Closed whedon closed 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:.
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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
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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
PDF failed to compile for issue #3490 with the following error:
Can't find any papers to compile :-(
@whedon generate paper from branch joos
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@whedon commands
@whedon generate pdf from branch joos
Attempting PDF compilation from custom branch joos. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
👋🏼 @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!!
:wave: @nnadeau, please update us on how your review is going (this is an automated reminder).
:wave: @destogl, please update us on how your review is going (this is an automated reminder).
@adi3 , before getting started, I think there may be an issue with the "submitting author":
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":
— 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.
@adi3 @klevis-a, i did a first pass of the repo from a software architecture point of view, see the issues linked above
@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:
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!
@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.
@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?
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.
@klevis-a I've discussed this with the editorial team and this is how we can proceed -
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.
@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.
@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.
@destogl @nnadeau - 👋 please update us on how your review is going
@whedon generate paper from branch joos
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@whedon commands
@whedon generate pdf from branch joos
Attempting PDF compilation from custom branch joos. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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:
Please also consider a newly opened issues.
@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.
@whedon generate pdf from branch joos
Attempting PDF compilation from custom branch joos. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
wonderful updates @klevis-a , especially the usage of yarn
. Paper is good to go from my end. Kudos!
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.
@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
@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.
@destogl - 👋 please update us on how your review is going
@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!
@destogl - 👋 please update us on how your review is going
@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.
@adi3 I will finish it this week. Thanks for reaching out and for the huge patience!
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 :)
@destogl thank you for the kind words and for making time to review our software. @heath-henninger and I, very much appreciate your efforts!
@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.
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!
@whedon generate pdf from branch joos
Attempting PDF compilation from custom branch joos. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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!
Thank you, @adi3!
Just released version 0.2.0. This is archived on Zenodo with a DOI of 10.5281/zenodo.5781772.
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
: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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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.)
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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
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Software paper
Review checklist for @nnadeau
Conflict of interest
Code of Conduct
General checks
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Documentation
Software paper