[REVIEW]: Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU #4840

editorialbot · 2022-10-10T19:42:50Z

Submitting author: @edeno ()
Repository: https://github.com/Eden-Kramer-Lab/spectral_connectivity
Branch with paper.md (empty if default branch):
Version: v1.1.0
Editor: @emdupre
Reviewers: @AJQuinn, @sappelhoff, @EtienneCmb
Archive: 10.5281/zenodo.7416614

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/27eb33e699c9ea723783c44576d081bb"><img src="https://joss.theoj.org/papers/27eb33e699c9ea723783c44576d081bb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/27eb33e699c9ea723783c44576d081bb/status.svg)](https://joss.theoj.org/papers/27eb33e699c9ea723783c44576d081bb)

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

@AJQuinn & @sappelhoff & @EtienneCmb, 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 @emdupre 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 @AJQuinn

📝 Checklist for @sappelhoff

📝 Checklist for @EtienneCmb

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-10-10T19:42:52Z

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 · 2022-10-10T19:42:54Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (331.1 files/s, 111252.9 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Jupyter Notebook                  2              0           2763           2512
Python                           13            778           1355           2330
TeX                               1             25              0            315
DOS Batch                         1             36              2            243
make                              2             32              6            199
Markdown                          3             52              0            167
YAML                              5              9             20            113
reStructuredText                  5             32             52             43
Bourne Again Shell                1              1              0              2
--------------------------------------------------------------------------------
SUM:                             33            965           4198           5924
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-10-10T19:42:55Z

Wordcount for paper.md is 684

editorialbot · 2022-10-10T19:43:09Z

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

OK DOIs

- 10.1016/j.jneumeth.2014.11.012 is OK
- 10.1109/ICDSP.2007.4288544 is OK
- 10.1007/PL00007990 is OK
- 10.1007/s005290050005 is OK
- 10.1073/pnas.1017041108 is OK
- 10.48550/arXiv.2201.11941 is OK
- 10.1101/2021.02.03.429582 is OK
- 10.1016/j.neuroimage.2008.02.020 is OK
- 10.2307/2287238 is OK
- 10.1016/0013-4694(83)90235-3 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1007/BF00198091 is OK
- 10.1016/S0165-0270(03)00052-9 is OK
- 10.1007/978-3-662-58485-9_11 is OK
- 10.1002/(sici)1097-0193(1999)8:4<194::aid-hbm4>3.0.co;2-c is OK
- 10.1523/JNEUROSCI.0854-21.2021 is OK
- 10.1016/j.clinph.2004.04.029 is OK
- 10.1103/PhysRevLett.100.234101 is OK
- 10.1002/hbm.20346 is OK
- 10.3389/fnsys.2021.645709 is OK
- 10.1016/j.neuroimage.2011.01.055 is OK
- 10.1016/j.neuroimage.2010.01.073 is OK
- 10.3389/fnins.2013.00267 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-10-10T19:44:04Z

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

emdupre · 2022-10-10T19:44:41Z

Hi @AJQuinn, @sappelhoff, and @EtienneCmb 👋 Thanks again for agreeing to review this submission ! The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @\editorialbot generate my checklist.

In working through the checklist, you're likely to have specific feedback on Spectral Connectivity. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

sappelhoff · 2022-10-10T20:49:52Z

Review checklist for @sappelhoff

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/Eden-Kramer-Lab/spectral_connectivity?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@edeno) 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?

AJQuinn · 2022-10-17T19:16:11Z

@editorialbot generate my checklist

emdupre · 2022-10-17T19:21:28Z

Hm, you might need to just create a new comment @AJQuinn -- I'm not sure that it will respond to edited comments ! Sorry for the confusion.

AJQuinn · 2022-10-17T22:05:54Z

Review checklist for @AJQuinn

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/Eden-Kramer-Lab/spectral_connectivity?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@edeno) 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?

sappelhoff · 2022-10-21T10:27:01Z

@emdupre I have completed my review. All issues that I raised have been addressed to my full satisfaction. I believe that spectral_connectivity is a valuable package that will serve the community well, as already evidenced in several publications. I recommend this paper for publication in JOSS.

For details, please see my checklist and all my linked issues and PRs in this review thread.

editorialbot · 2022-12-09T03:57:24Z

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

emdupre · 2022-12-09T04:37:25Z

@editorialbot set 10.5281/zenodo.7416614 as archive

editorialbot · 2022-12-09T04:37:27Z

Done! Archive is now 10.5281/zenodo.7416614

emdupre · 2022-12-09T18:19:26Z

Thank you, @edeno !

I noticed that the metadata on the archive has several small discrepancies from the paper metadata. In particular, could you please update the title to :

Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU

and double-check that the author information lists names and surnames correctly ? From my rendering, these appear inverted in the final citation (i.e., excerpting from the bib file):

author = {Eric, Denovellis and
          Maxym, Myroshnychenko and
          Mehrad, Sarmashghi and
          Emily, Stephen},

You can update these without creating a new archive by editing the existing archive's metadata as described here.

edeno · 2022-12-09T18:28:33Z

Ah yes. Silly mistake by me. Should be fixed now.

emdupre · 2022-12-09T20:04:05Z

Thank you ! I see that the author name changes have updated but not the title of the archive. Could you please confirm that ?

edeno · 2022-12-09T20:21:34Z

Sorry, I misunderstood what the title referred to. It should be fixed now?

emdupre · 2022-12-09T20:31:09Z

Thank you ; this now looks right on my end !

