[REVIEW]: Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion

[whedon]

Submitting author: @heath-henninger (Heath Henninger)
Repository: https://github.com/klevis-a/kinematics-vis.git
Version: v0.2.0
Editor: @adi3
Reviewer: @destogl, @nnadeau
Archive: 10.5281/zenodo.5781772

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/ef7f95fc8216dd7c6d37a6679374b175/status.svg)](https://joss.theoj.org/papers/ef7f95fc8216dd7c6d37a6679374b175)

Reviewers and authors:

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@destogl & @nnadeau, 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 @destogl

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 (@heath-henninger) 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 @nnadeau

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 (@heath-henninger) 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @destogl, @nnadeau 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:

1. 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:

@whedon commands

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.03 s (1310.0 files/s, 162041.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      32            621            173           3716
CSS                              3             60              2            416
HTML                             2             13              0            220
Markdown                         1             12              0             31
Bourne Shell                     2              0              0             27
DOS Batch                        2              0              0             27
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            43            706            175           4438
-------------------------------------------------------------------------------


Statistical information for the repository 'f6ff8c2f6f61e832d1e41930' was
gathered on 2021/07/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Klevis                         135          8091           3929           97.00
Klevis Aliaj                     5           360             12            3.00

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
Klevis Aliaj               4510         1252.8          6.9                3.84

[whedon]

PDF failed to compile for issue #3490 with the following error:

 Can't find any papers to compile :-(

[adi3]

@whedon generate paper from branch joos

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[adi3]

@whedon generate pdf from branch joos

[whedon]

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

[whedon]

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

[adi3]

👋🏼 @heath-henninger @destogl @nnadeau 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. When doing so, please mention openjournals/joss-reviews#3490 so that a link is created to this thread (and I can keep an eye on what is happening). 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.

Please feel free to ping me (@adi3) if you have any questions/concerns. Thank you for all your help!!

[whedon]

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

[whedon]

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

[engnadeau]

@adi3 , before getting started, I think there may be an issue with the "submitting author":

• the review has @heath-henninger as the submitting author, but it's an inactive account with no contributions to the repo
• @klevis-a is the sole contributor to the repo, but isn't mentioned anywhere here

[heath-henninger]

A valid comment Nicholas. As the PI on the grant that collected these kinematic data and stimulated the generation of the visualization and analysis application, I typically submit the manuscripts for peer-review. In this case Klevis, a recent PhD graduate from my lab, was the lead investigator who created the code in support of his dissertation research. This is definitely a case of our naiveté about the JOSS process versus the typical peer reviewed journal. I sense this requires us to switch the submitting author, but will this require the whole review process to begin again? Or can we shortcut the process with a simple assignment change? Any information is helpful. Heath From: Nicholas Nadeau, Ph.D., P.Eng. ***@***.*** Sent: Sunday, August 1, 2021 8:52 AM To: openjournals/joss-reviews ***@***.***> Cc: Heath Byron Henninger ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [REVIEW]: Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion (#3490) @adi3<https://github.com/adi3> , before getting started, I think there may be an issue with the "submitting author": * the review has @heath-henninger<https://github.com/heath-henninger> as the submitting author, but it's an inactive account with no contributions to the repo * @klevis-a<https://github.com/klevis-a> is the sole contributor to the repo, but isn't mentioned anywhere here — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3490 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUO5S32JPCMAF23H3GGS4ZDT2VNRNANCNFSM5AHVHJWA>.

[whedon]

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

[whedon]

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

[heath-henninger]

@adi3, we will likely use Zenodo as that is where our other open access kinematic data sets that drive Kinematics-vis live currently. Will that Zenodo DOI then be listed in the published manuscript? Will it move forward from DRAFT status after that link is published? Sorry for the questions...this is the first time we have published using the JoOS mechanism and it's quite different than the common print publications we deal with!

[klevis-a]

Thank you, @adi3!

Just released version 0.2.0. This is archived on Zenodo with a DOI of 10.5281/zenodo.5781772.

[adi3]

@heath-henninger yes, the DOI will be published in the manuscript. I believe I have everything from your side now to push this to publication.

[adi3]

@whedon set 10.5281/zenodo.5781772 as archive

[whedon]

OK. 10.5281/zenodo.5781772 is the archive.

[adi3]

@whedon set v0.2.0 as version

[whedon]

OK. v0.2.0 is the version.

[adi3]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3490 with the following error:

 Can't find any papers to compile :-(

[adi3]

@whedon recommend-accept from branch joos

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/j.jbiomech.2004.05.042 is OK
- 10.1016/j.jbiomech.2010.10.042 is OK
- 10.1016/s0021-9290(00)00032-4 is OK
- 10.1115/1.2894884 is OK
- 10.1016/j.gaitpost.2021.05.004 is OK
- 10.1016/j.jbiomech.2011.04.031 is OK
- 10.2106/jbjs.g.01483 is OK
- 10.1007/s11517-018-1903-3 is OK
- 10.1109/TBME.2007.901024 is OK

MISSING DOIs

- 10.1036/1097-8542.245400 may be a valid DOI for title: Euler angles

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2838

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2838, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joos 

[arfon]

@whedon accept deposit=true from branch joos

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03490 joss-papers#2839
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03490
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...

[arfon]

@destogl, @nnadeau – many thanks for your reviews here and to @adi3 for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@heath-henninger – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 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.03490/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03490/status.svg
   :target: https://doi.org/10.21105/joss.03490

This is how it will look in your documentation:

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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:

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[klevis-a]

Thank you @arfon and thank you @adi3! Working through the review process for JOSS has been cool. I very much enjoyed the transparency and automation. I am thankful for the acceptance and for all the hard work everyone has put into the journal.

@destogl, @nnadeau thank you for taking the time to review the manuscript and software, and for your feedback!