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[REVIEW]: The Geodynamic World Builder: A planetary structure creator for the geosciences #6671

Closed editorialbot closed 2 weeks ago

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@mfraters<!--end-author-handle-- (Menno Fraters) Repository: https://github.com/GeodynamicWorldBuilder/WorldBuilder/ Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@observingClouds<!--end-editor-- Reviewers: @busstoptaktik, @cpgr Archive: 10.5281/zenodo.13352667

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c7a291efd5527aca16fd4e9f660fd778"><img src="https://joss.theoj.org/papers/c7a291efd5527aca16fd4e9f660fd778/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c7a291efd5527aca16fd4e9f660fd778/status.svg)](https://joss.theoj.org/papers/c7a291efd5527aca16fd4e9f660fd778)

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

@busstoptaktik & @cpgr, 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 @cpgr

📝 Checklist for @busstoptaktik

editorialbot commented 4 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 4 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5194/se-10-1785-2019 is OK
- 10.1029/2018GC008057 is OK
- 10.1029/2021GC010265 is OK
- 10.21105/joss.01136 is OK
- 10.1007/s00024-002-8738-3 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.5194/gmd-14-3899-2021 is OK
- 10.1016/0040-1951(70)90115-0 is OK
- 10.5281/zenodo.10680530 is OK
- 10.1016/j.epsl.2023.118471 is OK
- 10.1093/gji/ggad230 is OK
- 10.3389/feart.2023.995041 is OK
- 10.1029/2022JB025877 is OK

MISSING DOIs

- No DOI given, and none found for title: A New Method for Assigning Thermal Structure to 2D...

INVALID DOIs

- None
editorialbot commented 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.41 s (1127.0 files/s, 353680.1 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
C/C++ Header                       157           8445          10371          39010
Markdown                           117           9746              0          29026
C++                                117           5264           4274          21735
JSON                                 8              7              0          11201
CMake                               15            280            177           1579
SVG                                  8              8              8           1356
YAML                                 9            189             35           1029
XML                                 15              0              0            812
TeX                                  2             26              3            332
Fortran 90                           4             32             78            119
Python                               5             52             62            107
C                                    3             22              4             77
TOML                                 1              7              4             35
Bourne Again Shell                   1              9              9             34
Windows Resource File                1              8              0             26
SWIG                                 1              0              0             11
-----------------------------------------------------------------------------------
SUM:                               464          24095          15025         106489
-----------------------------------------------------------------------------------

Commit count by author:

   642  MFraters
   525  Menno Fraters
    42  Rene Gassmoeller
    38  Juliane Dannberg
    38  Lorraine Hwang
    35  Timo Heister
    30  Magali Billen
    29  Wolfgang Bangerth
    24  danieldouglas92
    18  Arushi Saxena
     9  Wang-yijun
     8  Haoyuan Li
     6  asaxena
     6  cmills1095
     5  ljhwang
     4  lhy11009
     2  Yijun Wang
     1  Arushi
     1  cedrict
     1  kristofporkolab
editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 1389

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago

License info:

🟡 License found: GNU Lesser General Public License v2.1 (Check here for OSI approval)

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:

observingClouds commented 4 months ago

👋🏼 @MFraters @busstoptaktik, @cpgr this is the review thread for the paper. All of our communications will happen here from now on.

@busstoptaktik, @cpgr thank you for agreeing to review this submission.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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#6671 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@observingClouds) if you have any questions/concerns.

cpgr commented 4 months ago

Review checklist for @cpgr

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

busstoptaktik commented 4 months ago

Review checklist for @busstoptaktik

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

observingClouds commented 4 months ago

Dear @busstoptaktik, Dear @cpgr,

I just want to quickly check in how the review is moving along. I see that you both successfully created the reviewer checklist and checked the first items. Great! We aim to finish the review within 4 weeks, so please let me know if you have any questions.

Cheers

busstoptaktik commented 4 months ago

I have serious trouble compiling the software (using cmake, ninja, and a recent gcc), so comparing the paper and the actual software has proven tricky. Will submit an issue to the software repo, but busy the next 5 days, so that will be next week.

