation are not included as authors: Beckner, Day, Lijewski, Malone, Nonaka. There is also one author, Sexton, not listed as a core developer. Could you please comment on this?
  • There appears to be some automated testing and regression testing, but it is not clear to me how these are executed as part of the continuous integration or how to run these manually. Could you please make this clearer, preferably in the README?
kegiljarhus picture kegiljarhus on 27 Jul 2020

@eloisabentivegna @zingale Thanks for letting me help in the review. I have already cloned the repo and briefly looked through the awesome software and paper. I will be done with the first round of review (and by my first impression this is the final round too) by Friday afternoon this week.

bonh picture bonh on 28 Jul 2020
👍1

Hi @kegiljarhus, thanks for your review and update!

Could you raise those issues in Castro's repository? This will ensure your suggestions will enter the package's history and be properly credited. You can create a mention here by using this issue's URL in the repository's issue, if you wish (see https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#guiding-principles).

eloisabentivegna picture eloisabentivegna on 29 Jul 2020

@kegiljarhus thank you for the comments.

For the first, it is indeed the case that those names were listed on the developers page, but none of them have made any contributions in the last 6 years and some of the names don't show in the git history. According to our policy in the README.md, we consider developers as active if they've contributed in the last 3 years. I've moved the inactive names to a "Former Developers" category (through this PR: https://github.com/AMReX-Astro/Castro/pull/1150 ). I've also added Jean Sexton to the list of developers.

For the second, our testing is currently manually triggered on PRs using our regression testing framework here: https://github.com/AMReX-Codes/regression_testing . Part of the reason is because we need to test against 3 different repos (Castro, Microphysics, and AMReX) and we want to make sure that not just Castro changes are clean, but that changes to those other repos also don't affect Castro. Also, our test suite is expensive to run and also uses GPUs, so we use a local machine to do this. For most PRs you'll see a link to the test results. The master list of CPU tests is here: http://groot.astro.sunysb.edu/Castro/test-suite/gfortran/ and for GPUs is here: http://groot.astro.sunysb.edu/Castro/test-suite/gpu/

zingale picture zingale on 29 Jul 2020

Note: in addition to being triggered manually on PRs, the test suite also runs nightly using the latest AMReX, Castro, and Microphysics.

zingale picture zingale on 29 Jul 2020

Thank you for the suggestions, @eloisabentivegna. Since @zingale already updated the developer list, and the pull request links to this review, I believe that is sufficient and we do not need to create a new issue. The comments on testing are also satisfactory from my side.

kegiljarhus picture kegiljarhus on 30 Jul 2020
👍1

@whedon add @joshia5 as reviewer

eloisabentivegna picture eloisabentivegna on 31 Jul 2020

OK, @joshia5 is now a reviewer

whedon picture whedon on 31 Jul 2020

https://github.com/AMReX-Astro/Castro/issues/1154

bonh picture bonh on 31 Jul 2020

https://github.com/AMReX-Astro/Castro/issues/1155

bonh picture bonh on 31 Jul 2020

@eloisabentivegna On references: "Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)?" As this is not my field of expertise I am not really able to determine if the references concerning the physics and mathematics for this particular problem are complete and/or appropriate.

bonh picture bonh on 31 Jul 2020

@eloisabentivegna On Functionality: "Have the functional claims of the software been confirmed?" I do not have a hpc cluster available for testing so I am not really able to confirm the code to be able to conduct "massively parallel [...] simulations"

Same for Performance.

Same for Accuracy.

Same for Installation on a hpc cluster.

bonh picture bonh on 31 Jul 2020

@zingale Really impressive work!

bonh picture bonh on 31 Jul 2020

@whedon generate pdf from branch development

joshia5 picture joshia5 on 31 Jul 2020 
Attempting PDF compilation from custom branch development. Reticulating splines etc...
whedon picture whedon on 31 Jul 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 31 Jul 2020

@bonh, thanks for your questions about the reference list box -- please feel free to leave it unticked.

