[REVIEW]: SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency #3653

whedon · 2021-08-24T12:27:28Z

Submitting author: @antoinediez (Antoine Diez)
Repository: https://github.com/antoinediez/Sisyphe
Version: v1.0
Editor: @pdebuyl
Reviewer: @lorenzo-rovigatti, @junghans
Archive: 10.5281/zenodo.5532924

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Reviewer instructions & questions

@lorenzo-rovigatti & @junghans, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

Review checklist for @lorenzo-rovigatti

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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 (@antoinediez) 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 @junghans

✨ 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 (@antoinediez) 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 · 2021-08-24T12:27:31Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lorenzo-rovigatti, @junghans 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.

⭐ Important ⭐

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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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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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whedon · 2021-08-24T12:27:44Z

Wordcount for paper.md is 1005

whedon · 2021-08-24T12:27:50Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.44 s (266.0 files/s, 107151.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            27           3451             81          10525
JavaScript                      14           2404           2467           9203
Python                          21           1206           2156           3274
SVG                              2              0              0           2672
CSS                              9            200             57           1154
TeX                              1             55              4            578
reStructuredText                28           2577           2288            470
Markdown                         2             46              0            129
Jupyter Notebook                10              0           1959             88
DOS Batch                        1              8              1             26
make                             1              5              7             11
YAML                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           117           9956           9027          28139
-------------------------------------------------------------------------------


Statistical information for the repository 'c23e03744e8da25d31ee0339' was
gathered on 2021/08/24.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Antoine Diez                    32         40852          17140          100.00

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
Antoine Diez              23712           58.0          0.1               17.24

whedon · 2021-08-24T12:27:51Z

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

OK DOIs

- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/bfb0093177 is OK
- 10.1103/PhysRevLett.75.1226 is OK
- 10.1142/S0218202508003005 is OK
- 10.1007/s11537-007-0647-x is OK
- 10.4310/cms.2009.v7.n2.a9 is OK
- 10.1007/978-0-8176-4946-3_12 is OK
- 10.1016/j.jfa.2014.02.030 is OK
- 10.1007/s00205-014-0800-7 is OK
- 10.1142/S0218202516500330 is OK
- 10.1080/07362994.2018.1486202 is OK
- 10.1142/9789813272880_0206 is OK
- 10.1142/S0218202519500374 is OK
- 10.1007/978-3-030-15096-9_2 is OK
- 10.1142/S021820252040014X is OK
- 10.1002/pamm.201800291 is OK
- 10.1142/S0218202517400061 is OK
- 10.1137/18M1192184 is OK
- 10.1073/pnas.1806579115 is OK
- 10.1016/j.physrep.2012.03.004 is OK
- 10.1214/15-AIHP701 is OK
- 10.1214/aoap/1028903535 is OK
- 10.1109/ICNN.1995.488968 is OK
- 10.1016/j.jcp.2019.108877 is OK
- 10.1103/PhysRevE.77.046113 is OK
- 10.1007/s10955-014-1119-3 is OK
- 10.1103/PhysRevE.58.4828 is OK
- 10.1073/pnas.1202032109 is OK
- 10.1103/PhysRevE.92.032722 is OK
- 10.1007/978-1-4757-3437-9 is OK
- 10.1109/78.984773 is OK
- 10.3182/20090706-3-FR-2004.00129 is OK
- 10.1198/106186004X12803 is OK

MISSING DOIs

- 10.1007/bfb0085169 may be a valid DOI for title: Topics in propagation of chaos
- 10.1142/s0218202521500342 may be a valid DOI for title: From particle swarm optimization to consensus based optimization: stochastic modeling and mean-field limit

INVALID DOIs

- None

whedon · 2021-08-24T12:28:00Z

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

pdebuyl · 2021-08-24T12:35:54Z

@lorenzo-rovigatti @junghans make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines linked to at the top of this review page.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here. As this is the first JOSS review for one of you (unless I missed something), do not hesitate to ask questions if you have doubts about the procedure. You can also take a look at earlier reviews to get an idea of how the reviews proceed https://github.com/openjournals/joss-reviews/issues?q=is%3Aissue+label%3Aaccepted+

