[REVIEW]: GASTLI: A Python package for coupled interior–atmosphere modelling of volatile-rich planets

editorialbot commented 1 week ago

Submitting author: !--author-handle-->@lorenaacuna@JBorrow<!--end-editor-- Reviewers: @ivalaginja, @MartianColonist Archive: Pending

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Reviewers and authors:

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Reviewer instructions & questions

@ivalaginja & @MartianColonist, 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:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @JBorrow 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 @ivalaginja

📝 Checklist for @MartianColonist

editorialbot commented 1 week ago

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editorialbot commented 1 week ago

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

✅ OK DOIs

- 10.1088/0067-0049/192/1/3 is OK
- 10.1088/0067-0049/208/1/4 is OK
- 10.1088/0067-0049/220/1/15 is OK
- 10.3847/1538-4365/aaa5a8 is OK
- 10.3847/1538-4365/ab2241 is OK
- 10.1093/mnras/stac1133 is OK
- 10.1093/mnras/stab2250 is OK
- 10.3847/0004-637X/831/2/180 is OK
- 10.3390/atmos10110664 is OK
- 10.48550/arXiv.2402.19466 is OK
- 10.1051/0004-6361/201833873 is OK
- 10.1088/0004-637X/792/1/1 is OK
- 10.3847/0004-637X/831/1/64 is OK
- 10.1088/0004-637X/775/2/105 is OK
- 10.1088/0004-637X/813/1/47 is OK
- 10.1051/0004-6361/201629800 is OK
- 10.3847/2041-8205/831/2/L16 is OK
- 10.3847/1538-4357/aa965a is OK
- 10.3847/2041-8213/ab9530 is OK
- 10.3847/1538-4357/abfa99 is OK
- 10.3847/1538-4357/ac66e2 is OK
- 10.1051/0004-6361/202039885 is OK
- 10.1051/0004-6361/202142374 is OK
- 10.1051/0004-6361/202245736 is OK
- 10.1051/0004-6361/202243207 is OK
- 10.1051/0004-6361/201833963 is OK
- 10.3847/1538-4357/abfc48 is OK
- 10.48550/arXiv.2302.07902 is OK
- 10.1051/0004-6361/202038367 is OK
- 10.48550/arXiv.2406.10032 is OK
- 10.1088/0004-637X/775/1/80 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Structure interne et minéralogie des exoplanètes t...
- No DOI given, and none found for title: Sesame: the Los Alamos National Laboratory equatio...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1078.0 files/s, 287482.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 95                      10           1951           1731           3335
Python                          22            779           1038           1627
TeX                              1             36              0            557
reStructuredText                 8            361           1175            207
Meson                            1             43             18            153
Fortran 90                       2             43             18             79
Markdown                         1             18              0             46
YAML                             2              4              4             29
DOS Batch                        1              8              1             26
TOML                             1              2              0             25
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            50           3249           3992           6093
-------------------------------------------------------------------------------

Commit count by author:

   178  lorenaacuna

editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1383

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot commented 1 week ago

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

ivalaginja commented 1 week ago

Review checklist for @ivalaginja

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/lorenaacuna/GASTLI?
[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 (@lorenaacuna) 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
[ ] 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

[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)?
[ ] 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?

MartianColonist commented 1 week ago

Review checklist for @MartianColonist

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/lorenaacuna/GASTLI?
[ ] 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 (@lorenaacuna) 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?

MartianColonist commented 1 week ago

@lorenaacuna, I'm looking forward to reviewing your JOSS manuscript and Python package!

One quick thing: the embedded images aren't showing in the notebooks in the docs (probably because they are PDFs). Can you try converting them to pngs to see if they'll render that way?

ivalaginja commented 5 days ago

@lorenaaacuna, could you elaborate why in the package documentation under https://gastli.readthedocs.io/en/latest/#development, there are six people listed as main developers, while the paper only lists five co-authors? I see that the sixth one is mentioned in the acknowledgments of the paper. How come? This could be totally fine, I am just trying to make sure I understand how the choice was made.

openjournals / joss-reviews