[REVIEW]: STEDY - Software for TEnsegrity DYnamics

[whedon]

Submitting author: @vaishnavtv (Venkata Vaishnav Tadiparthi)
Repository: https://github.com/uqLab/stedy
Version: v0.1.0
Editor: @labarba
Reviewer: @Kevin-Mattheus-Moerman, @ctdegroot, @apsabelhaus
Archive: 10.5281/zenodo.2527084

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/932cce456c4dd1514e6c4e46d2088ad7/status.svg)](http://joss.theoj.org/papers/932cce456c4dd1514e6c4e46d2088ad7)

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) 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

@Kevin-Mattheus-Moerman & @ctdegroot, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @labarba know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @Kevin-Mattheus-Moerman

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v0.1.0)?
• Authorship: Has the submitting author (@vaishnavtv) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @ctdegroot

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v0.1.0)?
• Authorship: Has the submitting author (@vaishnavtv) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @apsabelhaus

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v0.1.0)?
• Authorship: Has the submitting author (@vaishnavtv) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Kevin-Mattheus-Moerman, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ 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:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[Kevin-Mattheus-Moerman]

@labarba over at #1000 @apsabelhaus agreed to be reviewer, perhaps you could add him here.

[Kevin-Mattheus-Moerman]

@apsabelhaus let me introduce you to JOSS and reviewing for JOSS. JOSS is a free, open access, and open source journal. Reviews take place here, i.e. in Github issues. As you can see the top of this issue has checklists for the reviewers which will guide them through the review process. A set of checklists will be created for you if you join as reviewer. As described in our review guidelines the review focuses on the software and a short paper. Reviewers can comment on this work here in this issue and are encouraged to created dedicated issues on the software repository, and link to them here, for larger items. Let me know if you have more questions.

[Kevin-Mattheus-Moerman]

@labarba so far @vaishnavtv has worked on these issues which I've posted on the software repository:

• README issues isrlab/stedy#1 README issues
• Example TemplateForUser_DBar.m does not exist isrlab/stedy#2 Example TemplateForUser_DBar.m does not exist
• Comments about / errors in example: Template_DBar isrlab/stedy#3 Comments about / errors in example: Template_DBar
• Error in examples Arm.m and Ball.m isrlab/stedy#4 Error in examples Arm.m and Ball.m

[labarba]

I manually added the header comment to add @apsabelhaus as reviewer — thank you, all.

[labarba]

@Kevin-Mattheus-Moerman : I forgot how to give @apsabelhaus the permissions to edit the reviewer checklist or send him the appropriate invitation. Do you remember? I went to the Teams section of the open journals org, and couldn't immediately identify a team to add him. Help…

[Kevin-Mattheus-Moerman]

@labarba The first step is to do this:
@whedon add @apsabelhaus as reviewer

[Kevin-Mattheus-Moerman]

Then the reviewer should accept this invitation: https://github.com/openjournals/joss-reviews/invitations

[labarba]

The @whedon add commands sets things up only if used in the Pre-Review issue, before starting the review. Once we're here, adding a reviewer is a manual process.

[vaishnavtv]

You can find the pre-print of the cited reference here.

I hope the review is going smoothly. Please let us know if anything else is required.

[vaishnavtv]

Any issues with the review? It has been almost two weeks since the last update. Kindly let us know if there are problems with the software.

[ctdegroot]

@vaishnavtv Please have patience. As you know peer review takes time and reviewers cannot drop everything immediately to tend to a review. I will review within the next two weeks.

[labarba]

@vaishnavtv I kindly ask you that you be patient, and allow the review to proceed at a pace that reflects the fact that everyone here is a volunteer.

[ctdegroot]

@vaishnavtv In the paper, the affiliations are incomplete. The position of each author (i.e. Graduate Research Assistant or Associate Professor) is not part of the affiliation and is not required. Additionally, provide more details on affiliation (i.e. department/faculty, city, state, country).

