[REVIEW]: biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals #2621

whedon · 2020-08-31T19:44:39Z

Submitting author: @JanCBrammer (Jan C. Brammer)
Repository: https://github.com/JanCBrammer/biopeaks
Version: v1.4.1
Editor: @oliviaguest
Reviewer: @TomDonoghue, @sappelhoff, @jamesheathers
Archive: 10.5281/zenodo.4133324

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/610ce9dc258bcf3d5ccd311e349b946a/status.svg)](https://joss.theoj.org/papers/610ce9dc258bcf3d5ccd311e349b946a)

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Reviewer instructions & questions

@TomDonoghue & @sappelhoff & @jamesheathers, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @TomDonoghue

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 repository url?
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 (@JanCBrammer) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
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?

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 repository url?
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 (@JanCBrammer) 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

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed? Question/suggestions about benchmark files JanCBrammer/biopeaks#14 (comment)
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. complete install instructions for users who already have python JanCBrammer/biopeaks#13
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). Make use of a dedicated example file in "getting-started" section in docs JanCBrammer/biopeaks#12
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)? Discussion: Adopting a consistent style for docstrings JanCBrammer/biopeaks#11 Suggestion: Add docs on how docs are being built JanCBrammer/biopeaks#10
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified? Add code coverage to tests JanCBrammer/biopeaks#8
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 Making community and contributing guidelines more visible JanCBrammer/biopeaks#9

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
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? Feedback JOSS paper JanCBrammer/biopeaks#6

Review checklist for @jamesheathers

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 repository url?
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 (@JanCBrammer) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
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?

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

whedon · 2020-08-31T19:44:43Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @TomDonoghue, @sappelhoff, @jamesheathers it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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

@whedon generate pdf

whedon · 2020-08-31T19:45:05Z

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

OK DOIs

- 10.5281/ZENODO.3597887 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1016/0013-4694(92)90009-7 is OK
- 10.1080/03091902.2019.1640306 is OK
- 10.3758/s13428-011-0107-7 is OK
- 10.1088/0967-3334/37/7/N38 is OK
- 10.1111/1469-8986.3510127 is OK
- 10.1371/journal.pone.0076585 is OK
- 10.1088/1361-6579/aad7e6 is OK

MISSING DOIs

- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data Structures for Statistical Computing in Python

INVALID DOIs

- https://doi.org/10.1038/s41592-019-0686-2 is INVALID because of 'https://doi.org/' prefix

whedon · 2020-08-31T19:45:58Z

👉 Check article proof 📄 👈

oliviaguest · 2020-08-31T19:59:26Z

👋👋👋

Hey @JanCBrammer, @TomDonoghue, @sappelhoff, @jamesheathers! Welcome to where the review itself will take place. Please make sure to read the instructions above.

For any and all things worthy of discussion or comment, use this issue right here — so drop comments or questions for me, the author, etc., here. For any very code-specific things please feel free to start an issue on the repo of the code itself (if appropriate!) and link back to it from here. For an example of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

JanCBrammer · 2020-09-10T06:52:21Z

@sappelhoff, thanks for your thorough and helpful review so far, much appreciated! I'm offline next week (week 38), so I won't get around to address your questions and suggestions until the week after the next (week 39). Looking forward to it :)

oliviaguest · 2020-09-21T10:12:20Z

Hey, no super pressure but when you (@TomDonoghue, @sappelhoff, @jamesheathers) get a chance could you give us a rough estimate for an ETA on your reviews, please? ☺️

sappelhoff · 2020-09-21T20:18:05Z

My final evaluation is on hold until @JanCBrammer has addressed or replied to some of my remarks. But other than that, I am basically done reviewing - see the linked issues and prs. :-)

oliviaguest · 2020-09-22T12:14:34Z

@sappelhoff oh, amazing! Great work — thanks. 👍

TomDonoghue · 2020-09-22T16:56:37Z

I should be able to do my review by the end of the week!

oliviaguest · 2020-09-23T06:42:22Z

@TomDonoghue Oh, great! I'll set up a reminder for both of us.

oliviaguest · 2020-09-23T06:43:07Z

@whedon remind @TomDonoghue in 9 days

whedon · 2020-09-23T06:43:10Z

Reminder set for @TomDonoghue in 9 days

oliviaguest · 2020-10-25T17:50:00Z

@JanCBrammer awesome, I think all reviewers are happy now. Can you please deposit the code on zenodo or similar and post the DOI back here? ☺️

JanCBrammer · 2020-10-26T08:49:28Z

@oliviaguest, I released a new version (v.1.4.1) containing the improvements related to this review. I've then deposited the repository at 10.5281/zenodo.4133324.

oliviaguest · 2020-10-26T13:58:43Z

@whedon set 10.5281/zenodo.4133324 as archive

whedon · 2020-10-26T13:58:48Z

OK. 10.5281/zenodo.4133324 is the archive.

oliviaguest · 2020-10-26T13:58:54Z

@whedon set v1.4.1 as version

whedon · 2020-10-26T13:58:59Z

OK. v1.4.1 is the version.

