[REVIEW]: ABSESpy: An agent-based modeling framework for social-ecological systems

[editorialbot]

Submitting author: @SongshGeo (Shuang Song)
Repository: https://github.com/ABSESpy/ABSESpy
Branch with paper.md (empty if default branch): dev
Version: 0.5.6
Editor: @crvernon
Reviewers: @wang-boyu, @jamesdamillington
Archive: 10.5281/zenodo.10935937

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52"><img src="https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52/status.svg)](https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52)

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

@wang-boyu & @jamesdamillington, 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 @crvernon 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 @wang-boyu

📝 Checklist for @jamesdamillington

[editorialbot]

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

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.34 s (144.6 files/s, 159873.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      17           4989          20714         163824
JSON                            39              0              0           5131
Python                          53           1186           1644           3594
CSS                             15            460            543           3354
Markdown                        41            440              0            880
Jupyter Notebook                12              0           4662            834
TeX                              1             35              0            432
YAML                            11             48            100            393
TOML                             2             14              2            108
make                             1             10              8             41
INI                              1              1              0              7
-------------------------------------------------------------------------------
SUM:                           193           7183          27673         178598
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1279

[editorialbot]

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

OK DOIs

- 10.1680/ensu.2011.164.2.129 is OK
- 10.4324/9781003021339 is OK
- 10.1016/j.envsoft.2015.08.018 is OK
- 10.1038/s41562-017-0181-7 is OK
- 10.1111/gwat.12569 is OK
- 10.1016/j.gloenvcha.2019.101972 is OK
- 10.1007/978-3-030-29443-4_9 is OK
- 10.1177/1745691614527464 is OK
- 10.21105/joss.03065 is OK
- 10.3389/fnins.2015.00332 is OK
- 10.1177/1464993413486544 is OK
- 10.5751/es-03610-150420 is OK
- 10.5751/ES-08748-210341 is OK
- 10.1038/s41562-022-01478-5 is OK
- 10.1201/9780429496639 is OK
- 10.1017/S1355770X12000460 is OK
- 10.1016/j.ecocom.2018.07.007 is OK
- 10.1146/annurev-environ-110615-085349 is OK
- 10.1016/j.ecolecon.2016.08.008 is OK
- 10.1007/978-3-319-67217-5_2 is OK
- 10.1007/978-3-030-61255-9_30 is OK

MISSING DOIs

- 10.18564/jasss.3423 may be a valid DOI for title: Agent-based modelling of social-ecological systems: achievements, challenges, and a way forward

INVALID DOIs

- None

[editorialbot]

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

[crvernon]

👋 @SongshGeo , @wang-boyu , and @jamesdamillington - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) 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.

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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #6298 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[wang-boyu]

Review checklist for @wang-boyu

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/ABSESpy/ABSESpy?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@SongshGeo) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[SongshGeo]

@crvernon Thanks for your efforts on our project! We are glad to hear this update.
I appreciate two reviewers, @wang-boyu and @jamesdamillington, for your time on reviewing our project. This is a long-term project, and we are still working to improve it. I want to make this project better through discussion with you. :)

[jamesdamillington]

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 https://github.com/ABSESpy/ABSESpy?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@SongshGeo) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[wang-boyu]

Raised ABSESpy/ABSESpy#36 for missing DOI and reference.

[wang-boyu]

@editorialbot generate pdf

[editorialbot]

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

[wang-boyu]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1201/9780429496639 is OK
- 10.1680/ensu.2011.164.2.129 is OK
- 10.1038/s41562-022-01478-5 is OK
- 10.4324/9781003021339 is OK
- 10.1016/j.envsoft.2015.08.018 is OK
- 10.1038/s41562-017-0181-7 is OK
- 10.1111/gwat.12569 is OK
- 10.1016/j.gloenvcha.2019.101972 is OK
- 10.1007/978-3-030-29443-4_9 is OK
- 10.1177/1745691614527464 is OK
- 10.5751/es-03610-150420 is OK
- 10.5751/ES-08748-210341 is OK
- 10.21105/joss.03065 is OK
- 10.1016/j.ecocom.2018.07.007 is OK
- 10.1007/978-3-030-61255-9_30 is OK
- 10.1017/S1355770X12000460 is OK
- 10.1146/annurev-environ-110615-085349 is OK
- 10.1016/j.ecolecon.2016.08.008 is OK
- 10.18564/jasss.3423 is OK
- 10.1007/978-3-319-67217-5_2 is OK
- 10.3389/fnins.2015.00332 is OK
- 10.1145/3557989.3566157 is OK
- 10.1177/1464993413486544 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

👋 @SongshGeo , @wang-boyu , and @jamesdamillington

Just checking in to see how things are going. Could you provide a brief update here in this thread? Thanks!

