[PRE 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: 2.1
Editor: Pending
Reviewers: Pending
Managing EiC: Warrick Ball

Status

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[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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.31 s (438.4 files/s, 202707.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          89           9711          15953          26967
reStructuredText                22            585            385           1244
Jupyter Notebook                 1              0           5087            371
Markdown                         6             92              0            364
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          10523          21477          30423
-------------------------------------------------------------------------------

Commit count by author:

  1741	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]

Paper file info:

📄 Wordcount for paper.md is 1205

🔴 Failed to discover a Statement of need section in paper

[editorialbot]

License info:

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

[editorialbot]

⚠️ An error happened when generating the pdf. Problem with affiliations for John Swinbank, perhaps the affiliations index need quoting?.

[warrickball]

Hi @matteobachetti, and thanks for your submission. I noticed that this submission is for Stingray v2 and Stingray v1 was previously published as a joint publication with AAS Journals. Is this submission also a joint submission with AAS Journals?

Also, for the sake of whichever editor and reviewers handle this, are there specific parts of the package that are new and warrant review, or has enough changed that it's worth treating this as a fresh review anyway?

I think the error in the paper is that John Swinbank has affiliation number 4 but no such affiliation is given. (The list skips from 3 to 5.)

Note also that we require a statement of need, and that the paper is currently a bit longer than our stated maximum of 1000 words (though not by much). If you could squeeze it down, that'll be great.

Our editors are all operating at capacity so I'm going to waitlist this submission but hopefully one will be available by the time you've addressed these initial points.

[matteobachetti]

@warrickball thanks! First of all, let me apologize for not specifying that the paper already went through pyOpenSci review here: pyOpenSci/software-submission#201 (at pyOpenSci the editors told us not to forget this, but of course I did).

There is no publication with AAS planned for now, this paper was really meant to give an update on the work we've been doing on the code since 2019, in connection with the pyOpenSci review.

[arfon]

@matteobachetti – it would be useful to have an explicit diff here that clearly demonstrates the code changes between v1 and v2 of this library.

@warrickball – assuming the scale/scope of the changes between v1 and v2 meet out 'substantial scholarly effort' criterion, we can proceed here without additional review (see https://joss.readthedocs.io/en/latest/editing.html#ropensci-reviewed-or-pyopensci-reviewed-and-accepted-submissions)

[matteobachetti]

@arfon, the first paper was in 2019, so basically everything you see in this changelog from 2020 on (from v.0.2 on!) was not in the first paper:
https://docs.stingray.science/en/stable/history.html

[matteobachetti]

In any case, thanks for the feedback! If you agree that the changes in the code are sufficient to justify a new paper, I can start working on the issues raised above from Tuesday on (upcoming proposal deadline! 😅)