[ctdegroot]

@vaishnavtv The paper contains insufficient references and the one reference that is included is not formatted properly (it appears twice). Please include at least a couple more references. For example, you mention some similar software called "Simscape Multibody". You should reference that. The first paragraph needs a reference or two also.

[ctdegroot]

@vaishnavtv Where can I find your automated tests?

[vaishnavtv]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1042 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 15 0 15 0 0 252 0 --:--:-- --:--:-- --:--:-- 254
Error reading bibliography ./JOSSpaper.bib (line 6, column 3):
unexpected "y"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[vaishnavtv]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[vaishnavtv]

@ctdegroot I have made the recommended changes to the paper - affiliations and references have been added. We were under the impression that our manuscript submitted for publication would suffice as it exhaustively covers all information pertinent to this submission as well. Thank you for the clarification.

For the automated tests, would the files provided in the Examples folder be sufficient?

[ctdegroot]

@vaishnavtv The paper looks good now.

I don't think that the files in the Examples folder are sufficient as test cases because they do not assert what result is expected. Let's imagine that I am a user that makes some changes/extensions to the code. How to I check that I haven't broken anything that already existed?

From the JOSS review criteria:

Good: An automated test suite hooked up to an external service such as Travis-CI or similar
OK: Documented manual steps that can be followed to check the expected functionality of the software (e.g. a sample input file to assert behaviour)
Bad (not acceptable): No way for you the reviewer to check whether the software works

To get the tests into the 'OK' category you will need to provide some reference results that can be checked (preferably automatically) with the code outputs.

One other note, is that you should remove all of the ".DS_Store" files that are in some of the example folders. Normally you can put this in your .gitignore file to prevent them from being tracked in the future.

[vaishnavtv]

@ctdegroot
As recommended, I have added a Tests folder to the repository. The user can simply run TestPendulum.m to check the results of their changes to the code. I have also modified the Contributing Guidelines document to reflect this update.

I have removed all the .DS_Store files as well.

[labarba]

👋 @apsabelhaus — We're waiting for you to finish the checklist. Are you still working on your review? Or are you ready to make a recommendation?

[apsabelhaus]

Hi all, thanks again for your patience, the semester just finished up here, so I'm going to work on this now.

[apsabelhaus]

Hi all - an update from me. Almost ready for publication, only item left is 'functionality.' There's one last, potentially significant, issue to be addressed. I'll keep a close eye on this review throughout the week so the authors can get it done before the holidays.

[apsabelhaus]

All boxes checked from me. I recommend publication.

[labarba]

@whedon accept

[whedon]

No archive DOI set. Exiting...

[labarba]

Oops. Forgot one thing ... @vaishnavtv: Could you now make a deposit in an archive, such as Zenodo, and give us the DOI here?

[labarba]

@whedon set 10.5281/zenodo.2527084 as archive

[whedon]

OK. 10.5281/zenodo.2527084 is the archive.

[labarba]

👋 @vaishnavtv — Could you edit the metadata over at Zenodo, so that the title and list of authors match this submission?

[labarba]

Hi there, @vaishnavtv — As soon as you correct the metadata of the Zenodo entry, I can get you paper published here in JOSS. Let me know!

[vaishnavtv]

Happy new year!
@labarba, it’s done.
Is there anything else we need to add?

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#419

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#419, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[labarba]

@whedon accept deposit=true

[whedon]

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

[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.01042 joss-papers#420
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01042
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...

[labarba]

Congratulations, @vaishnavtv — your paper is published, and is the first JOSS paper of 2019!

And a big, happy Thank You to our reviewers: @Kevin-Mattheus-Moerman, @ctdegroot, @apsabelhaus

[labarba]

https://twitter.com/JOSS_TheOJ/status/1080093912616837120

[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:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01042/status.svg)](https://doi.org/10.21105/joss.01042)

HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.01042/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01042/status.svg
   :target: https://doi.org/10.21105/joss.01042

This is how it will look in your documentation:

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[vaishnavtv]

Thank you @labarba and to all the reviewers, for your helpful inputs in the review process!