[REVIEW]: OTTO: A Python package to simulate, solve and visualize the source-tracking POMDP #4266

editorialbot · 2022-03-22T21:33:33Z

Submitting author: @auroreloisy (Aurore Loisy)
Repository: https://github.com/C0PEP0D/otto
Branch with paper.md (empty if default branch):
Version: v1.0.1
Editor: @VivianePons
Reviewers: @11michalis11, @RomainAzais
Archive: 10.5281/zenodo.6651884

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/51c451ddeeb1affdb1533a4fa1582f4c"><img src="https://joss.theoj.org/papers/51c451ddeeb1affdb1533a4fa1582f4c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/51c451ddeeb1affdb1533a4fa1582f4c/status.svg)](https://joss.theoj.org/papers/51c451ddeeb1affdb1533a4fa1582f4c)

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

@11michalis11, @RomainAzais 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 @VivianePons 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 @11michalis11

📝 Checklist for @RomainAzais

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

editorialbot · 2022-03-22T21:33:34Z

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

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editorialbot · 2022-03-22T21:33:41Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (560.4 files/s, 50671.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          61            905           1190           4013
SVG                              1              1              1            505
reStructuredText                23            274            290            406
Markdown                         2            160              0            362
TeX                              1             26              0            230
YAML                             2              7             12             36
DOS Batch                        1              8              1             26
Bourne Shell                     1              5              0             19
make                             1              4              7              9
INI                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            94           1390           1501           5609
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-03-22T21:33:44Z

Wordcount for paper.md is 668

editorialbot · 2022-03-22T21:33:46Z

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

OK DOIs

- 10.1103/PhysRevE.101.043110 is OK
- 10.7554/eLife.04220 is OK
- 10.7554/elife.52371 is OK
- 10.1073/pnas.1618055114 is OK
- 10.1016/J.INFFUS.2017.10.009 is OK
- 10.1073/pnas.1221091110 is OK
- 10.1007/s10514-006-7536-7 is OK
- 10.3389/fnbot.2010.00001 is OK
- 10.1073/pnas.1606075113 is OK
- 10.1146/annurev-conmatphys-031720-032754 is OK
- 10.1016/J.INFFUS.2015.06.008 is OK
- 10.1142/4042 is OK
- 10.2307/1542524 is OK
- 10.1038/nature05464 is OK
- 10.1371/journal.pcbi.1003861 is OK
- 10.5281/zenodo.6125391 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-03-22T21:35:33Z

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

auroreloisy · 2022-03-23T06:00:43Z

@VivianePons <https://github.com/VivianePons> Thank you for handling this manuscript, should I provide you with additional reviewers suggestions?

…

On Tue, Mar 22, 2022 at 10:35 PM The Open Journals editorial robot < ***@***.***> wrote: 👉📄 Download article proof <https://raw.githubusercontent.com/openjournals/joss-papers/joss.04266/joss.04266/10.21105.joss.04266.pdf> 📄 View article proof on GitHub <https://github.com/openjournals/joss-papers/blob/joss.04266/joss.04266/10.21105.joss.04266.pdf> 📄 👈 — Reply to this email directly, view it on GitHub <#4266 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMQVCOHU5RMBNC2DGGUEOG3VBI4K7ANCNFSM5RMEMA3Q> . You are receiving this because you were mentioned.Message ID: ***@***.***>

MichalisPanayides · 2022-03-30T11:42:18Z

Review checklist for @11michalis11

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/C0PEP0D/otto?
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 (@auroreloisy) 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?

VivianePons · 2022-03-30T18:50:11Z

@auroreloisy Thank you, I think I still have a few names to check. I just contacted someone.

VivianePons · 2022-04-01T18:16:34Z

@editorialbot add @RomainAzais as reviewer

editorialbot · 2022-04-01T18:16:35Z

@RomainAzais added to the reviewers list!

MichalisPanayides · 2022-04-04T17:43:54Z

Just finished my review. All the comments can be found at the issue created on the repository 👍

auroreloisy · 2022-04-05T13:49:54Z

@11michalis11 Thank you for your positive feedback and for your help with improving our submission, we have replied in the issue.
@VivianePons We have addressed all the comments in the the last commit

auroreloisy · 2022-05-06T09:35:45Z

Dear @RomainAzais, we hope everything is going alright with the review, as nothing has moved in the last 5 weeks. Let us know if we can help with anything.

auroreloisy · 2022-05-12T11:15:53Z

@VivianePons Have you heard back from @RomainAzais by any chance? It's been 6 weeks since they were assigned and nothing has moved.

