[REVIEW]: GeophysicalModelGenerator.jl: A Julia package to visualise geoscientific data and create numerical model setups

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@boriskaus@rwegener2<!--end-editor-- Reviewers: @anowacki, @AnantHariharan1996 Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/55e0a26869bba1d825de1088b75996a4"><img src="https://joss.theoj.org/papers/55e0a26869bba1d825de1088b75996a4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/55e0a26869bba1d825de1088b75996a4/status.svg)](https://joss.theoj.org/papers/55e0a26869bba1d825de1088b75996a4)

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

@anowacki & @AnantHariharan1996, 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 @rwegener2 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 @AnantHariharan1996

📝 Checklist for @anowacki

editorialbot commented 3 months ago

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For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.11 s (1141.6 files/s, 173965.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           58           2613           3803           6351
Markdown                        46           1096              0           3825
SVG                              2              0              0            302
YAML                             9             14             12            209
Lisp                             1             23              0            119
TeX                              1             16              0             94
TOML                             3              8              0             76
CSV                              1              1              0             18
XML                              1              0              0             12
-------------------------------------------------------------------------------
SUM:                           122           3771           3815          11006
-------------------------------------------------------------------------------

Commit count by author:

   592  Boris Kaus
    62  mthielma
    59  Marcel Thielmann
    35  Pascal Aellig
    25  Arne_Spang
    21  Luca De Siena
    19  ChristianSchuler
    16  ArneSpang
    14  APiccolo89
    13  LukasFuchs
    11  TatjanaWeiler
     7  Albert de Montserrat
     5  Hendrik Ranocha
     5  dependabot[bot]
     1  Arne Spang
     1  jfrasunk
     1  nicolasriel

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2219

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 months ago

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

OK DOIs

- 10.5194/se-10-1785-2019 is OK
- 10.1029/2019GC008515 is OK
- 10.5194/gmd-12-1-2019 is OK
- 10.5194/se-12-2671-2021 is OK
- 10.1029/2023GC011356 is OK
- 10.1029/2021JB023488 is OK
- 10.51363/unifr.sth.2022.001 is OK
- 10.1111/j.1365-246X.1969.tb00259.x is OK
- 10.1137/141000671 is OK
- 10.1029/2023GL104895 is OK
- 10.1029/2023GL103132 is OK
- 2128/9842 is OK
- 10.1038/s41598-023-47104-w is OK
- 10.1029/2018GC008057 is OK
- 10.1038/s41598-017-11039-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

rwegener2 commented 3 months ago

👋🏼 @boriskaus @anowacki @AnantHariharan1996 this is the review thread for the paper. All of our communications will happen here from now on.

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#REVIEW_NUMBER 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 (@rwegener2) if you have any questions/concerns.

AnantHariharan1996 commented 3 months ago

Review checklist for @AnantHariharan1996

Conflict of interest

[x] 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

[x] 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/JuliaGeodynamics/GeophysicalModelGenerator.jl?
[ ] 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 (@boriskaus) 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.
[x] 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?

editorialbot commented 3 months ago

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

rwegener2 commented 3 months ago

Hi @anowacki anything questions getting started with your review? The first step is to run @editorialbot generate my checklist to generate your checklist, then follow steps listed in the comment that gets automatically generated. Feel free to ping me if anything isn't clear!

anowacki commented 2 months ago

Review checklist for @anowacki

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@boriskaus) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

anowacki commented 2 months ago

@rwegener2 Apologies—I hadn't realised that I needed to run things to ggenerate the checklist. I will get on with this now.

anowacki commented 2 months ago

@rwegener2 I have finished my review and have no comments or issues that need to be addressed before acceptance. Thanks for your contribution to the community, @boriskaus!

rwegener2 commented 2 months ago

Thanks @anowacki!

@AnantHariharan1996 how are things going for you? If you have any questions please don't hesitate to ask!

rwegener2 commented 1 month ago

Hi @AnantHariharan1996 👋🏻 Just checking in. How is the review going?

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