Mesa 3.1.5__tar.gz → 3.2.0__tar.gz

{mesa-3.1.5 → mesa-3.2.0}/.github/workflows/build_lint.yml

@@ -84,4 +84,4 @@ jobs:
     - name: Test examples
       run: |
         cd mesa-examples
-        pytest -rA -Werror -Wdefault::FutureWarning test_examples.py
+        pytest -rA -Werror -Wdefault::FutureWarning -Wi::DeprecationWarning test_examples.py

{mesa-3.1.5 → mesa-3.2.0}/.gitignore

@@ -69,6 +69,7 @@ target/
 
 # Jupyter and iPython notebook checkpoints
 *.ipynb_checkpoints
+*.virtual_documents
 
 # Spyder app workspace config file
 .spyderworkspace

{mesa-3.1.5 → mesa-3.2.0}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.9.4
+  rev: v0.9.9
   hooks:
     # Run the linter.
     - id: ruff

mesa-3.2.0/CITATION.cff

@@ -0,0 +1,62 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Hoeven
+  given-names: Ewout
+  name-particle: ter
+  orcid: "https://orcid.org/0009-0002-0805-3425"
+- family-names: Kwakkel
+  given-names: Jan
+  orcid: "https://orcid.org/0000-0001-9447-2954"
+- family-names: Hess
+  given-names: Vincent
+  orcid: "https://orcid.org/0000-0002-9242-8500"
+- family-names: Pike
+  given-names: Thomas
+  orcid: "https://orcid.org/0000-0003-1576-0283"
+- family-names: Wang
+  given-names: Boyu
+  orcid: "https://orcid.org/0000-0001-9879-2138"
+- family-names: rht
+  orcid: "https://orcid.org/0009-0002-6902-111X"
+- family-names: Kazil
+  given-names: Jackie
+  orcid: "https://orcid.org/0000-0002-8300-7384"
+doi: 10.5281/zenodo.15090710
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Hoeven
+    given-names: Ewout
+    name-particle: ter
+    orcid: "https://orcid.org/0009-0002-0805-3425"
+  - family-names: Kwakkel
+    given-names: Jan
+    orcid: "https://orcid.org/0000-0001-9447-2954"
+  - family-names: Hess
+    given-names: Vincent
+    orcid: "https://orcid.org/0000-0002-9242-8500"
+  - family-names: Pike
+    given-names: Thomas
+    orcid: "https://orcid.org/0000-0003-1576-0283"
+  - family-names: Wang
+    given-names: Boyu
+    orcid: "https://orcid.org/0000-0001-9879-2138"
+  - family-names: rht
+    orcid: "https://orcid.org/0009-0002-6902-111X"
+  - family-names: Kazil
+    given-names: Jackie
+    orcid: "https://orcid.org/0000-0002-8300-7384"
+  date-published: 2025-03-28
+  doi: 10.21105/joss.07668
+  issn: 2475-9066
+  issue: 107
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 7668
+  title: "Mesa 3: Agent-based modeling with Python in 2025"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.07668"
+  volume: 10
+title: "Mesa 3: Agent-based modeling with Python in 2025"

{mesa-3.1.5 → mesa-3.2.0}/CONTRIBUTING.md

@@ -53,7 +53,7 @@ Learn the tools, talk to us about what you want to change, and open a small PR.
 Awesome! You have the basics of open-source software development (if not check above), but not much modelling experience.
 
 First step is to start thinking like a modeller. To understand the fine details about our library and contribute meaningfully, get some modelling experience:
-- Go though our [Introductory Tutorial](https://mesa.readthedocs.io/latest/tutorials/intro_tutorial.html) and [Visualization Tutorial](https://mesa.readthedocs.io/latest/tutorials/visualization_tutorial.html). While going through them, dive into the source code to really see what everything does.
+- Go though our series of introductory tutorials at [Getting Started](https://mesa.readthedocs.io/latest/getting_started.html). While going through them, dive into the source code to really see what everything does.
 - Follow an ABM course (if possible). They might be a bit outdated programming language wise, but conceptual they're sound.
   - This MOOC on ABM concepts: [Agent Based Modeling](https://ocw.tudelft.nl/course-lectures/agent-based-modeling/)
   - This MOOC on practical ABM modelling: [Agent-Based Models with Python: An Introduction to Mesa](https://www.complexityexplorer.org/courses/172-agent-based-models-with-python-an-introduction-to-mesa)

