[REVIEW]: Efficient Polyhedral Gravity Modeling in Modern C++ and Python

[editorialbot]

Submitting author: @schuhmaj (Jonas Schuhmacher)
Repository: https://github.com/esa/polyhedral-gravity-model
Branch with paper.md (empty if default branch): main
Version: 3.2.0
Editor: @dfm
Reviewers: @mikegrudic, @santisoler
Archive: 10.5281/zenodo.11221939

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7d01f903d9d137c08240185331f91606/status.svg)](https://joss.theoj.org/papers/7d01f903d9d137c08240185331f91606)

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

@mikegrudic & @santisoler, 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 @santisoler

📝 Checklist for @mikegrudic

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (865.5 files/s, 93256.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             17            409            221           2324
C/C++ Header                    17            270           1060            700
Python                          11            244            321            668
Markdown                         3            148              0            417
CMake                           15            116            103            288
YAML                             8             14             30            260
reStructuredText                11            207            287            255
Jupyter Notebook                 1              0            651            160
TeX                              1             15              0            147
DOS Batch                        1              8              1             26
make                             1              4              7              9
INI                              1              0              0              4
-------------------------------------------------------------------------------
SUM:                            87           1435           2681           5258
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1026

[editorialbot]

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

OK DOIs

- 10.1007/s00190-009-0310-9 is OK
- 10.1190/geo2010-0334.1 is OK
- 10.1111/1365-2478.13134 is OK
- 10.1038/s44172-022-00050-3 is OK
- 10.1190/1.1444944 is OK
- 10.1007/s001900050074 is OK
- 10.1145/2629697 is OK
- 10.1016/j.earscirev.2021.103739 is OK
- 10.21105/joss.02338 is OK
- 10.1109/iciecs.2010.5677738 is OK

MISSING DOIs

- 10.5270/esa-gnc-icatt-2023-067 may be a valid DOI for title: Investigation of the Robustness of Neural Density Fields

INVALID DOIs

- None

[dfm]

@mikegrudic, @santisoler — This is the review thread for the paper. All of our correspondence 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#6384 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. Please get your review started as soon as possible!

[editorialbot]

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

[santisoler]

Review checklist for @santisoler

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/esa/polyhedral-gravity-model?
• 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 (@schuhmaj) 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?

[santisoler]

Hello @schuhmaj. Thanks for submitting this paper to JOSS. As you might have noticed I've started with the review process. I still need to go through some of the items on the checklist. While I do so I'll be opening issues and PRs in your repo (as the ones you can already see). Feel free to reply and tackle them in whatever order you like. They won't block my review process: even if I open an issue, I'll continue with the rest of the checklist.

The suggestions I make for solving the issues I identify and the PRs I open are mere suggestions to solve them. Don't feel obliged to accept them if you don't agree with my take. Feel free to suggest alternative ways of solving them, and to justify your disagreement if you have any.

On contribution and authorship

I do have a question that I'll ask you in this Issue. I noticed that gomezzz made significant contributions to the submitted repository, particularly in esa/polyhedral-gravity-model@f3cc4d9. Is there a reason why gomezzz is not listed in the list of submitting authors?

I'm not asking them to be added, I'm just curious about their involvement in the submitted paper.

(I'm not pinging gomezzz to avoid sending unrequested notifications. I leave the decision to ping them or not to the editor @dfm).

[mikegrudic]

Review checklist for @mikegrudic

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/esa/polyhedral-gravity-model?
• 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 (@schuhmaj) 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?

[schuhmaj]

Hi @santisoler, Thanks a lot for taking the time to do our JOSS review. I will address the issues that have already been opened and those that will come up in the forthcoming days.

Regarding the authorship, the project was initially developed in schuhmaj/polyhedral-gravity-model
The init commit from gomezzz roughly corresponds to the final commit in schuhmaj/polyhedral-gravity-model.
We did not transfer the repository at that time to keep a copy of the "original," while the ESA repository started with a fresh commit history.

gomezzz has been (and sort of still is 🙂 since he suggested the JOSS submission) my major advisor from the ESA side through code reviews and suggestions.