MFraters commented 4 months ago

@busstoptaktik, I am sorry to hear that you have issues with compiling the code. If you would be able post your operating system and your gcc version (and cmake and ninja versions if not too much trouble) before that time I can try to reproduce the issue based on that in the meantime. If not, I of course completely understand and then I am looking forward to your issue in the software repository next week.

busstoptaktik commented 2 months ago

Everything seems fine, although I have still not been able to compile the material on (Windows 10, gcc 14.1, cmake 3.24.3, ninja 1.11.1). I have, however, no reason to believe this is due to anything but a local glitch, so with this caveat, I have checked off the tick boxes in the "Functionality" section as well

cpgr commented 2 months ago

Just confirming that I was able to build this project (OSX), and could reproduce the example in the paper, as well as run all of the tutorials

observingClouds commented 2 months ago

@busstoptaktik, @cpgr thank you very much for your review. Do you have any issues that need to be addressed before acceptance? I could not find any PRs or issues in the code repository created during this review process. I might have missed them though. Please link any potential issues, PRs here, by mentioning this page in the respective issue.

Thanks!

observingClouds commented 2 months ago

@busstoptaktik, coming back to your initial issues with the compilation, has this been resolved by you switching to a different machine or has there been some fixes being made? I would just like to get a feeling whether the compilation issue is across a broad range of platforms or if it was rather due to a potential "glitch" on one of your machines.

Thanks!

busstoptaktik commented 1 month ago

I would just like to get a feeling whether the compilation issue is across a broad range of platforms or if it was rather due to a potential "glitch" on one of your machines.

As noted by @MFraters here, this is a general limitation regarding compilation on the Windows platform, where only MSVC is supported, which is unfortunate, but not a show-stopper

observingClouds commented 1 month ago

@busstoptaktik thank you for the additional comments and evaluation. As this only effects the windows platform I'm happy to move on with the submission, close the review process and work with @MFraters through the post-review steps before accepting the submission for publication.

@busstoptaktik, @cpgr thank you very much for your time and effort. We appreciate it!

observingClouds commented 1 month ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

observingClouds commented 1 month ago

@MFraters could you please have a look at the above author tasks and post the information here so I can then recommend the paper for acceptance?

observingClouds commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5194/se-10-1785-2019 is OK
- 10.1029/2018GC008057 is OK
- 10.1029/2021GC010265 is OK
- 10.21105/joss.01136 is OK
- 10.1007/s00024-002-8738-3 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.5194/gmd-14-3899-2021 is OK
- 10.1016/0040-1951(70)90115-0 is OK
- 10.5281/zenodo.10680530 is OK
- 10.1016/j.epsl.2023.118471 is OK
- 10.1093/gji/ggad230 is OK
- 10.3389/feart.2023.995041 is OK
- 10.1029/2022JB025877 is OK

MISSING DOIs

- No DOI given, and none found for title: A New Method for Assigning Thermal Structure to 2D...

INVALID DOIs

- None
observingClouds commented 1 month ago

@MFraters could you check above's missing DOI? You mentioned in https://github.com/openjournals/joss-reviews/issues/6470#issuecomment-1998062987 that you would now be able to update the AGU poster reference.

observingClouds commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

observingClouds commented 1 month ago

@MFraters reading through the paper I have a few more comments:

MFraters commented 1 month ago

Thanks @busstoptaktik and @cpgr for your review and finding the issue with mingw builds, and of course thanks @observingClouds for your work and your further comments! I will go through the issues in the next few days. It will take me a bit to make the new release (as mentioned in your post-review checklist) since it requires carefully going through some steps.

@MFraters could you check above's missing DOI? You mentioned in #6470 (comment) that you would now be able to update the AGU poster reference.

Unfortunately the paper is not yet submitted. How do you want pro procede with this? The abstract can be found here: https://agu.confex.com/agu/fm23/meetingapp.cgi/Paper/1363473, but doesn't have a doi.