{mesa-3.1.5 → mesa-3.2.0}/HISTORY.md

@@ -1,6 +1,102 @@
 ---
 title: Release History
 ---
+# 3.2.0 (2025-05-04)
+## Highlights
+Mesa 3.2.0 is a feature-packed release, which stabilizes our discrete space, improves many of our visualisation capabilities, improves our tutorial organization, adds the experimental meta-agents, and includes other quality of life enhancements.
+
+We also celebrate the publication of our peer-reviewed [Mesa 3 paper](https://doi.org/10.21105/joss.07668) in JOSS. See the updated [Citing Mesa](https://github.com/projectmesa/mesa?tab=readme-ov-file#citing-mesa) section on how to cite us.
+
+### Stabilization of Discrete Space
+The experimental Cell Space system has been stabilized and is now available as `mesa.discrete_space` ([#2610](https://github.com/projectmesa/mesa/pull/2610)). This powerful spatial modeling framework enables cell-centric simulations with integrated PropertyLayers and improved agent movement capabilities. Key improvements include:
+
+- Support for dynamic modifications to discrete spaces during simulation ([#2755](https://github.com/projectmesa/mesa/pull/2755))
+- Methods to add/remove cells and connections in real-time
+- Full integration with PropertyLayers ([#2440](https://github.com/projectmesa/mesa/pull/2440)) for representing environmental variables
+- Compatible with all examples and existing visualizations
+
+The PropertyLayer itself has also been stabilized, allowing for efficient management of spatial environmental properties like terrain, resources, or any grid-based variables. Core examples including [Schelling](https://github.com/projectmesa/mesa/tree/main/mesa/examples/basic/schelling), [Game of Life](https://github.com/projectmesa/mesa/tree/main/mesa/examples/basic/conways_game_of_life), [Boltzmann Wealth](https://github.com/projectmesa/mesa/tree/main/mesa/examples/basic/boltzmann_wealth_model), and [Virus on Network](https://github.com/projectmesa/mesa/tree/main/mesa/examples/basic/virus_on_network) have been updated to use the new discrete space system.
+
+### Enhanced Visualization Experience
+The SolaraViz visualization system has received substantial upgrades:
+
+- **Command Console** ([#2697](https://github.com/projectmesa/mesa/pull/2697)): An interactive Python console embedded directly in the visualization, allowing real-time model inspection and manipulation
+- **Asynchronous Updates** ([#2656](https://github.com/projectmesa/mesa/pull/2656)): Visualization now runs in a separate thread, dramatically improving performance for complex models
+- **Dark Mode** ([#2689](https://github.com/projectmesa/mesa/pull/2689)): Support for Solara Dark theme, automatically matching system preferences
+- **Improved Error Handling** ([#2747](https://github.com/projectmesa/mesa/pull/2747), [#2753](https://github.com/projectmesa/mesa/pull/2753)): Better visualization of errors with options to view detailed traceback information
+- **Enhanced UI**: Arrow key navigation ([#2725](https://github.com/projectmesa/mesa/pull/2725)), movable input field with auto-scroll ([#2710](https://github.com/projectmesa/mesa/pull/2710)), and other quality-of-life improvements
+- **PropertyLayer visualisation in Altair** ([#2643](https://github.com/projectmesa/mesa/pull/2643)): Support for visualising PropertyLayers using the Altair frontend in Solara.
+
+### Restructured and updated tutorial
+Our [introduction tutorial](https://mesa.readthedocs.io/latest/overview.html) has been completely restructured ([#2731](https://github.com/projectmesa/mesa/pull/2731)). Instead of one huge notebook, the tutorial is now divided into smaller, focused modules that build progressively:
+
+- **Creating Your First Model**: Essential basics to get started
+- **Adding Space**: Learn how to use the new discrete space system
+- **Collecting Data**: Effectively gather model statistics
+- **AgentSet**: Master agent management techniques
+- **Visualization**: Series of modules covering basic to advanced visualization
+
+
+### Introducing Meta-Agents
+Complex systems often have multiple levels of components. An organization is not one entity, but is made of departments, sub-departments, and people. A person is not a single entity, but it is made of micro biomes, organs and cells. A city is not a single entity, but it is made of districts, neighborhoods, buildings, and people. A forest comprises an ecosystem of trees, plants, animals, and microorganisms.
+
