From e7d1feef6da363c4a49d504fae116903af1bc1d9 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 23 Oct 2024 15:34:23 +0200
Subject: [PATCH 01/74] start

---
 mesa/visualization/components/matplotlib.py |  2 ++
 mesa/visualization/components/util.py       | 16 ++++++++++++++++
 2 files changed, 18 insertions(+)
 create mode 100644 mesa/visualization/components/util.py

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index bea633d6c8b..be9e7640c22 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -37,6 +37,8 @@ def MakeSpaceMatplotlib(model):
     return MakeSpaceMatplotlib
 
 
+
+
 @solara.component
 def SpaceMatplotlib(
     model,
diff --git a/mesa/visualization/components/util.py b/mesa/visualization/components/util.py
new file mode 100644
index 00000000000..f3af21e1a27
--- /dev/null
+++ b/mesa/visualization/components/util.py
@@ -0,0 +1,16 @@
+from mesa.space import _Grid, ContinuousSpace
+from mesa.experimental.cell_space import DiscreteSpace
+
+
+def get_agents_olstyle_grid(space: _Grid):
+    for entry in space:
+        if entry:
+            yield entry
+
+
+def get_agents_newstyle_grid(space: DiscreteSpace):
+    for agent in space.all_cells.agents:
+        yield agent
+
+def get_agent_continuous(space: ContinuousSpace):
+    pass

From bbb0122a382df6f955491b070c0745284a970806 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 23 Oct 2024 17:28:09 +0200
Subject: [PATCH 02/74] ongoin

---
 mesa/space.py                         | 170 ++++++++++++++------------
 mesa/visualization/components/util.py | 115 ++++++++++++++++-
 2 files changed, 203 insertions(+), 82 deletions(-)

diff --git a/mesa/space.py b/mesa/space.py
index fc089b0f258..8dbf3b3d83e 100644
--- a/mesa/space.py
+++ b/mesa/space.py
@@ -128,7 +128,7 @@ def __init__(self, width: int, height: int, torus: bool) -> None:
         # Cutoff used inside self.move_to_empty. The parameters are fitted on Python
         # 3.11 and it was verified that they are roughly the same for 3.10. Refer to
         # the code in PR#1565 to check for their stability when a new release gets out.
-        self.cutoff_empties = 7.953 * self.num_cells**0.384
+        self.cutoff_empties = 7.953 * self.num_cells ** 0.384
 
     @staticmethod
     def default_val() -> None:
@@ -151,12 +151,14 @@ def build_empties(self) -> None:
         self._empties_built = True
 
     @overload
-    def __getitem__(self, index: int | Sequence[Coordinate]) -> list[GridContent]: ...
+    def __getitem__(self, index: int | Sequence[Coordinate]) -> list[GridContent]:
+        ...
 
     @overload
     def __getitem__(
-        self, index: tuple[int | slice, int | slice]
-    ) -> GridContent | list[GridContent]: ...
+            self, index: tuple[int | slice, int | slice]
+    ) -> GridContent | list[GridContent]:
+        ...
 
     def __getitem__(self, index):
         """Access contents from the grid."""
@@ -202,11 +204,11 @@ def coord_iter(self) -> Iterator[tuple[GridContent, Coordinate]]:
                 yield self._grid[row][col], (row, col)  # agent, position
 
     def iter_neighborhood(
-        self,
-        pos: Coordinate,
-        moore: bool,
-        include_center: bool = False,
-        radius: int = 1,
+            self,
+            pos: Coordinate,
+            moore: bool,
+            include_center: bool = False,
+            radius: int = 1,
     ) -> Iterator[Coordinate]:
         """Return an iterator over cell coordinates that are in the neighborhood of a certain point.
 
@@ -229,11 +231,11 @@ def iter_neighborhood(
         yield from self.get_neighborhood(pos, moore, include_center, radius)
 
     def get_neighborhood(
-        self,
-        pos: Coordinate,
-        moore: bool,
-        include_center: bool = False,
-        radius: int = 1,
+            self,
+            pos: Coordinate,
+            moore: bool,
+            include_center: bool = False,
+            radius: int = 1,
     ) -> Sequence[Coordinate]:
         """Return a list of cells that are in the neighborhood of a certain point.
 
@@ -268,10 +270,10 @@ def get_neighborhood(
 
         # First we check if the neighborhood is inside the grid
         if (
-            x >= radius
-            and self.width - x > radius
-            and y >= radius
-            and self.height - y > radius
+                x >= radius
+                and self.width - x > radius
+                and y >= radius
+                and self.height - y > radius
         ):
             # If the radius is smaller than the distance from the borders, we
             # can skip boundary checks.
@@ -312,11 +314,11 @@ def get_neighborhood(
         return tuple(neighborhood.keys())
 
     def iter_neighbors(
-        self,
-        pos: Coordinate,
-        moore: bool,
-        include_center: bool = False,
-        radius: int = 1,
+            self,
+            pos: Coordinate,
+            moore: bool,
+            include_center: bool = False,
+            radius: int = 1,
     ) -> Iterator[Agent]:
         """Return an iterator over neighbors to a certain point.
 
@@ -342,11 +344,11 @@ def iter_neighbors(
                 yield cell
 
     def get_neighbors(
-        self,
-        pos: Coordinate,
-        moore: bool,
-        include_center: bool = False,
-        radius: int = 1,
+            self,
+            pos: Coordinate,
+            moore: bool,
+            include_center: bool = False,
+            radius: int = 1,
     ) -> list[Agent]:
         """Return a list of neighbors to a certain point.
 
@@ -384,7 +386,7 @@ def out_of_bounds(self, pos: Coordinate) -> bool:
 
     @accept_tuple_argument
     def iter_cell_list_contents(
-        self, cell_list: Iterable[Coordinate]
+            self, cell_list: Iterable[Coordinate]
     ) -> Iterator[Agent]:
         """Returns an iterator of the agents contained in the cells identified in `cell_list`; cells with empty content are excluded.
 
@@ -412,9 +414,11 @@ def get_cell_list_contents(self, cell_list: Iterable[Coordinate]) -> list[Agent]
         """
         return list(self.iter_cell_list_contents(cell_list))
 
-    def place_agent(self, agent: Agent, pos: Coordinate) -> None: ...
+    def place_agent(self, agent: Agent, pos: Coordinate) -> None:
+        ...
 
-    def remove_agent(self, agent: Agent) -> None: ...
+    def remove_agent(self, agent: Agent) -> None:
+        ...
 
     def move_agent(self, agent: Agent, pos: Coordinate) -> None:
         """Move an agent from its current position to a new position.
@@ -429,11 +433,11 @@ def move_agent(self, agent: Agent, pos: Coordinate) -> None:
         self.place_agent(agent, pos)
 
     def move_agent_to_one_of(
-        self,
-        agent: Agent,
-        pos: list[Coordinate],
-        selection: str = "random",
-        handle_empty: str | None = None,
+            self,
+            agent: Agent,
+            pos: list[Coordinate],
+            selection: str = "random",
+            handle_empty: str | None = None,
     ) -> None:
         """Move an agent to one of the given positions.
 
@@ -493,7 +497,7 @@ def _distance_squared(self, pos1: Coordinate, pos2: Coordinate) -> float:
         if self.torus:
             dx = min(dx, self.width - dx)
             dy = min(dy, self.height - dy)
-        return dx**2 + dy**2
+        return dx ** 2 + dy ** 2
 
     def swap_pos(self, agent_a: Agent, agent_b: Agent) -> None:
         """Swap agents positions."""
@@ -552,8 +556,8 @@ def exists_empty_cells(self) -> bool:
 def is_single_argument_function(function):
     """Check if a function is a single argument function."""
     return (
-        inspect.isfunction(function)
-        and len(inspect.signature(function).parameters) == 1
+            inspect.isfunction(function)
+            and len(inspect.signature(function).parameters) == 1
     )
 
 
@@ -579,7 +583,7 @@ class PropertyLayer:
     propertylayer_experimental_warning_given = False
 
     def __init__(
-        self, name: str, width: int, height: int, default_value, dtype=np.float64
+            self, name: str, width: int, height: int, default_value, dtype=np.float64
     ):
         """Initializes a new PropertyLayer instance.
 
@@ -607,7 +611,7 @@ def __init__(
 
         # Check that width and height are positive integers
         if (not isinstance(width, int) or width < 1) or (
-            not isinstance(height, int) or height < 1
+                not isinstance(height, int) or height < 1
         ):
             raise ValueError(
                 f"Width and height must be positive integers, got {width} and {height}."
@@ -655,8 +659,8 @@ def set_cells(self, value, condition=None):
                 condition_result = vectorized_condition(self.data)
 
             if (
-                not isinstance(condition_result, np.ndarray)
-                or condition_result.shape != self.data.shape
+                    not isinstance(condition_result, np.ndarray)
+                    or condition_result.shape != self.data.shape
             ):
                 raise ValueError(
                     "Result of condition must be a NumPy array with the same shape as the grid."
@@ -775,11 +779,11 @@ class _PropertyGrid(_Grid):
     """
 
     def __init__(
-        self,
-        width: int,
-        height: int,
-        torus: bool,
-        property_layers: None | PropertyLayer | list[PropertyLayer] = None,
+            self,
+            width: int,
+            height: int,
+            torus: bool,
+            property_layers: None | PropertyLayer | list[PropertyLayer] = None,
     ):
         """Initializes a new _PropertyGrid instance with specified dimensions and optional property layers.
 
@@ -846,7 +850,7 @@ def remove_property_layer(self, property_name: str):
         del self.properties[property_name]
 
     def get_neighborhood_mask(
-        self, pos: Coordinate, moore: bool, include_center: bool, radius: int
+            self, pos: Coordinate, moore: bool, include_center: bool, radius: int
     ) -> np.ndarray:
         """Generate a boolean mask representing the neighborhood.
 
@@ -870,12 +874,12 @@ def get_neighborhood_mask(
         return mask
 
     def select_cells(
-        self,
-        conditions: dict | None = None,
-        extreme_values: dict | None = None,
-        masks: np.ndarray | list[np.ndarray] = None,
-        only_empty: bool = False,
-        return_list: bool = True,
+            self,
+            conditions: dict | None = None,
+            extreme_values: dict | None = None,
+            masks: np.ndarray | list[np.ndarray] = None,
+            only_empty: bool = False,
+            return_list: bool = True,
     ) -> list[Coordinate] | np.ndarray:
         """Select cells based on property conditions, extreme values, and/or masks, with an option to only select empty cells.
 
@@ -1031,11 +1035,11 @@ def remove_agent(self, agent: Agent) -> None:
         agent.pos = None
 
     def iter_neighbors(  # noqa: D102
-        self,
-        pos: Coordinate,
-        moore: bool,
-        include_center: bool = False,
-        radius: int = 1,
+            self,
+            pos: Coordinate,
+            moore: bool,
+            include_center: bool = False,
+            radius: int = 1,
     ) -> Iterator[Agent]:
         return itertools.chain.from_iterable(
             super().iter_neighbors(pos, moore, include_center, radius)
@@ -1043,7 +1047,7 @@ def iter_neighbors(  # noqa: D102
 
     @accept_tuple_argument
     def iter_cell_list_contents(
-        self, cell_list: Iterable[Coordinate]
+            self, cell_list: Iterable[Coordinate]
     ) -> Iterator[Agent]:
         """Returns an iterator of the agents contained in the cells identified in `cell_list`.
 
@@ -1083,7 +1087,7 @@ def torus_adj_2d(self, pos: Coordinate) -> Coordinate:
         return pos[0] % self.width, pos[1] % self.height
 
     def get_neighborhood(
-        self, pos: Coordinate, include_center: bool = False, radius: int = 1
+            self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> list[Coordinate]:
         """Return a list of coordinates that are in the neighborhood of a certain point.
 
@@ -1171,7 +1175,7 @@ def get_neighborhood(
         return neighborhood
 
     def iter_neighborhood(
-        self, pos: Coordinate, include_center: bool = False, radius: int = 1
+            self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> Iterator[Coordinate]:
         """Return an iterator over cell coordinates that are in the neighborhood of a certain point.
 
@@ -1187,7 +1191,7 @@ def iter_neighborhood(
         yield from self.get_neighborhood(pos, include_center, radius)
 
     def iter_neighbors(
-        self, pos: Coordinate, include_center: bool = False, radius: int = 1
+            self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> Iterator[Agent]:
         """Return an iterator over neighbors to a certain point.
 
@@ -1205,7 +1209,7 @@ def iter_neighbors(
         return self.iter_cell_list_contents(neighborhood)
 
     def get_neighbors(
-        self, pos: Coordinate, include_center: bool = False, radius: int = 1
+            self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> list[Agent]:
         """Return a list of neighbors to a certain point.
 
@@ -1221,6 +1225,10 @@ def get_neighbors(
         """
         return list(self.iter_neighbors(pos, include_center, radius))
 
+    def __iter__(self) -> Iterator[GridContent]:
+        """Create an iterator returns the agents in the space"""
+        for entry in self._agent_to_index:
+            yield entry
 
 class HexSingleGrid(_HexGrid, SingleGrid):
     """Hexagonal SingleGrid: a SingleGrid where neighbors are computed according to a hexagonal tiling of the grid.
@@ -1301,12 +1309,12 @@ class ContinuousSpace:
     """
 
     def __init__(
-        self,
-        x_max: float,
-        y_max: float,
-        torus: bool,
-        x_min: float = 0,
-        y_min: float = 0,
+            self,
+            x_max: float,
+            y_max: float,
+            torus: bool,
+            x_min: float = 0,
+            y_min: float = 0,
     ) -> None:
         """Create a new continuous space.
 
@@ -1390,7 +1398,7 @@ def remove_agent(self, agent: Agent) -> None:
         agent.pos = None
 
     def get_neighbors(
-        self, pos: FloatCoordinate, radius: float, include_center: bool = True
+            self, pos: FloatCoordinate, radius: float, include_center: bool = True
     ) -> list[Agent]:
         """Get all agents within a certain radius.
 
@@ -1410,14 +1418,14 @@ def get_neighbors(
             deltas = np.minimum(deltas, self.size - deltas)
         dists = deltas[:, 0] ** 2 + deltas[:, 1] ** 2
 
-        (idxs,) = np.where(dists <= radius**2)
+        (idxs,) = np.where(dists <= radius ** 2)
         neighbors = [
             self._index_to_agent[x] for x in idxs if include_center or dists[x] > 0
         ]
         return neighbors
 
     def get_heading(
-        self, pos_1: FloatCoordinate, pos_2: FloatCoordinate
+            self, pos_1: FloatCoordinate, pos_2: FloatCoordinate
     ) -> FloatCoordinate:
         """Get the heading vector between two points, accounting for toroidal space.
 
@@ -1492,6 +1500,11 @@ def out_of_bounds(self, pos: FloatCoordinate) -> bool:
         x, y = pos
         return x < self.x_min or x >= self.x_max or y < self.y_min or y >= self.y_max
 
+    def __iter__(self) -> Iterator[GridContent]:
+        """Create an iterator returns the agents in the space"""
+        for entry in self._agent_to_index:
+            yield entry
+
 
 class NetworkGrid:
     """Network Grid where each node contains zero or more agents."""
@@ -1518,7 +1531,7 @@ def place_agent(self, agent: Agent, node_id: int) -> None:
         agent.pos = node_id
 
     def get_neighborhood(
-        self, node_id: int, include_center: bool = False, radius: int = 1
+            self, node_id: int, include_center: bool = False, radius: int = 1
     ) -> list[int]:
         """Get all adjacent nodes within a certain radius.
 
@@ -1544,7 +1557,7 @@ def get_neighborhood(
         return neighborhood
 
     def get_neighbors(
-        self, node_id: int, include_center: bool = False, radius: int = 1
+            self, node_id: int, include_center: bool = False, radius: int = 1
     ) -> list[Agent]:
         """Get all agents in adjacent nodes (within a certain radius).
 
@@ -1624,3 +1637,8 @@ def iter_cell_list_contents(self, cell_list: list[int]) -> Iterator[Agent]:
             self.G.nodes[node_id]["agent"]
             for node_id in itertools.filterfalse(self.is_cell_empty, cell_list)
         )
+
+    def __iter__(self) -> Iterator[GridContent]:
+        """Create an iterator returns the agents in the space"""
+        for node_id in self.G.nodes:
+            yield self.g.nodes[node_id]["agent"]
diff --git a/mesa/visualization/components/util.py b/mesa/visualization/components/util.py
index f3af21e1a27..315b641affe 100644
--- a/mesa/visualization/components/util.py
+++ b/mesa/visualization/components/util.py
@@ -1,16 +1,119 @@
-from mesa.space import _Grid, ContinuousSpace
+from typing import Callable
+
+from mesa.space import _Grid, ContinuousSpace, _HexGrid, NetworkGrid
 from mesa.experimental.cell_space import DiscreteSpace
 
 
-def get_agents_olstyle_grid(space: _Grid):
+__all__ = ["get_agent_continuous",
+           "get_agents_olstyle_grid",
+           "get_agents_newstyle_grid"]
+
+OldStyleSpace = _Grid | ContinuousSpace | _HexGrid | NetworkGrid
+Space = OldStyleSpace | DiscreteSpace
+
+def get_agents_olstyle_space(space: OldStyleSpace):
     for entry in space:
         if entry:
             yield entry
 
-
-def get_agents_newstyle_grid(space: DiscreteSpace):
+def get_agents_newstyle_space(space: DiscreteSpace):
     for agent in space.all_cells.agents:
         yield agent
 
-def get_agent_continuous(space: ContinuousSpace):
-    pass
+
+def _get_oldstyle_agent_data(agents, agent_portrayal):
+    """Helper function to get agent data for visualization."""
+    x, y, s, c, m = [], [], [], [], []
+    for agent in agents:
+        data = agent_portrayal(agent)
+        x.append(pos[0] + 0.5)  # Center the agent in the cell
+        y.append(pos[1] + 0.5)  # Center the agent in the cell
+        default_size = (180 / max(space.width, space.height)) ** 2
+        s.append(data.get("size", default_size))
+        c.append(data.get("color", "tab:blue"))
+        m.append(data.get("shape", "o"))
+    return {"x": x, "y": y, "s": s, "c": c, "m": m}
+
+
+# fixme:
+#  how we get the data depends on the space and I don't like it.
+#  can't we separate more cleanly the data and any post
+#  space specific refinements?
+#  or gather data depending on the space?
+# fixme:
+#  what routes do we have?
+#  network (2 options)
+#  continuous (1 option)
+#  orthogonal grids (7 options?)
+#  voronoi (1 option)
+
+
+def get_agent_data(space: Space, agent_portrayal: Callable):
+    # fixme should we cover networks here at all?
+
+    match space:
+        case _Grid():  # matches also hexgrids
+            agents = get_agents_olstyle_space(space)
+        case ContinuousSpace():
+            agents = get_agents_olstyle_space(space)
+        case NetworkGrid():
+            agents = get_agents_olstyle_space(space)
+        case DiscreteSpace():
+            agents = get_agents_newstyle_space(space)
+        case _:
+            raise NotImplementedError(f"Unknown space of type {type(space)}")
+
+    x, y, s, c, m = [], [], [], [], []
+    for agent in agents:
+        data = agent_portrayal(agent)
+
+        if isinstance(space, DiscreteSpace):
+            x_i, y_i = agent.cell.coordinate
+        else:
+            x_i, y_i = agent.pos
+
+        x.append(x_i)
+        y.append(y_i)
+        s.append(data.get("size", None))  # we use None here as a flag to fall back on default
+        c.append(data.get("color", "tab:blue"))
+        m.append(data.get("shape", "o"))
+
+
+
+
+
+if __name__ == '__main__':
+    from mesa import Agent, Model
+    from mesa.space import SingleGrid
+    from mesa.experimental.cell_space import OrthogonalMooreGrid, CellAgent
+
+    model = Model()
+    space = SingleGrid(10, 10, True)
+    for _ in range(10):
+        agent = Agent(model)
+        pos = model.random.choice(list(space.empties))
+        space.place_agent(agent, pos)
+
+    agents = list(get_agents_olstyle_space(space))
+    assert len(agents) == 10
+
+
+    model = Model()
+    space = OrthogonalMooreGrid((10, 10), capacity=1, torus=True, random=model.random)
+    for _ in range(10):
+        agent = CellAgent(model)
+        cell = space.select_random_empty_cell()
+        agent.cell = cell
+
+    agents = list(get_agents_newstyle_space(space))
+    assert len(agents) == 10
+
+    model = Model()
+    space = ContinuousSpace(10, 10, True)
+    for _ in range(10):
+        agent = Agent(model)
+        pos = (agent.random.random()*space.width, agent.random.random()*space.height)
+        space.place_agent(agent, pos)
+
+    agents = list(get_agents_olstyle_space(space))
+    assert len(agents) == 10
\ No newline at end of file

From 4197325ad0de6149a29a1eca2adb820b3e5d382c Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 25 Oct 2024 17:08:53 +0200
Subject: [PATCH 03/74] creating a mess

---
 mesa/examples/advanced/wolf_sheep/app.py    |  28 +-
 mesa/visualization/components/matplotlib.py | 367 ++++++++++++--------
 2 files changed, 243 insertions(+), 152 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index b5ac6e8bf47..ab581048337 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,3 +1,8 @@
+import sys
+import os.path
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+
+
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
 from mesa.examples.advanced.wolf_sheep.model import WolfSheep
 from mesa.visualization import (
@@ -16,24 +21,25 @@ def wolf_sheep_portrayal(agent):
         return
 
     portrayal = {
-        "size": 25,
-        "shape": "s",  # square marker
+        "s": 25,
     }
 
     if isinstance(agent, Wolf):
-        portrayal["color"] = WOLF_COLOR
-        portrayal["Layer"] = 3
+        portrayal["c"] = "tab:orange"
+        portrayal["marker"] = "o"
     elif isinstance(agent, Sheep):
-        portrayal["color"] = SHEEP_COLOR
-        portrayal["Layer"] = 2
+        portrayal["c"] = "tab:blue"
+        portrayal["zorder"] = 2
+        portrayal["marker"] = "o"
     elif isinstance(agent, GrassPatch):
         if agent.fully_grown:
-            portrayal["color"] = "#00FF00"
+            portrayal["c"] = "tab:green"
         else:
-            portrayal["color"] = "#84e184"
-        # portrayal["shape"] = "rect"
+            portrayal["c"] = "tab:brown"
+        portrayal["marker"] = "s"
         # portrayal["Filled"] = "true"
-        portrayal["Layer"] = 1
+        portrayal["zorder"] = 1
+        portrayal["s"] = 75
 
     return portrayal
 
@@ -65,7 +71,7 @@ def wolf_sheep_portrayal(agent):
 space_component = make_space_matplotlib(wolf_sheep_portrayal)
 lineplot_component = make_plot_measure(["Wolves", "Sheep", "Grass"])
 
-model = WolfSheep()
+model = WolfSheep(grass=True)
 
 
 page = SolaraViz(
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index be9e7640c22..1590ab9d613 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -10,11 +10,18 @@
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
 from matplotlib.figure import Figure
 
+from collections import defaultdict
+from typing import Callable
+
 import mesa
-from mesa.experimental.cell_space import Grid, VoronoiGrid
-from mesa.space import PropertyLayer
+from mesa.experimental.cell_space import Grid, VoronoiGrid, OrthogonalMooreGrid, OrthogonalVonNeumannGrid, HexGrid
+from mesa.space import PropertyLayer, SingleGrid, MultiGrid, HexSingleGrid, HexMultiGrid, ContinuousSpace, NetworkGrid
 from mesa.visualization.utils import update_counter
 
+OrthogonalGrid = SingleGrid | MultiGrid | OrthogonalMooreGrid | OrthogonalVonNeumannGrid
+HexGrid = HexSingleGrid | HexMultiGrid | HexGrid
+Network = NetworkGrid | mesa.experimental.cell_space.Network
+
 
 def make_space_matplotlib(agent_portrayal=None, propertylayer_portrayal=None):
     """Create a Matplotlib-based space visualization component.
@@ -27,7 +34,6 @@ def make_space_matplotlib(agent_portrayal=None, propertylayer_portrayal=None):
         function: A function that creates a SpaceMatplotlib component
     """
     if agent_portrayal is None:
-
         def agent_portrayal(a):
             return {"id": a.unique_id}
 
@@ -37,19 +43,16 @@ def MakeSpaceMatplotlib(model):
     return MakeSpaceMatplotlib
 
 
-
-
 @solara.component
 def SpaceMatplotlib(
-    model,
-    agent_portrayal,
-    propertylayer_portrayal,
-    dependencies: list[any] | None = None,
+        model,
+        agent_portrayal,
+        propertylayer_portrayal,
+        dependencies: list[any] | None = None,
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
-    space_fig = Figure()
-    space_ax = space_fig.subplots()
+
     space = getattr(model, "grid", None)
     if space is None:
         space = getattr(model, "space", None)
@@ -57,22 +60,25 @@ def SpaceMatplotlib(
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:
         case mesa.space._Grid():
-            _draw_grid(space, space_ax, agent_portrayal, propertylayer_portrayal, model)
-        case mesa.space.ContinuousSpace():
-            _draw_continuous_space(space, space_ax, agent_portrayal, model)
+            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal)
+        # case mesa.space.ContinuousSpace():
+        #     _draw_continuous_space(space, space_ax, agent_portrayal, model)
         case mesa.space.NetworkGrid():
-            _draw_network_grid(space, space_ax, agent_portrayal)
-        case VoronoiGrid():
-            _draw_voronoi(space, space_ax, agent_portrayal)
-        case Grid():  # matches OrthogonalMooreGrid, OrthogonalVonNeumannGrid, and Hexgrid
-            # fixme add a separate draw method for hexgrids in the future
-            _draw_discrete_space_grid(space, space_ax, agent_portrayal)
-        case None:
-            if propertylayer_portrayal:
-                draw_property_layers(space_ax, space, propertylayer_portrayal, model)
+            fig, ax = _draw_network_grid(space, agent_portrayal)
+        # case VoronoiGrid():
+        #     _draw_voronoi(space, space_ax, agent_portrayal)
+        case OrthogonalMooreGrid():  # matches OrthogonalMooreGrid, OrthogonalVonNeumannGrid, and Hexgrid
+            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal)
+        case OrthogonalVonNeumannGrid():  # matches OrthogonalMooreGrid, OrthogonalVonNeumannGrid, and Hexgrid
+            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal)
+        case mesa.experimental.cell_space.Network():
+            fig, ax = _draw_network_grid(space, agent_portrayal)
+        # case None:
+        #     if propertylayer_portrayal:
+        #         draw_property_layers(space_ax, space, propertylayer_portrayal, model)
 
     solara.FigureMatplotlib(
-        space_fig, format="png", bbox_inches="tight", dependencies=dependencies
+        fig, format="png", bbox_inches="tight", dependencies=dependencies
     )
 
 
@@ -148,107 +154,222 @@ def draw_property_layers(ax, space, propertylayer_portrayal, model):
             )
 
 
-def _draw_grid(space, space_ax, agent_portrayal, propertylayer_portrayal, model):
-    if propertylayer_portrayal:
-        draw_property_layers(space_ax, space, propertylayer_portrayal, model)
+def collect_agent_data(space: OrthogonalGrid | HexGrid | Network | ContinuousSpace, agent_portrayal: Callable):
+    """Collect the plotting data for all agents in the space.
+
+    Args:
+        space: The space containing the Agents.
+        agent_portrayal: A callable that is called with the agent and returns a dict
+        loc: a boolean indicating whether to gather agent x, y data or not
+
+    Notes:
+        agent portray dict is limited to s (size of marker), c (color of marker, and marker (marker style)
+        see `Matplotlib`_.
 
