[REVIEW]: SelfEEG: A Python library for Self-Supervised Learning in Electroencephalography

[editorialbot]

Submitting author: @fedepup (Federico Del Pup)
Repository: https://github.com/MedMaxLab/selfEEG
Branch with paper.md (empty if default branch):
Version: v0.1.1
Editor: @emdupre
Reviewers: @vferat, @wmvanvliet
Archive: 10.5281/zenodo.10813095

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ab7eaf53973996e7c8d49dada734de78"><img src="https://joss.theoj.org/papers/ab7eaf53973996e7c8d49dada734de78/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ab7eaf53973996e7c8d49dada734de78/status.svg)](https://joss.theoj.org/papers/ab7eaf53973996e7c8d49dada734de78)

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

@vferat & @wmvanvliet & @Bsingstad, 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 @wmvanvliet

📝 Checklist for @Bsingstad

📝 Checklist for @vferat

[editorialbot]

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]

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

OK DOIs

- 10.1001/jamainternmed.2018.7117 is OK
- 10.1109/TNNLS.2022.3190448 is OK
- 10.1088/1741-2552/abca18 is OK
- 10.1109/ACCESS.2023.3344531 is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1088/1741-2552/ab4af6 is OK
- 10.3390/app13095472 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.19 s (775.1 files/s, 128088.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24           2401           5788           7347
Jupyter Notebook                12              0           3971           2565
reStructuredText                97            552            564            491
Markdown                         8            196              0            457
YAML                             4             22             17            109
TeX                              1             11              0             70
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              1              0              6
-------------------------------------------------------------------------------
SUM:                           149           3195          10348          11080
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 979

[editorialbot]

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

[emdupre]

👋 Hi @vferat, @wmvanvliet, @Bsingstad, and thank you again for agreeing to review this submission for SelfEEG !

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 SelfEEG. Whenever possible, please open relevant issues on the 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 !

[Bsingstad]

Review checklist for @Bsingstad

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/MedMaxLab/selfEEG?
• 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 (@fedepup) 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?

[wmvanvliet]

Review checklist for @wmvanvliet

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/MedMaxLab/selfEEG?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license? Copyright holder in LICENSE.md MedMaxLab/selfEEG#1
• Contribution and authorship: Has the submitting author (@fedepup) 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? pup_fede_cnd conda channel not found? MedMaxLab/selfEEG#2
• 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). Some doc tweaks MedMaxLab/selfEEG#3
• 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)? Some spelling/grammar tweaks to the paper MedMaxLab/selfEEG#5
• 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?

[wmvanvliet]

Excellent work, @fedepup and team! I think this package will definitely help with the development of self-supervised learning techniques on EEG data.

[vferat]

Review checklist for @vferat

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/MedMaxLab/selfEEG?
• 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 (@fedepup) 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?

[fedepup]

Excellent work, @fedepup and team! I think this package will definitely help with the development of self-supervised learning techniques on EEG data.

Thank you very much, @wmvanvliet!

[fedepup]

@editorialbot generate pdf

[editorialbot]

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

[fedepup]

I've generated a new PDF draft to include changes made during wmvanvliet's review.

[emdupre]

👋 Hi everyone ! I just wanted to check-in on how this review is going for you, @Bsingstad and @vferat.

If you have any questions that I can answer, please don't hesitate to let me know. And thank you again for your help in reviewing SelfEEG !

[vferat]

Hey @emdupre,
The review is coming along, I'm a bit busy this week, but I expect to finish by next week.

[vferat]

Review completed !

Thanks to the authors for their responsiveness! The library delivers on its promise to simplify access to EEG data
All my comments have been addressed and I can only recommend to accept this publication.

Thank to all authors for making this tool available to the community !

[fedepup]

Thanks to the authors for their responsiveness! The library delivers on its promise to simplify access to EEG data
All my comments have been addressed and I can only recommend to accept this publication.

Thank you very much, @vferat!

[fedepup]

Hi @emdupre. To help you have a clear view of all the revisions made during vferat and wmvanvliet review, I would like to write a little summary.

wmvanvliet:

1. General Checks: The copyright holder's name was changed to MedMax Team Copyright holder in LICENSE.md MedMaxLab/selfEEG#1
2. Installation: Corrected the wrongly reported conda channel pup_fede_cnd conda channel not found? MedMaxLab/selfEEG#2
3. Functionality: Minor revision to improve compatibility with python < 3.11 Make selfeeg compatible with python<3.11 MedMaxLab/selfEEG#4
4. documentation: Corrected spelling/grammar typos and improved notebooks readability Some doc tweaks MedMaxLab/selfEEG#3
5. Paper: Corrected spelling/grammar typos Some spelling/grammar tweaks to the paper MedMaxLab/selfEEG#5 (I also specified name and surname of every author since mine was detected wrongly MedMaxLab/selfEEG@4154e64)

vferat

1. Functionality: there was a small bug in the dataloading module when assigning float values to the window length or the sampling rate. Corrected and explained here [JOSS] Review  MedMaxLab/selfEEG#6 (comment)
2. Documentation: Added a new tutorial notebook with a more concrete use case on real-world data (EEGMMI dataset, preprocessed version) and updated notebooks in the Notebooks folder MedMaxLab/selfEEG@e573df1
3. Maintenance (optional but important): Improved tests by adding a matrix with different os/python versions and the nighlty version of pytorch Improve unittest MedMaxLab/selfEEG#7 and added a basic list of pre-commit Add pre-commit MedMaxLab/selfEEG#8

[emdupre]

Thank you for your write-up, @fedepup ! I appreciate this summary 🙏 And thank you very much to @wmvanvliet and @vferat for your reviews !

