From 2e47f56fbdae2e338ee0cd830c493c6fefd50df8 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 30 Dec 2024 20:52:12 +0100
Subject: [PATCH 01/84] initial draft

---
 .../continuous_space/continuous_space.py      | 113 ++++++++++++++++++
 .../continuous_space_agents.py                |  61 ++++++++++
 .../continuous_space/for_development.py       |  26 ++++
 3 files changed, 200 insertions(+)
 create mode 100644 mesa/experimental/continuous_space/continuous_space.py
 create mode 100644 mesa/experimental/continuous_space/continuous_space_agents.py
 create mode 100644 mesa/experimental/continuous_space/for_development.py

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
new file mode 100644
index 00000000000..423519c121a
--- /dev/null
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -0,0 +1,113 @@
+"""A Continous Space class."""
+
+
+import warnings
+from collections.abc import Sequence
+from random import Random
+
+import numpy as np
+from scipy.spatial.distance import cdist
+
+from mesa.agent import Agent, AgentSet
+
+
+class ContinuousSpace:
+    """Continuous space where each agent can have an arbitrary position.
+
+    """
+
+    def __init__(
+        self,
+        dimensions: Sequence[Sequence[float]],
+        torus: bool = False,
+        random: Random | None = None,
+    ) -> None:
+        """Create a new continuous space."""
+        if random is None:
+            warnings.warn(
+                "Random number generator not specified, this can make models non-reproducible. Please pass a random number generator explicitly",
+                UserWarning,
+                stacklevel=2,
+            )
+            random = Random()
+        self.random = random
+
+        self.dimensions = np.asarray(dimensions)
+        self.ndims = self.dimensions.shape[0]
+        self.size = self.dimensions[:, 1] - self.dimensions[:, 0]
+        self.center = np.sum(self.dimensions, axis=1) / 2
+
+        self.torus = torus
+
+
+        n = 100
+        self._agent_positions = np.zeros((n, self.dimensions.shape[0]))
+        self._positions_in_use = np.zeros((n,), dtype=bool)  # effectively a mask over _agent_positions
+        self._index_to_agent: dict[int, Agent] = {}
+        self._agent_to_index: dict[Agent, int | None] = {}
+
+    @property
+    def agents(self) -> AgentSet:
+        """Return an AgentSet with the agents in the space."""
+        return AgentSet(list(self._agent_to_index), random=self.random)
+
+    @property
+    def agent_positions(self) -> np.ndarray:
+        """Return the positions of the agents in the space."""
+        return self._agent_positions[self._positions_in_use]
+
+    def _get_index_for_agent(self, agent: Agent) -> int:
+        """Helper method to get the index for the agent.
+
+        This method manages the numpy array with the agent positions and ensuring it is
+        enlarged if and when needed.
+
+        """
+        try:
+           return self._agent_to_index[agent]
+        except KeyError:
+            indices = np.where(self._positions_in_use == False)[0]
+
+            if indices.size:
+                index = indices[0]
+            else:
+                # we are out of space
+                fraction = 0.2  # we add 20%
+                n = int(round(fraction * self._agent_positions.shape[0]))
+                self._agent_positions = np.vstack([self._agent_positions,
+                                                  np.zeros((n, self.dimensions.shape[0]),)]
+                                                  )
+                self._positions_in_use = np.hstack([self._positions_in_use,
+                                                    np.zeros((n,), dtype=bool)])
+                index = np.where(self._positions_in_use == False)[0][0]
+
+        self._positions_in_use[index] = True
+        self._agent_to_index[agent] = index
+        self._index_to_agent[index] = agent
+
+        return index
+
+    def _remove_agent(self, agent: Agent) -> None:
+        """Remove an agent from the space."""
+        index = self._get_index_for_agent(agent)
+        self._agent_to_index.pop(agent, None)
+        self._index_to_agent.pop(index, None)
+        self._positions_in_use[index] = False
+
+    def calculate_distances(self, point):
+        """Calculate the distance between the point and all agents."""
+        if self.torus:
+            delta = np.abs(point[np.newaxis, :] - self._agent_positions)
+            delta = np.minimum(delta, 1 - delta)
+            dists = np.linalg.norm(delta, axis=1)
+        else:
+            dists = cdist(point[np.newaxis, :], self._agent_positions)
+        return dists
+
+    def in_bounds(self, point) -> bool:
+        """Check if point is inside the bounds of the space."""
+        return ((point >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])).all()
+
+    def torus_correct(self, point) -> np.ndarray:
+        """Apply a torus correction to the point."""
+        return self.dimensions[:, 0] + np.mod(point - self.dimensions[:, 0], self.size)
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
new file mode 100644
index 00000000000..51dd4788fa8
--- /dev/null
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -0,0 +1,61 @@
+from __future__ import annotations
+
+from typing import Protocol
+
+import numpy as np
+
+from mesa.agent import Agent
+from mesa.experimental.continuous_space.continuous_space import ContinuousSpace
+
+
+class HasPositionProtocol(Protocol):
+    """Protocol for continuous space position holders."""
+
+    position: np.ndarray
+
+class ContinuousSpaceAgent(Agent):
+    __slots__ = ["space", "_mesa_index"]
+
+    @property
+    def position(self) -> np.ndarray:
+        return self.space._agent_positions[self._mesa_index]
+
+    @position.setter
+    def position(self, value: np.ndarray) -> None:
+        if not self.space.in_bounds(value):
+            if self.space.torus:
+                value =  self.space.torus_correct(value)
+            else:
+                raise ValueError(f"point {value} is outside the bounds of the space")
+
+        self.space._agent_positions[self._mesa_index] = value
+
+    def __init__(self, space: ContinuousSpace, model):
+        super().__init__(model)
+        self.space: ContinuousSpace = space
+        self._mesa_index = self.space._get_index_for_agent(self)
+        self.position[:] = np.NaN
+
+    def remove(self) -> None:
+        super().remove()
+        self.space._remove_agent(self)
+        self._mesa_index = None
+        self.space = None
+
+    def get_neigbors_in_radius(self, radius=1):
+        distances = self.space.calculate_distances(self.position)
+        indices = np.where(distances < radius)[0]
+
+        # don't forget to remove our self
+        agents = [self.space._index_to_agent[index] for index in indices if index != self._mesa_index]
+        return agents
+
+    def get_nearest_neighbors(self, k=1):
+        distances = self.space.calculate_distances(self.position)
+
+        k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
+        indices = np.argpartition(distances, k)[:k]
+
+        # don't forget to remove our self
+        agents = [self.space._index_to_agent[index] for index in indices if index != self._mesa_index]
+        return agents
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
new file mode 100644
index 00000000000..e6e78b5b042
--- /dev/null
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -0,0 +1,26 @@
+
+
+# to be removed once further into the development
+
+
+from random import Random
+
+import numpy as np
+from continuous_space import ContinuousSpace
+from continuous_space_agents import ContinuousSpaceAgent
+
+from mesa import Model
+
+if __name__ == "__main__":
+
+    dimensions = [[0,1], [0,1]]
+
+    model = Model(seed=42)
+    space = ContinuousSpace(dimensions, random=Random(42), torus=True)
+
+    for _ in range(101):
+        agent = ContinuousSpaceAgent(space, model, )
+        agent.position = [agent.random.random(), agent.random.random()]
+        agent.position += [1, 0.01]
+
+    print("blaat")

From 6ef0b13d801354799f9513fdf4f0622e0957670d Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 30 Dec 2024 21:11:10 +0100
Subject: [PATCH 02/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 423519c121a..dea37683384 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -97,11 +97,11 @@ def _remove_agent(self, agent: Agent) -> None:
     def calculate_distances(self, point):
         """Calculate the distance between the point and all agents."""
         if self.torus:
-            delta = np.abs(point[np.newaxis, :] - self._agent_positions)
+            delta = np.abs(point[np.newaxis, :] - self.agent_positions)
             delta = np.minimum(delta, 1 - delta)
             dists = np.linalg.norm(delta, axis=1)
         else:
-            dists = cdist(point[np.newaxis, :], self._agent_positions)
+            dists = cdist(point[np.newaxis, :], self.agent_positions)
         return dists
 
     def in_bounds(self, point) -> bool:

From a8bd211b677edd79542da11fa4579cb01e9bac3a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Dec 2024 20:13:11 +0000
Subject: [PATCH 03/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../continuous_space/continuous_space.py      | 32 +++++++++++--------
 .../continuous_space_agents.py                | 17 +++++++---
 .../continuous_space/for_development.py       | 11 +++----
 3 files changed, 37 insertions(+), 23 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index dea37683384..3ea195e2d17 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -1,6 +1,5 @@
 """A Continous Space class."""
 
-
 import warnings
 from collections.abc import Sequence
 from random import Random
@@ -12,9 +11,7 @@
 
 
 class ContinuousSpace:
-    """Continuous space where each agent can have an arbitrary position.
-
-    """
+    """Continuous space where each agent can have an arbitrary position."""
 
     def __init__(
         self,
@@ -39,10 +36,11 @@ def __init__(
 
         self.torus = torus
 
-
         n = 100
         self._agent_positions = np.zeros((n, self.dimensions.shape[0]))
-        self._positions_in_use = np.zeros((n,), dtype=bool)  # effectively a mask over _agent_positions
+        self._positions_in_use = np.zeros(
+            (n,), dtype=bool
+        )  # effectively a mask over _agent_positions
         self._index_to_agent: dict[int, Agent] = {}
         self._agent_to_index: dict[Agent, int | None] = {}
 
@@ -64,7 +62,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
 
         """
         try:
-           return self._agent_to_index[agent]
+            return self._agent_to_index[agent]
         except KeyError:
             indices = np.where(self._positions_in_use == False)[0]
 
@@ -74,11 +72,17 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 # we are out of space
                 fraction = 0.2  # we add 20%
                 n = int(round(fraction * self._agent_positions.shape[0]))
-                self._agent_positions = np.vstack([self._agent_positions,
-                                                  np.zeros((n, self.dimensions.shape[0]),)]
-                                                  )
-                self._positions_in_use = np.hstack([self._positions_in_use,
-                                                    np.zeros((n,), dtype=bool)])
+                self._agent_positions = np.vstack(
+                    [
+                        self._agent_positions,
+                        np.zeros(
+                            (n, self.dimensions.shape[0]),
+                        ),
+                    ]
+                )
+                self._positions_in_use = np.hstack(
+                    [self._positions_in_use, np.zeros((n,), dtype=bool)]
+                )
                 index = np.where(self._positions_in_use == False)[0][0]
 
         self._positions_in_use[index] = True
@@ -106,7 +110,9 @@ def calculate_distances(self, point):
 
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
-        return ((point >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])).all()
+        return (
+            (point >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])
+        ).all()
 
     def torus_correct(self, point) -> np.ndarray:
         """Apply a torus correction to the point."""
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 51dd4788fa8..68b73bd4e92 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -13,8 +13,9 @@ class HasPositionProtocol(Protocol):
 
     position: np.ndarray
 
+
 class ContinuousSpaceAgent(Agent):
-    __slots__ = ["space", "_mesa_index"]
+    __slots__ = ["_mesa_index", "space"]
 
     @property
     def position(self) -> np.ndarray:
@@ -24,7 +25,7 @@ def position(self) -> np.ndarray:
     def position(self, value: np.ndarray) -> None:
         if not self.space.in_bounds(value):
             if self.space.torus:
-                value =  self.space.torus_correct(value)
+                value = self.space.torus_correct(value)
             else:
                 raise ValueError(f"point {value} is outside the bounds of the space")
 
@@ -47,7 +48,11 @@ def get_neigbors_in_radius(self, radius=1):
         indices = np.where(distances < radius)[0]
 
         # don't forget to remove our self
-        agents = [self.space._index_to_agent[index] for index in indices if index != self._mesa_index]
+        agents = [
+            self.space._index_to_agent[index]
+            for index in indices
+            if index != self._mesa_index
+        ]
         return agents
 
     def get_nearest_neighbors(self, k=1):
@@ -57,5 +62,9 @@ def get_nearest_neighbors(self, k=1):
         indices = np.argpartition(distances, k)[:k]
 
         # don't forget to remove our self
-        agents = [self.space._index_to_agent[index] for index in indices if index != self._mesa_index]
+        agents = [
+            self.space._index_to_agent[index]
+            for index in indices
+            if index != self._mesa_index
+        ]
         return agents
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index e6e78b5b042..175e6d1ac79 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,25 +1,24 @@
-
-
 # to be removed once further into the development
 
 
 from random import Random
 
-import numpy as np
 from continuous_space import ContinuousSpace
 from continuous_space_agents import ContinuousSpaceAgent
 
 from mesa import Model
 
 if __name__ == "__main__":
-
-    dimensions = [[0,1], [0,1]]
+    dimensions = [[0, 1], [0, 1]]
 
     model = Model(seed=42)
     space = ContinuousSpace(dimensions, random=Random(42), torus=True)
 
     for _ in range(101):
-        agent = ContinuousSpaceAgent(space, model, )
+        agent = ContinuousSpaceAgent(
+            space,
+            model,
+        )
         agent.position = [agent.random.random(), agent.random.random()]
         agent.position += [1, 0.01]
 

From 797e6810a796f1aaa366d061c7883f24aa31c890 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 30 Dec 2024 21:40:38 +0100
Subject: [PATCH 04/84] ruff

---
 mesa/experimental/continuous_space/continuous_space.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 3ea195e2d17..ad297263265 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -64,9 +64,9 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         try:
             return self._agent_to_index[agent]
         except KeyError:
-            indices = np.where(self._positions_in_use == False)[0]
+            indices = np.where(not self._positions_in_use)[0]
 
-            if indices.size:
+            if indices.size>0:
                 index = indices[0]
             else:
                 # we are out of space

From 27827366b1cae3e91756b202bcc5535994a494c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Dec 2024 21:25:59 +0000
Subject: [PATCH 05/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index ad297263265..10bcf87fcc8 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -66,7 +66,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         except KeyError:
             indices = np.where(not self._positions_in_use)[0]
 
-            if indices.size>0:
+            if indices.size > 0:
                 index = indices[0]
             else:
                 # we are out of space

From d0b05ec51f07cc8f07715191ff7e1e29ae1963df Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 30 Dec 2024 22:26:53 +0100
Subject: [PATCH 06/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 10bcf87fcc8..01344c5af75 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -83,7 +83,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 self._positions_in_use = np.hstack(
                     [self._positions_in_use, np.zeros((n,), dtype=bool)]
                 )
-                index = np.where(self._positions_in_use == False)[0][0]
+                index = np.where(not self._positions_in_use)[0][0]
 
         self._positions_in_use[index] = True
         self._agent_to_index[agent] = index

From 611af520b754c8a463db68f00fc4531403f54c32 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 31 Dec 2024 14:05:59 +0100
Subject: [PATCH 07/84] first tests

---
 mesa/experimental/__init__.py                 |   2 +-
 .../experimental/continuous_space/__init__.py |   4 +
 .../continuous_space/continuous_space.py      |  16 +-
 .../continuous_space_agents.py                |   4 +-
 tests/test_continuous_space.py                | 166 ++++++++++++++++++
 5 files changed, 181 insertions(+), 11 deletions(-)
 create mode 100644 mesa/experimental/continuous_space/__init__.py
 create mode 100644 tests/test_continuous_space.py

diff --git a/mesa/experimental/__init__.py b/mesa/experimental/__init__.py
index 946b2ba53fc..3c6f50b0e28 100644
--- a/mesa/experimental/__init__.py
+++ b/mesa/experimental/__init__.py
@@ -15,6 +15,6 @@
     - Features graduate from experimental status once their APIs are stabilized
 """
 
-from mesa.experimental import cell_space, devs, mesa_signals
+from mesa.experimental import cell_space, devs, mesa_signals, continuous_space
 
 __all__ = ["cell_space", "devs", "mesa_signals"]
diff --git a/mesa/experimental/continuous_space/__init__.py b/mesa/experimental/continuous_space/__init__.py
new file mode 100644
index 00000000000..46bb85c4830
--- /dev/null
+++ b/mesa/experimental/continuous_space/__init__.py
@@ -0,0 +1,4 @@
+
+
+from mesa.experimental.continuous_space.continuous_space import ContinuousSpace
+from mesa.experimental.continuous_space.continuous_space_agents import ContinuousSpaceAgent
\ No newline at end of file
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 01344c5af75..577b688934c 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -1,4 +1,4 @@
-"""A Continous Space class."""
+"""A Continyous Space class."""
 
