[REVIEW]: Stingray 2: A fast and modern Python library for spectral timing #7389

editorialbot · 2024-10-21T21:03:15Z

Submitting author: @matteobachetti (Matteo Bachetti)
Repository: https://github.com/stingraysoftware/stingray
Branch with paper.md (empty if default branch): update_joss_paper
Version: v2.2
Editor: @warrickball
Reviewers: @warrickball
Archive: 10.5281/zenodo.1490116

Status

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Markdown: [![status](https://joss.theoj.org/papers/89b3bb065835f94b7945a8ee1f00e059/status.svg)](https://joss.theoj.org/papers/89b3bb065835f94b7945a8ee1f00e059)

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📝 Checklist for @warrickball

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editorialbot · 2024-10-21T21:03:19Z

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 · 2024-10-21T21:03:40Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.30 s (443.1 files/s, 204912.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          89           9711          15953          26967
reStructuredText                22            585            385           1244
Markdown                         6             95              0            373
Jupyter Notebook                 1              0           5087            371
SVG                              1              1              1            364
TeX                              2             27              0            363
YAML                             9             37             45            361
DOS Batch                        1             21              1            148
make                             1             22              5            107
INI                              1             15              0             86
TOML                             1             11              0             42
CSS                              1              1              0              6
-------------------------------------------------------------------------------
SUM:                           135          10526          21477          30432
-------------------------------------------------------------------------------

Commit count by author:

  1752	Matteo Bachetti
   447	Daniela Huppenkothen
   127	Himanshu Mishra
   103	mbachett
    84	John Swinbank
    78	Swapnil Sharma
    68	Usman Mahmood
    65	Haroon Rashid
    63	Abbie Stevens
    60	Usman
    58	Amogh Desai
    48	Gaurav17Joshi
    43	Mihir Tripathi
    33	Gullo
    32	Abigail Stevens
    26	Evandro M. Ribeiro
    26	pupperemeritus
    22	Brigitta Sipocz
    19	Evandro M Ribeiro
    17	Dhruv Vats
    14	Guglielmo Mastroserio
    12	tappina
     8	omargamal8
     7	Megan Davis
     7	Stuart Mumford
     6	Mihir
     6	devanshshukla99
     5	Abhinav Kumar
     5	Achilles Rasquinha
     5	Brigitta Sipőcz
     5	Riccardo Campana
     5	Tomasz Kolek
     5	_youteakay
     5	parkma99
     4	Evandro Martinez Ribeiro
     4	Nitish Garg
     4	da-ta-vinci21
     3	Anurag Hota
     3	Arnav Anand
     3	Nick Gorgone
     3	Rashmi
     3	sandeepkrjha
     3	sashank27
     2	Arfon Smith
     2	Marta
     2	Max M
     2	Saurav Sachidanand
     2	luzpaz
     1	Meg Davis
     1	Ricardo Valles Blanco
     1	Ricardo Vallés Blanco
     1	Sambhav Kothari
     1	Shriharsh Tendulkar
     1	Terrence Wong
     1	Your Name
     1	ajitjjadhav
     1	dependabot[bot]
     1	dhuppenkothen
     1	francescodoan
     1	paopaofi
     1	parulsethi
     1	pupper emeritus

editorialbot · 2024-10-21T21:03:42Z

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

✅ OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1007/978-981-16-4544-0_137-1 is OK
- 10.1093/mnras/stv191 is OK
- 10.3847/1538-4357/ac7959 is OK
- 10.3847/1538-4357/ab258d is OK
- 10.21105/joss.01393 is OK
- 10.1007/BF00648343 is OK
- 10.1086/342285 is OK
- 10.1086/167757 is OK
- 10.1086/156444 is OK
- 10.1007/s00159-014-0072-0 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A Poweful Test for Weak Periodic Signals with Unkn...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-21T21:03:43Z

Paper file info:

📄 Wordcount for paper.md is 1044

✅ The paper includes a Statement of need section

editorialbot · 2024-10-21T21:03:45Z

License info:

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

warrickball · 2024-10-21T21:03:50Z

Review checklist for @warrickball

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/stingraysoftware/stingray?
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 (@matteobachetti) 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?