Regarding the code tests, we only really expect reviewers to check the small-scale examples (as a rough rule of thumb, those that can be executed on a reasonable laptop). For all the other tests, please simply check that the results appear sensible and generally consistent.

Thanks for all the useful comments!

eloisabentivegna picture eloisabentivegna on 12 Aug 2020

So I am done :+1:

bonh picture bonh on 13 Aug 2020
👍1

@zingale, @eloisabentivegna following are my comments and questions:

  1. Explicit instructions or commands for loading modules could be given in the installation
    instructions, I found that python>=3.7 might not be preloaded on all systems

  2. I could not find significant commits in the repo for author John bell.

  3. I could run the test case but is there a specific version requirement on Paraview to visualize the output
    *plt files?
    What reader/format should I use while opening the files?

  4. In the paper, comparisons are made with other packages but for the checklist requirement,
    I cannot comment on whether these other packages are commonly used

  5. While the README mentions how to contribute to the software & Report issues, i
    could not find guidelines on how a third party can seek support.

  6. As I do not have research expertise in this field, I cannot comment on completeness of references

  7. license: it is mentioned in the commit comment of the license file that
    castro has gone through paperwork for BSD license, does this mean
    that the license is a BSD type ?

Thanks,
Aditya

joshia5 picture joshia5 on 8 Sep 2020
👍1

Thanks for the comments. I will answer them each inline here.

  1. Can you point out where we suggest python 3.7? It looks like we
    require 3.6. If you have suggestions for what types of machines
    you think there should be instructions for, please share. There
    are so many variations that it would be hard to cover them all.

    Python version 3.5 has reached "end of life":
    https://www.python.org/downloads/release/python-3510/ so we believe
    requiring 3.6 or later is reasonable.

    For working at supercomputing centers, we do provide instructions,
    linked to from this page of the docs (at the bottom):
    https://amrex-astro.github.io/Castro/docs/mpi_plus_x.html

zingale picture zingale on 15 Sep 2020
  1. Not all Castro developers write code. John contributed the initial
    version of the hydro solver (before Castro was in version control)
    and he works on the mathematical aspects of the algorithm
    development (most recently the SDC stuff).
zingale picture zingale on 15 Sep 2020
  1. We don't have experience with Paraview, so we will remove it's mention
    from the docs. All of the developers use yt.
zingale picture zingale on 15 Sep 2020
  1. I am not sure if there is something for us to address here
zingale picture zingale on 15 Sep 2020
  1. The last section of the README has a link to the castro-help mailing list.
    Further, the mailing list is featured under the "get help" button on the
    main website: https://amrex-astro.github.io/Castro/
zingale picture zingale on 15 Sep 2020
  1. We are not sure if there is something for us to address here
zingale picture zingale on 15 Sep 2020
  1. The license is OSI approved: https://opensource.org/BSD-3-Clause-LBNL
zingale picture zingale on 15 Sep 2020

@zingale, thanks for the replies. There is nothing for you to do regarding points 4. and 6. I will now wait for @joshia5 to comment back and share his final recommendation.

eloisabentivegna picture eloisabentivegna on 18 Sep 2020

@zingale. Thanks for your replies.
Regarding comment 1, I was on RHEL and Ubuntu systems.
@eloisabentivegna looks good to me.

joshia5 picture joshia5 on 19 Sep 2020

Thanks, @joshia5! And thanks again to @kegiljarhus and @bonh for your recommendation. I am pleased to start the pre-publication stage for this submission. 🎉

@zingale, could you please proceed issuing a tagged release and creating the archive? Let me know if you need assistance with these steps.

eloisabentivegna picture eloisabentivegna on 21 Sep 2020

@zingale, did you manage to create the release and the archive? Please let us know if you need assistance.

eloisabentivegna picture eloisabentivegna on 12 Oct 2020

sorry... I lost track on things for a bit. I'll do this now.