 import warnings
 from collections.abc import Sequence
@@ -18,6 +18,7 @@ def __init__(
         dimensions: Sequence[Sequence[float]],
         torus: bool = False,
         random: Random | None = None,
+        n_agents: int = 100,
     ) -> None:
         """Create a new continuous space."""
         if random is None:
@@ -36,10 +37,9 @@ def __init__(
 
         self.torus = torus
 
-        n = 100
-        self._agent_positions = np.zeros((n, self.dimensions.shape[0]))
+        self._agent_positions = np.zeros((n_agents, self.dimensions.shape[0]), dtype=float)
         self._positions_in_use = np.zeros(
-            (n,), dtype=bool
+            (n_agents,), dtype=bool
         )  # effectively a mask over _agent_positions
         self._index_to_agent: dict[int, Agent] = {}
         self._agent_to_index: dict[Agent, int | None] = {}
@@ -64,13 +64,13 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         try:
             return self._agent_to_index[agent]
         except KeyError:
-            indices = np.where(not self._positions_in_use)[0]
+            indices = np.where(~self._positions_in_use)[0]
 
             if indices.size > 0:
                 index = indices[0]
             else:
                 # we are out of space
-                fraction = 0.2  # we add 20%
+                fraction = 0.2  # we add 20%  Fixme
                 n = int(round(fraction * self._agent_positions.shape[0]))
                 self._agent_positions = np.vstack(
                     [
@@ -83,7 +83,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 self._positions_in_use = np.hstack(
                     [self._positions_in_use, np.zeros((n,), dtype=bool)]
                 )
-                index = np.where(not self._positions_in_use)[0][0]
+                index = np.where(~self._positions_in_use)[0][0]
 
         self._positions_in_use[index] = True
         self._agent_to_index[agent] = index
@@ -102,7 +102,7 @@ def calculate_distances(self, point):
         """Calculate the distance between the point and all agents."""
         if self.torus:
             delta = np.abs(point[np.newaxis, :] - self.agent_positions)
-            delta = np.minimum(delta, 1 - delta)
+            delta = np.minimum(delta, 1 - delta)  # fixme, should be based on size
             dists = np.linalg.norm(delta, axis=1)
         else:
             dists = cdist(point[np.newaxis, :], self.agent_positions)
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 68b73bd4e92..1f379c09b17 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -5,7 +5,7 @@
 import numpy as np
 
 from mesa.agent import Agent
-from mesa.experimental.continuous_space.continuous_space import ContinuousSpace
+from mesa.experimental.continuous_space import ContinuousSpace
 
 
 class HasPositionProtocol(Protocol):
@@ -45,7 +45,7 @@ def remove(self) -> None:
 
     def get_neigbors_in_radius(self, radius=1):
         distances = self.space.calculate_distances(self.position)
-        indices = np.where(distances < radius)[0]
+        indices = np.where(distances <= radius)[0]
 
         # don't forget to remove our self
         agents = [
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
new file mode 100644
index 00000000000..19cdc8e95cc
--- /dev/null
+++ b/tests/test_continuous_space.py
@@ -0,0 +1,166 @@
+import numpy as np
+import pytest
+
+from mesa import Model
+
+from mesa.experimental.continuous_space import ContinuousSpace, ContinuousSpaceAgent
+
+
+
+def test_continuous_space():
+    model = Model(seed=42)
+
+    dimensions = np.asarray([[0, 1],
+                             [-1, 0]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    # check some default fields
+    assert space.ndims == 2
+    assert np.all(space.size == [1, 1])
+    assert np.all(space.center == [0.5, -0.5])
+    assert len(space.agents) == 0
+
+    # check in_bounds
+    assert space.in_bounds([0.5, -0.5])
+    assert not space.in_bounds([-0.5, -0.5])
+    assert not space.in_bounds([ 1.5, -0.5])
+    assert not space.in_bounds([ 0.5,  0.5])
+    assert not space.in_bounds([ 0.5, -1.5])
+
+    # check torus correction
+    space = ContinuousSpace(dimensions, torus=True, random=model.random)
+    assert np.all(space.torus_correct([-0.5, 0.5]) == [0.5, -0.5])
+    assert np.all(space.torus_correct([0.5, -0.5]) == [0.5, -0.5])
+    assert np.all(space.torus_correct([0.5, -0.5]) == [0.5, -0.5])
+    assert np.all(space.torus_correct([1.5, -0.5]) == [0.5, -0.5])
+    assert np.all(space.torus_correct([0.5, -1.5]) == [0.5, -0.5])
+
+    # check 3d
+    dimensions = np.asarray([[0, 2],
+                             [-2, 0],
+                             [-2, 2]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    # check some default fields
+    assert space.ndims == 3
+    assert np.all(space.size == [2, 2, 4])
+    assert np.all(space.center == [1, -1, 0])
+
+    # check in_bounds
+    assert space.in_bounds([1, -1, 0])
+    assert not space.in_bounds([-0.5, -1, 0])
+    assert not space.in_bounds([2.5, -1, 0])
+    assert not space.in_bounds([ 1, 0.5, 0])
+    assert not space.in_bounds([ 1, -2.5, 0])
+    assert not space.in_bounds([ 1, -1, -3])
+    assert not space.in_bounds([ 1, -1, 3])
+    assert not space.in_bounds([-0.5, -1, 3])
+    assert not space.in_bounds([1, 0.5, 3])
+
+def test_continuous_agent():
+    model = Model(seed=42)
+
+    dimensions = np.asarray([[0, 1],
+                             [0, 1]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    for _ in range(10):
+        agent = ContinuousSpaceAgent(space, model)
+        agent.position = [agent.random.random(), agent.random.random()]
+
+    assert space.agent_positions.shape == (10, 2)
+    for agent in space.agents:
+        assert np.all(agent.position == space.agent_positions[space._get_index_for_agent(agent)])
+
+    # add more agents, triggering a resizeing of the array
+    for _ in range(100):
+        agent = ContinuousSpaceAgent(space, model)
+        agent.position = [agent.random.random(), agent.random.random()]
+
+    assert space.agent_positions.shape == (110, 2)
+    for agent in space.agents:
+        assert np.all(agent.position == space.agent_positions[space._get_index_for_agent(agent)])
+
+    # remove all agents and check if the view is updated throughout correctly
+    for i, agent in enumerate(space.agents):
+        agent.remove()
+        assert space.agent_positions.shape == (110-1-i, 2)
+
+
+# class TestSpaceToroidal(unittest.TestCase):
+#     """Testing a toroidal continuous space."""
+#
+#     def setUp(self):
+#         """Create a test space and populate with Mock Agents."""
+#         self.space = ContinuousSpace(70, 20, True, -30, -30)
+#         self.agents = []
+#         for i, pos in enumerate(TEST_AGENTS):
+#             a = MockAgent(i)
+#             self.agents.append(a)
+#             self.space.place_agent(a, pos)
+#
+#     def test_agent_positions(self):
+#         """Ensure that the agents are all placed properly."""
+#         for i, pos in enumerate(TEST_AGENTS):
+#             a = self.agents[i]
+#             assert a.pos == pos
+#
+#     def test_agent_matching(self):
+#         """Ensure that the agents are all placed and indexed properly."""
+#         for i, agent in self.space._index_to_agent.items():
+#             assert agent.pos == tuple(self.space._agent_points[i, :])
+#             assert i == self.space._agent_to_index[agent]
+#
+#     def test_distance_calculations(self):
+#         """Test toroidal distance calculations."""
+#         pos_1 = (-30, -30)
+#         pos_2 = (70, 20)
+#         assert self.space.get_distance(pos_1, pos_2) == 0
+#
+#         pos_3 = (-30, -20)
+#         assert self.space.get_distance(pos_1, pos_3) == 10
+#
+#         pos_4 = (20, -5)
+#         pos_5 = (20, -15)
+#         assert self.space.get_distance(pos_4, pos_5) == 10
+#
+#         pos_6 = (-30, -29)
+#         pos_7 = (21, -5)
+#         assert self.space.get_distance(pos_6, pos_7) == np.sqrt(49**2 + 24**2)
+#
+#     def test_heading(self):  # noqa: D102
+#         pos_1 = (-30, -30)
+#         pos_2 = (70, 20)
+#         self.assertEqual((0, 0), self.space.get_heading(pos_1, pos_2))
+#
+#         pos_1 = (65, -25)
+#         pos_2 = (-25, -25)
+#         self.assertEqual((10, 0), self.space.get_heading(pos_1, pos_2))
+#
+#     def test_neighborhood_retrieval(self):
+#         """Test neighborhood retrieval."""
+#         neighbors_1 = self.space.get_neighbors((-20, -20), 1)
+#         assert len(neighbors_1) == 2
+#
+#         neighbors_2 = self.space.get_neighbors((40, -10), 10)
+#         assert len(neighbors_2) == 0
+#
+#         neighbors_3 = self.space.get_neighbors((-30, -30), 10)
+#         assert len(neighbors_3) == 1
+#
+#     def test_bounds(self):
+#         """Test positions outside of boundary."""
+#         boundary_agents = []
+#         for i, pos in enumerate(OUTSIDE_POSITIONS):
+#             a = MockAgent(len(self.agents) + i)
+#             boundary_agents.append(a)
+#             self.space.place_agent(a, pos)
+#
+#         for a, pos in zip(boundary_agents, OUTSIDE_POSITIONS):
+#             adj_pos = self.space.torus_adj(pos)
+#             assert a.pos == adj_pos
+#
+#         a = self.agents[0]
+#         for pos in OUTSIDE_POSITIONS:
+#             assert self.space.out_of_bounds(pos)
+#             self.space.move_agent(a, pos)
\ No newline at end of file

From 85c0bc2a214786f1a01bb7938342b8b789b0376d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 31 Dec 2024 13:06:10 +0000
Subject: [PATCH 08/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/__init__.py                 |  2 +-
 .../experimental/continuous_space/__init__.py |  6 +--
 .../continuous_space/continuous_space.py      |  4 +-
 tests/test_continuous_space.py                | 42 +++++++++----------
 4 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/mesa/experimental/__init__.py b/mesa/experimental/__init__.py
index 3c6f50b0e28..34111682b15 100644
--- a/mesa/experimental/__init__.py
+++ b/mesa/experimental/__init__.py
@@ -15,6 +15,6 @@
     - Features graduate from experimental status once their APIs are stabilized
 """
 
-from mesa.experimental import cell_space, devs, mesa_signals, continuous_space
+from mesa.experimental import cell_space, continuous_space, devs, mesa_signals
 
 __all__ = ["cell_space", "devs", "mesa_signals"]
diff --git a/mesa/experimental/continuous_space/__init__.py b/mesa/experimental/continuous_space/__init__.py
index 46bb85c4830..db7d4b39cd3 100644
--- a/mesa/experimental/continuous_space/__init__.py
+++ b/mesa/experimental/continuous_space/__init__.py
@@ -1,4 +1,4 @@
-
-
 from mesa.experimental.continuous_space.continuous_space import ContinuousSpace
-from mesa.experimental.continuous_space.continuous_space_agents import ContinuousSpaceAgent
\ No newline at end of file
+from mesa.experimental.continuous_space.continuous_space_agents import (
+    ContinuousSpaceAgent,
+)
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 577b688934c..5b225a3decd 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -37,7 +37,9 @@ def __init__(
 
         self.torus = torus
 
-        self._agent_positions = np.zeros((n_agents, self.dimensions.shape[0]), dtype=float)
+        self._agent_positions = np.zeros(
+            (n_agents, self.dimensions.shape[0]), dtype=float
+        )
         self._positions_in_use = np.zeros(
             (n_agents,), dtype=bool
         )  # effectively a mask over _agent_positions
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 19cdc8e95cc..7c9d44f3295 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -1,17 +1,13 @@
 import numpy as np
-import pytest
 
 from mesa import Model
-
 from mesa.experimental.continuous_space import ContinuousSpace, ContinuousSpaceAgent
 
 
-
 def test_continuous_space():
     model = Model(seed=42)
 
-    dimensions = np.asarray([[0, 1],
-                             [-1, 0]])
+    dimensions = np.asarray([[0, 1], [-1, 0]])
     space = ContinuousSpace(dimensions, torus=False, random=model.random)
 
     # check some default fields
@@ -23,9 +19,9 @@ def test_continuous_space():
     # check in_bounds
     assert space.in_bounds([0.5, -0.5])
     assert not space.in_bounds([-0.5, -0.5])
-    assert not space.in_bounds([ 1.5, -0.5])
-    assert not space.in_bounds([ 0.5,  0.5])
-    assert not space.in_bounds([ 0.5, -1.5])
+    assert not space.in_bounds([1.5, -0.5])
+    assert not space.in_bounds([0.5, 0.5])
+    assert not space.in_bounds([0.5, -1.5])
 
     # check torus correction
     space = ContinuousSpace(dimensions, torus=True, random=model.random)
@@ -36,9 +32,7 @@ def test_continuous_space():
     assert np.all(space.torus_correct([0.5, -1.5]) == [0.5, -0.5])
 
     # check 3d
-    dimensions = np.asarray([[0, 2],
-                             [-2, 0],
-                             [-2, 2]])
+    dimensions = np.asarray([[0, 2], [-2, 0], [-2, 2]])
     space = ContinuousSpace(dimensions, torus=False, random=model.random)
 
     # check some default fields
@@ -50,18 +44,18 @@ def test_continuous_space():
     assert space.in_bounds([1, -1, 0])
     assert not space.in_bounds([-0.5, -1, 0])
     assert not space.in_bounds([2.5, -1, 0])
-    assert not space.in_bounds([ 1, 0.5, 0])
-    assert not space.in_bounds([ 1, -2.5, 0])
-    assert not space.in_bounds([ 1, -1, -3])
-    assert not space.in_bounds([ 1, -1, 3])
+    assert not space.in_bounds([1, 0.5, 0])
+    assert not space.in_bounds([1, -2.5, 0])
+    assert not space.in_bounds([1, -1, -3])
+    assert not space.in_bounds([1, -1, 3])
     assert not space.in_bounds([-0.5, -1, 3])
     assert not space.in_bounds([1, 0.5, 3])
 
+
 def test_continuous_agent():
     model = Model(seed=42)
 
-    dimensions = np.asarray([[0, 1],
-                             [0, 1]])
+    dimensions = np.asarray([[0, 1], [0, 1]])
     space = ContinuousSpace(dimensions, torus=False, random=model.random)
 
     for _ in range(10):
@@ -70,7 +64,9 @@ def test_continuous_agent():
 
     assert space.agent_positions.shape == (10, 2)
     for agent in space.agents:
-        assert np.all(agent.position == space.agent_positions[space._get_index_for_agent(agent)])
+        assert np.all(
+            agent.position == space.agent_positions[space._get_index_for_agent(agent)]
+        )
 
     # add more agents, triggering a resizeing of the array
     for _ in range(100):
@@ -79,12 +75,14 @@ def test_continuous_agent():
 
     assert space.agent_positions.shape == (110, 2)
     for agent in space.agents:
-        assert np.all(agent.position == space.agent_positions[space._get_index_for_agent(agent)])
+        assert np.all(
+            agent.position == space.agent_positions[space._get_index_for_agent(agent)]
+        )
 
     # remove all agents and check if the view is updated throughout correctly
     for i, agent in enumerate(space.agents):
         agent.remove()
-        assert space.agent_positions.shape == (110-1-i, 2)
+        assert space.agent_positions.shape == (110 - 1 - i, 2)
 
 
 # class TestSpaceToroidal(unittest.TestCase):
@@ -128,7 +126,7 @@ def test_continuous_agent():
 #         pos_7 = (21, -5)
 #         assert self.space.get_distance(pos_6, pos_7) == np.sqrt(49**2 + 24**2)
 #
-#     def test_heading(self):  # noqa: D102
+#     def test_heading(self):
 #         pos_1 = (-30, -30)
 #         pos_2 = (70, 20)
 #         self.assertEqual((0, 0), self.space.get_heading(pos_1, pos_2))
@@ -163,4 +161,4 @@ def test_continuous_agent():
 #         a = self.agents[0]
 #         for pos in OUTSIDE_POSITIONS:
 #             assert self.space.out_of_bounds(pos)
-#             self.space.move_agent(a, pos)
\ No newline at end of file
+#             self.space.move_agent(a, pos)

From 2e31c49826b04bcd1c6a6ffb9d6e36b97310d5b2 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 31 Dec 2024 14:40:33 +0100
Subject: [PATCH 09/84] docstring for agent