pdebuyl · 2021-08-24T12:36:43Z

@antoinediez please check the missing dois

antoinediez · 2021-08-24T12:49:11Z

@whedon generate pdf

whedon · 2021-08-24T12:49:41Z

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

antoinediez · 2021-08-24T12:50:34Z

@whedon check references

whedon · 2021-08-24T12:50:55Z

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

OK DOIs

- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/bfb0085169 is OK
- 10.1007/bfb0093177 is OK
- 10.1103/PhysRevLett.75.1226 is OK
- 10.1142/S0218202508003005 is OK
- 10.1007/s11537-007-0647-x is OK
- 10.4310/cms.2009.v7.n2.a9 is OK
- 10.1007/978-0-8176-4946-3_12 is OK
- 10.1016/j.jfa.2014.02.030 is OK
- 10.1007/s00205-014-0800-7 is OK
- 10.1142/S0218202516500330 is OK
- 10.1080/07362994.2018.1486202 is OK
- 10.1142/9789813272880_0206 is OK
- 10.1142/S0218202519500374 is OK
- 10.1007/978-3-030-15096-9_2 is OK
- 10.1142/S021820252040014X is OK
- 10.1002/pamm.201800291 is OK
- 10.1142/S0218202517400061 is OK
- 10.1137/18M1192184 is OK
- 10.1142/s0218202521500342 is OK
- 10.1073/pnas.1806579115 is OK
- 10.1016/j.physrep.2012.03.004 is OK
- 10.1214/15-AIHP701 is OK
- 10.1214/aoap/1028903535 is OK
- 10.1109/ICNN.1995.488968 is OK
- 10.1016/j.jcp.2019.108877 is OK
- 10.1103/PhysRevE.77.046113 is OK
- 10.1007/s10955-014-1119-3 is OK
- 10.1103/PhysRevE.58.4828 is OK
- 10.1073/pnas.1202032109 is OK
- 10.1103/PhysRevE.92.032722 is OK
- 10.1007/978-1-4757-3437-9 is OK
- 10.1109/78.984773 is OK
- 10.3182/20090706-3-FR-2004.00129 is OK
- 10.1198/106186004X12803 is OK

MISSING DOIs

- None

INVALID DOIs

- None

antoinediez · 2021-08-31T21:10:00Z

@whedon generate pdf

whedon · 2021-08-31T21:10:31Z

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

whedon · 2021-09-07T12:27:41Z

👋 @lorenzo-rovigatti, please update us on how your review is going (this is an automated reminder).

whedon · 2021-09-07T12:27:41Z

👋 @junghans, please update us on how your review is going (this is an automated reminder).

junghans · 2021-09-07T15:22:33Z

👋 @junghans, please update us on how your review is going (this is an automated reminder).

Done.

pdebuyl · 2021-09-13T14:13:40Z

Thanks @junghans for the review!

pdebuyl · 2021-09-13T14:14:36Z

@lorenzo-rovigatti I see that you have checked a number of items already. Do you need extra information to proceed? You can contact the authors here or, if it makes sense, open an issue at the project directly.

pdebuyl · 2021-09-13T14:15:41Z

PS: @lorenzo-rovigatti check the issue there as well antoinediez/Sisyphe#2

lorenzo-rovigatti · 2021-09-13T21:04:48Z

Yes, I started working on the review but then I had to stop for a few days. I'll get back to it this week. Sorry for any delay this may cause!

whedon · 2021-09-28T12:11:59Z

Attempting dry run of processing paper acceptance...

whedon · 2021-09-28T12:12:21Z

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

OK DOIs

- 10.1137/15M1019726 is OK
- 10.1007/978-3-662-12616-5 is OK
- 10.1007/978-3-319-16375-8 is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/bfb0085169 is OK
- 10.1007/bfb0093177 is OK
- 10.1103/PhysRevLett.75.1226 is OK
- 10.1142/S0218202508003005 is OK
- 10.1007/s11537-007-0647-x is OK
- 10.4310/cms.2009.v7.n2.a9 is OK
- 10.1007/978-0-8176-4946-3_12 is OK
- 10.1016/j.jfa.2014.02.030 is OK
- 10.1007/s00205-014-0800-7 is OK
- 10.1142/S0218202516500330 is OK
- 10.1080/07362994.2018.1486202 is OK
- 10.1142/9789813272880_0206 is OK
- 10.1142/S0218202519500374 is OK
- 10.1007/978-3-030-15096-9_2 is OK
- 10.1142/S021820252040014X is OK
- 10.1002/pamm.201800291 is OK
- 10.1142/S0218202517400061 is OK
- 10.1137/18M1192184 is OK
- 10.1142/s0218202521500342 is OK
- 10.1073/pnas.1806579115 is OK
- 10.1016/j.physrep.2012.03.004 is OK
- 10.1214/15-AIHP701 is OK
- 10.1214/aoap/1028903535 is OK
- 10.1109/ICNN.1995.488968 is OK
- 10.1016/j.jcp.2019.108877 is OK
- 10.1103/PhysRevE.77.046113 is OK
- 10.1007/s10955-014-1119-3 is OK
- 10.1103/PhysRevE.58.4828 is OK
- 10.1073/pnas.1202032109 is OK
- 10.1103/PhysRevE.92.032722 is OK
- 10.1007/978-1-4757-3437-9 is OK
- 10.1109/78.984773 is OK
- 10.3182/20090706-3-FR-2004.00129 is OK
- 10.1198/106186004X12803 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-09-28T12:12:34Z

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

Check final proof 👉 openjournals/joss-papers#2619

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2619, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

pdebuyl · 2021-09-28T12:12:54Z

Thank you @antoinediez for the update. All is ok with the paper, one of the editors-in-chief will pick up the submission.