@Bsingstad, please let us know when you've finalized your review -- or if there are any blockers that we should be aware of ! And thank you again for your work on reviewing SelfEEG to date 🌻

[Bsingstad]

Sorry for my silence here. I will try to finish my review during this week.

[emdupre]

Hi @Bsingstad, thank you for following up on this ! Please let me know if you would still be able to complete your review within the next week, or if you anticipate a longer delay.

[editorialbot]

That doesn't look like a valid DOI value

[emdupre]

@editorialbot set v0.1.1 as version

[editorialbot]

Done! version is now v0.1.1

[emdupre]

Thank you, @fedepup !

As you can see, I'm having a little difficulty setting the archive with a non-valid DOI. I hope / expect that this will be resolved soon on the DataCite side, but in the meantime I'll try to confirm what we can do on our end.

[fedepup]

Hi @emdupre. The SelEEG v0.1.1 DOI on Zenodo now works. Il Gio 14 Mar 2024, 06:02 Elizabeth DuPre ***@***.***> ha scritto:

…

Thank you, @fedepup <https://github.com/fedepup> ! As you can see, I'm having a little difficulty setting the archive with a non-valid DOI. I hope / expect that this will be resolved soon on the DataCite side, but in the meantime I'll try to confirm what we can do on our end. — Reply to this email directly, view it on GitHub <#6224 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A4NECZKR5TDDIAE6E2QJUSDYYEVPTAVCNFSM6AAAAABBYYQR7GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJWGQ4DQMRTGM> . You are receiving this because you were mentioned. Message ID: ***@***.***>

[emdupre]

@editorialbot set 10.5281/zenodo.10813095 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10813095

[emdupre]

@editorialbot generate pdf

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[emdupre]

@editorialbot generate pdf

[editorialbot]

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

[emdupre]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1001/jamainternmed.2018.7117 is OK
- 10.1109/TNNLS.2022.3190448 is OK
- 10.1088/1741-2552/abca18 is OK
- 10.1109/ACCESS.2023.3344531 is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1088/1741-2552/ab4af6 is OK
- 10.3390/app13095472 is OK
- 10.1016/j.eswa.2024.123550 is OK

MISSING DOIs

- No DOI given, and none found for title: Lightly
- No DOI given, and none found for title: VISSL

INVALID DOIs

- None

[emdupre]

Thank you, @fedepup ! I'm now happy to recommend SelfEEG to the EiC team for publication in JOSS ✨🚀 And my personal congratulations on this impressive work !

Thank you, too, to @wmvanvliet and @vferat for your reviews ! JOSS works because of your work 💐

[emdupre]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1001/jamainternmed.2018.7117 is OK
- 10.1109/TNNLS.2022.3190448 is OK
- 10.1088/1741-2552/abca18 is OK
- 10.1109/ACCESS.2023.3344531 is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1088/1741-2552/ab4af6 is OK
- 10.3390/app13095472 is OK
- 10.1016/j.eswa.2024.123550 is OK

MISSING DOIs

- No DOI given, and none found for title: Lightly
- No DOI given, and none found for title: VISSL

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#5134, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Del Pup
  given-names: Federico
  orcid: "https://orcid.org/0009-0004-0698-962X"
- family-names: Zanola
  given-names: Andrea
  orcid: "https://orcid.org/0000-0001-6973-8634"
- family-names: Tshimanga
  given-names: Louis Fabrice
  orcid: "https://orcid.org/0009-0002-1240-4830"
- family-names: Mazzon
  given-names: Paolo Emilio
- family-names: Atzori
  given-names: Manfredo
  orcid: "https://orcid.org/0000-0001-5397-2063"
doi: 10.5281/zenodo.10813095
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Del Pup
    given-names: Federico
    orcid: "https://orcid.org/0009-0004-0698-962X"
  - family-names: Zanola
    given-names: Andrea
    orcid: "https://orcid.org/0000-0001-6973-8634"
  - family-names: Tshimanga
    given-names: Louis Fabrice
    orcid: "https://orcid.org/0009-0002-1240-4830"
  - family-names: Mazzon
    given-names: Paolo Emilio
  - family-names: Atzori
    given-names: Manfredo
    orcid: "https://orcid.org/0000-0001-5397-2063"
  date-published: 2024-03-17
  doi: 10.21105/joss.06224
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6224
  title: "SelfEEG: A Python library for Self-Supervised Learning in
    Electroencephalography"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06224"
  volume: 9
title: "SelfEEG: A Python library for Self-Supervised Learning in
  Electroencephalography"

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.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06224 joss-papers#5140
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06224
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@vferat, @wmvanvliet – many thanks for your reviews here and to @emdupre for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@fedepup – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 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.06224/status.svg)](https://doi.org/10.21105/joss.06224)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06224">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06224/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06224/status.svg
   :target: https://doi.org/10.21105/joss.06224

This is how it will look in your documentation:

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