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[REVIEW]: Wearablehrv: A Python package for the validation of heart rate and heart rate variability in wearables #6240

Closed editorialbot closed 1 week ago

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@aminsinichi<!--end-author-handle-- (Mohammadamin Sinichi) Repository: https://github.com/Aminsinichi/wearable-hrv/ Branch with paper.md (empty if default branch): Version: 0.2.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @AKuederle, @richrobe Archive: 10.5281/zenodo.12917981

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Markdown: [![status](https://joss.theoj.org/papers/a10cca1568263ddfa4e87f02fba1ba4d/status.svg)](https://joss.theoj.org/papers/a10cca1568263ddfa4e87f02fba1ba4d)

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

@jamesheathers & @AKuederle, 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 @oliviaguest 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 @AKuederle

📝 Checklist for @richrobe

editorialbot commented 7 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 7 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (216.3 files/s, 138003.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6           1015           1447           2614
TeX                              1             23              0            301
Markdown                         2             60              0            130
Jupyter Notebook                 1              0           1320             86
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            11           1099           2771           3149
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 7 months ago

Wordcount for paper.md is 1252

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.25080/majora-92bf1922-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/mcse.2007.55 is OK
- 10.1109/mcse.2007.53 is OK
- 10.5334/jors.305 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/joss.01026 is OK
- 10.5281/zenodo.883859 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1097/PSY.0000000000000133 is OK
- 10.1109/EMBC.2016.7591347 is OK
- 10.1038/tp.2016.73 is OK
- 10.1016/j.ijpsycho.2017.07.015 is OK
- 10.1088/0031-9155/19/3/003 is OK
- 10.1088/0967-3334/28/3/R01 is OK
- 10.1016/j.ijcard.2012.03.119 is OK
- 10.3389/fspor.2021.585870 is OK
- 10.1038/s41746-020-0226-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None
oliviaguest commented 7 months ago

:wave: Hi @jamesheathers, @AKuederle, thank you so much for helping out at JOSS. If you need any pointers, please feel free to look at previous reviews (which can be found by looking at published papers) and the documentation. If you need to comment on the code itself, opening an issue at the repo and then linking to it from here (to help me/others keep track) is the way to go. For comments on the paper, you can also open issues or PRs (say for typos), but those can be directly posted as replies in this issue. Thanks, and feel free to reach out if you need me. :relaxed:

oliviaguest commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

editorialbot commented 7 months ago

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

Aminsinichi commented 7 months ago

Thank you all for taking the time; very much appreciate it, and looking forward to hearing your thoughts and comments.

@oliviaguest, just a side note (I am not sure how important it is), but version 1.0.10 is currently published (https://pypi.org/project/wearablehrv/).

Thank you!

AKuederle commented 7 months ago

@oliviaguest @Aminsinichi I am really sorry that I haven't started my review yet! I got swammped with some other work the last couple of weeks. My plan is to do the review next week. I hope this does not cause to much of a delay.

oliviaguest commented 7 months ago

@Aminsinichi awesome! is the version above correct?

Aminsinichi commented 7 months ago

@oliviaguest Thank you very much! Yes, version 1.0.10 is currently running.

AKuederle commented 6 months ago

Review checklist for @AKuederle

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

oliviaguest commented 5 months ago

@AKuederle what is the status of your review at the moment? 😊

AKuederle commented 5 months ago

@oliviaguest Thanks for the reminder!

I opened some issues in the repo a while back to help the author improve their code, as I had some trouble understanding it/getting things to run:

https://github.com/Aminsinichi/wearable-hrv/issues/5 https://github.com/Aminsinichi/wearable-hrv/issues/4 https://github.com/Aminsinichi/wearable-hrv/issues/6 https://github.com/Aminsinichi/wearable-hrv/issues/1 https://github.com/Aminsinichi/wearable-hrv/issues/2

I was not able to fully validate the funcitonality of the package, as I wanted to wait for the author to respond to all of my suggestions. In particular, I found the example quite hard to understand. I wanted to wait for potential improvement (as suggested in one the issues), to fully work through it.

I read through the paper and it is well written. I was missing the comparison to other papers/packages a little and opened an issue about it (https://github.com/Aminsinichi/wearable-hrv/issues/10)

Regrading general scope, the package primarily provides IO and plotting functionality. The analysis components are all handled by existing packages. The GUI they build around it seems to be nice, but I am not sure if it is good enough and easy enough for people to use it over custom solutions using the analysis packages directly.

Aminsinichi commented 5 months ago

Thank you very much to both of you! I will continue working through the remaining issues and also make sure to justify the added value of the package in the paper as well. I will also improve the documentation and examples as you suggested, which should hopefully help you to test the full capabilities.

Aminsinichi commented 5 months ago

I wanted to let you know that I incorporated the majority of the suggestions that were issued on GitHub. Thank you!

oliviaguest commented 4 months ago

@AKuederle oh, fantastic! @Aminsinichi great stuff. I will give the reviewers some time to have a look. Thank you, all. :relaxed:

oliviaguest commented 4 months ago

@jamesheathers, @AKuederle any chance you can give an ETA for taking a look and reviewing the changes?

AKuederle commented 3 months ago

Sorry that this took so long... I went through the changes made, and everything works as expected now. @Aminsinichi amazing job on the documentation. Really easy to follow now.

