[REVIEW]: Caustics: A Python Package for Accelerated Strong Gravitational Lensing Simulations

[editorialbot]

Submitting author: @ConnorStoneAstro (Connor Stone)
Repository: https://github.com/Ciela-Institute/caustics
Branch with paper.md (empty if default branch): JOSS
Version: v0.10.1
Editor: @ivastar
Reviewers: @andigu, @Jammy2211
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/995fa98462eb534a32952549ef2244f8/status.svg)](https://joss.theoj.org/papers/995fa98462eb534a32952549ef2244f8)

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

@andigu, 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 @ivastar 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 @andigu

📝 Checklist for @Jammy2211

[editorialbot]

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[ivastar]

@editorialbot assing @Jammy2211 as reviewer

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.21105/joss.03283 is OK
- 10.21105/joss.02825 is OK
- 10.3847/1538-4357/ac6de4 is OK
- 10.48550/arXiv.2404.14487 is OK
- 10.1093/mnras/stu1859 is OK
- 10.1051/0004-6361/202039363 is OK
- 10.1051/0004-6361/201015481 is OK
- 10.48550/arXiv.2302.05329 is OK
- 10.1103/PhysRevD.106.122001 is OK
- 10.3847/1538-4357/acf5cd is OK
- 10.1117/1.JATIS.9.2.028007 is OK
- 10.1093/mnras/stad2477 is OK
- 10.1093/mnras/staa1477 is OK
- 10.1093/mnras/stac311 is OK
- 10.3847/1538-4357/ab4c41 is OK
- 10.48550/arXiv.2206.14820 is OK
- 10.48550/arXiv.2010.07032 is OK
- 10.48550/arXiv.2211.04365 is OK
- 10.48550/arXiv.2402.08725 is OK
- 10.1093/mnras/staa278 is OK
- 10.48550/arXiv.1805.07439 is OK
- 10.1093/mnras/stx2052 is OK
- 10.3847/1538-4357/abd62b is OK
- 10.1093/mnras/stz3094 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.48550/arXiv.1701.02434 is OK
- 10.1086/670067 is OK
- 10.1088/1475-7516/2016/11/048 is OK
- 10.1038/nature23463 is OK
- 10.3847/2041-8213/aa9704 is OK
- 10.1093/mnras/stu1284 is OK
- 10.1086/506266 is OK
- 10.48550/arXiv.2211.03812 is OK
- 10.3847/1538-4357/accf84 is OK
- 10.1051/0004-6361/202243054 is OK
- 10.1088/0004-637X/811/1/20 is OK
- 10.1038/s41550-021-01450-9 is OK
- 10.3847/2041-8213/ac9d39 is OK

MISSING DOIs

- No DOI given, and none found for title: LENSTOOL: A Gravitational Lensing Software for Mod...
- No DOI given, and none found for title: GRAVLENS: Computational Methods for Gravitational ...
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Numba: A llvm-based python jit compiler
- No DOI given, and none found for title: Pyro: Deep universal probabilistic programming

INVALID DOIs

- None

[ivastar]

@editorialbot assign @Jammy2211 as reviewer

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (1199.6 files/s, 196687.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          93           3455           5728           7730
Jupyter Notebook                11              0           2181           1379
TeX                              1             46              0            685
Markdown                         9            164              0            655
YAML                            11             69             55            452
reStructuredText                 8             85             27            119
Dockerfile                       2             20             24             75
JSON                             2              4              0             64
TOML                             1              9              1             61
make                             1              4              6              9
Bourne Shell                     2              4              3              5
-------------------------------------------------------------------------------
SUM:                           141           3860           8025          11234
-------------------------------------------------------------------------------

Commit count by author:

   216	Connor Stone
   126	Adam Coogan
    38	AlexandreAdam
    27	Alexandre Adam
    21	Connor Stone, PhD
    20	Don Setiawan
    19	Andreas Filipp
    12	pre-commit-ci[bot]
    10	dependabot[bot]
     8	Cordero Core
     6	mjyb16
     1	Gabriel Missael Barco
     1	Landung 'Don' Setiawan

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 3248

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[ivastar]

@editorialbot add @Jammy2211 as reviewer

[editorialbot]

@Jammy2211 added to the reviewers list!

[ivastar]

@andigu, @Jammy2211 thank you for agreeing to review this submission! Check the comment at the top of this thread for instruction on the review and on the guidelines before you dive in. We are looking for reviews by the end of August/early September. Don't hesitate to contact me if you encounter any issues or have questions.

[andigu]

Review checklist for @andigu

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/Ciela-Institute/caustics?
• 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 (@ConnorStoneAstro) 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?

[ivastar]

@Jammy2211 pinging you about the review. Please let me know if you have any issues. It would be great if you can complete the checklist in the next week or so.

[Jammy2211]

Just finished an MNRAS review today so will look at this this week.

[Jammy2211]

Review checklist for @Jammy2211

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/Ciela-Institute/caustics?
• 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 (@ConnorStoneAstro) 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?

[Jammy2211]

Review complete, put two minor issues up which once complete mean I can recommend for acceptance:

Ciela-Institute/caustics#263
Ciela-Institute/caustics#262

[ivastar]

Thank you @Jammy2211! @ConnorStoneAstro the ball is in your court. Please ping me in this thread when the changes are completed.

[ConnorStoneAstro]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[Jammy2211]

All aspects of my review have been responded to so I recommend for acceptance :)

[ivastar]

@andigu if you are happy with the final submission, can you also recommend acceptance?

[andigu]

Yes, I can recommend for acceptance.