zingale picture zingale on 13 Oct 2020

Here's a Zenodo DOI for a tagged release:
https://zenodo.org/record/4085328

zingale picture zingale on 13 Oct 2020

sorry, that was the zenodo record
Here's the DOI: 10.5281/zenodo.4085328

zingale picture zingale on 13 Oct 2020

@whedon set 10.5281/zenodo.4085328 as archive

eloisabentivegna picture eloisabentivegna on 13 Oct 2020

OK. 10.5281/zenodo.4085328 is the archive.

whedon picture whedon on 13 Oct 2020

@zingale, I am wondering whether the release should have a traditional numerical tag, rather than a special label like "JOSS_paper", so users can readily identify whether a given code version precedes or follows the one published in JOSS.

@arfon, @danielskatz, what do you think?

eloisabentivegna picture eloisabentivegna on 13 Oct 2020

We don't enforce anything along those lines here and are happy to follow whatever conventions a project might already have in place.

arfon picture arfon on 14 Oct 2020

We don't enforce anything along those lines here and are happy to follow whatever conventions a project might already have in place.

OK! The project follows a mix of the usual convention (numerical) and special descriptive tags. If there's no requirement on our side, let's leave everything as is. Thanks!

eloisabentivegna picture eloisabentivegna on 14 Oct 2020

@whedon set JOSS_paper as version

eloisabentivegna picture eloisabentivegna on 14 Oct 2020

OK. JOSS_paper is the version.

whedon picture whedon on 14 Oct 2020

@whedon check references

eloisabentivegna picture eloisabentivegna on 14 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK

MISSING DOIs

- 10.21105/joss.01757 may be a valid DOI for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver
- 10.1088/1742-6596/1623/1/012021 may be a valid DOI for title: The Castro AMR Simulation Code: Current and Future Developments
- 10.1109/tpds.2020.3010016 may be a valid DOI for title: K-Athena: a performance portable structured grid finite volume magnetohydrodynamics code

INVALID DOIs

- https://doi.org/10.1016/j.jpdc.2014.07.003 is INVALID because of 'https://doi.org/' prefix
whedon picture whedon on 14 Oct 2020

Hi @zingale, I have created a PR on the Castro repository with fixes to the DOI problems above. Can you check that everything works, and merge?

eloisabentivegna picture eloisabentivegna on 16 Oct 2020

@whedon check references

eloisabentivegna picture eloisabentivegna on 17 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK

MISSING DOIs

- 10.21105/joss.01757 may be a valid DOI for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver
- 10.1088/1742-6596/1623/1/012021 may be a valid DOI for title: The Castro AMR Simulation Code: Current and Future Developments
- 10.1109/tpds.2020.3010016 may be a valid DOI for title: K-Athena: a performance portable structured grid finite volume magnetohydrodynamics code

INVALID DOIs

- https://doi.org/10.1016/j.jpdc.2014.07.003 is INVALID because of 'https://doi.org/' prefix
whedon picture whedon on 17 Oct 2020

@whedon check references from branch development

eloisabentivegna picture eloisabentivegna on 17 Oct 2020 
Attempting to check references... from custom branch development
whedon picture whedon on 17 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK

MISSING DOIs

- 10.21105/joss.01757 may be a valid DOI for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver
- 10.1088/1742-6596/1623/1/012021 may be a valid DOI for title: The Castro AMR Simulation Code: Current and Future Developments
- 10.1109/tpds.2020.3010016 may be a valid DOI for title: K-Athena: a performance portable structured grid finite volume magnetohydrodynamics code

INVALID DOIs

- https://doi.org/10.1016/j.jpdc.2014.07.003 is INVALID because of 'https://doi.org/' prefix
whedon picture whedon on 17 Oct 2020

@whedon generate pdf from branch development

eloisabentivegna picture eloisabentivegna on 17 Oct 2020 
Attempting PDF compilation from custom branch development. Reticulating splines etc...
whedon picture whedon on 17 Oct 2020