editorialbot · 2024-10-21T21:04:34Z

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

warrickball · 2024-10-21T21:08:25Z

This submission has already been reviewed by pyOpenSci: pyOpenSci/software-submission#201

warrickball · 2024-10-21T21:10:50Z

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

Read the text of the paper and offer comments/corrections (as either a list or a pull request)
Check that the archive title, author list, version tag, and the license are correct
Set archive DOI with @editorialbot set <DOI here> as archive
Set version with @editorialbot set <version here> as version
Double check rendering of paper with @editorialbot generate pdf
Specifically check the references with @editorialbot check references and ask author(s) to update as needed
Recommend acceptance with @editorialbot recommend-accept

warrickball · 2024-10-21T21:17:10Z

@editorialbot set 10.5281/zenodo.1490116 as archive

editorialbot · 2024-10-21T21:17:15Z

Done! archive is now 10.5281/zenodo.1490116

warrickball · 2024-10-21T21:21:25Z

@editorialbot set v2.1 as version

editorialbot · 2024-10-21T21:21:27Z

Done! version is now v2.1

matteobachetti · 2024-10-21T21:26:25Z

@warrickball please note that the version that received the review is 2.1, but the version including the changes made as part of the pyOpenSci review is 2.2 (which will be released tomorrow).

matteobachetti · 2024-10-22T11:51:15Z

Here is the new release: https://github.com/StingraySoftware/stingray/releases/tag/v2.2

matteobachetti · 2024-10-22T19:25:07Z

And the release on Zenodo: https://zenodo.org/records/13974481
(doi: 10.5281/zenodo.13974481)

warrickball · 2024-10-22T20:29:40Z

@editorialbot set v2.2 as version

editorialbot · 2024-10-22T20:29:42Z

Done! version is now v2.2

warrickball · 2024-10-23T22:07:27Z

I've opened a pull request with some editorial tweaks. Since I'm already thinking in AEiC mode, this should be the only pass, unless I need to fix any metadata that's generated when we do a dry run of the publication process.

I did also notice that the Zenodo archive doesn't include ORCIDs for any of the authors. That isn't a requirement for JOSS publication but you might want to add it. If you publish to Zenodo via GitHub integration, it might automatically pick up ORCIDs for those contributors who've added ORCID information to their GitHub profile.

matteobachetti · 2024-10-24T07:31:59Z

@warrickball I don't know how to pick up the OrcIDs, some people (me included) do have OrcID information on Github, but it wasn't pick up automatically. Is there any other step that needs to be taken?

warrickball · 2024-10-24T07:51:49Z

@warrickball I don't know how to pick up the OrcIDs, some people (me included) do have OrcID information on Github, but it wasn't pick up automatically. Is there any other step that needs to be taken?

Interesting! I don't know the process well but will see if I can find out more. It isn't an issue for the JOSS publication, so I'll advance with that anyway.

warrickball · 2024-10-24T07:52:16Z

@editorialbot recommend-accept

editorialbot · 2024-10-24T07:52:18Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-10-24T07:52:43Z

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

✅ OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1007/978-981-16-4544-0_137-1 is OK
- 10.1093/mnras/stv191 is OK
- 10.3847/1538-4357/ac7959 is OK
- 10.3847/1538-4357/ab258d is OK
- 10.21105/joss.01393 is OK
- 10.1007/BF00648343 is OK
- 10.1086/342285 is OK
- 10.1086/167757 is OK
- 10.1086/156444 is OK
- 10.1007/s00159-014-0072-0 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A Powerful Test for Weak Periodic Signals with Unk...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-24T07:54:08Z

👋 @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6048, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

warrickball · 2024-10-24T22:39:12Z

@editorialbot accept

editorialbot · 2024-10-24T22:39:14Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-10-24T22:46:03Z

