[REVIEW]: SWAMPE: A Shallow-Water Atmospheric Model in Python for Exoplanets

[editorialbot]

Submitting author: @kathlandgren (Ekaterina Landgren)
Repository: https://github.com/kathlandgren/SWAMPE
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @dfm
Reviewers: @mark-hammond, @imalsky
Archive: 10.5281/zenodo.7402247

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/ef9e88a2db11cb4c962b8a1925f94306/status.svg)](https://joss.theoj.org/papers/ef9e88a2db11cb4c962b8a1925f94306)

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

@mark-hammond & @imalsky, 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 @dfm 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 @mark-hammond

📝 Checklist for @imalsky

[editorialbot]

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[dfm]

@mark-hammond, @imalsky — This is the review thread for the paper. All of our communications will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4872 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

[mark-hammond]

Review checklist for @mark-hammond

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/kathlandgren/SWAMPE?
• 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 (@kathlandgren) 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?

[dfm]

@imalsky — A reminder to keep this on your radar. Please generate your checklist and start taking a look as soon as you can. Thanks!!

[imalsky]

Review checklist for @imalsky

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/kathlandgren/SWAMPE?
• 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 (@kathlandgren) 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?

[imalsky]

Thanks! I opened a review. My apologies if I get any of the process wrong, this is my first JOSS review.

…

On Mon, Oct 31, 2022 at 7:40 AM Dan Foreman-Mackey ***@***.***> wrote: @imalsky <https://github.com/imalsky> — A reminder to keep this on your radar. Please generate your checklist and start taking a look as soon as you can. Thanks!! — Reply to this email directly, view it on GitHub <#4872 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEHJJJO2AJQKLC6QEJIPRLWF7K5BANCNFSM6AAAAAARLMWYAU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[imalsky]

@dfm, is it recommended that I also make any suggestion for improvements/questions in the paper or code, or simply check the above guideline checklist?

[dfm]

@imalsky — absolutely! The checklist is our priority, but any other suggestions would be excellent. I recommend opening any comments as issues on the repo.

[imalsky]

Everything looks good to me! I had an issue open on the repo that I've now closed also

[mark-hammond]

Thank you for addressing the comments, I have ticked all the boxes now and closed the issue thread on the other repo. This is a great piece of code, thank you for sharing it in this way!

[dfm]

Awesome!! Thanks @mark-hammond and @imalsky for your constructive reviews! I really appreciate all the time that you volunteered to this process.

@kathlandgren — I have a couple of final edits to do then I'll have some quick tasks for you before we publish. I'm totally swamped today, but I'll get to this before the end of the week. Thanks for your patience!

[imalsky]

Thanks for inviting me! It was my pleasure

…

On Thu, Dec 1, 2022 at 3:20 AM Dan Foreman-Mackey ***@***.***> wrote: Awesome!! Thanks @mark-hammond <https://github.com/mark-hammond> and @imalsky <https://github.com/imalsky> for your constructive reviews! I really appreciate all the time that you volunteered to this process. @kathlandgren <https://github.com/kathlandgren> — I have a couple of final edits to do then I'll have some quick tasks for you before we publish. I'm totally swamped today, but I'll get to this before the end of the week. Thanks for your patience! — Reply to this email directly, view it on GitHub <#4872 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEHJJLZKCOYPZOV4E5VKODWLCCZJANCNFSM6AAAAAARLMWYAU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[dfm]

@editorialbot check references

[dfm]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.3847/2041-8213/aabcc8 is OK
- 10.1088/0004-637X/700/1/887 is OK
- 10.3847/0004-637X/821/1/9 is OK
- 10.1051/0004-6361/201321132 is OK
- 10.1086/506312 is OK
- 10.1093/mnras/stt1509 is OK
- 10.1016/j.icarus.2020.114065 is OK
- 10.1086/375015 is OK
- 10.1088/0004-637X/738/1/71 is OK
- 10.1088/0004-637X/776/2/134 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1103/PhysRevResearch.2.023068 is OK

MISSING DOIs

- 10.1029/96jc02776 may be a valid DOI for title: Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling
- 10.3847/0004-637x/829/1/52 may be a valid DOI for title: The impact of non-uniform thermal structure on the interpretation of exoplanet emission spectra
- 10.3847/1538-4365/aa7a06 may be a valid DOI for title: Resolving orbital and climate keys of earth and extraterrestrial environments with dynamics (ROCKE-3D) 1.0: a general circulation model for simulating the climates of rocky planets
- 10.1016/j.ocemod.2011.02.013 may be a valid DOI for title: What processes drive the ocean heat transport?
- 10.1086/523957 may be a valid DOI for title: Hydrodynamic simulations of unevenly irradiated Jovian planets
- 10.1175/1520-0493(2001)129<2346:svfswe>2.0.co;2 may be a valid DOI for title: Spectral viscosity for shallow water equations in spherical geometry
- 10.1029/2019ms002015 may be a valid DOI for title: The GFDL Earth System Model version 4.1 (GFDL-ESM 4.1): Overall coupled model description and simulation characteristics

INVALID DOIs

- None

[dfm]

@kathlandgren — I've opened a PR with some minor edits to the paper. After merging or responding to that, here are the final steps that I'll need from you:

1. Take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
2. Increment the version number of the software and report that version number back here.
3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

[kathlandgren]

@dfm Thank you for the edits and for your help!

Version is: v1.0.0

DOI of the release is: 10.5281/zenodo.7402247

[dfm]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[dfm]

@editorialbot set 10.5281/zenodo.7402247 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7402247

[dfm]

@editorialbot generate pdf

@kathlandgren — Thanks! Can you take one last look through the proofs 👇 and make sure that you're happy?

[editorialbot]

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

[kathlandgren]

The proofs look great to me!

[dfm]

@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

- 10.1029/96jc02776 is OK
- 10.3847/2041-8213/aabcc8 is OK
- 10.3847/0004-637x/829/1/52 is OK
- 10.1088/0004-637X/700/1/887 is OK
- 10.3847/0004-637X/821/1/9 is OK
- 10.1051/0004-6361/201321132 is OK
- 10.1086/506312 is OK
- 10.1093/mnras/stt1509 is OK
- 10.3847/1538-4365/aa7a06 is OK
- 10.1016/j.ocemod.2011.02.013 is OK
- 10.1016/j.icarus.2020.114065 is OK
- 10.1086/375015 is OK
- 10.1088/0004-637X/738/1/71 is OK
- 10.1086/523957 is OK
- 10.1088/0004-637X/776/2/134 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1175/1520-0493(2001)129<2346:svfswe>2.0.co;2 is OK
- 10.1103/PhysRevResearch.2.023068 is OK
- 10.1029/2019ms002015 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/aass-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#3781, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[dfm]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04872 joss-papers#3782
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04872
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[dfm]

@mark-hammond, @imalsky — Many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@kathlandgren — Your paper is now accepted and published in JOSS! ⚡🚀💥

[editorialbot]

🎉🎉🎉 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.04872/status.svg)](https://doi.org/10.21105/joss.04872)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04872">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04872/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04872/status.svg
   :target: https://doi.org/10.21105/joss.04872

This is how it will look in your documentation:

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