[REVIEW]: LBR-Stack: ROS 2 and Python Integration of KUKA FRI for Med and IIWA Robots

[editorialbot]

Submitting author: @mhubii (Martin Huber)
Repository: https://github.com/lbr-stack/lbr_stack_doc
Branch with paper.md (empty if default branch): main
Version: joss
Editor: @adi3
Reviewers: @CameronDevine, @dmronga
Archive: 10.5281/zenodo.13897377

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c43c82bed833c02503dd47f2637192ef"><img src="https://joss.theoj.org/papers/c43c82bed833c02503dd47f2637192ef/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c43c82bed833c02503dd47f2637192ef/status.svg)](https://joss.theoj.org/papers/c43c82bed833c02503dd47f2637192ef)

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

@CameronDevine & @bmagyar & @vincentberenz, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @adi3 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 ✨

Checklists

📝 Checklist for @CameronDevine

📝 Checklist for @dmronga

[editorialbot]

Hello humans, 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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (764.7 files/s, 33762.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             42              0            142
TeX                              1             10              0             98
YAML                             3              5              0             66
Python                           1             16             17             54
DOS Batch                        1              8              1             26
JSON                             1              0              0             22
reStructuredText                 3              7             29             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            13             92             54            428
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 988

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/SII55687.2023.10039308 is OK
- 10.1109/MRA.2018.2877776 is OK
- 10.1109/IROS.2004.1389727 is OK
- 10.1126/scirobotics.abm6074 is OK
- 10.21105/joss.00456 is OK

MISSING DOIs

- 10.1109/tmi.2016.2620723 may be a valid DOI for title: Towards MRI-based autonomous robotic US acquisitions: a first feasibility study

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[adi3]

@vincentberenz looks like we already had a reviewer in place and we limit papers to 2 reviews. So let me ping you for our next submission, that should also align well with your January timeline :) Thanks!

[adi3]

@editorialbot remove @vincentberenz from reviewers

[editorialbot]

@vincentberenz removed from the reviewers list!

[adi3]

👋🏼 @mhubii this is the review thread for the paper. All of our communications will happen here from now on.

👋🏼 @CameronDevine, @bmagyar - you both should generate your checklists with the JOSS requirements. As you go over the submission, please check the items that you feel have been satisfied and let the author know where further work needs to be done.

Here is a little more context for first-time reviewers :) - 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 #6138 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 @editorialbot 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!!

[bmagyar]

Review checklist for @bmagyar

Conflict of interest

• 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

• 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 https://github.com/lbr-stack/lbr_stack_doc?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mhubii) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

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

[CameronDevine]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[CameronDevine]

Review checklist for @CameronDevine

Conflict of interest

• 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

• 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 https://github.com/lbr-stack/lbr_stack_doc?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mhubii) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

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

[CameronDevine]

@adi3 Before I get too far into this review, I would like to make sure we are all in agreement about the scope of this review. In the past, when I have both submitted and reviewed JOSS papers, the codebase and paper have been in a single repository. In this case, the codebase appears to be spread among multiple repositories all housed in a common GitHub organization. Therefore, should @bmagyar and I review all the repositories in the GitHub organization?

One exception to this rule would, I assume, be the lbr-stack/pymoveit2 repository which is a fork of another repository.

Finally, the checklist asks if the source code is available at https://github.com/lbr-stack/lbr_stack_doc, which it is not. Does this need to be changed?

[mhubii]

First of all, thank you very much for reviewing.

Correct, pymoveit2 is an unrelated fork that I will remove for clarification.

Have a good start into the new year!

[adi3]

@arfon some valid points by @CameronDevine above. How should we go about handling multi-repo codebases?

[arfon]

@arfon some valid points by @CameronDevine above. How should we go about handling multi-repo codebases?

This does happen sometimes, and if you believe the structure of the project is reasonable, then it's acceptable for the review to be across multiple codebases.

[CameronDevine]

@arfon @adi3 in my reviewer checklist there is an item: "Repository: Is the source code for this software available at the https://github.com/lbr-stack/lbr_stack_doc?" As this is not true, how should I proceed?

[mhubii]

Hi All, sorry for the confusion. Let me give you a brief explanation.

The architecture is as follows (paper figure 2):

Top: fri (KUKA's library, unaltered, only CMake support added)
Middle: fri_vendor (expose fri cmake target to ament cmake for ROS 2), pyFRI (Python bindings for fri)
Bottom: lbr_fri_ros2_stack (all ROS 2 integration)

Why this separation? The ROS ecosystem offers a lot but comes with a steep learning curve and currently limited cross platform support. Hence, for some users it is easiest to just pip install stuff, whereas more experienced users can really benefit from ROS.

[adi3]

@CameronDevine In light of explanation provided by @mhubii I recommend checking off that item on your list. Thanks!

[adi3]

@bmagyar could you please give us an idea of when you could start off your review? Appreciate your help!

[mhubii]

thank you for the feedback @CameronDevine. Hope things are going well!

As rightfully indicated, the license is now OSI compliant. Copyright notices where third-party software was used are included.

