[REVIEW]: Pybotics: Python Toolbox for Robotics

whedon commented 5 years ago

Submitting author: @nnadeau (Nicholas A. Nadeau) Repository: https://github.com/nnadeau/pybotics Version: 0.7.1 Editor: @kyleniemeyer Reviewer: @adi3, @CameronDevine Archive: 10.5281/zenodo.3464685

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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.)

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@adi3 & @CameronDevine, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @adi3

Conflict of interest

[x] 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

[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 repository url?
[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 (@nnadeau) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @CameronDevine

Conflict of interest

[x] 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

[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 repository url?
[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 (@nnadeau) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @adi3, @CameronDevine it looks like you're currently assigned to review this paper :tada:.

: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 😿

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kyleniemeyer commented 5 years ago

👋 @nnadeau @adi3 @CameronDevine

engnadeau commented 5 years ago

Thanks for volunteering to review, @adi3 and @CameronDevine

adi3 commented 5 years ago

@nnadeau Great work in the repo! I'm yet to test it out on my machine but I did a quick overview and I'm already a fan. Regarding the review, I'd like you to add a few things in the Development section of the readme.

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

Step 3 of your development process should have the contributor run tests to make sure the changes have not broken anything. Please list out specific commands and outputs the contributor should expect before the feature is ready for PR.

In addition, please add a quick line and a link to the issues board of your repo so users know where they can get support.

engnadeau commented 5 years ago

@adi3 thanks for the review. The following changes have been made:

Added issue templates: https://github.com/nnadeau/pybotics/commit/7d53e8f31756c316a0c84662a094a644bb376e3a
As a CONTRIBUTING.md already existed, I updated README.md with additional community info, direct links to the relevant docs/issues, and extended the testing how-to: https://github.com/nnadeau/pybotics/commit/2fe8b2127d560c676666c1a041d903716d3b18f8

adi3 commented 5 years ago

@nnadeau Thanks for updating that.

With reference to this quote from your paper:

It was designed to provide a simple, clear, and concise interface to quickly simulate and evaluate common robot concepts, such as kinematics, dynamics, trajectory generations, and calibration.

I see the how the library helps with kinematics and calibration easily; both your examples and the source code show it clearly. I'm less certain about the dynamics and trajectory generations part of it. Of course, the kinematics and calibration features are important for calculating solutions of dynamics and trajectory, but to actually mention it as an advantage of your library, please implement either (1) an out-of-the-box feature relating to them, or (2) an example script showing how the existing features lead to dynamics and planning equations.

Ditto for the mention of Machine learning in the Readme.

engnadeau commented 5 years ago

@adi3 good catch! I've added additional examples (https://github.com/nnadeau/pybotics/pull/728). Specifically:

Example:

adi3 commented 5 years ago

@nnadeau Stellar work! I'm impressed by the utility of your library. I'll likely use it my work at some point.

I'm having some trouble running your tests. This is the error I get: No such file or directory: 'black': 'black'. I'm not conversant with poetry so some pointers here would be useful.

adi3 commented 5 years ago

@nnadeau Stellar work! I'm impressed by the utility of your library. I'll likely use it my work at some point.

I'm having some trouble running your tests. This is the error I get: No such file or directory: 'black': 'black'. I'm not conversant with poetry so some pointers here would be useful.

My bad. Running poetry install got all this fixed. Your tests run fine and at this point, I am satisfied with your submission. Pending a references check, I will be happy to recommend your paper for publication.

adi3 commented 5 years ago

@whedon commands

whedon commented 5 years ago

Here are some things you can ask me to do:

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EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

adi3 commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.3390/robotics8020033 may be missing for title: Impedance Control Self-Calibration of a Collaborative Robot Using Kinematic Coupling
- https://doi.org/10.1109/jra.1987.1087086 may be missing for title: Introduction to Robotics Mechanics and Control
- https://doi.org/10.1109/mcse.2011.37 may be missing for title: The NumPy array: a structure for efficient numerical computation
- https://doi.org/10.1109/iros.2018.8593598 may be missing for title: Evolutionary motion control optimization in physical human-robot interaction

INVALID DOIs

- None

adi3 commented 5 years ago

@nnadeau can you please update your .bib file to include the missing DOIs? See whedon output above.

danielskatz commented 5 years ago

Please be aware that whedon is not perfect at this, and sometimes gives wrong suggestions.

engnadeau commented 5 years ago

@adi3 @danielskatz DOIs updated: https://github.com/nnadeau/pybotics/pull/729

Missing DOIs:

Craig2005 (popular robotics textbook)
jones2001scipy (recommended citation for library: https://www.scipy.org/citing.html#scipy-the-library)
pedregosa2011scikit (recommended citation for library: https://scikit-learn.org/stable/about.html#citing-scikit-learn)

engnadeau commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

engnadeau commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.3390/robotics8020033 is OK
- 10.1007/978-3-319-54413-7 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/IROS.2018.8593598 is OK

MISSING DOIs

- https://doi.org/10.1109/jra.1987.1087086 may be missing for title: Introduction to Robotics Mechanics and Control

INVALID DOIs

- None

adi3 commented 5 years ago

@kyleniemeyer I am finished with my review and I recommend this paper for publication. Thank you for facilitating the process.

engnadeau commented 5 years ago

@CameronDevine, https://github.com/nnadeau/pybotics/issues/730 is fixed. Thanks for the idea.

CameronDevine commented 5 years ago

Once nnadeau/pybotics#731 is closed I will be ready to recommend this paper for publication.

engnadeau commented 5 years ago

@CameronDevine good to go! https://github.com/nnadeau/pybotics/issues/731 closed with https://github.com/nnadeau/pybotics/pull/732

CameronDevine commented 5 years ago

@kyleniemeyer, I recommend this paper for publication.

kyleniemeyer commented 5 years ago

Thanks @CameronDevine @adi3 ! I'll do my checks now.

kyleniemeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kyleniemeyer commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.3390/robotics8020033 is OK
- 10.1007/978-3-319-54413-7 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/IROS.2018.8593598 is OK

MISSING DOIs

- https://doi.org/10.1109/jra.1987.1087086 may be missing for title: Introduction to Robotics Mechanics and Control

INVALID DOIs

- None

kyleniemeyer commented 5 years ago

Hi @nnadeau, just a few minor edits needed for the paper, in the references:

the title in the Corke reference doesn't look completely correct, please check.

The SciPy reference should be

@Misc{,
author =    {Eric Jones and Travis Oliphant and Pearu Peterson and others},
title =     {{SciPy}: Open source scientific tools for {Python}},
year =      {2001--},
url = "http://www.scipy.org/",
note = {[Online; accessed <today>]}
}

in the Nadeau 2018 reference, please put { } around words that should be capitalized, like IEEE, RSJ, and IROS (or just the whole conference name)

We can ignore the warning about the missing DOI from whedon, that looks to be a review of the book you cited.

engnadeau commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

engnadeau commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

engnadeau commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

engnadeau commented 5 years ago

@kyleniemeyer

updated Corke citation title to match recommended title on the toolbox's website (https://github.com/nnadeau/pybotics/commit/fe145a340f4d178c46a6abae523618756f4eda85)
escaped ampersand in Corke title (https://github.com/nnadeau/pybotics/commit/58a4533baf4bbb4b9c59c78b000a3dc385245744)
fixed scipy citation (https://github.com/nnadeau/pybotics/commit/609da085f9481c55fad66d7f63b233e2a2b221c0)
added {} to Nadeau citation (https://github.com/nnadeau/pybotics/commit/924dd59c8dcc039ac860d646fbae7ec981a78e64)

engnadeau commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

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