[REVIEW]: Agentpy: A package for agent-based modeling in Python

[whedon]

Submitting author: @JoelForamitti (Joël Foramitti)
Repository: https://github.com/JoelForamitti/agentpy
Version: v0.1.1
Editor: @sbenthall
Reviewer: @jamesdamillington, @martibosch
Archive: 10.5281/zenodo.4946508

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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

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

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✨ 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 @jamesdamillington

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 (@JoelForamitti) 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: 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?
• 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: Do the authors clearly state 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 @martibosch

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 (@JoelForamitti) 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: 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?
• 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: Do the authors clearly state 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jamesdamillington, @martibosch 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 😿

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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]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.41 s (144.7 files/s, 165391.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          27            776            923           2113
reStructuredText                18            208            144            455
Jupyter Notebook                 6              0          62148            386
Markdown                         2             24              0             84
TeX                              1              8              1             70
YAML                             2              1              1             34
DOS Batch                        1              8              1             26
make                             1              4              7              9
CSS                              1              1              2              6
-------------------------------------------------------------------------------
SUM:                            59           1030          63227           3183
-------------------------------------------------------------------------------


Statistical information for the repository '4f497de77da3cb9525eb4407' was
gathered on 2021/02/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
JoelForamitti                   13           208            128            2.44
Joël Foramitti                  44          8561           4859           97.56

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
JoelForamitti              3812         1832.7          1.8                9.76

[whedon]

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

OK DOIs

- 10.1177/0963721419834547 is OK
- 10.3389/fevo.2018.00237 is OK

MISSING DOIs

- 10.1038/460685a may be a valid DOI for title: The economy needs agent-based modelling
- 10.1057/jos.2009.28 may be a valid DOI for title: Managing business complexity: discovering strategic solutions with agent-based modeling and simulation

INVALID DOIs

- https://doi.org/10.1002/wcc.647 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/wics.1356 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cosrev.2017.03.001 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

[sbenthall]

@JoelForamitti One thing you can always do while waiting for reviews is correct the DOI's noted as missing or invalid by the whedon bot. Those will need to be resolved before publication.

[jofmi]

@whedon check references

[whedon]

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

OK DOIs

- 10.1177/0963721419834547 is OK
- 10.3389/fevo.2018.00237 is OK
- 10.1038/460685a is OK
- 10.1002/wcc.647 is OK
- 10.1002/wics.1356 is OK
- 10.1016/j.cosrev.2017.03.001 is OK
- 10.1093/acprof:oso/9780195172119.001.0001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[jamesdamillington]

Apologies, yes this is still on my todo list. Teaching a priority, but this will follow very soon

[martibosch]

Hello! I have my thesis defense the 30th of March, so I will get to this review after that. Sorry for the inconveniences, I hope that this timing still works for you.

[sbenthall]

Hello. Gentle reminder to @martibosch and @jamesdamillington to please review this work.

[jamesdamillington]

@JoelForamitti Although you do include related information elsewhere in the paper, there does not seem to be "a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is". @whedon also discovered this (on 26 Feb). I think the section is required for the journal.

[jofmi]

@jamesdamillington, thank you for your comment! From other publications in JOSS (see e.g. this recent one) I had the impression that it is allowed to explain the need without an explicit section title of that name. @sbenthall, could you confirm or refute this?

[jamesdamillington]

@JoelForamitti @sbenthall I've completed my review at JOSS Review (JM) and conditionally accept the submission depending on the issues highlighted there. Looks good! Any queries on my comments, just let me know.

[jofmi]

Thanks a lot @jamesdamillington. I will wait for the second review from @martibosch as well as a response from @sbenthall on the 'statement of need' section before starting to work on a revision!

[sbenthall]

I'm actually not sure myself. I'll need to ask somebody with more experience. @xuanxu can you answer this question about Statement of Need?

[xuanxu]

Yes, the Statement of need is a required section and we just recently changed the documentation to better reflect this and avoid exceptions like the mentioned paper.

[jofmi]

Ok, thanks! I will include it in the revised version

[sbenthall]

Hello @martibosch this is a gentle reminder that this submission is waiting for your review

[martibosch]

Hello all! I am sorry for my delay, these were (and still are) some crazy days with the end of my thesis and some proposal deadlines to find further funding opportunities.

I have finished my review, I find the package to be very neat and easy (enjoyable) to use, which is great. The examples are clear and properly cover all the features except the scenario comparison, which is why I submitted a dedicated issue. Besides this, I only have some minor corrections in the manuscript which are addressed in another issue.

Overall, I find that agentpy is a great piece of work, my remarks are minor and should be quite easy to address. Looking forward to use it for my research!

Best,
Martí

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03065 joss-papers#2406
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03065
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @JoelForamitti on your article's publication in JOSS!

Many thanks to @jamesdamillington and @martibosch for reviewing this, and @sbenthall for editing.

[whedon]

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

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[jofmi]

Fantastic, thanks again to everyone!

[jofmi]

Hi @kyleniemeyer, I realized there is typo in the acknowledgements! Is there a way to still fix this?

[kyleniemeyer]

@JoelForamitti yes, I think if you update the paper source, @arfon can update the published version

[jofmi]

ok, thanks @kyleniemeyer!

@arfon, I have just made a commit that fixed the typo: jofmi/agentpy@480da12

[arfon]

@JoelForamitti – that should be updated now. The updated paper might take a few hours to show up properly on the JOSS site due to caching.

[jofmi]

@arfon fantastic, thanks a lot!