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[REVIEW]: SelfEEG: A Python library for Self-Supervised Learning in Electroencephalography #6224

Closed editorialbot closed 8 months ago

editorialbot commented 10 months ago

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

Status

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

πŸ“ Checklist for @wmvanvliet

πŸ“ Checklist for @Bsingstad

πŸ“ Checklist for @vferat

editorialbot commented 10 months ago

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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 10 months ago
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 commented 10 months ago
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 commented 10 months ago

Wordcount for paper.md is 979

editorialbot commented 10 months ago

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

emdupre commented 10 months ago

πŸ‘‹ 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 commented 10 months ago

Review checklist for @Bsingstad

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

wmvanvliet commented 10 months ago

Review checklist for @wmvanvliet

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

wmvanvliet commented 9 months ago

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

vferat commented 9 months ago

Review checklist for @vferat

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

fedepup commented 9 months ago

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 commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

fedepup commented 9 months ago

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

emdupre commented 9 months ago

πŸ‘‹ 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 commented 9 months ago

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

vferat commented 9 months ago

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 commented 9 months ago

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 commented 9 months ago

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 MedMaxLab/selfEEG#1
  2. Installation: Corrected the wrongly reported conda channel MedMaxLab/selfEEG#2
  3. Functionality: Minor revision to improve compatibility with python < 3.11 MedMaxLab/selfEEG#4
  4. documentation: Corrected spelling/grammar typos and improved notebooks readability MedMaxLab/selfEEG#3
  5. Paper: Corrected spelling/grammar typos MedMaxLab/selfEEG#5 (I also specified name and surname of every author since mine was detected wrongly https://github.com/MedMaxLab/selfEEG/commit/4154e642b52c1d2ae6374c0f71121b2ffe25ebba)

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 https://github.com/MedMaxLab/selfEEG/issues/6#issuecomment-1904160507
  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@e573df17acc1f15a77b0fc94b92aeaa8d23ae3b2
  3. Maintenance (optional but important): Improved tests by adding a matrix with different os/python versions and the nighlty version of pytorch MedMaxLab/selfEEG#7 and added a basic list of pre-commit MedMaxLab/selfEEG#8
emdupre commented 9 months ago

Thank you for your write-up, @fedepup ! I appreciate this summary πŸ™ 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 commented 9 months ago

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

emdupre commented 9 months ago

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.

fedepup commented 9 months ago

@emdupre - Thanks for your constant monitoring on this review process. Considering how smoothly things have gone so far and, more importantly, how the revisions have already greatly improved the quality of selfEEG, I'm confident that the entire review process will be completed within the expected time.

@Bsingstad - As already said in the pre-review process, I will try to solve any raised issue as soon as possible, possibly within the same day. Thanks again for having accepted to review selfEEG.

emdupre commented 8 months ago

πŸ‘‹ Hi everyone !

I just wanted to follow-up on this review for SelfEEG. Given that we're now outside of the six week review window, we'll need to wrap up our initial reviews. @Bsingstad, if you're able to provide comments by Monday, 4 March we would still be consider those. Otherwise, we'll need to conclude the initial review.

Thank you again to everyone for all of your input throughout this review process !

emdupre commented 8 months ago

Hi again,

Now that we've passed this final deadline, I'll need to remove @Bsingstad from the reviewer list. Thank you, though, for your enthusiasm for SelfEEG.

As @wmvanvliet and @vferat have already confirmed their completed reviews, I'll then proceed to perform a few final editorial checks.

If there are any questions or concerns at this point, please let me know !

emdupre commented 8 months ago

@editorialbot remove @Bsingstad from reviewers

editorialbot commented 8 months ago

@Bsingstad removed from the reviewers list!

emdupre commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

emdupre commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago
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
fedepup commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

fedepup commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago
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

- None

INVALID DOIs

- None
fedepup commented 8 months ago

Hi @emdupre. Yesterday a paper on torchEEG was published on Expert Systems with Applications. Therefore, I've updated the paper and added the new reference. You can find all the modifications here MedMaxLab/SelfEEG@c7475baa2b539901d9b426ccbde2e0d5038b17c3.

I also take the chance to ask if there are other additional steps I need to perform at this stage of the peer-review.

emdupre commented 8 months ago

Thanks for checking in, @fedepup ! I've now had a chance to review SelfEEG and am happy with the state of the submission πŸš€

I do, though, have a few small editorial requests before we can proceed (the torchEEG citation was actually one of my original requests, so thanks for taking care of that !):

emdupre commented 8 months ago

After making these changes, could you then please:

I'll then be able to proceed with processing the submission πŸš€

emdupre commented 8 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

fedepup commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

fedepup commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago
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
wmvanvliet commented 8 months ago

Line 63 of the paper: Few examples are should be A few examples are

fedepup commented 8 months ago

Line 63 of the paper: Few examples are should be A few examples are

Thanks! Corrected.

fedepup commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

fedepup commented 8 months ago

HI @emdupre. Here I report all the requested information and revisions.

Paper

Tagged release and repository archive

Title, list of authors, license (MIT), affiliations and version tag reported in the archive are the same as in the paper or GitHub repository.

Additional Notes

Zenodo's DOI registration is currently affected by a service incident at DataCite. So, the provided link does not work at the moment, although it is correct. If you check the DOI that represent all versions of selfEEG ( https://zenodo.org/doi/10.5281/zenodo.10813094 ), you can see that this works. You can also check that the one provided for the specific release (v0.1.1) is correct.

Thanks again.

emdupre commented 8 months ago

@editorialbot set 10.5281/zenodo.10813095 as archive

editorialbot commented 8 months ago

That doesn't look like a valid DOI value