[REVIEW]: Openseize: A digital signal processing package for large EEG datasets in Python

[editorialbot]

Submitting author: @mscaudill (Matthew Caudill)
Repository: https://github.com/mscaudill/openseize
Branch with paper.md (empty if default branch):
Version: v1.1.0-joss
Editor: @samhforbes
Reviewers: @szorowi1, @AJQuinn
Archive: 10.5281/zenodo.7760376

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f737f4eb377a3bed6602dac51f6b13b4"><img src="https://joss.theoj.org/papers/f737f4eb377a3bed6602dac51f6b13b4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f737f4eb377a3bed6602dac51f6b13b4/status.svg)](https://joss.theoj.org/papers/f737f4eb377a3bed6602dac51f6b13b4)

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

@szorowi1 & @AJQuinn, 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 @samhforbes 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 @szorowi1

[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:

@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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.27 s (305.9 files/s, 80737.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           2061           3953           3451
Markdown                        35            294              0           1467
Jupyter Notebook                 7              0           9248            965
YAML                             9             49             46            351
TeX                              1             17              1            158
TOML                             1             10              4             87
CSS                              1              3              2              4
-------------------------------------------------------------------------------
SUM:                            84           2434          13254           6483
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 915

[editorialbot]

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

OK DOIs

- 10.1371/journal.pone.0039127 is OK
- 10.1016/j.yebeh.2009.02.035 is OK
- 10.3389/fnsys.2011.00059 is OK
- 10.3389/fncel.2021.649262 is OK
- 10.5014/ajot.61.2.176 is OK
- 10.3758/BF03196680 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1177/155005941104200412 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.jneumeth.2003.10.009 is OK
- 10.21105/joss.01272 is OK
- 10.1155/2011/156869 is OK
- 10.1155/2011/879716 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[samhforbes]

Hi @szorowi1, @AJQuinn thanks for agreeing to review. This is our review thread. Please generate your checklist with the above command seen in the top post, and raise any issues about the software in the issues tab of the repository directly, linking back to here, Any wider issues you'd like to discuss please flag here of course, and let me know if there's anything I can help with. Thanks again!

[AJQuinn]

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/mscaudill/openseize?
• 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 (@mscaudill) 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?

[szorowi1]

Review checklist for @szorowi1

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/mscaudill/openseize?
• 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 (@mscaudill) 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?

[samhforbes]

Hi @szorowi1, @AJQuinn how are things going? Please let me know if I can help with anything.

[szorowi1]

Hi @samhforbes, thanks for the follow-up! I believe my review is complete.

OpenSeize looks like a great package! I was able to successfully reproduce the outputs of the tutorials, and the documentation is excellent. I opened a minor PR in the parent repo to fix one bug. Otherwise, it all looks great to me!

[samhforbes]

Thanks @szorowi1 !

[mscaudill]

Many thanks @szorowi1 for the fast review and the PR to fix the link in the documentation!

[samhforbes]

Hi @AJQuinn I can see there are some things you haven't completed on the checklist. Are there any issues that need to be raised / addressed?

[AJQuinn]

Hi @samhforbes - apologies for the delay. No substantial issues, I've been testing the package for a bit and just submitted my review issue with a handful of suggested documentation changes.

Very impressed overall, expect to complete the review soon.

[AJQuinn]

My comments have been well addressed and I'm happy to sign off my review. This is a useful, well constructed and throughly documented package that I'm glad to recommend to JOSS.

[mscaudill]

Hi @samhforbes Not sure if you were pinged on the last comment but it looks like the reviews of Openseize are complete.

Best
Matt

[samhforbes]

Thanks @mscaudill. This is exciting and is looking good. I can see the reviewers are happy and I have also had a look and am really pleased with how everything works.

[samhforbes]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1371/journal.pone.0039127 is OK
- 10.1016/j.yebeh.2009.02.035 is OK
- 10.3389/fnsys.2011.00059 is OK
- 10.3389/fncel.2021.649262 is OK
- 10.5014/ajot.61.2.176 is OK
- 10.3758/BF03196680 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1177/155005941104200412 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.jneumeth.2003.10.009 is OK
- 10.21105/joss.01272 is OK
- 10.1155/2011/156869 is OK
- 10.1155/2011/879716 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[samhforbes]

@editorialbot generate pdf

[editorialbot]

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

[samhforbes]

@mscaudill can you please check the version number is accurate, confirm the author list, and then archive it somewhere with a stable DOI (Zenodo, or figshare for example) - making sure the authors and title match that of the paper. Then could you please post the DOI here.

[samhforbes]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[mscaudill]

Hi @openjournals/bcm-eics

The proof of the paper looks great. Thank you!

[mscaudill]

Hi @samhforbes

I apologize for reaching back out to you since you turned Openseize over to the bcm-eic but I haven't heard anything from them in over a week and I wanted to make sure that I haven't been forgotten.

Thanks
Matt

[samhforbes]

Hi @mscaudill I'm sure it hasn't been lost -- that said I note that the teams feature might be ending which means the notification might not have gone through.
@openjournals/bcm-eics @Kevin-Mattheus-Moerman just tagging you in in case the GitHub teams have already been deprecated unbeknownst to editorialbot.

[Kevin-Mattheus-Moerman]

@samhforbes @mscaudill apologies for the delay in processing the final steps. I will work on this now.

[Kevin-Mattheus-Moerman]

@mscaudill I have just one minor comment:

• In your affiliations, please spell out USA as Unites States of America

[mscaudill]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[mscaudill]

@Kevin-Mattheus-Moerman Thank you for catching this. I've updated the affiliations and generated the PDF in this discussion thread as well as the repository.

• In your affiliations, please spell out USA as Unites States of America

Best
Matt

[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: Caudill
  given-names: Matthew S.
  orcid: "https://orcid.org/0000-0002-3656-9261"
doi: 10.5281/zenodo.7760376
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Caudill
    given-names: Matthew S.
    orcid: "https://orcid.org/0000-0002-3656-9261"
  date-published: 2023-04-05
  doi: 10.21105/joss.05126
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5126
  title: "Openseize: A digital signal processing package for large EEG
    datasets in Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05126"
  volume: 8
title: "Openseize: A digital signal processing package for large EEG
  datasets in Python"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.05126 joss-papers#4104
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05126
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...

[Kevin-Mattheus-Moerman]

Congratulations on this publication @mscaudill

Thanks for editing this one @samhforbes!

And a special thanks to the reviewers: @szorowi1, @AJQuinn

[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.05126/status.svg)](https://doi.org/10.21105/joss.05126)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05126">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05126/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05126/status.svg
   :target: https://doi.org/10.21105/joss.05126

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[mscaudill]

Thank you @samhforbes @AJQuinn @szorowi1 and @Kevin-Mattheus-Moerman for reviewing, editing and most importantly improving Openseize. It was a pleasure.

Best
Matt