[REVIEW]: NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling #6448

editorialbot · 2024-03-06T17:49:54Z

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

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b89b0f085fc62dd87d6797ded45e4a32"><img src="https://joss.theoj.org/papers/b89b0f085fc62dd87d6797ded45e4a32/status.svg"></a>
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

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-03-06T17:49:57Z

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:

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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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editorialbot · 2024-03-06T17:50:15Z

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 · 2024-03-06T17:50:18Z

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 · 2024-03-06T17:50:22Z

Paper file info:

📄 Wordcount for paper.md is 1173

✅ The paper includes a Statement of need section

editorialbot · 2024-03-06T17:50:25Z

License info:

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

editorialbot · 2024-03-06T17:51:02Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

observingClouds · 2024-03-06T17:58:53Z

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 · 2024-03-06T18:02:35Z

@editorialbot remind @capitalaslash in two weeks

editorialbot · 2024-03-06T18:02:37Z

Reminder set for @capitalaslash in two weeks

observingClouds · 2024-03-06T18:02:57Z

@editorialbot remind @esclapez in two weeks

editorialbot · 2024-03-06T18:02:59Z

Reminder set for @esclapez in two weeks

esclapez · 2024-03-06T20:25:29Z

Review checklist for @esclapez

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

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 https://github.com/dshawul/NebulaSEM?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
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?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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: 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?
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?

capitalaslash · 2024-03-19T14:59:30Z

Review checklist for @capitalaslash

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

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 https://github.com/dshawul/NebulaSEM?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
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?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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: 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?
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?

capitalaslash · 2024-03-20T11:03:03Z

added dshawul/NebulaSEM/pull/1

editorialbot · 2024-03-20T18:02:42Z

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

editorialbot · 2024-03-20T18:03:00Z

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

capitalaslash · 2024-04-02T10:20:19Z

added dshawul/NebulaSEM/pull/2

esclapez · 2024-04-03T20:37:40Z

added dshawul/NebulaSEM/pull/3

capitalaslash · 2024-04-12T13:42:33Z

added dshawul/NebulaSEM/issues/4

capitalaslash · 2024-04-15T10:02:22Z

@editorialbot generate pdf

editorialbot · 2024-04-15T10:03:33Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

observingClouds · 2024-04-30T03:30:46Z

@editorialbot generate pdf

observingClouds · 2024-04-30T03:30:58Z

@editorialbot check references

editorialbot · 2024-04-30T03:31:20Z

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 · 2024-04-30T03:31:55Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

dshawul · 2024-04-30T03:46:13Z

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

observingClouds · 2024-04-30T06:00:36Z

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

observingClouds · 2024-04-30T16:55:02Z

@editorialbot generate pdf

observingClouds · 2024-04-30T16:56:10Z

@editorialbot check references

editorialbot · 2024-04-30T16:56:19Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-04-30T16:56:27Z

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 · 2024-04-30T16:59:01Z

@editorialbot recommend-accept

editorialbot · 2024-04-30T16:59:03Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-04-30T16:59:18Z

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 · 2024-04-30T17:00:42Z

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

Check final proof 👉📄 Download article

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

observingClouds · 2024-04-30T17:07:35Z

@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).

danielabdi-noaa · 2024-04-30T17:11:33Z

@observingClouds Thank you very much for editing the paper! I'd also like to express my gratitude to @capitalaslash and @esclapez for their reviews and contributions!

kthyng · 2024-04-30T17:56:04Z

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

Are checklists all checked off?
Check that version was updated and make sure the version from JOSS matches github and Zenodo.
Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
Check paper.

kthyng · 2024-04-30T18:00:45Z

Everything looks great!

kthyng · 2024-04-30T18:00:50Z

@editorialbot accept

editorialbot · 2024-04-30T18:00:52Z

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

editorialbot · 2024-04-30T18:07:40Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Abdi
  given-names: Daniel S.
  orcid: "https://orcid.org/0000-0003-0671-2941"
contact:
- family-names: Abdi
  given-names: Daniel S.
  orcid: "https://orcid.org/0000-0003-0671-2941"
doi: 10.5281/zenodo.11088210
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Abdi
    given-names: Daniel S.
    orcid: "https://orcid.org/0000-0003-0671-2941"
  date-published: 2024-04-30
  doi: 10.21105/joss.06448
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6448
  title: "NebulaSEM: A high-order discontinuous Galerkin spectral
    element code for atmospheric modeling"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06448"
  volume: 9
title: "NebulaSEM: A high-order discontinuous Galerkin spectral element
  code for atmospheric modeling"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-04-30T18:07:49Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-04-30T18:07:50Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06448 joss-papers#5290
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06448
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-04-30T18:17:35Z

Congratulations on your new publication @dshawul! Many thanks to @observingClouds and to reviewers @capitalaslash and @esclapez for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

editorialbot · 2024-04-30T18:17:37Z

🎉🎉🎉 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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06448/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06448/status.svg
   :target: https://doi.org/10.21105/joss.06448

This is how it will look in your documentation:

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editorialbot added C C++ CMake review Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Mar 6, 2024

editorialbot assigned observingClouds Mar 6, 2024

editorialbot mentioned this issue Mar 6, 2024

[PRE REVIEW]: NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling #6180

Closed

observingClouds removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 6, 2024

observingClouds mentioned this issue Apr 30, 2024

JOSS paper check dshawul/NebulaSEM#9

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Apr 30, 2024

editorialbot added accepted published Papers published in JOSS labels Apr 30, 2024

kthyng closed this as completed Apr 30, 2024

[REVIEW]: NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling #6448

[REVIEW]: NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling #6448

Comments

editorialbot commented Mar 6, 2024 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Mar 6, 2024

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observingClouds commented Mar 6, 2024

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observingClouds commented Mar 6, 2024

editorialbot commented Mar 6, 2024

esclapez commented Mar 6, 2024 • edited

Review checklist for @esclapez

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

capitalaslash commented Mar 19, 2024 • edited

Review checklist for @capitalaslash

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

capitalaslash commented Mar 20, 2024

editorialbot commented Mar 20, 2024

editorialbot commented Mar 20, 2024

capitalaslash commented Apr 2, 2024

esclapez commented Apr 3, 2024

capitalaslash commented Apr 12, 2024

capitalaslash commented Apr 15, 2024

editorialbot commented Apr 15, 2024

observingClouds commented Apr 30, 2024

observingClouds commented Apr 30, 2024

editorialbot commented Apr 30, 2024

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dshawul commented Apr 30, 2024

observingClouds commented Apr 30, 2024

observingClouds commented Apr 30, 2024

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observingClouds commented Apr 30, 2024

danielabdi-noaa commented Apr 30, 2024

kthyng commented Apr 30, 2024 • edited

kthyng commented Apr 30, 2024

kthyng commented Apr 30, 2024

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kthyng commented Apr 30, 2024

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editorialbot commented Mar 6, 2024 •

edited

esclapez commented Mar 6, 2024 •

edited

capitalaslash commented Mar 19, 2024 •

edited

kthyng commented Apr 30, 2024 •

edited