-    agent_data = _get_agent_data(space, agent_portrayal)
 
-    space_ax.set_xlim(0, space.width)
-    space_ax.set_ylim(0, space.height)
-    _split_and_scatter(agent_data, space_ax)
+    .. _Matplotlib: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
+
+    """
+    default_size = (180 / max(space.width, space.height)) ** 2
+
+    arguments = dict(x=[], y=[], s=[], c=[], marker=[])
+    for agent in space.agents:
+        portray = agent_portrayal(agent)
+        loc = agent.pos
+        if loc is None:
+            loc = agent.cell.coordinate
+        x, y = loc
+        arguments["x"].append(x)
+        arguments["y"].append(y)
+
+        arguments['s'].append(portray.get("s", default_size))
+        arguments['c'].append(portray.get("c", "tab:blue"))
+        arguments['marker'].append(portray.get("marker", "o"))
+
+    return {k: np.asarray(v) for k, v in arguments.items()}
+
+
+def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
+    arguments = collect_agent_data(space, agent_portrayal)
+
+    fig, ax = plt.subplots()
+    ax.set_xlim(0, space.width)
+    ax.set_ylim(0, space.height)
 
     # Draw grid lines
     for x in range(space.width + 1):
-        space_ax.axvline(x, color="gray", linestyle=":")
+        ax.axvline(x, color="gray", linestyle=":")
     for y in range(space.height + 1):
-        space_ax.axhline(y, color="gray", linestyle=":")
+        ax.axhline(y, color="gray", linestyle=":")
 
+    x = arguments.pop('x') + 0.5
+    y = arguments.pop('y') + 0.5
+    marker = arguments.pop('marker')
 
-def _get_agent_data(space, agent_portrayal):
-    """Helper function to get agent data for visualization."""
-    x, y, s, c, m = [], [], [], [], []
-    for agents, pos in space.coord_iter():
-        if not agents:
-            continue
-        if not isinstance(agents, list):
-            agents = [agents]  # noqa PLW2901
-        for agent in agents:
-            data = agent_portrayal(agent)
-            x.append(pos[0] + 0.5)  # Center the agent in the cell
-            y.append(pos[1] + 0.5)  # Center the agent in the cell
-            default_size = (180 / max(space.width, space.height)) ** 2
-            s.append(data.get("size", default_size))
-            c.append(data.get("color", "tab:blue"))
-            m.append(data.get("shape", "o"))
-    return {"x": x, "y": y, "s": s, "c": c, "m": m}
-
-
-def _split_and_scatter(portray_data, space_ax):
-    """Helper function to split and scatter agent data."""
-    for marker in set(portray_data["m"]):
-        mask = [m == marker for m in portray_data["m"]]
-        space_ax.scatter(
-            [x for x, show in zip(portray_data["x"], mask) if show],
-            [y for y, show in zip(portray_data["y"], mask) if show],
-            s=[s for s, show in zip(portray_data["s"], mask) if show],
-            c=[c for c, show in zip(portray_data["c"], mask) if show],
-            marker=marker,
-        )
+    for mark in np.unique(marker):
+        mask = marker == mark
+        ax.scatter(x[mask], y[mask], marker=mark, **{k: v[mask] for k, v in arguments.items()})
+
+    return fig, ax
+
+
+# def draw_hex_grid(space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
+#     ...
+#
+def collect_agent_data_for_networks(space, agent_portrayal):
+    arguments = defaultdict(list)
+    for agent in space.agents:
+        portray = agent_portrayal(agent)
+        for k, v in agent_portrayal.items():
+            arguments[k].append(v)
+
+    return arguments
+
+def draw_network(space: Network, agent_portrayal: Callable):
+    """Visualize a network space.
+
+    Args:
+        space: the space to visualize
+        agent_portrayal: a callable that is called with the agent and returns a dict
+
+    Notes:
+        this uses networkx.draw under the hood so agent portrayal fields should match those used there
+        i.e., node_side, node_color, node_shape, edge_color
+
+
+    """
+    arguments = collect_agent_data_for_networks(agent_portrayal)
+
+    fig, ax = plt.subplots()
+    graph = space.G
+    pos = nx.spring_layout(graph, seed=0)
+    nx.draw(
+        graph,
+        ax=ax,
+        pos=pos,
+        **arguments,
+    )
 
+    return fig, ax
+
+
+# def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
+#     ...
+#
+# def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
+#     ...
+
+# def _draw_grid(space, space_ax, agent_portrayal, propertylayer_portrayal, model):
+#     if propertylayer_portrayal:
+#         draw_property_layers(space_ax, space, propertylayer_portrayal, model)
+#
+#     agent_data = _get_agent_data(space, agent_portrayal)
+#
+#     space_ax.set_xlim(0, space.width)
+#     space_ax.set_ylim(0, space.height)
+#     _split_and_scatter(agent_data, space_ax)
+#
+#     # Draw grid lines
+#     for x in range(space.width + 1):
+#         space_ax.axvline(x, color="gray", linestyle=":")
+#     for y in range(space.height + 1):
+#         space_ax.axhline(y, color="gray", linestyle=":")
+#
+#
+# def _get_agent_data(space, agent_portrayal):
+#     """Helper function to get agent data for visualization."""
+#     x, y, s, c, m = [], [], [], [], []
+#     for agents, pos in space.coord_iter():
+#         if not agents:
+#             continue
+#         if not isinstance(agents, list):
+#             agents = [agents]  # noqa PLW2901
+#         for agent in agents:
+#             data = agent_portrayal(agent)
+#             x.append(pos[0] + 0.5)  # Center the agent in the cell
+#             y.append(pos[1] + 0.5)  # Center the agent in the cell
+#             default_size = (180 / max(space.width, space.height)) ** 2
+#             s.append(data.get("size", default_size))
+#             c.append(data.get("color", "tab:blue"))
+#             m.append(data.get("shape", "o"))
+#     return {"x": x, "y": y, "s": s, "c": c, "m": m}
+#
+#
+# def _split_and_scatter(portray_data, space_ax):
+#     """Helper function to split and scatter agent data."""
+#     for marker in set(portray_data["m"]):
+#         mask = [m == marker for m in portray_data["m"]]
+#         space_ax.scatter(
+#             [x for x, show in zip(portray_data["x"], mask) if show],
+#             [y for y, show in zip(portray_data["y"], mask) if show],
+#             s=[s for s, show in zip(portray_data["s"], mask) if show],
+#             c=[c for c, show in zip(portray_data["c"], mask) if show],
+#             marker=marker,
+#         )
+
+def collect_agent_data_for_networks(space, agent_portrayal):
+    arguments = defaultdict(list)
+    for agent in space.agents:
+        portray = agent_portrayal(agent)
+        for k, v in agent_portrayal.items():
+            arguments[k].append(v)
+
+    return arguments
 
 def _draw_network_grid(space, space_ax, agent_portrayal):
+    arguments = collect_agent_data_for_networks(agent_portrayal)
+
     graph = space.G
     pos = nx.spring_layout(graph, seed=0)
     nx.draw(
         graph,
         ax=space_ax,
         pos=pos,
-        **agent_portrayal(graph),
+        **arguments,
     )
 
 
-def _draw_continuous_space(space, space_ax, agent_portrayal, model):
-    def portray(space):
-        x = []
-        y = []
-        s = []  # size
-        c = []  # color
-        m = []  # shape
-        for agent in space._agent_to_index:
-            data = agent_portrayal(agent)
-            _x, _y = agent.pos
-            x.append(_x)
-            y.append(_y)
-
-            # This is matplotlib's default marker size
-            default_size = 20
-            size = data.get("size", default_size)
-            s.append(size)
-            color = data.get("color", "tab:blue")
-            c.append(color)
-            mark = data.get("shape", "o")
-            m.append(mark)
-        return {"x": x, "y": y, "s": s, "c": c, "m": m}
-
-    # Determine border style based on space.torus
-    border_style = "solid" if not space.torus else (0, (5, 10))
-
-    # Set the border of the plot
-    for spine in space_ax.spines.values():
-        spine.set_linewidth(1.5)
-        spine.set_color("black")
-        spine.set_linestyle(border_style)
-
-    width = space.x_max - space.x_min
-    x_padding = width / 20
-    height = space.y_max - space.y_min
-    y_padding = height / 20
-    space_ax.set_xlim(space.x_min - x_padding, space.x_max + x_padding)
-    space_ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
-
-    # Portray and scatter the agents in the space
-    _split_and_scatter(portray(space), space_ax)
+# def _draw_continuous_space(space, space_ax, agent_portrayal, model):
+#     def portray(space):
+#         x = []
+#         y = []
+#         s = []  # size
+#         c = []  # color
+#         m = []  # shape
+#         for agent in space._agent_to_index:
+#             data = agent_portrayal(agent)
+#             _x, _y = agent.pos
+#             x.append(_x)
+#             y.append(_y)
+#
+#             # This is matplotlib's default marker size
+#             default_size = 20
+#             size = data.get("size", default_size)
+#             s.append(size)
+#             color = data.get("color", "tab:blue")
+#             c.append(color)
+#             mark = data.get("shape", "o")
+#             m.append(mark)
+#         return {"x": x, "y": y, "s": s, "c": c, "m": m}
+#
+#     # Determine border style based on space.torus
+#     border_style = "solid" if not space.torus else (0, (5, 10))
+#
+#     # Set the border of the plot
+#     for spine in space_ax.spines.values():
+#         spine.set_linewidth(1.5)
+#         spine.set_color("black")
+#         spine.set_linestyle(border_style)
+#
+#     width = space.x_max - space.x_min
+#     x_padding = width / 20
+#     height = space.y_max - space.y_min
+#     y_padding = height / 20
+#     space_ax.set_xlim(space.x_min - x_padding, space.x_max + x_padding)
+#     space_ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
+#
+#     # Portray and scatter the agents in the space
+#     _split_and_scatter(portray(space), space_ax)
 
 
 def _draw_voronoi(space, space_ax, agent_portrayal):
@@ -299,42 +420,6 @@ def portray(g):
         space_ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in black
 
 
-def _draw_discrete_space_grid(space: Grid, space_ax, agent_portrayal):
-    if space._ndims != 2:
-        raise ValueError("Space must be 2D")
-
-    def portray(g):
-        x = []
-        y = []
-        s = []  # size
-        c = []  # color
-
-        for cell in g.all_cells:
-            for agent in cell.agents:
-                data = agent_portrayal(agent)
-                x.append(cell.coordinate[0])
-                y.append(cell.coordinate[1])
-                if "size" in data:
-                    s.append(data["size"])
-                if "color" in data:
-                    c.append(data["color"])
-        out = {"x": x, "y": y}
-        out["s"] = s
-        if len(c) > 0:
-            out["c"] = c
-
-        return out
-
-    space_ax.set_xlim(0, space.width)
-    space_ax.set_ylim(0, space.height)
-
-    # Draw grid lines
-    for x in range(space.width + 1):
-        space_ax.axvline(x, color="gray", linestyle=":")
-    for y in range(space.height + 1):
-        space_ax.axhline(y, color="gray", linestyle=":")
-
-    space_ax.scatter(**portray(space))
 
 
 def make_plot_measure(measure: str | dict[str, str] | list[str] | tuple[str]):

From 8e7b6c6f713cbed0d7962c88c7fefd6b8cd57ad9 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 09:01:27 +0100
Subject: [PATCH 04/74] ongoing refactor

---
 mesa/visualization/components/matplotlib.py | 90 +++------------------
 1 file changed, 12 insertions(+), 78 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 1590ab9d613..b4d66f4087e 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -64,7 +64,7 @@ def SpaceMatplotlib(
         # case mesa.space.ContinuousSpace():
         #     _draw_continuous_space(space, space_ax, agent_portrayal, model)
         case mesa.space.NetworkGrid():
-            fig, ax = _draw_network_grid(space, agent_portrayal)
+            fig, ax = draw_network(space, agent_portrayal)
         # case VoronoiGrid():
         #     _draw_voronoi(space, space_ax, agent_portrayal)
         case OrthogonalMooreGrid():  # matches OrthogonalMooreGrid, OrthogonalVonNeumannGrid, and Hexgrid
@@ -72,10 +72,10 @@ def SpaceMatplotlib(
         case OrthogonalVonNeumannGrid():  # matches OrthogonalMooreGrid, OrthogonalVonNeumannGrid, and Hexgrid
             fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal)
         case mesa.experimental.cell_space.Network():
-            fig, ax = _draw_network_grid(space, agent_portrayal)
-        # case None:
-        #     if propertylayer_portrayal:
-        #         draw_property_layers(space_ax, space, propertylayer_portrayal, model)
+            fig, ax = draw_network(space, agent_portrayal)
+        case None:
+            if propertylayer_portrayal:
+                draw_property_layers(space_ax, space, propertylayer_portrayal, model)
 
     solara.FigureMatplotlib(
         fig, format="png", bbox_inches="tight", dependencies=dependencies
@@ -193,17 +193,17 @@ def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, prope
     arguments = collect_agent_data(space, agent_portrayal)
 
     fig, ax = plt.subplots()
-    ax.set_xlim(0, space.width)
-    ax.set_ylim(0, space.height)
+    ax.set_xlim(-0.5, space.width-0.5)
+    ax.set_ylim(-0.5, space.height-0.5)
 
     # Draw grid lines
-    for x in range(space.width + 1):
+    for x in np.arange(-0.5, space.width-0.5, 1):
         ax.axvline(x, color="gray", linestyle=":")
-    for y in range(space.height + 1):
+    for y in np.arange(-0.5, space.height-0.5, 1):
         ax.axhline(y, color="gray", linestyle=":")
 
-    x = arguments.pop('x') + 0.5
-    y = arguments.pop('y') + 0.5
+    x = arguments.pop('x')
+    y = arguments.pop('y')
     marker = arguments.pop('marker')
 
     for mark in np.unique(marker):
@@ -216,6 +216,7 @@ def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, prope
 # def draw_hex_grid(space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
 #     ...
 #
+
 def collect_agent_data_for_networks(space, agent_portrayal):
     arguments = defaultdict(list)
     for agent in space.agents:
@@ -259,74 +260,7 @@ def draw_network(space: Network, agent_portrayal: Callable):
 # def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
 #     ...
 
-# def _draw_grid(space, space_ax, agent_portrayal, propertylayer_portrayal, model):
-#     if propertylayer_portrayal:
-#         draw_property_layers(space_ax, space, propertylayer_portrayal, model)
-#
-#     agent_data = _get_agent_data(space, agent_portrayal)
-#
-#     space_ax.set_xlim(0, space.width)
-#     space_ax.set_ylim(0, space.height)
-#     _split_and_scatter(agent_data, space_ax)
-#
-#     # Draw grid lines
-#     for x in range(space.width + 1):
-#         space_ax.axvline(x, color="gray", linestyle=":")
-#     for y in range(space.height + 1):
-#         space_ax.axhline(y, color="gray", linestyle=":")
-#
-#
-# def _get_agent_data(space, agent_portrayal):
-#     """Helper function to get agent data for visualization."""
-#     x, y, s, c, m = [], [], [], [], []
-#     for agents, pos in space.coord_iter():
-#         if not agents:
-#             continue
-#         if not isinstance(agents, list):
-#             agents = [agents]  # noqa PLW2901
-#         for agent in agents:
-#             data = agent_portrayal(agent)
-#             x.append(pos[0] + 0.5)  # Center the agent in the cell
-#             y.append(pos[1] + 0.5)  # Center the agent in the cell
-#             default_size = (180 / max(space.width, space.height)) ** 2
-#             s.append(data.get("size", default_size))
-#             c.append(data.get("color", "tab:blue"))
-#             m.append(data.get("shape", "o"))
-#     return {"x": x, "y": y, "s": s, "c": c, "m": m}
-#
-#
-# def _split_and_scatter(portray_data, space_ax):
-#     """Helper function to split and scatter agent data."""
-#     for marker in set(portray_data["m"]):
-#         mask = [m == marker for m in portray_data["m"]]
-#         space_ax.scatter(
-#             [x for x, show in zip(portray_data["x"], mask) if show],
-#             [y for y, show in zip(portray_data["y"], mask) if show],
-#             s=[s for s, show in zip(portray_data["s"], mask) if show],
-#             c=[c for c, show in zip(portray_data["c"], mask) if show],
-#             marker=marker,
-#         )
 
-def collect_agent_data_for_networks(space, agent_portrayal):
-    arguments = defaultdict(list)
-    for agent in space.agents:
-        portray = agent_portrayal(agent)
-        for k, v in agent_portrayal.items():
-            arguments[k].append(v)
-
-    return arguments
-
-def _draw_network_grid(space, space_ax, agent_portrayal):
-    arguments = collect_agent_data_for_networks(agent_portrayal)
-
-    graph = space.G
-    pos = nx.spring_layout(graph, seed=0)
-    nx.draw(
-        graph,
-        ax=space_ax,
-        pos=pos,
-        **arguments,
-    )
 
 
 # def _draw_continuous_space(space, space_ax, agent_portrayal, model):

From bdb23cbd10b864e53e51401c9df3667db900fa3e Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 11:08:27 +0100
Subject: [PATCH 05/74] Update matplotlib.py

---
 mesa/visualization/components/matplotlib.py | 274 ++++++++++++--------
 1 file changed, 162 insertions(+), 112 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index b4d66f4087e..38400d10c32 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -1,6 +1,8 @@
 """Matplotlib based solara components for visualization MESA spaces and plots."""
 
 import warnings
+from collections import defaultdict
+from collections.abc import Callable
 
 import matplotlib.pyplot as plt
 import networkx as nx
@@ -10,16 +12,25 @@
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
 from matplotlib.figure import Figure
 
-from collections import defaultdict
-from typing import Callable
-
 import mesa
-from mesa.experimental.cell_space import Grid, VoronoiGrid, OrthogonalMooreGrid, OrthogonalVonNeumannGrid, HexGrid
-from mesa.space import PropertyLayer, SingleGrid, MultiGrid, HexSingleGrid, HexMultiGrid, ContinuousSpace, NetworkGrid
+from mesa.experimental.cell_space import (
+    OrthogonalMooreGrid,
+    OrthogonalVonNeumannGrid,
+    VoronoiGrid,
+)
+from mesa.space import (
+    ContinuousSpace,
+    HexMultiGrid,
+    HexSingleGrid,
+    MultiGrid,
+    NetworkGrid,
+    PropertyLayer,
+    SingleGrid,
+)
 from mesa.visualization.utils import update_counter
 
 OrthogonalGrid = SingleGrid | MultiGrid | OrthogonalMooreGrid | OrthogonalVonNeumannGrid
-HexGrid = HexSingleGrid | HexMultiGrid | HexGrid
+HexGrid = HexSingleGrid | HexMultiGrid | mesa.experimental.cell_space.HexGrid
 Network = NetworkGrid | mesa.experimental.cell_space.Network
 
 
@@ -60,22 +71,30 @@ def SpaceMatplotlib(
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:
         case mesa.space._Grid():
-            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal)
-        # case mesa.space.ContinuousSpace():
-        #     _draw_continuous_space(space, space_ax, agent_portrayal, model)
+            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal, model)
+        case OrthogonalMooreGrid():
+            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal, model)
+        case OrthogonalVonNeumannGrid():
+            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal, model)
+        case HexSingleGrid():
+            fig, ax = draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model)
+        case HexSingleGrid():
+            fig, ax = draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model)
+        case mesa.experimental.cell_space.HexGrid():
+            fig, ax = draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model)
+        case mesa.space.ContinuousSpace():
+            fig, ax = draw_continuous_space(space, agent_portrayal)
         case mesa.space.NetworkGrid():
             fig, ax = draw_network(space, agent_portrayal)
-        # case VoronoiGrid():
-        #     _draw_voronoi(space, space_ax, agent_portrayal)
-        case OrthogonalMooreGrid():  # matches OrthogonalMooreGrid, OrthogonalVonNeumannGrid, and Hexgrid
-            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal)
-        case OrthogonalVonNeumannGrid():  # matches OrthogonalMooreGrid, OrthogonalVonNeumannGrid, and Hexgrid
-            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal)
+        case VoronoiGrid():
+            fig, ax = draw_voroinoi_grid(space, agent_portrayal)
         case mesa.experimental.cell_space.Network():
             fig, ax = draw_network(space, agent_portrayal)
         case None:
+            fig = Figure()
+            ax = fig.subplots(111)
             if propertylayer_portrayal:
-                draw_property_layers(space_ax, space, propertylayer_portrayal, model)
+                draw_property_layers(ax, space, propertylayer_portrayal, model)
 
     solara.FigureMatplotlib(
         fig, format="png", bbox_inches="tight", dependencies=dependencies
@@ -172,7 +191,7 @@ def collect_agent_data(space: OrthogonalGrid | HexGrid | Network | ContinuousSpa
     """
     default_size = (180 / max(space.width, space.height)) ** 2
 
-    arguments = dict(x=[], y=[], s=[], c=[], marker=[])
+    arguments = {"x":[], "y":[], "s":[], "c":[], "marker":[]}
     for agent in space.agents:
         portray = agent_portrayal(agent)
         loc = agent.pos
@@ -182,17 +201,31 @@ def collect_agent_data(space: OrthogonalGrid | HexGrid | Network | ContinuousSpa
         arguments["x"].append(x)
         arguments["y"].append(y)
 
-        arguments['s'].append(portray.get("s", default_size))
-        arguments['c'].append(portray.get("c", "tab:blue"))
-        arguments['marker'].append(portray.get("marker", "o"))
+        arguments["s"].append(portray.get("s", default_size))
+        arguments["c"].append(portray.get("c", "tab:blue"))
+        arguments["marker"].append(portray.get("marker", "o"))
 
     return {k: np.asarray(v) for k, v in arguments.items()}
 
 
-def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
+def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model):
+    """Visualize a orthogonal grid..
+
+    Args:
+        space: the space to visualize
+        agent_portrayal: a callable that is called with the agent and returns a dict
+        propertylayer_portrayal: a callable that is called with the agent and returns a dict
+        model: a model instance
+
+    Returns:
+        A Figure and Axes instance
+
+    """
     arguments = collect_agent_data(space, agent_portrayal)
 
-    fig, ax = plt.subplots()
+    fig = Figure()
+    ax = fig.add_subplot(111)
+
     ax.set_xlim(-0.5, space.width-0.5)
     ax.set_ylim(-0.5, space.height-0.5)
 
@@ -202,26 +235,54 @@ def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, prope
     for y in np.arange(-0.5, space.height-0.5, 1):
         ax.axhline(y, color="gray", linestyle=":")
 
-    x = arguments.pop('x')
-    y = arguments.pop('y')
-    marker = arguments.pop('marker')
+    _scatter(ax, arguments)
 
-    for mark in np.unique(marker):
-        mask = marker == mark
-        ax.scatter(x[mask], y[mask], marker=mark, **{k: v[mask] for k, v in arguments.items()})
+    if propertylayer_portrayal:
+        draw_property_layers(ax, space, propertylayer_portrayal, model)
 
     return fig, ax
 
 
-# def draw_hex_grid(space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
-#     ...
-#
+def draw_hex_grid(space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model):
+    """Visualize a hex grid.
+
+    Args:
+        space: the space to visualize
+        agent_portrayal: a callable that is called with the agent and returns a dict
+        propertylayer_portrayal: a callable that is called with the agent and returns a dict
+        model: a model instance
+
+    Returns:
+        A Figure and Axes instance
+
+    """
+    arguments = collect_agent_data(space, agent_portrayal)
+
+    # give all odd rows an offset in the x direction
+    logical = np.mod(arguments["y"], 2) == 1
+    arguments["x"] = arguments["x"][logical] + 1
+
+    fig = Figure()
+    ax = fig.add_subplot(111)
+
+    _scatter(ax, arguments)
+
+    if propertylayer_portrayal:
+        draw_property_layers(ax, space, propertylayer_portrayal, model)
+    return fig, ax
 
 def collect_agent_data_for_networks(space, agent_portrayal):
+    """Collect the plotting data for all agents in the network.
+
+    Args:
+        space: the space to visualize
+        agent_portrayal: a callable that is called with the agent and returns a dict
+
+    """
     arguments = defaultdict(list)
     for agent in space.agents:
         portray = agent_portrayal(agent)
-        for k, v in agent_portrayal.items():
+        for k, v in portray.items():
             arguments[k].append(v)
 
     return arguments
@@ -254,80 +315,57 @@ def draw_network(space: Network, agent_portrayal: Callable):
     return fig, ax
 
 
-# def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
-#     ...
-#
-# def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable):
-#     ...
-
-
-
-
-# def _draw_continuous_space(space, space_ax, agent_portrayal, model):
-#     def portray(space):
-#         x = []
-#         y = []
-#         s = []  # size
-#         c = []  # color
-#         m = []  # shape
-#         for agent in space._agent_to_index:
-#             data = agent_portrayal(agent)
-#             _x, _y = agent.pos
-#             x.append(_x)
-#             y.append(_y)
-#
-#             # This is matplotlib's default marker size
-#             default_size = 20
-#             size = data.get("size", default_size)
-#             s.append(size)
-#             color = data.get("color", "tab:blue")
-#             c.append(color)
-#             mark = data.get("shape", "o")
-#             m.append(mark)
-#         return {"x": x, "y": y, "s": s, "c": c, "m": m}
-#
-#     # Determine border style based on space.torus
-#     border_style = "solid" if not space.torus else (0, (5, 10))
-#
-#     # Set the border of the plot
-#     for spine in space_ax.spines.values():
-#         spine.set_linewidth(1.5)
-#         spine.set_color("black")
-#         spine.set_linestyle(border_style)
-#
-#     width = space.x_max - space.x_min
-#     x_padding = width / 20
-#     height = space.y_max - space.y_min
-#     y_padding = height / 20
-#     space_ax.set_xlim(space.x_min - x_padding, space.x_max + x_padding)
-#     space_ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
-#
-#     # Portray and scatter the agents in the space
-#     _split_and_scatter(portray(space), space_ax)
-
-
-def _draw_voronoi(space, space_ax, agent_portrayal):
-    def portray(g):
-        x = []
-        y = []
-        s = []  # size
-        c = []  # color
-
-        for cell in g.all_cells:
-            for agent in cell.agents:
-                data = agent_portrayal(agent)
-                x.append(cell.coordinate[0])
-                y.append(cell.coordinate[1])
-                if "size" in data:
-                    s.append(data["size"])
-                if "color" in data:
-                    c.append(data["color"])
-        out = {"x": x, "y": y}
-        out["s"] = s
-        if len(c) > 0:
-            out["c"] = c
-
-        return out
+def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
+    """Visualize a continuous space.
+
+    Args:
+        space: the space to visualize
+        agent_portrayal: a callable that is called with the agent and returns a dict
+
+    Returns:
+        A Figure and Axes instance
+
+    """
+    arguments = collect_agent_data(space, agent_portrayal)
+
+    fig = Figure()
+    ax = fig.add_subplot(111)
+
+    border_style = "solid" if not space.torus else (0, (5, 10))
+
+    # Set the border of the plot
+    for spine in ax.spines.values():
+        spine.set_linewidth(1.5)
+        spine.set_color("black")
+        spine.set_linestyle(border_style)
+
+    width = space.x_max - space.x_min
+    x_padding = width / 20
+    height = space.y_max - space.y_min
+    y_padding = height / 20
+
+    ax.set_xlim(space.x_min - x_padding, space.x_max + x_padding)
+    ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
+
+    _scatter(ax, arguments)
+    return fig, ax
+
+
+def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
+    """Visualize a voronoi grid.
+
+    Args:
+        space: the space to visualize
+        agent_portrayal: a callable that is called with the agent and returns a dict
+
+    Returns:
+        A Figure and Axes instance
+
+    """
+    arguments = collect_agent_data(space, agent_portrayal)
+
+    fig = Figure()
+    ax = fig.add_subplot(111)
 
     x_list = [i[0] for i in space.centroids_coordinates]
     y_list = [i[1] for i in space.centroids_coordinates]
@@ -340,20 +378,32 @@ def portray(g):
     x_padding = width / 20
     height = y_max - y_min
     y_padding = height / 20
-    space_ax.set_xlim(x_min - x_padding, x_max + x_padding)
-    space_ax.set_ylim(y_min - y_padding, y_max + y_padding)
-    space_ax.scatter(**portray(space))
+    ax.set_xlim(x_min - x_padding, x_max + x_padding)
+    ax.set_ylim(y_min - y_padding, y_max + y_padding)
+
+    _scatter(ax, arguments)
+
 
     for cell in space.all_cells:
         polygon = cell.properties["polygon"]
-        space_ax.fill(
+        ax.fill(
             *zip(*polygon),
             alpha=min(1, cell.properties[space.cell_coloring_property]),
-            c="red",
+            c="red", zorder=0
         )  # Plot filled polygon
-        space_ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in black
+        ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in black
+    return fig, ax
+
 
 
+def _scatter(ax, arguments):
+    x = arguments.pop("x")
+    y = arguments.pop("y")
+    marker = arguments.pop("marker")
+
+    for mark in np.unique(marker):
+        mask = marker == mark
+        ax.scatter(x[mask], y[mask], marker=mark, **{k: v[mask] for k, v in arguments.items()})
 
 
 def make_plot_measure(measure: str | dict[str, str] | list[str] | tuple[str]):

From 9f543da57c4a745b8d050bafc1fec80e8531eb97 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 27 Oct 2024 10:25:58 +0000
Subject: [PATCH 06/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/advanced/wolf_sheep/app.py    |   7 +-
 mesa/space.py                               | 163 ++++++++++----------
 mesa/visualization/components/matplotlib.py |  70 ++++++---
 mesa/visualization/components/util.py       |  37 +++--
 4 files changed, 152 insertions(+), 125 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index ab581048337..46f577b4ba0 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,6 +1,9 @@
-import sys
 import os.path
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+import sys
+
+sys.path.insert(
+    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
+)
 
 
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
diff --git a/mesa/space.py b/mesa/space.py
index 5881baa6934..49fb1c9b880 100644
--- a/mesa/space.py
+++ b/mesa/space.py
@@ -139,7 +139,7 @@ def __init__(self, width: int, height: int, torus: bool) -> None:
         # Cutoff used inside self.move_to_empty. The parameters are fitted on Python
         # 3.11 and it was verified that they are roughly the same for 3.10. Refer to
         # the code in PR#1565 to check for their stability when a new release gets out.
-        self.cutoff_empties = 7.953 * self.num_cells ** 0.384
+        self.cutoff_empties = 7.953 * self.num_cells**0.384
 
     @staticmethod
     def default_val() -> None:
@@ -162,8 +162,7 @@ def build_empties(self) -> None:
         self._empties_built = True
 
     @overload
-    def __getitem__(self, index: int | Sequence[Coordinate]) -> list[GridContent]:
-        ...
+    def __getitem__(self, index: int | Sequence[Coordinate]) -> list[GridContent]: ...
 
     @property
     def agents(self) -> AgentSet:
@@ -187,9 +186,8 @@ def agents(self) -> AgentSet:
 
     @overload
     def __getitem__(
-            self, index: tuple[int | slice, int | slice]
-    ) -> GridContent | list[GridContent]:
-        ...
+        self, index: tuple[int | slice, int | slice]
+    ) -> GridContent | list[GridContent]: ...
 
     def __getitem__(self, index):
         """Access contents from the grid."""
@@ -235,11 +233,11 @@ def coord_iter(self) -> Iterator[tuple[GridContent, Coordinate]]:
                 yield self._grid[row][col], (row, col)  # agent, position
 
     def iter_neighborhood(
-            self,
-            pos: Coordinate,
-            moore: bool,
-            include_center: bool = False,
-            radius: int = 1,
+        self,
+        pos: Coordinate,
+        moore: bool,
+        include_center: bool = False,
+        radius: int = 1,
     ) -> Iterator[Coordinate]:
         """Return an iterator over cell coordinates that are in the neighborhood of a certain point.
 
@@ -262,11 +260,11 @@ def iter_neighborhood(
         yield from self.get_neighborhood(pos, moore, include_center, radius)
 
     def get_neighborhood(
-            self,
-            pos: Coordinate,
-            moore: bool,
-            include_center: bool = False,
-            radius: int = 1,
+        self,
+        pos: Coordinate,
+        moore: bool,
+        include_center: bool = False,
+        radius: int = 1,
     ) -> Sequence[Coordinate]:
         """Return a list of cells that are in the neighborhood of a certain point.
 
@@ -301,10 +299,10 @@ def get_neighborhood(
 
         # First we check if the neighborhood is inside the grid
         if (
-                x >= radius
-                and self.width - x > radius
-                and y >= radius
-                and self.height - y > radius
+            x >= radius
+            and self.width - x > radius
+            and y >= radius
+            and self.height - y > radius
         ):
             # If the radius is smaller than the distance from the borders, we
             # can skip boundary checks.
@@ -345,11 +343,11 @@ def get_neighborhood(
         return tuple(neighborhood.keys())
 
     def iter_neighbors(
-            self,
-            pos: Coordinate,
-            moore: bool,
-            include_center: bool = False,
-            radius: int = 1,
+        self,
+        pos: Coordinate,
+        moore: bool,
+        include_center: bool = False,
+        radius: int = 1,
     ) -> Iterator[Agent]:
         """Return an iterator over neighbors to a certain point.
 
@@ -375,11 +373,11 @@ def iter_neighbors(
                 yield cell
 
     def get_neighbors(
-            self,
-            pos: Coordinate,
-            moore: bool,
-            include_center: bool = False,
-            radius: int = 1,
+        self,
+        pos: Coordinate,
+        moore: bool,
+        include_center: bool = False,
+        radius: int = 1,
     ) -> list[Agent]:
         """Return a list of neighbors to a certain point.
 
@@ -417,7 +415,7 @@ def out_of_bounds(self, pos: Coordinate) -> bool:
 
     @accept_tuple_argument
     def iter_cell_list_contents(
-            self, cell_list: Iterable[Coordinate]
+        self, cell_list: Iterable[Coordinate]
     ) -> Iterator[Agent]:
         """Returns an iterator of the agents contained in the cells identified in `cell_list`; cells with empty content are excluded.
 
@@ -445,11 +443,9 @@ def get_cell_list_contents(self, cell_list: Iterable[Coordinate]) -> list[Agent]
         """
         return list(self.iter_cell_list_contents(cell_list))
 
-    def place_agent(self, agent: Agent, pos: Coordinate) -> None:
-        ...
+    def place_agent(self, agent: Agent, pos: Coordinate) -> None: ...
 
-    def remove_agent(self, agent: Agent) -> None:
-        ...
+    def remove_agent(self, agent: Agent) -> None: ...
 
     def move_agent(self, agent: Agent, pos: Coordinate) -> None:
         """Move an agent from its current position to a new position.
@@ -464,11 +460,11 @@ def move_agent(self, agent: Agent, pos: Coordinate) -> None:
         self.place_agent(agent, pos)
 
     def move_agent_to_one_of(
-            self,
-            agent: Agent,
-            pos: list[Coordinate],
-            selection: str = "random",
-            handle_empty: str | None = None,
+        self,
+        agent: Agent,
+        pos: list[Coordinate],
+        selection: str = "random",
+        handle_empty: str | None = None,
     ) -> None:
         """Move an agent to one of the given positions.
 
@@ -528,7 +524,7 @@ def _distance_squared(self, pos1: Coordinate, pos2: Coordinate) -> float:
         if self.torus:
             dx = min(dx, self.width - dx)
             dy = min(dy, self.height - dy)
-        return dx ** 2 + dy ** 2
+        return dx**2 + dy**2
 
     def swap_pos(self, agent_a: Agent, agent_b: Agent) -> None:
         """Swap agents positions."""
@@ -587,8 +583,8 @@ def exists_empty_cells(self) -> bool:
 def is_single_argument_function(function):
     """Check if a function is a single argument function."""
     return (
-            inspect.isfunction(function)
-            and len(inspect.signature(function).parameters) == 1
+        inspect.isfunction(function)
+        and len(inspect.signature(function).parameters) == 1
     )
 
 
@@ -614,7 +610,7 @@ class PropertyLayer:
     propertylayer_experimental_warning_given = False
 
     def __init__(
-            self, name: str, width: int, height: int, default_value, dtype=np.float64
+        self, name: str, width: int, height: int, default_value, dtype=np.float64
     ):
         """Initializes a new PropertyLayer instance.
 