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

whedon picture whedon on 17 Oct 2020

@arfon, @zingale, the new changes do not seem to be picked up from the development branch. Any idea why? A quick fix would probably be merging them into master, but it would be interesting to find out why we can use the development branch.

eloisabentivegna picture eloisabentivegna on 17 Oct 2020

@whedon check references from branch development

arfon picture arfon on 17 Oct 2020 
Attempting to check references... from custom branch development
whedon picture whedon on 17 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK

MISSING DOIs

- 10.21105/joss.01757 may be a valid DOI for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver
- 10.1088/1742-6596/1623/1/012021 may be a valid DOI for title: The Castro AMR Simulation Code: Current and Future Developments
- 10.1109/tpds.2020.3010016 may be a valid DOI for title: K-Athena: a performance portable structured grid finite volume magnetohydrodynamics code

INVALID DOIs

- https://doi.org/10.1016/j.jpdc.2014.07.003 is INVALID because of 'https://doi.org/' prefix
whedon picture whedon on 17 Oct 2020

@whedon check references from branch development

arfon picture arfon on 17 Oct 2020 
Attempting to check references... from custom branch development
whedon picture whedon on 17 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3847/1538-4357/ab4f75 is OK
- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/1742-6596/1623/1/012021 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1109/tpds.2020.3010016 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK
- 10.1016/j.jpdc.2014.07.003 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 17 Oct 2020

@whedon generate pdf from branch development

arfon picture arfon on 17 Oct 2020 
Attempting PDF compilation from custom branch development. Reticulating splines etc...
whedon picture whedon on 17 Oct 2020

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

whedon picture whedon on 17 Oct 2020

@eloisabentivegna - does this look better?

arfon picture arfon on 17 Oct 2020

@eloisabentivegna - does this look better?

Yes, great!

eloisabentivegna picture eloisabentivegna on 17 Oct 2020

The proof looks good to me! @zingale, I have added one last missing DOI, and issued a PR on the Castro repo. Once that is fixed, we should be done.

eloisabentivegna picture eloisabentivegna on 20 Oct 2020

awesome. Thanks. I merged that.

zingale picture zingale on 21 Oct 2020

@whedon check references from branch development

eloisabentivegna picture eloisabentivegna on 21 Oct 2020 
Attempting to check references... from custom branch development
whedon picture whedon on 21 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3847/1538-4357/ab4f75 is OK
- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/1742-6596/1623/1/012021 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1109/tpds.2020.3010016 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1109/P3HPC49587.2019.00012 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 21 Oct 2020

@whedon generate pdf from branch development

eloisabentivegna picture eloisabentivegna on 21 Oct 2020 
Attempting PDF compilation from custom branch development. Reticulating splines etc...
whedon picture whedon on 21 Oct 2020

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

whedon picture whedon on 21 Oct 2020

The proof looks fine now. I will issue the accept command next. Congratulations to the authors, and many heartfelt thanks to @kegiljarhus, @bonh, and @joshia5 for the careful reviews! 🎉

eloisabentivegna picture eloisabentivegna on 21 Oct 2020

@whedon accept

eloisabentivegna picture eloisabentivegna on 21 Oct 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 21 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK

MISSING DOIs

- 10.21105/joss.01757 may be a valid DOI for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver
- 10.1088/1742-6596/1623/1/012021 may be a valid DOI for title: The Castro AMR Simulation Code: Current and Future Developments
- 10.1109/tpds.2020.3010016 may be a valid DOI for title: K-Athena: a performance portable structured grid finite volume magnetohydrodynamics code

INVALID DOIs

- https://doi.org/10.1016/j.jpdc.2014.07.003 is INVALID because of 'https://doi.org/' prefix
whedon picture whedon on 21 Oct 2020

: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/1837

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1837, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon picture whedon on 21 Oct 2020

@whedon accept from branch development

eloisabentivegna picture eloisabentivegna on 22 Oct 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 22 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3847/1538-4357/ab4f75 is OK
- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/1742-6596/1623/1/012021 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1109/tpds.2020.3010016 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1109/P3HPC49587.2019.00012 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 22 Oct 2020

: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/1838

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1838, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true from branch development

whedon picture whedon on 22 Oct 2020

Hi @zingale, I'm the EIC on duty this week doing some final checks. Could you fix these in the paper before we accept?

