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[REVIEW]: Efficient Polyhedral Gravity Modeling in Modern C++ and Python #6384

Closed editorialbot closed 4 months ago

editorialbot commented 8 months ago

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

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7d01f903d9d137c08240185331f91606"><img src="https://joss.theoj.org/papers/7d01f903d9d137c08240185331f91606/status.svg"></a>
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 commented 8 months ago

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 commented 8 months ago 
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 commented 8 months ago

Wordcount for paper.md is 1026

editorialbot commented 8 months ago 
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 commented 8 months ago

@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 commented 8 months ago

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

santisoler commented 8 months ago

Review checklist for @santisoler

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

santisoler commented 7 months ago

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 https://github.com/esa/polyhedral-gravity-model/commit/f3cc4d9d80c3ca23fffa342d9ac178a4582c0899. 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 commented 7 months ago

Review checklist for @mikegrudic

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

schuhmaj commented 7 months ago

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 commented 7 months ago

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 commented 7 months ago

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.

mikegrudic commented 7 months ago

Hi @schuhmaj,

Just did a pass through the code. Overall I think the software and paper are of high quality. I raised one issue re: documentation, but that's the one thing I would need to see to sign off on this. However, I strongly concur with all of @santisoler's issues and PRs and recommend addressing them.

Cheers, Mike

santisoler commented 7 months ago

Hi @schuhmaj. Thanks again for submitting this article to JOSS. I finished my review process. I think this article is in a very good shape to be published. I would only ask the authors to address some of the issues mentioned in the opened Issues and Pull Requests, which have been linked to this Review Issue.

~Regarding the checklist, I think the authors have covered all points, except for the one mentioned by @mikegrudic related to a missing statement of need in the documentation (https://github.com/esa/polyhedral-gravity-model/issues/30).~

In conclusion, I think the article should be considered as ready for publication after these issues have been solved. I really enjoyed reviewing this article and going through the code, and I'm looking forward to continuing the conversation.

Kind regards, Santiago Soler

Edit 2024-04-15: Strikethrough the sentence regarding unchecked item in checklist regarding the missing statement in docs.

dfm commented 6 months ago

@schuhmaj — I wanted to check in here on the status of your work addressing the comments from @santisoler and @mikegrudic. Taking a peek at the repo, it looks like you're making good progress. When you get a chance, could you post a summary back here? Thanks!

@santisoler, @mikegrudic — Thanks so much for your constructive reviews!!

schuhmaj commented 6 months ago

Hi @dfm

The "needed" requested changes are included in the paper and the implementation. These are all integrated, yet the associated version 2.2 is not yet published since it changes behavior without a syntactical change. A potential existing user might run into trouble blindly upgrading. Our current approach is to defer that a bit until I am finished - presumably finished this week - with https://github.com/esa/polyhedral-gravity-model/issues/36, which integrates an "optional" improvement that one will notice improving the first-time-user experience. I would ping you when it is merged & the changes are successfully released to conda and PyPi.

In any case, also at this place, thank you very much, @santisoler and @mikegrudic, for taking the time to review our submission 🙂 It got better by a lot!

Summary

Documentation related

Implementation related

(Optional) Implementation related - Work in Progress

What is still missing is an "optional" improvement

I am currently working on this issue in PR https://github.com/esa/polyhedral-gravity-model/issues/36

dfm commented 6 months ago

@schuhmaj — Thanks for this thorough summary! Let me know when https://github.com/esa/polyhedral-gravity-model/pull/36 is finished and we'll go through the final editorial steps.

schuhmaj commented 6 months ago

@dfm Thanks for the patience - I am ready for the next steps 🙂

The PR https://github.com/esa/polyhedral-gravity-model/pull/36 has been merged, and version v3.0 incorporating all of the JOSS feedback is deployed and installable via PyPi and Conda.

dfm commented 5 months ago

@editorialbot generate pdf

dfm commented 5 months ago

@editorialbot check references

editorialbot commented 5 months ago 
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 commented 5 months ago

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

dfm commented 5 months ago

@mikegrudic, @santisoler — Thanks for your thorough and constructive reviews!!

@schuhmaj — I'm so sorry for the delay on my end now! I've opened a small PR with a minor edit to the manuscript, please take a look and merge or let me know what you think.

Once you've done that:

  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.
dfm commented 5 months ago

@schuhmaj — Checking in here about these last few steps. We're very close to publication!

schuhmaj commented 5 months ago

@schuhmaj — Checking in here about these last few steps. We're very close to publication!

I'm working on it; sorry that it takes so long; we've had some issues with our macOS x86_64 toolchain. However, this is now fixed.

schuhmaj commented 5 months ago

@dfm The final version for the JOSS release is 3.2.0 The source code is published on Zenodo:

Schuhmacher, J., Blazquez, E., Gratl, F., Izzo, D., & Gómez, P. (2024). Efficient Polyhedral Gravity Modeling in Modern C++ and Python (3.2.0). Zenodo. https://doi.org/10.5281/zenodo.11221939

Ready for the next steps 🙂

dfm commented 5 months ago

@editorialbot set 3.2.0 as version

editorialbot commented 5 months ago

Done! version is now 3.2.0

dfm commented 5 months ago

@editorialbot set 10.5281/zenodo.11221939 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.11221939

dfm commented 5 months ago

@editorialbot check references

dfm commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

dfm commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

dfm commented 5 months ago

I'm not sure why this is failing, but we're looking into it and I'll do the final processing ASAP after that's worked out!

dfm commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

danielskatz commented 5 months ago

@editorialbot generate pdf

since this is now working on another repo, after not working there yesterday...

xuanxu commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

danielskatz commented 5 months ago

I'll leave this to @xuanxu :)

editorialbot commented 5 months ago

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

dfm commented 4 months ago

@editorialbot generate pdf

dfm commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago 
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 commented 4 months ago

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

dfm commented 4 months ago

@editorialbot recommend-accept

editorialbot commented 4 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 4 months ago 
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