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[REVIEW]: Reggae: A Parametric Tuner for PBJam, and a Visualization Tool for Red Giant Oscillation Spectra #6588

Closed editorialbot closed 2 months ago

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@darthoctopus<!--end-author-handle-- (Joel Ong J. M.) Repository: https://github.com/darthoctopus/reggae Branch with paper.md (empty if default branch): joss Version: 0.1.0 Editor: !--editor-->@dfm<!--end-editor-- Reviewers: @sybreton, @sblunt Archive: 10.5281/zenodo.12730547

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status

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Markdown: [![status](https://joss.theoj.org/papers/e6adb7a3b7cabe398f6c23297da1d3b3/status.svg)](https://joss.theoj.org/papers/e6adb7a3b7cabe398f6c23297da1d3b3)

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 commented 6 months 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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 6 months ago

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 commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 960

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

🔴 Failed to discover a valid open source license

editorialbot commented 6 months ago 
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 commented 6 months ago

@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 commented 6 months ago

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

sybreton commented 6 months ago

Review checklist for @sybreton

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

sybreton commented 6 months ago

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 commented 6 months ago

@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 commented 5 months ago

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 commented 5 months ago

@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 commented 5 months ago

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

dfm commented 5 months ago

@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 commented 5 months ago

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

sblunt commented 4 months ago

Review checklist for @sblunt

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

dfm commented 4 months ago

@sybreton, @sblunt, @darthoctopus — I'm just stopping by to check in on how this review is going. Please let me know if there's anything I can do to help get this over the line ASAP!

sblunt commented 3 months ago

Sorry for the holdup. I've been having a lot of trouble getting the code installed, and I'm trying to figure out if it's an issue with my machine. Will send more updates soon!

sybreton commented 3 months ago

@dfm - Sorry I have been wanting to answer you for a few day already ! No particular issues to mention on my side, once @darthoctopus will have added the few items I required for the documentation (https://github.com/darthoctopus/reggae/issues/9#issuecomment-2135446923) I should be able to tick the missing boxes for this part. I started reading the software paper and it is already in a very good state, so things should go smoothly on this side too.

dfm commented 3 months ago

@sblunt, @sybreton — Thanks for your work on this so far!!

@darthoctopus — It looks to me like the ball is in your court to respond to the issues the reviewers have opened. Can you update this thread and let us know what your ETA is? Thanks!

darthoctopus commented 3 months ago

Hi all,

Apologies for the delay. Working my way through these issues now — I should have responses ready to the currently open issues by the end of the week.

darthoctopus commented 3 months ago

thanks all for your patience — we've responded (hopefully adequately) to all open issues

sblunt commented 3 months ago

I'm very happy with the state of the code, documentation, and paper after the most recent round of comments!

sybreton commented 2 months ago

On my side I validated all the items of the checklist and I am also completely satisfied with the additions that have been made!

darthoctopus commented 2 months ago

hi @dfm , could you please advise on the next steps in the review process?

darthoctopus commented 2 months ago

@editorialbot set 10.5281/zenodo.12730547 as archive

editorialbot commented 2 months ago

I'm sorry @darthoctopus, I'm afraid I can't do that. That's something only editors are allowed to do.

dfm commented 2 months ago

@editorialbot generate pdf

dfm commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago 
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/ac97e7 is OK
- 10.3847/1538-4357/acbf2f is OK
- 10.1007/s10509-009-0216-2 is OK
- 10.3847/1538-4357/ab9ffb is OK
- 10.3847/1538-4357/ad2ae5 is OK
- 10.48550/arXiv.2406.05447 is OK
- 10.1051/0004-6361/201832822 is OK
- 10.1007/978-1-4020-5803-5 is OK
- 10.1051/0004-6361/201118519 is OK
- 10.1007/s41116-019-0020-1 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: PBJam 2.0: Mixed Modes are Everywhere, But We’ve G...

INVALID DOIs

- None
editorialbot commented 2 months ago

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

dfm commented 2 months ago

@sybreton, @sblunt — Thanks for your thorough and constructive reviews!!

@darthoctopus — I've opened a small PR with some minor edits to the manuscript, please take a look and merge or let me know what you think.

Once you've done that:

  1. Take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
  2. Increment the version number of the software and report that version number back here.
  3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.
darthoctopus commented 2 months ago

Hi Dan,

I've had a look at the merge request and it looks reasonable — the backslash before the closing quote was needed to get inara to compile a pdf on my work machine, but it compiles now on my laptop without it. Thanks for helping us with the references — I must confess to not having noticed them missing before. I have merged it now.

I have incremented the version number from 0.0.1 to 0.1.0, and deposited the repository on Zenodo; the DOI is 10.5281/zenodo.12730547 .

darthoctopus commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

dfm commented 2 months ago

@darthoctopus — Thanks. One last edit that I missed: can you add the # References section heading back to the bottom of the manuscript?

Also: please update the Zenodo metadata to have the same title as the manuscript.

darthoctopus commented 2 months ago

Hi Dan,

Sure, I have just now made both of these changes (sorry for the delay)

dfm commented 2 months ago

@editorialbot set 10.5281/zenodo.12730547 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.12730547

dfm commented 2 months ago

@editorialbot set 0.1.0 as version

editorialbot commented 2 months ago

Done! version is now 0.1.0

dfm commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 2 months ago 
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/ac97e7 is OK
- 10.3847/1538-4357/acbf2f is OK
- 10.1007/s10509-009-0216-2 is OK
- 10.3847/1538-4357/ab9ffb is OK
- 10.3847/1538-4357/ad2ae5 is OK
- 10.48550/arXiv.2406.05447 is OK
- 10.1051/0004-6361/201832822 is OK
- 10.1007/978-1-4020-5803-5 is OK
- 10.1051/0004-6361/201118519 is OK
- 10.1007/s41116-019-0020-1 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: PBJam 2.0: Mixed Modes are Everywhere, But We’ve G...

INVALID DOIs

- None
editorialbot commented 2 months 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/5616, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm commented 2 months ago

@editorialbot accept

editorialbot commented 2 months ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 2 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Ong given-names: J. M. Joel orcid: "https://orcid.org/0000-0001-7664-648X" - family-names: Nielsen given-names: Martin B. orcid: "https://orcid.org/0000-0001-9169-2599" - family-names: Hatt given-names: Emily J. orcid: "https://orcid.org/0000-0002-1389-1549" - family-names: Davies given-names: Guy R. orcid: "https://orcid.org/0000-0002-4290-7351" contact: - family-names: Ong given-names: J. M. Joel orcid: "https://orcid.org/0000-0001-7664-648X" doi: 10.5281/zenodo.12730547 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Ong given-names: J. M. Joel orcid: "https://orcid.org/0000-0001-7664-648X" - family-names: Nielsen given-names: Martin B. orcid: "https://orcid.org/0000-0001-9169-2599" - family-names: Hatt given-names: Emily J. orcid: "https://orcid.org/0000-0002-1389-1549" - family-names: Davies given-names: Guy R. orcid: "https://orcid.org/0000-0002-4290-7351" date-published: 2024-07-13 doi: 10.21105/joss.06588 issn: 2475-9066 issue: 99 journal: Journal of Open Source Software publisher: name: Open Journals start: 6588 title: "Reggae: A Parametric Tuner for PBJam, and a Visualization Tool for Red Giant Oscillation Spectra" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06588" volume: 9 title: "Reggae: A Parametric Tuner for PBJam, and a Visualization Tool for Red Giant Oscillation Spectra" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 2 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 2 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5617
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06588
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

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