[REVIEW]: NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling

[editorialbot]

Submitting author: !--author-handle-->@dshawul<!--end-author-handle-- (Daniel Abdi) Repository: https://github.com/dshawul/NebulaSEM Branch with paper.md (empty if default branch): master Version: v2.0 Editor: !--editor-->@observingClouds<!--end-editor-- Reviewers: @capitalaslash, @esclapez Archive: 10.5281/zenodo.11088210

Status

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Markdown: [![status](https://joss.theoj.org/papers/b89b0f085fc62dd87d6797ded45e4a32/status.svg)](https://joss.theoj.org/papers/b89b0f085fc62dd87d6797ded45e4a32)

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

@capitalaslash & @esclapez, 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 @observingClouds 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 @esclapez

📝 Checklist for @capitalaslash

[editorialbot]

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:

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1016/j.advengsoft.2014.05.002 is OK
- 10.1175/1520-0469(1993)050<1865:BCEWAS>2.0.CO;2 is OK
- 10.2514/3.8290 is OK
- 10.1137/100791634 is OK
- 10.1175/1520-0469(1981)038<0988:SATSOA>2.0.CO;2 is OK
- 10.1175/1520-0493(1963)091<0099:GCEWTP>2.3.CO;2 is OK
- 10.7551/mitpress/3014.001.0001 is OK
- 10.1177/1094342017694427 is OK
- 10.1155/2015/295393 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (1430.1 files/s, 234465.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             32            680           1203           6804
C/C++ Header                    23            548            582           5165
Markdown                         7            113              0            477
CMake                           31             34             82            377
Bourne Shell                     3             20             12            123
TeX                              1              4              0            101
YAML                             3             10              4             56
-------------------------------------------------------------------------------
SUM:                           100           1409           1883          13103
-------------------------------------------------------------------------------

Commit count by author:

   287  Daniel Abdi
    59  dshawul
    21  Daniel Shawul
     8  U-Daniel-pc\dshawul

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1173

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 2-Clause "Simplified" License (Valid open source OSI approved license)

[editorialbot]

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

[observingClouds]

Dear @capitalaslash, Dear @esclapez, Thank you very much for agreeing to review this submission. Please carefully read the instructions mentioned above and start the review process by creating your review checklist with the command @editorialbot generate my checklist. Please be reminded that we like to have individual discussion points in separate issues in the software repository to keep this thread light and have a better overview about open/closed discussion points.

I'll check back in two weeks how the review is progressing with the aim to finish the review within 6 weeks. In the meantime feel free to reach out and ask any questions.

Cheers, Hauke

[observingClouds]

@editorialbot remind @capitalaslash in two weeks

[editorialbot]

Reminder set for @capitalaslash in two weeks

[observingClouds]

@editorialbot remind @esclapez in two weeks

[editorialbot]

Reminder set for @esclapez in two weeks

[esclapez]

Review checklist for @esclapez

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/dshawul/NebulaSEM?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@dshawul) 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?

[capitalaslash]

Review checklist for @capitalaslash

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/dshawul/NebulaSEM?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@dshawul) 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?

[capitalaslash]

added dshawul/NebulaSEM/pull/1

[editorialbot]

:wave: @capitalaslash, please update us on how your review is going (this is an automated reminder).

[editorialbot]

:wave: @esclapez, please update us on how your review is going (this is an automated reminder).

[capitalaslash]

added dshawul/nebulaSEM/pull/2

[esclapez]

added dshawul/NebulaSEM/pull/3

[capitalaslash]

added dshawul/NebulaSEM/issues/4

[capitalaslash]

@editorialbot generate pdf

[editorialbot]

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

[observingClouds]

Thank you @capitalaslash, @esclapez and @dshawul for being active and responsive and moving the review process quickly forward. I see that you have opened a few PRs that have all been merged or otherwise addressed.

@capitalaslash, I see that you have completed your checklist. Could you please confirm that you have finished your review?

@esclapez, would you be able to finish the review and outstanding items within the next week?

Thank you!

[capitalaslash]

hey @observingClouds yes my review is over. Thanks to @dshawul for quickly addressing all my concerns, my review is positive and I recommend to publish.

