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

[editorialbot]

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

Status badge code:

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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

@warrickball, 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 @warrickball 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 @warrickball

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

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]

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]

Paper file info:

📄 Wordcount for paper.md is 1044

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[warrickball]

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]

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

[warrickball]

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

[warrickball]

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]

@editorialbot set 10.5281/zenodo.1490116 as archive