+This reality is the motivation for meta-agents. It allows users to represent these multiple levels, where each level can have meta-agents with constituting agents.
+- **Meta agents** [#2748](https://github.com/projectmesa/mesa/pull/2748)
+
+To demonstrate meta-agents capability there are two examples:
+
+1.  Dynamic meta-agent creation - [Alliance formation](https://mesa.readthedocs.io/latest/examples/advanced/alliance_formation.html), which shows emergent meta-agent formation through a game theoretic based alliance formation.
+2. Deliberate meta-agent creation - [Warehouse model](https://github.com/projectmesa/mesa-examples/tree/main/examples/warehouse), which provides a pseudo warehouse model to demonstrate meta-agent functionality.
+
+Let us know what you think on our [Matrix Channel](https://matrix.to/#/#project-mesa:matrix.org)
+
+### Other improvements
+- AgentSet's `agg` method now supports multiple aggregation functions in a single call ([#2743](https://github.com/projectmesa/mesa/pull/2743))
+- Many documentation improvements have been made based on feedback by our JOSS reviewers
+
+## What's Changed
+### 🎉 New features added
+* Stabilize experimental Cell Space as `mesa.discrete_space` by @quaquel in https://github.com/projectmesa/mesa/pull/2610
+* Feat: Added Command Console by @Sahil-Chhoker in https://github.com/projectmesa/mesa/pull/2697
+* Stabilize PropertyLayer by @EwoutH in https://github.com/projectmesa/mesa/pull/2440
+### 🛠 Enhancements made
+* Visualisation: Add dark mode by @sanika-n in https://github.com/projectmesa/mesa/pull/2689
+* Creating threads to update visualization asynchronously  by @HMNS19 in https://github.com/projectmesa/mesa/pull/2656
+* Movable Input Field with auto-scroll by @Sahil-Chhoker in https://github.com/projectmesa/mesa/pull/2710
+* Feat: Added arrow key navigation by @Sahil-Chhoker in https://github.com/projectmesa/mesa/pull/2725
+* added property_layer with altair by @sanika-n in https://github.com/projectmesa/mesa/pull/2643
+* Debug option for errors in visualisation by @colinfrisch in https://github.com/projectmesa/mesa/pull/2747
+* Debug option for errors in visualisation front end by @colinfrisch in https://github.com/projectmesa/mesa/pull/2753
+* Add support for dynamic discrete spaces by @quaquel in https://github.com/projectmesa/mesa/pull/2755
+* Support multiple functions in AgentSet `agg` method by @EwoutH in https://github.com/projectmesa/mesa/pull/2743
+### 🔍 Examples updated
+* Move boltzmann to cell spaces by @quaquel in https://github.com/projectmesa/mesa/pull/2680
+* Move Game of life to cell space by @quaquel in https://github.com/projectmesa/mesa/pull/2681
+* Move Schelling to discrete space by @quaquel in https://github.com/projectmesa/mesa/pull/2684
+* Move virus_on_a_network to discrete_space by @quaquel in https://github.com/projectmesa/mesa/pull/2688
+* Update boid_flockers example include flight direction by @sanika-n in https://github.com/projectmesa/mesa/pull/2696
+### 📜 Documentation improvements
+* docs: Split off the overview page, extend with spaces/activation by @EwoutH in https://github.com/projectmesa/mesa/pull/2673
+* docs: Add Roles section to CONTRIBUTING.md by @EwoutH in https://github.com/projectmesa/mesa/pull/2694
+* [JOSS] Docs: Clarify difference between core and user examples by @EwoutH in https://github.com/projectmesa/mesa/pull/2706
+* [JOSS] docs: Improve batch_run documentation for parallel processing by @EwoutH in https://github.com/projectmesa/mesa/pull/2707
+* JOSS Tutorial Fixes by @tpike3 in https://github.com/projectmesa/mesa/pull/2708
+* Clean-up old images, compress wolf-sheep image, remove version switch artifact by @EwoutH in https://github.com/projectmesa/mesa/pull/2717
+* docs: Update citation to JOSS article by @EwoutH in https://github.com/projectmesa/mesa/pull/2740
+* update intro tutorial discrete space by @tpike3 in https://github.com/projectmesa/mesa/pull/2731
+* docs: fix broken links to Readthedocs in example descriptions by @reyan-singh in https://github.com/projectmesa/mesa/pull/2757
+### 🧪 Experimental features
+* Meta agents by @tpike3 in https://github.com/projectmesa/mesa/pull/2748
+### 🐛 Bugs fixed
+* Minor (bug) fixes to discrete_space by @quaquel in https://github.com/projectmesa/mesa/pull/2687
+* Fixed Marker in mpl by @sanika-n in https://github.com/projectmesa/mesa/pull/2670
+
+## New Contributors
+* @colinfrisch made their first contribution in https://github.com/projectmesa/mesa/pull/2747