[jamesdamillington]

@crvernon I've been struggling to get things running on my linux machine. Initially it was an issue at my end but now @SongshGeo thinks it might be an issue with python versioning and is investigating, so I'm waiting for the result of that. Have I got that right @SongshGeo ?

[SongshGeo]

@jamesdamillington was right. A new release with compatible improvements (and some other useful changes) is coming soon. I've been working on that in the past few days. Thanks for the patience @wang-boyu @crvernon

[crvernon]

👋 @SongshGeo , @wang-boyu , and @jamesdamillington

Could you provide a brief update to how things are going in this thread? Thanks!

[jamesdamillington]

I have completed my review of the software and checked off all items in my checklist satisfactorily.

Before I can check off items regarding the paper, I have comments for @SongshGeo and colleagues to address as follows:

• Line 24: 'research' not 'researches'
• Line 44: rather than 'et al.' maybe use actual words (e.g. 'and others') so as not to confuse against the file suffixes which are similar abbreviations
• Line 55: What do you mean by 'practicing' here? This doesn't seem right. Please edit to clarify
• Lines 57-65: I'm surprised these three points (Perceptions, Decision-making, Response) don't match the words used in Fig 2 (Options, Evaluate, Behaviour). Or are the latter three (in the Fig) all part of the 'decision-making' step? Aligning the steps in the list with the figure would be useful, I think
• Line 76: I think 'vary' should be 'varying'
• Line 93: 'more accurate' - this is a relative statement, so please clarify 'more accurate' than what?
• Line 99: ( wang2022h? )) is not included in the reference list
• Line 100: it's good that you recognise the similarity here to AgentPy but you don't then clearly explain how absespy is beneficial for SES researchers - maybe you could highlight the explicit functionality for representing the 'nature' side of CHANS (AgentPy really focuses on the 'human' side).
• Line 108: 'merely heuristic' - I think this is a little over-critical of NetLogo, which can incorporate 'real-world' (I think you mean 'empirical'?) data although not at the scale absespy could. I suggest you edit here to focus on the value of absespy for working with large-scale, empirical data so that models can run more efficiently than would be possible for the same data in NetLogo. You might also highlight your TimeDriver module which is a benefit over NetLogo's more simple 'ticks'

[crvernon]

@SongshGeo it looks like one of your co-authors names appear differently between what is in the paper (Elías José Mantilla) versus what is in the Zenodo archive (Elías José Mantilla Ibarra).

Also, you have ORCIDs for some authors in archive that do not have the ORCID listed in the paper.

Please make these consistent.

No need to conduct another release. Thanks!

[SongshGeo]

@crvernon Hi, Sorry. I sometimes struggle with Western names 😂. Now, I updated the ORCIDs in the paper and the name in the Zenodo archive.

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

👋 - @SongshGeo I am recommending that this submission be accepted for publication. An EiC will review shortly and if all goes well this will go live soon! Thanks to @wang-boyu and @jamesdamillington for a timely and constructive review!

[crvernon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1201/9780429496639 is OK
- 10.1680/ensu.2011.164.2.129 is OK
- 10.1038/s41562-022-01478-5 is OK
- 10.4324/9781003021339 is OK
- 10.1016/j.envsoft.2015.08.018 is OK
- 10.1038/s41562-017-0181-7 is OK
- 10.1111/gwat.12569 is OK
- 10.1016/j.gloenvcha.2019.101972 is OK
- 10.1007/978-3-030-29443-4_9 is OK
- 10.1177/1745691614527464 is OK
- 10.5751/es-03610-150420 is OK
- 10.5751/ES-08748-210341 is OK
- 10.21105/joss.03065 is OK
- 10.1016/j.ecocom.2018.07.007 is OK
- 10.1017/S1355770X12000460 is OK
- 10.1146/annurev-environ-110615-085349 is OK
- 10.1016/j.ecolecon.2016.08.008 is OK
- 10.18564/jasss.3423 is OK
- 10.3389/fnins.2015.00332 is OK
- 10.1145/3557989.3566157 is OK
- 10.1177/1464993413486544 is OK
- 10.1073/pnas.2215674121 is OK
- 10.1073/pnas.2215676120 is OK
- 10.5334/jors.148 is OK