@@ -642,7 +638,7 @@ def __init__(
 
         # Check that width and height are positive integers
         if (not isinstance(width, int) or width < 1) or (
-                not isinstance(height, int) or height < 1
+            not isinstance(height, int) or height < 1
         ):
             raise ValueError(
                 f"Width and height must be positive integers, got {width} and {height}."
@@ -690,8 +686,8 @@ def set_cells(self, value, condition=None):
                 condition_result = vectorized_condition(self.data)
 
             if (
-                    not isinstance(condition_result, np.ndarray)
-                    or condition_result.shape != self.data.shape
+                not isinstance(condition_result, np.ndarray)
+                or condition_result.shape != self.data.shape
             ):
                 raise ValueError(
                     "Result of condition must be a NumPy array with the same shape as the grid."
@@ -810,11 +806,11 @@ class _PropertyGrid(_Grid):
     """
 
     def __init__(
-            self,
-            width: int,
-            height: int,
-            torus: bool,
-            property_layers: None | PropertyLayer | list[PropertyLayer] = None,
+        self,
+        width: int,
+        height: int,
+        torus: bool,
+        property_layers: None | PropertyLayer | list[PropertyLayer] = None,
     ):
         """Initializes a new _PropertyGrid instance with specified dimensions and optional property layers.
 
@@ -881,7 +877,7 @@ def remove_property_layer(self, property_name: str):
         del self.properties[property_name]
 
     def get_neighborhood_mask(
-            self, pos: Coordinate, moore: bool, include_center: bool, radius: int
+        self, pos: Coordinate, moore: bool, include_center: bool, radius: int
     ) -> np.ndarray:
         """Generate a boolean mask representing the neighborhood.
 
@@ -905,12 +901,12 @@ def get_neighborhood_mask(
         return mask
 
     def select_cells(
-            self,
-            conditions: dict | None = None,
-            extreme_values: dict | None = None,
-            masks: np.ndarray | list[np.ndarray] = None,
-            only_empty: bool = False,
-            return_list: bool = True,
+        self,
+        conditions: dict | None = None,
+        extreme_values: dict | None = None,
+        masks: np.ndarray | list[np.ndarray] = None,
+        only_empty: bool = False,
+        return_list: bool = True,
     ) -> list[Coordinate] | np.ndarray:
         """Select cells based on property conditions, extreme values, and/or masks, with an option to only select empty cells.
 
@@ -1066,11 +1062,11 @@ def remove_agent(self, agent: Agent) -> None:
         agent.pos = None
 
     def iter_neighbors(  # noqa: D102
-            self,
-            pos: Coordinate,
-            moore: bool,
-            include_center: bool = False,
-            radius: int = 1,
+        self,
+        pos: Coordinate,
+        moore: bool,
+        include_center: bool = False,
+        radius: int = 1,
     ) -> Iterator[Agent]:
         return itertools.chain.from_iterable(
             super().iter_neighbors(pos, moore, include_center, radius)
@@ -1078,7 +1074,7 @@ def iter_neighbors(  # noqa: D102
 
     @accept_tuple_argument
     def iter_cell_list_contents(
-            self, cell_list: Iterable[Coordinate]
+        self, cell_list: Iterable[Coordinate]
     ) -> Iterator[Agent]:
         """Returns an iterator of the agents contained in the cells identified in `cell_list`.
 
@@ -1118,7 +1114,7 @@ def torus_adj_2d(self, pos: Coordinate) -> Coordinate:
         return pos[0] % self.width, pos[1] % self.height
 
     def get_neighborhood(
-            self, pos: Coordinate, include_center: bool = False, radius: int = 1
+        self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> list[Coordinate]:
         """Return a list of coordinates that are in the neighborhood of a certain point.
 
@@ -1206,7 +1202,7 @@ def get_neighborhood(
         return neighborhood
 
     def iter_neighborhood(
-            self, pos: Coordinate, include_center: bool = False, radius: int = 1
+        self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> Iterator[Coordinate]:
         """Return an iterator over cell coordinates that are in the neighborhood of a certain point.
 
@@ -1222,7 +1218,7 @@ def iter_neighborhood(
         yield from self.get_neighborhood(pos, include_center, radius)
 
     def iter_neighbors(
-            self, pos: Coordinate, include_center: bool = False, radius: int = 1
+        self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> Iterator[Agent]:
         """Return an iterator over neighbors to a certain point.
 
@@ -1240,7 +1236,7 @@ def iter_neighbors(
         return self.iter_cell_list_contents(neighborhood)
 
     def get_neighbors(
-            self, pos: Coordinate, include_center: bool = False, radius: int = 1
+        self, pos: Coordinate, include_center: bool = False, radius: int = 1
     ) -> list[Agent]:
         """Return a list of neighbors to a certain point.
 
@@ -1258,8 +1254,8 @@ def get_neighbors(
 
     def __iter__(self) -> Iterator[GridContent]:
         """Create an iterator returns the agents in the space"""
-        for entry in self._agent_to_index:
-            yield entry
+        yield from self._agent_to_index
+
 
 class HexSingleGrid(_HexGrid, SingleGrid):
     """Hexagonal SingleGrid: a SingleGrid where neighbors are computed according to a hexagonal tiling of the grid.
@@ -1340,12 +1336,12 @@ class ContinuousSpace:
     """
 
     def __init__(
-            self,
-            x_max: float,
-            y_max: float,
-            torus: bool,
-            x_min: float = 0,
-            y_min: float = 0,
+        self,
+        x_max: float,
+        y_max: float,
+        torus: bool,
+        x_min: float = 0,
+        y_min: float = 0,
     ) -> None:
         """Create a new continuous space.
 
@@ -1442,7 +1438,7 @@ def remove_agent(self, agent: Agent) -> None:
         agent.pos = None
 
     def get_neighbors(
-            self, pos: FloatCoordinate, radius: float, include_center: bool = True
+        self, pos: FloatCoordinate, radius: float, include_center: bool = True
     ) -> list[Agent]:
         """Get all agents within a certain radius.
 
@@ -1462,14 +1458,14 @@ def get_neighbors(
             deltas = np.minimum(deltas, self.size - deltas)
         dists = deltas[:, 0] ** 2 + deltas[:, 1] ** 2
 
-        (idxs,) = np.where(dists <= radius ** 2)
+        (idxs,) = np.where(dists <= radius**2)
         neighbors = [
             self._index_to_agent[x] for x in idxs if include_center or dists[x] > 0
         ]
         return neighbors
 
     def get_heading(
-            self, pos_1: FloatCoordinate, pos_2: FloatCoordinate
+        self, pos_1: FloatCoordinate, pos_2: FloatCoordinate
     ) -> FloatCoordinate:
         """Get the heading vector between two points, accounting for toroidal space.
 
@@ -1546,8 +1542,7 @@ def out_of_bounds(self, pos: FloatCoordinate) -> bool:
 
     def __iter__(self) -> Iterator[GridContent]:
         """Create an iterator returns the agents in the space"""
-        for entry in self._agent_to_index:
-            yield entry
+        yield from self._agent_to_index
 
 
 class NetworkGrid:
@@ -1596,7 +1591,7 @@ def place_agent(self, agent: Agent, node_id: int) -> None:
         agent.pos = node_id
 
     def get_neighborhood(
-            self, node_id: int, include_center: bool = False, radius: int = 1
+        self, node_id: int, include_center: bool = False, radius: int = 1
     ) -> list[int]:
         """Get all adjacent nodes within a certain radius.
 
@@ -1622,7 +1617,7 @@ def get_neighborhood(
         return neighborhood
 
     def get_neighbors(
-            self, node_id: int, include_center: bool = False, radius: int = 1
+        self, node_id: int, include_center: bool = False, radius: int = 1
     ) -> list[Agent]:
         """Get all agents in adjacent nodes (within a certain radius).
 
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 38400d10c32..bba07d420bd 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -45,6 +45,7 @@ def make_space_matplotlib(agent_portrayal=None, propertylayer_portrayal=None):
         function: A function that creates a SpaceMatplotlib component
     """
     if agent_portrayal is None:
+
         def agent_portrayal(a):
             return {"id": a.unique_id}
 
@@ -56,10 +57,10 @@ def MakeSpaceMatplotlib(model):
 
 @solara.component
 def SpaceMatplotlib(
-        model,
-        agent_portrayal,
-        propertylayer_portrayal,
-        dependencies: list[any] | None = None,
+    model,
+    agent_portrayal,
+    propertylayer_portrayal,
+    dependencies: list[any] | None = None,
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
@@ -71,17 +72,29 @@ def SpaceMatplotlib(
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:
         case mesa.space._Grid():
-            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal, model)
+            fig, ax = draw_orthogonal_grid(
+                space, agent_portrayal, propertylayer_portrayal, model
+            )
         case OrthogonalMooreGrid():
-            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal, model)
+            fig, ax = draw_orthogonal_grid(
+                space, agent_portrayal, propertylayer_portrayal, model
+            )
         case OrthogonalVonNeumannGrid():
-            fig, ax = draw_orthogonal_grid(space, agent_portrayal, propertylayer_portrayal, model)
+            fig, ax = draw_orthogonal_grid(
+                space, agent_portrayal, propertylayer_portrayal, model
+            )
         case HexSingleGrid():
-            fig, ax = draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model)
+            fig, ax = draw_hex_grid(
+                space, agent_portrayal, propertylayer_portrayal, model
+            )
         case HexSingleGrid():
-            fig, ax = draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model)
+            fig, ax = draw_hex_grid(
+                space, agent_portrayal, propertylayer_portrayal, model
+            )
         case mesa.experimental.cell_space.HexGrid():
-            fig, ax = draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model)
+            fig, ax = draw_hex_grid(
+                space, agent_portrayal, propertylayer_portrayal, model
+            )
         case mesa.space.ContinuousSpace():
             fig, ax = draw_continuous_space(space, agent_portrayal)
         case mesa.space.NetworkGrid():
@@ -173,7 +186,10 @@ def draw_property_layers(ax, space, propertylayer_portrayal, model):
             )
 
 
-def collect_agent_data(space: OrthogonalGrid | HexGrid | Network | ContinuousSpace, agent_portrayal: Callable):
+def collect_agent_data(
+    space: OrthogonalGrid | HexGrid | Network | ContinuousSpace,
+    agent_portrayal: Callable,
+):
     """Collect the plotting data for all agents in the space.
 
     Args:
@@ -191,7 +207,7 @@ def collect_agent_data(space: OrthogonalGrid | HexGrid | Network | ContinuousSpa
     """
     default_size = (180 / max(space.width, space.height)) ** 2
 
-    arguments = {"x":[], "y":[], "s":[], "c":[], "marker":[]}
+    arguments = {"x": [], "y": [], "s": [], "c": [], "marker": []}
     for agent in space.agents:
         portray = agent_portrayal(agent)
         loc = agent.pos
@@ -208,7 +224,12 @@ def collect_agent_data(space: OrthogonalGrid | HexGrid | Network | ContinuousSpa
     return {k: np.asarray(v) for k, v in arguments.items()}
 
 
-def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model):
+def draw_orthogonal_grid(
+    space: OrthogonalGrid,
+    agent_portrayal: Callable,
+    propertylayer_portrayal: Callable,
+    model,
+):
     """Visualize a orthogonal grid..
 
     Args:
@@ -226,13 +247,13 @@ def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, prope
     fig = Figure()
     ax = fig.add_subplot(111)
 
-    ax.set_xlim(-0.5, space.width-0.5)
-    ax.set_ylim(-0.5, space.height-0.5)
+    ax.set_xlim(-0.5, space.width - 0.5)
+    ax.set_ylim(-0.5, space.height - 0.5)
 
     # Draw grid lines
-    for x in np.arange(-0.5, space.width-0.5, 1):
+    for x in np.arange(-0.5, space.width - 0.5, 1):
         ax.axvline(x, color="gray", linestyle=":")
-    for y in np.arange(-0.5, space.height-0.5, 1):
+    for y in np.arange(-0.5, space.height - 0.5, 1):
         ax.axhline(y, color="gray", linestyle=":")
 
     _scatter(ax, arguments)
@@ -243,7 +264,9 @@ def draw_orthogonal_grid(space: OrthogonalGrid, agent_portrayal: Callable, prope
     return fig, ax
 
 
-def draw_hex_grid(space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model):
+def draw_hex_grid(
+    space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model
+):
     """Visualize a hex grid.
 
     Args:
@@ -271,6 +294,7 @@ def draw_hex_grid(space: HexGrid, agent_portrayal: Callable, propertylayer_portr
         draw_property_layers(ax, space, propertylayer_portrayal, model)
     return fig, ax
 
+
 def collect_agent_data_for_networks(space, agent_portrayal):
     """Collect the plotting data for all agents in the network.
 
@@ -287,6 +311,7 @@ def collect_agent_data_for_networks(space, agent_portrayal):
 
     return arguments
 
+
 def draw_network(space: Network, agent_portrayal: Callable):
     """Visualize a network space.
 
@@ -383,19 +408,18 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
 
     _scatter(ax, arguments)
 
-
     for cell in space.all_cells:
         polygon = cell.properties["polygon"]
         ax.fill(
             *zip(*polygon),
             alpha=min(1, cell.properties[space.cell_coloring_property]),
-            c="red", zorder=0
+            c="red",
+            zorder=0,
         )  # Plot filled polygon
         ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in black
     return fig, ax
 
 
-
 def _scatter(ax, arguments):
     x = arguments.pop("x")
     y = arguments.pop("y")
@@ -403,7 +427,9 @@ def _scatter(ax, arguments):
 
     for mark in np.unique(marker):
         mask = marker == mark
-        ax.scatter(x[mask], y[mask], marker=mark, **{k: v[mask] for k, v in arguments.items()})
+        ax.scatter(
+            x[mask], y[mask], marker=mark, **{k: v[mask] for k, v in arguments.items()}
+        )
 
 
 def make_plot_measure(measure: str | dict[str, str] | list[str] | tuple[str]):
diff --git a/mesa/visualization/components/util.py b/mesa/visualization/components/util.py
index 315b641affe..ae3461903b1 100644
--- a/mesa/visualization/components/util.py
+++ b/mesa/visualization/components/util.py
@@ -1,24 +1,26 @@
-from typing import Callable
+from collections.abc import Callable
 
-from mesa.space import _Grid, ContinuousSpace, _HexGrid, NetworkGrid
 from mesa.experimental.cell_space import DiscreteSpace
+from mesa.space import ContinuousSpace, NetworkGrid, _Grid, _HexGrid
 
-
-__all__ = ["get_agent_continuous",
-           "get_agents_olstyle_grid",
-           "get_agents_newstyle_grid"]
+__all__ = [
+    "get_agent_continuous",
+    "get_agents_olstyle_grid",
+    "get_agents_newstyle_grid",
+]
 
 OldStyleSpace = _Grid | ContinuousSpace | _HexGrid | NetworkGrid
 Space = OldStyleSpace | DiscreteSpace
 
+
 def get_agents_olstyle_space(space: OldStyleSpace):
     for entry in space:
         if entry:
             yield entry
 
+
 def get_agents_newstyle_space(space: DiscreteSpace):
-    for agent in space.all_cells.agents:
-        yield agent
+    yield from space.all_cells.agents
 
 
 def _get_oldstyle_agent_data(agents, agent_portrayal):
@@ -74,18 +76,17 @@ def get_agent_data(space: Space, agent_portrayal: Callable):
 
         x.append(x_i)
         y.append(y_i)
-        s.append(data.get("size", None))  # we use None here as a flag to fall back on default
+        s.append(
+            data.get("size", None)
+        )  # we use None here as a flag to fall back on default
         c.append(data.get("color", "tab:blue"))
         m.append(data.get("shape", "o"))
 
 
-
-
-
-if __name__ == '__main__':
+if __name__ == "__main__":
     from mesa import Agent, Model
+    from mesa.experimental.cell_space import CellAgent, OrthogonalMooreGrid
     from mesa.space import SingleGrid
-    from mesa.experimental.cell_space import OrthogonalMooreGrid, CellAgent
 
     model = Model()
     space = SingleGrid(10, 10, True)
@@ -97,7 +98,6 @@ def get_agent_data(space: Space, agent_portrayal: Callable):
     agents = list(get_agents_olstyle_space(space))
     assert len(agents) == 10
 
-
     model = Model()
     space = OrthogonalMooreGrid((10, 10), capacity=1, torus=True, random=model.random)
     for _ in range(10):
@@ -112,8 +112,11 @@ def get_agent_data(space: Space, agent_portrayal: Callable):
     space = ContinuousSpace(10, 10, True)
     for _ in range(10):
         agent = Agent(model)
-        pos = (agent.random.random()*space.width, agent.random.random()*space.height)
+        pos = (
+            agent.random.random() * space.width,
+            agent.random.random() * space.height,
+        )
         space.place_agent(agent, pos)
 
     agents = list(get_agents_olstyle_space(space))
-    assert len(agents) == 10
\ No newline at end of file
+    assert len(agents) == 10

From 355ab0dd182651256c18cc4c8945c1c16b3e6e18 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 11:26:46 +0100
Subject: [PATCH 07/74] Update matplotlib.py

---
 mesa/visualization/components/matplotlib.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index bba07d420bd..cf37f036d58 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -1,5 +1,7 @@
 """Matplotlib based solara components for visualization MESA spaces and plots."""
 
+
+
 import warnings
 from collections import defaultdict
 from collections.abc import Callable

From 4436072159281cb51fab033a404450fafc1831b9 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 11:27:26 +0100
Subject: [PATCH 08/74] undo space changes

this has become outdated with adding space.agents
---
 mesa/space.py | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/mesa/space.py b/mesa/space.py
index 49fb1c9b880..df501b8639c 100644
--- a/mesa/space.py
+++ b/mesa/space.py
@@ -1252,10 +1252,6 @@ def get_neighbors(
         """
         return list(self.iter_neighbors(pos, include_center, radius))
 
-    def __iter__(self) -> Iterator[GridContent]:
-        """Create an iterator returns the agents in the space"""
-        yield from self._agent_to_index
-
 
 class HexSingleGrid(_HexGrid, SingleGrid):
     """Hexagonal SingleGrid: a SingleGrid where neighbors are computed according to a hexagonal tiling of the grid.
@@ -1540,10 +1536,6 @@ def out_of_bounds(self, pos: FloatCoordinate) -> bool:
         x, y = pos
         return x < self.x_min or x >= self.x_max or y < self.y_min or y >= self.y_max
 
-    def __iter__(self) -> Iterator[GridContent]:
-        """Create an iterator returns the agents in the space"""
-        yield from self._agent_to_index
-
 
 class NetworkGrid:
     """Network Grid where each node contains zero or more agents."""
@@ -1697,8 +1689,3 @@ def iter_cell_list_contents(self, cell_list: list[int]) -> Iterator[Agent]:
             self.G.nodes[node_id]["agent"]
             for node_id in itertools.filterfalse(self.is_cell_empty, cell_list)
         )
-
-    def __iter__(self) -> Iterator[GridContent]:
-        """Create an iterator returns the agents in the space"""
-        for node_id in self.G.nodes:
-            yield self.g.nodes[node_id]["agent"]

From 022cfdcdb470014406cff7d2d4d2ba5bd71dcfbc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 27 Oct 2024 10:27:50 +0000
Subject: [PATCH 09/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index cf37f036d58..bba07d420bd 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -1,7 +1,5 @@
 """Matplotlib based solara components for visualization MESA spaces and plots."""
 
-
-
 import warnings
 from collections import defaultdict
 from collections.abc import Callable

From aad49e2efad5e13d05e14a03adc0826b99419bce Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 18:02:37 +0100
Subject: [PATCH 10/74] Delete util.py

---
 mesa/visualization/components/util.py | 122 --------------------------
 1 file changed, 122 deletions(-)
 delete mode 100644 mesa/visualization/components/util.py

diff --git a/mesa/visualization/components/util.py b/mesa/visualization/components/util.py
deleted file mode 100644
index ae3461903b1..00000000000
--- a/mesa/visualization/components/util.py
+++ /dev/null
@@ -1,122 +0,0 @@
-from collections.abc import Callable
-
-from mesa.experimental.cell_space import DiscreteSpace
-from mesa.space import ContinuousSpace, NetworkGrid, _Grid, _HexGrid
-
-__all__ = [
-    "get_agent_continuous",
-    "get_agents_olstyle_grid",
-    "get_agents_newstyle_grid",
-]
-
-OldStyleSpace = _Grid | ContinuousSpace | _HexGrid | NetworkGrid
-Space = OldStyleSpace | DiscreteSpace
-
-
-def get_agents_olstyle_space(space: OldStyleSpace):
-    for entry in space:
-        if entry:
-            yield entry
-
-
-def get_agents_newstyle_space(space: DiscreteSpace):
-    yield from space.all_cells.agents
-
-
-def _get_oldstyle_agent_data(agents, agent_portrayal):
-    """Helper function to get agent data for visualization."""
-    x, y, s, c, m = [], [], [], [], []
-    for agent in agents:
-        data = agent_portrayal(agent)
-        x.append(pos[0] + 0.5)  # Center the agent in the cell
-        y.append(pos[1] + 0.5)  # Center the agent in the cell
-        default_size = (180 / max(space.width, space.height)) ** 2
-        s.append(data.get("size", default_size))
-        c.append(data.get("color", "tab:blue"))
-        m.append(data.get("shape", "o"))
-    return {"x": x, "y": y, "s": s, "c": c, "m": m}
-
-
-# fixme:
-#  how we get the data depends on the space and I don't like it.
-#  can't we separate more cleanly the data and any post
-#  space specific refinements?
-#  or gather data depending on the space?
-# fixme:
-#  what routes do we have?
-#  network (2 options)
-#  continuous (1 option)
-#  orthogonal grids (7 options?)
-#  voronoi (1 option)
-
-
-def get_agent_data(space: Space, agent_portrayal: Callable):
-    # fixme should we cover networks here at all?
-
-    match space:
-        case _Grid():  # matches also hexgrids
-            agents = get_agents_olstyle_space(space)
-        case ContinuousSpace():
-            agents = get_agents_olstyle_space(space)
-        case NetworkGrid():
-            agents = get_agents_olstyle_space(space)
-        case DiscreteSpace():
-            agents = get_agents_newstyle_space(space)
-        case _:
-            raise NotImplementedError(f"Unknown space of type {type(space)}")
-
-    x, y, s, c, m = [], [], [], [], []
-    for agent in agents:
-        data = agent_portrayal(agent)
-
-        if isinstance(space, DiscreteSpace):
-            x_i, y_i = agent.cell.coordinate
-        else:
-            x_i, y_i = agent.pos
-
-        x.append(x_i)
-        y.append(y_i)
-        s.append(
-            data.get("size", None)
-        )  # we use None here as a flag to fall back on default
-        c.append(data.get("color", "tab:blue"))
-        m.append(data.get("shape", "o"))
-
-
-if __name__ == "__main__":
-    from mesa import Agent, Model
-    from mesa.experimental.cell_space import CellAgent, OrthogonalMooreGrid
-    from mesa.space import SingleGrid
-
-    model = Model()
-    space = SingleGrid(10, 10, True)
-    for _ in range(10):
-        agent = Agent(model)
-        pos = model.random.choice(list(space.empties))
-        space.place_agent(agent, pos)
-
-    agents = list(get_agents_olstyle_space(space))
-    assert len(agents) == 10
-
-    model = Model()
-    space = OrthogonalMooreGrid((10, 10), capacity=1, torus=True, random=model.random)
-    for _ in range(10):
-        agent = CellAgent(model)
-        cell = space.select_random_empty_cell()
-        agent.cell = cell
-
-    agents = list(get_agents_newstyle_space(space))
-    assert len(agents) == 10
-
-    model = Model()
-    space = ContinuousSpace(10, 10, True)
-    for _ in range(10):
-        agent = Agent(model)
-        pos = (
-            agent.random.random() * space.width,
-            agent.random.random() * space.height,
-        )
-        space.place_agent(agent, pos)
-
-    agents = list(get_agents_olstyle_space(space))
-    assert len(agents) == 10

From 5c2ddcbaebc6844c36a6f52ebbd41c57b340637e Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 18:03:00 +0100
Subject: [PATCH 11/74] add width and height property to voroinoi

---
 mesa/experimental/cell_space/voronoi.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/mesa/experimental/cell_space/voronoi.py b/mesa/experimental/cell_space/voronoi.py
index 2cde122cbb6..7239ff0cc72 100644
--- a/mesa/experimental/cell_space/voronoi.py
+++ b/mesa/experimental/cell_space/voronoi.py
@@ -208,6 +208,20 @@ def __init__(
         self._connect_cells()
         self._build_cell_polygons()
 
+    @property
+    def width(self):
+        x_list = [i[0] for i in self.centroids_coordinates]
+        x_max = max(x_list)
+        x_min = min(x_list)
+        return x_max - x_min
+
+    @property
+    def height(self):
+        y_list = [i[1] for i in self.centroids_coordinates]
+        y_max = max(y_list)
+        y_min = min(y_list)
+        return y_max - y_min
+
     def _connect_cells(self) -> None:
         """Connect cells to neighbors based on given centroids and using Delaunay Triangulation."""
         self.triangulation = Delaunay()

From 327b5398419f619b369329cb59c7ab2c0434ee43 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 18:03:08 +0100
Subject: [PATCH 12/74] add tests

---
 mesa/visualization/components/matplotlib.py |  13 +-
 tests/test_components_matplotlib.py         | 132 ++++++++++++++++++++
 2 files changed, 140 insertions(+), 5 deletions(-)
 create mode 100644 tests/test_components_matplotlib.py

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index bba07d420bd..d9002845be8 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -227,7 +227,7 @@ def collect_agent_data(
 def draw_orthogonal_grid(
     space: OrthogonalGrid,
     agent_portrayal: Callable,
-    propertylayer_portrayal: Callable,
+    propertylayer_portrayal: Callable | None,
     model,
 ):
     """Visualize a orthogonal grid..
@@ -283,7 +283,7 @@ def draw_hex_grid(
 
     # give all odd rows an offset in the x direction
     logical = np.mod(arguments["y"], 2) == 1
-    arguments["x"] = arguments["x"][logical] + 1
+    arguments["x"][logical] += + 1
 
     fig = Figure()
     ax = fig.add_subplot(111)
@@ -321,13 +321,16 @@ def draw_network(space: Network, agent_portrayal: Callable):
 
     Notes:
         this uses networkx.draw under the hood so agent portrayal fields should match those used there
-        i.e., node_side, node_color, node_shape, edge_color
+        i.e., node_size and node_color.
 
 
     """
-    arguments = collect_agent_data_for_networks(agent_portrayal)
+    # FIXME this plotting is not correct. The x,y coordinates reflect the nodes in the network
+    #  not the location of the agents on those nodes
+    arguments = collect_agent_data_for_networks(space, agent_portrayal)
 
-    fig, ax = plt.subplots()
+    fig = Figure()
+    ax = fig.add_subplot(111)
     graph = space.G
     pos = nx.spring_layout(graph, seed=0)
     nx.draw(
diff --git a/tests/test_components_matplotlib.py b/tests/test_components_matplotlib.py
new file mode 100644
index 00000000000..591fa3b1d5b
--- /dev/null
+++ b/tests/test_components_matplotlib.py
@@ -0,0 +1,132 @@
+"""tests for matplotlib components."""
+
+from mesa import Agent, Model
+from mesa.experimental.cell_space import (
+    CellAgent,
+    HexGrid,
+    OrthogonalMooreGrid,
+    VoronoiGrid,
+    Network
+)
+from mesa.space import ContinuousSpace, HexSingleGrid, SingleGrid, NetworkGrid
+from mesa.visualization.components.matplotlib import (
+    draw_continuous_space,
+    draw_hex_grid,
+    draw_orthogonal_grid,
+    draw_voroinoi_grid,
+    draw_network
+)
+
+
+def agent_portrayal(agent):
+    """Simple portrayal of an agent.
+
+    Args:
+        agent (Agent): The agent to portray
+
+    """
+    return {"s": 10,
+            "c": "tab:blue",
+            "marker": "s" if (agent.unique_id % 2) == 0 else "o"}
+def test_draw_hex_grid():
+    """Test drawing hexgrids."""
+    model = Model(seed=42)
+    grid = HexSingleGrid(10, 10, torus=True)
+    for _ in range(10):
+        agent = Agent(model)
+        grid.move_to_empty(agent)
+    draw_hex_grid(grid, agent_portrayal, None, model)
+
+
+    model = Model(seed=42)
+    grid = HexGrid((10, 10), torus=True, random=model.random, capacity=1)
+    for _ in range(10):
+        agent = CellAgent(model)
+        agent.cell = grid.select_random_empty_cell()
+
+    draw_hex_grid(grid, agent_portrayal, None, model)
+
+def test_draw_voroinoi_grid():
+    """Test drawing voroinoi grids."""
+    model = Model(seed=42)
+
+    coordinates = model.rng.random((100, 2)) * 10
+
+    grid = VoronoiGrid(coordinates.tolist(), random=model.random, capacity=1)
+    for _ in range(10):
+        agent = CellAgent(model)
+        agent.cell = grid.select_random_empty_cell()
+
+    draw_voroinoi_grid(grid, agent_portrayal)
+
+def test_draw_orthogonal_grid():
+    """Test drawing orthogonal grids."""
+    model = Model(seed=42)
+    grid = SingleGrid(10, 10, torus=True)
+    for _ in range(10):
+        agent = Agent(model)
+        grid.move_to_empty(agent)
+    draw_orthogonal_grid(grid, agent_portrayal, None, model)
+
+
+    model = Model(seed=42)
+    grid = OrthogonalMooreGrid((10, 10), torus=True, random=model.random, capacity=1)
+    for _ in range(10):
+        agent = CellAgent(model)
+        agent.cell = grid.select_random_empty_cell()
+
+    draw_orthogonal_grid(grid, agent_portrayal, None, model)
+
+def test_draw_continuous_space():
+    """Test drawing continuous space."""
+    model = Model(seed=42)
+    space = ContinuousSpace(10, 10, torus=True)
+    for _ in range(10):
+        x = model.random.random() * 10
+        y = model.random.random() * 10
+        agent = Agent(model)
+        space.place_agent(agent, (x, y))
+    draw_continuous_space(space, agent_portrayal)
+
+def test_draw_network():
+    """Test drawing network."""
+
+    def agent_portrayal(agent):
+        """Simple portrayal of an agent.
+
+        Args:
+            agent (Agent): The agent to portray
+
+        """
+        return {"node_size": 10,
+                "node_color": "tab:blue"}
+
+    import networkx as nx
+
+    n = 10
+    m = 20
+    seed = 42
+    graph = nx.gnm_random_graph(n, m, seed=seed)  # noqa: N806
+
+
+    model = Model(seed=42)
+    grid = NetworkGrid(graph)
+    for _ in range(10):
+        agent = Agent(model)
+        pos = agent.random.randint(0, len(graph.nodes)-1)
+        grid.place_agent(agent, pos)
+    draw_network(grid, agent_portrayal)
+
+
+    model = Model(seed=42)
+    grid = Network(graph, random=model.random, capacity=1)
+    for _ in range(10):
+        agent = CellAgent(model)
+        agent.cell = grid.select_random_empty_cell()
+
+    draw_network(grid, agent_portrayal)
+
+
+def test_draw_property_layers():
+    """Test drawing property layers."""
+    pass

From d8a409ab69aeab5a2975a639be3673ff03741fce Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 27 Oct 2024 17:03:16 +0000
Subject: [PATCH 13/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py |  2 +-
 tests/test_components_matplotlib.py         | 32 +++++++++++----------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index d9002845be8..83b5d4ee2e8 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -283,7 +283,7 @@ def draw_hex_grid(
 
     # give all odd rows an offset in the x direction
     logical = np.mod(arguments["y"], 2) == 1
-    arguments["x"][logical] += + 1
+    arguments["x"][logical] += +1
 
     fig = Figure()
     ax = fig.add_subplot(111)
diff --git a/tests/test_components_matplotlib.py b/tests/test_components_matplotlib.py
index 591fa3b1d5b..8284e48423f 100644
--- a/tests/test_components_matplotlib.py
+++ b/tests/test_components_matplotlib.py
@@ -4,17 +4,17 @@
 from mesa.experimental.cell_space import (
     CellAgent,
     HexGrid,
+    Network,
     OrthogonalMooreGrid,
     VoronoiGrid,
-    Network
 )
-from mesa.space import ContinuousSpace, HexSingleGrid, SingleGrid, NetworkGrid
+from mesa.space import ContinuousSpace, HexSingleGrid, NetworkGrid, SingleGrid
 from mesa.visualization.components.matplotlib import (
     draw_continuous_space,
     draw_hex_grid,
+    draw_network,
     draw_orthogonal_grid,
     draw_voroinoi_grid,
-    draw_network
 )
 
 
@@ -25,9 +25,13 @@ def agent_portrayal(agent):
         agent (Agent): The agent to portray
 
     """
-    return {"s": 10,
-            "c": "tab:blue",
-            "marker": "s" if (agent.unique_id % 2) == 0 else "o"}
+    return {
+        "s": 10,
+        "c": "tab:blue",
+        "marker": "s" if (agent.unique_id % 2) == 0 else "o",
+    }
+
+
 def test_draw_hex_grid():
     """Test drawing hexgrids."""
     model = Model(seed=42)
@@ -37,7 +41,6 @@ def test_draw_hex_grid():
         grid.move_to_empty(agent)
     draw_hex_grid(grid, agent_portrayal, None, model)
 
-
     model = Model(seed=42)
     grid = HexGrid((10, 10), torus=True, random=model.random, capacity=1)
     for _ in range(10):
@@ -46,6 +49,7 @@ def test_draw_hex_grid():
 
     draw_hex_grid(grid, agent_portrayal, None, model)
 
+
 def test_draw_voroinoi_grid():
     """Test drawing voroinoi grids."""
     model = Model(seed=42)
@@ -59,6 +63,7 @@ def test_draw_voroinoi_grid():
 
     draw_voroinoi_grid(grid, agent_portrayal)
 
+
 def test_draw_orthogonal_grid():
     """Test drawing orthogonal grids."""
     model = Model(seed=42)
@@ -68,7 +73,6 @@ def test_draw_orthogonal_grid():
         grid.move_to_empty(agent)
     draw_orthogonal_grid(grid, agent_portrayal, None, model)
 
-
     model = Model(seed=42)
     grid = OrthogonalMooreGrid((10, 10), torus=True, random=model.random, capacity=1)
     for _ in range(10):
@@ -77,6 +81,7 @@ def test_draw_orthogonal_grid():
 
     draw_orthogonal_grid(grid, agent_portrayal, None, model)
 
+
 def test_draw_continuous_space():
     """Test drawing continuous space."""
     model = Model(seed=42)
@@ -88,6 +93,7 @@ def test_draw_continuous_space():
         space.place_agent(agent, (x, y))
     draw_continuous_space(space, agent_portrayal)
 
+
 def test_draw_network():
     """Test drawing network."""
 