---
 .../continuous_space_agents.py                | 90 ++++++++++++++++---
 1 file changed, 76 insertions(+), 14 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 1f379c09b17..8c987d2029b 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Protocol
+from typing import Protocol, overload
 
 import numpy as np
 
@@ -15,10 +15,18 @@ class HasPositionProtocol(Protocol):
 
 
 class ContinuousSpaceAgent(Agent):
+    """A continuous space agent.
+
+    Attributes:
+        space (ContinuousSpace): the continuous space in which the agent is located
+        position (np.ndarray): the position of the agent
+
+    """
     __slots__ = ["_mesa_index", "space"]
 
     @property
     def position(self) -> np.ndarray:
+        """Position of the agent."""
         return self.space._agent_positions[self._mesa_index]
 
     @position.setter
@@ -32,39 +40,93 @@ def position(self, value: np.ndarray) -> None:
         self.space._agent_positions[self._mesa_index] = value
 
     def __init__(self, space: ContinuousSpace, model):
+        """Initialize a continuous space agent.
+
+        Args:
+            space: the continuous space in which the agent is located
+            model: the model to which the agent belongs
+
+        """
         super().__init__(model)
         self.space: ContinuousSpace = space
         self._mesa_index = self.space._get_index_for_agent(self)
         self.position[:] = np.NaN
 
     def remove(self) -> None:
+        """Remove and delete the agent from the model."""
         super().remove()
         self.space._remove_agent(self)
         self._mesa_index = None
         self.space = None
 
-    def get_neigbors_in_radius(self, radius=1):
+    @overload
+    def get_neighbors_in_radius(self, radius:int=1, include_distance:bool=False) -> list[ContinuousSpaceAgent]: ...
+
+    @overload
+    def get_neighbors_in_radius(self, radius=1, include_distance:bool=True) -> list[tuple[ContinuousSpaceAgent, float]]: ...
+
+
+    def get_neighbors_in_radius(self, radius=1, include_distance = False):
+        """Get neighbors within radius.
+
+        Args:
+            radius: radius within which to look for neighbors
+            include_distance: include the distance information for each neighbor
+
+        """
         distances = self.space.calculate_distances(self.position)
         indices = np.where(distances <= radius)[0]
 
-        # don't forget to remove our self
-        agents = [
-            self.space._index_to_agent[index]
-            for index in indices
-            if index != self._mesa_index
-        ]
+        if include_distance:
+            # don't forget to remove our self
+            agents = [
+                (self.space._index_to_agent[index], distances[index])
+                for index in indices
+                if index != self._mesa_index
+            ]
+        else:
+            # don't forget to remove our self
+            agents = [
+                self.space._index_to_agent[index]
+                for index in indices
+                if index != self._mesa_index
+            ]
         return agents
 
-    def get_nearest_neighbors(self, k=1):
+    @overload
+    def get_nearest_neighbors(self, k:int=1, include_distance:bool=False) -> list[ContinuousSpaceAgent]: ...
+
+    @overload
+    def get_nearest_neighbors(self, k=1, include_distance:bool=True) -> list[tuple[ContinuousSpaceAgent, float]]: ...
+
+
+    def get_nearest_neighbors(self, k=1, include_distance = False):
+        """Get neighbors within radius.
+
+        Args:
+            k: the number of nearest neighbors to return
+            include_distance: include the distance information for each neighbor
+
+        """
+
         distances = self.space.calculate_distances(self.position)
 
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
         indices = np.argpartition(distances, k)[:k]
 
         # don't forget to remove our self
-        agents = [
-            self.space._index_to_agent[index]
-            for index in indices
-            if index != self._mesa_index
-        ]
+        if include_distance:
+            # don't forget to remove our self
+            agents = [
+                (self.space._index_to_agent[index], distances[index])
+                for index in indices
+                if index != self._mesa_index
+            ]
+        else:
+            # don't forget to remove our self
+            agents = [
+                self.space._index_to_agent[index]
+                for index in indices
+                if index != self._mesa_index
+            ]
         return agents

From 322a50e9d42a01a443829b0440fbdd86c7666db2 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Tue, 31 Dec 2024 14:40:50 +0100
Subject: [PATCH 10/84] Update continuous_space_agents.py

---
 mesa/experimental/continuous_space/continuous_space_agents.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 8c987d2029b..a19cc2c000e 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -1,3 +1,5 @@
+"""Continuous space agents."""
+
 from __future__ import annotations
 
 from typing import Protocol, overload

From aee0ff8afcc1327b686fb104c816f595e0898b9a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 31 Dec 2024 13:41:42 +0000
Subject: [PATCH 11/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../continuous_space_agents.py                | 24 ++++++++++++-------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index a19cc2c000e..f361e4f4ed6 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -24,6 +24,7 @@ class ContinuousSpaceAgent(Agent):
         position (np.ndarray): the position of the agent
 
     """
+
     __slots__ = ["_mesa_index", "space"]
 
     @property
@@ -62,13 +63,16 @@ def remove(self) -> None:
         self.space = None
 
     @overload
-    def get_neighbors_in_radius(self, radius:int=1, include_distance:bool=False) -> list[ContinuousSpaceAgent]: ...
+    def get_neighbors_in_radius(
+        self, radius: int = 1, include_distance: bool = False
+    ) -> list[ContinuousSpaceAgent]: ...
 
     @overload
-    def get_neighbors_in_radius(self, radius=1, include_distance:bool=True) -> list[tuple[ContinuousSpaceAgent, float]]: ...
-
+    def get_neighbors_in_radius(
+        self, radius=1, include_distance: bool = True
+    ) -> list[tuple[ContinuousSpaceAgent, float]]: ...
 
-    def get_neighbors_in_radius(self, radius=1, include_distance = False):
+    def get_neighbors_in_radius(self, radius=1, include_distance=False):
         """Get neighbors within radius.
 
         Args:
@@ -96,13 +100,16 @@ def get_neighbors_in_radius(self, radius=1, include_distance = False):
         return agents
 
     @overload
-    def get_nearest_neighbors(self, k:int=1, include_distance:bool=False) -> list[ContinuousSpaceAgent]: ...
+    def get_nearest_neighbors(
+        self, k: int = 1, include_distance: bool = False
+    ) -> list[ContinuousSpaceAgent]: ...
 
     @overload
-    def get_nearest_neighbors(self, k=1, include_distance:bool=True) -> list[tuple[ContinuousSpaceAgent, float]]: ...
+    def get_nearest_neighbors(
+        self, k=1, include_distance: bool = True
+    ) -> list[tuple[ContinuousSpaceAgent, float]]: ...
 
-
-    def get_nearest_neighbors(self, k=1, include_distance = False):
+    def get_nearest_neighbors(self, k=1, include_distance=False):
         """Get neighbors within radius.
 
         Args:
@@ -110,7 +117,6 @@ def get_nearest_neighbors(self, k=1, include_distance = False):
             include_distance: include the distance information for each neighbor
 
         """
-
         distances = self.space.calculate_distances(self.position)
 
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later

From 85665c5195a3344b6eafc2871f4598d71f275753 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 1 Jan 2025 15:22:56 +0100
Subject: [PATCH 12/84] add scipy as dependency

---
 mesa/experimental/continuous_space/continuous_space.py     | 4 ++--
 .../continuous_space/continuous_space_agents.py            | 4 ++++
 mesa/experimental/continuous_space/for_development.py      | 7 ++++---
 pyproject.toml                                             | 1 +
 4 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 5b225a3decd..442564427cb 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -103,8 +103,8 @@ def _remove_agent(self, agent: Agent) -> None:
     def calculate_distances(self, point):
         """Calculate the distance between the point and all agents."""
         if self.torus:
-            delta = np.abs(point[np.newaxis, :] - self.agent_positions)
-            delta = np.minimum(delta, 1 - delta)  # fixme, should be based on size
+            delta = np.abs(point[np.newaxis, :] - self._agent_positions)
+            delta = np.minimum(delta, 1 - delta)  # fixme, should be based on size or maxima?
             dists = np.linalg.norm(delta, axis=1)
         else:
             dists = cdist(point[np.newaxis, :], self.agent_positions)
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index f361e4f4ed6..72d0c156cf6 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -122,6 +122,10 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
         indices = np.argpartition(distances, k)[:k]
 
+        # fixme
+        #  indices mismatch, because it is the index in the distances
+        #  but this is not the same as the indices in agent_positions
+
         # don't forget to remove our self
         if include_distance:
             # don't forget to remove our self
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index 175e6d1ac79..667a88e293a 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,5 +1,5 @@
 # to be removed once further into the development
-
+import numpy as np
 
 from random import Random
 
@@ -14,12 +14,13 @@
     model = Model(seed=42)
     space = ContinuousSpace(dimensions, random=Random(42), torus=True)
 
-    for _ in range(101):
+    for _ in range(2):
         agent = ContinuousSpaceAgent(
             space,
             model,
         )
         agent.position = [agent.random.random(), agent.random.random()]
-        agent.position += [1, 0.01]
+
+    distances = space.calculate_distances(np.asarray([0.5, 0.5]))
 
     print("blaat")
diff --git a/pyproject.toml b/pyproject.toml
index 51265df9301..db68f3986c6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,6 +38,7 @@ dependencies = [
   "numpy",
   "pandas",
   "tqdm",
+  "scipy"
 ]
 dynamic = ["version"]
 

From cdbeb2abe906b8f9c482f3cbe677e31fa30461bd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 1 Jan 2025 14:23:13 +0000
Subject: [PATCH 13/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/continuous_space/continuous_space.py | 4 +++-
 mesa/experimental/continuous_space/for_development.py  | 3 +--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 442564427cb..73ad0b73df9 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -104,7 +104,9 @@ def calculate_distances(self, point):
         """Calculate the distance between the point and all agents."""
         if self.torus:
             delta = np.abs(point[np.newaxis, :] - self._agent_positions)
-            delta = np.minimum(delta, 1 - delta)  # fixme, should be based on size or maxima?
+            delta = np.minimum(
+                delta, 1 - delta
+            )  # fixme, should be based on size or maxima?
             dists = np.linalg.norm(delta, axis=1)
         else:
             dists = cdist(point[np.newaxis, :], self.agent_positions)
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index 667a88e293a..52704b667ca 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,8 +1,7 @@
 # to be removed once further into the development
-import numpy as np
-
 from random import Random
 
+import numpy as np
 from continuous_space import ContinuousSpace
 from continuous_space_agents import ContinuousSpaceAgent
 

From 04f66f9921dead239a5a0d197354beff87825e02 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 1 Jan 2025 15:43:46 +0100
Subject: [PATCH 14/84] Update continuous_space_agents.py

---
 mesa/experimental/continuous_space/continuous_space_agents.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 72d0c156cf6..e9b64147bfb 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -53,7 +53,7 @@ def __init__(self, space: ContinuousSpace, model):
         super().__init__(model)
         self.space: ContinuousSpace = space
         self._mesa_index = self.space._get_index_for_agent(self)
-        self.position[:] = np.NaN
+        self.position[:] = np.nan
 
     def remove(self) -> None:
         """Remove and delete the agent from the model."""

From a2d113efaa566b5fcd0f7c7ff2a39f984e3f96f5 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 1 Jan 2025 16:14:26 +0100
Subject: [PATCH 15/84] ensure aligntment between agents and distances

---
 .../continuous_space/continuous_space.py         |  9 ++++++---
 .../continuous_space/continuous_space_agents.py  | 16 ++++++++--------
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 73ad0b73df9..f655b8d5e26 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -40,6 +40,7 @@ def __init__(
         self._agent_positions = np.zeros(
             (n_agents, self.dimensions.shape[0]), dtype=float
         )
+        self._agents = np.zeros((n_agents, ), dtype=object)
         self._positions_in_use = np.zeros(
             (n_agents,), dtype=bool
         )  # effectively a mask over _agent_positions
@@ -49,7 +50,7 @@ def __init__(
     @property
     def agents(self) -> AgentSet:
         """Return an AgentSet with the agents in the space."""
-        return AgentSet(list(self._agent_to_index), random=self.random)
+        return AgentSet(self._agents[self._positions_in_use], random=self.random)
 
     @property
     def agent_positions(self) -> np.ndarray:
@@ -88,6 +89,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 index = np.where(~self._positions_in_use)[0][0]
 
         self._positions_in_use[index] = True
+        self._agents[index] = agent
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
 
@@ -99,18 +101,19 @@ def _remove_agent(self, agent: Agent) -> None:
         self._agent_to_index.pop(agent, None)
         self._index_to_agent.pop(index, None)
         self._positions_in_use[index] = False
+        self._agents[index] = None
 
     def calculate_distances(self, point):
         """Calculate the distance between the point and all agents."""
         if self.torus:
-            delta = np.abs(point[np.newaxis, :] - self._agent_positions)
+            delta = np.abs(point[np.newaxis, :] - self.agent_positions)
             delta = np.minimum(
                 delta, 1 - delta
             )  # fixme, should be based on size or maxima?
             dists = np.linalg.norm(delta, axis=1)
         else:
             dists = cdist(point[np.newaxis, :], self.agent_positions)
-        return dists
+        return dists, self._agents[self._positions_in_use]
 
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index e9b64147bfb..58f6a1e03d5 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -80,20 +80,20 @@ def get_neighbors_in_radius(self, radius=1, include_distance=False):
             include_distance: include the distance information for each neighbor
 
         """
-        distances = self.space.calculate_distances(self.position)
-        indices = np.where(distances <= radius)[0]
+        dists, agents = self.space.calculate_distances(self.position)
+        indices = np.where(dists <= radius)[0]
 
         if include_distance:
             # don't forget to remove our self
             agents = [
-                (self.space._index_to_agent[index], distances[index])
+                (agents[index], dists[index])
                 for index in indices
                 if index != self._mesa_index
             ]
         else:
             # don't forget to remove our self
             agents = [
-                self.space._index_to_agent[index]
+                agents[index]
                 for index in indices
                 if index != self._mesa_index
             ]
@@ -117,10 +117,10 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
             include_distance: include the distance information for each neighbor
 
         """
-        distances = self.space.calculate_distances(self.position)
+        dists, agents = self.space.calculate_distances(self.position)
 
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
-        indices = np.argpartition(distances, k)[:k]
+        indices = np.argpartition(dists, k)[:k]
 
         # fixme
         #  indices mismatch, because it is the index in the distances
@@ -130,14 +130,14 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
         if include_distance:
             # don't forget to remove our self
             agents = [
-                (self.space._index_to_agent[index], distances[index])
+                (agents[index], dists[index])
                 for index in indices
                 if index != self._mesa_index
             ]
         else:
             # don't forget to remove our self
             agents = [
-                self.space._index_to_agent[index]
+                agents[index]
                 for index in indices
                 if index != self._mesa_index
             ]

From 76f3ccd665ed40a29d7e89fab761b1a01d5cdf52 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 1 Jan 2025 15:14:34 +0000
Subject: [PATCH 16/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../continuous_space/continuous_space.py             |  2 +-
 .../continuous_space/continuous_space_agents.py      | 12 ++----------
 2 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index f655b8d5e26..86c3c99ca2b 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -40,7 +40,7 @@ def __init__(
         self._agent_positions = np.zeros(
             (n_agents, self.dimensions.shape[0]), dtype=float
         )
-        self._agents = np.zeros((n_agents, ), dtype=object)
+        self._agents = np.zeros((n_agents,), dtype=object)
         self._positions_in_use = np.zeros(
             (n_agents,), dtype=bool
         )  # effectively a mask over _agent_positions
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 58f6a1e03d5..4643e8325c2 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -92,11 +92,7 @@ def get_neighbors_in_radius(self, radius=1, include_distance=False):
             ]
         else:
             # don't forget to remove our self
-            agents = [
-                agents[index]
-                for index in indices
-                if index != self._mesa_index
-            ]
+            agents = [agents[index] for index in indices if index != self._mesa_index]
         return agents
 
     @overload
@@ -136,9 +132,5 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
             ]
         else:
             # don't forget to remove our self
-            agents = [
-                agents[index]
-                for index in indices
-                if index != self._mesa_index
-            ]
+            agents = [agents[index] for index in indices if index != self._mesa_index]
         return agents

From d8b62b096dd8558e9b432e21752e771ca3f18525 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 1 Jan 2025 16:31:15 +0100
Subject: [PATCH 17/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 86c3c99ca2b..b1d68b04cb7 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -44,6 +44,7 @@ def __init__(
         self._positions_in_use = np.zeros(
             (n_agents,), dtype=bool
         )  # effectively a mask over _agent_positions
+
         self._index_to_agent: dict[int, Agent] = {}
         self._agent_to_index: dict[Agent, int | None] = {}
 
@@ -86,6 +87,9 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 self._positions_in_use = np.hstack(
                     [self._positions_in_use, np.zeros((n,), dtype=bool)]
                 )
+                self._agents = np.hstack(
+                    [self._agents, np.zeros((n,), dtype=object)]
+                )
                 index = np.where(~self._positions_in_use)[0][0]
 
         self._positions_in_use[index] = True

From c5ad8bb96f4a0e419a25ed94acd301a7fea95696 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 1 Jan 2025 16:04:26 +0000
Subject: [PATCH 18/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/continuous_space/continuous_space.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index b1d68b04cb7..5652d1aea9e 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -87,9 +87,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 self._positions_in_use = np.hstack(
                     [self._positions_in_use, np.zeros((n,), dtype=bool)]
                 )
-                self._agents = np.hstack(
-                    [self._agents, np.zeros((n,), dtype=object)]
-                )
+                self._agents = np.hstack([self._agents, np.zeros((n,), dtype=object)])
                 index = np.where(~self._positions_in_use)[0][0]
 
         self._positions_in_use[index] = True

From 5695c3b71ae07ae49ebbf59da90399732cfc42f4 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 1 Jan 2025 17:12:07 +0100
Subject: [PATCH 19/84] typing fix

---
 mesa/experimental/continuous_space/continuous_space.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 5652d1aea9e..6c4d796373d 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -119,9 +119,9 @@ def calculate_distances(self, point):
 
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
-        return (
+        return bool((
             (point >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])
-        ).all()
+        ).all())
 
     def torus_correct(self, point) -> np.ndarray:
         """Apply a torus correction to the point."""

