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

whedon commented 2 years ago

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

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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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✨ 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 @destogl

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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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whedon commented 2 years ago

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 commented 2 years ago

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

 Can't find any papers to compile :-(

adi3 commented 2 years ago

@whedon generate paper from branch joos

whedon commented 2 years ago

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

@whedon commands

adi3 commented 2 years ago

@whedon generate pdf from branch joos

whedon commented 2 years ago

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

whedon commented 2 years ago

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

adi3 commented 2 years ago

👋🏼 @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 commented 2 years ago

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

whedon commented 2 years ago

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

engnadeau commented 2 years ago

@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 commented 2 years ago

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)

@adi3https://github.com/adi3 , before getting started, I think there may be an issue with the "submitting author":

the review has @heath-henningerhttps://github.com/heath-henninger as the submitting author, but it's an inactive account with no contributions to the repo
@klevis-ahttps://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 GitHubhttps://github.com/openjournals/joss-reviews/issues/3490#issuecomment-890533820, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUO5S32JPCMAF23H3GGS4ZDT2VNRNANCNFSM5AHVHJWA.

engnadeau commented 2 years ago

@adi3 @klevis-a, i did a first pass of the repo from a software architecture point of view, see the issues linked above

adi3 commented 2 years ago

@nnadeau thank you for bringing up the point about the submitting author. @heath-henninger appreciate the additional clarity you provided. We do expect the submitting author to have made substantial contributions to the repository, but I will make an exception to continue with this review for two reasons:

@klevis-a, who made all (or at least most of) the commits to the repository, is still listed as the primary author of the paper, and
@heath-henninger did have a role in the authorship and contributed to the work that went in the paper; it seems now he is simply handling the logistics of the publication process.

Separately - @klevis-a please see the list of issues opened above and let @nnadeau know when you have them ready for review.

Thanks everyone for your contribution so far!

klevis-a commented 2 years ago

@nnadeau thank you for taking time to review our submission. @nnadeau @adi3, this software was written to help me visually understand how we quantify human motion. It provided much of the insight that helped us publish "Beyond Euler/Cardan analysis: True glenohumeral axial rotation during arm elevation and rotation". Furthermore, other biomechanics researchers have found it helpful for understanding and teaching Euler/Cardan angles. I have already finished my graduate studies as of May of this year and moved on. And, I don't have the time to address the issues regarding standard packaging, unit tests, and continuous integration. Writing good unit tests can take as long (if not longer) than writing the actual software. I do believe that these topics are important, but unfortunately my time is limited.

If you would still consider the software for publication without me having to address the unit tests, continuous integration, and standard packaging then I can start addressing the other issues. If not, then I understand the choice. The journal (rightfully so) may need to uphold certain standards, but I won't be able to fulfill them.

adi3 commented 2 years ago

@klevis-a thank your for the clear response.

@heath-henninger do you have alternate resources to fix the editorial issues raised in this review, or perhaps you could do them yourself?

heath-henninger commented 2 years ago

Unfortunately not. Klevis was a bit of a unicorn in my research team with his extensive background in code and software development. I hired him specifically because he could do great things that my team was otherwise unprepared to accomplish. Believe that we will feel his absence now that he has graduated.

And this includes me. I am an experimental biomechanist by trade…so my coding experience ends at Matlab and some FORTRAN in the early 90s :-)

On Aug 3, 2021, at 5:21 AM, Adi Singh @.***> wrote:

@klevis-ahttps://github.com/klevis-a thank your for the clear response.

@heath-henningerhttps://github.com/heath-henninger do you have alternate resources to fix the editorial issues raised in this review, or perhaps you could do them yourself?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/3490#issuecomment-891764734, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUO5S35ORY6J7TKMQCSVAJLT27GMPANCNFSM5AHVHJWA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email.

adi3 commented 2 years ago

@klevis-a I've discussed this with the editorial team and this is how we can proceed -

You do not need to go with standard packaging, as long as installation instructions are clearly documented in the Readme.
In the absence of automated tests (and CI/CD), we would at least need documented manual steps that can be followed to objectively check the expected functionality of the software (e.g., a sample input file to assert behavior).

I believe you'll be able to work on the other issues as is. Let us know once you've fixed all the tickets opened by @nnadeau.

klevis-a commented 2 years ago

@adi3 thank you for being flexible! Yes, I can provide manual steps that can be followed to objectively check the expected functionality of the software. And I'll start working on the other tickets.

klevis-a commented 2 years ago

@nnadeau @adi3 I have now addressed the currently open issues. I have left them open since I thought they would be easier to track this way. @nnadeau feel free to close them as you review the changes. Otherwise, I can close them - whichever makes this process easier.

adi3 commented 2 years ago

@destogl @nnadeau - 👋 please update us on how your review is going

destogl commented 2 years ago

@whedon generate paper from branch joos

whedon commented 2 years ago

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

@whedon commands

destogl commented 2 years ago

@whedon generate pdf from branch joos

whedon commented 2 years ago

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

whedon commented 2 years ago

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

destogl commented 2 years ago

@adi3 Thanks for your patience. The holiday season behind brought hard-time to focus on this review. Next time I have to plan better and let you know.

