Installation issue fixed

Dockerfile

@@ -1,7 +1,9 @@
 # We can't use slim because we need either git/wget/curl to
 # download mesa-examples, and so installing them requires
 # updating the system anyway.
-FROM python:bookworm
+FROM python:3.12-bookworm
+
+
 LABEL maintainer="projectmesa [email protected]"
 
 # To use this Dockerfile:
@@ -29,7 +31,7 @@ COPY . /opt/mesa
 
 EXPOSE 8765/tcp
 
-RUN pip3 install -e /opt/mesa[rec]
+RUN pip3 install -e '/opt/mesa[rec]'
 
 CMD ["sh", "-c", "cd $MODEL_DIR && solara run app.py --host=0.0.0.0"]
 

HISTORY.md

@@ -699,7 +699,7 @@ We're proud to release the first Mesa 3.0 beta! This pre-release announces that
 In this beta, not so much has changed as in the alphas (we're stabilizing, that's a good sign), but there are still a few notable things:
 - Agents now have to be initialized without their `unique_id`. See [#2328](https://github.com/projectmesa/mesa/pull/2328) and the [Migration guide](https://mesa.readthedocs.io/latest/migration_guide.html#automatic-assignment-of-unique-id-to-agents).
 - PropertyLayers can now be visualized! See [#2336](https://github.com/projectmesa/mesa/pull/2336) for details and some examples, and [mesa-examples#214](https://github.com/projectmesa/mesa-examples/pull/214) as a simple example model.
-- We reduced the core dependencies of Mesa, so that's a lighter and simpler install. You can now use extras to install the dependencies, for example add `[viz]` to install all visualisation dependencies: `pip install -U --pre mesa[viz]`. See [#2265](https://github.com/projectmesa/mesa/pull/2265) for details.
+- We reduced the core dependencies of Mesa, so that's a lighter and simpler install. You can now use extras to install the dependencies, for example add `[viz]` to install all visualisation dependencies: `pip install -U --pre "mesa[viz]"`. See [#2265](https://github.com/projectmesa/mesa/pull/2265) for details.
 - The [Mesa Overview](https://mesa.readthedocs.io/latest/overview.html) as fully updated for 3.0. We highly recommend reading though it!
 - We made some more progress on the experimental Cell Space, adding movement and integrating the PropertyLayer. Among others, Agents have nu initial movement capabilities for grids. Development continues during the betas and
 

docs/conf.py

@@ -131,6 +131,10 @@
 # documentation.
 html_theme_options = {
     "navbar_start": ["navbar-logo"],
+    "navigation_depth": 4,
+    "show_nav_level": 2,
+    "collapse_navigation": True,
+    "show_toc_level": 2,
 }
 
 # Add any paths that contain custom themes here, relative to this directory.

docs/index.md

@@ -44,13 +44,12 @@ pip install -U mesa
 ```
 To also install our recommended dependencies:
 ```bash
-pip install -U mesa[rec]
+pip install -U "mesa[rec]"
 ```
 
 The `[rec]` option installs additional recommended dependencies needed for visualization, plotting, and network modeling capabilities.
 
-On a Mac, this command might cause an error stating `zsh: no matches found: mesa[all]`.
-In that case, change the command to `pip install -U "mesa[rec]"`.
+Note: On macOS with zsh, the square brackets `[rec]` are interpreted as glob patterns by the shell. Always use quotes as shown in the command above to prevent shell expansion errors.
 
 Furthermore, if you are using `nix`, Mesa comes with a flake with devShells and a runnable app:
 
@@ -95,8 +94,22 @@ Our [CITATION.cff](https://github.com/projectmesa/mesa/blob/main/CITATION.cff) c
 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
-:maxdepth: 7
+:maxdepth: 2
+:caption: Contents
+
+getting_started
+overview
+mesa
+examples
+best-practices
+mesa_extension
+migration_guide
+apis/api_main
+GSoC
+```
+   overview
+   tutorials/index
+
 
 Getting started <getting_started>
 Overview <overview>

docs/overview.md

@@ -298,21 +298,9 @@ 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
 
-```{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>
 
 
-```
+
+
+
+

docs/tutorials/0_first_model.ipynb

@@ -58,7 +58,7 @@
     "Install Mesa:\n",
     "\n",
     "```bash\n",
-    "pip install mesa[rec] \n",
+    "pip install \"mesa[rec]\"\n",
     "```\n",
     "\n",
     "Install Jupyter notebook (optional):\n",
@@ -89,7 +89,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {

docs/tutorials/10_comparing_scenarios.ipynb

@@ -41,7 +41,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {

docs/tutorials/1_adding_space.ipynb

@@ -43,7 +43,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {

docs/tutorials/2_collecting_data.ipynb

@@ -43,7 +43,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {

docs/tutorials/3_agentset.ipynb

@@ -43,7 +43,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {

docs/tutorials/9_batch_run.ipynb

@@ -41,7 +41,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {

mesa/examples/advanced/alliance_formation/Readme.md

@@ -24,7 +24,7 @@ If you would like to see an example of explicit meta-agent formation see the [wa
 This model requires Mesa's recommended install and scipy
 
 ```
-    $ pip install mesa[rec]
+    $ pip install "mesa[rec]"
 ```
 
 ## How to Run