  • [x] The paper is missing an explicit Statement of Need section, which we have made a required component of articles. (You can likely use text already in the first page)
  • [x] In the second paragraph, can you use the @author:2001 citation for the Collela 1990 reference, so that it appears as "Collela (1990)"
  • [x] please put a comma after "e.g." in paragraph four (and in any other places where i.e. or e.g. are used)
  • [x] The references are missing the journal names—likely this is due to the .bib file using astro-specific macros (\apj, etc.) that need to be replaced with spelled-out versions
kyleniemeyer picture kyleniemeyer on 22 Oct 2020

Hi Kyle, thanks for the comments. I think I've addressed them all.

zingale picture zingale on 23 Oct 2020
👍1

@whedon generate pdf

kyleniemeyer picture kyleniemeyer on 23 Oct 2020

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

whedon picture whedon on 23 Oct 2020

@whedon generate pdf from branch development

kyleniemeyer picture kyleniemeyer on 23 Oct 2020 
Attempting PDF compilation from custom branch development. Reticulating splines etc...
whedon picture whedon on 23 Oct 2020

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

whedon picture whedon on 23 Oct 2020

@whedon accept

kyleniemeyer picture kyleniemeyer on 23 Oct 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 23 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK

MISSING DOIs

- 10.21105/joss.01757 may be a valid DOI for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver
- 10.1088/1742-6596/1623/1/012021 may be a valid DOI for title: The Castro AMR Simulation Code: Current and Future Developments
- 10.1109/tpds.2020.3010016 may be a valid DOI for title: K-Athena: a performance portable structured grid finite volume magnetohydrodynamics code

INVALID DOIs

- https://doi.org/10.1016/j.jpdc.2014.07.003 is INVALID because of 'https://doi.org/' prefix
whedon picture whedon on 23 Oct 2020

: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/1846

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1846, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon picture whedon on 23 Oct 2020

@whedon accept from branch development

kyleniemeyer picture kyleniemeyer on 23 Oct 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 23 Oct 2020 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3847/1538-4357/ab4f75 is OK
- 10.21105/joss.01370 is OK
- 10.5281/zenodo.3633773 is OK
- 10.3847/1538-4357/ab4e1d is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1088/0067-0049/196/2/20 is OK
- 10.1088/0067-0049/204/1/7 is OK
- 10.1088/1742-6596/1623/1/012021 is OK
- 10.1088/0004-637X/765/1/39 is OK
- 10.1088/1742-6596/1031/1/012024 is OK
- 10.1109/tpds.2020.3010016 is OK
- 10.1086/317361 is OK
- 10.1088/0067-0049/211/2/19 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1109/P3HPC49587.2019.00012 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 23 Oct 2020

: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/1847

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1847, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true from branch development

whedon picture whedon on 23 Oct 2020

@whedon accept deposit=true from branch development

kyleniemeyer picture kyleniemeyer on 23 Oct 2020 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 23 Oct 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon picture whedon on 23 Oct 2020

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/1848
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02513
  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...

whedon picture whedon on 23 Oct 2020

Congrats @zingale on your article's publication in JOSS!

Many thanks to @kegiljarhus, @bonh, and @joshia5 for reviewing this submission, and @eloisabentivegna for editing it.

kyleniemeyer picture kyleniemeyer on 23 Oct 2020
😄1

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

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.02513/status.svg)](https://doi.org/10.21105/joss.02513)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02513">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02513/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02513/status.svg
   :target: https://doi.org/10.21105/joss.02513

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

whedon picture whedon on 23 Oct 2020
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