@klevis-a, @heath-henninger: Here are my overall comments on software:

The live code demo was very useful. Thanks for creating it. This is especially useful for target users.
Regarding "Substantial scholarly effort": my main area of research and interest is robotics, although in my research I was "touching" kinematics of humans, I don't have in-depth knowledge of the field. Nevertheless, the kinematics challenged the software is addressing is very well known and discussed in robotics, and there we manged to find a suitable standard for data-representation. Therefore, I clearly see contribution of this software and regarding discussion in klevis-a/kinematics-vis#8 I am convicted in added values for the biomechanics research community.

Please also consider a newly opened issues.

klevis-a commented 2 years ago

@destogl thank you for chiming in on the contribution of the software - I appreciate it. We also think that it adds value to the biomechanics community, but of course, we are a bit biased.

The software has been especially useful in convincing other biomechanics researchers that Euler angles cannot be added or subtracted. My first Ph.D. project was in robotics so this was almost a given to me. But the practice of subtracting Euler angles is still widely practiced in the biomechanics community.

klevis-a commented 2 years ago

@whedon generate pdf from branch joos

whedon commented 2 years ago

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

whedon commented 2 years ago

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

engnadeau commented 2 years ago

wonderful updates @klevis-a , especially the usage of yarn. Paper is good to go from my end. Kudos!

klevis-a commented 2 years ago

Thank you @nnadeau! I opened a pull request based on the switch to yarn, but I couldn't assign you as a Reviewer. But I take it you approve, so I'll merge it to master.

heath-henninger commented 2 years ago

@adi3 are there any remaining outstanding issues with this submission? Looking to make sure we are not missing anything that remains to be completed. Thanks! Heath

adi3 commented 2 years ago

@heath-henninger looks like @nnadeau is done with his review (Thank you Nicholas!), and @destogl has only 3 more items remaining (Thank you so far Denis!). As soon as these last items are marked completed, I will be happy to move this forward to publication.

adi3 commented 2 years ago

@destogl - 👋 please update us on how your review is going

adi3 commented 2 years ago

@destogl - I see you're almost done with your checklist. Could you please plan to finish it sometime this week so we can move ahead with publishing this paper? Greatly appreciate your help!

adi3 commented 2 years ago

@destogl - 👋 please update us on how your review is going

adi3 commented 2 years ago

@destogl - are you still able to finish this review? I see you only have a couple of items left, so would be great to get a response from you on when you can have them completed. Alternatively, please let me know if you are unable to continue so we can look for another reviewer. Thank you.

destogl commented 2 years ago

@adi3 I will finish it this week. Thanks for reaching out and for the huge patience!

destogl commented 2 years ago

Dear all,

Thank you for your patience and for the opportunity for his review. I am deeply sorry that my review took so long, I will work to change this in the future and check my notifications regularly.

@adi3 my review is finished.

@klevis-a and @heath-henninger congratulation for the great work! I am fully supporting acceptance of its publication. The improvements @klevis-a did after my review are great and now I as non-biomechanic person can understand how the software works.

A one closing note: @klevis-a I think you can close klevis-a/kinematics-vis#8 it does not seem to be relevant anymore.

I wish you all much success in the future and to continue producing great open-source software :)

klevis-a commented 2 years ago

@destogl thank you for the kind words and for making time to review our software. @heath-henninger and I, very much appreciate your efforts!

heath-henninger commented 2 years ago

@destogl I echo @klevis-a's comments, thank you for the kind words and review! We hope this platform will find wide utilization in biomechanics laboratories and courses to help learning and reinforcing kinematics concepts more intuitively.

adi3 commented 2 years ago

Hurray! @destogl thank you so much for your thorough review! We appreciate all the effort you put into it.

@klevis-a @heath-henninger - I have just one more formality required from you. Can you please issue a new tagged release of the software and archive it on Zenodo, figshare or another archiving platform of your choice? Then report the release's version number and the archive's DOI on this thread. Thank you, and congratulations!

adi3 commented 2 years ago

@whedon generate pdf from branch joos

whedon commented 2 years ago

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

whedon commented 2 years ago

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

heath-henninger commented 2 years ago

@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 commented 2 years ago

Thank you, @adi3!

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

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