+* @reyan-singh made their first contribution in https://github.com/projectmesa/mesa/pull/2757
+
+**Full Changelog**: https://github.com/projectmesa/mesa/compare/v3.1.4...v3.2.0
+
 # 3.1.5 (2025-03-26)
 ## Highlights
 Mesa 3.1.5 is a maintenance release focused on improving documentation and cleaning up our resources. This update includes no breaking changes and is compatible with previous 3.1.x releases.
@@ -384,7 +480,7 @@ Install Mesa 3.0:
 pip install --upgrade mesa
 ```
 
-If building a new model, we recommend checking out the updated [Mesa Overview](https://mesa.readthedocs.io/latest/overview.html) and [Introductory Tutorial](https://mesa.readthedocs.io/latest/tutorials/intro_tutorial.html).
+If building a new model, we recommend checking out the updated [Mesa Overview](https://mesa.readthedocs.io/latest/overview.html) and [Introductory Tutorial](https://mesa.readthedocs.io/latest/tutorials/0_first_model.html).
 
 For updating existing models, we recommend upgrading in steps:
 1. Update to latest Mesa 2.x

{mesa-3.1.5 → mesa-3.2.0}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: Mesa
-Version: 3.1.5
+Version: 3.2.0
 Summary: Agent-based modeling (ABM) in Python
 Project-URL: homepage, https://github.com/projectmesa/mesa
 Project-URL: repository, https://github.com/projectmesa/mesa
-Author-email: Project Mesa Team <projectmesa@googlegroups.com>
+Author-email: Project Mesa Team <maintainers@projectmesa.dev>
 License: Apache 2.0
 License-File: LICENSE
 License-File: NOTICE
@@ -87,12 +87,13 @@ Description-Content-Type: text/markdown
 
 # Mesa: Agent-based modeling in Python
 
-| | |
-| --- | --- |
-| CI/CD | [![GitHub Actions build status](https://github.com/projectmesa/mesa/workflows/build/badge.svg)](https://github.com/projectmesa/mesa/actions) [![Coverage status](https://codecov.io/gh/projectmesa/mesa/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa) |
+|         | |
+|---------| --- |
+| CI/CD   | [![GitHub Actions build status](https://github.com/projectmesa/mesa/workflows/build/badge.svg)](https://github.com/projectmesa/mesa/actions) [![Coverage status](https://codecov.io/gh/projectmesa/mesa/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa) |
 | Package | [![PyPI - Version](https://img.shields.io/pypi/v/mesa.svg?logo=pypi&label=PyPI&logoColor=gold)](https://pypi.org/project/Mesa/) [![PyPI - Downloads](https://img.shields.io/pypi/dm/mesa.svg?color=blue&label=Downloads&logo=pypi&logoColor=gold)](https://pypi.org/project/Mesa/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mesa.svg?logo=python&label=Python&logoColor=gold)](https://pypi.org/project/Mesa/) |
-| Meta | [![linting - Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch) [![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) |
-| Chat | [![chat](https://img.shields.io/matrix/project-mesa:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#project-mesa:matrix.org) |
+| Meta    | [![linting - Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch) [![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) |
+| Chat    | [![chat](https://img.shields.io/matrix/project-mesa:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#project-mesa:matrix.org) |
+| Cite    | [![DOI](https://joss.theoj.org/papers/10.21105/joss.07668/status.svg)](https://doi.org/10.21105/joss.07668) |
 
 Mesa allows users to quickly create agent-based models using built-in
 core components (such as spatial grids and agent schedulers) or
@@ -220,4 +221,7 @@ Don't forget to checkout the [Contributors guide](https://github.com/projectmesa
 
 ## Citing Mesa
 
-To cite Mesa in your publication, you can use the [CITATION.bib](https://github.com/projectmesa/mesa/blob/main/CITATION.bib).
+To cite Mesa in your publication, you can refer to our peer-reviewed article in the Journal of Open Source Software (JOSS):
+- ter Hoeven, E., Kwakkel, J., Hess, V., Pike, T., Wang, B., rht, & Kazil, J. (2025). Mesa 3: Agent-based modeling with Python in 2025. Journal of Open Source Software, 10(107), 7668. https://doi.org/10.21105/joss.07668
+
+Our [CITATION.cff](https://github.com/projectmesa/mesa/blob/main/CITATION.cff) can be used to generate APA, BibTeX and other citation formats.

{mesa-3.1.5 → mesa-3.2.0}/README.md

@@ -1,11 +1,12 @@
 # Mesa: Agent-based modeling in Python
 
-| | |
-| --- | --- |
