[REVIEW]: The Geodynamic World Builder: A planetary structure creator for the geosciences
editorialbot opened this issue · comments
Submitting author: @MFraters (Menno Fraters)
Repository: https://github.com/GeodynamicWorldBuilder/WorldBuilder/
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @observingClouds
Reviewers: @busstoptaktik, @cpgr
Archive: Pending
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: [](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
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:
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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
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
Paper file info:
📄 Wordcount for paper.md is 1389
✅ The paper includes a Statement of need section
License info:
🟡 License found: GNU Lesser General Public License v2.1 (Check here for OSI approval)
👋🏼 @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.
Review checklist for @cpgr
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/GeodynamicWorldBuilder/WorldBuilder/?
- 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 (@MFraters) 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?
Review checklist for @busstoptaktik
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/GeodynamicWorldBuilder/WorldBuilder/?
- 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 (@MFraters) 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?
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
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.
@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.