Thanks @junghans and @lorenzo-rovigatti for the review!

danielskatz · 2021-09-28T12:56:20Z

@antoinediez - I've suggested some minor changes to the paper in antoinediez/Sisyphe#5 - please merge this, or let me know what you disagree with, then we can proceed to acceptance and publication.

antoinediez · 2021-09-28T13:07:44Z

Hi @danielskatz !
Thanks for updating the paper, this is merged.

danielskatz · 2021-09-28T13:18:53Z

@whedon recommend-accept

whedon · 2021-09-28T13:18:56Z

Attempting dry run of processing paper acceptance...

whedon · 2021-09-28T13:19:13Z

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

OK DOIs

- 10.1137/15M1019726 is OK
- 10.1007/978-3-662-12616-5 is OK
- 10.1007/978-3-319-16375-8 is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/bfb0085169 is OK
- 10.1007/bfb0093177 is OK
- 10.1103/PhysRevLett.75.1226 is OK
- 10.1142/S0218202508003005 is OK
- 10.1007/s11537-007-0647-x is OK
- 10.4310/cms.2009.v7.n2.a9 is OK
- 10.1007/978-0-8176-4946-3_12 is OK
- 10.1016/j.jfa.2014.02.030 is OK
- 10.1007/s00205-014-0800-7 is OK
- 10.1142/S0218202516500330 is OK
- 10.1080/07362994.2018.1486202 is OK
- 10.1142/9789813272880_0206 is OK
- 10.1142/S0218202519500374 is OK
- 10.1007/978-3-030-15096-9_2 is OK
- 10.1142/S021820252040014X is OK
- 10.1002/pamm.201800291 is OK
- 10.1142/S0218202517400061 is OK
- 10.1137/18M1192184 is OK
- 10.1142/s0218202521500342 is OK
- 10.1073/pnas.1806579115 is OK
- 10.1016/j.physrep.2012.03.004 is OK
- 10.1214/15-AIHP701 is OK
- 10.1214/aoap/1028903535 is OK
- 10.1109/ICNN.1995.488968 is OK
- 10.1016/j.jcp.2019.108877 is OK
- 10.1103/PhysRevE.77.046113 is OK
- 10.1007/s10955-014-1119-3 is OK
- 10.1103/PhysRevE.58.4828 is OK
- 10.1073/pnas.1202032109 is OK
- 10.1103/PhysRevE.92.032722 is OK
- 10.1007/978-1-4757-3437-9 is OK
- 10.1109/78.984773 is OK
- 10.3182/20090706-3-FR-2004.00129 is OK
- 10.1198/106186004X12803 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-09-28T13:19:26Z

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

Check final proof 👉 openjournals/joss-papers#2620

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2620, 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 · 2021-09-28T13:20:13Z

@whedon accept deposit=true

whedon · 2021-09-28T13:20:18Z

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

whedon · 2021-09-28T13:21:03Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-09-28T13:21:04Z

🚨🚨🚨 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.03653 joss-papers#2621
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03653
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2021-09-28T13:26:04Z

Congratulations to @antoinediez (Antoine Diez)!!

And thanks to @lorenzo-rovigatti and @junghans for reviewing, and to @pdebuyl for editing!
We couldn't do this without you!

whedon · 2021-09-28T13:26:10Z

🎉🎉🎉 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.03653/status.svg)](https://doi.org/10.21105/joss.03653)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03653/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03653/status.svg
   :target: https://doi.org/10.21105/joss.03653

This is how it will look in your documentation:

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whedon added Python review labels Aug 24, 2021

whedon assigned pdebuyl Aug 24, 2021

whedon mentioned this issue Aug 24, 2021

[PRE REVIEW]: SiSyPHE: A Python package for the Simulation of Systems of Particles with High Efficiency #3425

Closed

whedon assigned junghans and lorenzo-rovigatti Aug 25, 2021

This was referenced Aug 30, 2021

Add contribution guidelines antoinediez/Sisyphe#1

Closed

Add CI / improve testing antoinediez/Sisyphe#2

Closed

JOSS Paper title to broad antoinediez/Sisyphe#3

Closed

junghans changed the title ~~[REVIEW]: SiSyPHE: A Python package for the Simulation of Systems of Particles with High Efficiency~~ [REVIEW]: SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency Aug 31, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 28, 2021

whedon added accepted published Papers published in JOSS labels Sep 28, 2021

danielskatz closed this as completed Sep 28, 2021

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[REVIEW]: SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency #3653

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whedon commented Aug 24, 2021 • edited Loading

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