@@ -98,26 +104,23 @@ def agent_portrayal(agent):
             agent (Agent): The agent to portray
 
         """
-        return {"node_size": 10,
-                "node_color": "tab:blue"}
+        return {"node_size": 10, "node_color": "tab:blue"}
 
     import networkx as nx
 
     n = 10
     m = 20
     seed = 42
-    graph = nx.gnm_random_graph(n, m, seed=seed)  # noqa: N806
-
+    graph = nx.gnm_random_graph(n, m, seed=seed)
 
     model = Model(seed=42)
     grid = NetworkGrid(graph)
     for _ in range(10):
         agent = Agent(model)
-        pos = agent.random.randint(0, len(graph.nodes)-1)
+        pos = agent.random.randint(0, len(graph.nodes) - 1)
         grid.place_agent(agent, pos)
     draw_network(grid, agent_portrayal)
 
-
     model = Model(seed=42)
     grid = Network(graph, random=model.random, capacity=1)
     for _ in range(10):
@@ -129,4 +132,3 @@ def agent_portrayal(agent):
 
 def test_draw_property_layers():
     """Test drawing property layers."""
-    pass

From c3ca9d7ec6009b6284afb48f9d0ffc60b8184de2 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 27 Oct 2024 20:27:50 +0100
Subject: [PATCH 14/74] add mesh to draw_hexgrid

---
 mesa/visualization/components/matplotlib.py | 31 ++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 83b5d4ee2e8..4b6f3f7fa44 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -1,6 +1,7 @@
 """Matplotlib based solara components for visualization MESA spaces and plots."""
 
 import warnings
+import itertools
 from collections import defaultdict
 from collections.abc import Callable
 
@@ -8,6 +9,12 @@
 import networkx as nx
 import numpy as np
 import solara
+
+from matplotlib.collections import PatchCollection
+from matplotlib.patches import RegularPolygon
+import math
+
+
 from matplotlib.cm import ScalarMappable
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
 from matplotlib.figure import Figure
@@ -282,14 +289,36 @@ def draw_hex_grid(
     arguments = collect_agent_data(space, agent_portrayal)
 
     # give all odd rows an offset in the x direction
+    offset = math.sqrt(0.75)
+
     logical = np.mod(arguments["y"], 2) == 1
-    arguments["x"][logical] += +1
+    arguments["y"] = arguments["y"].astype(float) * offset
+    arguments["x"] = arguments["x"].astype(float)
+    arguments["x"][logical] += 0.5
 
     fig = Figure()
     ax = fig.add_subplot(111)
+    ax.set_xlim(-1, space.width+0.5)
+    ax.set_ylim(-offset, space.height*offset)
 
     _scatter(ax, arguments)
 
+    def setup_hexmesh(width, height, ):
+        """Helper function for creating the hexmaesh."""
+        # fixme: this should be done once, rather than in each update
+
+        patches = []
+        for x, y in itertools.product(range(width), range(height)):
+            if y % 2 == 1:
+                x += 0.5
+            y *= offset
+            hex = RegularPolygon((x, y), numVertices=6, radius=math.sqrt(1 / 3),
+                                 orientation=np.radians(120))
+            patches.append(hex)
+        mesh = PatchCollection(patches, edgecolor='k', facecolor=(1, 1, 1, 0), linestyle='dotted', lw=1)
+        return mesh
+    ax.add_collection(setup_hexmesh(space.width, space.height, ))
+
     if propertylayer_portrayal:
         draw_property_layers(ax, space, propertylayer_portrayal, model)
     return fig, ax

From 519670fb5b71fcb75e5299cd97eb900f917c73c0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 27 Oct 2024 19:28:20 +0000
Subject: [PATCH 15/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 40 +++++++++++++--------
 1 file changed, 26 insertions(+), 14 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 4b6f3f7fa44..64f0e49b205 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -1,7 +1,8 @@
 """Matplotlib based solara components for visualization MESA spaces and plots."""
 
-import warnings
 import itertools
+import math
+import warnings
 from collections import defaultdict
 from collections.abc import Callable
 
@@ -9,15 +10,11 @@
 import networkx as nx
 import numpy as np
 import solara
-
-from matplotlib.collections import PatchCollection
-from matplotlib.patches import RegularPolygon
-import math
-
-
 from matplotlib.cm import ScalarMappable
+from matplotlib.collections import PatchCollection
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
 from matplotlib.figure import Figure
+from matplotlib.patches import RegularPolygon
 
 import mesa
 from mesa.experimental.cell_space import (
@@ -298,12 +295,15 @@ def draw_hex_grid(
 
     fig = Figure()
     ax = fig.add_subplot(111)
-    ax.set_xlim(-1, space.width+0.5)
-    ax.set_ylim(-offset, space.height*offset)
+    ax.set_xlim(-1, space.width + 0.5)
+    ax.set_ylim(-offset, space.height * offset)
 
     _scatter(ax, arguments)
 
-    def setup_hexmesh(width, height, ):
+    def setup_hexmesh(
+        width,
+        height,
+    ):
         """Helper function for creating the hexmaesh."""
         # fixme: this should be done once, rather than in each update
 
@@ -312,12 +312,24 @@ def setup_hexmesh(width, height, ):
             if y % 2 == 1:
                 x += 0.5
             y *= offset
-            hex = RegularPolygon((x, y), numVertices=6, radius=math.sqrt(1 / 3),
-                                 orientation=np.radians(120))
+            hex = RegularPolygon(
+                (x, y),
+                numVertices=6,
+                radius=math.sqrt(1 / 3),
+                orientation=np.radians(120),
+            )
             patches.append(hex)
-        mesh = PatchCollection(patches, edgecolor='k', facecolor=(1, 1, 1, 0), linestyle='dotted', lw=1)
+        mesh = PatchCollection(
+            patches, edgecolor="k", facecolor=(1, 1, 1, 0), linestyle="dotted", lw=1
+        )
         return mesh
-    ax.add_collection(setup_hexmesh(space.width, space.height, ))
+
+    ax.add_collection(
+        setup_hexmesh(
+            space.width,
+            space.height,
+        )
+    )
 
     if propertylayer_portrayal:
         draw_property_layers(ax, space, propertylayer_portrayal, model)

From 80f10bfd47f3d4370b4895c3443330466dbf8962 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 07:55:48 +0100
Subject: [PATCH 16/74] remove properties again

---
 mesa/experimental/cell_space/voronoi.py | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/mesa/experimental/cell_space/voronoi.py b/mesa/experimental/cell_space/voronoi.py
index 7239ff0cc72..01281bf8563 100644
--- a/mesa/experimental/cell_space/voronoi.py
+++ b/mesa/experimental/cell_space/voronoi.py
@@ -208,19 +208,6 @@ def __init__(
         self._connect_cells()
         self._build_cell_polygons()
 
-    @property
-    def width(self):
-        x_list = [i[0] for i in self.centroids_coordinates]
-        x_max = max(x_list)
-        x_min = min(x_list)
-        return x_max - x_min
-
-    @property
-    def height(self):
-        y_list = [i[1] for i in self.centroids_coordinates]
-        y_max = max(y_list)
-        y_min = min(y_list)
-        return y_max - y_min
 
     def _connect_cells(self) -> None:
         """Connect cells to neighbors based on given centroids and using Delaunay Triangulation."""

From a30b14296e06f80899fd28695b55d5a846d5c29e Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 07:55:55 +0100
Subject: [PATCH 17/74] ongoing work

---
 mesa/visualization/components/matplotlib.py | 138 +++++++++++---------
 1 file changed, 74 insertions(+), 64 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 64f0e49b205..344393fc472 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -10,6 +10,12 @@
 import networkx as nx
 import numpy as np
 import solara
+
+from matplotlib.collections import PatchCollection
+from matplotlib.patches import RegularPolygon
+import math
+
+
 from matplotlib.cm import ScalarMappable
 from matplotlib.collections import PatchCollection
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
@@ -49,7 +55,6 @@ def make_space_matplotlib(agent_portrayal=None, propertylayer_portrayal=None):
         function: A function that creates a SpaceMatplotlib component
     """
     if agent_portrayal is None:
-
         def agent_portrayal(a):
             return {"id": a.unique_id}
 
@@ -61,10 +66,10 @@ def MakeSpaceMatplotlib(model):
 
 @solara.component
 def SpaceMatplotlib(
-    model,
-    agent_portrayal,
-    propertylayer_portrayal,
-    dependencies: list[any] | None = None,
+        model,
+        agent_portrayal,
+        propertylayer_portrayal,
+        dependencies: list[any] | None = None,
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
@@ -191,8 +196,11 @@ def draw_property_layers(ax, space, propertylayer_portrayal, model):
 
 
 def collect_agent_data(
-    space: OrthogonalGrid | HexGrid | Network | ContinuousSpace,
-    agent_portrayal: Callable,
+        space: OrthogonalGrid | HexGrid | Network | ContinuousSpace,
+        agent_portrayal: Callable,
+        c_default="tab:blue",
+        marker_default="o",
+        s_default=25
 ):
     """Collect the plotting data for all agents in the space.
 
@@ -200,6 +208,9 @@ def collect_agent_data(
         space: The space containing the Agents.
         agent_portrayal: A callable that is called with the agent and returns a dict
         loc: a boolean indicating whether to gather agent x, y data or not
+        c_default: default color
+        marker_default: default marker
+        s_default: default size
 
     Notes:
         agent portray dict is limited to s (size of marker), c (color of marker, and marker (marker style)
@@ -209,30 +220,26 @@ def collect_agent_data(
     .. _Matplotlib: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
 
     """
-    default_size = (180 / max(space.width, space.height)) ** 2
-
-    arguments = {"x": [], "y": [], "s": [], "c": [], "marker": []}
+    arguments = {"loc": [], "s": [], "c": [], "marker": []}
     for agent in space.agents:
         portray = agent_portrayal(agent)
         loc = agent.pos
         if loc is None:
             loc = agent.cell.coordinate
-        x, y = loc
-        arguments["x"].append(x)
-        arguments["y"].append(y)
 
-        arguments["s"].append(portray.get("s", default_size))
-        arguments["c"].append(portray.get("c", "tab:blue"))
-        arguments["marker"].append(portray.get("marker", "o"))
+        arguments['loc'] = loc
+        arguments["s"].append(portray.get("s", s_default))
+        arguments["c"].append(portray.get("c", c_default))
+        arguments["marker"].append(portray.get("marker", marker_default))
 
     return {k: np.asarray(v) for k, v in arguments.items()}
 
 
 def draw_orthogonal_grid(
-    space: OrthogonalGrid,
-    agent_portrayal: Callable,
-    propertylayer_portrayal: Callable | None,
-    model,
+        space: OrthogonalGrid,
+        agent_portrayal: Callable,
+        propertylayer_portrayal: Callable | None,
+        model,
 ):
     """Visualize a orthogonal grid..
 
@@ -246,7 +253,8 @@ def draw_orthogonal_grid(
         A Figure and Axes instance
 
     """
-    arguments = collect_agent_data(space, agent_portrayal)
+    s_default = (180 / max(space.width, space.height)) ** 2
+    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
     fig = Figure()
     ax = fig.add_subplot(111)
@@ -269,7 +277,7 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-    space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model
+        space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model
 ):
     """Visualize a hex grid.
 
@@ -283,7 +291,8 @@ def draw_hex_grid(
         A Figure and Axes instance
 
     """
-    arguments = collect_agent_data(space, agent_portrayal)
+    s_default = (180 / max(space.width, space.height)) ** 2
+    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
     # give all odd rows an offset in the x direction
     offset = math.sqrt(0.75)
@@ -306,6 +315,7 @@ def setup_hexmesh(
     ):
         """Helper function for creating the hexmaesh."""
         # fixme: this should be done once, rather than in each update
+        # fixme check coordinate system in hexgrid (see https://www.redblobgames.com/grids/hexagons/#coordinates-offset)
 
         patches = []
         for x, y in itertools.product(range(width), range(height)):
@@ -336,23 +346,6 @@ def setup_hexmesh(
     return fig, ax
 
 
-def collect_agent_data_for_networks(space, agent_portrayal):
-    """Collect the plotting data for all agents in the network.
-
-    Args:
-        space: the space to visualize
-        agent_portrayal: a callable that is called with the agent and returns a dict
-
-    """
-    arguments = defaultdict(list)
-    for agent in space.agents:
-        portray = agent_portrayal(agent)
-        for k, v in portray.items():
-            arguments[k].append(v)
-
-    return arguments
-
-
 def draw_network(space: Network, agent_portrayal: Callable):
     """Visualize a network space.
 
@@ -366,20 +359,32 @@ def draw_network(space: Network, agent_portrayal: Callable):
 
 
     """
-    # FIXME this plotting is not correct. The x,y coordinates reflect the nodes in the network
-    #  not the location of the agents on those nodes
-    arguments = collect_agent_data_for_networks(space, agent_portrayal)
+    graph = space.G
+    pos = nx.spring_layout(graph, seed=0)
+    x, y = list(zip(*pos.values()))
+    xmin, xmax = min(x), max(x)
+    ymin, ymax = min(y), max(y)
+
+    width = xmax - xmin
+    height = ymax - ymin
+
+    s_default = (180 / max(width, height)) ** 2
+    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
+
+
+    # fixme check if this code works
+    #  it won't work in the current format because pos is a dict
+    arguments['loc'] = pos[arguments['loc']]
 
     fig = Figure()
     ax = fig.add_subplot(111)
-    graph = space.G
-    pos = nx.spring_layout(graph, seed=0)
-    nx.draw(
-        graph,
-        ax=ax,
-        pos=pos,
-        **arguments,
-    )
+    ax.set_axis_off()
+    ax.set_xlim(xmin=xmin, xmax=xmax)
+    ax.set_ylim(ymin=ymin, ymax=ymax)
+
+    _scatter(ax, arguments)
+
+    nx.draw_networkx_edges(graph, pos, ax=ax)
 
     return fig, ax
 
@@ -395,7 +400,13 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
         A Figure and Axes instance
 
     """
-    arguments = collect_agent_data(space, agent_portrayal)
+    width = space.x_max - space.x_min
+    x_padding = width / 20
+    height = space.y_max - space.y_min
+    y_padding = height / 20
+
+    s_default = (180 / max(width, height)) ** 2
+    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
     fig = Figure()
     ax = fig.add_subplot(111)
@@ -408,11 +419,6 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
         spine.set_color("black")
         spine.set_linestyle(border_style)
 
-    width = space.x_max - space.x_min
-    x_padding = width / 20
-    height = space.y_max - space.y_min
-    y_padding = height / 20
-
     ax.set_xlim(space.x_min - x_padding, space.x_max + x_padding)
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
@@ -431,11 +437,6 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
         A Figure and Axes instance
 
     """
-    arguments = collect_agent_data(space, agent_portrayal)
-
-    fig = Figure()
-    ax = fig.add_subplot(111)
-
     x_list = [i[0] for i in space.centroids_coordinates]
     y_list = [i[1] for i in space.centroids_coordinates]
     x_max = max(x_list)
@@ -447,6 +448,13 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
     x_padding = width / 20
     height = y_max - y_min
     y_padding = height / 20
+
+    s_default = (180 / max(width, height)) ** 2
+    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
+
+    fig = Figure()
+    ax = fig.add_subplot(111)
+
     ax.set_xlim(x_min - x_padding, x_max + x_padding)
     ax.set_ylim(y_min - y_padding, y_max + y_padding)
 
@@ -465,8 +473,10 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
 
 
 def _scatter(ax, arguments):
-    x = arguments.pop("x")
-    y = arguments.pop("y")
+    loc = arguments.pop['loc']
+
+    x = loc[:, 0]
+    y = loc[:, 1]
     marker = arguments.pop("marker")
 
     for mark in np.unique(marker):

From f54f52b621ee4339901137673482927605b3d832 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 06:56:51 +0000
Subject: [PATCH 18/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/cell_space/voronoi.py     |  1 -
 mesa/visualization/components/matplotlib.py | 43 +++++++++------------
 2 files changed, 18 insertions(+), 26 deletions(-)

diff --git a/mesa/experimental/cell_space/voronoi.py b/mesa/experimental/cell_space/voronoi.py
index 01281bf8563..2cde122cbb6 100644
--- a/mesa/experimental/cell_space/voronoi.py
+++ b/mesa/experimental/cell_space/voronoi.py
@@ -208,7 +208,6 @@ def __init__(
         self._connect_cells()
         self._build_cell_polygons()
 
-
     def _connect_cells(self) -> None:
         """Connect cells to neighbors based on given centroids and using Delaunay Triangulation."""
         self.triangulation = Delaunay()
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 344393fc472..10fde0a1e2e 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -3,19 +3,12 @@
 import itertools
 import math
 import warnings
-from collections import defaultdict
 from collections.abc import Callable
 
 import matplotlib.pyplot as plt
 import networkx as nx
 import numpy as np
 import solara
-
-from matplotlib.collections import PatchCollection
-from matplotlib.patches import RegularPolygon
-import math
-
-
 from matplotlib.cm import ScalarMappable
 from matplotlib.collections import PatchCollection
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
@@ -55,6 +48,7 @@ def make_space_matplotlib(agent_portrayal=None, propertylayer_portrayal=None):
         function: A function that creates a SpaceMatplotlib component
     """
     if agent_portrayal is None:
+
         def agent_portrayal(a):
             return {"id": a.unique_id}
 
@@ -66,10 +60,10 @@ def MakeSpaceMatplotlib(model):
 
 @solara.component
 def SpaceMatplotlib(
-        model,
-        agent_portrayal,
-        propertylayer_portrayal,
-        dependencies: list[any] | None = None,
+    model,
+    agent_portrayal,
+    propertylayer_portrayal,
+    dependencies: list[any] | None = None,
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
@@ -196,11 +190,11 @@ def draw_property_layers(ax, space, propertylayer_portrayal, model):
 
 
 def collect_agent_data(
-        space: OrthogonalGrid | HexGrid | Network | ContinuousSpace,
-        agent_portrayal: Callable,
-        c_default="tab:blue",
-        marker_default="o",
-        s_default=25
+    space: OrthogonalGrid | HexGrid | Network | ContinuousSpace,
+    agent_portrayal: Callable,
+    c_default="tab:blue",
+    marker_default="o",
+    s_default=25,
 ):
     """Collect the plotting data for all agents in the space.
 
@@ -227,7 +221,7 @@ def collect_agent_data(
         if loc is None:
             loc = agent.cell.coordinate
 
-        arguments['loc'] = loc
+        arguments["loc"] = loc
         arguments["s"].append(portray.get("s", s_default))
         arguments["c"].append(portray.get("c", c_default))
         arguments["marker"].append(portray.get("marker", marker_default))
@@ -236,10 +230,10 @@ def collect_agent_data(
 
 
 def draw_orthogonal_grid(
-        space: OrthogonalGrid,
-        agent_portrayal: Callable,
-        propertylayer_portrayal: Callable | None,
-        model,
+    space: OrthogonalGrid,
+    agent_portrayal: Callable,
+    propertylayer_portrayal: Callable | None,
+    model,
 ):
     """Visualize a orthogonal grid..
 
@@ -277,7 +271,7 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-        space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model
+    space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model
 ):
     """Visualize a hex grid.
 
@@ -371,10 +365,9 @@ def draw_network(space: Network, agent_portrayal: Callable):
     s_default = (180 / max(width, height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-
     # fixme check if this code works
     #  it won't work in the current format because pos is a dict
-    arguments['loc'] = pos[arguments['loc']]
+    arguments["loc"] = pos[arguments["loc"]]
 
     fig = Figure()
     ax = fig.add_subplot(111)
@@ -473,7 +466,7 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
 
 
 def _scatter(ax, arguments):
-    loc = arguments.pop['loc']
+    loc = arguments.pop["loc"]
 
     x = loc[:, 0]
     y = loc[:, 1]

From 295b819e01f1a35dcae1f89f2fccf90dc4fa5b8c Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 08:12:14 +0100
Subject: [PATCH 19/74] ruff fix and update to plot

---
 mesa/visualization/components/matplotlib.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 10fde0a1e2e..efd20edeb1d 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -289,6 +289,8 @@ def draw_hex_grid(
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
     # give all odd rows an offset in the x direction
+    # give all rows an offset in the y direction
+    # numbers here are based on a distance of 1 between centers of hexes
     offset = math.sqrt(0.75)
 
     logical = np.mod(arguments["y"], 2) == 1
@@ -314,8 +316,8 @@ def setup_hexmesh(
         patches = []
         for x, y in itertools.product(range(width), range(height)):
             if y % 2 == 1:
-                x += 0.5
-            y *= offset
+                x += 0.5  # noqa: PLW2901
+            y *= offset    # noqa: PLW2901
             hex = RegularPolygon(
                 (x, y),
                 numVertices=6,
@@ -466,7 +468,7 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
 
 
 def _scatter(ax, arguments):
-    loc = arguments.pop["loc"]
+    loc = arguments.pop("loc")
 
     x = loc[:, 0]
     y = loc[:, 1]

From b9ecc228790bfdb1eca5e2ddfe87f83c031516d7 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 07:12:30 +0000
Subject: [PATCH 20/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index efd20edeb1d..cb2a68fc5e0 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -317,7 +317,7 @@ def setup_hexmesh(
         for x, y in itertools.product(range(width), range(height)):
             if y % 2 == 1:
                 x += 0.5  # noqa: PLW2901
-            y *= offset    # noqa: PLW2901
+            y *= offset  # noqa: PLW2901
             hex = RegularPolygon(
                 (x, y),
                 numVertices=6,

From 101aad66204927283684dbc3ab64e5c9310da98f Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 08:38:28 +0100
Subject: [PATCH 21/74] make tests work again

only network still needs fixing
---
 mesa/visualization/components/matplotlib.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index cb2a68fc5e0..e1e978660e5 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -221,7 +221,7 @@ def collect_agent_data(
         if loc is None:
             loc = agent.cell.coordinate
 
-        arguments["loc"] = loc
+        arguments["loc"].append(loc)
         arguments["s"].append(portray.get("s", s_default))
         arguments["c"].append(portray.get("c", c_default))
         arguments["marker"].append(portray.get("marker", marker_default))
@@ -293,10 +293,11 @@ def draw_hex_grid(
     # numbers here are based on a distance of 1 between centers of hexes
     offset = math.sqrt(0.75)
 
-    logical = np.mod(arguments["y"], 2) == 1
-    arguments["y"] = arguments["y"].astype(float) * offset
-    arguments["x"] = arguments["x"].astype(float)
-    arguments["x"][logical] += 0.5
+    loc = arguments['loc'].astype(float)
+
+    logical = np.mod(loc[:, 1], 2) == 1
+    loc[:, 1] *= offset
+    loc[:, 0][logical] += 0.5
 
     fig = Figure()
     ax = fig.add_subplot(111)

From 9477f66654d5ac0e5d723cc1443528c5d3cd8b86 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 07:38:49 +0000
Subject: [PATCH 22/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index e1e978660e5..aac1d2f6314 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -293,7 +293,7 @@ def draw_hex_grid(
     # numbers here are based on a distance of 1 between centers of hexes
     offset = math.sqrt(0.75)
 
-    loc = arguments['loc'].astype(float)
+    loc = arguments["loc"].astype(float)
 
     logical = np.mod(loc[:, 1], 2) == 1
     loc[:, 1] *= offset

From 9904d256ea8b986d325b2ac61735bba7c16fd57f Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 09:01:28 +0100
Subject: [PATCH 23/74] fix networks

---
 mesa/visualization/components/matplotlib.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index aac1d2f6314..10577be8436 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -368,8 +368,9 @@ def draw_network(space: Network, agent_portrayal: Callable):
     s_default = (180 / max(width, height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-    # fixme check if this code works
-    #  it won't work in the current format because pos is a dict
+    # this assumes that nodes are identified by an integer
+    # which is true for default nx graphs but might user changeable
+    pos = np.asarray(list(pos.values()))
     arguments["loc"] = pos[arguments["loc"]]
 
     fig = Figure()

From 15fa02a9a38294cb3d823714b775793f51e08389 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 09:10:35 +0100
Subject: [PATCH 24/74] correctly update x,y for hexgrids

---
 mesa/visualization/components/matplotlib.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 10577be8436..e9ca7ecf826 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -293,11 +293,19 @@ def draw_hex_grid(
     # numbers here are based on a distance of 1 between centers of hexes
     offset = math.sqrt(0.75)
 
+
+    # logical = np.mod(arguments["y"], 2) == 1
+    # arguments["y"] = arguments["y"].astype(float) * offset
+    # arguments["x"] = arguments["x"].astype(float)
+    # arguments["x"][logical] += 0.5
+
     loc = arguments["loc"].astype(float)
 
     logical = np.mod(loc[:, 1], 2) == 1
-    loc[:, 1] *= offset
     loc[:, 0][logical] += 0.5
+    loc[:, 1] *= offset
+    arguments["loc"] = loc
+
 
     fig = Figure()
     ax = fig.add_subplot(111)

From dbeb9224f575ac4f96dbe8bb127eaab1a3fba3bc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 08:10:51 +0000
Subject: [PATCH 25/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index e9ca7ecf826..d6003c0ff43 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -293,7 +293,6 @@ def draw_hex_grid(
     # numbers here are based on a distance of 1 between centers of hexes
     offset = math.sqrt(0.75)
 
-
     # logical = np.mod(arguments["y"], 2) == 1
     # arguments["y"] = arguments["y"].astype(float) * offset
     # arguments["x"] = arguments["x"].astype(float)
@@ -306,7 +305,6 @@ def draw_hex_grid(
     loc[:, 1] *= offset
     arguments["loc"] = loc
 
-
     fig = Figure()
     ax = fig.add_subplot(111)
     ax.set_xlim(-1, space.width + 0.5)

From 669aa0bfaffd6ded5601d43567fe87e0e082102a Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 12:12:53 +0100
Subject: [PATCH 26/74] correction for how hexgrids are wired

---
 mesa/visualization/components/matplotlib.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index d6003c0ff43..cf092fc4e11 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -300,7 +300,7 @@ def draw_hex_grid(
 
     loc = arguments["loc"].astype(float)
 
-    logical = np.mod(loc[:, 1], 2) == 1
+    logical = np.mod(loc[:, 1], 2) == 0
     loc[:, 0][logical] += 0.5
     loc[:, 1] *= offset
     arguments["loc"] = loc
@@ -322,7 +322,7 @@ def setup_hexmesh(
 
         patches = []
         for x, y in itertools.product(range(width), range(height)):
-            if y % 2 == 1:
+            if y % 2 == 0:
                 x += 0.5  # noqa: PLW2901
             y *= offset  # noqa: PLW2901
             hex = RegularPolygon(

From 1bbe3795ac4dbd4a60b95b19961a9b9b70773072 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 15:44:40 +0100
Subject: [PATCH 27/74] simplification of case match structure

---
 mesa/visualization/components/matplotlib.py | 82 +++++++--------------
 1 file changed, 26 insertions(+), 56 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index cf092fc4e11..72920d0e077 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -72,52 +72,35 @@ def SpaceMatplotlib(
     if space is None:
         space = getattr(model, "space", None)
 
+    fig = Figure()
+    ax = fig.subplots(111)
+
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:
-        case mesa.space._Grid():
-            fig, ax = draw_orthogonal_grid(
-                space, agent_portrayal, propertylayer_portrayal, model
-            )
-        case OrthogonalMooreGrid():
-            fig, ax = draw_orthogonal_grid(
-                space, agent_portrayal, propertylayer_portrayal, model
-            )
-        case OrthogonalVonNeumannGrid():
-            fig, ax = draw_orthogonal_grid(
-                space, agent_portrayal, propertylayer_portrayal, model
-            )
-        case HexSingleGrid():
-            fig, ax = draw_hex_grid(
-                space, agent_portrayal, propertylayer_portrayal, model
+        case mesa.space._Grid() | OrthogonalMooreGrid() | OrthogonalVonNeumannGrid():
+            draw_orthogonal_grid(
+                space, agent_portrayal, propertylayer_portrayal, model, ax
             )
-        case HexSingleGrid():
-            fig, ax = draw_hex_grid(
-                space, agent_portrayal, propertylayer_portrayal, model
-            )
-        case mesa.experimental.cell_space.HexGrid():
-            fig, ax = draw_hex_grid(
-                space, agent_portrayal, propertylayer_portrayal, model
+        case HexSingleGrid() | HexSingleGrid() | mesa.experimental.cell_space.HexGrid():
+            draw_hex_grid(
+                space, agent_portrayal, propertylayer_portrayal, model, ax
             )
+        case mesa.space.NetworkGrid() | mesa.experimental.cell_space.Network():
+            draw_network(space, agent_portrayal, ax)
         case mesa.space.ContinuousSpace():
-            fig, ax = draw_continuous_space(space, agent_portrayal)
-        case mesa.space.NetworkGrid():
-            fig, ax = draw_network(space, agent_portrayal)
+            draw_continuous_space(space, agent_portrayal, ax)
         case VoronoiGrid():
-            fig, ax = draw_voroinoi_grid(space, agent_portrayal)
-        case mesa.experimental.cell_space.Network():
-            fig, ax = draw_network(space, agent_portrayal)
+            draw_voroinoi_grid(space, agent_portrayal, ax)
         case None:
-            fig = Figure()
-            ax = fig.subplots(111)
             if propertylayer_portrayal:
-                draw_property_layers(ax, space, propertylayer_portrayal, model)
+                draw_property_layers(space, propertylayer_portrayal, model, ax)
 
     solara.FigureMatplotlib(
         fig, format="png", bbox_inches="tight", dependencies=dependencies
     )
 
 
-def draw_property_layers(ax, space, propertylayer_portrayal, model):
+def draw_property_layers(space, propertylayer_portrayal, model, ax):
     """Draw PropertyLayers on the given axes.
 