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: Bachetti
  given-names: Matteo
  orcid: "https://orcid.org/0000-0002-4576-9337"
- family-names: Huppenkothen
  given-names: Daniela
  orcid: "https://orcid.org/0000-0002-1169-7486"
- family-names: Stevens
  given-names: Abigail
  orcid: "https://orcid.org/0000-0002-5041-3079"
- family-names: Swinbank
  given-names: John
- family-names: Mastroserio
  given-names: Guglielmo
  orcid: "https://orcid.org/0000-0003-4216-7936"
- family-names: Lucchini
  given-names: Matteo
  orcid: "https://orcid.org/0000-0002-2235-3347"
- family-names: Lai
  given-names: Eleonora Veronica
  orcid: "https://orcid.org/0000-0002-6421-2198"
- family-names: Buchner
  given-names: Johannes
  orcid: "https://orcid.org/0000-0003-0426-6634"
- family-names: Desai
  given-names: Amogh
  orcid: "https://orcid.org/0000-0002-6015-9553"
- family-names: Joshi
  given-names: Gaurav
  orcid: "https://orcid.org/0009-0009-2305-5008"
- family-names: Pisanu
  given-names: Francesco
  orcid: "https://orcid.org/0000-0003-0799-5760"
- family-names: Pisupati
  given-names: Sri Guru Datta
  orcid: "https://orcid.org/0009-0006-3745-5553"
- family-names: Sharma
  given-names: Swapnil
- family-names: Tripathi
  given-names: Mihir
  orcid: "https://orcid.org/0009-0007-2723-0315"
- family-names: Vats
  given-names: Dhruv
  orcid: "https://orcid.org/0009-0001-0542-0755"
doi: 10.5281/zenodo.1490116
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bachetti
    given-names: Matteo
    orcid: "https://orcid.org/0000-0002-4576-9337"
  - family-names: Huppenkothen
    given-names: Daniela
    orcid: "https://orcid.org/0000-0002-1169-7486"
  - family-names: Stevens
    given-names: Abigail
    orcid: "https://orcid.org/0000-0002-5041-3079"
  - family-names: Swinbank
    given-names: John
  - family-names: Mastroserio
    given-names: Guglielmo
    orcid: "https://orcid.org/0000-0003-4216-7936"
  - family-names: Lucchini
    given-names: Matteo
    orcid: "https://orcid.org/0000-0002-2235-3347"
  - family-names: Lai
    given-names: Eleonora Veronica
    orcid: "https://orcid.org/0000-0002-6421-2198"
  - family-names: Buchner
    given-names: Johannes
    orcid: "https://orcid.org/0000-0003-0426-6634"
  - family-names: Desai
    given-names: Amogh
    orcid: "https://orcid.org/0000-0002-6015-9553"
  - family-names: Joshi
    given-names: Gaurav
    orcid: "https://orcid.org/0009-0009-2305-5008"
  - family-names: Pisanu
    given-names: Francesco
    orcid: "https://orcid.org/0000-0003-0799-5760"
  - family-names: Pisupati
    given-names: Sri Guru Datta
    orcid: "https://orcid.org/0009-0006-3745-5553"
  - family-names: Sharma
    given-names: Swapnil
  - family-names: Tripathi
    given-names: Mihir
    orcid: "https://orcid.org/0009-0007-2723-0315"
  - family-names: Vats
    given-names: Dhruv
    orcid: "https://orcid.org/0009-0001-0542-0755"
  date-published: 2024-10-24
  doi: 10.21105/joss.07389
  issn: 2475-9066
  issue: 102
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7389
  title: "Stingray 2: A fast and modern Python library for spectral
    timing"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07389"
  volume: 9
title: "Stingray 2: A fast and modern Python library for spectral
  timing"

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.

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editorialbot · 2024-10-24T22:46:07Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-10-24T22:46:08Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2024-10-24T22:46:08Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07389 joss-papers#6056
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07389
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

warrickball · 2024-10-24T22:49:50Z

Congratulations @matteobachetti, your paper has been published in JOSS!

editorialbot · 2024-10-24T22:49:55Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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matteobachetti · 2024-10-25T05:53:04Z

Thank you @warrickball!

editorialbot added review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences labels Oct 21, 2024

editorialbot assigned warrickball Oct 21, 2024

editorialbot mentioned this issue Oct 21, 2024

[PRE REVIEW]: Stingray 2: A fast and modern Python library for spectral timing #7345

Closed

warrickball added the pyOpenSci Submissions associated with pyOpenSci label Oct 21, 2024

warrickball mentioned this issue Oct 23, 2024

JOSS editorial tweaks StingraySoftware/stingray#854

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editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 24, 2024

editorialbot added accepted published Papers published in JOSS labels Oct 24, 2024

warrickball closed this as completed Oct 24, 2024

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[REVIEW]: Stingray 2: A fast and modern Python library for spectral timing #7389

[REVIEW]: Stingray 2: A fast and modern Python library for spectral timing #7389

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[REVIEW]: Stingray 2: A fast and modern Python library for spectral timing #7389

[REVIEW]: Stingray 2: A fast and modern Python library for spectral timing #7389

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Review checklist for @warrickball

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

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