I'm now happy to recommend Spectral Connectivity to the EIC team for publication, and I just want to add my congratulations to you on such an impressive effort ! 🎉

emdupre · 2022-12-09T20:31:18Z

@editorialbot recommend-accept

editorialbot · 2022-12-09T20:31:19Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-12-09T20:31:47Z

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

OK DOIs

- 10.1016/j.jneumeth.2014.11.012 is OK
- 10.1109/ICDSP.2007.4288544 is OK
- 10.1007/PL00007990 is OK
- 10.1007/s005290050005 is OK
- 10.1073/pnas.1017041108 is OK
- 10.48550/ARXIV.2201.11941 is OK
- 10.1101/2021.02.03.429582 is OK
- 10.1016/j.neuroimage.2008.02.020 is OK
- 10.2307/2287238 is OK
- 10.1016/0013-4694(83)90235-3 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1007/BF00198091 is OK
- 10.1016/S0165-0270(03)00052-9 is OK
- 10.1007/978-3-662-58485-9_11 is OK
- 10.1002/(sici)1097-0193(1999)8:4<194::aid-hbm4>3.0.co;2-c is OK
- 10.1523/JNEUROSCI.0854-21.2021 is OK
- 10.1016/j.clinph.2004.04.029 is OK
- 10.1103/PhysRevLett.100.234101 is OK
- 10.1002/hbm.20346 is OK
- 10.3389/fnsys.2021.645709 is OK
- 10.1016/j.neuroimage.2011.01.055 is OK
- 10.1016/j.neuroimage.2010.01.073 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.3389/978-2-88919-608-1 is OK
- 10.22541/au.159363438.81020330 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-12-09T20:33:06Z

👋 @openjournals/bcm-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#3787, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

edeno · 2022-12-09T21:00:53Z

I found a couple of small typos that I fixed. We are happy how it looks otherwise.

Kevin-Mattheus-Moerman · 2022-12-12T22:26:28Z

@edeno I am the AEiC for this track and here to help process this work for acceptance in JOSS. I have reviewed the archive and the paper and all seems in order. I only have one minor editorial point:

Please add the affiliation country to all affiliations, and do not use acronyms, i.e use United States of America instead of USA.

Please let me know when you've worked on the above. Thanks.

edeno · 2022-12-13T00:48:01Z

Hi @Kevin-Mattheus-Moerman,

I added the affiliation country to the archive and the paper.md. Please let me know if there's another place it should be added.

Kevin-Mattheus-Moerman · 2022-12-13T14:40:32Z

@editorialbot generate pdf

editorialbot · 2022-12-13T14:41:44Z

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

Kevin-Mattheus-Moerman · 2022-12-13T14:45:12Z

@edeno all looks good now so we'll proceed with acceptance. Thanks

Kevin-Mattheus-Moerman · 2022-12-13T14:46:02Z

@editorialbot accept

editorialbot · 2022-12-13T14:46:04Z

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

editorialbot · 2022-12-13T14:47:50Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-12-13T14:47:51Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2022-12-13T14:47:52Z

🚨🚨🚨 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.04840 joss-papers#3800
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04840
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2022-12-13T14:59:22Z

@edeno congratulations on this JOSS publication! 🎉

Thanks @emdupre for editing!

And also thank you to the reviewers @AJQuinn, @sappelhoff, and @EtienneCmb!!!!!

editorialbot · 2022-12-13T14:59:24Z

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04840/status.svg)](https://doi.org/10.21105/joss.04840)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04840">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04840/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04840/status.svg
   :target: https://doi.org/10.21105/joss.04840

This is how it will look in your documentation:

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editorialbot added Makefile review Shell TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Oct 10, 2022

editorialbot assigned emdupre Oct 10, 2022

editorialbot mentioned this issue Oct 10, 2022

[PRE REVIEW]: Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU #4766

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 9, 2022

editorialbot added accepted published Papers published in JOSS labels Dec 13, 2022

Kevin-Mattheus-Moerman closed this as completed Dec 13, 2022

editorialbot mentioned this issue Jul 1, 2024

[PRE REVIEW]: WhaleConnect: A General-Purpose, Cross-Platform Network Communication Application #6946

Closed

[REVIEW]: Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU #4840

[REVIEW]: Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU #4840

Comments

editorialbot commented Oct 10, 2022 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Oct 10, 2022

editorialbot commented Oct 10, 2022

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editorialbot commented Oct 10, 2022

editorialbot commented Oct 10, 2022

emdupre commented Oct 10, 2022

sappelhoff commented Oct 10, 2022 • edited Loading

Review checklist for @sappelhoff

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

AJQuinn commented Oct 17, 2022 • edited Loading

emdupre commented Oct 17, 2022

AJQuinn commented Oct 17, 2022 • edited Loading

Review checklist for @AJQuinn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

sappelhoff commented Oct 21, 2022

editorialbot commented Dec 9, 2022

emdupre commented Dec 9, 2022

editorialbot commented Dec 9, 2022

emdupre commented Dec 9, 2022 • edited Loading

edeno commented Dec 9, 2022

emdupre commented Dec 9, 2022

edeno commented Dec 9, 2022

emdupre commented Dec 9, 2022

emdupre commented Dec 9, 2022

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edeno commented Dec 9, 2022

Kevin-Mattheus-Moerman commented Dec 12, 2022 • edited Loading

edeno commented Dec 13, 2022 • edited Loading

Kevin-Mattheus-Moerman commented Dec 13, 2022

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Kevin-Mattheus-Moerman commented Dec 13, 2022

Kevin-Mattheus-Moerman commented Dec 13, 2022

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Kevin-Mattheus-Moerman commented Dec 13, 2022

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editorialbot commented Oct 10, 2022 •

edited

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sappelhoff commented Oct 10, 2022 •

edited

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AJQuinn commented Oct 17, 2022 •

edited

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AJQuinn commented Oct 17, 2022 •

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emdupre commented Dec 9, 2022 •

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edeno commented Dec 13, 2022 •

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