[PRE REVIEW]: Mesa 3: Agent-based modelling with Python in 2024

[editorialbot]

Submitting author: @EwoutH (Ewout ter Hoeven)
Repository: https://github.com/projectmesa/mesa
Branch with paper.md (empty if default branch): paper_2024
Version: v3.1
Editor: @gkthiruvathukal
Reviewers: Pending
Managing EiC: Daniel S. Katz

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/0c0e31521267ed506b9f352cba409559/status.svg)](https://joss.theoj.org/papers/0c0e31521267ed506b9f352cba409559)

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Software report:

github.com/AlDanial/cloc v 1.98  T=0.15 s (1021.5 files/s, 177295.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          86           3392           3808           9905
Markdown                        35           1289             26           3428
Jupyter Notebook                 5              0           2145            752
YAML                            12             19             39            356
DOS Batch                        1             29              1            212
TeX                              2             14              0            145
make                             1             28              6            143
TOML                             1              9             17            127
Text                             3             16              0             69
JSON                             1              0              0             12
Dockerfile                       1              9             19              9
Bourne Shell                     1              1              0              7
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           150           4806           6061          15167
-------------------------------------------------------------------------------

Commit count by author:

   420	rht
   288	Ewout ter Hoeven
   284	jackiekazil
   120	David Masad
   115	Jan Kwakkel
   101	Corvince
    71	tpike3
    63	Jackie Kazil
    58	Tortar
    42	Taylor Mutch
    42	pre-commit-ci[bot]
    24	cauemello
    23	Dustin J. Mitchell
    22	Jeetu
    19	corvince
    17	ReblochonMasque
    16	Tom Pike
    13	Drewrey Lupton
    13	Jon Schiefelbein
    13	Wang Boyu
    12	SebastianoF
    12	Thomas Johnson
    11	dependabot[bot]
    10	Animesh Rawat
    10	Matt Davis
     8	James Arruda
     8	Nathan Miller
     8	Stephen Mubita
     7	Ankit Kumar
     7	Joe Dight
     7	gcallah
     7	ihopethiswillfi
     7	rlskoeser
     6	Achal Jain
     6	Heß
     6	Jessica Garson
     6	Spartan-71
     6	Steven MacLeod
     6	deepsource-autofix[bot]
     5	Dan Cunningham
     5	Daniel Chen
     5	Keith Richards
     5	Sascha Holzhauer
     5	Yannick Jadoul
     5	devforfu
     5	nissu99
     4	Ash Hoover
     4	Brian Russo
     4	Colin Maxwell
     4	DanielWeitzenfeld
     4	James Hovet
     4	Jangsea Park
     4	Max Orhai
     4	Nathan Verzemnieks
     4	Raúl Reguillo Carmona
     4	jess010
     4	jkerfs
     4	jonahaag
     3	AdamZh0u
     3	Benjamin Crane
     3	Bill Tucker
     3	Glenn Lehman
     3	ItsQuinnMoore
     3	Jatin Khilnani
     3	Jeremy Silver
     3	Keelan
     3	Martin Breuss
     3	Paul Gowder
     3	Yigit Guneli
     3	trickroll
     3	uec561
     2	Adam Zh0u
     2	Casper Smet
     2	Catherine Devlin
     2	Daniel Furman
     2	David
     2	David Balash
     2	Florian Kohrt
     2	Gonçalo Pascoal
     2	Jeremy Foote
     2	Luke Meyers
     2	Mat-pa
     2	Rebecca Sutton Koeser
     2	Ron Dotsch
     2	Sahil Chhoker
     2	Simon Podhajsky
     2	Victor Norman
     2	Vincent Hess
     2	federico
     2	houssam7737
     1	A Lee
     1	Abdallah Akrab
     1	Aditya Tiwari
     1	Alex
     1	Allen Lee
     1	Bubu
     1	Charlie Roe
     1	Christopher Akiki
     1	DarshPareek
     1	Deborah Duong
     1	Dev Test
     1	Edward Betts
     1	Eleonore9
     1	EwoutH
     1	Francis dela Cruz
     1	Giacomo Ravaioli
     1	Grace Z
     1	Houssam Kherraz
     1	Ikko Eltociear Ashimine
     1	J. Fernando Sánchez
     1	Jack at Omen Apps
     1	Jacob Hwang
     1	James Paterson
     1	Jared Norman
     1	Jisk Attema
     1	JoeHelbing
     1	Josiah Vinson
     1	LizaRoelofsen
     1	Luca Verginer
     1	LuciaBaldassini
     1	Maarten van der Sande
     1	Maarten-vd-Sande
     1	Majd Al-Shihabi
     1	Matt Wiens
     1	Megan Sosey
     1	Nick Aldershof
     1	Nouamane Tazi
     1	Oliver Katz
     1	Oren Bochman
     1	Paolo Gervasoni Vila
     1	Rebecca Davidsson
     1	Robert Hopkins
     1	Sahil Singh
     1	Sangamesh Itagi
     1	Sebastian Ortan
     1	Shengyu Huang
     1	Sherman
     1	Shubhanshu Mishra
     1	Sophia Wassermann
     1	Spencer Williams
     1	Steffen Rehberg
     1	Stephen Mann
     1	Taylor Mitchell
     1	Valentina Kiryushkina
     1	Vítor Fróis
     1	Wouter
     1	WouterVrielink
     1	Yasin Amini
     1	alba ramos
     1	clumdee
     1	electric-souperman
     1	gary
     1	gboeing
     1	jurreaserna
     1	kennethells
     1	logeaux
     1	maskarb
     1	nvrzm
     1	puer-robustus
     1	sahusiddharth
     1	schand5
     1	subhamonsey
     1	tcdejong
     1	vhess
     1	werwty

