[REVIEW]: Pybullet Industrial: A process-aware robot simulation

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@liquidcronos@adi3<!--end-editor-- Reviewers: @CameronDevine, @sea-bass Archive: 10.5281/zenodo.7833292

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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 & @sea-bass, 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 @sea-bass

📝 Checklist for @CameronDevine

editorialbot commented 1 year ago

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

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (970.8 files/s, 46332.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Markdown                         6             74              0            195
YAML                             4             28             44            120
TeX                              1              7              0             57
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SUM:                            11            109             44            372
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gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1096

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-662-62138-7_41 is OK
- 10.1109/IROS.2013.6696520 is OK

MISSING DOIs

- 10.1109/iros.2004.1389727 may be a valid DOI for title: Design and use paradigms for gazebo, an open-source multi-robot simulator

INVALID DOIs

- None

editorialbot commented 1 year ago

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

arfon commented 1 year ago

@CameronDevine, @sea-bass This is the review thread for the paper. All of the communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

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 https://github.com/openjournals/joss-reviews/issues/5174 so that a link is created to this thread (and @adi3 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

adi3 commented 1 year ago

@CameronDevine @sea-bass - can we have an update on when you can kick-off your review of this submission? Thanks!

sea-bass commented 1 year ago

@CameronDevine @sea-bass - can we have an update on when you can kick-off your review of this submission? Thanks!

I planned to do mine this coming weekend, so it should be soon.

CameronDevine commented 1 year ago

@adi3 I have spring break coming up next week, which should allow me plenty of time to complete the review.

sea-bass commented 1 year ago

Review checklist for @sea-bass

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/WBK-Robotics/pybullet_industrial?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@liquidcronos) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

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

sea-bass commented 1 year ago

Hello all, my review is complete.

Overall, the software is in very good shape and checks all the boxes. Only found some minor things, but getting set up with the tool was easy and the claims were verifiable.

The paper, on the other hand, is a bit short on references, but critically it abruptly stops after outlining many of their features (they could do a bit more on that front). So I think my biggest piece of feedback to the authors is to add a section showing examples/applications of their work in action, plus a conclusion summarizing their work and outlining future work.

See https://github.com/WBK-Robotics/pybullet_industrial/issues/40 for documentation review and https://github.com/WBK-Robotics/pybullet_industrial/issues/41 for software review. Once my comments are addressed, I'd be happy to take another quick look and help move this forward!

CameronDevine commented 1 year ago

Review checklist for @CameronDevine

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/WBK-Robotics/pybullet_industrial?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@liquidcronos) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

The findings from my review are summarized here:

I agree with @sea-bass that the paper should include a conclusion. (See https://github.com/WBK-Robotics/pybullet_industrial/issues/40)
The examples are currently undocumented. (See https://github.com/WBK-Robotics/pybullet_industrial/issues/42)
One of the examples requires matplotlib but it isn't a dependency of the library (See https://github.com/WBK-Robotics/pybullet_industrial/issues/43)
The community guidelines do not provide any directions on how to seek support (See https://github.com/WBK-Robotics/pybullet_industrial/issues/44)

Once these issues are resolved I think this will make an excellent contribution to JOSS. Personally, this package would have been very useful to me while completing my PhD thesis.

liquidcronos commented 1 year ago

Thank you very much for your reviews and the valuable feedback.

I have updated the code to reflect your suggestions, and thus removed the bugs from the examples and added docstrings explaining their usage. You can see this in the Issues you opened. I am currently working on incorporating your feedback into the paper and will share the new version with you shortly

liquidcronos commented 1 year ago

Hey @CameronDevine , I have now included a conclusion to the paper along with changes @sea-bass requested. Let me know if this resolves your reservations about the paper.

liquidcronos commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

liquidcronos commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

liquidcronos commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

liquidcronos commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

liquidcronos commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

sea-bass commented 1 year ago

@adi3 , the authors have gone through all my feedback and I am happy to approve this submission for publication!

CameronDevine commented 1 year ago

For me, there is one last outstanding issue.

https://github.com/WBK-Robotics/pybullet_industrial/issues/42#issuecomment-1465760402

Once this is complete I will be more than happy to approve the submission.

CameronDevine commented 1 year ago

All of the issues I have raised have now been addressed. I also approve this submission for publication.

liquidcronos commented 1 year ago

Hey @adi3, Since all reviewers have approved the paper, i was wondering what the next steps are. Is there anything else I can do?

adi3 commented 1 year ago

@CameronDevine @sea-bass thank you for completing your respective reviews. I appreciate your thoroughness!

@liquidcronos Looks like everything is set. Congratulations! I need one final formality to be done from your side. Please make a tagged release of the project and archive it. Then report the version number and archive DOI here. Once I have that, I will send this for publication. Cheers!

liquidcronos commented 1 year ago

Hey @adi3, thank you very much!

I have drafted a new release with version v1.0.2 the corresponding doi is: 10.5281/zenodo.7833292

adi3 commented 1 year ago

@editorialbot set 10.5281/zenodo.7833292 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7833292

adi3 commented 1 year ago

@editorialbot set v1.0.2 as version

editorialbot commented 1 year ago

Done! version is now v1.0.2

adi3 commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.48550/arXiv.2302.13442 is OK
- 10.1007/978-3-662-62138-7_41 is OK
- 10.1109/IROS.2013.6696520 is OK

MISSING DOIs

- 10.1109/iros.2004.1389727 may be a valid DOI for title: Design and use paradigms for gazebo, an open-source multi-robot simulator

INVALID DOIs

- https://doi.org/10.1016/j.procir.2014.10.032 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0146-664X(82)90169-1 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/j.procir.2014.10.032' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.
Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/0146-664X(82)90169-1' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

adi3 commented 1 year ago

@liquidcronos please fix the Invalid and Missing DOIs as shown above

liquidcronos commented 1 year ago

Hey @adi3,

I have added the missing DOI and formatted the remaining two to comply with the standards of the editorial bot

kyleniemeyer commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "organization" (NAME) ["@", #<BibTeX::Entry >, {:title=>["Design and use paradigms for gazebo, an open-source multi-robot simulator"], :author=>["Koenig, Nathan and Howard, Andrew"], :booktitle=>["2004 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)(IEEE Cat. No. 04CH37566)"], :volume=>["3"], :pages=>["2149--2154"], :doi=>["10.1109/IROS.2004.1389727"]}]

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance.

kyleniemeyer commented 1 year ago

Hi @liquidcronos, I think the error in the BibTeX comes from a missing comma after the doi field in the gazebo entry.

liquidcronos commented 1 year ago

Hey @kyleniemeyer , thanks for letting me know. It should be fixed now. The editorialbot didnt spot this error last time, is there some way i can call the bot directly in the future to avoid you and adi3 always having to check?

kyleniemeyer commented 1 year ago

@liquidcronos The editorialbot command check references should catch some of these, as this is a step performed in the dry run of acceptance. However, some additional steps are only done at the very end.

kyleniemeyer commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

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