diff --git a/Dockerfile b/Dockerfile
index a5af06e220b..8b121a83577 100644
--- a/Dockerfile
+++ b/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 maintainers@projectmesa.dev"
 
 # 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"]
 
diff --git a/HISTORY.md b/HISTORY.md
index b1e8e35083c..f31d0ee36a7 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -736,7 +736,7 @@ 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
 
diff --git a/docs/conf.py b/docs/conf.py
index 9d6ce6a64ae..f765063dff7 100644
--- a/docs/conf.py
+++ b/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.
diff --git a/docs/index.md b/docs/index.md
index 1d3ca9a6167..29753f45442 100644
--- a/docs/index.md
+++ b/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>
diff --git a/docs/overview.md b/docs/overview.md
index a4ce4cba4e5..5e0a7f4438b 100644
--- a/docs/overview.md
+++ b/docs/overview.md
@@ -317,4 +317,4 @@ Comparing Scenarios <tutorials/10_comparing_scenarios>
 Best Practices <best-practices>
 
 
-```
\ No newline at end of file
+```
diff --git a/docs/tutorials/0_first_model.ipynb b/docs/tutorials/0_first_model.ipynb
index d814be5346b..f337bf94bea 100644
--- a/docs/tutorials/0_first_model.ipynb
+++ b/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]\""
    ]
   },
   {
diff --git a/docs/tutorials/10_comparing_scenarios.ipynb b/docs/tutorials/10_comparing_scenarios.ipynb
index 00a8b7d4d05..86e6d6bb9eb 100644
--- a/docs/tutorials/10_comparing_scenarios.ipynb
+++ b/docs/tutorials/10_comparing_scenarios.ipynb
@@ -41,7 +41,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {
diff --git a/docs/tutorials/1_adding_space.ipynb b/docs/tutorials/1_adding_space.ipynb
index 92181efe0ba..f5ce078064e 100644
--- a/docs/tutorials/1_adding_space.ipynb
+++ b/docs/tutorials/1_adding_space.ipynb
@@ -43,7 +43,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {
diff --git a/docs/tutorials/2_collecting_data.ipynb b/docs/tutorials/2_collecting_data.ipynb
index f5fc42e65a8..1fb1130466e 100644
--- a/docs/tutorials/2_collecting_data.ipynb
+++ b/docs/tutorials/2_collecting_data.ipynb
@@ -43,7 +43,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {
diff --git a/docs/tutorials/3_agentset.ipynb b/docs/tutorials/3_agentset.ipynb
index fdf9e42f804..88d774aa6aa 100644
--- a/docs/tutorials/3_agentset.ipynb
+++ b/docs/tutorials/3_agentset.ipynb
@@ -43,7 +43,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {
diff --git a/docs/tutorials/9_batch_run.ipynb b/docs/tutorials/9_batch_run.ipynb
index 98ee83e09bd..d323729af92 100644
--- a/docs/tutorials/9_batch_run.ipynb
+++ b/docs/tutorials/9_batch_run.ipynb
@@ -41,7 +41,7 @@
     }
    },
    "source": [
-    "%pip install --quiet mesa[rec]"
+    "%pip install --quiet \"mesa[rec]\""
    ]
   },
   {
diff --git a/mesa/examples/advanced/alliance_formation/Readme.md b/mesa/examples/advanced/alliance_formation/Readme.md
index bb04dea94d0..94741b7050d 100644
--- a/mesa/examples/advanced/alliance_formation/Readme.md
+++ b/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