-| CI/CD | [![GitHub Actions build status](https://github.com/projectmesa/mesa/workflows/build/badge.svg)](https://github.com/projectmesa/mesa/actions) [![Coverage status](https://codecov.io/gh/projectmesa/mesa/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa) |
+|         | |
+|---------| --- |
+| CI/CD   | [![GitHub Actions build status](https://github.com/projectmesa/mesa/workflows/build/badge.svg)](https://github.com/projectmesa/mesa/actions) [![Coverage status](https://codecov.io/gh/projectmesa/mesa/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa) |
 | Package | [![PyPI - Version](https://img.shields.io/pypi/v/mesa.svg?logo=pypi&label=PyPI&logoColor=gold)](https://pypi.org/project/Mesa/) [![PyPI - Downloads](https://img.shields.io/pypi/dm/mesa.svg?color=blue&label=Downloads&logo=pypi&logoColor=gold)](https://pypi.org/project/Mesa/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mesa.svg?logo=python&label=Python&logoColor=gold)](https://pypi.org/project/Mesa/) |
-| Meta | [![linting - Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch) [![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) |
-| Chat | [![chat](https://img.shields.io/matrix/project-mesa:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#project-mesa:matrix.org) |
+| Meta    | [![linting - Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch) [![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) |
+| Chat    | [![chat](https://img.shields.io/matrix/project-mesa:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#project-mesa:matrix.org) |
+| Cite    | [![DOI](https://joss.theoj.org/papers/10.21105/joss.07668/status.svg)](https://doi.org/10.21105/joss.07668) |
 
 Mesa allows users to quickly create agent-based models using built-in
 core components (such as spatial grids and agent schedulers) or
@@ -133,4 +134,7 @@ Don't forget to checkout the [Contributors guide](https://github.com/projectmesa
 
 ## Citing Mesa
 
-To cite Mesa in your publication, you can use the [CITATION.bib](https://github.com/projectmesa/mesa/blob/main/CITATION.bib).
+To cite Mesa in your publication, you can refer to our peer-reviewed article in the Journal of Open Source Software (JOSS):
+- ter Hoeven, E., Kwakkel, J., Hess, V., Pike, T., Wang, B., rht, & Kazil, J. (2025). Mesa 3: Agent-based modeling with Python in 2025. Journal of Open Source Software, 10(107), 7668. https://doi.org/10.21105/joss.07668
+
+Our [CITATION.cff](https://github.com/projectmesa/mesa/blob/main/CITATION.cff) can be used to generate APA, BibTeX and other citation formats.

{mesa-3.1.5 → mesa-3.2.0}/docs/apis/api_main.md

@@ -7,6 +7,7 @@ model
 agent
 time
 space
+discrete_space
 datacollection
 batchrunner
 visualization

mesa-3.2.0/docs/apis/discrete_space.md

@@ -0,0 +1,41 @@
+## Discrete Space
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.__init__
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.cell
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.cell_agent
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.cell_collection
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.discrete_space
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.grid
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.network
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: mesa.discrete_space.voronoi
+   :members:
+```

mesa-3.2.0/docs/apis/experimental.md

@@ -0,0 +1,39 @@
+# Experimental
+This namespace contains experimental features. These are under development, and their API is not necessarily stable.
+
+
+## Devs
+
+```{eval-rst}
+.. automodule:: experimental.devs.eventlist
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: experimental.devs.simulator
+   :members:
+```
+
+## Continuous Space
+
+```{eval-rst}
+.. automodule:: experimental.continuous_space.continuous_space
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: experimental.continuous_space.continuous_space_agents
+   :members:
+```
+
+## Continuous Space
+
+```{eval-rst}
+.. automodule:: experimental.continuous_space.continuous_space
+   :members:
+```
+
+```{eval-rst}
+.. automodule:: experimental.continuous_space.continuous_space_agents
+   :members:
+```

{mesa-3.1.5 → mesa-3.2.0}/docs/apis/visualization.md

@@ -52,4 +52,13 @@ For a detailed tutorial, please refer to our [Visualization Tutorial](../tutoria
    :members:
    :undoc-members:
    :show-inheritance:
+```
+
+## Command Console
+
+```{eval-rst}
+.. automodule:: mesa.visualization.command_console
+   :members:
+   :undoc-members:
+   :show-inheritance:
 ```

