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[PRE REVIEW]: MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco #6844

Closed editorialbot closed 2 months ago

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@Aravind-Sundararajan<!--end-author-handle-- (Aravind Sundararajan) Repository: https://github.com/Aravind-Sundararajan/MocoExtendProblem Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @0todd0000, @aasadi1 Managing EiC: Kevin M. Moerman

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Author instructions

Thanks for submitting your paper to JOSS @Aravind-Sundararajan. Currently, there isn't a JOSS editor assigned to your paper.

@Aravind-Sundararajan if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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editorialbot commented 5 months ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.29 s (696.0 files/s, 424496.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                             86              0           1585         111339
C/C++ Header                    50            471           1193           3063
MATLAB                          29            440            803           1840
C++                             32            358            392           1292
TeX                              1             17              0            124
Markdown                         2             40              0            103
CMake                            1             11              4             97
YAML                             1              0              5             30
-------------------------------------------------------------------------------
SUM:                           202           1337           3982         117888
-------------------------------------------------------------------------------

Commit count by author:

   141  Aravind-Sundararajan
    85  AspectWaltz
    38  Varun Joshi
     3  Aravind Sundararajan
editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1423

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

Aravind-Sundararajan commented 5 months ago

@editorialbot commands

editorialbot commented 5 months ago

Hello @Aravind-Sundararajan, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
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Aravind-Sundararajan commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

Aravind-Sundararajan commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

Aravind-Sundararajan commented 5 months ago

@editorialbot check references

editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1137/16M1062569 is OK
- 10.1371/journal.pcbi.1008493 is OK
- 10.1002/cnm.3777 is OK
- 10.1098/rsif.2019.0402 is OK
- 10.1371/journal.pcbi.1010466 is OK
- 10.1371/journal.pcbi.1006223 is OK
- 10.1186/s12984-023-01279-5 is OK
- 10.1007/s10107-004-0559-y is OK

MISSING DOIs

- No DOI given, and none found for title: Optimal control gait simulations of older adults p...
- No DOI given, and none found for title: Optimal Control Simulations of 3-D Walking in Huma...
- No DOI given, and none found for title: mexplus

INVALID DOIs

- None
Aravind-Sundararajan commented 5 months ago

@editorialbot generate preprint

editorialbot commented 5 months ago

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

Kevin-Mattheus-Moerman commented 5 months ago

@editorialbot assign me as editor

editorialbot commented 5 months ago

Assigned! @Kevin-Mattheus-Moerman is now the editor

Kevin-Mattheus-Moerman commented 5 months ago

@Aravind-Sundararajan thanks for this submission. I will be the editor for this submission. I will soon start looking for reviewers. If you'd like to suggest reviewers that is fine/helpful. You can mention their GitHub handles here but leave out the @ symbol so they are not tagged.

For the moment, can you:

Aravind-Sundararajan commented 5 months ago

Hello @Kevin-Mattheus-Moerman, thank you for taking the time to do this pre-review.

As for DOIs, Mexplus is a project hosted on github, and the other two references are conference abstracts for presentations at podium or posters.

I have edited the authors list so the affiliations spell out United States of America.

I have also gone ahead and updated my readme and added the COC and CONTRIBUTING files. Let me know if there is anything else I can do here.

As far as reviewers, am I allowed to suggest people who did not yet volunteer? My thinking was to suggest users on OpenSim

Kevin-Mattheus-Moerman commented 5 months ago

@Aravind-Sundararajan great looks like an improvement.

Kevin-Mattheus-Moerman commented 5 months ago

@chrisdembia @cvhammond @marcopus @Ipuch @Modenaxe @aaa34169 @moorepants @nickbianco @jimmyDunne would you be interested in reviewing this submission for JOSS: The Journal of Open Source Software, the title is: "MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco".

JOSS reviews happen here on GitHub and focus on the software as well as a short paper. More on our review process can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

If you are interested please let me know here, thanks!

Ipuch commented 5 months ago

Thank you for considering me for the review of the submission. I am unable to participate as I do not have access to a MATLAB license at the moment. This limits my ability to thoroughly evaluate the software.

Regards, Pierre

cvhammond commented 4 months ago

I apologize, I don't currently have the bandwidth to review right now. Please feel free to continue to tag me in these posts as I may have time in the future.

nickbianco commented 4 months ago

Seems like a great contribution @Aravind-Sundararajan! Unfortunately, I also do not currently have the bandwidth for a review. Also, I am still actively developing Moco, so a review from me seems like a bit of a conflict of interest.

aaa34169 commented 4 months ago

sorry, i am not avalaible for any extra reviewing so far.

Kevin-Mattheus-Moerman commented 4 months ago

@chrisdembia @marcopus @Modenaxe @moorepants @jimmyDunne would you be interested in reviewing this submission for JOSS: The Journal of Open Source Software, the title is: "MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco".

JOSS reviews happen here on GitHub and focus on the software as well as a short paper. More on our review process can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

If you are interested please let me know here, thanks!

marcopus commented 4 months ago

Sorry but I have to decline, I lack bandwidth and to be fair I'm long out of the musculoskeletal simulation field.

Aravind-Sundararajan commented 4 months ago

@Kevin-Mattheus-Moerman May I suggest 0todd0000 and dhruv.gupta@kuleuven.be?

Kevin-Mattheus-Moerman commented 3 months ago

@chrisdembia @Modenaxe @moorepants @jimmyDunne @0todd0000 @jorandevet @johnjdavisiv

would you be interested in reviewing this submission for JOSS: The Journal of Open Source Software, the title is: "MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco".

JOSS reviews happen here on GitHub and focus on the software as well as a short paper. More on our review process can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

If you are interested please let me know here, thanks!