From 3a985d807c5922977078adde8b8c156c7620a2f9 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 1 Jan 2025 17:34:03 +0100
Subject: [PATCH 20/84] tests for distance calculations

---
 .../continuous_space/continuous_space.py      | 22 ++++----
 tests/test_continuous_space.py                | 53 +++++++++++++------
 2 files changed, 49 insertions(+), 26 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 6c4d796373d..1708483b827 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -30,18 +30,18 @@ def __init__(
             random = Random()
         self.random = random
 
-        self.dimensions = np.asarray(dimensions)
-        self.ndims = self.dimensions.shape[0]
-        self.size = self.dimensions[:, 1] - self.dimensions[:, 0]
-        self.center = np.sum(self.dimensions, axis=1) / 2
+        self.dimensions: np.array = np.asarray(dimensions)
+        self.ndims : int = self.dimensions.shape[0]
+        self.size: np.array = self.dimensions[:, 1] - self.dimensions[:, 0]
+        self.center: np.array = np.sum(self.dimensions, axis=1) / 2
 
-        self.torus = torus
+        self.torus: bool = torus
 
-        self._agent_positions = np.zeros(
+        self._agent_positions: np.array = np.zeros(
             (n_agents, self.dimensions.shape[0]), dtype=float
         )
-        self._agents = np.zeros((n_agents,), dtype=object)
-        self._positions_in_use = np.zeros(
+        self._agents: np.array = np.zeros((n_agents,), dtype=object)
+        self._positions_in_use: np.array = np.zeros(
             (n_agents,), dtype=bool
         )  # effectively a mask over _agent_positions
 
@@ -105,8 +105,10 @@ def _remove_agent(self, agent: Agent) -> None:
         self._positions_in_use[index] = False
         self._agents[index] = None
 
-    def calculate_distances(self, point):
+    def calculate_distances(self, point) -> tuple[np.ndarray, np.ndarray]:
         """Calculate the distance between the point and all agents."""
+        point = np.asanyarray(point)
+
         if self.torus:
             delta = np.abs(point[np.newaxis, :] - self.agent_positions)
             delta = np.minimum(
@@ -114,7 +116,7 @@ def calculate_distances(self, point):
             )  # fixme, should be based on size or maxima?
             dists = np.linalg.norm(delta, axis=1)
         else:
-            dists = cdist(point[np.newaxis, :], self.agent_positions)
+            dists = cdist(point[np.newaxis, :], self.agent_positions)[:, 0]
         return dists, self._agents[self._positions_in_use]
 
     def in_bounds(self, point) -> bool:
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 7c9d44f3295..889129e072c 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -84,6 +84,42 @@ def test_continuous_agent():
         agent.remove()
         assert space.agent_positions.shape == (110 - 1 - i, 2)
 
+def test_distances():
+    # non torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.1, 0.1]
+
+    distances, agents = space.calculate_distances([0.1, 0.9])
+    assert np.all(distances == [0.8,])
+    assert np.all(agents == [agent,])
+
+    distances, agents = space.calculate_distances([0.9, 0.1])
+    assert np.all(distances == [0.8,])
+    assert np.all(agents == [agent, ])
+
+    # torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=True, random=model.random)
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.1, 0.1]
+
+    distances, agents = space.calculate_distances([0.1, 0.9])
+    assert np.all(np.isclose(distances, [0.2,]))
+    assert np.all(agents == [agent,])
+
+    distances, agents = space.calculate_distances([0.9, 0.1])
+    assert np.all(np.isclose(distances, [0.2,]))
+    assert np.all(agents == [agent, ])
+
+    distances, agents = space.calculate_distances([0.9, 0.9])
+    assert np.all(np.isclose(distances, [0.2*2**0.5,]))
+    assert np.all(agents == [agent, ])
 
 # class TestSpaceToroidal(unittest.TestCase):
 #     """Testing a toroidal continuous space."""
@@ -146,19 +182,4 @@ def test_continuous_agent():
 #         neighbors_3 = self.space.get_neighbors((-30, -30), 10)
 #         assert len(neighbors_3) == 1
 #
-#     def test_bounds(self):
-#         """Test positions outside of boundary."""
-#         boundary_agents = []
-#         for i, pos in enumerate(OUTSIDE_POSITIONS):
-#             a = MockAgent(len(self.agents) + i)
-#             boundary_agents.append(a)
-#             self.space.place_agent(a, pos)
-#
-#         for a, pos in zip(boundary_agents, OUTSIDE_POSITIONS):
-#             adj_pos = self.space.torus_adj(pos)
-#             assert a.pos == adj_pos
-#
-#         a = self.agents[0]
-#         for pos in OUTSIDE_POSITIONS:
-#             assert self.space.out_of_bounds(pos)
-#             self.space.move_agent(a, pos)
+

From 94963cdcdd2b48e0277bc53b49c542e6eace6717 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 1 Jan 2025 16:36:39 +0000
Subject: [PATCH 21/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../continuous_space/continuous_space.py      |  8 +-
 tests/test_continuous_space.py                | 79 ++++++++++++++++---
 2 files changed, 72 insertions(+), 15 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 1708483b827..886f40c0a67 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -31,7 +31,7 @@ def __init__(
         self.random = random
 
         self.dimensions: np.array = np.asarray(dimensions)
-        self.ndims : int = self.dimensions.shape[0]
+        self.ndims: int = self.dimensions.shape[0]
         self.size: np.array = self.dimensions[:, 1] - self.dimensions[:, 0]
         self.center: np.array = np.sum(self.dimensions, axis=1) / 2
 
@@ -121,9 +121,9 @@ def calculate_distances(self, point) -> tuple[np.ndarray, np.ndarray]:
 
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
-        return bool((
-            (point >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])
-        ).all())
+        return bool(
+            ((point >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])).all()
+        )
 
     def torus_correct(self, point) -> np.ndarray:
         """Apply a torus correction to the point."""
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 889129e072c..bb5405ad8ca 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -84,6 +84,7 @@ def test_continuous_agent():
         agent.remove()
         assert space.agent_positions.shape == (110 - 1 - i, 2)
 
+
 def test_distances():
     # non torus
     model = Model(seed=42)
@@ -94,12 +95,32 @@ def test_distances():
     agent.position = [0.1, 0.1]
 
     distances, agents = space.calculate_distances([0.1, 0.9])
-    assert np.all(distances == [0.8,])
-    assert np.all(agents == [agent,])
+    assert np.all(
+        distances
+        == [
+            0.8,
+        ]
+    )
+    assert np.all(
+        agents
+        == [
+            agent,
+        ]
+    )
 
     distances, agents = space.calculate_distances([0.9, 0.1])
-    assert np.all(distances == [0.8,])
-    assert np.all(agents == [agent, ])
+    assert np.all(
+        distances
+        == [
+            0.8,
+        ]
+    )
+    assert np.all(
+        agents
+        == [
+            agent,
+        ]
+    )
 
     # torus
     model = Model(seed=42)
@@ -110,16 +131,53 @@ def test_distances():
     agent.position = [0.1, 0.1]
 
     distances, agents = space.calculate_distances([0.1, 0.9])
-    assert np.all(np.isclose(distances, [0.2,]))
-    assert np.all(agents == [agent,])
+    assert np.all(
+        np.isclose(
+            distances,
+            [
+                0.2,
+            ],
+        )
+    )
+    assert np.all(
+        agents
+        == [
+            agent,
+        ]
+    )
 
     distances, agents = space.calculate_distances([0.9, 0.1])
-    assert np.all(np.isclose(distances, [0.2,]))
-    assert np.all(agents == [agent, ])
+    assert np.all(
+        np.isclose(
+            distances,
+            [
+                0.2,
+            ],
+        )
+    )
+    assert np.all(
+        agents
+        == [
+            agent,
+        ]
+    )
 
     distances, agents = space.calculate_distances([0.9, 0.9])
-    assert np.all(np.isclose(distances, [0.2*2**0.5,]))
-    assert np.all(agents == [agent, ])
+    assert np.all(
+        np.isclose(
+            distances,
+            [
+                0.2 * 2**0.5,
+            ],
+        )
+    )
+    assert np.all(
+        agents
+        == [
+            agent,
+        ]
+    )
+
 
 # class TestSpaceToroidal(unittest.TestCase):
 #     """Testing a toroidal continuous space."""
@@ -182,4 +240,3 @@ def test_distances():
 #         neighbors_3 = self.space.get_neighbors((-30, -30), 10)
 #         assert len(neighbors_3) == 1
 #
-

From acd0ef0e4016b2221763e8498ea566fbb2880444 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 1 Jan 2025 19:09:36 +0100
Subject: [PATCH 22/84] ruff related fixes

---
 mesa/experimental/__init__.py                                 | 2 +-
 mesa/experimental/continuous_space/__init__.py                | 2 ++
 mesa/experimental/continuous_space/continuous_space_agents.py | 4 ----
 tests/test_continuous_space.py                                | 3 +++
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/mesa/experimental/__init__.py b/mesa/experimental/__init__.py
index 34111682b15..6898d06f403 100644
--- a/mesa/experimental/__init__.py
+++ b/mesa/experimental/__init__.py
@@ -17,4 +17,4 @@
 
 from mesa.experimental import cell_space, continuous_space, devs, mesa_signals
 
-__all__ = ["cell_space", "devs", "mesa_signals"]
+__all__ = ["cell_space", "devs", "mesa_signals", "continuous_space"]
diff --git a/mesa/experimental/continuous_space/__init__.py b/mesa/experimental/continuous_space/__init__.py
index db7d4b39cd3..f5cfe92e57c 100644
--- a/mesa/experimental/continuous_space/__init__.py
+++ b/mesa/experimental/continuous_space/__init__.py
@@ -2,3 +2,5 @@
 from mesa.experimental.continuous_space.continuous_space_agents import (
     ContinuousSpaceAgent,
 )
+
+__all__ = ["ContinuousSpace", "ContinuousSpaceAgent"]
\ No newline at end of file
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 4643e8325c2..2a878732dcb 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -118,10 +118,6 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
         indices = np.argpartition(dists, k)[:k]
 
-        # fixme
-        #  indices mismatch, because it is the index in the distances
-        #  but this is not the same as the indices in agent_positions
-
         # don't forget to remove our self
         if include_distance:
             # don't forget to remove our self
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index bb5405ad8ca..6c00f0be54d 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -5,6 +5,7 @@
 
 
 def test_continuous_space():
+    """Test ContinuousSpace class."""
     model = Model(seed=42)
 
     dimensions = np.asarray([[0, 1], [-1, 0]])
@@ -53,6 +54,7 @@ def test_continuous_space():
 
 
 def test_continuous_agent():
+    """Test ContinuousSpaceAgent class."""
     model = Model(seed=42)
 
     dimensions = np.asarray([[0, 1], [0, 1]])
@@ -86,6 +88,7 @@ def test_continuous_agent():
 
 
 def test_distances():
+    """Test ContinuousSpace.distance method."""
     # non torus
     model = Model(seed=42)
     dimensions = np.asarray([[0, 1], [0, 1]])

From 5b676d0e4664365917340809b229117b4a6b5159 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 1 Jan 2025 18:09:45 +0000
Subject: [PATCH 23/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/__init__.py                  | 2 +-
 mesa/experimental/continuous_space/__init__.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/experimental/__init__.py b/mesa/experimental/__init__.py
index 6898d06f403..8f0ac91df48 100644
--- a/mesa/experimental/__init__.py
+++ b/mesa/experimental/__init__.py
@@ -17,4 +17,4 @@
 
 from mesa.experimental import cell_space, continuous_space, devs, mesa_signals
 
-__all__ = ["cell_space", "devs", "mesa_signals", "continuous_space"]
+__all__ = ["cell_space", "continuous_space", "devs", "mesa_signals"]
diff --git a/mesa/experimental/continuous_space/__init__.py b/mesa/experimental/continuous_space/__init__.py
index f5cfe92e57c..56dab0ef693 100644
--- a/mesa/experimental/continuous_space/__init__.py
+++ b/mesa/experimental/continuous_space/__init__.py
@@ -3,4 +3,4 @@
     ContinuousSpaceAgent,
 )
 
-__all__ = ["ContinuousSpace", "ContinuousSpaceAgent"]
\ No newline at end of file
+__all__ = ["ContinuousSpace", "ContinuousSpaceAgent"]

From c8119ede2165fd5357d85796827765547c32f548 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Thu, 2 Jan 2025 16:24:35 +0100
Subject: [PATCH 24/84] wip

---
 mesa/examples/basic/boid_flockers/agents.py   | 68 ++++++++-----------
 mesa/examples/basic/boid_flockers/app.py      |  5 ++
 mesa/examples/basic/boid_flockers/model.py    | 53 +++++----------
 .../continuous_space/continuous_space.py      | 27 ++++++--
 .../continuous_space_agents.py                | 28 ++------
 mesa/visualization/mpl_space_drawing.py       | 14 ++--
 tests/test_continuous_space.py                |  2 +
 7 files changed, 91 insertions(+), 106 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 2ff00cbaef2..531d70cac89 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -6,10 +6,10 @@
 
 import numpy as np
 
-from mesa import Agent
+from mesa.experimental.continuous_space import ContinuousSpaceAgent
 
 
-class Boid(Agent):
+class Boid(ContinuousSpaceAgent):
     """A Boid-style flocker agent.
 