     Args:
@@ -234,14 +217,16 @@ def draw_orthogonal_grid(
     agent_portrayal: Callable,
     propertylayer_portrayal: Callable | None,
     model,
+    ax
 ):
-    """Visualize a orthogonal grid..
+    """Visualize a orthogonal grid.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
         propertylayer_portrayal: a callable that is called with the agent and returns a dict
         model: a model instance
+        ax: a Matplotlib Axes instance
 
     Returns:
         A Figure and Axes instance
@@ -250,9 +235,6 @@ def draw_orthogonal_grid(
     s_default = (180 / max(space.width, space.height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-    fig = Figure()
-    ax = fig.add_subplot(111)
-
     ax.set_xlim(-0.5, space.width - 0.5)
     ax.set_ylim(-0.5, space.height - 0.5)
 
@@ -267,11 +249,9 @@ def draw_orthogonal_grid(
     if propertylayer_portrayal:
         draw_property_layers(ax, space, propertylayer_portrayal, model)
 
-    return fig, ax
-
 
 def draw_hex_grid(
-    space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model
+    space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model, ax
 ):
     """Visualize a hex grid.
 
@@ -280,6 +260,7 @@ def draw_hex_grid(
         agent_portrayal: a callable that is called with the agent and returns a dict
         propertylayer_portrayal: a callable that is called with the agent and returns a dict
         model: a model instance
+        ax: a Matplotlib Axes instance
 
     Returns:
         A Figure and Axes instance
@@ -305,8 +286,6 @@ def draw_hex_grid(
     loc[:, 1] *= offset
     arguments["loc"] = loc
 
-    fig = Figure()
-    ax = fig.add_subplot(111)
     ax.set_xlim(-1, space.width + 0.5)
     ax.set_ylim(-offset, space.height * offset)
 
@@ -346,15 +325,15 @@ def setup_hexmesh(
 
     if propertylayer_portrayal:
         draw_property_layers(ax, space, propertylayer_portrayal, model)
-    return fig, ax
 
 
-def draw_network(space: Network, agent_portrayal: Callable):
+def draw_network(space: Network, agent_portrayal: Callable, ax):
     """Visualize a network space.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
+        ax: a Matplotlib Axes instance
 
     Notes:
         this uses networkx.draw under the hood so agent portrayal fields should match those used there
@@ -379,25 +358,22 @@ def draw_network(space: Network, agent_portrayal: Callable):
     pos = np.asarray(list(pos.values()))
     arguments["loc"] = pos[arguments["loc"]]
 
-    fig = Figure()
     ax = fig.add_subplot(111)
     ax.set_axis_off()
     ax.set_xlim(xmin=xmin, xmax=xmax)
     ax.set_ylim(ymin=ymin, ymax=ymax)
 
     _scatter(ax, arguments)
-
     nx.draw_networkx_edges(graph, pos, ax=ax)
 
-    return fig, ax
-
 
-def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
+def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax):
     """Visualize a continuous space.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
+        ax: a Matplotlib Axes instance
 
     Returns:
         A Figure and Axes instance
@@ -411,8 +387,6 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
     s_default = (180 / max(width, height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-    fig = Figure()
-    ax = fig.add_subplot(111)
 
     border_style = "solid" if not space.torus else (0, (5, 10))
 
@@ -426,15 +400,15 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable):
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
     _scatter(ax, arguments)
-    return fig, ax
 
 
-def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
+def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax):
     """Visualize a voronoi grid.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
+        ax: a Matplotlib Axes instance
 
     Returns:
         A Figure and Axes instance
@@ -455,9 +429,6 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
     s_default = (180 / max(width, height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-    fig = Figure()
-    ax = fig.add_subplot(111)
-
     ax.set_xlim(x_min - x_padding, x_max + x_padding)
     ax.set_ylim(y_min - y_padding, y_max + y_padding)
 
@@ -472,7 +443,6 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable):
             zorder=0,
         )  # Plot filled polygon
         ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in black
-    return fig, ax
 
 
 def _scatter(ax, arguments):

From fc63cf4cd8909b95048fb9a91efd939deef76537 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 15:44:59 +0100
Subject: [PATCH 28/74] update to tests because draw functions take an axes
 instance as argument

---
 tests/test_components_matplotlib.py | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/tests/test_components_matplotlib.py b/tests/test_components_matplotlib.py
index 8284e48423f..d630f59812c 100644
--- a/tests/test_components_matplotlib.py
+++ b/tests/test_components_matplotlib.py
@@ -16,6 +16,7 @@
     draw_orthogonal_grid,
     draw_voroinoi_grid,
 )
+import matplotlib.pyplot as plt
 
 
 def agent_portrayal(agent):
@@ -39,7 +40,9 @@ def test_draw_hex_grid():
     for _ in range(10):
         agent = Agent(model)
         grid.move_to_empty(agent)
-    draw_hex_grid(grid, agent_portrayal, None, model)
+
+    fig, ax = plt.subplots()
+    draw_hex_grid(grid, agent_portrayal, None, model, ax)
 
     model = Model(seed=42)
     grid = HexGrid((10, 10), torus=True, random=model.random, capacity=1)
@@ -47,7 +50,8 @@ def test_draw_hex_grid():
         agent = CellAgent(model)
         agent.cell = grid.select_random_empty_cell()
 
-    draw_hex_grid(grid, agent_portrayal, None, model)
+    fig, ax = plt.subplots()
+    draw_hex_grid(grid, agent_portrayal, None, model, ax)
 
 
 def test_draw_voroinoi_grid():
@@ -61,7 +65,8 @@ def test_draw_voroinoi_grid():
         agent = CellAgent(model)
         agent.cell = grid.select_random_empty_cell()
 
-    draw_voroinoi_grid(grid, agent_portrayal)
+    fig, ax = plt.subplots()
+    draw_voroinoi_grid(grid, agent_portrayal, ax)
 
 
 def test_draw_orthogonal_grid():
@@ -71,7 +76,9 @@ def test_draw_orthogonal_grid():
     for _ in range(10):
         agent = Agent(model)
         grid.move_to_empty(agent)
-    draw_orthogonal_grid(grid, agent_portrayal, None, model)
+
+    fig, ax = plt.subplots()
+    draw_orthogonal_grid(grid, agent_portrayal, None, model, ax)
 
     model = Model(seed=42)
     grid = OrthogonalMooreGrid((10, 10), torus=True, random=model.random, capacity=1)
@@ -79,7 +86,8 @@ def test_draw_orthogonal_grid():
         agent = CellAgent(model)
         agent.cell = grid.select_random_empty_cell()
 
-    draw_orthogonal_grid(grid, agent_portrayal, None, model)
+    fig, ax = plt.subplots()
+    draw_orthogonal_grid(grid, agent_portrayal, None, model, ax)
 
 
 def test_draw_continuous_space():
@@ -91,7 +99,9 @@ def test_draw_continuous_space():
         y = model.random.random() * 10
         agent = Agent(model)
         space.place_agent(agent, (x, y))
-    draw_continuous_space(space, agent_portrayal)
+
+    fig, ax = plt.subplots()
+    draw_continuous_space(space, agent_portrayal, ax)
 
 
 def test_draw_network():
@@ -119,7 +129,9 @@ def agent_portrayal(agent):
         agent = Agent(model)
         pos = agent.random.randint(0, len(graph.nodes) - 1)
         grid.place_agent(agent, pos)
-    draw_network(grid, agent_portrayal)
+
+    fig, ax = plt.subplots()
+    draw_network(grid, agent_portrayal, ax)
 
     model = Model(seed=42)
     grid = Network(graph, random=model.random, capacity=1)
@@ -127,7 +139,8 @@ def agent_portrayal(agent):
         agent = CellAgent(model)
         agent.cell = grid.select_random_empty_cell()
 
-    draw_network(grid, agent_portrayal)
+    fig, ax = plt.subplots()
+    draw_network(grid, agent_portrayal, ax)
 
 
 def test_draw_property_layers():

From 8a558167e02afea32afacf172c19042f75c30d62 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 14:45:10 +0000
Subject: [PATCH 29/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 13 +++++++------
 tests/test_components_matplotlib.py         |  3 ++-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 72920d0e077..3e2e074840c 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -82,9 +82,7 @@ def SpaceMatplotlib(
                 space, agent_portrayal, propertylayer_portrayal, model, ax
             )
         case HexSingleGrid() | HexSingleGrid() | mesa.experimental.cell_space.HexGrid():
-            draw_hex_grid(
-                space, agent_portrayal, propertylayer_portrayal, model, ax
-            )
+            draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model, ax)
         case mesa.space.NetworkGrid() | mesa.experimental.cell_space.Network():
             draw_network(space, agent_portrayal, ax)
         case mesa.space.ContinuousSpace():
@@ -217,7 +215,7 @@ def draw_orthogonal_grid(
     agent_portrayal: Callable,
     propertylayer_portrayal: Callable | None,
     model,
-    ax
+    ax,
 ):
     """Visualize a orthogonal grid.
 
@@ -251,7 +249,11 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-    space: HexGrid, agent_portrayal: Callable, propertylayer_portrayal: Callable, model, ax
+    space: HexGrid,
+    agent_portrayal: Callable,
+    propertylayer_portrayal: Callable,
+    model,
+    ax,
 ):
     """Visualize a hex grid.
 
@@ -387,7 +389,6 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax)
     s_default = (180 / max(width, height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-
     border_style = "solid" if not space.torus else (0, (5, 10))
 
     # Set the border of the plot
diff --git a/tests/test_components_matplotlib.py b/tests/test_components_matplotlib.py
index d630f59812c..1b45d95e5a2 100644
--- a/tests/test_components_matplotlib.py
+++ b/tests/test_components_matplotlib.py
@@ -1,5 +1,7 @@
 """tests for matplotlib components."""
 
+import matplotlib.pyplot as plt
+
 from mesa import Agent, Model
 from mesa.experimental.cell_space import (
     CellAgent,
@@ -16,7 +18,6 @@
     draw_orthogonal_grid,
     draw_voroinoi_grid,
 )
-import matplotlib.pyplot as plt
 
 
 def agent_portrayal(agent):

From 84954fd655001009d7766e36dbb67aced0fc1fcf Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 15:46:03 +0100
Subject: [PATCH 30/74] fix for failing tests

---
 mesa/visualization/components/matplotlib.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 3e2e074840c..f6439d601c7 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -360,7 +360,6 @@ def draw_network(space: Network, agent_portrayal: Callable, ax):
     pos = np.asarray(list(pos.values()))
     arguments["loc"] = pos[arguments["loc"]]
 
-    ax = fig.add_subplot(111)
     ax.set_axis_off()
     ax.set_xlim(xmin=xmin, xmax=xmax)
     ax.set_ylim(ymin=ymin, ymax=ymax)

From 24e3154e0f79bf1e327b6154c51e9b3899578a7d Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 15:55:26 +0100
Subject: [PATCH 31/74] move propertlayer drawing out of specific draw_x
 functions

---
 mesa/visualization/components/matplotlib.py | 26 +++++++--------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index f6439d601c7..b984be13e14 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -9,6 +9,7 @@
 import networkx as nx
 import numpy as np
 import solara
+
 from matplotlib.cm import ScalarMappable
 from matplotlib.collections import PatchCollection
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
@@ -30,6 +31,7 @@
     PropertyLayer,
     SingleGrid,
 )
+from mesa import Model
 from mesa.visualization.utils import update_counter
 
 OrthogonalGrid = SingleGrid | MultiGrid | OrthogonalMooreGrid | OrthogonalVonNeumannGrid
@@ -79,19 +81,19 @@ def SpaceMatplotlib(
     match space:
         case mesa.space._Grid() | OrthogonalMooreGrid() | OrthogonalVonNeumannGrid():
             draw_orthogonal_grid(
-                space, agent_portrayal, propertylayer_portrayal, model, ax
+                space, agent_portrayal, ax
             )
-        case HexSingleGrid() | HexSingleGrid() | mesa.experimental.cell_space.HexGrid():
-            draw_hex_grid(space, agent_portrayal, propertylayer_portrayal, model, ax)
+        case HexSingleGrid() | HexMultiGrid() | mesa.experimental.cell_space.HexGrid():
+            draw_hex_grid(space, agent_portrayal, ax)
         case mesa.space.NetworkGrid() | mesa.experimental.cell_space.Network():
             draw_network(space, agent_portrayal, ax)
         case mesa.space.ContinuousSpace():
             draw_continuous_space(space, agent_portrayal, ax)
         case VoronoiGrid():
             draw_voroinoi_grid(space, agent_portrayal, ax)
-        case None:
-            if propertylayer_portrayal:
-                draw_property_layers(space, propertylayer_portrayal, model, ax)
+
+    if propertylayer_portrayal:
+        draw_property_layers(space, propertylayer_portrayal, model, ax)
 
     solara.FigureMatplotlib(
         fig, format="png", bbox_inches="tight", dependencies=dependencies
@@ -213,8 +215,6 @@ def collect_agent_data(
 def draw_orthogonal_grid(
     space: OrthogonalGrid,
     agent_portrayal: Callable,
-    propertylayer_portrayal: Callable | None,
-    model,
     ax,
 ):
     """Visualize a orthogonal grid.
@@ -222,8 +222,6 @@ def draw_orthogonal_grid(
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
-        propertylayer_portrayal: a callable that is called with the agent and returns a dict
-        model: a model instance
         ax: a Matplotlib Axes instance
 
     Returns:
@@ -244,15 +242,10 @@ def draw_orthogonal_grid(
 
     _scatter(ax, arguments)
 
-    if propertylayer_portrayal:
-        draw_property_layers(ax, space, propertylayer_portrayal, model)
-
 
 def draw_hex_grid(
     space: HexGrid,
     agent_portrayal: Callable,
-    propertylayer_portrayal: Callable,
-    model,
     ax,
 ):
     """Visualize a hex grid.
@@ -325,9 +318,6 @@ def setup_hexmesh(
         )
     )
 
-    if propertylayer_portrayal:
-        draw_property_layers(ax, space, propertylayer_portrayal, model)
-
 
 def draw_network(space: Network, agent_portrayal: Callable, ax):
     """Visualize a network space.

From 81d90e7b6f5e508f7a7adde438cef24292835be6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 14:58:42 +0000
Subject: [PATCH 32/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index b984be13e14..88570d1de6f 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -9,7 +9,6 @@
 import networkx as nx
 import numpy as np
 import solara
-
 from matplotlib.cm import ScalarMappable
 from matplotlib.collections import PatchCollection
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
@@ -31,7 +30,6 @@
     PropertyLayer,
     SingleGrid,
 )
-from mesa import Model
 from mesa.visualization.utils import update_counter
 
 OrthogonalGrid = SingleGrid | MultiGrid | OrthogonalMooreGrid | OrthogonalVonNeumannGrid
@@ -80,9 +78,7 @@ def SpaceMatplotlib(
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:
         case mesa.space._Grid() | OrthogonalMooreGrid() | OrthogonalVonNeumannGrid():
-            draw_orthogonal_grid(
-                space, agent_portrayal, ax
-            )
+            draw_orthogonal_grid(space, agent_portrayal, ax)
         case HexSingleGrid() | HexMultiGrid() | mesa.experimental.cell_space.HexGrid():
             draw_hex_grid(space, agent_portrayal, ax)
         case mesa.space.NetworkGrid() | mesa.experimental.cell_space.Network():

From 36b9623f812508a554cbeb646bd53f7f1258bd97 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 17:19:00 +0100
Subject: [PATCH 33/74] add tests for and fixes errors in draw_property_layers

---
 mesa/visualization/components/matplotlib.py | 25 +++++++++++----
 tests/test_components_matplotlib.py         | 35 ++++++++++++---------
 2 files changed, 40 insertions(+), 20 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 88570d1de6f..eddadbbafb9 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -5,6 +5,8 @@
 import warnings
 from collections.abc import Callable
 
+from typing import Dict
+
 import matplotlib.pyplot as plt
 import networkx as nx
 import numpy as np
@@ -96,17 +98,30 @@ def SpaceMatplotlib(
     )
 
 
-def draw_property_layers(space, propertylayer_portrayal, model, ax):
+def draw_property_layers(space, propertylayer_portrayal: Dict[str:Dict], ax):
     """Draw PropertyLayers on the given axes.
 
     Args:
-        ax (matplotlib.axes.Axes): The axes to draw on.
         space (mesa.space._Grid): The space containing the PropertyLayers.
-        propertylayer_portrayal (dict): Dictionary of PropertyLayer portrayal specifications.
+        propertylayer_portrayal (dict): the key is the name of the layer, the value is a dict with
+                                        fields specifying how the layer is to be portrayed
         model (mesa.Model): The model instance.
+        ax (matplotlib.axes.Axes): The axes to draw on.
+
+    Notes:
+        valid fields in in the inner dict of propertylayer_portrayal are "alpha", "vmin", "vmax", "color" or "colormap", and "colorbar"
+        so you can do `{"some_layer":{"colormap":'viridis', 'alpha':.25, "colorbar":False}}`
+
     """
+    try:
+        # old style spaces
+        property_layers = space.properties
+    except AttributeError:
+        # new style spaces
+        property_layers = space.property_layers
+
     for layer_name, portrayal in propertylayer_portrayal.items():
-        layer = getattr(model, layer_name, None)
+        layer = property_layers.get(layer_name, None)
         if not isinstance(layer, PropertyLayer):
             continue
 
@@ -138,7 +153,6 @@ def draw_property_layers(space, propertylayer_portrayal, model, ax):
             )
             im = ax.imshow(
                 rgba_data.transpose(1, 0, 2),
-                extent=(0, width, 0, height),
                 origin="lower",
             )
             if colorbar:
@@ -157,7 +171,6 @@ def draw_property_layers(space, propertylayer_portrayal, model, ax):
                 alpha=alpha,
                 vmin=vmin,
                 vmax=vmax,
-                extent=(0, width, 0, height),
                 origin="lower",
             )
             if colorbar:
diff --git a/tests/test_components_matplotlib.py b/tests/test_components_matplotlib.py
index 1b45d95e5a2..df9d5e91326 100644
--- a/tests/test_components_matplotlib.py
+++ b/tests/test_components_matplotlib.py
@@ -3,6 +3,7 @@
 import matplotlib.pyplot as plt
 
 from mesa import Agent, Model
+from mesa.space import PropertyLayer
 from mesa.experimental.cell_space import (
     CellAgent,
     HexGrid,
@@ -17,6 +18,7 @@
     draw_network,
     draw_orthogonal_grid,
     draw_voroinoi_grid,
+    draw_property_layers
 )
 
 
@@ -43,7 +45,7 @@ def test_draw_hex_grid():
         grid.move_to_empty(agent)
 
     fig, ax = plt.subplots()
-    draw_hex_grid(grid, agent_portrayal, None, model, ax)
+    draw_hex_grid(grid, agent_portrayal, ax)
 
     model = Model(seed=42)
     grid = HexGrid((10, 10), torus=True, random=model.random, capacity=1)
@@ -52,7 +54,7 @@ def test_draw_hex_grid():
         agent.cell = grid.select_random_empty_cell()
 
     fig, ax = plt.subplots()
-    draw_hex_grid(grid, agent_portrayal, None, model, ax)
+    draw_hex_grid(grid, agent_portrayal, ax)
 
 
 def test_draw_voroinoi_grid():
@@ -79,7 +81,7 @@ def test_draw_orthogonal_grid():
         grid.move_to_empty(agent)
 
     fig, ax = plt.subplots()
-    draw_orthogonal_grid(grid, agent_portrayal, None, model, ax)
+    draw_orthogonal_grid(grid, agent_portrayal, ax)
 
     model = Model(seed=42)
     grid = OrthogonalMooreGrid((10, 10), torus=True, random=model.random, capacity=1)
@@ -88,7 +90,7 @@ def test_draw_orthogonal_grid():
         agent.cell = grid.select_random_empty_cell()
 
     fig, ax = plt.subplots()
-    draw_orthogonal_grid(grid, agent_portrayal, None, model, ax)
+    draw_orthogonal_grid(grid, agent_portrayal, ax)
 
 
 def test_draw_continuous_space():
@@ -107,16 +109,6 @@ def test_draw_continuous_space():
 
 def test_draw_network():
     """Test drawing network."""
-
-    def agent_portrayal(agent):
-        """Simple portrayal of an agent.
-
-        Args:
-            agent (Agent): The agent to portray
-
-        """
-        return {"node_size": 10, "node_color": "tab:blue"}
-
     import networkx as nx
 
     n = 10
@@ -146,3 +138,18 @@ def agent_portrayal(agent):
 
 def test_draw_property_layers():
     """Test drawing property layers."""
+
+    model = Model(seed=42)
+    grid = SingleGrid(10, 10, torus=True)
+    grid.add_property_layer(PropertyLayer("test", grid.width, grid.height, 0))
+
+    fig, ax = plt.subplots()
+    draw_property_layers(grid, {"test":{"colormap":"viridis", "colorbar":True}}, ax)
+
+    model = Model(seed=42)
+    grid = OrthogonalMooreGrid((10, 10), torus=True, random=model.random, capacity=1)
+    grid.add_property_layer(PropertyLayer("test", grid.width, grid.height, 0))
+
+    fig, ax = plt.subplots()
+    draw_property_layers(grid, {"test":{"colormap":"viridis", "colorbar":True}}, ax)
+

From 5c28476a1797d8cfc8e3e9353702dea887e31e28 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:19:09 +0000
Subject: [PATCH 34/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py |  4 +---
 tests/test_components_matplotlib.py         | 17 ++++++++++-------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index eddadbbafb9..e9790837080 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -5,8 +5,6 @@
 import warnings
 from collections.abc import Callable
 
-from typing import Dict
-
 import matplotlib.pyplot as plt
 import networkx as nx
 import numpy as np
@@ -98,7 +96,7 @@ def SpaceMatplotlib(
     )
 
 
-def draw_property_layers(space, propertylayer_portrayal: Dict[str:Dict], ax):
+def draw_property_layers(space, propertylayer_portrayal: dict[str:dict], ax):
     """Draw PropertyLayers on the given axes.
 
     Args:
diff --git a/tests/test_components_matplotlib.py b/tests/test_components_matplotlib.py
index df9d5e91326..c85dd1ce292 100644
--- a/tests/test_components_matplotlib.py
+++ b/tests/test_components_matplotlib.py
@@ -3,7 +3,6 @@
 import matplotlib.pyplot as plt
 
 from mesa import Agent, Model
-from mesa.space import PropertyLayer
 from mesa.experimental.cell_space import (
     CellAgent,
     HexGrid,
@@ -11,14 +10,20 @@
     OrthogonalMooreGrid,
     VoronoiGrid,
 )
-from mesa.space import ContinuousSpace, HexSingleGrid, NetworkGrid, SingleGrid
+from mesa.space import (
+    ContinuousSpace,
+    HexSingleGrid,
+    NetworkGrid,
+    PropertyLayer,
+    SingleGrid,
+)
 from mesa.visualization.components.matplotlib import (
     draw_continuous_space,
     draw_hex_grid,
     draw_network,
     draw_orthogonal_grid,
+    draw_property_layers,
     draw_voroinoi_grid,
-    draw_property_layers
 )
 
 
@@ -138,18 +143,16 @@ def test_draw_network():
 
 def test_draw_property_layers():
     """Test drawing property layers."""
-
     model = Model(seed=42)
     grid = SingleGrid(10, 10, torus=True)
     grid.add_property_layer(PropertyLayer("test", grid.width, grid.height, 0))
 
     fig, ax = plt.subplots()
-    draw_property_layers(grid, {"test":{"colormap":"viridis", "colorbar":True}}, ax)
+    draw_property_layers(grid, {"test": {"colormap": "viridis", "colorbar": True}}, ax)
 
     model = Model(seed=42)
     grid = OrthogonalMooreGrid((10, 10), torus=True, random=model.random, capacity=1)
     grid.add_property_layer(PropertyLayer("test", grid.width, grid.height, 0))
 
     fig, ax = plt.subplots()
-    draw_property_layers(grid, {"test":{"colormap":"viridis", "colorbar":True}}, ax)
-
+    draw_property_layers(grid, {"test": {"colormap": "viridis", "colorbar": True}}, ax)

From 0cec04e6d31b5cd54dcd2f0f0617c62011d08565 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 17:40:01 +0100
Subject: [PATCH 35/74] Update matplotlib.py

---
 mesa/visualization/components/matplotlib.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index e9790837080..138e5c128b0 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -5,6 +5,8 @@
 import warnings
 from collections.abc import Callable
 
+from typing import Dict, Any
+
 import matplotlib.pyplot as plt
 import networkx as nx
 import numpy as np
@@ -96,7 +98,7 @@ def SpaceMatplotlib(
     )
 
 
-def draw_property_layers(space, propertylayer_portrayal: dict[str:dict], ax):
+def draw_property_layers(space, propertylayer_portrayal: Dict[str, Dict[str, Any]], ax):
     """Draw PropertyLayers on the given axes.
 
     Args:

From b07620f719c13404474095c3bd06cb281a7ef8ff Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:40:43 +0000
Subject: [PATCH 36/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 138e5c128b0..17ede9a1dbd 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -4,8 +4,7 @@
 import math
 import warnings
 from collections.abc import Callable
-
-from typing import Dict, Any
+from typing import Any
 
 import matplotlib.pyplot as plt
 import networkx as nx
@@ -98,7 +97,7 @@ def SpaceMatplotlib(
     )
 
 
-def draw_property_layers(space, propertylayer_portrayal: Dict[str, Dict[str, Any]], ax):
+def draw_property_layers(space, propertylayer_portrayal: dict[str, dict[str, Any]], ax):
     """Draw PropertyLayers on the given axes.
 
     Args:

From 315e7eb411beaad7effe2fb281cd60f70a4f43b9 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 17:50:13 +0100
Subject: [PATCH 37/74] cleanup

---
 mesa/examples/advanced/wolf_sheep/app.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index 46f577b4ba0..5270be7a753 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,11 +1,3 @@
-import os.path
-import sys
-
-sys.path.insert(
-    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
-)
-
-
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
 from mesa.examples.advanced.wolf_sheep.model import WolfSheep
 from mesa.visualization import (

From f685db486cdd007bc439a14aa59373c1a4ceabed Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 17:54:29 +0100
Subject: [PATCH 38/74] some further cleanup

---
 mesa/visualization/components/matplotlib.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 17ede9a1dbd..a4c66fb20bf 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -33,6 +33,8 @@
 )
 from mesa.visualization.utils import update_counter
 
+
+# For typing
 OrthogonalGrid = SingleGrid | MultiGrid | OrthogonalMooreGrid | OrthogonalVonNeumannGrid
 HexGrid = HexSingleGrid | HexMultiGrid | mesa.experimental.cell_space.HexGrid
 Network = NetworkGrid | mesa.experimental.cell_space.Network
@@ -90,7 +92,7 @@ def SpaceMatplotlib(
             draw_voroinoi_grid(space, agent_portrayal, ax)
 
     if propertylayer_portrayal:
-        draw_property_layers(space, propertylayer_portrayal, model, ax)
+        draw_property_layers(space, propertylayer_portrayal, ax)
 
     solara.FigureMatplotlib(
         fig, format="png", bbox_inches="tight", dependencies=dependencies

From 4c727ecd07614df688cf5a553f2c35a3e966590a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:54:38 +0000
Subject: [PATCH 39/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index a4c66fb20bf..32fe33166a2 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -33,7 +33,6 @@
 )
 from mesa.visualization.utils import update_counter
 
-
 # For typing
 OrthogonalGrid = SingleGrid | MultiGrid | OrthogonalMooreGrid | OrthogonalVonNeumannGrid
 HexGrid = HexSingleGrid | HexMultiGrid | mesa.experimental.cell_space.HexGrid

From c102abb24609982199472e1403969133a5acbeda Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 18:11:13 +0100
Subject: [PATCH 40/74] further annotation of code

---
 mesa/visualization/components/matplotlib.py | 46 ++++++++++++++-------
 1 file changed, 32 insertions(+), 14 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 32fe33166a2..4c20117d1e9 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -105,7 +105,6 @@ def draw_property_layers(space, propertylayer_portrayal: dict[str, dict[str, Any
         space (mesa.space._Grid): The space containing the PropertyLayers.
         propertylayer_portrayal (dict): the key is the name of the layer, the value is a dict with
                                         fields specifying how the layer is to be portrayed
-        model (mesa.Model): The model instance.
         ax (matplotlib.axes.Axes): The axes to draw on.
 
     Notes:
@@ -237,9 +236,14 @@ def draw_orthogonal_grid(
         A Figure and Axes instance
 
     """
+    # gather agent data
     s_default = (180 / max(space.width, space.height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
+    # plot the agents
+    _scatter(ax, arguments)
+
+    # further styling
     ax.set_xlim(-0.5, space.width - 0.5)
     ax.set_ylim(-0.5, space.height - 0.5)
 
@@ -249,7 +253,7 @@ def draw_orthogonal_grid(
     for y in np.arange(-0.5, space.height - 0.5, 1):
         ax.axhline(y, color="gray", linestyle=":")
 
-    _scatter(ax, arguments)
+
 
 
 def draw_hex_grid(
@@ -270,19 +274,20 @@ def draw_hex_grid(
         A Figure and Axes instance
 
     """
+    # gather data
     s_default = (180 / max(space.width, space.height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-    # give all odd rows an offset in the x direction
+
+    # for hexgrids we have to go from logical coordinates to visual coordinates
+    # this is a bit messy.
+
+    # give all even rows an offset in the x direction
     # give all rows an offset in the y direction
+
     # numbers here are based on a distance of 1 between centers of hexes
     offset = math.sqrt(0.75)
 
-    # logical = np.mod(arguments["y"], 2) == 1
-    # arguments["y"] = arguments["y"].astype(float) * offset
-    # arguments["x"] = arguments["x"].astype(float)
-    # arguments["x"][logical] += 0.5
-
     loc = arguments["loc"].astype(float)
 
     logical = np.mod(loc[:, 1], 2) == 0
@@ -290,11 +295,13 @@ def draw_hex_grid(
     loc[:, 1] *= offset
     arguments["loc"] = loc
 
+    # plot the agents
+    _scatter(ax, arguments)
+
+    # further styling and adding of grid
     ax.set_xlim(-1, space.width + 0.5)
     ax.set_ylim(-offset, space.height * offset)
 
-    _scatter(ax, arguments)
-
     def setup_hexmesh(
         width,
         height,
@@ -320,6 +327,7 @@ def setup_hexmesh(
         )
         return mesh
 
+    # add grid
     ax.add_collection(
         setup_hexmesh(
             space.width,
@@ -342,6 +350,7 @@ def draw_network(space: Network, agent_portrayal: Callable, ax):
 
 
     """
+    # gather locations for nodes in network
     graph = space.G
     pos = nx.spring_layout(graph, seed=0)
     x, y = list(zip(*pos.values()))
@@ -351,6 +360,7 @@ def draw_network(space: Network, agent_portrayal: Callable, ax):
     width = xmax - xmin
     height = ymax - ymin
 
+    # gather agent data
     s_default = (180 / max(width, height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
@@ -359,11 +369,15 @@ def draw_network(space: Network, agent_portrayal: Callable, ax):
     pos = np.asarray(list(pos.values()))
     arguments["loc"] = pos[arguments["loc"]]
 
+    # plot the agents
+    _scatter(ax, arguments)
+
+
+    # further styling
     ax.set_axis_off()
     ax.set_xlim(xmin=xmin, xmax=xmax)
     ax.set_ylim(ymin=ymin, ymax=ymax)
 
-    _scatter(ax, arguments)
     nx.draw_networkx_edges(graph, pos, ax=ax)
 
 
@@ -379,17 +393,21 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax)
         A Figure and Axes instance
 
     """
+    # space related setup
     width = space.x_max - space.x_min
     x_padding = width / 20
     height = space.y_max - space.y_min
     y_padding = height / 20
 
+    # gather agent data
     s_default = (180 / max(width, height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-    border_style = "solid" if not space.torus else (0, (5, 10))
+    # plot the agents
+    _scatter(ax, arguments)
 
-    # Set the border of the plot
+    # further visual styling
+    border_style = "solid" if not space.torus else (0, (5, 10))
     for spine in ax.spines.values():
         spine.set_linewidth(1.5)
         spine.set_color("black")
@@ -398,7 +416,7 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax)
     ax.set_xlim(space.x_min - x_padding, space.x_max + x_padding)
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
-    _scatter(ax, arguments)
+
 
 
 def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax):

From cad794f20915c7038f189d47f6531d44d3c70d95 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:45:34 +0000
Subject: [PATCH 41/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 4c20117d1e9..a6981c9db13 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -254,8 +254,6 @@ def draw_orthogonal_grid(
         ax.axhline(y, color="gray", linestyle=":")
 
 
-
-
 def draw_hex_grid(
     space: HexGrid,
     agent_portrayal: Callable,
@@ -278,7 +276,6 @@ def draw_hex_grid(
     s_default = (180 / max(space.width, space.height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
 
-
     # for hexgrids we have to go from logical coordinates to visual coordinates
     # this is a bit messy.
 