MISSING DOIs

- No DOI given, and none found for title: Applying Plural Rationality to Some Wicked Problem...
- No DOI given, and none found for title: Plural Rationality and Interactive Decision Proces...
- No DOI given, and none found for title: Towards a Community Framework for Agent-Based Mode...
- No DOI given, and none found for title: Utilizing Python for agent-based modeling: The Mes...
- No DOI given, and none found for title: MODFLOW 6 modular hydrologic model version 6.2. 1:...
- No DOI given, and none found for title: Complexity: A guided tour
- No DOI given, and none found for title: Understanding Institutional Diversity
- 10.1007/978-3-319-67217-5_2 may be a valid DOI for title: ABCE: A Python library for economic agent-based mo...
- No DOI given, and none found for title: NetLogo: A simple environment for modeling complex...

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5228, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[SongshGeo]

@crvernon Hi, I cannot download the proof article from the above link. When I tried to check the PDF file from JOSS's GitHub repo, I got the following error:

Error rendering embedded code
Invalid PDF

[kthyng]

Hi I can take over from here. My steps are:

• Check that version was updated
• Check that software archive exists, has been input to JOSS, and title and author list look good
• Check paper

[kthyng]

@SongshGeo Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. I think "earth" and "anthropocene" should be capitalized right?

[SongshGeo]

@kthyng Hi, sure! Now they are up-in-date in this PR.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Song
  given-names: Shuang
  orcid: "https://orcid.org/0000-0002-8112-8780"
- family-names: Wang
  given-names: Shuai
  orcid: "https://orcid.org/0000-0003-1595-9858"
- family-names: Jiao
  given-names: Chentai
  orcid: "https://orcid.org/0000-0003-1737-9814"
- family-names: Ibarra
  given-names: Elías José Mantilla
contact:
- family-names: Wang
  given-names: Shuai
  orcid: "https://orcid.org/0000-0003-1595-9858"
doi: 10.5281/zenodo.10935937
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Song
    given-names: Shuang
    orcid: "https://orcid.org/0000-0002-8112-8780"
  - family-names: Wang
    given-names: Shuai
    orcid: "https://orcid.org/0000-0003-1595-9858"
  - family-names: Jiao
    given-names: Chentai
    orcid: "https://orcid.org/0000-0003-1737-9814"
  - family-names: Ibarra
    given-names: Elías José Mantilla
  date-published: 2024-04-10
  doi: 10.21105/joss.06298
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6298
  title: "ABSESpy: An agent-based modeling framework for
    social-ecological systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06298"
  volume: 9
title: "ABSESpy: An agent-based modeling framework for social-ecological
  systems"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06298 joss-papers#5234
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06298
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...

[kthyng]

Congrats on your new publication @SongshGeo! Many thanks to editor @crvernon and reviewers @wang-boyu and @jamesdamillington for your time, hard work, and expertise!!

[editorialbot]

🎉🎉🎉 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.06298/status.svg)](https://doi.org/10.21105/joss.06298)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06298">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06298/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06298/status.svg
   :target: https://doi.org/10.21105/joss.06298

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
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[kthyng]

@SongshGeo if you're interested in reviewing for JOSS in the future, please sign up here: https://reviewers.joss.theoj.org/

[SongshGeo]

@kthyng @crvernon @jamesdamillington @wang-boyu

Thanks for the efforts from you all. The comments helped us improve our package.
Sure! I'm delighted to help with potential reviews in the future. I signed up just now.

By the way, does anyone know how to change JOSS's badge style? It seems not supported by Shields. I cannot add ?style= to make it consistent with my other badges.

[kthyng]

@SongshGeo I got an answer for you: We (JOSS) make them badges ourselves and they can't be re-styled. Sorry!

[SongshGeo]

@kthyng OK! It's such a pity!