{mesa-3.1.5 → mesa-3.2.0}/docs/conf.py

@@ -1,4 +1,3 @@
-# noqa: D100
 #!/usr/bin/env python3
 #
 # Mesa documentation build configuration file, created by
@@ -16,8 +15,8 @@
 import os
 import os.path as osp
 import pathlib
-import sys
 import string
+import sys
 from datetime import date
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -47,7 +46,7 @@ extensions = [
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",  # for google style docstrings
     "myst_nb",  # For Markdown and Jupyter notebooks
-    "sphinx_copybutton" # For copying the code in the documentation
+    "sphinx_copybutton",  # For copying the code in the documentation
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -131,11 +130,7 @@ html_theme = "pydata_sphinx_theme"
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-    "navbar_start": ["navbar-logo", "version-switcher"],  # Show switcher in navbar
-    "switcher": {
-        "json_url": "https://mesa.readthedocs.io/latest/_static/switcher.json",  # URL of your switcher.json file
-        "version_match": version  # Automatically matches the current version
-    }
+    "navbar_start": ["navbar-logo"],
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -177,7 +172,7 @@ html_static_path = ["_static"]
 
 # Custom sidebar templates, maps document names to template names.
 html_sidebars = {
-    'migration_guide': [],  # No sidebar migration
+    "migration_guide": [],  # No sidebar migration
 }
 
 # Additional templates that should be rendered to pages, maps page names to
@@ -297,8 +292,9 @@ texinfo_documents = [
 intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}
 
 
-
-def write_example_md_file(agent_filename, model_filename, readme_filename, app_filename, md_filepath, template):
+def write_example_md_file(
+    agent_filename, model_filename, readme_filename, app_filename, md_filepath, template
+):
     with open(agent_filename) as content_file:
         agent_file = content_file.read()
     with open(model_filename) as content_file:
@@ -310,17 +306,30 @@ def write_example_md_file(agent_filename, model_filename, readme_filename, app_f
 
     with open(md_filepath, "w") as fh:
         content = template.substitute(
-            dict(agent_file=agent_file, model_file=model_file,
-                 readme_file=readme_file, app_file=app_file)
+            dict(
+                agent_file=agent_file,
+                model_file=model_file,
+                readme_file=readme_file,
+                app_file=app_file,
+            )
         )
         fh.write(content)
 
+
 def setup_examples_pages():
     # create md files for all examples
     # check what examples exist
     examples_folder = osp.abspath(osp.join(HERE, "..", "mesa", "examples"))
-    basic_examples = [("basic", f.path) for f in os.scandir(osp.join(examples_folder, "basic")) if f.is_dir() and not f.name.startswith("__") ]
-    advanced_examples = [("advanced", f.path) for f in os.scandir(osp.join(examples_folder, "advanced")) if f.is_dir() and not f.name.startswith("__")]
+    basic_examples = [
+        ("basic", f.path)
+        for f in os.scandir(osp.join(examples_folder, "basic"))
+        if f.is_dir() and not f.name.startswith("__")
+    ]
+    advanced_examples = [
+        ("advanced", f.path)
+        for f in os.scandir(osp.join(examples_folder, "advanced"))
+        if f.is_dir() and not f.name.startswith("__")
+    ]
     examples = basic_examples + advanced_examples
 