Ready to be excepted from my side :)

Aminsinichi commented 3 months ago

So happy to hear this! Thank you so much for all your super useful comments!

Aminsinichi commented 3 months ago

Hi @oliviaguest. Just so you know, there have been no contact, review points, or comments on the repository by the other reviewer (i.e., @jamesheathers) since the beginning of the review process.

oliviaguest commented 3 months ago

I am really sorry about this. I will try and reach out to him, but also I will try and find you another review too.

oliviaguest commented 3 months ago

@richrobe do you have the time to review this for JOSS? If you have not reviewed for us before, please let me know and I can say more. 😊

richrobe commented 3 months ago

Hi @oliviaguest, thank you for the invitation! I had a brief look at the package and I don't have anything further to add to the comments of my lab colleague @AKuederle 😊

oliviaguest commented 3 months ago

Hi @oliviaguest, thank you for the invitation! I had a brief look at the package and I don't have anything further to add to the comments of my lab colleague @AKuederle 😊

Oh, thanks for the prompt reply. Is this because you think you can't add to the review or shall I add you as a reviewer and you can go through the list in your own pace?

richrobe commented 3 months ago

I think I can't add much as a reviewer as all major points have been covered, but I can also go through the list once more if you want!

Aminsinichi commented 2 months ago

@oliviaguest Dear Olivia, Just a kind request: if you could assign a second reviewer, I would be very grateful. Many thanks!

arfon commented 2 months ago

:wave: @richrobe @arianesasso @VBlesius – would any of you be willing to review this submission for JOSS? The submission under consideration is Wearablehrv: A Python package for the validation of heart rate and heart rate variability in wearables

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, and past papers you have published in JOSS, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

arfon commented 2 months ago

@editorialbot assign me as editor

:wave: @Aminsinichi – I'm going to be taking over this paper to help Olivia out a bit here.

editorialbot commented 2 months ago

Assigned! @arfon is now the editor

arfon commented 2 months ago

I think I can't add much as a reviewer as all major points have been covered, but I can also go through the list once more if you want!

@richrobe – I'm afraid I missed this comment above. For completeness, if you're willing to act as a second reviewer still, I would formally add you as a reviewer here, and then you would need to make your own checklist and complete that. Is that something you're willing to do?

richrobe commented 2 months ago

@arfon Sure, I can do that!

arfon commented 2 months ago

@editorialbot add @richrobe as reviewer

editorialbot commented 2 months ago

@richrobe added to the reviewers list!

arfon commented 2 months ago

@arfon Sure, I can do that!

Thanks so much @richrobe. Please go ahead and get started. As a reminder, to get started, you just need to type the following into a new comment here:

@editorialbot generate my checklist
richrobe commented 2 months ago

Review checklist for @richrobe

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

richrobe commented 2 months ago

Hi @arfon, I checked all items on my review checklist - so from my side, it's good to go!

arfon commented 1 month ago

@editorialbot remove @jamesheathers as reviewer

editorialbot commented 1 month ago

@jamesheathers removed from the reviewers list!

arfon commented 1 month ago

@Aminsinichi – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

Aminsinichi commented 1 month ago

@arfon - Thank you very much! I arranged the following:

Let me know if anything else is required from my side.

samhforbes commented 2 weeks ago

Hi @Aminsinichi thanks for doing that - taking a look now

samhforbes commented 2 weeks ago

@editorialbot check references

editorialbot commented 2 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.25080/majora-92bf1922-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/mcse.2007.55 is OK
- 10.1109/mcse.2007.53 is OK
- 10.5334/jors.305 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/joss.01026 is OK
- 10.5281/zenodo.883859 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1097/PSY.0000000000000133 is OK
- 10.1109/EMBC.2016.7591347 is OK
- 10.1038/tp.2016.73 is OK
- 10.1016/j.ijpsycho.2017.07.015 is OK
- 10.1088/0031-9155/19/3/003 is OK
- 10.1088/0967-3334/28/3/R01 is OK
- 10.1016/j.ijcard.2012.03.119 is OK
- 10.3389/fspor.2021.585870 is OK
- 10.1038/s41746-020-0226-6 is OK
- 10.1088/1361-6579/ab86d6 is OK
- 10.3758/s13428-020-01516-y is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: ipywidgets Documentation
- No DOI given, and none found for title: The Python Library Reference, release 3.8.2
- No DOI given, and none found for title: An introduction to tkinter
- No DOI given, and none found for title: Collaborative data science
- No DOI given, and none found for title: pyHRV: Development and evaluation of an open-sourc...

❌ MISSING DOIs

- 10.2307/2987937 may be a valid DOI for title: Measurement in Medicine: The Analysis of Method Co...

❌ INVALID DOIs

- https://doi.org/10.1016/S0031-9406(05)61211-4 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0169-2070(93)90079-3 is INVALID because of 'https://doi.org/' prefix
samhforbes commented 2 weeks ago

Hi @Aminsinichi can you please check whether the suggested missing DOI should be added, and the two invalid DOIs are corrected?

samhforbes commented 2 weeks ago

@editorialbot set v0.2.0 as version

editorialbot commented 2 weeks ago

Done! version is now v0.2.0

samhforbes commented 2 weeks ago

@editorialbot set https://doi.org/10.5281/zenodo.12917981 as archive

editorialbot commented 2 weeks ago

Done! archive is now 10.5281/zenodo.12917981