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

Closed whedon closed 3 years ago

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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

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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @meg-simula 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 ✨

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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 :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.

:star: Important :star:

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:

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whedon commented 3 years ago

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

 Can't find any papers to compile :-(
whedon commented 3 years ago 
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 commented 3 years ago

@whedon generate pdf from branch JOSS

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...
meg-simula commented 3 years ago

@whedon check references from branch JOSS

whedon commented 3 years ago 
Attempting to check references... from custom branch JOSS
whedon commented 3 years ago 
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 commented 3 years ago

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

meg-simula commented 3 years ago

👋🏼 @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 commented 3 years ago

@whedon remind @alcantarar in 2 days 🙄

whedon commented 3 years ago

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

melund commented 3 years ago

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

whedon commented 3 years ago

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

whedon commented 3 years ago

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

alcantarar commented 3 years ago

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

alcantarar commented 3 years ago

👋🏾 @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 commented 3 years ago

Thanks @alcantarar for the constructive review and comments!

meg-simula commented 3 years ago

@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 commented 3 years ago

@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 commented 3 years ago

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

felixchenier commented 3 years ago

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

melund commented 3 years ago

@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 commented 3 years ago

@whedon generate pdf from branch JOSS

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...
whedon commented 3 years ago

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

felixchenier commented 3 years ago

@whedon generate pdf from branch JOSS

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...
whedon commented 3 years ago

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

felixchenier commented 3 years ago

@meg-simula @melund @alcantarar

Thank you for your time, reviews and kind comments. I have introduced the changes suggested by @alcantarar (https://github.com/felixchenier/kineticstoolkit/issues/66) into the new current version.

I hope that everything has been addressed.

Kind regards,

Félix

meg-simula commented 3 years ago

Excellent, thank you @melund, @alcantarar and @felixchenier. I'll do a final pass now.

meg-simula commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

 Can't find any papers to compile :-(
meg-simula commented 3 years ago

@whedon generate pdf from branch JOSS

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...
whedon commented 3 years ago

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

meg-simula commented 3 years ago

@whedon check references from branch JOSS

whedon commented 3 years ago 
Attempting to check references... from custom branch JOSS
whedon commented 3 years ago 
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 commented 3 years ago

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

meg-simula commented 3 years ago

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

felixchenier commented 3 years ago

@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 commented 3 years ago

@whedon set 10.5281/zenodo.5590654 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5590654 is the archive.

meg-simula commented 3 years ago

@whedon set 0.6.2 as version

whedon commented 3 years ago

OK. 0.6.2 is the version.

meg-simula commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago

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

 Can't find any papers to compile :-(
felixchenier commented 3 years ago

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