     with open(os.path.join(HERE, "example_template.txt")) as fh:
@@ -329,7 +338,9 @@ def setup_examples_pages():
     root_folder = pathlib.Path(os.path.join(HERE, "examples"))
     root_folder.mkdir(parents=True, exist_ok=True)
     pathlib.Path(os.path.join(root_folder, "basic")).mkdir(parents=True, exist_ok=True)
-    pathlib.Path(os.path.join(root_folder, "advanced")).mkdir(parents=True, exist_ok=True)
+    pathlib.Path(os.path.join(root_folder, "advanced")).mkdir(
+        parents=True, exist_ok=True
+    )
 
     examples_md = []
     for kind, example in examples:
@@ -344,7 +355,14 @@ def setup_examples_pages():
         examples_md.append((base_name, f"{kind}/{base_name}"))
 
         md_filepath = os.path.join(HERE, "examples", kind, md_filename)
-        write_example_md_file(agent_filename, model_filename, readme_filename, app_filename, md_filepath, template)
+        write_example_md_file(
+            agent_filename,
+            model_filename,
+            readme_filename,
+            app_filename,
+            md_filepath,
+            template,
+        )
 
     # create overview of examples.md
     with open(os.path.join(HERE, "examples_overview_template.txt")) as fh:
@@ -357,14 +375,21 @@ def setup_examples_pages():
         content = template.substitute(
             dict(
                 readme=readme_md,
-                example_paths="\n".join([f"{' '.join(a.split('_'))} </examples/{b}>" for a, b in examples_md]),
+                example_paths="\n".join(
+                    [
+                        f"{' '.join(a.split('_'))} </examples/{b}>"
+                        for a, b in examples_md
+                    ]
+                ),
             )
         )
         fh.write(content)
 
+
 def setup(app):
     setup_examples_pages()
 
+
 #
 if __name__ == "__main__":
-    setup_examples_pages()
+    setup_examples_pages()

{mesa-3.1.5 → mesa-3.2.0}/docs/getting_started.md

@@ -7,8 +7,15 @@ Mesa is a modular framework for building, analyzing and visualizing agent-based
 If you want to get a quick start on how to build agent based models with MESA, check the overview and tutorials:
 
 - [Overview of the MESA library](overview): Learn about the core concepts and components of Mesa.
-- [Introductory Tutorial](tutorials/intro_tutorial): Learn how to create your first Mesa model.
-- [Visualization Tutorial](tutorials/visualization_tutorial): Learn how to create interactive visualizations for your models.
+- [Creating Your First Model](tutorials/0_first_model): Learn how to create your first Mesa model.
+- [Adding Space](tutorials/1_adding_space): Learn how to add space to your Mesa model and understand Mesa's space architecture.
+- [Collecting Data](tutorials/2_collecting_data): Learn how to collect model level and agent level data with Mesa' DataCollector.
+- [AgentSet](tutorials/3_agentset): Learn how to more effectively manage agents with  Mesa's AgentSet.
+- [Basic Visualization](tutorials/4_visualization_basic): Learn how to build an interactive dashboard with Mesa's visualization module.
+- [Dynamic Agent Visualization](tutorials/5_visualization_dynamic_agents): Learn how to dynamically represent your agents in your interactive dashboard.
+- [Custom Visualization Components](tutorials/6_visualization_custom): Learn how to add custom visual components to your interactive dashboard.
+- [Parameter Sweeps](tutorials/7_batch_run): Learn how to conduct parameter sweeps on multiple processors with Mesa's BatchRunner.
+- [Comparing Scenarios](tutorials/8_comparing_scenarios): Think through how to analyze your parameter sweep results to find insight in your Mesa simulations.
 