RomainAzais · 2022-05-12T11:27:53Z

Hello!
Sorry for my very late reply. I've been super busy the last few weeks.
But as I said to @VivianePons earlier this morning, I'm going to take care of the review in the next few days.
Romain

RomainAzais · 2022-05-13T08:41:59Z

Review checklist for @RomainAzais

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/C0PEP0D/otto?
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 (@auroreloisy) 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?

auroreloisy · 2022-06-02T12:53:10Z

Hi @RomainAzais, just wondering when you think you'll be able to complete the review. We're happy to help with any issue.

RomainAzais · 2022-06-03T11:41:38Z

Hi @auroreloisy,
I'm almost done. I'll complete it by the end of next week.

RomainAzais · 2022-06-09T10:21:15Z

Hello,

My overall opinion of OTTO is very positive: the installation and testing procedures are clear, the readme file and the documentation are very complete and at the right level of detail, and the examples help to understand how to use it. I only encountered a small bug during the installation (with tensorflow apparently) but it has been solved. Setting up a ci/cd pipeline might avoid this kind of mishap.

My only (slightly) negative comment is related to the discussion on the review thread: reading only the paper, I expect (as a non-specialist) to be able to use OTTO on custom state spaces, where I can decide on target and tracker (starting) positions. (Perhaps this is a bias induced by the introduction of the paper on applications of this type of model.)

The documentation is precise on the model and strategies considered and helps to understand that this is not what is treated with this package. If I understood correctly, OTTO is more a tool for rigorous study and comparison of heuristic policies than a practical tool to be used on real-world examples. In my opinion, a sentence or two should be added in the paper to clarify the purpose of the package.

I still checked the "statement of need" box because this point is not blocking for me. On this subject, note that if we follow the checklist to the letter, a "statement of need" section should be present in the paper.

It was a pleasure to use and review OTTO. Thanks for the quick feedback during the review process, and sorry for my late feedback in this busy end of year period.

R.

auroreloisy · 2022-06-09T17:07:42Z

Dear @RomainAzais,
thank you very much for spending time on reviewing OTTO, and for your positive feedback.
Following your suggestion, we have added the following sentence in the paper to clarify the purpose of the package: "It is primarily designed to rigorously study the statistical properties of near-optimal strategies and of their heuristic approximations."
(cf commit and commit).
Regarding the "Statement of Need", it is actually present in the paper (first section).

Dear @VivianePons : we believe we have now addressed all issues raised by the reviewers.

VivianePons · 2022-06-10T14:06:09Z

@editorialbot generate pdf

auroreloisy · 2022-06-10T14:30:59Z

@VivianePons actually the invalid doi should be active on the 15 june (upcoming publication that uses OTTO by us)

RomainAzais · 2022-06-13T15:10:38Z

Regarding the "Statement of Need", it is actually present in the paper (first section).

My mistake, I guess I was expecting it at the "summary" place. But that's perfectly fine.

@RomainAzais can you confirm that you're satisfied with the answer from @auroreloisy to your comment?

Yes, I am.

auroreloisy · 2022-06-15T08:16:16Z

@VivianePons I have just updated the reference, it works now

VivianePons · 2022-06-15T15:35:05Z

@editorialbot generate pdf

editorialbot · 2022-06-15T15:36:19Z

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

VivianePons · 2022-06-15T15:36:36Z

@editorialbot check references

editorialbot · 2022-06-15T15:36:45Z

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

OK DOIs

- 10.1103/PhysRevE.101.043110 is OK
- 10.7554/eLife.04220 is OK
- 10.7554/elife.52371 is OK
- 10.1073/pnas.1618055114 is OK
- 10.1098/rspa.2022.0118 is OK
- 10.1016/J.INFFUS.2017.10.009 is OK
- 10.1073/pnas.1221091110 is OK
- 10.1007/s10514-006-7536-7 is OK
- 10.3389/fnbot.2010.00001 is OK
- 10.1073/pnas.1606075113 is OK
- 10.1146/annurev-conmatphys-031720-032754 is OK
- 10.1016/J.INFFUS.2015.06.008 is OK
- 10.1142/4042 is OK
- 10.2307/1542524 is OK
- 10.1038/nature05464 is OK
- 10.1371/journal.pcbi.1003861 is OK
- 10.5281/zenodo.6125391 is OK

MISSING DOIs

- None

INVALID DOIs

- None

VivianePons · 2022-06-15T15:42:54Z

Thank you @auroreloisy, I believe we have now everything and we will move to the last steps before final acceptance. Congrats! And thank you to @11michalis11 and @RomainAzais for the reviews.

