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

Closed editorialbot closed 1 day ago

editorialbot commented 1 week ago

Submitting author: !--author-handle-->@matteobachetti<!--end-author-handle-- (Matteo Bachetti) Repository: https://github.com/stingraysoftware/stingray Branch with paper.md (empty if default branch): update_joss_paper Version: 2.1 Editor: !--editor-->@warrickball<!--end-editor-- Reviewers: !--reviewers-list-->@warrickball<!--end-reviewers-list-- Managing EiC: Warrick Ball

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/89b3bb065835f94b7945a8ee1f00e059"><img src="https://joss.theoj.org/papers/89b3bb065835f94b7945a8ee1f00e059/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/89b3bb065835f94b7945a8ee1f00e059/status.svg)](https://joss.theoj.org/papers/89b3bb065835f94b7945a8ee1f00e059)

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editorialbot commented 1 week ago

Hello human, 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 commented 1 week ago 
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 commented 1 week ago

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 commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1205

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 1 week ago

License info:

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

editorialbot commented 1 week ago

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

warrickball commented 1 week ago

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 commented 1 week ago

@warrickball thanks! First of all, let me apologize for not specifying that the paper already went through pyOpenSci review here: https://github.com/pyOpenSci/software-submission/issues/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 commented 1 week ago

@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 commented 1 week ago

@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 commented 1 week ago

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! 😅)

matteobachetti commented 1 week ago

@editorialbot commands

editorialbot commented 1 week ago

Hello @matteobachetti, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

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@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
matteobachetti commented 1 week ago

@editorialbot check repository @editorialbot generate pdf

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.31 s (438.4 files/s, 202773.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          89           9711          15953          26967
reStructuredText                22            585            385           1244
Markdown                         6             92              0            379
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          10523          21477          30438
-------------------------------------------------------------------------------

Commit count by author:

  1743  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 commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1258

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

matteobachetti commented 1 week ago

@editorialbot check repository

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.32 s (428.3 files/s, 198066.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          89           9711          15953          26967
reStructuredText                22            585            385           1244
Markdown                         6             92              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          10523          21477          30432
-------------------------------------------------------------------------------

Commit count by author:

  1744  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 commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1156

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

matteobachetti commented 1 week ago

@editorialbot check repository

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.31 s (430.4 files/s, 199019.4 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             93              0            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          10524          21477          30430
-------------------------------------------------------------------------------

Commit count by author:

  1745  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 commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1108

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

matteobachetti commented 1 week ago

@editorialbot check repository

matteobachetti commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.32 s (423.5 files/s, 195854.2 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:

  1747  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 commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1042

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

editorialbot commented 1 week ago

:warning: An error happened when generating the pdf.

matteobachetti commented 1 week ago

@warrickball I still have a few words to cut (and if you ask how many, it's 42, Douglas Adams would be proud). However, I get an error from the pdf generation which I don't understand: 

/opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych/parser.rb:62:in `_native_parse': (tmp/89fbb0b4faffadd5c23d73ca35df12df/joss/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError)
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych/parser.rb:62:in `parse'
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych.rb:455:in `parse_stream'
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych.rb:399:in `parse'
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych.rb:323:in `safe_load'
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych.rb:369:in `load'
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych.rb:671:in `block in load_file'
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych.rb:670:in `open'
    from /opt/hostedtoolcache/Ruby/3.3.4/x64/lib/ruby/3.3.0/psych.rb:670:in `load_file'
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.3.0/gems/theoj-1.10.0/lib/theoj/paper.rb:113:in `load_metadata'
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.3.0/gems/theoj-1.10.0/lib/theoj/paper.rb:20:in `initialize'
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.3.0/gems/theoj-1.10.0/lib/theoj/paper.rb:82:in `new'
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.3.0/gems/theoj-1.10.0/lib/theoj/paper.rb:82:in `from_repo'
    from /home/runner/work/_actions/xuanxu/paper-action/main/get_paper.rb:12:in `<main>'
Error: Process completed with exit code 1.

I don't understand what key it is missing in line 2 column 1 🤔

warrickball commented 1 week ago

Thanks for cutting it down! I'm willing to let 1042 words through and will see if I can reproduce the PDF generation error.

warrickball commented 1 week ago

It looks to me like this commit nudged the indentation of the index field for each affiliation by removing one leading space. I couldn't build the paper as it is but aligning them with the name line above again got the paper to build for me.

matteobachetti commented 1 week ago

Ouch. Done!

matteobachetti commented 6 days ago

@editorialbot generate pdf

editorialbot commented 6 days ago

:warning: An error happened when generating the pdf.

matteobachetti commented 6 days ago

@editorialbot generate pdf

editorialbot commented 6 days ago

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

editorialbot commented 6 days ago

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

warrickball commented 6 days ago

@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)