     The agent follows three behaviors to flock:
@@ -23,13 +23,16 @@ class Boid(Agent):
     any other Boid.
     """
 
+
     def __init__(
         self,
         model,
-        speed,
-        direction,
-        vision,
-        separation,
+        space,
+        position=(0,0),
+        speed=1,
+        direction=(1,1),
+        vision=1,
+        separation=1,
         cohere=0.03,
         separate=0.015,
         match=0.05,
@@ -46,7 +49,8 @@ def __init__(
             separate: Relative importance of avoiding close neighbors (default: 0.015)
             match: Relative importance of matching neighbors' directions (default: 0.05)
         """
-        super().__init__(model)
+        super().__init__(space, model)
+        self.position = position
         self.speed = speed
         self.direction = direction
         self.vision = vision
@@ -56,48 +60,36 @@ def __init__(
         self.match_factor = match
         self.neighbors = []
 
+    @property
+    def pos(self):
+        return self.position
+
+    @pos.setter
+    def pos(self, value):
+        pass
+
+
     def step(self):
         """Get the Boid's neighbors, compute the new vector, and move accordingly."""
-        self.neighbors = self.model.space.get_neighbors(self.pos, self.vision, False)
+        neighbors, distances = self.get_neighbors_in_radius(radius=self.vision, include_distance=True)
+        self.neighbors = neighbors.tolist()
 
         # If no neighbors, maintain current direction
-        if not self.neighbors:
-            new_pos = self.pos + self.direction * self.speed
-            self.model.space.move_agent(self, new_pos)
+        if neighbors.size==0:
+            self.position += self.direction * self.speed
             return
 
-        # Initialize vectors for the three flocking behaviors
-        cohere = np.zeros(2)  # Cohesion vector
-        match_vector = np.zeros(2)  # Alignment vector
-        separation_vector = np.zeros(2)  # Separation vector
-
-        # Calculate the contribution of each neighbor to the three behaviors
-        for neighbor in self.neighbors:
-            heading = self.model.space.get_heading(self.pos, neighbor.pos)
-            distance = self.model.space.get_distance(self.pos, neighbor.pos)
-
-            # Cohesion - steer towards the average position of neighbors
-            cohere += heading
-
-            # Separation - avoid getting too close
-            if distance < self.separation:
-                separation_vector -= heading
-
-            # Alignment - match neighbors' flying direction
-            match_vector += neighbor.direction
+        delta = self.space.calculate_difference_vector(self.position, [n._mesa_index for n in neighbors])
 
-        # Weight each behavior by its factor and normalize by number of neighbors
-        n = len(self.neighbors)
-        cohere = cohere * self.cohere_factor
-        separation_vector = separation_vector * self.separate_factor
-        match_vector = match_vector * self.match_factor
+        cohere = np.sum(delta, axis=0) * self.cohere_factor
+        separation_vector = -1 * np.sum(delta[distances < self.separation], axis=0) * self.separate_factor
+        match_vector = np.sum(np.asarray([n.direction for n in neighbors]), axis=0) * self.match_factor
 
         # Update direction based on the three behaviors
-        self.direction += (cohere + separation_vector + match_vector) / n
+        self.direction += (cohere + separation_vector + match_vector) / len(neighbors)
 
         # Normalize direction vector
         self.direction /= np.linalg.norm(self.direction)
 
         # Move boid
-        new_pos = self.pos + self.direction * self.speed
-        self.model.space.move_agent(self, new_pos)
+        self.position += self.direction * self.speed
diff --git a/mesa/examples/basic/boid_flockers/app.py b/mesa/examples/basic/boid_flockers/app.py
index 16b1ccf7f68..f728550673a 100644
--- a/mesa/examples/basic/boid_flockers/app.py
+++ b/mesa/examples/basic/boid_flockers/app.py
@@ -1,3 +1,8 @@
+import sys, os
+
+
+sys.path.insert(0, os.path.abspath('../../../..'))
+
 from mesa.examples.basic.boid_flockers.model import BoidFlockers
 from mesa.visualization import Slider, SolaraViz, make_space_component
 
diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index 5b4974f3a20..c1cb7b661db 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -9,7 +9,7 @@
 
 from mesa import Model
 from mesa.examples.basic.boid_flockers.agents import Boid
-from mesa.space import ContinuousSpace
+from mesa.experimental.continuous_space import ContinuousSpace
 
 
 class BoidFlockers(Model):
@@ -17,7 +17,7 @@ class BoidFlockers(Model):
 
     def __init__(
         self,
-        population=100,
+        population_size=100,
         width=100,
         height=100,
         speed=1,
@@ -31,7 +31,7 @@ def __init__(
         """Create a new Boids Flocking model.
 
         Args:
-            population: Number of Boids in the simulation (default: 100)
+            population_size: Number of Boids in the simulation (default: 100)
             width: Width of the space (default: 100)
             height: Height of the space (default: 100)
             speed: How fast the Boids move (default: 1)
@@ -44,48 +44,22 @@ def __init__(
         """
         super().__init__(seed=seed)
 
-        # Model Parameters
-        self.population = population
-        self.vision = vision
-        self.speed = speed
-        self.separation = separation
-
         # Set up the space
-        self.space = ContinuousSpace(width, height, torus=True)
-
-        # Store flocking weights
-        self.factors = {"cohere": cohere, "separate": separate, "match": match}
+        self.space = ContinuousSpace([[0, width],
+                                      [0, height]],
+                                     torus=True, random=self.random)
 
         # Create and place the Boid agents
-        self.make_agents()
+        position = self.rng.random(size=(population_size, 2)) * self.space.size
+        direction = self.rng.uniform(-1, 1, size=(population_size, 2))
+        Boid.create_agents(self, population_size, self.space, position=position, direction=direction,
+                           cohere=cohere, separate=separate, match=match, speed=speed, vision=vision,
+                           separation=separation)
 
         # For tracking statistics
         self.average_heading = None
         self.update_average_heading()
 
-    def make_agents(self):
-        """Create and place all Boid agents randomly in the space."""
-        for _ in range(self.population):
-            # Random position
-            x = self.random.random() * self.space.x_max
-            y = self.random.random() * self.space.y_max
-            pos = np.array((x, y))
-
-            # Random initial direction
-            direction = np.random.random(2) * 2 - 1  # Random vector between -1 and 1
-            direction /= np.linalg.norm(direction)  # Normalize
-
-            # Create and place the Boid
-            boid = Boid(
-                model=self,
-                speed=self.speed,
-                direction=direction,
-                vision=self.vision,
-                separation=self.separation,
-                **self.factors,
-            )
-            self.space.place_agent(boid, pos)
-
     def update_average_heading(self):
         """Calculate the average heading (direction) of all Boids."""
         if not self.agents:
@@ -103,3 +77,8 @@ def step(self):
         """
         self.agents.shuffle_do("step")
         self.update_average_heading()
+
+
+if __name__ == '__main__':
+    model = BoidFlockers()
+    model.step()
\ No newline at end of file
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 886f40c0a67..7e640fff094 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -105,19 +105,36 @@ def _remove_agent(self, agent: Agent) -> None:
         self._positions_in_use[index] = False
         self._agents[index] = None
 
-    def calculate_distances(self, point) -> tuple[np.ndarray, np.ndarray]:
+    def calculate_difference_vector(self, point: np.ndarray, indices=None) -> np.ndarray:
+        """Calculate the difference vector between the point and all agents"""
+        point = np.asanyarray(point)
+        positions = self._agent_positions[indices] if indices is not None else self.agent_positions
+
+        if self.torus:
+            delta = np.abs(point[np.newaxis, :] - positions)
+            delta = np.minimum(
+                delta, self.size - delta
+            )  # fixme, should be based on size or maxima?
+        else:
+            delta = point[np.newaxis, :] - positions
+
+        return delta
+
+    def calculate_distances(self, point, indices=None) -> tuple[np.ndarray, np.ndarray]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
+        positions = self._agent_positions[indices] if indices is not None else self.agent_positions
+        agents = self._agents[indices] if indices is not None else self._agents[self._positions_in_use]
 
         if self.torus:
-            delta = np.abs(point[np.newaxis, :] - self.agent_positions)
+            delta = np.abs(point[np.newaxis, :] - positions)
             delta = np.minimum(
-                delta, 1 - delta
+                delta, self.size - delta
             )  # fixme, should be based on size or maxima?
             dists = np.linalg.norm(delta, axis=1)
         else:
-            dists = cdist(point[np.newaxis, :], self.agent_positions)[:, 0]
-        return dists, self._agents[self._positions_in_use]
+            dists = cdist(point[np.newaxis, :], positions)[:, 0]
+        return dists, agents
 
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 2a878732dcb..f55e88e9fe8 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -65,12 +65,12 @@ def remove(self) -> None:
     @overload
     def get_neighbors_in_radius(
         self, radius: int = 1, include_distance: bool = False
-    ) -> list[ContinuousSpaceAgent]: ...
+    ) -> np.ndarray[ContinuousSpaceAgent]: ...
 
     @overload
     def get_neighbors_in_radius(
         self, radius=1, include_distance: bool = True
-    ) -> list[tuple[ContinuousSpaceAgent, float]]: ...
+    ) -> tuple[np.ndarray[ContinuousSpaceAgent], np.ndarray[float]]: ...
 
     def get_neighbors_in_radius(self, radius=1, include_distance=False):
         """Get neighbors within radius.
@@ -82,18 +82,12 @@ def get_neighbors_in_radius(self, radius=1, include_distance=False):
         """
         dists, agents = self.space.calculate_distances(self.position)
         indices = np.where(dists <= radius)[0]
+        indices = indices[indices != self._mesa_index]
 
         if include_distance:
-            # don't forget to remove our self
-            agents = [
-                (agents[index], dists[index])
-                for index in indices
-                if index != self._mesa_index
-            ]
+            return agents[indices], dists[indices]
         else:
-            # don't forget to remove our self
-            agents = [agents[index] for index in indices if index != self._mesa_index]
-        return agents
+            return agents[indices]
 
     @overload
     def get_nearest_neighbors(
@@ -118,15 +112,7 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
         indices = np.argpartition(dists, k)[:k]
 
-        # don't forget to remove our self
         if include_distance:
-            # don't forget to remove our self
-            agents = [
-                (agents[index], dists[index])
-                for index in indices
-                if index != self._mesa_index
-            ]
+            return agents[indices], dists[indices]
         else:
-            # don't forget to remove our self
-            agents = [agents[index] for index in indices if index != self._mesa_index]
-        return agents
+            return agents[indices]
diff --git a/mesa/visualization/mpl_space_drawing.py b/mesa/visualization/mpl_space_drawing.py
index 784d370eba0..1adacce03f2 100644
--- a/mesa/visualization/mpl_space_drawing.py
+++ b/mesa/visualization/mpl_space_drawing.py
@@ -143,7 +143,7 @@ def draw_space(
             draw_orthogonal_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, **space_drawing_kwargs)
-        case mesa.space.ContinuousSpace():
+        case mesa.space.ContinuousSpace() | mesa.experimental.continuous_space.ContinuousSpace():
             draw_continuous_space(space, agent_portrayal, ax=ax)
         case VoronoiGrid():
             draw_voronoi_grid(space, agent_portrayal, ax=ax)
@@ -472,9 +472,13 @@ def draw_continuous_space(
         fig, ax = plt.subplots()
 
     # space related setup
-    width = space.x_max - space.x_min
+    width = space.size[0]
+    height = space.size[1]
+
+
+    # width = space.x_max - space.x_min
     x_padding = width / 20
-    height = space.y_max - space.y_min
+    # height = space.y_max - space.y_min
     y_padding = height / 20
 
     # gather agent data
@@ -491,8 +495,8 @@ def draw_continuous_space(
         spine.set_color("black")
         spine.set_linestyle(border_style)
 
-    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)
+    ax.set_xlim(space.dimensions[0, 0] - x_padding, space.dimensions[0, 1] + x_padding)
+    ax.set_ylim(space.dimensions[1, 0] - y_padding, space.dimensions[1, 1] + y_padding)
 
     return ax
 
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 6c00f0be54d..52fdd895fe7 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -1,3 +1,5 @@
+"""Tests for continuous space."""
+
 import numpy as np
 
 from mesa import Model

From b7c39144597add921f8f0cdcc29e3c1dadc8ee97 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Thu, 2 Jan 2025 16:28:02 +0100
Subject: [PATCH 25/84] wip

---
 mesa/examples/basic/boid_flockers/app.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/examples/basic/boid_flockers/app.py b/mesa/examples/basic/boid_flockers/app.py
index f728550673a..2a544c4ffec 100644
--- a/mesa/examples/basic/boid_flockers/app.py
+++ b/mesa/examples/basic/boid_flockers/app.py
@@ -22,7 +22,7 @@ def boid_draw(agent):
         "value": 42,
         "label": "Random Seed",
     },
-    "population": Slider(
+    "population_size": Slider(
         label="Number of boids",
         value=100,
         min=10,

From a08e29b81d232aacc186d83b9dd104628320b190 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Jan 2025 15:28:56 +0000
Subject: [PATCH 26/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/basic/boid_flockers/agents.py   | 27 ++++++++++++-------
 mesa/examples/basic/boid_flockers/app.py      |  6 ++---
 mesa/examples/basic/boid_flockers/model.py    | 26 ++++++++++++------
 .../continuous_space/continuous_space.py      | 22 ++++++++++++---
 mesa/visualization/mpl_space_drawing.py       |  6 +++--
 5 files changed, 61 insertions(+), 26 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 531d70cac89..e6144e0aaaa 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -23,14 +23,13 @@ class Boid(ContinuousSpaceAgent):
     any other Boid.
     """
 
-
     def __init__(
         self,
         model,
         space,
-        position=(0,0),
+        position=(0, 0),
         speed=1,
-        direction=(1,1),
+        direction=(1, 1),
         vision=1,
         separation=1,
         cohere=0.03,
@@ -68,22 +67,32 @@ def pos(self):
     def pos(self, value):
         pass
 
-
     def step(self):
         """Get the Boid's neighbors, compute the new vector, and move accordingly."""
-        neighbors, distances = self.get_neighbors_in_radius(radius=self.vision, include_distance=True)
+        neighbors, distances = self.get_neighbors_in_radius(
+            radius=self.vision, include_distance=True
+        )
         self.neighbors = neighbors.tolist()
 
         # If no neighbors, maintain current direction
-        if neighbors.size==0:
+        if neighbors.size == 0:
             self.position += self.direction * self.speed
             return
 
-        delta = self.space.calculate_difference_vector(self.position, [n._mesa_index for n in neighbors])
+        delta = self.space.calculate_difference_vector(
+            self.position, [n._mesa_index for n in neighbors]
+        )
 
         cohere = np.sum(delta, axis=0) * self.cohere_factor
-        separation_vector = -1 * np.sum(delta[distances < self.separation], axis=0) * self.separate_factor
-        match_vector = np.sum(np.asarray([n.direction for n in neighbors]), axis=0) * self.match_factor
+        separation_vector = (
+            -1
+            * np.sum(delta[distances < self.separation], axis=0)
+            * self.separate_factor
+        )
+        match_vector = (
+            np.sum(np.asarray([n.direction for n in neighbors]), axis=0)
+            * self.match_factor
+        )
 
         # Update direction based on the three behaviors
         self.direction += (cohere + separation_vector + match_vector) / len(neighbors)
diff --git a/mesa/examples/basic/boid_flockers/app.py b/mesa/examples/basic/boid_flockers/app.py
index 2a544c4ffec..174e2736a2a 100644
--- a/mesa/examples/basic/boid_flockers/app.py
+++ b/mesa/examples/basic/boid_flockers/app.py
@@ -1,7 +1,7 @@
-import sys, os
+import os
+import sys
 
-
-sys.path.insert(0, os.path.abspath('../../../..'))
+sys.path.insert(0, os.path.abspath("../../../.."))
 
 from mesa.examples.basic.boid_flockers.model import BoidFlockers
 from mesa.visualization import Slider, SolaraViz, make_space_component
diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index c1cb7b661db..edae3b2c752 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -45,16 +45,26 @@ def __init__(
         super().__init__(seed=seed)
 
         # Set up the space
-        self.space = ContinuousSpace([[0, width],
-                                      [0, height]],
-                                     torus=True, random=self.random)
+        self.space = ContinuousSpace(
+            [[0, width], [0, height]], torus=True, random=self.random
+        )
 
         # Create and place the Boid agents
         position = self.rng.random(size=(population_size, 2)) * self.space.size
         direction = self.rng.uniform(-1, 1, size=(population_size, 2))
-        Boid.create_agents(self, population_size, self.space, position=position, direction=direction,
-                           cohere=cohere, separate=separate, match=match, speed=speed, vision=vision,
-                           separation=separation)
+        Boid.create_agents(
+            self,
+            population_size,
+            self.space,
+            position=position,
+            direction=direction,
+            cohere=cohere,
+            separate=separate,
+            match=match,
+            speed=speed,
+            vision=vision,
+            separation=separation,
+        )
 
         # For tracking statistics
         self.average_heading = None
@@ -79,6 +89,6 @@ def step(self):
         self.update_average_heading()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     model = BoidFlockers()
-    model.step()
\ No newline at end of file
+    model.step()
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 7e640fff094..ff24115fb45 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -105,10 +105,16 @@ def _remove_agent(self, agent: Agent) -> None:
         self._positions_in_use[index] = False
         self._agents[index] = None
 
