[REVIEW]: RydIQule Version 2: Enhancing graph-based modeling of Rydberg atoms

[editorialbot]

Submitting author: @dihm (David H Meyer)
Repository: https://github.com/QTC-UMD/rydiqule
Branch with paper.md (empty if default branch): joss
Version: v2.1.2
Editor: @phibeck
Reviewers: @a-eghrari, @nikolasibalic
Archive: 10.5281/zenodo.18341352

Status

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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

@acrlakshman & @a-eghrari, 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/pre-2026-submission/reviewer_guidelines.html. Any questions/concerns please let @phibeck 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 @acrlakshman

📝 Checklist for @a-eghrari

📝 Checklist for @nikolasibalic

[editorialbot]

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]

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

✅ OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.cpc.2012.11.019 is OK
- 10.1016/j.cpc.2017.12.001 is OK
- 10.48550/arXiv.2011.07979 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.7093266 is OK
- 10.48550/arXiv.2501.06134 is OK
- 10.1063/1.5115323 is OK
- 10.1016/j.cpc.2017.06.015 is OK
- 10.1016/j.cpc.2020.107814 is OK
- 10.1088/1361-6455/aa743a is OK
- 10.1016/j.cpc.2023.108952 is OK
- 10.1088/1361-6455/ab52ef is OK
- 10.1038/s42254-024-00756-7 is OK
- 10.1109/TQE.2021.3065227 is OK
- 10.1103/PhysRevA.109.L021702 is OK
- 10.1063/5.0158150 is OK
- 10.1063/5.0222827 is OK
- 10.1364/opticaopen.27941730.v1 is OK
- 10.36227/techrxiv.24236953.v1 is OK
- 10.48550/arXiv.2404.17962 is OK
- 10.48550/arXiv.2209.00908 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: AtomicDensityMatrix
- No DOI given, and none found for title: Realizing Quantum Wireless Sensing Without Extra R...
- No DOI given, and none found for title: Warm Vapor Rydberg EIT spectra in Doppler-free con...

❌ MISSING DOIs

- 10.25080/tcwv9851 may be a valid DOI for title: Exploring Network Structure, Dynamics, and Functio...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.12 s (702.8 files/s, 238006.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40           2711           6201           4925
Jupyter Notebook                12              0           9616           1606
reStructuredText                20            702            563           1363
SVG                              2              0              0            430
TeX                              1             30              0            371
Markdown                         3             59              4            301
YAML                             4             46             13            281
TOML                             1             18              4            148
DOS Batch                        1              9              1             33
make                             1              5              7             14
Bourne Shell                     1              0              0              2
Text                             1              0              0              2
-------------------------------------------------------------------------------
SUM:                            87           3580          16409           9476
-------------------------------------------------------------------------------

Commit count by author:

    87	David Meyer
    27	Carter Montag
     6	Ben Miller
     3	OmarNagib
     1	Kevin Cox

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1529

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

[a-eghrari]

Review checklist for @a-eghrari

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/QTC-UMD/rydiqule?
• 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 (@dihm) 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?

[phibeck]

@a-eghrari, @acrlakshman thanks again for reviewing! Just checking in on your review. Please let me know if you have any questions about the process. Feel free to create issues in project repository directly or write them down as comments here, but please do link the issues in this review so it's easy to follow for everyone.

@acrlakshman please create your checklist first using the command @editorialbot generate my checklist.

[acrlakshman]

Review checklist for @acrlakshman

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/QTC-UMD/rydiqule?
• 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 (@dihm) 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?

[phibeck]

👋 Hi @a-eghrari and @acrlakshman, just sending a quick reminder in case you find time in the following days to take another look at the package, and to let me know if any questions came up in the meantime. Thanks!

[acrlakshman]

👋 Hi @a-eghrari and @acrlakshman, just sending a quick reminder in case you find time in the following days to take another look at the package, and to let me know if any questions came up in the meantime. Thanks!

Yes, I will be doing my review next week and submitting it.