@@ -372,7 +369,6 @@ def draw_network(space: Network, agent_portrayal: Callable, ax):
     # plot the agents
     _scatter(ax, arguments)
 
-
     # further styling
     ax.set_axis_off()
     ax.set_xlim(xmin=xmin, xmax=xmax)
@@ -417,8 +413,6 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax)
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
 
-
-
 def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax):
     """Visualize a voronoi grid.
 

From dfe15df194fdb7724c540d067413b90162ea3272 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 19:30:37 +0100
Subject: [PATCH 42/74] minor updates

---
 mesa/examples/advanced/wolf_sheep/app.py    | 6 +++++-
 mesa/visualization/components/matplotlib.py | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index 5270be7a753..7ccdc938193 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,3 +1,7 @@
+import sys
+import os.path
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
 from mesa.examples.advanced.wolf_sheep.model import WolfSheep
 from mesa.visualization import (
@@ -64,7 +68,7 @@ def wolf_sheep_portrayal(agent):
 
 
 space_component = make_space_matplotlib(wolf_sheep_portrayal)
-lineplot_component = make_plot_measure(["Wolves", "Sheep", "Grass"])
+lineplot_component = make_plot_measure({"Wolves":"tab:orange", "Sheep":"tab:blue", "Grass":"tab:green"})
 
 model = WolfSheep(grass=True)
 
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index a6981c9db13..5d8df4b4fba 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -75,7 +75,7 @@ def SpaceMatplotlib(
         space = getattr(model, "space", None)
 
     fig = Figure()
-    ax = fig.subplots(111)
+    ax = fig.subplots()
 
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:

From 95b963fec9f456fce0516500459fa44f89dcf1c8 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 20:52:52 +0100
Subject: [PATCH 43/74] Update matplotlib.py

first step towards addressing #2243
---
 mesa/visualization/components/matplotlib.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 5d8df4b4fba..23db6a52614 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -333,13 +333,16 @@ def setup_hexmesh(
     )
 
 
-def draw_network(space: Network, agent_portrayal: Callable, ax):
+def draw_network(space: Network, agent_portrayal: Callable, ax,
+                 layout_alg=nx.spring_layout, layout_kwargs={"seed":0}):
     """Visualize a network space.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
         ax: a Matplotlib Axes instance
+        layout_alg: a networkx layout algorithm or other callable with the same behavior
+        layout_kwargs: a dictionary of keyword arguments for the layout algorithm
 
     Notes:
         this uses networkx.draw under the hood so agent portrayal fields should match those used there
@@ -349,7 +352,7 @@ def draw_network(space: Network, agent_portrayal: Callable, ax):
     """
     # gather locations for nodes in network
     graph = space.G
-    pos = nx.spring_layout(graph, seed=0)
+    pos = layout_alg(graph, **layout_kwargs)
     x, y = list(zip(*pos.values()))
     xmin, xmax = min(x), max(x)
     ymin, ymax = min(y), max(y)

From d5f69c1bf2659811ac69bda11a435c318fbefadf Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 20:57:53 +0100
Subject: [PATCH 44/74] add boolean kwarg to control grid drawing

---
 mesa/visualization/components/matplotlib.py | 46 +++++++++++++--------
 1 file changed, 28 insertions(+), 18 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 23db6a52614..521588f869f 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -224,6 +224,7 @@ def draw_orthogonal_grid(
     space: OrthogonalGrid,
     agent_portrayal: Callable,
     ax,
+    draw_grid:bool =True
 ):
     """Visualize a orthogonal grid.
 
@@ -231,6 +232,7 @@ def draw_orthogonal_grid(
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
         ax: a Matplotlib Axes instance
+        draw_grid: whether to draw the grid
 
     Returns:
         A Figure and Axes instance
@@ -247,26 +249,27 @@ def draw_orthogonal_grid(
     ax.set_xlim(-0.5, space.width - 0.5)
     ax.set_ylim(-0.5, space.height - 0.5)
 
-    # Draw grid lines
-    for x in np.arange(-0.5, space.width - 0.5, 1):
-        ax.axvline(x, color="gray", linestyle=":")
-    for y in np.arange(-0.5, space.height - 0.5, 1):
-        ax.axhline(y, color="gray", linestyle=":")
+    if draw_grid:
+        # Draw grid lines
+        for x in np.arange(-0.5, space.width - 0.5, 1):
+            ax.axvline(x, color="gray", linestyle=":")
+        for y in np.arange(-0.5, space.height - 0.5, 1):
+            ax.axhline(y, color="gray", linestyle=":")
 
 
 def draw_hex_grid(
     space: HexGrid,
     agent_portrayal: Callable,
     ax,
+    draw_grid: bool = True
 ):
     """Visualize a hex grid.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
-        propertylayer_portrayal: a callable that is called with the agent and returns a dict
-        model: a model instance
         ax: a Matplotlib Axes instance
+        draw_grid: whether to draw the grid
 
     Returns:
         A Figure and Axes instance
@@ -324,23 +327,26 @@ def setup_hexmesh(
         )
         return mesh
 
-    # add grid
-    ax.add_collection(
-        setup_hexmesh(
-            space.width,
-            space.height,
+    if draw_grid:
+        # add grid
+        ax.add_collection(
+            setup_hexmesh(
+                space.width,
+                space.height,
+            )
         )
-    )
 
 
-def draw_network(space: Network, agent_portrayal: Callable, ax,
-                 layout_alg=nx.spring_layout, layout_kwargs={"seed":0}):
+def draw_network(space: Network, agent_portrayal: Callable, ax, draw_grid: bool=True,
+                 layout_alg=nx.spring_layout, layout_kwargs={"seed":0},
+                 ):
     """Visualize a network space.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
         ax: a Matplotlib Axes instance
+        draw_grid: whether to draw the grid
         layout_alg: a networkx layout algorithm or other callable with the same behavior
         layout_kwargs: a dictionary of keyword arguments for the layout algorithm
 
@@ -359,6 +365,8 @@ def draw_network(space: Network, agent_portrayal: Callable, ax,
 
     width = xmax - xmin
     height = ymax - ymin
+    x_padding = width / 20
+    y_padding = height / 20
 
     # gather agent data
     s_default = (180 / max(width, height)) ** 2
@@ -374,10 +382,12 @@ def draw_network(space: Network, agent_portrayal: Callable, ax,
 
     # further styling
     ax.set_axis_off()
-    ax.set_xlim(xmin=xmin, xmax=xmax)
-    ax.set_ylim(ymin=ymin, ymax=ymax)
+    ax.set_xlim(xmin=xmin-x_padding, xmax=xmax+x_padding)
+    ax.set_ylim(ymin=ymin-y_padding, ymax=ymax+y_padding)
 
-    nx.draw_networkx_edges(graph, pos, ax=ax)
+    if draw_grid:
+        # fixme we need to draw the empty nodes as well
+        nx.draw_networkx_edges(graph, pos, ax=ax)
 
 
 def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax):

From 9d2c970bc7f9d91bc2adf414d8b7aebde378889e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 20:06:13 +0000
Subject: [PATCH 45/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/advanced/wolf_sheep/app.py    | 11 ++++++---
 mesa/visualization/components/matplotlib.py | 25 ++++++++++-----------
 2 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index 7ccdc938193..f34d19d32eb 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,6 +1,9 @@
-import sys
 import os.path
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+import sys
+
+sys.path.insert(
+    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
+)
 
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
 from mesa.examples.advanced.wolf_sheep.model import WolfSheep
@@ -68,7 +71,9 @@ def wolf_sheep_portrayal(agent):
 
 
 space_component = make_space_matplotlib(wolf_sheep_portrayal)
-lineplot_component = make_plot_measure({"Wolves":"tab:orange", "Sheep":"tab:blue", "Grass":"tab:green"})
+lineplot_component = make_plot_measure(
+    {"Wolves": "tab:orange", "Sheep": "tab:blue", "Grass": "tab:green"}
+)
 
 model = WolfSheep(grass=True)
 
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 521588f869f..58030c407fc 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -221,10 +221,7 @@ def collect_agent_data(
 
 
 def draw_orthogonal_grid(
-    space: OrthogonalGrid,
-    agent_portrayal: Callable,
-    ax,
-    draw_grid:bool =True
+    space: OrthogonalGrid, agent_portrayal: Callable, ax, draw_grid: bool = True
 ):
     """Visualize a orthogonal grid.
 
@@ -258,10 +255,7 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-    space: HexGrid,
-    agent_portrayal: Callable,
-    ax,
-    draw_grid: bool = True
+    space: HexGrid, agent_portrayal: Callable, ax, draw_grid: bool = True
 ):
     """Visualize a hex grid.
 
@@ -337,9 +331,14 @@ def setup_hexmesh(
         )
 
 
-def draw_network(space: Network, agent_portrayal: Callable, ax, draw_grid: bool=True,
-                 layout_alg=nx.spring_layout, layout_kwargs={"seed":0},
-                 ):
+def draw_network(
+    space: Network,
+    agent_portrayal: Callable,
+    ax,
+    draw_grid: bool = True,
+    layout_alg=nx.spring_layout,
+    layout_kwargs={"seed": 0},
+):
     """Visualize a network space.
 
     Args:
@@ -382,8 +381,8 @@ def draw_network(space: Network, agent_portrayal: Callable, ax, draw_grid: bool=
 
     # further styling
     ax.set_axis_off()
-    ax.set_xlim(xmin=xmin-x_padding, xmax=xmax+x_padding)
-    ax.set_ylim(ymin=ymin-y_padding, ymax=ymax+y_padding)
+    ax.set_xlim(xmin=xmin - x_padding, xmax=xmax + x_padding)
+    ax.set_ylim(ymin=ymin - y_padding, ymax=ymax + y_padding)
 
     if draw_grid:
         # fixme we need to draw the empty nodes as well

From aa2110f239d86421f7f566d1dda87673a16959c7 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 21:18:33 +0100
Subject: [PATCH 46/74] Update matplotlib.py

---
 mesa/visualization/components/matplotlib.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 58030c407fc..63ca5bc0a43 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -386,7 +386,8 @@ def draw_network(
 
     if draw_grid:
         # fixme we need to draw the empty nodes as well
-        nx.draw_networkx_edges(graph, pos, ax=ax)
+        edge_collection = nx.draw_networkx_edges(graph, pos, ax=ax, alpha=0.5, style='--')
+        edge_collection.set_zorder(0)
 
 
 def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax):

From cdea05172c37791e9366568eaf6dc6a3092c0d51 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 20:20:59 +0000
Subject: [PATCH 47/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 63ca5bc0a43..7905997a7f9 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -386,7 +386,9 @@ def draw_network(
 
     if draw_grid:
         # fixme we need to draw the empty nodes as well
-        edge_collection = nx.draw_networkx_edges(graph, pos, ax=ax, alpha=0.5, style='--')
+        edge_collection = nx.draw_networkx_edges(
+            graph, pos, ax=ax, alpha=0.5, style="--"
+        )
         edge_collection.set_zorder(0)
 
 

From 22f57e47de4b510a138573f3147768fca5d7145a Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 21:48:22 +0100
Subject: [PATCH 48/74] ruff related fix

---
 mesa/visualization/components/matplotlib.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 7905997a7f9..d08de57d1ec 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -337,7 +337,7 @@ def draw_network(
     ax,
     draw_grid: bool = True,
     layout_alg=nx.spring_layout,
-    layout_kwargs={"seed": 0},
+    layout_kwargs=None,
 ):
     """Visualize a network space.
 
@@ -355,6 +355,9 @@ def draw_network(
 
 
     """
+    if layout_kwargs is None:
+        layout_kwargs = {"seed": 0}
+
     # gather locations for nodes in network
     graph = space.G
     pos = layout_alg(graph, **layout_kwargs)

From 511214e6591f7c4fb87429283100289ef33e7e35 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 28 Oct 2024 21:49:12 +0100
Subject: [PATCH 49/74] Update app.py

---
 mesa/examples/advanced/wolf_sheep/app.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index f34d19d32eb..bea98fd3630 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,10 +1,3 @@
-import os.path
-import sys
-
-sys.path.insert(
-    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
-)
-
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
 from mesa.examples.advanced.wolf_sheep.model import WolfSheep
 from mesa.visualization import (

From 0fa5c1f78836c84b552e324814f1f9de5e3c774f Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 16:53:42 +0100
Subject: [PATCH 50/74] make ax optional

---
 mesa/visualization/components/matplotlib.py | 39 +++++++++++++++------
 1 file changed, 28 insertions(+), 11 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index d08de57d1ec..7e81cdb1f44 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -10,6 +10,8 @@
 import networkx as nx
 import numpy as np
 import solara
+
+from matplotlib.axes import Axes
 from matplotlib.cm import ScalarMappable
 from matplotlib.collections import PatchCollection
 from matplotlib.colors import LinearSegmentedColormap, Normalize, to_rgba
@@ -221,20 +223,23 @@ def collect_agent_data(
 
 
 def draw_orthogonal_grid(
-    space: OrthogonalGrid, agent_portrayal: Callable, ax, draw_grid: bool = True
+    space: OrthogonalGrid, agent_portrayal: Callable, ax: Axes = None, draw_grid: bool = True
 ):
     """Visualize a orthogonal grid.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
-        ax: a Matplotlib Axes instance
+        ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
         draw_grid: whether to draw the grid
 
     Returns:
         A Figure and Axes instance
 
     """
+    if ax is None:
+        fig, ax = plt.subplots()
+
     # gather agent data
     s_default = (180 / max(space.width, space.height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
@@ -255,20 +260,23 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-    space: HexGrid, agent_portrayal: Callable, ax, draw_grid: bool = True
+    space: HexGrid, agent_portrayal: Callable, ax: Axes = None , draw_grid: bool = True
 ):
     """Visualize a hex grid.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
-        ax: a Matplotlib Axes instance
+        ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
         draw_grid: whether to draw the grid
 
     Returns:
         A Figure and Axes instance
 
     """
+    if ax is None:
+        fig, ax = plt.subplots()
+
     # gather data
     s_default = (180 / max(space.width, space.height)) ** 2
     arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
@@ -334,7 +342,7 @@ def setup_hexmesh(
 def draw_network(
     space: Network,
     agent_portrayal: Callable,
-    ax,
+    ax: Axes = None ,
     draw_grid: bool = True,
     layout_alg=nx.spring_layout,
     layout_kwargs=None,
@@ -344,7 +352,7 @@ def draw_network(
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
-        ax: a Matplotlib Axes instance
+        ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
         draw_grid: whether to draw the grid
         layout_alg: a networkx layout algorithm or other callable with the same behavior
         layout_kwargs: a dictionary of keyword arguments for the layout algorithm
@@ -355,6 +363,8 @@ def draw_network(
 
 
     """
+    if ax is None:
+        fig, ax = plt.subplots()
     if layout_kwargs is None:
         layout_kwargs = {"seed": 0}
 
@@ -395,18 +405,21 @@ def draw_network(
         edge_collection.set_zorder(0)
 
 
-def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax):
+def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax: Axes = None ):
     """Visualize a continuous space.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
-        ax: a Matplotlib Axes instance
+        ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
 
     Returns:
         A Figure and Axes instance
 
     """
+    if ax is None:
+        fig, ax = plt.subplots()
+
     # space related setup
     width = space.x_max - space.x_min
     x_padding = width / 20
@@ -431,18 +444,21 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax)
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
 
-def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax):
+def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax: Axes = None ):
     """Visualize a voronoi grid.
 
     Args:
         space: the space to visualize
         agent_portrayal: a callable that is called with the agent and returns a dict
-        ax: a Matplotlib Axes instance
+        ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
 
     Returns:
         A Figure and Axes instance
 
     """
+    if ax is None:
+        fig, ax = plt.subplots()
+
     x_list = [i[0] for i in space.centroids_coordinates]
     y_list = [i[1] for i in space.centroids_coordinates]
     x_max = max(x_list)
@@ -474,7 +490,8 @@ def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax):
         ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in black
 
 
-def _scatter(ax, arguments):
+def _scatter(ax: Axes, arguments):
+    """Helper function for plotting the agents."""
     loc = arguments.pop("loc")
 
     x = loc[:, 0]

From 7914328e9d2403b0245ffc10e56e924dfdf215db Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 15:53:55 +0000
Subject: [PATCH 51/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 7e81cdb1f44..b7dad465e57 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -10,7 +10,6 @@
 import networkx as nx
 import numpy as np
 import solara
-
 from matplotlib.axes import Axes
 from matplotlib.cm import ScalarMappable
 from matplotlib.collections import PatchCollection
@@ -223,7 +222,10 @@ def collect_agent_data(
 
 
 def draw_orthogonal_grid(
-    space: OrthogonalGrid, agent_portrayal: Callable, ax: Axes = None, draw_grid: bool = True
+    space: OrthogonalGrid,
+    agent_portrayal: Callable,
+    ax: Axes = None,
+    draw_grid: bool = True,
 ):
     """Visualize a orthogonal grid.
 
@@ -260,7 +262,7 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-    space: HexGrid, agent_portrayal: Callable, ax: Axes = None , draw_grid: bool = True
+    space: HexGrid, agent_portrayal: Callable, ax: Axes = None, draw_grid: bool = True
 ):
     """Visualize a hex grid.
 
@@ -342,7 +344,7 @@ def setup_hexmesh(
 def draw_network(
     space: Network,
     agent_portrayal: Callable,
-    ax: Axes = None ,
+    ax: Axes = None,
     draw_grid: bool = True,
     layout_alg=nx.spring_layout,
     layout_kwargs=None,
@@ -405,7 +407,9 @@ def draw_network(
         edge_collection.set_zorder(0)
 
 
-def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax: Axes = None ):
+def draw_continuous_space(
+    space: ContinuousSpace, agent_portrayal: Callable, ax: Axes = None
+):
     """Visualize a continuous space.
 
     Args:
@@ -444,7 +448,7 @@ def draw_continuous_space(space: ContinuousSpace, agent_portrayal: Callable, ax:
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
 
-def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax: Axes = None ):
+def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax: Axes = None):
     """Visualize a voronoi grid.
 
     Args:

From d9db041353de050253215193ffeeedc9b5f3b188 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 17:22:17 +0100
Subject: [PATCH 52/74] add a draw_space function and improve typing

---
 mesa/visualization/components/matplotlib.py | 50 ++++++++++++++-------
 1 file changed, 33 insertions(+), 17 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index b7dad465e57..0ce58eed49d 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -76,30 +76,46 @@ def SpaceMatplotlib(
         space = getattr(model, "space", None)
 
     fig = Figure()
-    ax = fig.subplots()
+    ax = fig.add_subplot()
+
+    draw_space(space, agent_portrayal, propertylayer_portrayal=propertylayer_portrayal, ax=ax)
+
+    solara.FigureMatplotlib(
+        fig, format="png", bbox_inches="tight", dependencies=dependencies
+    )
+
+
+def draw_space(space, agent_portrayal: Callable, propertylayer_portrayal: dict | None = None, ax: Axes | None = None):
+    """Draw a Matplotlib-based visualization of the space.
+
+    Args:
+        space: the space of the mesa model
+        agent_portrayal: A callable that returns a dict specifying how to show the agent
+        propertylayer_portrayal: a dict specifying how to show propertylayer(s)
+        ax: the axes upon which to draw the plot
+
+    """
+    if ax is None:
+        fig, ax = plt.subplots()
 
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:
         case mesa.space._Grid() | OrthogonalMooreGrid() | OrthogonalVonNeumannGrid():
-            draw_orthogonal_grid(space, agent_portrayal, ax)
+            draw_orthogonal_grid(space, agent_portrayal, ax=ax)
         case HexSingleGrid() | HexMultiGrid() | mesa.experimental.cell_space.HexGrid():
-            draw_hex_grid(space, agent_portrayal, ax)
+            draw_hex_grid(space, agent_portrayal, ax=ax)
         case mesa.space.NetworkGrid() | mesa.experimental.cell_space.Network():
-            draw_network(space, agent_portrayal, ax)
+            draw_network(space, agent_portrayal, ax=ax)
         case mesa.space.ContinuousSpace():
-            draw_continuous_space(space, agent_portrayal, ax)
+            draw_continuous_space(space, agent_portrayal, ax=ax)
         case VoronoiGrid():
-            draw_voroinoi_grid(space, agent_portrayal, ax)
+            draw_voroinoi_grid(space, agent_portrayal, ax=ax)
 
     if propertylayer_portrayal:
-        draw_property_layers(space, propertylayer_portrayal, ax)
-
-    solara.FigureMatplotlib(
-        fig, format="png", bbox_inches="tight", dependencies=dependencies
-    )
+        draw_property_layers(space, propertylayer_portrayal, ax=ax)
 
 
-def draw_property_layers(space, propertylayer_portrayal: dict[str, dict[str, Any]], ax):
+def draw_property_layers(space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes):
     """Draw PropertyLayers on the given axes.
 
     Args:
@@ -224,7 +240,7 @@ def collect_agent_data(
 def draw_orthogonal_grid(
     space: OrthogonalGrid,
     agent_portrayal: Callable,
-    ax: Axes = None,
+    ax: Axes | None = None,
     draw_grid: bool = True,
 ):
     """Visualize a orthogonal grid.
@@ -262,7 +278,7 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-    space: HexGrid, agent_portrayal: Callable, ax: Axes = None, draw_grid: bool = True
+    space: HexGrid, agent_portrayal: Callable, ax: Axes | None = None, draw_grid: bool = True
 ):
     """Visualize a hex grid.
 
@@ -344,7 +360,7 @@ def setup_hexmesh(
 def draw_network(
     space: Network,
     agent_portrayal: Callable,
-    ax: Axes = None,
+    ax: Axes | None = None,
     draw_grid: bool = True,
     layout_alg=nx.spring_layout,
     layout_kwargs=None,
@@ -408,7 +424,7 @@ def draw_network(
 
 
 def draw_continuous_space(
-    space: ContinuousSpace, agent_portrayal: Callable, ax: Axes = None
+    space: ContinuousSpace, agent_portrayal: Callable, ax: Axes | None = None
 ):
     """Visualize a continuous space.
 
@@ -448,7 +464,7 @@ def draw_continuous_space(
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
 
-def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax: Axes = None):
+def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax: Axes | None = None):
     """Visualize a voronoi grid.
 
     Args:

From f9adfba63763642680eb00192c9ad4493f3908ac Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 16:22:27 +0000
Subject: [PATCH 53/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 24 ++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 0ce58eed49d..f6a34d6937a 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -78,14 +78,21 @@ def SpaceMatplotlib(
     fig = Figure()
     ax = fig.add_subplot()
 
-    draw_space(space, agent_portrayal, propertylayer_portrayal=propertylayer_portrayal, ax=ax)
+    draw_space(
+        space, agent_portrayal, propertylayer_portrayal=propertylayer_portrayal, ax=ax
+    )
 
     solara.FigureMatplotlib(
         fig, format="png", bbox_inches="tight", dependencies=dependencies
     )
 
 
-def draw_space(space, agent_portrayal: Callable, propertylayer_portrayal: dict | None = None, ax: Axes | None = None):
+def draw_space(
+    space,
+    agent_portrayal: Callable,
+    propertylayer_portrayal: dict | None = None,
+    ax: Axes | None = None,
+):
     """Draw a Matplotlib-based visualization of the space.
 
     Args:
@@ -115,7 +122,9 @@ def draw_space(space, agent_portrayal: Callable, propertylayer_portrayal: dict |
         draw_property_layers(space, propertylayer_portrayal, ax=ax)
 
 
-def draw_property_layers(space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes):
+def draw_property_layers(
+    space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes
+):
     """Draw PropertyLayers on the given axes.
 
     Args:
@@ -278,7 +287,10 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-    space: HexGrid, agent_portrayal: Callable, ax: Axes | None = None, draw_grid: bool = True
+    space: HexGrid,
+    agent_portrayal: Callable,
+    ax: Axes | None = None,
+    draw_grid: bool = True,
 ):
     """Visualize a hex grid.
 
@@ -464,7 +476,9 @@ def draw_continuous_space(
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
 
-def draw_voroinoi_grid(space: VoronoiGrid, agent_portrayal: Callable, ax: Axes | None = None):
+def draw_voroinoi_grid(
+    space: VoronoiGrid, agent_portrayal: Callable, ax: Axes | None = None
+):
     """Visualize a voronoi grid.
 
     Args:

From aad0a8cdc197817582f7cdad23e92056450fc9f5 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 17:25:39 +0100
Subject: [PATCH 54/74] Update matplotlib.py

---
 mesa/visualization/components/matplotlib.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index f6a34d6937a..843a8ef73a2 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -224,7 +224,7 @@ def collect_agent_data(
         s_default: default size
 
     Notes:
-        agent portray dict is limited to s (size of marker), c (color of marker, and marker (marker style)
+        agent portray dict is limited to size (size of marker), color (color of marker, and marker (marker style)
         see `Matplotlib`_.
 
 
@@ -239,8 +239,8 @@ def collect_agent_data(
             loc = agent.cell.coordinate
 
         arguments["loc"].append(loc)
-        arguments["s"].append(portray.get("s", s_default))
-        arguments["c"].append(portray.get("c", c_default))
+        arguments["s"].append(portray.get("size", s_default))
+        arguments["c"].append(portray.get("color", c_default))
         arguments["marker"].append(portray.get("marker", marker_default))
 
     return {k: np.asarray(v) for k, v in arguments.items()}

From 6d7fae8013903484200ff1b207c3224b7d049b21 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 17:36:59 +0100
Subject: [PATCH 55/74] reorganization of file and warning added for ignored
 fields

---
 mesa/visualization/components/matplotlib.py | 95 +++++++++++----------
 1 file changed, 50 insertions(+), 45 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 843a8ef73a2..1c48833a490 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -87,6 +87,51 @@ def SpaceMatplotlib(
     )
 
 
+def collect_agent_data(
+    space: OrthogonalGrid | HexGrid | Network | ContinuousSpace | VoronoiGrid,
+    agent_portrayal: Callable,
+    color="tab:blue",
+    size=25,
+    marker="o",
+):
+    """Collect the plotting data for all agents in the space.
+
+    Args:
+        space: The space containing the Agents.
+        agent_portrayal: A callable that is called with the agent and returns a dict
+        loc: a boolean indicating whether to gather agent x, y data or not
+        color: default color
+        marker: default marker
+        size: default size
+
+    Notes:
+        agent portray dict is limited to size (size of marker), color (color of marker, and marker (marker style)
+        see `Matplotlib`_.
+
+
+    .. _Matplotlib: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
+
+    """
+    arguments = {"loc": [], "s": [], "c": [], "marker": []}
+    for agent in space.agents:
+        portray = agent_portrayal(agent)
+        loc = agent.pos
+        if loc is None:
+            loc = agent.cell.coordinate
+
+        arguments["loc"].append(loc)
+        arguments["s"].append(portray.pop("size", size))
+        arguments["c"].append(portray.pop("color", color))
+        arguments["marker"].append(portray.pop("marker", marker))
+
+        if len(portray) > 0:
+            ignored_fields = list(portray.keys())
+            msg = ", ".join(ignored_fields)
+            warnings.warn(f"the following fields are not used in agent portrayal and thus ignored: {msg}.")
+
+    return {k: np.asarray(v) for k, v in arguments.items()}
+
+
 def draw_space(
     space,
     agent_portrayal: Callable,
@@ -206,46 +251,6 @@ def draw_property_layers(
             )
 
 
-def collect_agent_data(
-    space: OrthogonalGrid | HexGrid | Network | ContinuousSpace,
-    agent_portrayal: Callable,
-    c_default="tab:blue",
-    marker_default="o",
-    s_default=25,
-):
-    """Collect the plotting data for all agents in the space.
-
-    Args:
-        space: The space containing the Agents.
-        agent_portrayal: A callable that is called with the agent and returns a dict
-        loc: a boolean indicating whether to gather agent x, y data or not
-        c_default: default color
-        marker_default: default marker
-        s_default: default size
-
-    Notes:
-        agent portray dict is limited to size (size of marker), color (color of marker, and marker (marker style)
-        see `Matplotlib`_.
-
-
-    .. _Matplotlib: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
-
-    """
-    arguments = {"loc": [], "s": [], "c": [], "marker": []}
-    for agent in space.agents:
-        portray = agent_portrayal(agent)
-        loc = agent.pos
-        if loc is None:
-            loc = agent.cell.coordinate
-
-        arguments["loc"].append(loc)
-        arguments["s"].append(portray.get("size", s_default))
-        arguments["c"].append(portray.get("color", c_default))
-        arguments["marker"].append(portray.get("marker", marker_default))
-
-    return {k: np.asarray(v) for k, v in arguments.items()}
-
-
 def draw_orthogonal_grid(
     space: OrthogonalGrid,
     agent_portrayal: Callable,
@@ -269,7 +274,7 @@ def draw_orthogonal_grid(
 
     # gather agent data
     s_default = (180 / max(space.width, space.height)) ** 2
-    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
+    arguments = collect_agent_data(space, agent_portrayal, size=s_default)
 
     # plot the agents
     _scatter(ax, arguments)
@@ -309,7 +314,7 @@ def draw_hex_grid(
 
     # gather data
     s_default = (180 / max(space.width, space.height)) ** 2
-    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
+    arguments = collect_agent_data(space, agent_portrayal, size=s_default)
 
     # for hexgrids we have to go from logical coordinates to visual coordinates
     # this is a bit messy.
@@ -412,7 +417,7 @@ def draw_network(
 
     # gather agent data
     s_default = (180 / max(width, height)) ** 2
-    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
+    arguments = collect_agent_data(space, agent_portrayal, size=s_default)
 
     # this assumes that nodes are identified by an integer
     # which is true for default nx graphs but might user changeable
@@ -460,7 +465,7 @@ def draw_continuous_space(
 
     # gather agent data
     s_default = (180 / max(width, height)) ** 2
-    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
+    arguments = collect_agent_data(space, agent_portrayal, size=s_default)
 
     # plot the agents
     _scatter(ax, arguments)
@@ -506,7 +511,7 @@ def draw_voroinoi_grid(
     y_padding = height / 20
 
     s_default = (180 / max(width, height)) ** 2
-    arguments = collect_agent_data(space, agent_portrayal, s_default=s_default)
+    arguments = collect_agent_data(space, agent_portrayal, size=s_default)
 
     ax.set_xlim(x_min - x_padding, x_max + x_padding)
     ax.set_ylim(y_min - y_padding, y_max + y_padding)

From de5ec29940736d1cd47a67736aae1d841f95126f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 16:38:02 +0000
Subject: [PATCH 56/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 1c48833a490..d44c8ad607f 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -127,7 +127,9 @@ def collect_agent_data(
         if len(portray) > 0:
             ignored_fields = list(portray.keys())
             msg = ", ".join(ignored_fields)
-            warnings.warn(f"the following fields are not used in agent portrayal and thus ignored: {msg}.")
+            warnings.warn(
+                f"the following fields are not used in agent portrayal and thus ignored: {msg}."
+            )
 
     return {k: np.asarray(v) for k, v in arguments.items()}
 

From e6938c1623217b39395bae275f4b811a185e74cc Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 17:58:43 +0100
Subject: [PATCH 57/74] further doc updates

---
 mesa/visualization/components/matplotlib.py | 37 ++++++++++++++++-----
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index d44c8ad607f..188afd5a291 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -40,12 +40,22 @@
 Network = NetworkGrid | mesa.experimental.cell_space.Network
 
 
-def make_space_matplotlib(agent_portrayal=None, propertylayer_portrayal=None):
+def make_space_matplotlib(agent_portrayal: Callable | None = None,
+                          propertylayer_portrayal: dict | None = None,
+                          post_process: Callable | None = None,
+                          **space_drawing_kwargs):
     """Create a Matplotlib-based space visualization component.
 