-    def calculate_difference_vector(self, point: np.ndarray, indices=None) -> np.ndarray:
+    def calculate_difference_vector(
+        self, point: np.ndarray, indices=None
+    ) -> np.ndarray:
         """Calculate the difference vector between the point and all agents"""
         point = np.asanyarray(point)
-        positions = self._agent_positions[indices] if indices is not None else self.agent_positions
+        positions = (
+            self._agent_positions[indices]
+            if indices is not None
+            else self.agent_positions
+        )
 
         if self.torus:
             delta = np.abs(point[np.newaxis, :] - positions)
@@ -123,8 +129,16 @@ def calculate_difference_vector(self, point: np.ndarray, indices=None) -> np.nda
     def calculate_distances(self, point, indices=None) -> tuple[np.ndarray, np.ndarray]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
-        positions = self._agent_positions[indices] if indices is not None else self.agent_positions
-        agents = self._agents[indices] if indices is not None else self._agents[self._positions_in_use]
+        positions = (
+            self._agent_positions[indices]
+            if indices is not None
+            else self.agent_positions
+        )
+        agents = (
+            self._agents[indices]
+            if indices is not None
+            else self._agents[self._positions_in_use]
+        )
 
         if self.torus:
             delta = np.abs(point[np.newaxis, :] - positions)
diff --git a/mesa/visualization/mpl_space_drawing.py b/mesa/visualization/mpl_space_drawing.py
index 1adacce03f2..db7916258b0 100644
--- a/mesa/visualization/mpl_space_drawing.py
+++ b/mesa/visualization/mpl_space_drawing.py
@@ -143,7 +143,10 @@ def draw_space(
             draw_orthogonal_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, **space_drawing_kwargs)
-        case mesa.space.ContinuousSpace() | mesa.experimental.continuous_space.ContinuousSpace():
+        case (
+            mesa.space.ContinuousSpace()
+            | mesa.experimental.continuous_space.ContinuousSpace()
+        ):
             draw_continuous_space(space, agent_portrayal, ax=ax)
         case VoronoiGrid():
             draw_voronoi_grid(space, agent_portrayal, ax=ax)
@@ -475,7 +478,6 @@ def draw_continuous_space(
     width = space.size[0]
     height = space.size[1]
 
-
     # width = space.x_max - space.x_min
     x_padding = width / 20
     # height = space.y_max - space.y_min

From 238d105724975bf81ad222bb1c6bb14a057f2a42 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Thu, 2 Jan 2025 17:02:26 +0100
Subject: [PATCH 27/84] Update configurations.py

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

diff --git a/benchmarks/configurations.py b/benchmarks/configurations.py
index e1e193c4e6d..a865325e145 100644
--- a/benchmarks/configurations.py
+++ b/benchmarks/configurations.py
@@ -90,14 +90,14 @@
             "seeds": 25,
             "replications": 3,
             "steps": 20,
-            "parameters": {"population": 200, "width": 100, "height": 100, "vision": 5},
+            "parameters": {"population_size": 200, "width": 100, "height": 100, "vision": 5},
         },
         "large": {
             "seeds": 10,
             "replications": 3,
             "steps": 10,
             "parameters": {
-                "population": 400,
+                "population_size": 400,
                 "width": 150,
                 "height": 150,
                 "vision": 15,

From 07e5da4f057e640b2f7be55c4da565c7f47472cd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Jan 2025 16:02:38 +0000
Subject: [PATCH 28/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 benchmarks/configurations.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/benchmarks/configurations.py b/benchmarks/configurations.py
index a865325e145..62f52bf3181 100644
--- a/benchmarks/configurations.py
+++ b/benchmarks/configurations.py
@@ -90,7 +90,12 @@
             "seeds": 25,
             "replications": 3,
             "steps": 20,
-            "parameters": {"population_size": 200, "width": 100, "height": 100, "vision": 5},
+            "parameters": {
+                "population_size": 200,
+                "width": 100,
+                "height": 100,
+                "vision": 5,
+            },
         },
         "large": {
             "seeds": 10,

From 1b5b08247f62ce7de2c77772f98245320315844a Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Thu, 2 Jan 2025 18:36:35 +0100
Subject: [PATCH 29/84] updates

---
 mesa/examples/basic/boid_flockers/model.py         | 14 +++++++++++---
 .../continuous_space/continuous_space.py           | 14 +++++---------
 2 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index edae3b2c752..c7fb65d1571 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -4,6 +4,12 @@
 A Mesa implementation of Craig Reynolds's Boids flocker model.
 Uses numpy arrays to represent vectors.
 """
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../../../.."))
+
+
 
 import numpy as np
 
@@ -46,7 +52,7 @@ def __init__(
 
         # Set up the space
         self.space = ContinuousSpace(
-            [[0, width], [0, height]], torus=True, random=self.random
+            [[0, width], [0, height]], torus=True, random=self.random, n_agents=population_size
         )
 
         # Create and place the Boid agents
@@ -90,5 +96,7 @@ def step(self):
 
 
 if __name__ == "__main__":
-    model = BoidFlockers()
-    model.step()
+    model = BoidFlockers(population_size=200, width=100, height=100, vision=5, seed=42)
+
+    for i in range(100):
+        model.step()
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index ff24115fb45..906a73d7540 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -115,14 +115,13 @@ def calculate_difference_vector(
             if indices is not None
             else self.agent_positions
         )
+        delta = point[np.newaxis, :] - positions
 
         if self.torus:
-            delta = np.abs(point[np.newaxis, :] - positions)
+            delta = np.abs(delta, out=delta)
             delta = np.minimum(
-                delta, self.size - delta
-            )  # fixme, should be based on size or maxima?
-        else:
-            delta = point[np.newaxis, :] - positions
+                delta, self.size - delta, out=delta
+            )
 
         return delta
 
@@ -141,10 +140,7 @@ def calculate_distances(self, point, indices=None) -> tuple[np.ndarray, np.ndarr
         )
 
         if self.torus:
-            delta = np.abs(point[np.newaxis, :] - positions)
-            delta = np.minimum(
-                delta, self.size - delta
-            )  # fixme, should be based on size or maxima?
+            delta = self.calculate_difference_vector(point)
             dists = np.linalg.norm(delta, axis=1)
         else:
             dists = cdist(point[np.newaxis, :], positions)[:, 0]

From c46c8901ac23074fe5393c8ce2634baa88b1f9a4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Jan 2025 17:38:55 +0000
Subject: [PATCH 30/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/basic/boid_flockers/model.py             | 7 +++++--
 mesa/experimental/continuous_space/continuous_space.py | 4 +---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index c7fb65d1571..0902edd5bfe 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -4,13 +4,13 @@
 A Mesa implementation of Craig Reynolds's Boids flocker model.
 Uses numpy arrays to represent vectors.
 """
+
 import os
 import sys
 
 sys.path.insert(0, os.path.abspath("../../../.."))
 
 
-
 import numpy as np
 
 from mesa import Model
@@ -52,7 +52,10 @@ def __init__(
 
         # Set up the space
         self.space = ContinuousSpace(
-            [[0, width], [0, height]], torus=True, random=self.random, n_agents=population_size
+            [[0, width], [0, height]],
+            torus=True,
+            random=self.random,
+            n_agents=population_size,
         )
 
         # Create and place the Boid agents
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 906a73d7540..6474cb1fc33 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -119,9 +119,7 @@ def calculate_difference_vector(
 
         if self.torus:
             delta = np.abs(delta, out=delta)
-            delta = np.minimum(
-                delta, self.size - delta, out=delta
-            )
+            delta = np.minimum(delta, self.size - delta, out=delta)
 
         return delta
 

From 357bc750bf32fb936d3022347fdf5349f2445e62 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Thu, 2 Jan 2025 20:20:59 +0100
Subject: [PATCH 31/84] ongoing

---
 mesa/examples/basic/boid_flockers/profile.svg | 491 ++++++++++++++++++
 .../continuous_space_agents.py                |   1 +
 2 files changed, 492 insertions(+)
 create mode 100644 mesa/examples/basic/boid_flockers/profile.svg

