Closed editorialbot closed 4 months ago
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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
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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
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SUM: 87 1435 2681 5258
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1026
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
@mikegrudic, @santisoler β This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!
π 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!
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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.
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).
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 π since he suggested the JOSS submission) my major advisor from the ESA side through code reviews and suggestions.
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 . :)
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.
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
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.
@schuhmaj β 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 β Thanks so much for your constructive reviews!!
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 π It got better by a lot!
README.md
and docs
by correcting examples and stating the relevant details more clearly
CONTRIBUTING.md
paper
formulations
requirements
of the jupyter example notebook
ninja-build
density
parameter, which was previously always 1.0
being suboptimal in case of changes
-1.0
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
@schuhmaj β 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.
@dfm Thanks for the patience - I am ready for the next steps π
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.
@editorialbot generate pdf
@editorialbot check references
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@mikegrudic, @santisoler β Thanks for your thorough and constructive reviews!!
@schuhmaj β 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:
@schuhmaj β Checking in here about these last few steps. We're very close to publication!
@schuhmaj β 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.
@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., & GΓ³mez, 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 π
@editorialbot set 3.2.0 as version
Done! version is now 3.2.0
@editorialbot set 10.5281/zenodo.11221939 as archive
Done! archive is now 10.5281/zenodo.11221939
@editorialbot check references
@editorialbot generate pdf
:warning: An error happened when generating the pdf.
@editorialbot generate pdf
:warning: An error happened when generating the pdf.
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!
@editorialbot generate pdf
:warning: An error happened when generating the pdf.
@editorialbot generate pdf
since this is now working on another repo, after not working there yesterday...
@editorialbot generate pdf
:warning: An error happened when generating the pdf.
I'll leave this to @xuanxu :)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
@editorialbot check references
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
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
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 badge code:
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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dfm know.
β¨ 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 β¨
Checklists
π Checklist for @santisoler
π Checklist for @mikegrudic