[REVIEW]: squishyplanet: modeling transits of non-spherical exoplanets in JAX

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@ben-cassese@mbobra<!--end-editor-- Reviewers: @rferrerc, @catrionamurray Archive: 10.5281/zenodo.13377036

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/2b62acea4e4d6c0de73309184861d1e9/status.svg)](https://joss.theoj.org/papers/2b62acea4e4d6c0de73309184861d1e9)

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

@rferrerc & @catrionamurray, 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 @mbobra 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 @catrionamurray

📝 Checklist for @rferrerc

editorialbot commented 1 month 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:

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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 1 month ago

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

OK DOIs

- 10.3847/1538-3881/ab4fee is OK
- 10.1086/345520 is OK
- 10.1086/683602 is OK
- 10.21105/joss.03285 is OK
- 10.5281/zenodo.10736936 is OK
- 10.1051/0004-6361/201628579 is OK
- 10.1038/s41586-022-05677-y is OK
- 10.5281/zenodo.11062823 is OK
- 10.1088/0004-637X/796/1/67 is OK
- 10.3847/1538-3881/aae8e5 is OK
- 10.1086/373893 is OK
- 10.1088/0004-637X/709/2/1219 is OK

MISSING DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

INVALID DOIs

- None

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (680.6 files/s, 182765.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            832           1920           4804
Jupyter Notebook                 7              0           2183           1579
TeX                              1             14              0            206
Markdown                         5             69              0            156
YAML                             5             20             32             93
reStructuredText                 5             84             90             86
TOML                             1              6              0             48
JSON                             1              0              0             46
DOS Batch                        1              8              1             26
INI                              1              4              4             21
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            46           1041           4237           7074
-------------------------------------------------------------------------------

Commit count by author:

    86  Ben-Cassese
     1  Ben Cassese

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1062

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

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:

mbobra commented 1 month ago

👋 @rferrerc @catrionamurray

Thank you so much for agreeing to review! You can find the article in the comment boxe above ⬆️ and the software repository linked in the first comment box on this issue. To generate your checklist, use the following command:

@editorialbot generate my checklist

I think you're good to go. Again, JOSS is an open review process and we encourage communication between the reviewers, the submitting author, and the editor. And please feel free to ask me questions, I'm always around.

Can you please respond here (or give a thumbs up) so I know you're in the right place and found all the materials?

catrionamurray commented 1 month ago

Review checklist for @catrionamurray

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/ben-cassese/squishyplanet?
[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 (@ben-cassese) 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?

rferrerc commented 1 month ago

Review checklist for @rferrerc

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/ben-cassese/squishyplanet?
[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 (@ben-cassese) 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?

rferrerc commented 2 weeks ago

Hi @mbobra , I have finished the review for this submission; the paper, software and documentation all check all the items in the checklist now.

mbobra commented 1 week ago

Hi @mbobra , I have finished the review for this submission; the paper, software and documentation all check all the items in the checklist now.

Thank you for your thorough review, @rferrerc! Your volunteer time keeps JOSS running and I sincerely appreciate it.

mbobra commented 1 week ago

👋 @catrionamurray Do you think the submitting author sufficiently addressed ben-cassese/squishyplanet/issues/11?

catrionamurray commented 1 week ago

@editorialbot generate pdf

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:

catrionamurray commented 1 week ago

I have updated the checklist and posted a small error in the same Github Issue: https://github.com/ben-cassese/squishyplanet/issues/11. However, it's a very small error and once we fix it I am happy that the checklist has been completed.

ben-cassese commented 4 days ago

Hi all! Just wanted to note that I've now resolved that last issue, and with it I think all of @catrionamurray's major concerns. Let me know if that's correct, or if there's anything more I can address. Thanks!

mbobra commented 3 days ago

Congratulations, @ben-cassese -- we're almost ready to publish the paper! Could you please cut a release of squishyplanet (please use whatever versioning system you wish), deposit it in Zenodo, and put the link to the Zenodo deposit in this thread? Please make sure that the author list and title on the Zenodo deposit matches the author list and title on the JOSS paper. Then I can move forward with accepting the paper.

catrionamurray commented 3 days ago

I'm happy it's ready on my side! Thanks for the cool tool @ben-cassese and for your help with the review process!

ben-cassese commented 3 days ago

Thank you so much @catrionamurray and @rferrerc for your reviews! We appreciate all the time you spent helping improve this package.

Thanks to you as well @mbobra! This was a great first experience submitting to JOSS. The deposit is here: https://zenodo.org/records/13377037. Let me know if there's anything else I should provide!

mbobra commented 2 days ago

@editorialbot generate pdf

editorialbot commented 2 days ago

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

mbobra commented 2 days ago

@editorialbot check references

editorialbot commented 2 days ago

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

✅ OK DOIs

- 10.3847/1538-3881/ab4fee is OK
- 10.1086/345520 is OK
- 10.1086/683602 is OK
- 10.21105/joss.03285 is OK
- 10.5281/zenodo.10736936 is OK
- 10.1051/0004-6361/201628579 is OK
- 10.1038/s41586-022-05677-y is OK
- 10.5281/zenodo.11062823 is OK
- 10.1088/0004-637X/796/1/67 is OK
- 10.3847/1538-3881/aae8e5 is OK
- 10.1086/373893 is OK
- 10.1088/0004-637X/709/2/1219 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

mbobra commented 2 days ago

@editorialbot set 10.5281/zenodo.13377036 as archive

editorialbot commented 2 days ago

Done! archive is now 10.5281/zenodo.13377036

mbobra commented 2 days ago

@editorialbot set v0.2.0 as version

editorialbot commented 2 days ago

Done! version is now v0.2.0

mbobra commented 2 days ago

@editorialbot recommend-accept

editorialbot commented 2 days ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 days ago

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

✅ OK DOIs

- 10.3847/1538-3881/ab4fee is OK
- 10.1086/345520 is OK
- 10.1086/683602 is OK
- 10.21105/joss.03285 is OK
- 10.5281/zenodo.10736936 is OK
- 10.1051/0004-6361/201628579 is OK
- 10.1038/s41586-022-05677-y is OK
- 10.5281/zenodo.11062823 is OK
- 10.1088/0004-637X/796/1/67 is OK
- 10.3847/1538-3881/aae8e5 is OK
- 10.1086/373893 is OK
- 10.1088/0004-637X/709/2/1219 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 2 days ago

:wave: @openjournals/aass-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/5820, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

mbobra commented 2 days ago

Thank you both so very much for your thorough reviews, @rferrerc and @catrionamurray! Your volunteer time keeps JOSS running and I sincerely appreciate it ☀️

And thank you for your submission and all the edits, @ben-cassese -- I hope you feel it improved the submission. This is a nice paper!

openjournals / joss-reviews