diff --git a/mesa/examples/basic/boid_flockers/profile.svg b/mesa/examples/basic/boid_flockers/profile.svg
new file mode 100644
index 00000000000..53d45336f85
--- /dev/null
+++ b/mesa/examples/basic/boid_flockers/profile.svg
@@ -0,0 +1,491 @@
+<?xml version="1.0" standalone="no"?><!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"><svg version="1.1" width="1200" height="1450" onload="init(evt)" viewBox="0 0 1200 1450" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:fg="http://github.com/jonhoo/inferno"><!--Flame graph stack visualization. See https://github.com/brendangregg/FlameGraph for latest version, and http://www.brendangregg.com/flamegraphs.html for examples.--><!--NOTES: --><defs><linearGradient id="background" y1="0" y2="1" x1="0" x2="0"><stop stop-color="#eeeeee" offset="5%"/><stop stop-color="#eeeeb0" offset="95%"/></linearGradient></defs><style type="text/css">
+text { font-family:monospace; font-size:12px }
+#title { text-anchor:middle; font-size:17px; }
+#matched { text-anchor:end; }
+#search { text-anchor:end; opacity:0.1; cursor:pointer; }
+#search:hover, #search.show { opacity:1; }
+#subtitle { text-anchor:middle; font-color:rgb(160,160,160); }
+#unzoom { cursor:pointer; }
+#frames > *:hover { stroke:black; stroke-width:0.5; cursor:pointer; }
+.hide { display:none; }
+.parent { opacity:0.5; }
+</style><script type="text/ecmascript"><![CDATA[
+        var nametype = 'Function:';
+        var fontsize = 12;
+        var fontwidth = 0.59;
+        var xpad = 10;
+        var inverted = true;
+        var searchcolor = 'rgb(230,0,230)';
+        var fluiddrawing = true;
+        var truncate_text_right = false;
+    ]]><![CDATA["use strict";
+var details, searchbtn, unzoombtn, matchedtxt, svg, searching, frames, known_font_width;
+function init(evt) {
+    details = document.getElementById("details").firstChild;
+    searchbtn = document.getElementById("search");
+    unzoombtn = document.getElementById("unzoom");
+    matchedtxt = document.getElementById("matched");
+    svg = document.getElementsByTagName("svg")[0];
+    frames = document.getElementById("frames");
+    known_font_width = get_monospace_width(frames);
+    total_samples = parseInt(frames.attributes.total_samples.value);
+    searching = 0;
+
+    // Use GET parameters to restore a flamegraph's state.
+    var restore_state = function() {
+        var params = get_params();
+        if (params.x && params.y)
+            zoom(find_group(document.querySelector('[*|x="' + params.x + '"][y="' + params.y + '"]')));
+        if (params.s)
+            search(params.s);
+    };
+
+    if (fluiddrawing) {
+        // Make width dynamic so the SVG fits its parent's width.
+        svg.removeAttribute("width");
+        // Edge requires us to have a viewBox that gets updated with size changes.
+        var isEdge = /Edge\/\d./i.test(navigator.userAgent);
+        if (!isEdge) {
+            svg.removeAttribute("viewBox");
+        }
+        var update_for_width_change = function() {
+            if (isEdge) {
+                svg.attributes.viewBox.value = "0 0 " + svg.width.baseVal.value + " " + svg.height.baseVal.value;
+            }
+
+            // Keep consistent padding on left and right of frames container.
+            frames.attributes.width.value = svg.width.baseVal.value - xpad * 2;
+
+            // Text truncation needs to be adjusted for the current width.
+            update_text_for_elements(frames.children);
+
+            // Keep search elements at a fixed distance from right edge.
+            var svgWidth = svg.width.baseVal.value;
+            searchbtn.attributes.x.value = svgWidth - xpad;
+            matchedtxt.attributes.x.value = svgWidth - xpad;
+        };
+        window.addEventListener('resize', function() {
+            update_for_width_change();
+        });
+        // This needs to be done asynchronously for Safari to work.
+        setTimeout(function() {
+            unzoom();
+            update_for_width_change();
+            restore_state();
+        }, 0);
+    } else {
+        restore_state();
+    }
+}
+// event listeners
+window.addEventListener("click", function(e) {
+    var target = find_group(e.target);
+    if (target) {
+        if (target.nodeName == "a") {
+            if (e.ctrlKey === false) return;
+            e.preventDefault();
+        }
+        if (target.classList.contains("parent")) unzoom();
+        zoom(target);
+
+        // set parameters for zoom state
+        var el = target.querySelector("rect");
+        if (el && el.attributes && el.attributes.y && el.attributes["fg:x"]) {
+            var params = get_params()
+            params.x = el.attributes["fg:x"].value;
+            params.y = el.attributes.y.value;
+            history.replaceState(null, null, parse_params(params));
+        }
+    }
+    else if (e.target.id == "unzoom") {
+        unzoom();
+
+        // remove zoom state
+        var params = get_params();
+        if (params.x) delete params.x;
+        if (params.y) delete params.y;
+        history.replaceState(null, null, parse_params(params));
+    }
+    else if (e.target.id == "search") search_prompt();
+}, false)
+// mouse-over for info
+// show
+window.addEventListener("mouseover", function(e) {
+    var target = find_group(e.target);
+    if (target) details.nodeValue = nametype + " " + g_to_text(target);
+}, false)
+// clear
+window.addEventListener("mouseout", function(e) {
+    var target = find_group(e.target);
+    if (target) details.nodeValue = ' ';
+}, false)
+// ctrl-F for search
+window.addEventListener("keydown",function (e) {
+    if (e.keyCode === 114 || (e.ctrlKey && e.keyCode === 70)) {
+        e.preventDefault();
+        search_prompt();
+    }
+}, false)
+// functions
+function get_params() {
+    var params = {};
+    var paramsarr = window.location.search.substr(1).split('&');
+    for (var i = 0; i < paramsarr.length; ++i) {
+        var tmp = paramsarr[i].split("=");
+        if (!tmp[0] || !tmp[1]) continue;
+        params[tmp[0]]  = decodeURIComponent(tmp[1]);
+    }
+    return params;
+}
+function parse_params(params) {
+    var uri = "?";
+    for (var key in params) {
+        uri += key + '=' + encodeURIComponent(params[key]) + '&';
+    }
+    if (uri.slice(-1) == "&")
+        uri = uri.substring(0, uri.length - 1);
+    if (uri == '?')
+        uri = window.location.href.split('?')[0];
+    return uri;
+}
+function find_child(node, selector) {
+    var children = node.querySelectorAll(selector);
+    if (children.length) return children[0];
+    return;
+}
+function find_group(node) {
+    var parent = node.parentElement;
+    if (!parent) return;
+    if (parent.id == "frames") return node;
+    return find_group(parent);
+}
+function orig_save(e, attr, val) {
+    if (e.attributes["fg:orig_" + attr] != undefined) return;
+    if (e.attributes[attr] == undefined) return;
+    if (val == undefined) val = e.attributes[attr].value;
+    e.setAttribute("fg:orig_" + attr, val);
+}
+function orig_load(e, attr) {
+    if (e.attributes["fg:orig_"+attr] == undefined) return;
+    e.attributes[attr].value = e.attributes["fg:orig_" + attr].value;
+    e.removeAttribute("fg:orig_" + attr);
+}
+function g_to_text(e) {
+    var text = find_child(e, "title").firstChild.nodeValue;
+    return (text)
+}
+function g_to_func(e) {
+    var func = g_to_text(e);
+    // if there's any manipulation we want to do to the function
+    // name before it's searched, do it here before returning.
+    return (func);
+}
+function get_monospace_width(frames) {
+    // Given the id="frames" element, return the width of text characters if
+    // this is a monospace font, otherwise return 0.
+    text = find_child(frames.children[0], "text");
+    originalContent = text.textContent;
+    text.textContent = "!";
+    bangWidth = text.getComputedTextLength();
+    text.textContent = "W";
+    wWidth = text.getComputedTextLength();
+    text.textContent = originalContent;
+    if (bangWidth === wWidth) {
+        return bangWidth;
+    } else {
+        return 0;
+    }
+}
+function update_text_for_elements(elements) {
+    // In order to render quickly in the browser, you want to do one pass of
+    // reading attributes, and one pass of mutating attributes. See
+    // https://web.dev/avoid-large-complex-layouts-and-layout-thrashing/ for details.
+
+    // Fall back to inefficient calculation, if we're variable-width font.
+    // TODO This should be optimized somehow too.
+    if (known_font_width === 0) {
+        for (var i = 0; i < elements.length; i++) {
+            update_text(elements[i]);
+        }
+        return;
+    }
+
+    var textElemNewAttributes = [];
+    for (var i = 0; i < elements.length; i++) {
+        var e = elements[i];
+        var r = find_child(e, "rect");
+        var t = find_child(e, "text");
+        var w = parseFloat(r.attributes.width.value) * frames.attributes.width.value / 100 - 3;
+        var txt = find_child(e, "title").textContent.replace(/\([^(]*\)$/,"");
+        var newX = format_percent((parseFloat(r.attributes.x.value) + (100 * 3 / frames.attributes.width.value)));
+
+        // Smaller than this size won't fit anything
+        if (w < 2 * known_font_width) {
+            textElemNewAttributes.push([newX, ""]);
+            continue;
+        }
+
+        // Fit in full text width
+        if (txt.length * known_font_width < w) {
+            textElemNewAttributes.push([newX, txt]);
+            continue;
+        }
+
+        var substringLength = Math.floor(w / known_font_width) - 2;
+        if (truncate_text_right) {
+            // Truncate the right side of the text.
+            textElemNewAttributes.push([newX, txt.substring(0, substringLength) + ".."]);
+            continue;
+        } else {
+            // Truncate the left side of the text.
+            textElemNewAttributes.push([newX, ".." + txt.substring(txt.length - substringLength, txt.length)]);
+            continue;
+        }
+    }
+
+    console.assert(textElemNewAttributes.length === elements.length, "Resize failed, please file a bug at https://github.com/jonhoo/inferno/");
+
+    // Now that we know new textContent, set it all in one go so we don't refresh a bazillion times.
+    for (var i = 0; i < elements.length; i++) {
+        var e = elements[i];
+        var values = textElemNewAttributes[i];
+        var t = find_child(e, "text");
+        t.attributes.x.value = values[0];
+        t.textContent = values[1];
+    }
+}
+
+function update_text(e) {
+    var r = find_child(e, "rect");
+    var t = find_child(e, "text");
+    var w = parseFloat(r.attributes.width.value) * frames.attributes.width.value / 100 - 3;
+    var txt = find_child(e, "title").textContent.replace(/\([^(]*\)$/,"");
+    t.attributes.x.value = format_percent((parseFloat(r.attributes.x.value) + (100 * 3 / frames.attributes.width.value)));
+
+    // Smaller than this size won't fit anything
+    if (w < 2 * fontsize * fontwidth) {
+        t.textContent = "";
+        return;
+    }
+    t.textContent = txt;
+    // Fit in full text width
+    if (t.getComputedTextLength() < w)
+        return;
+    if (truncate_text_right) {
+        // Truncate the right side of the text.
+        for (var x = txt.length - 2; x > 0; x--) {
+            if (t.getSubStringLength(0, x + 2) <= w) {
+                t.textContent = txt.substring(0, x) + "..";
+                return;
+            }
+        }
+    } else {
+        // Truncate the left side of the text.
+        for (var x = 2; x < txt.length; x++) {
+            if (t.getSubStringLength(x - 2, txt.length) <= w) {
+                t.textContent = ".." + txt.substring(x, txt.length);
+                return;
+            }
+        }
+    }
+    t.textContent = "";
+}
+// zoom
+function zoom_reset(e) {
+    if (e.tagName == "rect") {
+        e.attributes.x.value = format_percent(100 * parseInt(e.attributes["fg:x"].value) / total_samples);
+        e.attributes.width.value = format_percent(100 * parseInt(e.attributes["fg:w"].value) / total_samples);
+    }
+    if (e.childNodes == undefined) return;
+    for(var i = 0, c = e.childNodes; i < c.length; i++) {
+        zoom_reset(c[i]);
+    }
+}
+function zoom_child(e, x, zoomed_width_samples) {
+    if (e.tagName == "text") {
+        var parent_x = parseFloat(find_child(e.parentNode, "rect[x]").attributes.x.value);
+        e.attributes.x.value = format_percent(parent_x + (100 * 3 / frames.attributes.width.value));
+    } else if (e.tagName == "rect") {
+        e.attributes.x.value = format_percent(100 * (parseInt(e.attributes["fg:x"].value) - x) / zoomed_width_samples);
+        e.attributes.width.value = format_percent(100 * parseInt(e.attributes["fg:w"].value) / zoomed_width_samples);
+    }
+    if (e.childNodes == undefined) return;
+    for(var i = 0, c = e.childNodes; i < c.length; i++) {
+        zoom_child(c[i], x, zoomed_width_samples);
+    }
+}
+function zoom_parent(e) {
+    if (e.attributes) {
+        if (e.attributes.x != undefined) {
+            e.attributes.x.value = "0.0%";
+        }
+        if (e.attributes.width != undefined) {
+            e.attributes.width.value = "100.0%";
+        }
+    }
+    if (e.childNodes == undefined) return;
+    for(var i = 0, c = e.childNodes; i < c.length; i++) {
+        zoom_parent(c[i]);
+    }
+}
+function zoom(node) {
+    var attr = find_child(node, "rect").attributes;
+    var width = parseInt(attr["fg:w"].value);
+    var xmin = parseInt(attr["fg:x"].value);
+    var xmax = xmin + width;
+    var ymin = parseFloat(attr.y.value);
+    unzoombtn.classList.remove("hide");
+    var el = frames.children;
+    var to_update_text = [];
+    for (var i = 0; i < el.length; i++) {
+        var e = el[i];
+        var a = find_child(e, "rect").attributes;
+        var ex = parseInt(a["fg:x"].value);
+        var ew = parseInt(a["fg:w"].value);
+        // Is it an ancestor
+        if (!inverted) {
+            var upstack = parseFloat(a.y.value) > ymin;
+        } else {
+            var upstack = parseFloat(a.y.value) < ymin;
+        }
+        if (upstack) {
+            // Direct ancestor
+            if (ex <= xmin && (ex+ew) >= xmax) {
+                e.classList.add("parent");
+                zoom_parent(e);
+                to_update_text.push(e);
+            }
+            // not in current path
+            else
+                e.classList.add("hide");
+        }
+        // Children maybe
+        else {
+            // no common path
+            if (ex < xmin || ex >= xmax) {
+                e.classList.add("hide");
+            }
+            else {
+                zoom_child(e, xmin, width);
+                to_update_text.push(e);
+            }
+        }
+    }
+    update_text_for_elements(to_update_text);
+}
+function unzoom() {
+    unzoombtn.classList.add("hide");
+    var el = frames.children;
+    for(var i = 0; i < el.length; i++) {
+        el[i].classList.remove("parent");
+        el[i].classList.remove("hide");
+        zoom_reset(el[i]);
+    }
+    update_text_for_elements(el);
+}
+// search
+function reset_search() {
+    var el = document.querySelectorAll("#frames rect");
+    for (var i = 0; i < el.length; i++) {
+        orig_load(el[i], "fill")
+    }
+    var params = get_params();
+    delete params.s;
+    history.replaceState(null, null, parse_params(params));
+}
+function search_prompt() {
+    if (!searching) {
+        var term = prompt("Enter a search term (regexp " +
+            "allowed, eg: ^ext4_)", "");
+        if (term != null) {
+            search(term)
+        }
+    } else {
+        reset_search();
+        searching = 0;
+        searchbtn.classList.remove("show");
+        searchbtn.firstChild.nodeValue = "Search"
+        matchedtxt.classList.add("hide");
+        matchedtxt.firstChild.nodeValue = ""
+    }
+}
+function search(term) {
+    var re = new RegExp(term);
+    var el = frames.children;
+    var matches = new Object();
+    var maxwidth = 0;
+    for (var i = 0; i < el.length; i++) {
+        var e = el[i];
+        // Skip over frames which are either not visible, or below the zoomed-to frame
+        if (e.classList.contains("hide") || e.classList.contains("parent")) {
+            continue;
+        }
+        var func = g_to_func(e);
+        var rect = find_child(e, "rect");
+        if (func == null || rect == null)
+            continue;
+        // Save max width. Only works as we have a root frame
+        var w = parseInt(rect.attributes["fg:w"].value);
+        if (w > maxwidth)
+            maxwidth = w;
+        if (func.match(re)) {
+            // highlight
+            var x = parseInt(rect.attributes["fg:x"].value);
+            orig_save(rect, "fill");
+            rect.attributes.fill.value = searchcolor;
+            // remember matches
+            if (matches[x] == undefined) {
+                matches[x] = w;
+            } else {
+                if (w > matches[x]) {
+                    // overwrite with parent
+                    matches[x] = w;
+                }
+            }
+            searching = 1;
+        }
+    }
+    if (!searching)
+        return;
+    var params = get_params();
+    params.s = term;
+    history.replaceState(null, null, parse_params(params));
+
+    searchbtn.classList.add("show");
+    searchbtn.firstChild.nodeValue = "Reset Search";
+    // calculate percent matched, excluding vertical overlap
+    var count = 0;
+    var lastx = -1;
+    var lastw = 0;
+    var keys = Array();
+    for (k in matches) {
+        if (matches.hasOwnProperty(k))
+            keys.push(k);
+    }
+    // sort the matched frames by their x location
+    // ascending, then width descending
+    keys.sort(function(a, b){
+        return a - b;
+    });
+    // Step through frames saving only the biggest bottom-up frames
+    // thanks to the sort order. This relies on the tree property
+    // where children are always smaller than their parents.
+    for (var k in keys) {
+        var x = parseInt(keys[k]);
+        var w = matches[keys[k]];
+        if (x >= lastx + lastw) {
+            count += w;
+            lastx = x;
+            lastw = w;
+        }
+    }
+    // display matched percent
+    matchedtxt.classList.remove("hide");
+    var pct = 100 * count / maxwidth;
+    if (pct != 100) pct = pct.toFixed(1);
+    matchedtxt.firstChild.nodeValue = "Matched: " + pct + "%";
+}
+function format_percent(n) {
+    return n.toFixed(4) + "%";
+}
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\ No newline at end of file
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index f55e88e9fe8..f27dbda43d5 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -111,6 +111,7 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
 
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
         indices = np.argpartition(dists, k)[:k]
+        indices = indices[indices != self._mesa_index]
 
         if include_distance:
             return agents[indices], dists[indices]

From cc4a0959291531d29faee61035786426f7b915c4 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Thu, 2 Jan 2025 21:33:00 +0100
Subject: [PATCH 32/84] Update continuous_space.py

---
 .../continuous_space/continuous_space.py       | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 6474cb1fc33..c3ee6e7c771 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -115,11 +115,15 @@ def calculate_difference_vector(
             if indices is not None
             else self.agent_positions
         )
-        delta = point[np.newaxis, :] - positions
+        delta = positions - point[np.newaxis, :]
 
         if self.torus:
-            delta = np.abs(delta, out=delta)
-            delta = np.minimum(delta, self.size - delta, out=delta)
+            inverse_delta = delta - np.sign(delta) * self.size
+            logical = np.abs(delta) < np.abs(inverse_delta)
+            out = np.zeros(delta.shape)
+            out[logical] = delta[logical]
+            out[~logical] = inverse_delta[~logical]
+            delta = out
 
         return delta
 
@@ -138,7 +142,13 @@ def calculate_distances(self, point, indices=None) -> tuple[np.ndarray, np.ndarr
         )
 
         if self.torus:
-            delta = self.calculate_difference_vector(point)
+            delta = point[np.newaxis, :] - positions
+
+            delta = np.abs(delta, out=delta)
+            delta = np.minimum(
+                delta, self.size - delta, out=delta
+            )
+
             dists = np.linalg.norm(delta, axis=1)
         else:
             dists = cdist(point[np.newaxis, :], positions)[:, 0]

From f549eee8817e0539639ae374f7404cd66c82b492 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 09:56:02 +0100
Subject: [PATCH 33/84] revert mpl changes

---
 mesa/visualization/mpl_space_drawing.py | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/mesa/visualization/mpl_space_drawing.py b/mesa/visualization/mpl_space_drawing.py
index db7916258b0..2bfae564036 100644
--- a/mesa/visualization/mpl_space_drawing.py
+++ b/mesa/visualization/mpl_space_drawing.py
@@ -143,10 +143,7 @@ def draw_space(
             draw_orthogonal_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, **space_drawing_kwargs)
-        case (
-            mesa.space.ContinuousSpace()
-            | mesa.experimental.continuous_space.ContinuousSpace()
-        ):
+        case mesa.space.ContinuousSpace():
             draw_continuous_space(space, agent_portrayal, ax=ax)
         case VoronoiGrid():
             draw_voronoi_grid(space, agent_portrayal, ax=ax)
@@ -475,12 +472,9 @@ def draw_continuous_space(
         fig, ax = plt.subplots()
 
     # space related setup
-    width = space.size[0]
-    height = space.size[1]
-
-    # width = space.x_max - space.x_min
+    width = space.x_max - space.x_min
     x_padding = width / 20
-    # height = space.y_max - space.y_min
+    height = space.y_max - space.y_min
     y_padding = height / 20
 
     # gather agent data
@@ -497,8 +491,8 @@ def draw_continuous_space(
         spine.set_color("black")
         spine.set_linestyle(border_style)
 
-    ax.set_xlim(space.dimensions[0, 0] - x_padding, space.dimensions[0, 1] + x_padding)
-    ax.set_ylim(space.dimensions[1, 0] - y_padding, space.dimensions[1, 1] + y_padding)
+    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
 
@@ -598,4 +592,4 @@ def _scatter(ax: Axes, arguments, **kwargs):
                 zorder=z_order,
                 **{k: v[logical] for k, v in arguments.items()},
                 **kwargs,
-            )
+            )
\ No newline at end of file

From 4b3bb91ee681ccfb5003ec076667e33c197109b9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Jan 2025 08:56:10 +0000
Subject: [PATCH 34/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/continuous_space/continuous_space.py | 4 +---
 mesa/visualization/mpl_space_drawing.py                | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index c3ee6e7c771..8a3e70b3ca9 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -145,9 +145,7 @@ def calculate_distances(self, point, indices=None) -> tuple[np.ndarray, np.ndarr
             delta = point[np.newaxis, :] - positions
 
             delta = np.abs(delta, out=delta)
-            delta = np.minimum(
-                delta, self.size - delta, out=delta
-            )
+            delta = np.minimum(delta, self.size - delta, out=delta)
 
             dists = np.linalg.norm(delta, axis=1)
         else:
diff --git a/mesa/visualization/mpl_space_drawing.py b/mesa/visualization/mpl_space_drawing.py
index 2bfae564036..784d370eba0 100644
--- a/mesa/visualization/mpl_space_drawing.py
+++ b/mesa/visualization/mpl_space_drawing.py
@@ -592,4 +592,4 @@ def _scatter(ax: Axes, arguments, **kwargs):
                 zorder=z_order,
                 **{k: v[logical] for k, v in arguments.items()},
                 **kwargs,
-            )
\ No newline at end of file
+            )

From 8f0431235838e6f7f8e02f9f9222753c3a2e130c Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 10:39:27 +0100
Subject: [PATCH 35/84] fine tuning performance

---
 mesa/examples/basic/boid_flockers/agents.py   | 16 +---
 .../continuous_space/continuous_space.py      | 76 +++++++++++++------
 .../continuous_space_agents.py                | 10 +++
 3 files changed, 68 insertions(+), 34 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index e6144e0aaaa..96f12b4a585 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -59,20 +59,12 @@ def __init__(
         self.match_factor = match
         self.neighbors = []
 
-    @property
-    def pos(self):
-        return self.position
-
-    @pos.setter
-    def pos(self, value):
-        pass
-
     def step(self):
         """Get the Boid's neighbors, compute the new vector, and move accordingly."""
         neighbors, distances = self.get_neighbors_in_radius(
             radius=self.vision, include_distance=True
         )
-        self.neighbors = neighbors.tolist()
+        self.neighbors = neighbors
 
         # If no neighbors, maintain current direction
         if neighbors.size == 0:
@@ -80,10 +72,10 @@ def step(self):
             return
 
         delta = self.space.calculate_difference_vector(
-            self.position, [n._mesa_index for n in neighbors]
+            self.position, agents=neighbors
         )
 
-        cohere = np.sum(delta, axis=0) * self.cohere_factor
+        cohere_vector = np.sum(delta, axis=0) * self.cohere_factor
         separation_vector = (
             -1
             * np.sum(delta[distances < self.separation], axis=0)
@@ -95,7 +87,7 @@ def step(self):
         )
 
         # Update direction based on the three behaviors
-        self.direction += (cohere + separation_vector + match_vector) / len(neighbors)
+        self.direction += (cohere_vector + separation_vector + match_vector) / len(neighbors)
 