@auroreloisy : can you make a tagged release of the software (on Zenodo, figshare, or other). This needs to have the same title and authors as the submission. When done, send me the link and I will update the version and doi

auroreloisy · 2022-06-16T10:53:13Z

@VivianePons : here is the zenodo link https://zenodo.org/record/6651884

VivianePons · 2022-06-16T15:45:06Z

@editorialbot set v1.0.1 as version

editorialbot · 2022-06-16T15:45:08Z

Done! version is now v1.0.1

VivianePons · 2022-06-16T15:45:48Z

@editorialbot set 10.5281/zenodo.6651884 as archive

editorialbot · 2022-06-16T15:45:50Z

Done! Archive is now 10.5281/zenodo.6651884

VivianePons · 2022-06-16T15:46:15Z

@editorialbot recommend-accept

editorialbot · 2022-06-16T15:46:16Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-06-16T15:46:28Z

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

OK DOIs

- 10.1103/PhysRevE.101.043110 is OK
- 10.7554/eLife.04220 is OK
- 10.7554/elife.52371 is OK
- 10.1073/pnas.1618055114 is OK
- 10.1098/rspa.2022.0118 is OK
- 10.1016/J.INFFUS.2017.10.009 is OK
- 10.1073/pnas.1221091110 is OK
- 10.1007/s10514-006-7536-7 is OK
- 10.3389/fnbot.2010.00001 is OK
- 10.1073/pnas.1606075113 is OK
- 10.1146/annurev-conmatphys-031720-032754 is OK
- 10.1016/J.INFFUS.2015.06.008 is OK
- 10.1142/4042 is OK
- 10.2307/1542524 is OK
- 10.1038/nature05464 is OK
- 10.1371/journal.pcbi.1003861 is OK
- 10.5281/zenodo.6125391 is OK

MISSING DOIs

- None

INVALID DOIs

- None

VivianePons · 2022-06-16T15:46:49Z

Perfect, I just recommended acceptance, thank you all for the work on the paper!

editorialbot · 2022-06-16T15:47:54Z

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

Check final proof 👉 openjournals/joss-papers#3285

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3285, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2022-06-16T16:22:42Z

@editorialbot accept

editorialbot · 2022-06-16T16:22:43Z

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

editorialbot · 2022-06-16T16:24:26Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-06-16T16:24:27Z

🚨🚨🚨 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.04266 joss-papers#3286
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04266
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-06-16T16:28:47Z

@11michalis11, @RomainAzais – many thanks for your reviews here and to @VivianePons for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@auroreloisy – your paper is now accepted and published in JOSS ⚡🚀💥

editorialbot · 2022-06-16T16:28:49Z

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

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editorialbot added Python review Shell TeX labels Mar 22, 2022

editorialbot assigned VivianePons Mar 22, 2022

editorialbot mentioned this issue Mar 22, 2022

[PRE REVIEW]: OTTO: A Python package to simulate, solve and visualize the source-tracking POMDP #4233

Closed

MichalisPanayides mentioned this issue Apr 4, 2022

JOSS submission review #4266 C0PEP0D/otto#1

Closed

MichalisPanayides mentioned this issue Apr 25, 2022

2022-04-26 meeting overview MichalisPanayides/PhD-meetings#88

Open

4 tasks

RomainAzais mentioned this issue May 13, 2022

JOSS submission review #4266 (2nd review) C0PEP0D/otto#2

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 16, 2022

editorialbot added accepted published Papers published in JOSS labels Jun 16, 2022

arfon closed this as completed Jun 16, 2022

editorialbot mentioned this issue Jul 1, 2024

[PRE REVIEW]: AMaze: a benchmark generator for sighted maze-navigating agents #6945

Closed

editorialbot mentioned this issue Sep 28, 2024

[PRE REVIEW]: Pooltool: A Python package for realistic billiards simulation #7265

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[REVIEW]: OTTO: A Python package to simulate, solve and visualize the source-tracking POMDP #4266

[REVIEW]: OTTO: A Python package to simulate, solve and visualize the source-tracking POMDP #4266

Comments

editorialbot commented Mar 22, 2022 • edited Loading

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auroreloisy commented Mar 23, 2022 via email

MichalisPanayides commented Mar 30, 2022 • edited Loading

Review checklist for @11michalis11

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

VivianePons commented Mar 30, 2022

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editorialbot commented Apr 1, 2022

MichalisPanayides commented Apr 4, 2022

auroreloisy commented Apr 5, 2022

auroreloisy commented May 6, 2022 • edited Loading

auroreloisy commented May 12, 2022

RomainAzais commented May 12, 2022

RomainAzais commented May 13, 2022 • edited Loading

Review checklist for @RomainAzais

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

auroreloisy commented Jun 2, 2022

RomainAzais commented Jun 3, 2022

RomainAzais commented Jun 9, 2022

auroreloisy commented Jun 9, 2022

VivianePons commented Jun 10, 2022

auroreloisy commented Jun 10, 2022

RomainAzais commented Jun 13, 2022

auroreloisy commented Jun 15, 2022

VivianePons commented Jun 15, 2022

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VivianePons commented Jun 16, 2022

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