[REVIEW]: Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics #3714

whedon · 2021-09-10T12:23:38Z

Submitting author: @felixchenier (Félix Chénier)
Repository: https://github.com/felixchenier/kineticstoolkit
Version: 0.6.2
Editor: @meg-simula
Reviewer: @alcantarar, @melund
Archive: 10.5281/zenodo.5590654

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/05a091aa8cf7171d42d56e636c6d79fd/status.svg)](https://joss.theoj.org/papers/05a091aa8cf7171d42d56e636c6d79fd)

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Reviewer instructions & questions

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

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Review checklist for @alcantarar

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@felixchenier) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @melund

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@felixchenier) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 · 2021-09-10T12:23:41Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @alcantarar, @melund 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 a list of things I can do to help you, just type:

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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 · 2021-09-10T12:24:03Z

PDF failed to compile for issue #3714 with the following error:

 Can't find any papers to compile :-(

whedon · 2021-09-10T12:24:16Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=3.63 s (62.3 files/s, 215491.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0         681057
HTML                           132          17611            393          46552
JavaScript                      13           2405           2470           9212
Python                          36           2388           4207           6312
SVG                              1              0              0           2671
Jupyter Notebook                22              0           4620            831
CSS                              5            194             35            779
Markdown                         3             16              0             53
reStructuredText                 8             66            163             40
DOS Batch                        1              8              1             26
YAML                             1              1              0             15
make                             1              4              7              9
TOML                             1              0              0              3
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           226          22693          11896         747562
-------------------------------------------------------------------------------


Statistical information for the repository '662d8a4655e3f5a50958bf44' was
gathered on 2021/09/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Félix Chénier                157         48648          29969          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Félix Chénier           26994           55.5          8.5               14.89

meg-simula · 2021-09-10T12:24:38Z

@whedon generate pdf from branch JOSS

whedon · 2021-09-10T12:24:40Z

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

meg-simula · 2021-09-10T12:24:55Z

@whedon check references from branch JOSS

whedon · 2021-09-10T12:24:57Z

Attempting to check references... from custom branch JOSS

whedon · 2021-09-10T12:25:14Z

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

OK DOIs

- 10.1016/j.jbiomech.2004.05.042 is OK
- 10.21105/joss.02431 is OK
- 10.1016/j.cmpb.2016.11.007 is OK
- 10.21105/joss.02562 is OK
- 10.1109/SII.2019.8700380 is OK
- 10.1098/rsos.140449 is OK
- 10.1371/journal.pcbi.1006223 is OK
- 10.1016/j.piutam.2011.04.023 is OK
- 10.21105/joss.00927 is OK
- 10.1101/2021.02.27.432868 is OK
- 10.21105/joss.02911 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-09-10T12:25:16Z

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

meg-simula · 2021-09-10T12:28:34Z

👋🏼 @felixchenier @alcantarar @melund this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time. Also note that the current paper is in the branch JOSS, so use e.g.

-> @whedon generate pdf from branch JOSS
-> @whedon check references from branch JOSS

Please feel free to ping me (@meg-simula ) if you have any questions/concerns.

alcantarar · 2021-09-24T04:14:46Z

@whedon remind @alcantarar in 2 days 🙄

whedon · 2021-09-24T04:14:49Z

I'm sorry @alcantarar, I'm afraid I can't do that. That's something only editors are allowed to do.

melund · 2021-09-24T05:29:06Z

Sorry for the delay in getting to this. I hope to look at it in the weekend.

whedon · 2021-09-24T12:23:48Z

👋 @melund, please update us on how your review is going (this is an automated reminder).

whedon · 2021-09-24T12:23:48Z

👋 @alcantarar, please update us on how your review is going (this is an automated reminder).

alcantarar · 2021-09-26T17:28:11Z

I've been updating the checklist along the way, but haven't completed functionality testing/documentation.

alcantarar · 2021-09-27T21:41:10Z

👋🏾 @meg-simula I've completed my review. The repo looks good to me and any bugs I've found have been addressed except for 1 typo in the paper. I think this toolkit is a nice way to introduce beginner programmers to biomechanical analyses and research with tutorials on how to use the included functions to process a variety of timeseries data. It addresses the valid statement of need outlined in the paper.

@felixchenier, great work! 👍🏾 I particularly enjoyed the 2d kinematics tutorial and was impressed with the 3-D marker/segment visualization. Thanks for developing and maintaining this tool for the biomechanics community!

meg-simula · 2021-10-01T09:13:27Z

Thanks @alcantarar for the constructive review and comments!

meg-simula · 2021-10-01T09:14:47Z

@melund How is your review going? Do let us know if you need any input from the authors or me to proceed at this stage.

melund · 2021-10-01T09:31:38Z

@meg-simula Sorry about the delay. I might have been too optimistic about my time.