Kevin-Mattheus-Moerman commented 3 months ago

@Aravind-Sundararajan apologies for the delays finding reviewers so far. It seems many are preoccupied. Some searches via email also turned up empty so far. I will keep at it though so we'll hopefully be able to move on soon.

0todd0000 commented 3 months ago

Sorry for the delay. Yes, I'd be pleased to review!

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot add @0todd0000 as reviewer

editorialbot commented 3 months ago

@0todd0000 added to the reviewers list!

Kevin-Mattheus-Moerman commented 3 months ago

@chrisdembia @Modenaxe @moorepants @jimmyDunne @jorandevet @johnjdavisiv

would you be interested in reviewing this submission for JOSS: The Journal of Open Source Software, the title is: "MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco".

JOSS reviews happen here on GitHub and focus on the software as well as a short paper. More on our review process can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

If you are interested please let me know here, thanks!

jimmyDunne commented 3 months ago

Unable to do a review at this time, but thanks for the thought. Gluck

Kevin-Mattheus-Moerman commented 3 months ago

@jimmyDunne no worries, thanks for getting back to me. Do you know of anybody else that I should invite?

Kevin-Mattheus-Moerman commented 3 months ago

@chrisdembia @Modenaxe @moorepants @jorandevet @johnjdavisiv

would you be interested in reviewing this submission for JOSS: The Journal of Open Source Software, the title is: "MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco".

JOSS reviews happen here on GitHub and focus on the software as well as a short paper. More on our review process can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

If you are interested please let me know here, thanks!

Aravind-Sundararajan commented 2 months ago

@Kevin-Mattheus-Moerman I have been sending emails. How about dgupta7 (dhruv.gupta@kuleuven.be) I suggestested above or aasadi1 (azarangasadi@yahoo.com)

Kevin-Mattheus-Moerman commented 2 months ago

@dgupta7 @aasadi1

would you be interested in reviewing this submission for JOSS: The Journal of Open Source Software, the title is: "MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco".

JOSS reviews happen here on GitHub and focus on the software as well as a short paper. More on our review process can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

If you are interested please let me know here, thanks!

aasadi1 commented 2 months ago

Hi Kevin,Sure, I can help with the review.Regards,AzarangOn Aug 12, 2024, at 05:35, Kevin Mattheus Moerman @.***> wrote: @dgupta7 @aasadi1 would you be interested in reviewing this submission for JOSS: The Journal of Open Source Software, the title is: "MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco". JOSS reviews happen here on GitHub and focus on the software as well as a short paper. More on our review process can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you are interested please let me know here, thanks!

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot add @aasadi1 as reviewer

editorialbot commented 2 months ago

@aasadi1 added to the reviewers list!

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot start review

editorialbot commented 2 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7110.

dgupta7 commented 2 months ago

Hi Kevin,

Yea, I am happy to review.

Regards Dhruv Sent from my iPhone

On Aug 15, 2024, at 11:14 PM, The Open Journals editorial robot @.***> wrote:



Closed #6844https://github.com/openjournals/joss-reviews/issues/6844 as completed.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/6844#event-13902766284, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUMZWBW7334PI4CXF6BNBRLZRUKZRAVCNFSM6AAAAABI2KT3T6VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJTHEYDENZWGYZDQNA. You are receiving this because you were mentioned.Message ID: @.***>

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aasadi1 commented 3 weeks ago

I am following the tutorial and right now I'm running test_ExtendProblem_simple.m and I have a recommendation. Add a note in the documentation to change the openSim version in line 1, I changed mine to 4.4 so it ran. But now I get this error:

Error using createPointMass
Java exception occurred:
java.lang.RuntimeException: SimTK Exception thrown at Xml.cpp:115:
  Error detected by Simbody method Xml::writeToFile(): Failed to write to the Xml file
  './models/pointmass.osim' with error ' (line=1, col=1)'.
  (Required condition 'saveOK' was not met.)

    at org.opensim.modeling.opensimCommonJNI.OpenSimObject_print(Native Method)

    at org.opensim.modeling.OpenSimObject.print(OpenSimObject.java:603)

Error in test_ExtendProblem_simple (line 24)
p = createPointMass('./models/pointmass.osim', opensimroot);
Aravind-Sundararajan commented 3 weeks ago

I am following the tutorial and right now I'm running test_ExtendProblem_simple.m and I have a recommendation. Add a note in the documentation to change the openSim version in line 1, I changed mine to 4.4 so it ran. But now I get this error:

Error using createPointMass
Java exception occurred:
java.lang.RuntimeException: SimTK Exception thrown at Xml.cpp:115:
  Error detected by Simbody method Xml::writeToFile(): Failed to write to the Xml file
  './models/pointmass.osim' with error ' (line=1, col=1)'.
  (Required condition 'saveOK' was not met.)

  at org.opensim.modeling.opensimCommonJNI.OpenSimObject_print(Native Method)

  at org.opensim.modeling.OpenSimObject.print(OpenSimObject.java:603)

Error in test_ExtendProblem_simple (line 24)
p = createPointMass('./models/pointmass.osim', opensimroot);

I added a test_ExtendProblem_simple_compat.m where you will have to change the opensimroot to 'C:\opensim 4.4\'. After setting matlab to use my OpenSim 4.4 and rebuilding MocoExtendProblem, I was able to run test_ExtendProblem_simple_compat without issue.

It may be unable to write to the osim file because it is being used/opened by another program. Let me know if this is a sticking point and we can dig into it further.

Kevin-Mattheus-Moerman commented 2 weeks ago

@0todd0000, @aasadi1 can you please pick up this review again, or sumarise what the authors should work on? Thanks again for your help!