[gomezzz]

Hi @santisoler , thanks for reviewing ! To chime in from my end and just confirm, indeed, the majority of the code has actually been written by @schuhmaj . My role has been more on the side of ESA interface and code review as you can see in pull requests in the repo pointed out by @schuhmaj . :)

[santisoler]

Thanks @schuhmaj for the clarification, and thanks @gomezzz for confirming your role in the submitted repository. All good now on the Contribution and authorship end, I've already checked off that box in my checklist.

I'll continue with my review in the following days. Looking forward to it.

[editorialbot]

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

[dfm]

@editorialbot generate pdf

[dfm]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/s00190-009-0310-9 is OK
- 10.1190/geo2010-0334.1 is OK
- 10.1111/1365-2478.13134 is OK
- 10.1038/s44172-022-00050-3 is OK
- 10.5270/esa-gnc-icatt-2023-067 is OK
- 10.5270/esa-gnc-icatt-2023-057 is OK
- 10.1190/1.1444944 is OK
- 10.1007/s001900050074 is OK
- 10.1145/2629697 is OK
- 10.1016/j.earscirev.2021.103739 is OK
- 10.21105/joss.02338 is OK
- 10.1109/iciecs.2010.5677738 is OK

MISSING DOIs

- No DOI given, and none found for title: Efficient Polyhedral Gravity Modeling in Modern C+...
- No DOI given, and none found for title: Mascon models for small body gravity fields
- No DOI given, and none found for title: Eros polyhedral model
- No DOI given, and none found for title: The physics-informed neural network gravity model ...

INVALID DOIs

- None

[editorialbot]

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

[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

- 10.1007/s00190-009-0310-9 is OK
- 10.1190/geo2010-0334.1 is OK
- 10.1111/1365-2478.13134 is OK
- 10.1038/s44172-022-00050-3 is OK
- 10.5270/esa-gnc-icatt-2023-067 is OK
- 10.5270/esa-gnc-icatt-2023-057 is OK
- 10.1190/1.1444944 is OK
- 10.1007/s001900050074 is OK
- 10.1145/2629697 is OK
- 10.1016/j.earscirev.2021.103739 is OK
- 10.21105/joss.02338 is OK
- 10.1109/iciecs.2010.5677738 is OK

MISSING DOIs

- No DOI given, and none found for title: Efficient Polyhedral Gravity Modeling in Modern C+...
- No DOI given, and none found for title: Mascon models for small body gravity fields
- No DOI given, and none found for title: Eros polyhedral model
- No DOI given, and none found for title: The physics-informed neural network gravity model ...

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#5426, 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]

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: Schuhmacher
  given-names: Jonas
  orcid: "https://orcid.org/0009-0005-9693-4530"
- family-names: Blazquez
  given-names: Emmanuel
  orcid: "https://orcid.org/0000-0001-9697-582X"
- family-names: Gratl
  given-names: Fabio
  orcid: "https://orcid.org/0000-0001-5195-7919"
- family-names: Izzo
  given-names: Dario
  orcid: "https://orcid.org/0000-0002-9846-8423"
- family-names: Gómez
  given-names: Pablo
  orcid: "https://orcid.org/0000-0002-5631-8240"
doi: 10.5281/zenodo.11221939
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Schuhmacher
    given-names: Jonas
    orcid: "https://orcid.org/0009-0005-9693-4530"
  - family-names: Blazquez
    given-names: Emmanuel
    orcid: "https://orcid.org/0000-0001-9697-582X"
  - family-names: Gratl
    given-names: Fabio
    orcid: "https://orcid.org/0000-0001-5195-7919"
  - family-names: Izzo
    given-names: Dario
    orcid: "https://orcid.org/0000-0002-9846-8423"
  - family-names: Gómez
    given-names: Pablo
    orcid: "https://orcid.org/0000-0002-5631-8240"
  date-published: 2024-06-01
  doi: 10.21105/joss.06384
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6384
  title: Efficient Polyhedral Gravity Modeling in Modern C++ and Python
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06384"
  volume: 9
title: Efficient Polyhedral Gravity Modeling in Modern C++ and Python

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]

🐘🐘🐘 👉 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.06384 joss-papers#5427
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06384
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]

@mikegrudic, @santisoler — 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!!

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

[editorialbot]

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

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