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1485

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

✅ OK DOIs

- 10.1063/1.1571309 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Growing Artificial Societies: Social Science from ...
- No DOI given, and none found for title: Agent-based computational models and generative so...
- No DOI given, and none found for title: Mesa: An Agent-Based Modeling Framework.
- No DOI given, and none found for title: Utilizing python for agent-based modeling: The mes...
- No DOI given, and none found for title: Mesa-Geo: A GIS extension for the Mesa agent-based...

❌ MISSING DOIs

- 10.2307/134812 may be a valid DOI for title: Micromotives and Macrobehavior
- 10.1016/j.jclepro.2020.120296 may be a valid DOI for title: Sustainable food security decision-making: an agen...
- 10.1016/j.trd.2020.102455 may be a valid DOI for title: A post-disaster resource allocation framework for ...
- 10.1016/j.enbuild.2020.109763 may be a valid DOI for title: Towards agent-based building stock modeling: Botto...
- 10.1016/j.enpol.2017.08.024 may be a valid DOI for title: Putting renewable energy auctions into action–An a...
- 10.1016/j.eswa.2022.116604 may be a valid DOI for title: A multi-agent approach to the truck multi-drone ro...
- 10.1016/j.elerap.2022.101195 may be a valid DOI for title: Balancing consumer and business value of recommend...
- 10.1073/pnas.2215675120 may be a valid DOI for title: Uncertainty in boundedly rational household adapta...

❌ INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

AgentPy: A package for agent-based modeling in Python
Submitting author: @JoelForamitti
Handling editor: @sbenthall (Active)
Reviewers: @jamesdamillington, @martibosch
Similarity score: 0.7343

Agents.jl: agent-based modeling framework in Julia
Submitting author: @kavir1698
Handling editor: @jedbrown (Active)
Reviewers: @Datseris, @mozhgan-kch
Similarity score: 0.6969

Melodie: Agent-based Modeling in Python
Submitting author: @SongminYu
Handling editor: @jbytecode (Active)
Reviewers: @JoelForamitti, @rusu24edward
Similarity score: 0.6950

pylattica: a package for prototyping lattice models in chemistry and materials science
Submitting author: @mcgalcode
Handling editor: @richardjgowers (Retired)
Reviewers: @riesben, @amkrajewski
Similarity score: 0.6809

villager: A framework for designing and executing agent-based models in R
Submitting author: @thomasthelen
Handling editor: @marcosvital (Active)
Reviewers: @chrisaberson, @brunomontezano, @thodson-usgs
Similarity score: 0.6736

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

👋 @EwoutH - thanks for your submission. Here are some items that need work.

1. Please add countries to all affiliations in your .md file.
2. Note that when you refer explicitly to a reference, as in the second reference in your paper, you shouldn't use []s around it in the .md file, as shown in the JOSS example paper.
3. I see that your paper is a bit longer than normal for JOSS (1500 words vs a suggested max of 1000). Please consider if there is anything you could move to the repo or documentation, and point to in the paper.
4. You could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect.

Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when you've made changes in the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Finally, can we close openjournals/joss#1403 given that you have now submitted this paper, which seems fine to proceed with, other than the minor points above?

[EwoutH]

@danielskatz Thanks for the very quick pre-review assignment!