Looking forward for further feedback so we can work through this review :)

[adi3]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[adi3]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1109/SII55687.2023.10039308 is OK
- 10.1109/MRA.2018.2877776 is OK
- 10.1109/TMI.2016.2620723 is OK
- 10.1109/IROS.2004.1389727 is OK
- 10.1126/scirobotics.abm6074 is OK
- 10.21105/joss.00456 is OK
- 10.6092/JOSER_2014_05_01_p3 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: iiwa_ros: A ROS Stack for KUKA’s IIWA robots using...
- No DOI given, and none found for title: ROS 2 Stack for KUKA iiwa collaborative robots
- No DOI given, and none found for title: Generic and simple controls framework for ROS 2
- No DOI given, and none found for title: The fast research interface for the kuka lightweig...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[adi3]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1109/SII55687.2023.10039308 is OK
- 10.1109/MRA.2018.2877776 is OK
- 10.1109/TMI.2016.2620723 is OK
- 10.1109/IROS.2004.1389727 is OK
- 10.1126/scirobotics.abm6074 is OK
- 10.21105/joss.00456 is OK
- 10.6092/JOSER_2014_05_01_p3 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: iiwa_ros: A ROS Stack for KUKA’s IIWA robots using...
- No DOI given, and none found for title: ROS 2 Stack for KUKA iiwa collaborative robots
- No DOI given, and none found for title: Generic and simple controls framework for ROS 2
- No DOI given, and none found for title: The fast research interface for the kuka lightweig...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6060, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[crvernon]

@editorialbot generate pdf

🔍 checking out the following:

• reviewer checklists are completed or addressed
• version set
• archive set
• archive names (including order) and title in archive matches those specified in the paper
• archive uses the same license as the repo and is OSI approved as open source
• archive DOI and version match or redirect to those set by editor in review thread
• paper is error free - grammar and typos
• paper is error free - test links in the paper and bib
• paper is error free - refs preserve capitalization where necessary
• paper is error free - no invalid refs without justification

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[crvernon]

👋 @mhubii - I just need you to address the following before I move to accept this for publication:

In the paper:

• LINE 60: "...the work in (Hennersperger et al., 2017)..." should appear as "...the work in Hennersperger et al. (2017)..."
• LINE 83: The "g" in "gazebo" should be capitalized. You can do this by wrapping any characters you want to preserve formatting of in your bib file using curly brackets.
• LINE 96: "kuka" should be all caps.

Let me know when you have made these changes. Thank you.

[mhubii]

thank you for the hint, and apologies for the incorrect formatting. This is now fixed. I genuinely appreciate the work that you guys put into this journal!

@editorialbot generate pdf

[mhubii]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[crvernon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Huber
  given-names: Martin
  orcid: "https://orcid.org/0000-0003-4603-6773"
- family-names: Mower
  given-names: Christopher E.
  orcid: "https://orcid.org/0000-0002-3929-9391"
- family-names: Ourselin
  given-names: Sebastien
  orcid: "https://orcid.org/0000-0002-5694-5340"
- family-names: Vercauteren
  given-names: Tom
  orcid: "https://orcid.org/0000-0003-1794-0456"
- family-names: Bergeles
  given-names: Christos
  orcid: "https://orcid.org/0000-0002-9152-3194"
contact:
- family-names: Huber
  given-names: Martin
  orcid: "https://orcid.org/0000-0003-4603-6773"
doi: 10.5281/zenodo.13897377
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Huber
    given-names: Martin
    orcid: "https://orcid.org/0000-0003-4603-6773"
  - family-names: Mower
    given-names: Christopher E.
    orcid: "https://orcid.org/0000-0002-3929-9391"
  - family-names: Ourselin
    given-names: Sebastien
    orcid: "https://orcid.org/0000-0002-5694-5340"
  - family-names: Vercauteren
    given-names: Tom
    orcid: "https://orcid.org/0000-0003-1794-0456"
  - family-names: Bergeles
    given-names: Christos
    orcid: "https://orcid.org/0000-0002-9152-3194"
  date-published: 2024-11-15
  doi: 10.21105/joss.06138
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6138
  title: "LBR-Stack: ROS 2 and Python Integration of KUKA FRI for Med
    and IIWA Robots"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06138"
  volume: 9
title: "LBR-Stack: ROS 2 and Python Integration of KUKA FRI for Med and
  IIWA Robots"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

[editorialbot]

🚨🚨🚨 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.06138 joss-papers#6145
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06138
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...

[crvernon]

🥳 Congratulations on your new publication @mhubii! Many thanks to @adi3 for editing and @CameronDevine and @dmronga for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following

code snippets

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.06138/status.svg)](https://doi.org/10.21105/joss.06138)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06138/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.06138

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[CameronDevine]

Congratulations @mhubii! I'm glad to see that this paper is finally accepted. I do have some feedback for the JOSS editors relating to this review. Where is the best place to share this feedback?

[adi3]

@CameronDevine you're welcome to email your feedback directly to me at [email protected] and I can share with the broader team. Thanks again for all your help!