 ## Examples
 Mesa ships with a collection of example models. These are classic ABMs, so if you are familiar with ABMs and want to get a quick sense of how MESA works, these examples are great place to start. You can find them [here](examples).
@@ -46,8 +53,16 @@ Enjoy modelling with Mesa, and feel free to reach out!
 :hidden: true
 :maxdepth: 7
 
-tutorials/intro_tutorial
-tutorials/visualization_tutorial
+Overview <overview>
+Creating Your First Model <tutorials/0_first_model>
+Adding Space <tutorials/1_adding_space>
+Collecting Data <tutorials/2_collecting_data>
+AgentSet <tutorials/3_agentset>
+Basic Visualization <tutorials/4_visualization_basic>
+Dynamic Agent Visualization <tutorials/5_visualization_dynamic_agents>
+Custom Visualization Components <tutorials/6_visualization_custom>
+Parameter Sweeps <tutorials/7_batch_run>
+Comparing Scenarios <tutorials/8_comparing_scenarios>
 Best Practices <best-practices>
 
 

{mesa-3.1.5 → mesa-3.2.0}/docs/index.md

@@ -1,5 +1,9 @@
 # Mesa: Agent-based modeling in Python
 
+```{image} https://joss.theoj.org/papers/10.21105/joss.07668/status.svg
+:target: https://doi.org/10.21105/joss.07668
+```
+
 ```{image} https://github.com/projectmesa/mesa/workflows/build/badge.svg
 :target: https://github.com/projectmesa/mesa/actions
 ```
@@ -18,7 +22,7 @@
 
 [Mesa] is an Apache2 licensed agent-based modeling (or ABM) framework in Python.
 
-Mesa allows users to quickly create agent-based models using built-in core components (such as spatial grids and agent schedulers) or customized implementations; visualize them using a browser-based interface; and analyze their results using Python's data analysis tools. Its goal is to be the Python-based counterpart to NetLogo, Repast, or MASON.
+Mesa allows users to quickly create agent-based models using built-in core components (such as spatial grids and agent schedulers) or customized implementations; visualize them using a browser-based interface; and analyze their results using Python's data analysis tools. Mesa's goal is to make simulations accessible to everyone, so humanity can more effectively understand and solve complex problems.
 
 ![A screenshot of the Wolf Sheep model in Mesa|100%](images/wolf_sheep.png)
 *A visualisation of the Wolf Sheep model build with Mesa.*
@@ -67,7 +71,14 @@ Mesa is an open source project and welcomes contributions:
 - [Issue Tracker] - Report bugs or suggest features
 - [Contributors Guide] - Learn how to contribute
 
-The original Mesa conference paper is [available here](http://conference.scipy.org.s3-website-us-east-1.amazonaws.com/proceedings/scipy2015/jacqueline_kazil.html).
+### Citing Mesa
+
+To cite Mesa in your publication, you can refer to our peer-reviewed article in the Journal of Open Source Software (JOSS):
+- ter Hoeven, E., Kwakkel, J., Hess, V., Pike, T., Wang, B., rht, & Kazil, J. (2025). Mesa 3: Agent-based modeling with Python in 2025. Journal of Open Source Software, 10(107), 7668. https://doi.org/10.21105/joss.07668
+
+Our [CITATION.cff](https://github.com/projectmesa/mesa/blob/main/CITATION.cff) can be used to generate APA, BibTeX and other citation formats.
+
+The original Mesa conference paper from 2015 is [available here](http://conference.scipy.org.s3-website-us-east-1.amazonaws.com/proceedings/scipy2015/jacqueline_kazil.html).
 
 ```{toctree}
 :hidden: true

{mesa-3.1.5 → mesa-3.2.0}/docs/overview.md

@@ -299,4 +299,21 @@ This will create an interactive visualization of your model, including:
 - A plot of a model metric over time
 - A slider to adjust the number of agents
 
-You can also create custom visualization components using Matplotlib. For more advanced usage and customization options, please refer to the [visualization tutorial](tutorials/visualization_tutorial).
+```{toctree}
+:hidden: true
+:maxdepth: 7
+
+Overview <overview>
+Creating Your First Model <tutorials/0_first_model>
+Adding Space <tutorials/1_adding_space>
+Collecting Data <tutorials/2_collecting_data>
+AgentSet <tutorials/3_agentset>
+Basic Visualization <tutorials/4_visualization_basic>
+Dynamic Agent Visualization <tutorials/5_visualization_dynamic_agents>
+Custom Visualization Components <tutorials/6_visualization_custom>
+Parameter Sweeps <tutorials/7_batch_run>
+Comparing Scenarios <tutorials/8_comparing_scenarios>
+Best Practices <best-practices>
+
+
+```