     Args:
-        agent_portrayal (function): Function to portray agents
-        propertylayer_portrayal (dict): Dictionary of PropertyLayer portrayal specifications
+        agent_portrayal: Function to portray agents.
+        propertylayer_portrayal: Dictionary of PropertyLayer portrayal specifications
+        post_process : a callable that will be called with the Axes instance. Allows for fine tuning plots (e.g., control ticks)
+        space_drawing_kwargs : additional keyword arguments to be passed on to the underlying space drawer function. See
+                               the functions for drawing the various spaces for further details.
+
+    ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
+    "size", and "marker". Other field are ignored and will result in a user warning.
+
 
     Returns:
         function: A function that creates a SpaceMatplotlib component
@@ -53,10 +63,10 @@ def make_space_matplotlib(agent_portrayal=None, propertylayer_portrayal=None):
     if agent_portrayal is None:
 
         def agent_portrayal(a):
-            return {"id": a.unique_id}
+            return {}
 
     def MakeSpaceMatplotlib(model):
-        return SpaceMatplotlib(model, agent_portrayal, propertylayer_portrayal)
+        return SpaceMatplotlib(model, agent_portrayal, propertylayer_portrayal, post_process=post_process, **space_drawing_kwargs)
 
     return MakeSpaceMatplotlib
 
@@ -67,6 +77,8 @@ def SpaceMatplotlib(
     agent_portrayal,
     propertylayer_portrayal,
     dependencies: list[any] | None = None,
+    post_process: Callable| None = None,
+    **space_drawing_kwargs
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
@@ -79,7 +91,7 @@ def SpaceMatplotlib(
     ax = fig.add_subplot()
 
     draw_space(
-        space, agent_portrayal, propertylayer_portrayal=propertylayer_portrayal, ax=ax
+        space, agent_portrayal, propertylayer_portrayal=propertylayer_portrayal, ax=ax, post_process=post_process, **space_drawing_kwargs
     )
 
     solara.FigureMatplotlib(
@@ -139,6 +151,8 @@ def draw_space(
     agent_portrayal: Callable,
     propertylayer_portrayal: dict | None = None,
     ax: Axes | None = None,
+    space_drawing_kwargs: dict | None = None,
+    post_process: Callable| None = None,
 ):
     """Draw a Matplotlib-based visualization of the space.
 
@@ -147,6 +161,8 @@ def draw_space(
         agent_portrayal: A callable that returns a dict specifying how to show the agent
         propertylayer_portrayal: a dict specifying how to show propertylayer(s)
         ax: the axes upon which to draw the plot
+        postprocess: a user-specified callable to do post-processing called with the Axes instance. This callable
+        can be used for any further fine-tuning of the plot (e.g., changing ticks, etc.)
 
     """
     if ax is None:
@@ -155,11 +171,11 @@ def draw_space(
     # https://stackoverflow.com/questions/67524641/convert-multiple-isinstance-checks-to-structural-pattern-matching
     match space:
         case mesa.space._Grid() | OrthogonalMooreGrid() | OrthogonalVonNeumannGrid():
-            draw_orthogonal_grid(space, agent_portrayal, ax=ax)
+            draw_orthogonal_grid(space, agent_portrayal, ax=ax, **space_drawing_kwargs)
         case HexSingleGrid() | HexMultiGrid() | mesa.experimental.cell_space.HexGrid():
-            draw_hex_grid(space, agent_portrayal, ax=ax)
+            draw_hex_grid(space, agent_portrayal, ax=ax, **space_drawing_kwargs)
         case mesa.space.NetworkGrid() | mesa.experimental.cell_space.Network():
-            draw_network(space, agent_portrayal, ax=ax)
+            draw_network(space, agent_portrayal, ax=ax, **space_drawing_kwargs)
         case mesa.space.ContinuousSpace():
             draw_continuous_space(space, agent_portrayal, ax=ax)
         case VoronoiGrid():
@@ -168,6 +184,9 @@ def draw_space(
     if propertylayer_portrayal:
         draw_property_layers(space, propertylayer_portrayal, ax=ax)
 
+    if post_process is not None:
+        post_process(ax=ax)
+
 
 def draw_property_layers(
     space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes

From 292510694859281e9f66369946c6ee201376dddd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 16:59:33 +0000
Subject: [PATCH 58/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 31 +++++++++++++++------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 188afd5a291..cf6a9dec9c6 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -40,10 +40,12 @@
 Network = NetworkGrid | mesa.experimental.cell_space.Network
 
 
-def make_space_matplotlib(agent_portrayal: Callable | None = None,
-                          propertylayer_portrayal: dict | None = None,
-                          post_process: Callable | None = None,
-                          **space_drawing_kwargs):
+def make_space_matplotlib(
+    agent_portrayal: Callable | None = None,
+    propertylayer_portrayal: dict | None = None,
+    post_process: Callable | None = None,
+    **space_drawing_kwargs,
+):
     """Create a Matplotlib-based space visualization component.
 
     Args:
@@ -66,7 +68,13 @@ def agent_portrayal(a):
             return {}
 
     def MakeSpaceMatplotlib(model):
-        return SpaceMatplotlib(model, agent_portrayal, propertylayer_portrayal, post_process=post_process, **space_drawing_kwargs)
+        return SpaceMatplotlib(
+            model,
+            agent_portrayal,
+            propertylayer_portrayal,
+            post_process=post_process,
+            **space_drawing_kwargs,
+        )
 
     return MakeSpaceMatplotlib
 
@@ -77,8 +85,8 @@ def SpaceMatplotlib(
     agent_portrayal,
     propertylayer_portrayal,
     dependencies: list[any] | None = None,
-    post_process: Callable| None = None,
-    **space_drawing_kwargs
+    post_process: Callable | None = None,
+    **space_drawing_kwargs,
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
@@ -91,7 +99,12 @@ def SpaceMatplotlib(
     ax = fig.add_subplot()
 
     draw_space(
-        space, agent_portrayal, propertylayer_portrayal=propertylayer_portrayal, ax=ax, post_process=post_process, **space_drawing_kwargs
+        space,
+        agent_portrayal,
+        propertylayer_portrayal=propertylayer_portrayal,
+        ax=ax,
+        post_process=post_process,
+        **space_drawing_kwargs,
     )
 
     solara.FigureMatplotlib(
@@ -152,7 +165,7 @@ def draw_space(
     propertylayer_portrayal: dict | None = None,
     ax: Axes | None = None,
     space_drawing_kwargs: dict | None = None,
-    post_process: Callable| None = None,
+    post_process: Callable | None = None,
 ):
     """Draw a Matplotlib-based visualization of the space.
 

From 0ce0c7c4f74dea7a826ce02cb105b7edbc23f8ce Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 18:05:08 +0100
Subject: [PATCH 59/74] Update test_solara_viz.py

---
 tests/test_solara_viz.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_solara_viz.py b/tests/test_solara_viz.py
index a0d2b449399..f6b0a5ac64e 100644
--- a/tests/test_solara_viz.py
+++ b/tests/test_solara_viz.py
@@ -97,7 +97,7 @@ def test_call_space_drawer(mocker):  # noqa: D103
     mocker.patch.object(mesa.Model, "__init__", return_value=None)
 
     agent_portrayal = {
-        "Shape": "circle",
+        "marker": "circle",
         "color": "gray",
     }
     propertylayer_portrayal = None
@@ -106,7 +106,7 @@ def test_call_space_drawer(mocker):  # noqa: D103
     solara.render(SolaraViz(model, components=[make_space_matplotlib(agent_portrayal)]))
     # should call default method with class instance and agent portrayal
     mock_space_matplotlib.assert_called_with(
-        model, agent_portrayal, propertylayer_portrayal
+        model, agent_portrayal, propertylayer_portrayal, post_process=None
     )
 
     # specify no space should be drawn

From 9282bfeba6cdded42043ed92d36e924c9beeb6c7 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 18:14:30 +0100
Subject: [PATCH 60/74] ruff related fixes

---
 mesa/visualization/components/matplotlib.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index cf6a9dec9c6..3241e48fc4c 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -153,7 +153,8 @@ def collect_agent_data(
             ignored_fields = list(portray.keys())
             msg = ", ".join(ignored_fields)
             warnings.warn(
-                f"the following fields are not used in agent portrayal and thus ignored: {msg}."
+                f"the following fields are not used in agent portrayal and thus ignored: {msg}.",
+                stacklevel=2
             )
 
     return {k: np.asarray(v) for k, v in arguments.items()}
@@ -164,8 +165,8 @@ def draw_space(
     agent_portrayal: Callable,
     propertylayer_portrayal: dict | None = None,
     ax: Axes | None = None,
-    space_drawing_kwargs: dict | None = None,
     post_process: Callable | None = None,
+    **space_drawing_kwargs,
 ):
     """Draw a Matplotlib-based visualization of the space.
 
@@ -174,6 +175,9 @@ def draw_space(
         agent_portrayal: A callable that returns a dict specifying how to show the agent
         propertylayer_portrayal: a dict specifying how to show propertylayer(s)
         ax: the axes upon which to draw the plot
+        post_process: a callable called with the Axes instance
+        space_drawing_kwargs: any additional keyword arguments to be passed on to the underlying function for drawing the space.
+
         postprocess: a user-specified callable to do post-processing called with the Axes instance. This callable
         can be used for any further fine-tuning of the plot (e.g., changing ticks, etc.)
 

From d5b8ec6ebfd0742d8c76c3018f480830ce7ab191 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 17:14:40 +0000
Subject: [PATCH 61/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 3241e48fc4c..8b8db2f018d 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -154,7 +154,7 @@ def collect_agent_data(
             msg = ", ".join(ignored_fields)
             warnings.warn(
                 f"the following fields are not used in agent portrayal and thus ignored: {msg}.",
-                stacklevel=2
+                stacklevel=2,
             )
 
     return {k: np.asarray(v) for k, v in arguments.items()}

From ce2a8defb6748960cb8761235fe4df7bff145476 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 19:39:21 +0100
Subject: [PATCH 62/74] update example

---
 mesa/examples/advanced/wolf_sheep/app.py      | 27 ++++++++++---------
 .../basic/conways_game_of_life/app.py         |  9 +++++--
 2 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index bea98fd3630..f4c53171337 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -7,34 +7,28 @@
     make_space_matplotlib,
 )
 
-WOLF_COLOR = "#000000"
-SHEEP_COLOR = "#648FFF"
-
 
 def wolf_sheep_portrayal(agent):
     if agent is None:
         return
 
     portrayal = {
-        "s": 25,
+        "size": 25,
     }
 
     if isinstance(agent, Wolf):
-        portrayal["c"] = "tab:orange"
+        portrayal["color"] = "tab:orange"
         portrayal["marker"] = "o"
     elif isinstance(agent, Sheep):
-        portrayal["c"] = "tab:blue"
-        portrayal["zorder"] = 2
+        portrayal["color"] = "tab:blue"
         portrayal["marker"] = "o"
     elif isinstance(agent, GrassPatch):
         if agent.fully_grown:
-            portrayal["c"] = "tab:green"
+            portrayal["color"] = "tab:green"
         else:
-            portrayal["c"] = "tab:brown"
+            portrayal["color"] = "tab:brown"
         portrayal["marker"] = "s"
-        # portrayal["Filled"] = "true"
-        portrayal["zorder"] = 1
-        portrayal["s"] = 75
+        portrayal["size"] = 75
 
     return portrayal
 
@@ -63,7 +57,13 @@ def wolf_sheep_portrayal(agent):
 }
 
 
-space_component = make_space_matplotlib(wolf_sheep_portrayal)
+def post_process(ax):
+    ax.set_aspect("equal")
+    ax.set_xticks([])
+    ax.set_yticks([])
+
+
+space_component = make_space_matplotlib(wolf_sheep_portrayal, draw_grid=False, post_process=post_process)
 lineplot_component = make_plot_measure(
     {"Wolves": "tab:orange", "Sheep": "tab:blue", "Grass": "tab:green"}
 )
@@ -71,6 +71,7 @@ def wolf_sheep_portrayal(agent):
 model = WolfSheep(grass=True)
 
 
+
 page = SolaraViz(
     model,
     components=[space_component, lineplot_component],
diff --git a/mesa/examples/basic/conways_game_of_life/app.py b/mesa/examples/basic/conways_game_of_life/app.py
index 2c9dace8635..66bf5dfe5b2 100644
--- a/mesa/examples/basic/conways_game_of_life/app.py
+++ b/mesa/examples/basic/conways_game_of_life/app.py
@@ -1,12 +1,17 @@
+import sys
+import os.path
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+
+
 from mesa.examples.basic.conways_game_of_life.model import ConwaysGameOfLife
 from mesa.visualization import (
     SolaraViz,
     make_space_matplotlib,
 )
 
-
 def agent_portrayal(agent):
-    return {"color": "white" if agent.state == 0 else "black"}
+    return {"c": "white" if agent.state == 0 else "black",
+            "marker":'s'}
 
 
 model_params = {

From 9efaa99276678ef26a6d3db71b20f8a4f898b26c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 18:39:34 +0000
Subject: [PATCH 63/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/advanced/wolf_sheep/app.py        |  5 +++--
 mesa/examples/basic/conways_game_of_life/app.py | 11 +++++++----
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index f4c53171337..d4fd8189b48 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -63,7 +63,9 @@ def post_process(ax):
     ax.set_yticks([])
 
 
-space_component = make_space_matplotlib(wolf_sheep_portrayal, draw_grid=False, post_process=post_process)
+space_component = make_space_matplotlib(
+    wolf_sheep_portrayal, draw_grid=False, post_process=post_process
+)
 lineplot_component = make_plot_measure(
     {"Wolves": "tab:orange", "Sheep": "tab:blue", "Grass": "tab:green"}
 )
@@ -71,7 +73,6 @@ def post_process(ax):
 model = WolfSheep(grass=True)
 
 
-
 page = SolaraViz(
     model,
     components=[space_component, lineplot_component],
diff --git a/mesa/examples/basic/conways_game_of_life/app.py b/mesa/examples/basic/conways_game_of_life/app.py
index 66bf5dfe5b2..bafeb1a937b 100644
--- a/mesa/examples/basic/conways_game_of_life/app.py
+++ b/mesa/examples/basic/conways_game_of_life/app.py
@@ -1,6 +1,9 @@
-import sys
 import os.path
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+import sys
+
+sys.path.insert(
+    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
+)
 
 
 from mesa.examples.basic.conways_game_of_life.model import ConwaysGameOfLife
@@ -9,9 +12,9 @@
     make_space_matplotlib,
 )
 
+
 def agent_portrayal(agent):
-    return {"c": "white" if agent.state == 0 else "black",
-            "marker":'s'}
+    return {"c": "white" if agent.state == 0 else "black", "marker": "s"}
 
 
 model_params = {

From 3a753bbae3bc6ad869b036cdaece4e4b2c273039 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 19:54:07 +0100
Subject: [PATCH 64/74] ensure visualization.components is included in the docs

---
 docs/apis/visualization.md | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/docs/apis/visualization.md b/docs/apis/visualization.md
index 10349aaf240..7815ec568b8 100644
--- a/docs/apis/visualization.md
+++ b/docs/apis/visualization.md
@@ -19,3 +19,22 @@ For a detailed tutorial, please refer to our [Visualization Tutorial](../tutoria
    :undoc-members:
    :show-inheritance:
 ```
+
+
+## Matplotlib-based components
+
+```{eval-rst}
+.. automodule:: mesa.visualization.components.matplotlib
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
+## Altair-based components
+
+```{eval-rst}
+.. automodule:: mesa.visualization.components.altair
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
\ No newline at end of file

From 27e5e2636242745f6a0bef9e1c889f3cb1e6b9b9 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 20:09:18 +0100
Subject: [PATCH 65/74] add zorder in and update example

---
 mesa/examples/advanced/wolf_sheep/app.py    | 14 +++++++++++---
 mesa/visualization/components/matplotlib.py | 19 ++++++++++++++-----
 2 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index d4fd8189b48..6f30489c145 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,3 +1,9 @@
+import sys
+import os.path
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+
+
+
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
 from mesa.examples.advanced.wolf_sheep.model import WolfSheep
 from mesa.visualization import (
@@ -17,11 +23,13 @@ def wolf_sheep_portrayal(agent):
     }
 
     if isinstance(agent, Wolf):
-        portrayal["color"] = "tab:orange"
+        portrayal["color"] = "tab:red"
         portrayal["marker"] = "o"
+        portrayal["zorder"] = 2
     elif isinstance(agent, Sheep):
-        portrayal["color"] = "tab:blue"
+        portrayal["color"] = "tab:cyan"
         portrayal["marker"] = "o"
+        portrayal["zorder"] = 2
     elif isinstance(agent, GrassPatch):
         if agent.fully_grown:
             portrayal["color"] = "tab:green"
@@ -67,7 +75,7 @@ def post_process(ax):
     wolf_sheep_portrayal, draw_grid=False, post_process=post_process
 )
 lineplot_component = make_plot_measure(
-    {"Wolves": "tab:orange", "Sheep": "tab:blue", "Grass": "tab:green"}
+    {"Wolves": "tab:orange", "Sheep": "tab:cyan", "Grass": "tab:green"}
 )
 
 model = WolfSheep(grass=True)
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 8b8db2f018d..23e42d95060 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -118,6 +118,7 @@ def collect_agent_data(
     color="tab:blue",
     size=25,
     marker="o",
+    zorder:int = 1
 ):
     """Collect the plotting data for all agents in the space.
 
@@ -128,6 +129,7 @@ def collect_agent_data(
         color: default color
         marker: default marker
         size: default size
+        zorder: default zorder
 
     Notes:
         agent portray dict is limited to size (size of marker), color (color of marker, and marker (marker style)
@@ -137,7 +139,8 @@ def collect_agent_data(
     .. _Matplotlib: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
 
     """
-    arguments = {"loc": [], "s": [], "c": [], "marker": []}
+    arguments = {"s":[],"c":[], "marker":[], "zorder":[], 'loc':[]}
+
     for agent in space.agents:
         portray = agent_portrayal(agent)
         loc = agent.pos
@@ -148,6 +151,7 @@ def collect_agent_data(
         arguments["s"].append(portray.pop("size", size))
         arguments["c"].append(portray.pop("color", color))
         arguments["marker"].append(portray.pop("marker", marker))
+        arguments["zorder"].append(portray.pop("zorder", zorder))
 
         if len(portray) > 0:
             ignored_fields = list(portray.keys())
@@ -574,12 +578,17 @@ def _scatter(ax: Axes, arguments):
     x = loc[:, 0]
     y = loc[:, 1]
     marker = arguments.pop("marker")
+    zorder = arguments.pop("zorder")
+
 
     for mark in np.unique(marker):
-        mask = marker == mark
-        ax.scatter(
-            x[mask], y[mask], marker=mark, **{k: v[mask] for k, v in arguments.items()}
-        )
+        mark_mask = marker == mark
+        for z_order in np.unique(zorder):
+            zorder_mask = z_order == zorder
+            logical = mark_mask & zorder_mask
+            ax.scatter(
+                x[logical], y[logical], marker=mark, zorder=z_order, **{k: v[logical] for k, v in arguments.items()}
+            )
 
 
 def make_plot_measure(measure: str | dict[str, str] | list[str] | tuple[str]):

From f36fbbcd49e2ee6e589be78963283a4db548210d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 19:09:28 +0000
Subject: [PATCH 66/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/advanced/wolf_sheep/app.py    |  6 ++++--
 mesa/visualization/components/matplotlib.py | 11 +++++++----
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index 6f30489c145..1c60fe7b3b0 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,7 +1,9 @@
-import sys
 import os.path
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../../../')))
+import sys
 
+sys.path.insert(
+    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
+)
 
 
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 23e42d95060..d30f302a5a8 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -118,7 +118,7 @@ def collect_agent_data(
     color="tab:blue",
     size=25,
     marker="o",
-    zorder:int = 1
+    zorder: int = 1,
 ):
     """Collect the plotting data for all agents in the space.
 
@@ -139,7 +139,7 @@ def collect_agent_data(
     .. _Matplotlib: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
 
     """
-    arguments = {"s":[],"c":[], "marker":[], "zorder":[], 'loc':[]}
+    arguments = {"s": [], "c": [], "marker": [], "zorder": [], "loc": []}
 
     for agent in space.agents:
         portray = agent_portrayal(agent)
@@ -580,14 +580,17 @@ def _scatter(ax: Axes, arguments):
     marker = arguments.pop("marker")
     zorder = arguments.pop("zorder")
 
-
     for mark in np.unique(marker):
         mark_mask = marker == mark
         for z_order in np.unique(zorder):
             zorder_mask = z_order == zorder
             logical = mark_mask & zorder_mask
             ax.scatter(
-                x[logical], y[logical], marker=mark, zorder=z_order, **{k: v[logical] for k, v in arguments.items()}
+                x[logical],
+                y[logical],
+                marker=mark,
+                zorder=z_order,
+                **{k: v[logical] for k, v in arguments.items()},
             )
 
 

From 9c2e8cdbf81a9859e53551282e9672a121523f67 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 20:11:44 +0100
Subject: [PATCH 67/74] docstring fixes

---
 mesa/visualization/components/matplotlib.py | 30 ++++++++++-----------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index d30f302a5a8..318a3abe898 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -56,7 +56,7 @@ def make_space_matplotlib(
                                the functions for drawing the various spaces for further details.
 
     ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
-    "size", and "marker". Other field are ignored and will result in a user warning.
+    "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
 
     Returns:
@@ -180,10 +180,12 @@ def draw_space(
         propertylayer_portrayal: a dict specifying how to show propertylayer(s)
         ax: the axes upon which to draw the plot
         post_process: a callable called with the Axes instance
-        space_drawing_kwargs: any additional keyword arguments to be passed on to the underlying function for drawing the space.
-
         postprocess: a user-specified callable to do post-processing called with the Axes instance. This callable
         can be used for any further fine-tuning of the plot (e.g., changing ticks, etc.)
+        space_drawing_kwargs: any additional keyword arguments to be passed on to the underlying function for drawing the space.
+
+    ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
+    "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
     """
     if ax is None:
@@ -307,8 +309,8 @@ def draw_orthogonal_grid(
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
         draw_grid: whether to draw the grid
 
-    Returns:
-        A Figure and Axes instance
+    ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
+    "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
     """
     if ax is None:
@@ -347,8 +349,8 @@ def draw_hex_grid(
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
         draw_grid: whether to draw the grid
 
-    Returns:
-        A Figure and Axes instance
+    ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
+    "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
     """
     if ax is None:
@@ -434,10 +436,8 @@ def draw_network(
         layout_alg: a networkx layout algorithm or other callable with the same behavior
         layout_kwargs: a dictionary of keyword arguments for the layout algorithm
 
-    Notes:
-        this uses networkx.draw under the hood so agent portrayal fields should match those used there
-        i.e., node_size and node_color.
-
+    ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
+    "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
     """
     if ax is None:
@@ -492,8 +492,8 @@ def draw_continuous_space(
         agent_portrayal: a callable that is called with the agent and returns a dict
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
 
-    Returns:
-        A Figure and Axes instance
+    ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
+    "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
     """
     if ax is None:
@@ -533,8 +533,8 @@ def draw_voroinoi_grid(
         agent_portrayal: a callable that is called with the agent and returns a dict
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
 
-    Returns:
-        A Figure and Axes instance
+    ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
+    "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
     """
     if ax is None:

From cdbea6e2ffedba7879fea0cd9b25a7610c06ed69 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 20:24:25 +0100
Subject: [PATCH 68/74] cleanup

---
 mesa/examples/advanced/wolf_sheep/app.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index 1c60fe7b3b0..fc37949487f 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -1,11 +1,3 @@
-import os.path
-import sys
-
-sys.path.insert(
-    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
-)
-
-
 from mesa.examples.advanced.wolf_sheep.agents import GrassPatch, Sheep, Wolf
 from mesa.examples.advanced.wolf_sheep.model import WolfSheep
 from mesa.visualization import (

From f371ef0be8fb7b94917f85bde22f9868107b821b Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 20:29:25 +0100
Subject: [PATCH 69/74] rename to make_space_component, return ax and update
 docs

---
 docs/migration_guide.md                       |   4 +-
 docs/overview.md                              |   6 +-
 .../advanced/epstein_civil_violence/app.py    |   4 +-
 mesa/examples/advanced/pd_grid/app.py         |   4 +-
 mesa/examples/advanced/sugarscape_g1mt/app.py |   8 --
 mesa/examples/advanced/wolf_sheep/app.py      |   4 +-
 mesa/examples/basic/boid_flockers/app.py      |   4 +-
 .../basic/boltzmann_wealth_model/app.py       |   4 +-
 .../basic/conways_game_of_life/app.py         |   4 +-
 mesa/examples/basic/schelling/app.py          |   4 +-
 mesa/examples/basic/virus_on_network/app.py   |   4 +-
 mesa/visualization/__init__.py                |   4 +-
 mesa/visualization/components/matplotlib.py   | 119 +++++++++++-------
 tests/test_solara_viz.py                      |   6 +-
 14 files changed, 100 insertions(+), 79 deletions(-)

diff --git a/docs/migration_guide.md b/docs/migration_guide.md
index b4f54c3dfd7..016053e84fb 100644
--- a/docs/migration_guide.md
+++ b/docs/migration_guide.md
@@ -268,9 +268,9 @@ from mesa.experimental import SolaraViz
 SolaraViz(model_cls, model_params, agent_portrayal=agent_portrayal)
 
 # new
-from mesa.visualization import SolaraViz, make_space_matplotlib
+from mesa.visualization import SolaraViz, make_space_component
 
-SolaraViz(model, components=[make_space_matplotlib(agent_portrayal)])
+SolaraViz(model, components=[make_space_component(agent_portrayal)])
 ```
 