oliviaguest · 2020-10-26T13:59:45Z

@whedon generate pdf

whedon · 2020-10-26T14:00:42Z

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

oliviaguest · 2020-10-26T14:04:05Z

@whedon check references

whedon · 2020-10-26T14:04:30Z

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

OK DOIs

- 10.5281/ZENODO.3597887 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/0013-4694(92)90009-7 is OK
- 10.1080/03091902.2019.1640306 is OK
- 10.3758/s13428-011-0107-7 is OK
- 10.1088/0967-3334/37/7/N38 is OK
- 10.1111/1469-8986.3510127 is OK
- 10.1371/journal.pone.0076585 is OK
- 10.1088/1361-6579/aad7e6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest · 2020-10-26T14:05:33Z

@whedon accept

whedon · 2020-10-26T14:05:36Z

Attempting dry run of processing paper acceptance...

oliviaguest · 2020-10-26T14:05:46Z

@JanCBrammer does this all look good to you (the final PDF, etc.)?

whedon · 2020-10-26T14:06:15Z

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

OK DOIs

- 10.5281/ZENODO.3597887 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/0013-4694(92)90009-7 is OK
- 10.1080/03091902.2019.1640306 is OK
- 10.3758/s13428-011-0107-7 is OK
- 10.1088/0967-3334/37/7/N38 is OK
- 10.1111/1469-8986.3510127 is OK
- 10.1371/journal.pone.0076585 is OK
- 10.1088/1361-6579/aad7e6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2020-10-26T14:06:41Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1863

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1863, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

JanCBrammer · 2020-10-26T14:33:41Z

does this all look good to you (the final PDF, etc.)?

@oliviaguest, the final article proof looks good to me!

arfon · 2020-10-27T20:39:57Z

@whedon accept deposit=true

whedon · 2020-10-27T20:40:01Z

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

whedon · 2020-10-27T20:42:53Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-10-27T20:42:54Z

🚨🚨🚨 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.02621 joss-papers#1872
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02621
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2020-10-27T20:49:24Z

@TomDonoghue, @sappelhoff, @jamesheathers - many thanks for your reviews here and to @oliviaguest for editing this submission ✨

@JanCBrammer - your paper is now accepted into JOSS ⚡🚀💥

whedon · 2020-10-27T20:52:05Z

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

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02621/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02621/status.svg
   :target: https://doi.org/10.21105/joss.02621

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JanCBrammer · 2020-10-28T05:01:31Z

@oliviaguest, @TomDonoghue, @sappelhoff, @jamesheathers thank you all for your time and the thorough, helpful and timely reviews!

whedon added the review label Aug 31, 2020

whedon assigned oliviaguest Aug 31, 2020

whedon mentioned this issue Aug 31, 2020

[PRE REVIEW]: biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals #2593

Closed

whedon assigned jamesheathers, sappelhoff and TomDonoghue Sep 1, 2020

sappelhoff mentioned this issue Sep 28, 2020

custom zoom gets undone during manual peak editing + other issues JanCBrammer/biopeaks#15

Open

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 26, 2020

whedon added accepted published Papers published in JOSS labels Oct 27, 2020

arfon closed this as completed Oct 27, 2020

editorialbot mentioned this issue Jan 23, 2024

[PRE REVIEW]: JeFaPaTo - A joint toolbox for blinking analysis and facial features extraction #6267

Closed

editorialbot mentioned this issue Jul 30, 2024

[PRE REVIEW]: EMGFlow: A Python package for pre-processing and feature extraction of electromyographic signals #7054

Open

editorialbot mentioned this issue Sep 25, 2024

[PRE REVIEW]: respdetect: A Matlab tool for detecting breath events from whale biologger data #7282

Open

[REVIEW]: biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals #2621

[REVIEW]: biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals #2621

Comments

whedon commented Aug 31, 2020 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @TomDonoghue

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sappelhoff

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @jamesheathers

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Aug 31, 2020

whedon commented Aug 31, 2020

whedon commented Aug 31, 2020

oliviaguest commented Aug 31, 2020 • edited Loading

JanCBrammer commented Sep 10, 2020

oliviaguest commented Sep 21, 2020

sappelhoff commented Sep 21, 2020

oliviaguest commented Sep 22, 2020

TomDonoghue commented Sep 22, 2020

oliviaguest commented Sep 23, 2020

oliviaguest commented Sep 23, 2020

whedon commented Sep 23, 2020

oliviaguest commented Oct 25, 2020

JanCBrammer commented Oct 26, 2020

oliviaguest commented Oct 26, 2020

whedon commented Oct 26, 2020

oliviaguest commented Oct 26, 2020

whedon commented Oct 26, 2020

oliviaguest commented Oct 26, 2020

whedon commented Oct 26, 2020

oliviaguest commented Oct 26, 2020

whedon commented Oct 26, 2020

oliviaguest commented Oct 26, 2020

whedon commented Oct 26, 2020

oliviaguest commented Oct 26, 2020

whedon commented Oct 26, 2020

whedon commented Oct 26, 2020

JanCBrammer commented Oct 26, 2020

arfon commented Oct 27, 2020

whedon commented Oct 27, 2020

whedon commented Oct 27, 2020

whedon commented Oct 27, 2020

arfon commented Oct 27, 2020

whedon commented Oct 27, 2020

JanCBrammer commented Oct 28, 2020

whedon commented Aug 31, 2020 •

edited

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oliviaguest commented Aug 31, 2020 •

edited

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