1. Affiliations: would this be formatted correctly?

   affiliations:
     - name: Delft University of Technology (Faculty of Technology, Policy and Management), The Netherlands
       index: 1
     - name: Independent Researcher, Germany
       index: 2
     - name: George Mason University (Department of Computational Social Science), USA
       index: 3
     - name: University at Buffalo (Department of Geography), USA
       index: 4

2. Explicit citations: Good catch, should be addressed in projectmesa/mesa@5975ca5
3. Length: It's indeed a bit on the longer end, but we hope it's okay. It's 5 years of development by a large team of a major package in our space, and we went over the paper diligently multiple times to shorten it where feasible. We also hope the code blocks can be seem as "illustrations".
4. DOIs: You're right, for some reason Google Scholar didn't included them when generating BibTex. I've included them in projectmesa/mesa@6e42b29.

@editorialbot check references

[EwoutH]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1063/1.1571309 is OK
- 10.2307/134812 is OK
- 10.25080/Majora-7b98e3ed-009 is OK
- 10.1007/978-3-030-61255-9_30 is OK
- 10.1145/3557989.3566157 is OK
- 10.1016/j.jclepro.2020.120296 is OK
- 10.1016/j.trd.2020.102455 is OK
- 10.1016/j.enbuild.2020.109763 is OK
- 10.1016/j.enpol.2017.08.024 is OK
- 10.1016/j.eswa.2022.116604 is OK
- 10.1016/j.elerap.2022.101195 is OK
- 10.1073/pnas.2215675120 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Growing Artificial Societies: Social Science from ...
- No DOI given, and none found for title: Agent-based computational models and generative so...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[danielskatz]

@EwoutH - all of your responses seem fine.

[EwoutH]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

AgentPy: A package for agent-based modeling in Python
Submitting author: @JoelForamitti
Handling editor: @sbenthall (Active)
Reviewers: @jamesdamillington, @martibosch
Similarity score: 0.7290

Melodie: Agent-based Modeling in Python
Submitting author: @SongminYu
Handling editor: @jbytecode (Active)
Reviewers: @JoelForamitti, @rusu24edward
Similarity score: 0.6931

Agents.jl: agent-based modeling framework in Julia
Submitting author: @kavir1698
Handling editor: @jedbrown (Active)
Reviewers: @Datseris, @mozhgan-kch
Similarity score: 0.6910

pylattica: a package for prototyping lattice models in chemistry and materials science
Submitting author: @mcgalcode
Handling editor: @richardjgowers (Retired)
Reviewers: @riesben, @amkrajewski
Similarity score: 0.6818

villager: A framework for designing and executing agent-based models in R
Submitting author: @thomasthelen
Handling editor: @marcosvital (Active)
Reviewers: @chrisaberson, @brunomontezano, @thodson-usgs
Similarity score: 0.6708

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[EwoutH]

@danielskatz I should now have fully addressed all comments, thanks for your swift replies! If you need anything else from our side, please let us know.

@EwoutH if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

No one specific, but there seems quite a list of JOSS reviewers experienced with ABM: Programming language: Python, Keyword: agent-based

[danielskatz]

👋 @xuanxu - Would you be willing to edit this submission?

[danielskatz]

@editorialbot invite @xuanxu as editor

[editorialbot]

Invitation to edit this submission sent!

[EwoutH]

We have one maybe unusual request: On of our authors (@rht) would like to go under that name, his pseudonym he did all his work on Mesa under over the past years. He has an ORCID, but would like to omit his full name and country. Would that be possible in JOSS?

[danielskatz]

Yes, this is fine. List him as you choose.

[EwoutH]

Yes, this is fine. List him as you choose.

Perfect!

@xuanxu curious if you’re willing to act as editor on our submission!

[EwoutH]

Hi @danielskatz! How long does it usually take to find an editor and reviewers? I'm asking because I have a lot of time in January to work on the paper and process review feedback, but from February onward it will be a bit more tight.

Since we're a relatively large project in a relatively known field, I don't think it will be very difficult to find reviewers. Aside from these, I'm happy to help search for them!

[danielskatz]

Usually it's fairly fast, once we get an editor, though basically everything was on break the last couple of weeks...

[danielskatz]

👋 @gkthiruvathukal - Would you be able to edit this submission?

[danielskatz]

@editorialbot invite @gkthiruvathukal as editor

[editorialbot]

Invitation to edit this submission sent!

[gkthiruvathukal]

Hi @danielskatz! Happy new year! I'm happy to help.

[gkthiruvathukal]

@editorialbot assign me as editor

[editorialbot]

Assigned! @gkthiruvathukal is now the editor

[gkthiruvathukal]

Hi @jamesdamillington and @martibosch, as you have both been involved in a previous review for a Python package based on agent-based modeling, would you be willing to contribute a review for this JOSS submission?

[jamesdamillington]

@gkthiruvathukal Apologies, but I'm busy at the moment with many things, including my own journal editorial duties. Can I take the liberty of suggesting @JoelForamitti would be good for this