I still need to go through the documentation and really try out the functionality. I only just started on that part. I have no time this weekend, but I will try to do it some evening next week.

meg-simula · 2021-10-01T09:33:33Z

@melund We fully understand, your contribution and review is much appreciated!

felixchenier · 2021-10-04T13:13:16Z

@alcantarar Thank you Ryan for your very kind comments, it is much appreciated.

melund · 2021-10-08T20:14:57Z

@meg-simula. I have finished my review and worked my way through the documentation and all the tutorials It is a nice tool. I could see my self use the timeseries object in some of my own work. It also has many parts will be of great value to beginners in the area of biomechanics. Especially because the documentation and tutorials are so well written. I can recommend this for publication.

felixchenier · 2021-10-12T19:25:20Z

@whedon generate pdf from branch JOSS

whedon · 2021-10-20T16:41:23Z

Attempting to check references... from custom branch JOSS

whedon · 2021-10-20T16:41:37Z

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

OK DOIs

- 10.1016/j.jbiomech.2004.05.042 is OK
- 10.21105/joss.02431 is OK
- 10.1016/j.cmpb.2016.11.007 is OK
- 10.21105/joss.02562 is OK
- 10.1109/SII.2019.8700380 is OK
- 10.1098/rsos.140449 is OK
- 10.1371/journal.pcbi.1006223 is OK
- 10.1016/j.piutam.2011.04.023 is OK
- 10.21105/joss.00927 is OK
- 10.1101/2021.02.27.432868 is OK
- 10.21105/joss.02911 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1007/978-3-540-25944-2_157 is OK

MISSING DOIs

- None

INVALID DOIs

- None

meg-simula · 2021-10-20T16:43:39Z

@felixchenier Congratulations on an excellent paper, I'll send this off to the editors-in-chief for a final editorial decision now.

meg-simula · 2021-10-20T16:44:54Z

Ah, just forgot a few points. At this point could you:

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
Please list the DOI of the archived version here.

felixchenier · 2021-10-21T20:00:05Z

@meg-simula

[X] Make a tagged release of your software, and list the version tag of the archived version here.

0.6.2

[X] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[X] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[X] Please list the DOI of the archived version here.

10.5281/zenodo.5590654

meg-simula · 2021-10-22T09:13:22Z

@whedon set 10.5281/zenodo.5590654 as archive

whedon · 2021-10-22T09:13:26Z

OK. 10.5281/zenodo.5590654 is the archive.

meg-simula · 2021-10-22T09:14:06Z

@whedon set 0.6.2 as version

whedon · 2021-10-22T09:14:10Z

OK. 0.6.2 is the version.

meg-simula · 2021-10-22T09:14:20Z

@whedon recommend-accept

whedon · 2021-10-22T09:14:23Z

Attempting dry run of processing paper acceptance...

whedon · 2021-10-22T09:14:39Z

PDF failed to compile for issue #3714 with the following error:

 Can't find any papers to compile :-(

felixchenier · 2021-10-22T11:33:39Z

I just merged the JOSS branch into master, now that the paper is accepted. It should find the paper now.

Kevin-Mattheus-Moerman · 2021-10-23T13:33:09Z

@whedon recommend-accept

whedon · 2021-10-23T13:33:12Z

Attempting dry run of processing paper acceptance...

whedon · 2021-10-23T13:33:26Z

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

OK DOIs

- 10.1016/j.jbiomech.2004.05.042 is OK
- 10.21105/joss.02431 is OK
- 10.1016/j.cmpb.2016.11.007 is OK
- 10.21105/joss.02562 is OK
- 10.1109/SII.2019.8700380 is OK
- 10.1098/rsos.140449 is OK
- 10.1371/journal.pcbi.1006223 is OK
- 10.1016/j.piutam.2011.04.023 is OK
- 10.21105/joss.00927 is OK
- 10.1101/2021.02.27.432868 is OK
- 10.21105/joss.02911 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1007/978-3-540-25944-2_157 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-10-23T13:33:48Z

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

Check final proof 👉 openjournals/joss-papers#2704

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2704, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman · 2021-10-23T13:37:32Z

@whedon accept deposit=true

whedon · 2021-10-23T13:37:35Z

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

whedon · 2021-10-23T13:38:20Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-10-23T13:38:21Z

🚨🚨🚨 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.03714 joss-papers#2705
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03714
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2021-10-23T13:43:38Z

@felixchenier congratulations on getting your paper published in JOSS!

@meg-simula thanks for editing this submission, and thanks a million to @alcantarar and @melund for your review efforts!

whedon · 2021-10-23T13:43:43Z

🎉🎉🎉 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.03714/status.svg)](https://doi.org/10.21105/joss.03714)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03714">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03714/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03714/status.svg
   :target: https://doi.org/10.21105/joss.03714

This is how it will look in your documentation:

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felixchenier · 2021-10-23T16:08:13Z

Thank you all for this review, I wish you all the best.

whedon added Python review labels Sep 10, 2021

whedon assigned meg-simula Sep 10, 2021

whedon mentioned this issue Sep 10, 2021

[PRE REVIEW]: Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics #3343

Closed

whedon assigned alcantarar and melund Sep 11, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 22, 2021

whedon added accepted published Papers published in JOSS labels Oct 23, 2021

Kevin-Mattheus-Moerman closed this as completed Oct 23, 2021

editorialbot mentioned this issue Sep 28, 2023

[PRE REVIEW]: Learning from Crowds with Crowd-Kit #5898

Closed

editorialbot mentioned this issue Dec 19, 2023

[PRE REVIEW]: chemotools: A Python Package that Integrates Chemometrics and scikit-learn #6162

Closed

[REVIEW]: Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics #3714

[REVIEW]: Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics #3714

Comments

whedon commented Sep 10, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @alcantarar

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @melund

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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whedon commented Sep 10, 2021 •

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