$ git diff --stat v0.2 v2.0.0 stingray/*.py
 stingray/__init__.py           |    7 +
 stingray/_astropy_init.py      |   35 +--
 stingray/base.py               | 2828 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 stingray/bexvar.py             |  275 ++++++++++++++++++++
 stingray/bispectrum.py         |  105 ++++----
 stingray/conftest.py           |   34 +--
 stingray/covariancespectrum.py |  170 ++++++------
 stingray/crosscorrelation.py   |  175 +++++++++----
 stingray/crossspectrum.py      | 3031 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++----------------------------------------------------
 stingray/events.py             |  816 +++++++++++++++++++++++++++++++++++++---------------------
 stingray/filters.py            |   54 ++--
 stingray/fourier.py            | 2474 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 stingray/gti.py                | 1186 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------------------
 stingray/io.py                 | 1393 +++++++++++++++++++++++++++++++++++++++++++++++++++-----------------------------------------------
 stingray/lightcurve.py         | 1446 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-----------------------------------------------
 stingray/loggingconfig.py      |   39 +++
 stingray/lombscargle.py        |  686 +++++++++++++++++++++++++++++++++++++++++++++++++
 stingray/multitaper.py         |  791 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 stingray/power_colors.py       |  495 +++++++++++++++++++++++++++++++++++
 stingray/powerspectrum.py      | 1570 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++------------------------
 stingray/sampledata.py         |   13 +-
 stingray/spectroscopy.py       |   57 ++---
 stingray/stats.py              |  833 +++++++++++++++++++++++++++++++++++++++++++++++++++++++----
 stingray/utils.py              | 1681 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++------------
 stingray/varenergyspectrum.py  |  964 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++------------
 25 files changed, 17514 insertions(+), 3644 deletions(-)

@arfon — This isn't necessarily super accurate but I couldn't get cloc to parse a diff. From the code alone it looks like plenty of functionality was implemented since the first Stingray JOSS paper.

warrickball commented 6 days ago

@matteobachetti — I intend to take a closer look at this soon but at a quick glance I noticed a few references aren't rendering. Specifically, note all the lingering square brackets in this sentence:

Methods include Gaussian Process modeling of quasi-periodic oscillations [hubner] and Lomb-Scargle cross spectra [scargle]. We have introduced the Fourier-Domain Acceleration Search [ransom], the H-test [dejager] and Phase Dispersion Minimization [stellingwerf] statistics into the pulsar sub package.

I also don't see the JOSS reference to the original Stingray publication (Huppenkothen et al. 2019b) actually turn up in the text. The associated ApJ reference (Huppenkothen et al. 2019a) is in the summary.

Another few quick fixes while we're at it:

Don't worry too much about the typographic stuff. I can open a pull request to fix any minor things (like the last point) but it'll be more difficult for me to guess missing data, like exactly what you meant to cite in that sentence about methods that I quoted above.

matteobachetti commented 5 days ago

@warrickball sorry, I had gotten the syntax for citations wrong in various creative ways 😅 . Now all should appear correctly

matteobachetti commented 5 days ago

@editorialbot generate pdf

editorialbot commented 5 days ago

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

editorialbot commented 5 days ago

Five most similar historical JOSS papers:

Astronomical échelle spectroscopy data analysis with muler Submitting author: @gully Handling editor: @xuanxu (Active) Reviewers: @bmorris3, @wtgee Similarity score: 0.8103

DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data Submitting author: @finagle29 Handling editor: @arfon (Active) Reviewers: @crhea93, @arjunsavel Similarity score: 0.7958

SkyPy: A package for modelling the Universe Submitting author: @rrjbca Handling editor: @arfon (Active) Reviewers: @cescalara, @rmorgan10 Similarity score: 0.7880

The Python Sky Model 3 software Submitting author: @zonca Handling editor: @christinahedges (Retired) Reviewers: @patricialarsen, @smsharma Similarity score: 0.7782

SNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signals Submitting author: @JostMigenda Handling editor: @dfm (Active) Reviewers: @apizzuto, @PeterDenton Similarity score: 0.7761

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

matteobachetti commented 5 days ago

@editorialbot generate pdf

editorialbot commented 5 days ago

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

editorialbot commented 5 days ago

Five most similar historical JOSS papers:

Astronomical échelle spectroscopy data analysis with muler Submitting author: @gully Handling editor: @xuanxu (Active) Reviewers: @bmorris3, @wtgee Similarity score: 0.8094

DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data Submitting author: @finagle29 Handling editor: @arfon (Active) Reviewers: @crhea93, @arjunsavel Similarity score: 0.7970

SkyPy: A package for modelling the Universe Submitting author: @rrjbca Handling editor: @arfon (Active) Reviewers: @cescalara, @rmorgan10 Similarity score: 0.7813

SNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signals Submitting author: @JostMigenda Handling editor: @dfm (Active) Reviewers: @apizzuto, @PeterDenton Similarity score: 0.7793

The Python Sky Model 3 software Submitting author: @zonca Handling editor: @christinahedges (Retired) Reviewers: @patricialarsen, @smsharma Similarity score: 0.7739

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

warrickball commented 1 day ago

@editorialbot assign me as editor