@MFraters reading through the paper I have a few more comments:

* could you please ensure that the capitalization of the references in the bibliography is preserved (Double `{{ }}` in paper.bib usually work)

* could you please change the referencing style of some references in parenthesis following https://mystmd.org/guide/citations#table-pandoc-citations; so that e.g. `(Saxena et al. (2023), Gea et al. (2023), Sandiford & Craig (2023),46 and van der Wiel et al. (2024))` is more similar to `(Saxena et al., 2023; Gea et al., 2023; Sandiford & Craig, 2023 and van der Wiel et al., 2024)`
  Thank you!

Yes, I will address there, thanks!

observingClouds commented 1 month ago

Unfortunately the paper is not yet submitted. How do you want pro procede with this? The abstract can be found here: https://agu.confex.com/agu/fm23/meetingapp.cgi/Paper/1363473, but doesn't have a doi.

It's okay if we just use the URL. We prefer of course DOIs but if there is none, we can use the url.

MFraters commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

MFraters commented 1 month ago

@observingClouds I have addressed the comments about the paper. I am now working on getting the release out, but that may take a bit because I usually also confirm that the release is ready to merge in the projects that include it (In this case just ASPECT).

For the release it would be nice if I could already point to to this paper for people to cite. Is it possible to already get a doi reserved for the paper so that I can include it in the release?

observingClouds commented 1 month ago

The DOI will be https://doi.org/10.21105/joss.06671. It won't be registered after publication though.

MFraters commented 1 month ago

Thanks! It will use that in the release then. I don't think it will be a problem that it isn't registered yet, as long as it is reserved.

MFraters commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

MFraters commented 3 weeks ago

@observingClouds All your comments have been addressed and a release for version 1.0.0 has been made: https://github.com/GeodynamicWorldBuilder/WorldBuilder/releases/tag/v1.0.0

observingClouds commented 3 weeks ago

@editorialbot set v1.0.0 as version

editorialbot commented 3 weeks ago

Done! version is now v1.0.0

observingClouds commented 3 weeks ago

@editorialbot set 10.5281/zenodo.13352667 as archive

editorialbot commented 3 weeks ago

Done! archive is now 10.5281/zenodo.13352667

observingClouds commented 3 weeks ago

@MFraters thanks for the update and release of version 1.0.0. Looking at the archive at 10.5281/zenodo.13352667 I have three comment/questions:

Thank you!

MFraters commented 3 weeks ago

Thanks for the quick reply! 

* JOSS prefers if the archive title matches the manuscript title. Could you edit the metadata of the release and adapt the title?

Done

* The list of authors of the archive does not match the authors of the manuscript. Could you add everyone to the release or explain why the co-authors are not included?

Done

* the version of the archive seems off in some places. Instead of `v1.0.0` it is `v6`. Please fix this inconsistency.

Thanks for catching this. I forgot to set the version field. Fixed it.

observingClouds commented 3 weeks ago

@editorialbot check references

editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.5194/se-10-1785-2019 is OK
- 10.1029/2018GC008057 is OK
- 10.1029/2021GC010265 is OK
- 10.21105/joss.01136 is OK
- 10.1007/s00024-002-8738-3 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.5194/gmd-14-3899-2021 is OK
- 10.1016/0040-1951(70)90115-0 is OK
- 10.5281/zenodo.10680530 is OK
- 10.1016/j.epsl.2023.118471 is OK
- 10.1093/gji/ggad230 is OK
- 10.3389/feart.2023.995041 is OK
- 10.1029/2022JB025877 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A New Method for Assigning Thermal Structure to 2D...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
observingClouds commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

observingClouds commented 3 weeks ago

@editorialbot recommend-accept

editorialbot commented 3 weeks ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.5194/se-10-1785-2019 is OK
- 10.1029/2018GC008057 is OK
- 10.1029/2021GC010265 is OK
- 10.21105/joss.01136 is OK
- 10.1007/s00024-002-8738-3 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.5194/gmd-14-3899-2021 is OK
- 10.1016/0040-1951(70)90115-0 is OK
- 10.5281/zenodo.10680530 is OK
- 10.1016/j.epsl.2023.118471 is OK
- 10.1093/gji/ggad230 is OK
- 10.3389/feart.2023.995041 is OK
- 10.1029/2022JB025877 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A New Method for Assigning Thermal Structure to 2D...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 3 weeks ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5831, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept