[REVIEW]: sbp-env: A Python Package for Sampling-based Motion Planner and Samplers #3782

whedon · 2021-09-29T17:50:07Z

Submitting author: @soraxas (Tin Lai)
Repository: https://github.com/soraxas/sbp-env
Version: v1.1.1
Editor: @danielskatz
Reviewer: @KanishAnand, @OlgerSiebinga
Archive: 10.5281/zenodo.5572325

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Status

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Markdown: [![status](https://joss.theoj.org/papers/59cea6b194d33c2844b79084f0d940d8/status.svg)](https://joss.theoj.org/papers/59cea6b194d33c2844b79084f0d940d8)

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Review checklist for @KanishAnand

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Conflict of interest

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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?
Contribution and authorship: Has the submitting author (@soraxas) 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

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 and who the target audience is?
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?

Review checklist for @OlgerSiebinga

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@soraxas) 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

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 and who the target audience is?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-09-29T17:50:10Z

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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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:

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whedon · 2021-09-29T17:50:19Z

Wordcount for paper.md is 776

whedon · 2021-09-29T17:50:22Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (718.3 files/s, 95944.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          46           1331           1651           4214
reStructuredText                12            304            375            264
TeX                              1             28              0            214
Markdown                         2             54              0            122
YAML                             2              8              8             54
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            65           1737           2042           4903
-------------------------------------------------------------------------------


Statistical information for the repository '5f0bc2965922bee52ba859f0' was
gathered on 2021/09/29.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Oscar Lai                      161         10302           6725           49.29
Tin Lai                         38         10692           6827           50.71

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Oscar Lai                  1392           13.5         32.5               11.85
Tin Lai                    5814           54.4          4.9               14.26

whedon · 2021-09-29T17:50:23Z

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

OK DOIs

- 10/gdkx6g is OK
- 10.1109/access.2020.3023200 is OK
- 10/ghpwwm is OK
- 10/ghjdnk is OK
- 10.1109/robot.2005.1570709 is OK
- 10/gmv7jc is OK
- 10/d66p3t is OK
- 10/ghqdw7 is OK
- 10/ghvk26 is OK
- 10/gddhk5 is OK
- 10/gddhmf is OK
- 10/gg2n24 is OK
- 10.1109/isatp.2001.928961 is OK
- 10.1109/mra.2011.2181749 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-09-29T17:50:36Z

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

danielskatz · 2021-09-29T17:51:12Z

@KanishAnand and @OlgerSiebinga - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. 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.

Please read the first couple of comments in this issue carefully, so that you can accept the invitation from JOSS and be able to check items, and so that you don't get overwhelmed with notifications from other activities in JOSS.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3782 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 either of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

OlgerSiebinga · 2021-10-01T13:07:18Z

Quick update from my side. I started reviewing today and I have opened two issues in the repository:

soraxas/sbp-env#5 (comment)
soraxas/sbp-env#4 (comment)

One is a suggestion for a minor change, the other is an exception that occurs. This exception does not seem hard to fix or important, but I'm not sure I understand it enough to propose a fix. Just posting the links here to have everything in one place.

danielskatz · 2021-10-01T13:08:18Z

@OlgerSiebinga - can you mention openjournals/joss-reviews#3782 in those issues so that a link is created to this thread (and I can keep an eye on what is happening)

OlgerSiebinga · 2021-10-06T14:22:16Z

Hi All,

Another update from my side: I've ticked a lot of boxes today and created two more issues in the repository. Besides those issues, I have two other (small) remarks.:

I think the statement of need is missing from the documentation, so that should be added
I feel that the paper would benefit from some editing for language. I think there are some tense, punctuation, and number agreement issues. However, I'm not a native English speaker nor an experienced editor, so I'm not sure if I'm the right person to help out with this. Do you have ideas on how to proceed?

Besides that, everything looks good!

danielskatz · 2021-10-06T14:24:38Z

I'll proofread this at the end of the process, so you don't need to, but if there are things you want to flag or suggest, certainly you can feel free to.

OlgerSiebinga · 2021-10-06T14:31:43Z

ok! in that case, I think the paper is good as well.
Regarding the statement of need in the documentation, it is present in the readme file and I think that suffices. I missed that, my mistake.

danielskatz · 2021-10-06T14:34:29Z

I'll go ahead and proof-read the paper now - I usually wait until the end because there can be changes made during the review process, but given your comment, maybe it's a good idea to do now

danielskatz · 2021-10-06T14:49:44Z

@soraxas - see my suggested changes to the paper ☝️ ... Feel free to merge this, or comment on it...

KanishAnand · 2021-10-06T20:05:34Z

Hi @danielskatz

Regarding checkpoint "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 and who the target audience is?"
I think more about the target audience is mentioned in the Overview section of the paper instead of Statement of Need section, so should that be an issue?

danielskatz · 2021-10-06T20:07:01Z

Hi @danielskatz

Regarding checkpoint "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 and who the target audience is?" I think more about the target audience is mentioned in the Overview section of the paper instead of Statement of Need section, so should that be an issue?

As long as the information is in the paper, I think it's ok.

whedon · 2021-10-15T13:17:47Z

Attempting dry run of processing paper acceptance...

whedon · 2021-10-15T13:17:56Z

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

OK DOIs

- 10/gdkx6g is OK
- 10.1109/access.2020.3023200 is OK
- 10/ghpwwm is OK
- 10/ghjdnk is OK
- 10.1109/robot.2005.1570709 is OK
- 10/gmv7jc is OK
- 10/d66p3t is OK
- 10/ghqdw7 is OK
- 10/ghvk26 is OK
- 10/gddhk5 is OK
- 10/gddhmf is OK
- 10/gg2n24 is OK
- 10.1109/isatp.2001.928961 is OK
- 10.1109/mra.2011.2181749 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-10-15T13:18:12Z

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

Check final proof 👉 openjournals/joss-papers#2681

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2681, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz · 2021-10-15T13:39:48Z

👋 @soraxas - I've just realized that you've used shortDOIs for many references. I think these have been deprecated and for the purpose of long-term archiving, can you replace them by the traditional DOIs they represent? For example, http://doi.org/10/gg2n24 would be replaced by https://doi.org/10.1109/LRA.2020.2969145

soraxas · 2021-10-15T14:36:06Z

@whedon generate pdf

whedon · 2021-10-15T14:36:44Z

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

soraxas · 2021-10-15T14:38:00Z

@whedon check references

whedon · 2021-10-15T14:38:12Z

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

OK DOIs

- 10.1109/access.2014.2302442 is OK
- 10.1109/access.2020.3023200 is OK
- 10.1109/robio.2015.7419012 is OK
- 10.1109/csip.2012.6308826 is OK
- 10.1109/robot.2005.1570709 is OK
- 10.1109/robot.1996.509171 is OK
- 10.1109/icra.2019.8793618 is OK
- 10.1109/icra40945.2020.9197338 is OK
- 10.1007/978-3-319-03194-1_2 is OK
- 10.1109/mmar.2016.7575302 is OK
- 10.1109/lra.2020.2969145 is OK
- 10.1109/isatp.2001.928961 is OK
- 10.1109/mra.2011.2181749 is OK

MISSING DOIs

- None

INVALID DOIs

- 1010.1109/aim.2012.6265953 is INVALID

soraxas · 2021-10-15T14:41:09Z

@whedon check references

whedon · 2021-10-15T14:41:19Z

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

OK DOIs

- 10.1109/access.2014.2302442 is OK
- 10.1109/access.2020.3023200 is OK
- 10.1109/robio.2015.7419012 is OK
- 10.1109/csip.2012.6308826 is OK
- 10.1109/robot.2005.1570709 is OK
- 10.1109/aim.2012.6265953 is OK
- 10.1109/robot.1996.509171 is OK
- 10.1109/icra.2019.8793618 is OK
- 10.1109/icra40945.2020.9197338 is OK
- 10.1007/978-3-319-03194-1_2 is OK
- 10.1109/mmar.2016.7575302 is OK
- 10.1109/lra.2020.2969145 is OK
- 10.1109/isatp.2001.928961 is OK
- 10.1109/mra.2011.2181749 is OK

MISSING DOIs

- None

INVALID DOIs

- None

soraxas · 2021-10-15T14:42:00Z

Hi @danielskatz the DOIs should be all good to go

danielskatz · 2021-10-15T15:16:48Z

@whedon recommend-accept

whedon · 2021-10-15T15:16:53Z

Attempting dry run of processing paper acceptance...

