[REVIEW]: biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals
Closed this issue · 42 comments
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
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.
Status
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Markdown: [](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? 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. JanCBrammer/biopeaks#13
- Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). JanCBrammer/biopeaks#12
- Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)? JanCBrammer/biopeaks#11 JanCBrammer/biopeaks#10
- Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified? 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 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? 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?
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 🎉.
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.
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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
👋👋👋
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.
@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 :)
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?
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. :-)
@sappelhoff oh, amazing! Great work — thanks. 👍
I should be able to do my review by the end of the week!
@TomDonoghue Oh, great! I'll set up a reminder for both of us.
@whedon remind @TomDonoghue in 9 days
Reminder set for @TomDonoghue in 9 days
As an update: @JanCBrammer has addressed most of my suggestions by now. There are three remaining open issues from my side:
- consistent docstring documentation JanCBrammer/biopeaks#11
- test coverage reporting JanCBrammer/biopeaks#8
- developer documentation on how to build the docs JanCBrammer/biopeaks#10
It'd be nice to have these points addressed before a final evaluation.
Just a note that I have basically finished my first round of review. Thanks to @sappelhoff for making my job easier, as he already pointed out a lot of good suggestions! I made some additional suggestions, mostly by opening a couple issues on the tool repo. As a general note, I consider a few of the issues I opened as suggestions (not strictly required for the paper), and so to guide what I think is most important would be:
- I agree with @sappelhoff in particular on fixing up the documentation a bit (JanCBrammer/biopeaks#11)
- some small paper checks & fixes (JanCBrammer/biopeaks#16)
- noting test dependencies and how to run them, which I've added to an existing issue (JanCBrammer/biopeaks#8)
The other issues are potential clean ups / clarifications / extensions that may be useful for the module, but are perhaps a little longer term, and I don't think necessarily need to be done now.
When these things are all checked / done, I'm happy to come back and sign-off on the remaining points.
@sappelhoff, @TomDonoghue, thank you for you clear and thorough reviews! I'll try to address your issues over the coming two weeks. I'll keep you in the loop by tagging you once I've resolved an issue. Also, I will notify you here once I think the repo is ready for your final evaluation / sign-off (in case you don't have time and/or resources to keep track of single issues).
@sappelhoff, @TomDonoghue, I've addressed all "blocking" issues (JanCBrammer/biopeaks#8, JanCBrammer/biopeaks#10, JanCBrammer/biopeaks#11, JanCBrammer/biopeaks#16) and the repository is now ready for your final evaluation.
@jamesheathers please give us an ETA if you can here.
I checked all issues that I raised with @JanCBrammer and everything has been addressed to my full satisfaction. biopeaks is a useful piece of software that will make life easier for its users. The accompanying paper is well written, the documentation is up to date an thorough. Unit tests and coverage reports are in place, and best practices of open source software (and open science, where applicable) are being followed. I see a need for software like biopeaks that provides a GUI for users that are not (yet) familiar with scripting analyses.
I recommend accepting this project for a publication in JOSS.
Hello all,
My apologies for the delay. There was also another problem: I can't find anything to change here.
- I got this to run cleanly and straightforwardly with a fresh install of Miniconda
- All of the core functionality I would expect for a R-peak/systolic interval detector is present, and it all works to a higher reliability than simpler peak detection methods
- I gave it an engineer (not Python naive but biosignal analysis naive) and he was immediately able to get the software to function as intended and to my satisfaction
- Any additional suggestions for analytic functions I could make would go beyond the scope of the paper
- The documentation is extremely good
In short, I can't actually find anything I'd want to change that makes a reasonable contribution here. I don't think I've ever written an exclusively positive review before, but here we are. This will form a useful tool for beginner to intermediate biosignal analysts who wish to explore cardiac cyclic time series.
@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?
@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.
@whedon set 10.5281/zenodo.4133324 as archive
OK. 10.5281/zenodo.4133324 is the archive.
@whedon set v1.4.1 as version
OK. v1.4.1 is the version.
@whedon generate pdf
@whedon check references
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 accept
Attempting dry run of processing paper acceptance...
@JanCBrammer does this all look good to you (the final PDF, etc.)?
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
👋 @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
does this all look good to you (the final PDF, etc.)?
@oliviaguest, the final article proof looks good to me!
Doing it live! Attempting automated processing of paper acceptance...
🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦
🚨🚨🚨 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 👉 openjournals/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...
@TomDonoghue, @sappelhoff, @jamesheathers - many thanks for your reviews here and to @oliviaguest for editing this submission ✨
@JanCBrammer - your paper is now accepted into JOSS ⚡🚀💥
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉
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@oliviaguest, @TomDonoghue, @sappelhoff, @jamesheathers thank you all for your time and the thorough, helpful and timely reviews!