[REVIEW]: Reggae: A Parametric Tuner for PBJam, and a Visualization Tool for Red Giant Oscillation Spectra

[editorialbot]

Submitting author: @darthoctopus (Joel Ong J. M.)
Repository: https://github.com/darthoctopus/reggae
Branch with paper.md (empty if default branch): joss
Version: git
Editor: @dfm
Reviewers: @sybreton, @sblunt
Archive: Pending

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

@sybreton & @sblunt, 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 @dfm 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 @sybreton

📝 Checklist for @sblunt

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (763.7 files/s, 141587.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            850            731           1772
TeX                              1             16              0            253
Markdown                         2             25              0             61
-------------------------------------------------------------------------------
SUM:                            20            891            731           2086
-------------------------------------------------------------------------------

Commit count by author:

    26	Joel Ong

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 960

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/abcd39 is OK
- 10.1051/0004-6361/202346086 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.7215695 is OK
- 10.3847/1538-4357/acbf2f is OK
- 10.1007/s10509-009-0216-2 is OK
- 10.3847/1538-4357/ab9ffb is OK

MISSING DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Modal Analysis of Stellar Nonradial Oscillations b...
- No DOI given, and none found for title: Asteroseismic Signatures of Core Magnetism and Rot...
- No DOI given, and none found for title: Fossil Signatures of Main-sequence Convective Core...
- No DOI given, and none found for title: PBJam 2.0: Mixed Modes are Everywhere, But We’ve G...

INVALID DOIs

- None

[dfm]

@sybreton, @sblunt — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. As you go over the submission, please check any items that you feel have been satisfied. There are also 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#6588 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 the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

[editorialbot]

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

[sybreton]

Review checklist for @sybreton

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/darthoctopus/reggae?
• 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 (@darthoctopus) 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?

[sybreton]

Hi @dfm,

Before we go on, can you formally confirm that the COIs I might have with @darthoctopus have been waived ?
We have been co-authors on the following large collaboration papers:
https://ui.adsabs.harvard.edu/abs/2023AJ....166..167M/abstract
https://ui.adsabs.harvard.edu/abs/2023AJ....165..214C/abstract
https://ui.adsabs.harvard.edu/abs/2022AJ....163...79H/abstract
https://ui.adsabs.harvard.edu/abs/2021AJ....162..211H/abstract
but when he contacted me @warrickball told me that this should not represent an issue.

[dfm]

@sybreton — Many thanks for bringing this up! Like @warrickball says, this type of co-authorship within a large collaboration can typically be waived unless anyone involved in the review has any concerns (please feel free to send me an email or comment here if you have any!). The only comment I would have is that the COI policy should apply to all co-authors of this submission, so if you anticipate any larger conflicts there, please let me know! Thanks again!!

[sybreton]

Thanks for the information !
I went to check the co-author list in order to check possible COI, I hope everything should be fine:
Martin Nielsen is also among the co-authors of one of the paper already mentioned above:
https://ui.adsabs.harvard.edu/abs/2023AJ....166..167M/abstract
Martin Nielsen, Guy Davies and I are members of the PLATO consortium:
https://platomission.com/the-plato-consortium/plato-consortium-members/
Nevertheless, we are not involved on the same PLATO working packages, although I think I should mention that Martin is the author of a few functions that are included in my open source project related to the mission preparation:
https://gitlab.com/sybreton/star_privateer/-/blob/main/src/star_privateer/lomb_scargle.py?ref_type=heads
I have no perceived COI with Emily Hatt.

[dfm]

@sybreton — Thanks for checking this! This all sounds completely fine to me, especially now that you've disclosed this potential COIs. I'm happy to proceed with the review with you as a reviewer. Thanks again!!

[sybreton]

@dfm Perfect, thanks a lot for the check, I will proceed with the review !

[dfm]

@sblunt — Checking in here to make sure that this is on your radar. Please get started with your review ASAP. Thanks!

@sybreton — Also please let me know if there are any blockers on your end.

[sblunt]

Yes, sorry for the delay! I am working on it this week.

[sblunt]

Review checklist for @sblunt

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/darthoctopus/reggae?
• 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 (@darthoctopus) 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?