whedon · 2021-10-15T15:17:05Z

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

OK DOIs

- 10.1109/access.2014.2302442 is OK
- 10.1109/access.2020.3023200 is OK
- 10.1109/robio.2015.7419012 is OK
- 10.1109/csip.2012.6308826 is OK
- 10.1109/robot.2005.1570709 is OK
- 10.1109/aim.2012.6265953 is OK
- 10.1109/robot.1996.509171 is OK
- 10.1109/icra.2019.8793618 is OK
- 10.1109/icra40945.2020.9197338 is OK
- 10.1007/978-3-319-03194-1_2 is OK
- 10.1109/mmar.2016.7575302 is OK
- 10.1109/lra.2020.2969145 is OK
- 10.1109/isatp.2001.928961 is OK
- 10.1109/mra.2011.2181749 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-10-15T15:17:21Z

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

Check final proof 👉 openjournals/joss-papers#2682

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2682, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz · 2021-10-15T15:18:07Z

@whedon accept deposit=true

whedon · 2021-10-15T15:18:11Z

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

whedon · 2021-10-15T15:18:48Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-10-15T15:18:49Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03782 joss-papers#2683
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03782
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2021-10-15T16:06:57Z

Congratulations to @soraxas (Tin Lai)!!

And thanks to @KanishAnand and @OlgerSiebinga for reviewing!
We couldn't do this without you

whedon · 2021-10-15T16:07:25Z

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.03782/status.svg)](https://doi.org/10.21105/joss.03782)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03782">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03782/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03782/status.svg
   :target: https://doi.org/10.21105/joss.03782

This is how it will look in your documentation:

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whedon added Python review TeX labels Sep 29, 2021

whedon assigned danielskatz Sep 29, 2021

whedon mentioned this issue Sep 29, 2021

[PRE REVIEW]: sbp-env: A Python Package for Sampling-based Motion Planner and Samplers #3767

Closed

whedon assigned KanishAnand and OlgerSiebinga Sep 30, 2021

danielskatz mentioned this issue Oct 6, 2021

changes in paper text soraxas/sbp-env#8

Merged

This was referenced Oct 6, 2021

Python version compatibility with scipy soraxas/sbp-env#9

Closed

Path recognition issue soraxas/sbp-env#10

Closed

KanishAnand mentioned this issue Oct 11, 2021

Test Instructions soraxas/sbp-env#13

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 15, 2021

whedon added accepted published Papers published in JOSS labels Oct 15, 2021

danielskatz closed this as completed Oct 15, 2021

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[REVIEW]: sbp-env: A Python Package for Sampling-based Motion Planner and Samplers #3782

[REVIEW]: sbp-env: A Python Package for Sampling-based Motion Planner and Samplers #3782

Comments

whedon commented Sep 29, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @KanishAnand

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @OlgerSiebinga

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 29, 2021

whedon commented Sep 29, 2021

whedon commented Sep 29, 2021

whedon commented Sep 29, 2021

whedon commented Sep 29, 2021

danielskatz commented Sep 29, 2021

OlgerSiebinga commented Oct 1, 2021

danielskatz commented Oct 1, 2021

OlgerSiebinga commented Oct 6, 2021

danielskatz commented Oct 6, 2021

OlgerSiebinga commented Oct 6, 2021

danielskatz commented Oct 6, 2021

danielskatz commented Oct 6, 2021

KanishAnand commented Oct 6, 2021

danielskatz commented Oct 6, 2021

whedon commented Oct 15, 2021

whedon commented Oct 15, 2021

whedon commented Oct 15, 2021

danielskatz commented Oct 15, 2021

soraxas commented Oct 15, 2021

whedon commented Oct 15, 2021

soraxas commented Oct 15, 2021

whedon commented Oct 15, 2021

soraxas commented Oct 15, 2021

whedon commented Oct 15, 2021

soraxas commented Oct 15, 2021

danielskatz commented Oct 15, 2021

whedon commented Oct 15, 2021

whedon commented Oct 15, 2021

whedon commented Oct 15, 2021

danielskatz commented Oct 15, 2021

whedon commented Oct 15, 2021

whedon commented Oct 15, 2021

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danielskatz commented Oct 15, 2021

whedon commented Oct 15, 2021

whedon commented Sep 29, 2021 •

edited

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