 #### Plotting "measures"
diff --git a/docs/overview.md b/docs/overview.md
index 17ef67302fe..7d0c750ed84 100644
--- a/docs/overview.md
+++ b/docs/overview.md
@@ -168,11 +168,13 @@ The results are returned as a list of dictionaries, which can be easily converte
 Mesa now uses a new browser-based visualization system called SolaraViz. This allows for interactive, customizable visualizations of your models. Here's a basic example of how to set up a visualization:
 
 ```python
-from mesa.visualization import SolaraViz, make_space_matplotlib, make_plot_measure
+from mesa.visualization import SolaraViz, make_space_component, make_plot_measure
+
 
 def agent_portrayal(agent):
     return {"color": "blue", "size": 50}
 
+
 model_params = {
     "N": {
         "type": "SliderInt",
@@ -187,7 +189,7 @@ model_params = {
 page = SolaraViz(
     MyModel,
     [
-        make_space_matplotlib(agent_portrayal),
+        make_space_component(agent_portrayal),
         make_plot_measure("mean_age")
     ],
     model_params=model_params
diff --git a/mesa/examples/advanced/epstein_civil_violence/app.py b/mesa/examples/advanced/epstein_civil_violence/app.py
index 862ca6220d8..538ef186f57 100644
--- a/mesa/examples/advanced/epstein_civil_violence/app.py
+++ b/mesa/examples/advanced/epstein_civil_violence/app.py
@@ -8,7 +8,7 @@
     Slider,
     SolaraViz,
     make_plot_measure,
-    make_space_matplotlib,
+    make_space_component,
 )
 
 COP_COLOR = "#000000"
@@ -47,7 +47,7 @@ def citizen_cop_portrayal(agent):
     "max_jail_term": Slider("Max Jail Term", 30, 0, 50, 1),
 }
 
-space_component = make_space_matplotlib(citizen_cop_portrayal)
+space_component = make_space_component(citizen_cop_portrayal)
 chart_component = make_plot_measure([state.name.lower() for state in CitizenState])
 
 epstein_model = EpsteinCivilViolence()
diff --git a/mesa/examples/advanced/pd_grid/app.py b/mesa/examples/advanced/pd_grid/app.py
index c8ceec9fe16..6edf8140536 100644
--- a/mesa/examples/advanced/pd_grid/app.py
+++ b/mesa/examples/advanced/pd_grid/app.py
@@ -3,7 +3,7 @@
 """
 
 from mesa.examples.advanced.pd_grid.model import PdGrid
-from mesa.visualization import SolaraViz, make_plot_measure, make_space_matplotlib
+from mesa.visualization import SolaraViz, make_plot_measure, make_space_component
 from mesa.visualization.UserParam import Slider
 
 
@@ -32,7 +32,7 @@ def pd_agent_portrayal(agent):
 
 
 # Create grid visualization component using Altair
-grid_viz = make_space_matplotlib(agent_portrayal=pd_agent_portrayal)
+grid_viz = make_space_component(agent_portrayal=pd_agent_portrayal)
 
 # Create plot for tracking cooperating agents over time
 plot_component = make_plot_measure("Cooperating_Agents")
diff --git a/mesa/examples/advanced/sugarscape_g1mt/app.py b/mesa/examples/advanced/sugarscape_g1mt/app.py
index 7c8cc2cfead..752998891bd 100644
--- a/mesa/examples/advanced/sugarscape_g1mt/app.py
+++ b/mesa/examples/advanced/sugarscape_g1mt/app.py
@@ -1,11 +1,3 @@
-import os.path
-import sys
-
-sys.path.insert(
-    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
-)
-
-
 import numpy as np
 import solara
 from matplotlib.figure import Figure
diff --git a/mesa/examples/advanced/wolf_sheep/app.py b/mesa/examples/advanced/wolf_sheep/app.py
index fc37949487f..a8c0a1e9c49 100644
--- a/mesa/examples/advanced/wolf_sheep/app.py
+++ b/mesa/examples/advanced/wolf_sheep/app.py
@@ -4,7 +4,7 @@
     Slider,
     SolaraViz,
     make_plot_measure,
-    make_space_matplotlib,
+    make_space_component,
 )
 
 
@@ -65,7 +65,7 @@ def post_process(ax):
     ax.set_yticks([])
 
 
-space_component = make_space_matplotlib(
+space_component = make_space_component(
     wolf_sheep_portrayal, draw_grid=False, post_process=post_process
 )
 lineplot_component = make_plot_measure(
diff --git a/mesa/examples/basic/boid_flockers/app.py b/mesa/examples/basic/boid_flockers/app.py
index 482d582b8ba..bcecb0a3ebd 100644
--- a/mesa/examples/basic/boid_flockers/app.py
+++ b/mesa/examples/basic/boid_flockers/app.py
@@ -1,5 +1,5 @@
 from mesa.examples.basic.boid_flockers.model import BoidFlockers
-from mesa.visualization import Slider, SolaraViz, make_space_matplotlib
+from mesa.visualization import Slider, SolaraViz, make_space_component
 
 
 def boid_draw(agent):
@@ -51,7 +51,7 @@ def boid_draw(agent):
 
 page = SolaraViz(
     model,
-    [make_space_matplotlib(agent_portrayal=boid_draw)],
+    [make_space_component(agent_portrayal=boid_draw)],
     model_params=model_params,
     name="Boid Flocking Model",
 )
diff --git a/mesa/examples/basic/boltzmann_wealth_model/app.py b/mesa/examples/basic/boltzmann_wealth_model/app.py
index 7e3f41e64de..2ab6d06bf73 100644
--- a/mesa/examples/basic/boltzmann_wealth_model/app.py
+++ b/mesa/examples/basic/boltzmann_wealth_model/app.py
@@ -2,7 +2,7 @@
 from mesa.visualization import (
     SolaraViz,
     make_plot_measure,
-    make_space_matplotlib,
+    make_space_component,
 )
 
 
@@ -36,7 +36,7 @@ def agent_portrayal(agent):
 # Under the hood these are just classes that receive the model instance.
 # You can also author your own visualization elements, which can also be functions
 # that receive the model instance and return a valid solara component.
-SpaceGraph = make_space_matplotlib(agent_portrayal)
+SpaceGraph = make_space_component(agent_portrayal)
 GiniPlot = make_plot_measure("Gini")
 
 # Create the SolaraViz page. This will automatically create a server and display the
diff --git a/mesa/examples/basic/conways_game_of_life/app.py b/mesa/examples/basic/conways_game_of_life/app.py
index bafeb1a937b..aee1733e523 100644
--- a/mesa/examples/basic/conways_game_of_life/app.py
+++ b/mesa/examples/basic/conways_game_of_life/app.py
@@ -9,7 +9,7 @@
 from mesa.examples.basic.conways_game_of_life.model import ConwaysGameOfLife
 from mesa.visualization import (
     SolaraViz,
-    make_space_matplotlib,
+    make_space_component,
 )
 
 
@@ -30,7 +30,7 @@ def agent_portrayal(agent):
 # Under the hood these are just classes that receive the model instance.
 # You can also author your own visualization elements, which can also be functions
 # that receive the model instance and return a valid solara component.
-SpaceGraph = make_space_matplotlib(agent_portrayal)
+SpaceGraph = make_space_component(agent_portrayal)
 
 
 # Create the SolaraViz page. This will automatically create a server and display the
diff --git a/mesa/examples/basic/schelling/app.py b/mesa/examples/basic/schelling/app.py
index 72ae6ddc1ec..53fab7ba0f0 100644
--- a/mesa/examples/basic/schelling/app.py
+++ b/mesa/examples/basic/schelling/app.py
@@ -5,7 +5,7 @@
     Slider,
     SolaraViz,
     make_plot_measure,
-    make_space_matplotlib,
+    make_space_component,
 )
 
 
@@ -33,7 +33,7 @@ def agent_portrayal(agent):
 page = SolaraViz(
     model1,
     components=[
-        make_space_matplotlib(agent_portrayal),
+        make_space_component(agent_portrayal),
         make_plot_measure("happy"),
         get_happy_agents,
     ],
diff --git a/mesa/examples/basic/virus_on_network/app.py b/mesa/examples/basic/virus_on_network/app.py
index 0183d256790..7cf54f308d5 100644
--- a/mesa/examples/basic/virus_on_network/app.py
+++ b/mesa/examples/basic/virus_on_network/app.py
@@ -9,7 +9,7 @@
     VirusOnNetwork,
     number_infected,
 )
-from mesa.visualization import Slider, SolaraViz, make_space_matplotlib
+from mesa.visualization import Slider, SolaraViz, make_space_component
 
 
 def agent_portrayal(graph):
@@ -119,7 +119,7 @@ def make_plot(model):
     ),
 }
 
-SpacePlot = make_space_matplotlib(agent_portrayal)
+SpacePlot = make_space_component(agent_portrayal)
 
 model1 = VirusOnNetwork()
 
diff --git a/mesa/visualization/__init__.py b/mesa/visualization/__init__.py
index d6e50c37e36..0e1875c751c 100644
--- a/mesa/visualization/__init__.py
+++ b/mesa/visualization/__init__.py
@@ -1,7 +1,7 @@
 """Solara based visualization for Mesa models."""
 
 from .components.altair import make_space_altair
-from .components.matplotlib import make_plot_measure, make_space_matplotlib
+from .components.matplotlib import make_plot_measure, make_space_component
 from .solara_viz import JupyterViz, SolaraViz
 from .UserParam import Slider
 
@@ -10,6 +10,6 @@
     "SolaraViz",
     "Slider",
     "make_space_altair",
-    "make_space_matplotlib",
+    "make_space_component",
     "make_plot_measure",
 ]
diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 318a3abe898..f860660955b 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -40,11 +40,11 @@
 Network = NetworkGrid | mesa.experimental.cell_space.Network
 
 
-def make_space_matplotlib(
-    agent_portrayal: Callable | None = None,
-    propertylayer_portrayal: dict | None = None,
-    post_process: Callable | None = None,
-    **space_drawing_kwargs,
+def make_space_component(
+        agent_portrayal: Callable | None = None,
+        propertylayer_portrayal: dict | None = None,
+        post_process: Callable | None = None,
+        **space_drawing_kwargs,
 ):
     """Create a Matplotlib-based space visualization component.
 
@@ -63,7 +63,6 @@ def make_space_matplotlib(
         function: A function that creates a SpaceMatplotlib component
     """
     if agent_portrayal is None:
-
         def agent_portrayal(a):
             return {}
 
@@ -81,12 +80,12 @@ def MakeSpaceMatplotlib(model):
 
 @solara.component
 def SpaceMatplotlib(
-    model,
-    agent_portrayal,
-    propertylayer_portrayal,
-    dependencies: list[any] | None = None,
-    post_process: Callable | None = None,
-    **space_drawing_kwargs,
+        model,
+        agent_portrayal,
+        propertylayer_portrayal,
+        dependencies: list[any] | None = None,
+        post_process: Callable | None = None,
+        **space_drawing_kwargs,
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
@@ -113,26 +112,25 @@ def SpaceMatplotlib(
 
 
 def collect_agent_data(
-    space: OrthogonalGrid | HexGrid | Network | ContinuousSpace | VoronoiGrid,
-    agent_portrayal: Callable,
-    color="tab:blue",
-    size=25,
-    marker="o",
-    zorder: int = 1,
+        space: OrthogonalGrid | HexGrid | Network | ContinuousSpace | VoronoiGrid,
+        agent_portrayal: Callable,
+        color="tab:blue",
+        size=25,
+        marker="o",
+        zorder: int = 1,
 ):
     """Collect the plotting data for all agents in the space.
 
     Args:
         space: The space containing the Agents.
         agent_portrayal: A callable that is called with the agent and returns a dict
-        loc: a boolean indicating whether to gather agent x, y data or not
         color: default color
-        marker: default marker
         size: default size
+        marker: default marker
         zorder: default zorder
 
     Notes:
-        agent portray dict is limited to size (size of marker), color (color of marker, and marker (marker style)
+        agent portray dict is limited to size (size of marker), color (color of marker, zorder, and marker (marker style)
         see `Matplotlib`_.
 
 
@@ -165,12 +163,12 @@ def collect_agent_data(
 
 
 def draw_space(
-    space,
-    agent_portrayal: Callable,
-    propertylayer_portrayal: dict | None = None,
-    ax: Axes | None = None,
-    post_process: Callable | None = None,
-    **space_drawing_kwargs,
+        space,
+        agent_portrayal: Callable,
+        propertylayer_portrayal: dict | None = None,
+        ax: Axes | None = None,
+        post_process: Callable | None = None,
+        **space_drawing_kwargs,
 ):
     """Draw a Matplotlib-based visualization of the space.
 
@@ -184,6 +182,9 @@ def draw_space(
         can be used for any further fine-tuning of the plot (e.g., changing ticks, etc.)
         space_drawing_kwargs: any additional keyword arguments to be passed on to the underlying function for drawing the space.
 
+    Returns:
+        Returns the Axes object with the plot drawn onto it.
+
     ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
     "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
@@ -210,9 +211,11 @@ def draw_space(
     if post_process is not None:
         post_process(ax=ax)
 
+    return ax
+
 
 def draw_property_layers(
-    space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes
+        space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes
 ):
     """Draw PropertyLayers on the given axes.
 
@@ -296,10 +299,10 @@ def draw_property_layers(
 
 
 def draw_orthogonal_grid(
-    space: OrthogonalGrid,
-    agent_portrayal: Callable,
-    ax: Axes | None = None,
-    draw_grid: bool = True,
+        space: OrthogonalGrid,
+        agent_portrayal: Callable,
+        ax: Axes | None = None,
+        draw_grid: bool = True,
 ):
     """Visualize a orthogonal grid.
 
@@ -309,6 +312,9 @@ def draw_orthogonal_grid(
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
         draw_grid: whether to draw the grid
 
+    Returns:
+        Returns the Axes object with the plot drawn onto it.
+
     ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
     "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
@@ -334,12 +340,14 @@ def draw_orthogonal_grid(
         for y in np.arange(-0.5, space.height - 0.5, 1):
             ax.axhline(y, color="gray", linestyle=":")
 
+    return ax
+
 
 def draw_hex_grid(
-    space: HexGrid,
-    agent_portrayal: Callable,
-    ax: Axes | None = None,
-    draw_grid: bool = True,
+        space: HexGrid,
+        agent_portrayal: Callable,
+        ax: Axes | None = None,
+        draw_grid: bool = True,
 ):
     """Visualize a hex grid.
 
@@ -349,6 +357,9 @@ def draw_hex_grid(
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
         draw_grid: whether to draw the grid
 
+    Returns:
+        Returns the Axes object with the plot drawn onto it.
+
     ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
     "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
@@ -384,8 +395,8 @@ def draw_hex_grid(
     ax.set_ylim(-offset, space.height * offset)
 
     def setup_hexmesh(
-        width,
-        height,
+            width,
+            height,
     ):
         """Helper function for creating the hexmaesh."""
         # fixme: this should be done once, rather than in each update
@@ -416,15 +427,16 @@ def setup_hexmesh(
                 space.height,
             )
         )
+    return ax
 
 
 def draw_network(
-    space: Network,
-    agent_portrayal: Callable,
-    ax: Axes | None = None,
-    draw_grid: bool = True,
-    layout_alg=nx.spring_layout,
-    layout_kwargs=None,
+        space: Network,
+        agent_portrayal: Callable,
+        ax: Axes | None = None,
+        draw_grid: bool = True,
+        layout_alg=nx.spring_layout,
+        layout_kwargs=None,
 ):
     """Visualize a network space.
 
@@ -436,6 +448,9 @@ def draw_network(
         layout_alg: a networkx layout algorithm or other callable with the same behavior
         layout_kwargs: a dictionary of keyword arguments for the layout algorithm
 
+    Returns:
+        Returns the Axes object with the plot drawn onto it.
+
     ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
     "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
@@ -481,9 +496,11 @@ def draw_network(
         )
         edge_collection.set_zorder(0)
 
+    return ax
+
 
 def draw_continuous_space(
-    space: ContinuousSpace, agent_portrayal: Callable, ax: Axes | None = None
+        space: ContinuousSpace, agent_portrayal: Callable, ax: Axes | None = None
 ):
     """Visualize a continuous space.
 
@@ -492,6 +509,9 @@ def draw_continuous_space(
         agent_portrayal: a callable that is called with the agent and returns a dict
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
 
+    Returns:
+        Returns the Axes object with the plot drawn onto it.
+
     ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
     "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
@@ -522,9 +542,11 @@ def draw_continuous_space(
     ax.set_xlim(space.x_min - x_padding, space.x_max + x_padding)
     ax.set_ylim(space.y_min - y_padding, space.y_max + y_padding)
 
+    return ax
+
 
 def draw_voroinoi_grid(
-    space: VoronoiGrid, agent_portrayal: Callable, ax: Axes | None = None
+        space: VoronoiGrid, agent_portrayal: Callable, ax: Axes | None = None
 ):
     """Visualize a voronoi grid.
 
@@ -533,6 +555,9 @@ def draw_voroinoi_grid(
         agent_portrayal: a callable that is called with the agent and returns a dict
         ax: a Matplotlib Axes instance. If none is provided a new figure and ax will be created using plt.subplots
 
+    Returns:
+        Returns the Axes object with the plot drawn onto it.
+
     ``agent_portrayal`` is called with an agent and should return a dict. Valid fields in this dict are "color",
     "size", "marker", and "zorder". Other field are ignored and will result in a user warning.
 
@@ -570,6 +595,8 @@ def draw_voroinoi_grid(
         )  # Plot filled polygon
         ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in black
 
+    return ax
+
 
 def _scatter(ax: Axes, arguments):
     """Helper function for plotting the agents."""
diff --git a/tests/test_solara_viz.py b/tests/test_solara_viz.py
index f6b0a5ac64e..af6badd0bc2 100644
--- a/tests/test_solara_viz.py
+++ b/tests/test_solara_viz.py
@@ -8,7 +8,7 @@
 import mesa
 import mesa.visualization.components.altair
 import mesa.visualization.components.matplotlib
-from mesa.visualization.components.matplotlib import make_space_matplotlib
+from mesa.visualization.components.matplotlib import make_space_component
 from mesa.visualization.solara_viz import Slider, SolaraViz, UserInputs
 
 
@@ -103,7 +103,7 @@ def test_call_space_drawer(mocker):  # noqa: D103
     propertylayer_portrayal = None
     # initialize with space drawer unspecified (use default)
     # component must be rendered for code to run
-    solara.render(SolaraViz(model, components=[make_space_matplotlib(agent_portrayal)]))
+    solara.render(SolaraViz(model, components=[make_space_component(agent_portrayal)]))
     # should call default method with class instance and agent portrayal
     mock_space_matplotlib.assert_called_with(
         model, agent_portrayal, propertylayer_portrayal, post_process=None
@@ -132,7 +132,7 @@ def drawer(model):
         centroids_coordinates=[(0, 1), (0, 0), (1, 0)],
     )
     solara.render(
-        SolaraViz(voronoi_model, components=[make_space_matplotlib(agent_portrayal)])
+        SolaraViz(voronoi_model, components=[make_space_component(agent_portrayal)])
     )
 
 

From eabcbabfec15889c30b686ab06ce27f28e6d1c05 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 19:30:11 +0000
Subject: [PATCH 70/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 83 +++++++++++----------
 1 file changed, 42 insertions(+), 41 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index f860660955b..3c9ad970ce7 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -41,10 +41,10 @@
 
 
 def make_space_component(
-        agent_portrayal: Callable | None = None,
-        propertylayer_portrayal: dict | None = None,
-        post_process: Callable | None = None,
-        **space_drawing_kwargs,
+    agent_portrayal: Callable | None = None,
+    propertylayer_portrayal: dict | None = None,
+    post_process: Callable | None = None,
+    **space_drawing_kwargs,
 ):
     """Create a Matplotlib-based space visualization component.
 
@@ -63,6 +63,7 @@ def make_space_component(
         function: A function that creates a SpaceMatplotlib component
     """
     if agent_portrayal is None:
+
         def agent_portrayal(a):
             return {}
 
@@ -80,12 +81,12 @@ def MakeSpaceMatplotlib(model):
 
 @solara.component
 def SpaceMatplotlib(
-        model,
-        agent_portrayal,
-        propertylayer_portrayal,
-        dependencies: list[any] | None = None,
-        post_process: Callable | None = None,
-        **space_drawing_kwargs,
+    model,
+    agent_portrayal,
+    propertylayer_portrayal,
+    dependencies: list[any] | None = None,
+    post_process: Callable | None = None,
+    **space_drawing_kwargs,
 ):
     """Create a Matplotlib-based space visualization component."""
     update_counter.get()
@@ -112,12 +113,12 @@ def SpaceMatplotlib(
 
 
 def collect_agent_data(
-        space: OrthogonalGrid | HexGrid | Network | ContinuousSpace | VoronoiGrid,
-        agent_portrayal: Callable,
-        color="tab:blue",
-        size=25,
-        marker="o",
-        zorder: int = 1,
+    space: OrthogonalGrid | HexGrid | Network | ContinuousSpace | VoronoiGrid,
+    agent_portrayal: Callable,
+    color="tab:blue",
+    size=25,
+    marker="o",
+    zorder: int = 1,
 ):
     """Collect the plotting data for all agents in the space.
 
@@ -163,12 +164,12 @@ def collect_agent_data(
 
 
 def draw_space(
-        space,
-        agent_portrayal: Callable,
-        propertylayer_portrayal: dict | None = None,
-        ax: Axes | None = None,
-        post_process: Callable | None = None,
-        **space_drawing_kwargs,
+    space,
+    agent_portrayal: Callable,
+    propertylayer_portrayal: dict | None = None,
+    ax: Axes | None = None,
+    post_process: Callable | None = None,
+    **space_drawing_kwargs,
 ):
     """Draw a Matplotlib-based visualization of the space.
 
@@ -215,7 +216,7 @@ def draw_space(
 
 
 def draw_property_layers(
-        space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes
+    space, propertylayer_portrayal: dict[str, dict[str, Any]], ax: Axes
 ):
     """Draw PropertyLayers on the given axes.
 
@@ -299,10 +300,10 @@ def draw_property_layers(
 
 
 def draw_orthogonal_grid(
-        space: OrthogonalGrid,
-        agent_portrayal: Callable,
-        ax: Axes | None = None,
-        draw_grid: bool = True,
+    space: OrthogonalGrid,
+    agent_portrayal: Callable,
+    ax: Axes | None = None,
+    draw_grid: bool = True,
 ):
     """Visualize a orthogonal grid.
 
@@ -344,10 +345,10 @@ def draw_orthogonal_grid(
 
 
 def draw_hex_grid(
-        space: HexGrid,
-        agent_portrayal: Callable,
-        ax: Axes | None = None,
-        draw_grid: bool = True,
+    space: HexGrid,
+    agent_portrayal: Callable,
+    ax: Axes | None = None,
+    draw_grid: bool = True,
 ):
     """Visualize a hex grid.
 
@@ -395,8 +396,8 @@ def draw_hex_grid(
     ax.set_ylim(-offset, space.height * offset)
 
     def setup_hexmesh(
-            width,
-            height,
+        width,
+        height,
     ):
         """Helper function for creating the hexmaesh."""
         # fixme: this should be done once, rather than in each update
@@ -431,12 +432,12 @@ def setup_hexmesh(
 
 
 def draw_network(
-        space: Network,
-        agent_portrayal: Callable,
-        ax: Axes | None = None,
-        draw_grid: bool = True,
-        layout_alg=nx.spring_layout,
-        layout_kwargs=None,
+    space: Network,
+    agent_portrayal: Callable,
+    ax: Axes | None = None,
+    draw_grid: bool = True,
+    layout_alg=nx.spring_layout,
+    layout_kwargs=None,
 ):
     """Visualize a network space.
 
@@ -500,7 +501,7 @@ def draw_network(
 
 
 def draw_continuous_space(
-        space: ContinuousSpace, agent_portrayal: Callable, ax: Axes | None = None
+    space: ContinuousSpace, agent_portrayal: Callable, ax: Axes | None = None
 ):
     """Visualize a continuous space.
 
@@ -546,7 +547,7 @@ def draw_continuous_space(
 
 
 def draw_voroinoi_grid(
-        space: VoronoiGrid, agent_portrayal: Callable, ax: Axes | None = None
+    space: VoronoiGrid, agent_portrayal: Callable, ax: Axes | None = None
 ):
     """Visualize a voronoi grid.
 

From 40cc9e4a549cca4e709ea9a6b30132a29fec402e Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 20:39:47 +0100
Subject: [PATCH 71/74] Update visualization_tutorial.ipynb

---
 docs/tutorials/visualization_tutorial.ipynb | 284 +++++++++++++++-----
 1 file changed, 217 insertions(+), 67 deletions(-)

diff --git a/docs/tutorials/visualization_tutorial.ipynb b/docs/tutorials/visualization_tutorial.ipynb
index 7460ca30a19..aff166e9b82 100644
--- a/docs/tutorials/visualization_tutorial.ipynb
+++ b/docs/tutorials/visualization_tutorial.ipynb
@@ -3,9 +3,7 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "# Visualization Tutorial"
-   ]
+   "source": "# Visualization Tutorial"
   },
   {
    "cell_type": "markdown",
@@ -52,40 +50,50 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:46.075682Z",
+     "start_time": "2024-10-29T19:38:45.449918Z"
+    }
+   },
+   "source": [
+    "import mesa\n",
+    "print(f\"Mesa version: {mesa.__version__}\")\n",
+    "\n",
+    "from mesa.visualization import SolaraViz, make_plot_measure, make_space_component\n",
+    "\n",
+    "# Import the local MoneyModel.py\n",
+    "from MoneyModel import MoneyModel\n"
+   ],
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Mesa version: 3.0.0b1\n"
+      "Mesa version: 3.0.0b2\n"
      ]
     }
    ],
-   "source": [
-    "import mesa\n",
-    "print(f\"Mesa version: {mesa.__version__}\")\n",
-    "\n",
-    "from mesa.visualization import SolaraViz, make_plot_measure, make_space_matplotlib\n",
-    "# Import the local MoneyModel.py\n",
-    "from MoneyModel import MoneyModel\n"
-   ]
+   "execution_count": 1
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
-    "tags": []
+    "tags": [],
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:46.079286Z",
+     "start_time": "2024-10-29T19:38:46.076984Z"
+    }
    },
-   "outputs": [],
    "source": [
     "def agent_portrayal(agent):\n",
     "    return {\n",
     "        \"color\": \"tab:blue\",\n",
     "        \"size\": 50,\n",
     "    }"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": 2
   },
   {
    "cell_type": "markdown",
@@ -96,9 +104,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:46.081662Z",
+     "start_time": "2024-10-29T19:38:46.079838Z"
+    }
+   },
    "source": [
     "model_params = {\n",
     "    \"n\": {\n",
@@ -112,7 +123,9 @@
     "    \"width\": 10,\n",
     "    \"height\": 10,\n",
     "}"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": 3
   },
   {
    "cell_type": "markdown",
@@ -130,16 +143,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
-    "tags": []
+    "tags": [],
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:46.864371Z",
+     "start_time": "2024-10-29T19:38:46.082810Z"
+    }
    },
-   "outputs": [],
    "source": [
     "# Create initial model instance\n",
     "model1 = MoneyModel(50, 10, 10)\n",
     "\n",
-    "SpaceGraph = make_space_matplotlib(agent_portrayal)\n",
+    "SpaceGraph = make_space_component(agent_portrayal)\n",
     "GiniPlot = make_plot_measure(\"Gini\")\n",
     "\n",
     "page = SolaraViz(\n",
@@ -150,7 +165,27 @@
     ")\n",
     "# This is required to render the visualization in the Jupyter notebook\n",
     "page"
-   ]
+   ],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Cannot show ipywidgets in text"
+      ],
+      "text/html": [
+       "Cannot show widget. You probably want to rerun the code cell above (<i>Click in the code cell, and press Shift+Enter <kbd>⇧</kbd>+<kbd>↩</kbd></i>)."
+      ],
+      "application/vnd.jupyter.widget-view+json": {
+       "version_major": 2,
+       "version_minor": 0,
+       "model_id": "c9f2ef2b5a24483c92fa129213414a2c"
+      }
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "execution_count": 4
   },
   {
    "cell_type": "markdown",
@@ -169,23 +204,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:46.867576Z",
+     "start_time": "2024-10-29T19:38:46.865205Z"
+    }
+   },
    "source": [
     "import mesa\n",
     "print(f\"Mesa version: {mesa.__version__}\")\n",
     "\n",
-    "from mesa.visualization import SolaraViz, make_plot_measure, make_space_matplotlib\n",
+    "from mesa.visualization import SolaraViz, make_plot_measure, make_space_component\n",
     "# Import the local MoneyModel.py\n",
     "from MoneyModel import MoneyModel\n"
-   ]
+   ],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Mesa version: 3.0.0b2\n"
+     ]
+    }
+   ],
+   "execution_count": 5
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:46.870617Z",
+     "start_time": "2024-10-29T19:38:46.868336Z"
+    }
+   },
    "source": [
     "def agent_portrayal(agent):\n",
     "    size = 10\n",
@@ -207,18 +258,23 @@
     "    \"width\": 10,\n",
     "    \"height\": 10,\n",
     "}"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": 6
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:47.881911Z",
+     "start_time": "2024-10-29T19:38:46.871328Z"
+    }
+   },
    "source": [
     "# Create initial model instance\n",
     "model1 = MoneyModel(50, 10, 10)\n",
     "\n",
-    "SpaceGraph = make_space_matplotlib(agent_portrayal)\n",
+    "SpaceGraph = make_space_component(agent_portrayal)\n",
     "GiniPlot = make_plot_measure(\"Gini\")\n",
     "\n",
     "page = SolaraViz(\n",
@@ -229,7 +285,27 @@
     ")\n",
     "# This is required to render the visualization in the Jupyter notebook\n",
     "page"
-   ]
+   ],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Cannot show ipywidgets in text"
+      ],
+      "text/html": [
+       "Cannot show widget. You probably want to rerun the code cell above (<i>Click in the code cell, and press Shift+Enter <kbd>⇧</kbd>+<kbd>↩</kbd></i>)."
+      ],
+      "application/vnd.jupyter.widget-view+json": {
+       "version_major": 2,
+       "version_minor": 0,
+       "model_id": "da8518ec9ce74c068288bec0c8d3793e"
+      }
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "execution_count": 7
   },
   {
    "cell_type": "markdown",
@@ -250,9 +326,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:47.885386Z",
+     "start_time": "2024-10-29T19:38:47.882808Z"
+    }
+   },
    "source": [
     "import mesa\n",
     "print(f\"Mesa version: {mesa.__version__}\")\n",
@@ -260,16 +339,29 @@
     "from matplotlib.figure import Figure\n",
     "\n",
     "from mesa.visualization.utils import update_counter\n",
-    "from mesa.visualization import SolaraViz, make_plot_measure, make_space_matplotlib\n",
+    "from mesa.visualization import SolaraViz, make_plot_measure, make_space_component\n",
     "# Import the local MoneyModel.py\n",
     "from MoneyModel import MoneyModel\n"
-   ]
+   ],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Mesa version: 3.0.0b2\n"
+     ]
+    }
+   ],
+   "execution_count": 8
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:47.888491Z",
+     "start_time": "2024-10-29T19:38:47.886217Z"
+    }
+   },
    "source": [
     "def agent_portrayal(agent):\n",
     "    size = 10\n",
@@ -291,7 +383,9 @@
     "    \"width\": 10,\n",
     "    \"height\": 10,\n",
     "}"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": 9
   },
   {
    "cell_type": "markdown",
@@ -302,9 +396,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:47.893643Z",
+     "start_time": "2024-10-29T19:38:47.891084Z"
+    }
+   },
    "source": [
     "@solara.component\n",
     "def Histogram(model):\n",
@@ -318,26 +415,36 @@
     "    # because plt.hist is not thread-safe.\n",
     "    ax.hist(wealth_vals, bins=10)\n",
     "    solara.FigureMatplotlib(fig)"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": 10
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:47.896565Z",
+     "start_time": "2024-10-29T19:38:47.894387Z"
+    }
+   },
    "source": [
     "# Create initial model instance\n",
     "model1 = MoneyModel(50, 10, 10)\n",
     "\n",
-    "SpaceGraph = make_space_matplotlib(agent_portrayal)\n",
+    "SpaceGraph = make_space_component(agent_portrayal)\n",
     "GiniPlot = make_plot_measure(\"Gini\")"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": 11
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:49.471838Z",
+     "start_time": "2024-10-29T19:38:47.897295Z"
+    }
+   },
    "source": [
     "page = SolaraViz(\n",
     "    model1,\n",
@@ -347,7 +454,27 @@
     ")\n",
     "# This is required to render the visualization in the Jupyter notebook\n",
     "page"
-   ]
+   ],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Cannot show ipywidgets in text"
+      ],
+      "text/html": [
+       "Cannot show widget. You probably want to rerun the code cell above (<i>Click in the code cell, and press Shift+Enter <kbd>⇧</kbd>+<kbd>↩</kbd></i>)."
+      ],
+      "application/vnd.jupyter.widget-view+json": {
+       "version_major": 2,
+       "version_minor": 0,
+       "model_id": "bc71b89ee5684038a194eee4c36f4a4c"
+      }
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "execution_count": 12
   },
   {
    "cell_type": "markdown",
@@ -358,12 +485,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-29T19:38:49.505725Z",
+     "start_time": "2024-10-29T19:38:49.472599Z"
+    }
+   },
    "source": [
     "Histogram(model1)"
-   ]
+   ],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Cannot show ipywidgets in text"
+      ],
+      "text/html": [
+       "Cannot show widget. You probably want to rerun the code cell above (<i>Click in the code cell, and press Shift+Enter <kbd>⇧</kbd>+<kbd>↩</kbd></i>)."
+      ],
+      "application/vnd.jupyter.widget-view+json": {
+       "version_major": 2,
+       "version_minor": 0,
+       "model_id": "0491f167a1434a92b78535078bd082a8"
+      }
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "execution_count": 13
   },
   {
    "cell_type": "markdown",

From 8c3d928424b9615670a22a836a76f2cde3da3235 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 29 Oct 2024 20:48:23 +0100
Subject: [PATCH 72/74] docs

---
 mesa/visualization/components/matplotlib.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 3c9ad970ce7..8601d2392e2 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -130,12 +130,8 @@ def collect_agent_data(
         marker: default marker
         zorder: default zorder
 
-    Notes:
-        agent portray dict is limited to size (size of marker), color (color of marker, zorder, and marker (marker style)
-        see `Matplotlib`_.
-
-
-    .. _Matplotlib: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
+    agent_portrayal should return a dict, limited to size (size of marker), color (color of marker), zorder (z-order), 
+    and marker (marker style)
 
     """
     arguments = {"s": [], "c": [], "marker": [], "zorder": [], "loc": []}

From 642ba120af31d98fc5babe45b0e66e5f7f13ef87 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 19:49:44 +0000
Subject: [PATCH 73/74] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/components/matplotlib.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/visualization/components/matplotlib.py b/mesa/visualization/components/matplotlib.py
index 8601d2392e2..7e9982a7387 100644
--- a/mesa/visualization/components/matplotlib.py
+++ b/mesa/visualization/components/matplotlib.py
@@ -130,7 +130,7 @@ def collect_agent_data(
         marker: default marker
         zorder: default zorder
 
-    agent_portrayal should return a dict, limited to size (size of marker), color (color of marker), zorder (z-order), 
+    agent_portrayal should return a dict, limited to size (size of marker), color (color of marker), zorder (z-order),
     and marker (marker style)
 
     """

From 10c24c9e82c4e33a745e6faa8e7665482bd0edb5 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 30 Oct 2024 09:17:42 +0100
Subject: [PATCH 74/74] Update mesa/examples/basic/conways_game_of_life/app.py

Co-authored-by: Ewout ter Hoeven <E.M.terHoeven@student.tudelft.nl>
---
 mesa/examples/basic/conways_game_of_life/app.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/mesa/examples/basic/conways_game_of_life/app.py b/mesa/examples/basic/conways_game_of_life/app.py
index aee1733e523..7a45125a30a 100644
--- a/mesa/examples/basic/conways_game_of_life/app.py
+++ b/mesa/examples/basic/conways_game_of_life/app.py
@@ -1,11 +1,3 @@
-import os.path
-import sys
-
-sys.path.insert(
-    0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
-)
-
-
 from mesa.examples.basic.conways_game_of_life.model import ConwaysGameOfLife
 from mesa.visualization import (
     SolaraViz,