[esclapez]

added two minor PR7 and PR8

[esclapez]

Hi @observingClouds, my review is over too. Thanks @dshawul for your reactivity ! The review is also positive on my end and I recommend moving forward with publication.

[observingClouds]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• [x] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [x] Recommend acceptance with @editorialbot recommend-accept

[observingClouds]

@esclapez, @capitalaslash thank you very much for taking the time to review this submission. Your feedback has been very valuable. I will now work together with @dshawul on the last steps towards acceptance and publication.

[observingClouds]

@dshawul could you have a look at the above mentioned author tasks and post the DOI of the archived software version here? Thank you.

[dshawul]

@observingClouds Thank you! I have tried to address the author's checklists as follows

• The author and affiliations are correct
• I have created a release "NebulaSEM v2.0"
• Archived the release on Zenodo with the DOI
• The Zenodo archive author list is different in that it contains two github accounts of mine, and the two JOSS reviewers who contributed to the repo. I suppose that is Ok so just letting you know.
• The license on Zenodo says "Creative Commons License" while the github one has "BSD-2-clause simplified license". Is that Ok?

Sorry I am new to this.

[dshawul]

@observingClouds Sorry, I was not aware that you are able to edit the archive. I have now fixed both the "LICENSE" issue and the "Author's list" issue. Let me know if there are things that I missed.

[observingClouds]

Thanks @dshawul, no worries. Could you also adjust the title of the archived release? We prefer to have the JOSS release having the same title as the paper, i.e. "NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling". Thank you.

[observingClouds]

@editorialbot set 10.5281/zenodo.11088210 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11088210

[observingClouds]

@editorialbot set v2.0 as version

[editorialbot]

Done! version is now v2.0

[observingClouds]

@editorialbot generate pdf

[observingClouds]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.advengsoft.2014.05.002 is OK
- 10.1175/1520-0469(1993)050<1865:BCEWAS>2.0.CO;2 is OK
- 10.2514/3.8290 is OK
- 10.1137/100791634 is OK
- 10.1175/1520-0469(1981)038<0988:SATSOA>2.0.CO;2 is OK
- 10.1175/1520-0493(1963)091<0099:GCEWTP>2.3.CO;2 is OK
- 10.7551/mitpress/3014.001.0001 is OK
- 10.1177/1094342017694427 is OK
- 10.1155/2015/295393 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[dshawul]

@observingClouds I have now updated the title of the archive to match that of the JOSS paper. Thank you!

[observingClouds]

@dshawul please have a look at the above linked PR, which fixes a few last typos. Thank you.

[observingClouds]

@editorialbot generate pdf

[observingClouds]

@editorialbot check references

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1016/j.advengsoft.2014.05.002 is OK
- 10.1175/1520-0469(1993)050<1865:BCEWAS>2.0.CO;2 is OK
- 10.2514/3.8290 is OK
- 10.1137/100791634 is OK
- 10.1175/1520-0469(1981)038<0988:SATSOA>2.0.CO;2 is OK
- 10.1175/1520-0493(1963)091<0099:GCEWTP>2.3.CO;2 is OK
- 10.7551/mitpress/3014.001.0001 is OK
- 10.1177/1094342017694427 is OK
- 10.1155/2015/295393 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[observingClouds]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.advengsoft.2014.05.002 is OK
- 10.1175/1520-0469(1993)050<1865:BCEWAS>2.0.CO;2 is OK
- 10.2514/3.8290 is OK
- 10.1137/100791634 is OK
- 10.1175/1520-0469(1981)038<0988:SATSOA>2.0.CO;2 is OK
- 10.1175/1520-0493(1963)091<0099:GCEWTP>2.3.CO;2 is OK
- 10.7551/mitpress/3014.001.0001 is OK
- 10.1177/1094342017694427 is OK
- 10.1155/2015/295393 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5289, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[observingClouds]

@dshawul thank you for integrating the last changes. I have now recommended the manuscript for acceptance. The editor-in-chief will now take over in the next few days, makes a few more checks and then your manuscript should be soon published. In the meantime you can have a look at the final proof above and let us know if it does all look to your satisfaction (or not).