         # Normalize direction vector
         self.direction /= np.linalg.norm(self.direction)
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 8a3e70b3ca9..094a81c88bc 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -9,10 +9,41 @@
 
 from mesa.agent import Agent, AgentSet
 
+from line_profiler_pycharm import profile
 
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
 
+    @property
+    def x_min(self):
+        # compatability with solara_viz
+        return self.dimensions[0,0]
+
+    @property
+    def x_max(self):
+        # compatability with solara_viz
+        return self.dimensions[0,1]
+
+    @property
+    def y_min(self):
+        # compatability with solara_viz
+        return self.dimensions[1,0]
+
+    @property
+    def y_max(self):
+        # compatability with solara_viz
+        return self.dimensions[1,1]
+
+    @property
+    def width(self):
+        # compatability with solara_viz
+        return self.size[0]
+
+    @property
+    def height(self):
+        # compatability with solara_viz
+        return self.size[1]
+
     def __init__(
         self,
         dimensions: Sequence[Sequence[float]],
@@ -53,10 +84,10 @@ def agents(self) -> AgentSet:
         """Return an AgentSet with the agents in the space."""
         return AgentSet(self._agents[self._positions_in_use], random=self.random)
 
-    @property
-    def agent_positions(self) -> np.ndarray:
-        """Return the positions of the agents in the space."""
-        return self._agent_positions[self._positions_in_use]
+    # @property
+    # def agent_positions(self) -> np.ndarray:
+    #     """Return the positions of the agents in the space."""
+    #     return self._agent_positions[self._positions_in_use]
 
     def _get_index_for_agent(self, agent: Agent) -> int:
         """Helper method to get the index for the agent.
@@ -95,6 +126,9 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
 
+        self.agent_positions = self._agent_positions[self._positions_in_use]
+        self.active_agents = self._agents[self._positions_in_use]
+
         return index
 
     def _remove_agent(self, agent: Agent) -> None:
@@ -106,40 +140,38 @@ def _remove_agent(self, agent: Agent) -> None:
         self._agents[index] = None
 
     def calculate_difference_vector(
-        self, point: np.ndarray, indices=None
+        self, point: np.ndarray, agents=None
     ) -> np.ndarray:
-        """Calculate the difference vector between the point and all agents"""
+        """Calculate the difference vector between the point and all agents."""
         point = np.asanyarray(point)
-        positions = (
-            self._agent_positions[indices]
-            if indices is not None
-            else self.agent_positions
-        )
+        positions = self.agent_positions if agents is None else self._agent_positions[[self._agent_to_index[a] for a in agents]]
+
         delta = positions - point[np.newaxis, :]
 
         if self.torus:
             inverse_delta = delta - np.sign(delta) * self.size
+
+            # we need to use the lowest absolute value from delta and inverse delta
             logical = np.abs(delta) < np.abs(inverse_delta)
+
             out = np.zeros(delta.shape)
             out[logical] = delta[logical]
             out[~logical] = inverse_delta[~logical]
+
             delta = out
 
         return delta
 
-    def calculate_distances(self, point, indices=None) -> tuple[np.ndarray, np.ndarray]:
+    def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarray]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
-        positions = (
-            self._agent_positions[indices]
-            if indices is not None
-            else self.agent_positions
-        )
-        agents = (
-            self._agents[indices]
-            if indices is not None
-            else self._agents[self._positions_in_use]
-        )
+
+        if agents is None:
+            positions = self.agent_positions
+            agents = self.active_agents
+        else:
+            positions = self._agent_positions[[self._agent_to_index[a] for a in agents]]
+            agents = np.asarray(agents)
 
         if self.torus:
             delta = point[np.newaxis, :] - positions
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index f27dbda43d5..5c0aea15b58 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -42,6 +42,16 @@ def position(self, value: np.ndarray) -> None:
 
         self.space._agent_positions[self._mesa_index] = value
 
+    @property
+    def pos(self):
+        # just here for compatability with solara_viz.
+        return self.position
+
+    @pos.setter
+    def pos(self, value):
+        # just here for compatability solara_viz.
+        pass
+
     def __init__(self, space: ContinuousSpace, model):
         """Initialize a continuous space agent.
 

From 416455a1734fadb9b3426d369b37d1d013473bdc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Jan 2025 09:42:49 +0000
Subject: [PATCH 36/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/basic/boid_flockers/agents.py   |  8 ++++----
 .../continuous_space/continuous_space.py      | 19 ++++++++++---------
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 96f12b4a585..58151d442a0 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -71,9 +71,7 @@ def step(self):
             self.position += self.direction * self.speed
             return
 
-        delta = self.space.calculate_difference_vector(
-            self.position, agents=neighbors
-        )
+        delta = self.space.calculate_difference_vector(self.position, agents=neighbors)
 
         cohere_vector = np.sum(delta, axis=0) * self.cohere_factor
         separation_vector = (
@@ -87,7 +85,9 @@ def step(self):
         )
 
         # Update direction based on the three behaviors
-        self.direction += (cohere_vector + separation_vector + match_vector) / len(neighbors)
+        self.direction += (cohere_vector + separation_vector + match_vector) / len(
+            neighbors
+        )
 
         # Normalize direction vector
         self.direction /= np.linalg.norm(self.direction)
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 094a81c88bc..8dc78b1037e 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -9,7 +9,6 @@
 
 from mesa.agent import Agent, AgentSet
 
-from line_profiler_pycharm import profile
 
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
@@ -17,22 +16,22 @@ class ContinuousSpace:
     @property
     def x_min(self):
         # compatability with solara_viz
-        return self.dimensions[0,0]
+        return self.dimensions[0, 0]
 
     @property
     def x_max(self):
         # compatability with solara_viz
-        return self.dimensions[0,1]
+        return self.dimensions[0, 1]
 
     @property
     def y_min(self):
         # compatability with solara_viz
-        return self.dimensions[1,0]
+        return self.dimensions[1, 0]
 
     @property
     def y_max(self):
         # compatability with solara_viz
-        return self.dimensions[1,1]
+        return self.dimensions[1, 1]
 
     @property
     def width(self):
@@ -139,12 +138,14 @@ def _remove_agent(self, agent: Agent) -> None:
         self._positions_in_use[index] = False
         self._agents[index] = None
 
-    def calculate_difference_vector(
-        self, point: np.ndarray, agents=None
-    ) -> np.ndarray:
+    def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
         """Calculate the difference vector between the point and all agents."""
         point = np.asanyarray(point)
-        positions = self.agent_positions if agents is None else self._agent_positions[[self._agent_to_index[a] for a in agents]]
+        positions = (
+            self.agent_positions
+            if agents is None
+            else self._agent_positions[[self._agent_to_index[a] for a in agents]]
+        )
 
         delta = positions - point[np.newaxis, :]
 

From daa9b4797dbc8a460f9d9f5dc841390e437f4f7d Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 11:16:33 +0100
Subject: [PATCH 37/84] fine tuning

---
 .../continuous_space/continuous_space.py             | 12 ++++++------
 .../continuous_space/continuous_space_agents.py      |  1 +
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 8dc78b1037e..7eff8e76ee2 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -124,12 +124,14 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         self._agents[index] = agent
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
+        self._update_stuff()
 
+        return index
+
+    def _update_stuff(self):
         self.agent_positions = self._agent_positions[self._positions_in_use]
         self.active_agents = self._agents[self._positions_in_use]
 
-        return index
-
     def _remove_agent(self, agent: Agent) -> None:
         """Remove an agent from the space."""
         index = self._get_index_for_agent(agent)
@@ -137,6 +139,7 @@ def _remove_agent(self, agent: Agent) -> None:
         self._index_to_agent.pop(index, None)
         self._positions_in_use[index] = False
         self._agents[index] = None
+        self._update_stuff()
 
     def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
         """Calculate the difference vector between the point and all agents."""
@@ -175,11 +178,8 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             agents = np.asarray(agents)
 
         if self.torus:
-            delta = point[np.newaxis, :] - positions
-
-            delta = np.abs(delta, out=delta)
+            delta = np.abs(point[np.newaxis, :] - positions)
             delta = np.minimum(delta, self.size - delta, out=delta)
-
             dists = np.linalg.norm(delta, axis=1)
         else:
             dists = cdist(point[np.newaxis, :], positions)[:, 0]
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 5c0aea15b58..c0ac0a1ca85 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -9,6 +9,7 @@
 from mesa.agent import Agent
 from mesa.experimental.continuous_space import ContinuousSpace
 
+from line_profiler_pycharm import profile
 
 class HasPositionProtocol(Protocol):
     """Protocol for continuous space position holders."""

From 137162b3461c93e165d18bc4517cac0f53271517 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Jan 2025 10:16:51 +0000
Subject: [PATCH 38/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/continuous_space/continuous_space_agents.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index c0ac0a1ca85..5c0aea15b58 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -9,7 +9,6 @@
 from mesa.agent import Agent
 from mesa.experimental.continuous_space import ContinuousSpace
 
-from line_profiler_pycharm import profile
 
 class HasPositionProtocol(Protocol):
     """Protocol for continuous space position holders."""

From 5ce3d55c3febf2d524405502b56937b329032d11 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 11:22:53 +0100
Subject: [PATCH 39/84] Delete profile.svg

---
 mesa/examples/basic/boid_flockers/profile.svg | 491 ------------------
 1 file changed, 491 deletions(-)
 delete mode 100644 mesa/examples/basic/boid_flockers/profile.svg

diff --git a/mesa/examples/basic/boid_flockers/profile.svg b/mesa/examples/basic/boid_flockers/profile.svg
deleted file mode 100644
index 53d45336f85..00000000000
--- a/mesa/examples/basic/boid_flockers/profile.svg
+++ /dev/null
@@ -1,491 +0,0 @@
-<?xml version="1.0" standalone="no"?><!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"><svg version="1.1" width="1200" height="1450" onload="init(evt)" viewBox="0 0 1200 1450" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:fg="http://github.com/jonhoo/inferno"><!--Flame graph stack visualization. See https://github.com/brendangregg/FlameGraph for latest version, and http://www.brendangregg.com/flamegraphs.html for examples.--><!--NOTES: --><defs><linearGradient id="background" y1="0" y2="1" x1="0" x2="0"><stop stop-color="#eeeeee" offset="5%"/><stop stop-color="#eeeeb0" offset="95%"/></linearGradient></defs><style type="text/css">
-text { font-family:monospace; font-size:12px }
-#title { text-anchor:middle; font-size:17px; }
-#matched { text-anchor:end; }
-#search { text-anchor:end; opacity:0.1; cursor:pointer; }
-#search:hover, #search.show { opacity:1; }
-#subtitle { text-anchor:middle; font-color:rgb(160,160,160); }
-#unzoom { cursor:pointer; }
-#frames > *:hover { stroke:black; stroke-width:0.5; cursor:pointer; }
-.hide { display:none; }
-.parent { opacity:0.5; }
-</style><script type="text/ecmascript"><![CDATA[
-        var nametype = 'Function:';
-        var fontsize = 12;
-        var fontwidth = 0.59;
-        var xpad = 10;
-        var inverted = true;
-        var searchcolor = 'rgb(230,0,230)';
-        var fluiddrawing = true;
-        var truncate_text_right = false;
-    ]]><![CDATA["use strict";
-var details, searchbtn, unzoombtn, matchedtxt, svg, searching, frames, known_font_width;
-function init(evt) {
-    details = document.getElementById("details").firstChild;
-    searchbtn = document.getElementById("search");
-    unzoombtn = document.getElementById("unzoom");
-    matchedtxt = document.getElementById("matched");
-    svg = document.getElementsByTagName("svg")[0];
-    frames = document.getElementById("frames");
-    known_font_width = get_monospace_width(frames);
-    total_samples = parseInt(frames.attributes.total_samples.value);
-    searching = 0;
-
-    // Use GET parameters to restore a flamegraph's state.
-    var restore_state = function() {
-        var params = get_params();
-        if (params.x && params.y)
-            zoom(find_group(document.querySelector('[*|x="' + params.x + '"][y="' + params.y + '"]')));
-        if (params.s)
-            search(params.s);
-    };
-
-    if (fluiddrawing) {
-        // Make width dynamic so the SVG fits its parent's width.
-        svg.removeAttribute("width");
-        // Edge requires us to have a viewBox that gets updated with size changes.
-        var isEdge = /Edge\/\d./i.test(navigator.userAgent);
-        if (!isEdge) {
-            svg.removeAttribute("viewBox");
-        }
-        var update_for_width_change = function() {
-            if (isEdge) {
-                svg.attributes.viewBox.value = "0 0 " + svg.width.baseVal.value + " " + svg.height.baseVal.value;
-            }
-
-            // Keep consistent padding on left and right of frames container.
-            frames.attributes.width.value = svg.width.baseVal.value - xpad * 2;
-
-            // Text truncation needs to be adjusted for the current width.
-            update_text_for_elements(frames.children);
-
-            // Keep search elements at a fixed distance from right edge.
-            var svgWidth = svg.width.baseVal.value;
-            searchbtn.attributes.x.value = svgWidth - xpad;
-            matchedtxt.attributes.x.value = svgWidth - xpad;
-        };
-        window.addEventListener('resize', function() {
-            update_for_width_change();
-        });
-        // This needs to be done asynchronously for Safari to work.
-        setTimeout(function() {
-            unzoom();
-            update_for_width_change();
-            restore_state();
-        }, 0);
-    } else {
-        restore_state();
-    }
-}
-// event listeners
-window.addEventListener("click", function(e) {
-    var target = find_group(e.target);
-    if (target) {
-        if (target.nodeName == "a") {
-            if (e.ctrlKey === false) return;
-            e.preventDefault();
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\ No newline at end of file

From 96fc316c2fc13eb8243dd85063746131ca2739fe Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 11:25:11 +0100
Subject: [PATCH 40/84] ruff related

---
 mesa/examples/basic/boid_flockers/model.py    |  2 +-
 .../continuous_space/continuous_space.py      | 24 +++++++++----------
 .../continuous_space/for_development.py       |  2 +-
 3 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index 0902edd5bfe..497a69e9b06 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -101,5 +101,5 @@ def step(self):
 if __name__ == "__main__":
     model = BoidFlockers(population_size=200, width=100, height=100, vision=5, seed=42)
 
-    for i in range(100):
+    for _i in range(100):
         model.step()
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 7eff8e76ee2..f0266ff9fde 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -14,33 +14,33 @@ class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
 
     @property
-    def x_min(self):
-        # compatability with solara_viz
+    def x_min(self):  # noqa: D102
+        # compatibility with solara_viz
         return self.dimensions[0, 0]
 
     @property
-    def x_max(self):
-        # compatability with solara_viz
+    def x_max(self):  # noqa: D102
+        # compatibility with solara_viz
         return self.dimensions[0, 1]
 
     @property
-    def y_min(self):
-        # compatability with solara_viz
+    def y_min(self):  # noqa: D102
+        # compatibility with solara_viz
         return self.dimensions[1, 0]
 
     @property
-    def y_max(self):
-        # compatability with solara_viz
+    def y_max(self):  # noqa: D102
+        # compatibility with solara_viz
         return self.dimensions[1, 1]
 
     @property
-    def width(self):
-        # compatability with solara_viz
+    def width(self):  # noqa: D102
+        # compatibility with solara_viz
         return self.size[0]
 
     @property
-    def height(self):
-        # compatability with solara_viz
+    def height(self):  # noqa: D102
+        # compatibility with solara_viz
         return self.size[1]
 
     def __init__(
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index 52704b667ca..150c2fda7fb 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,4 +1,4 @@
-# to be removed once further into the development
+"""to be removed once further into the development"""
 from random import Random
 
 import numpy as np

From d6326fda83d559e816eee341dc0b7881ae9d2994 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 11:25:36 +0100
Subject: [PATCH 41/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index f0266ff9fde..76cb80cc363 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -129,6 +129,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         return index
 
     def _update_stuff(self):
+        """Fixme: Needs a better name."""
         self.agent_positions = self._agent_positions[self._positions_in_use]
         self.active_agents = self._agents[self._positions_in_use]
 

From 8d57c629e8042418f59d9ee95ce776491de11b67 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Jan 2025 10:27:20 +0000
Subject: [PATCH 42/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/continuous_space/for_development.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index 150c2fda7fb..2ec046dab18 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,4 +1,5 @@
 """to be removed once further into the development"""
+
 from random import Random
 
 import numpy as np

From afe44c350a31f306c643ed151fa1c40faf076a89 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 11:41:41 +0100
Subject: [PATCH 43/84] updates

---
 .../continuous_space/continuous_space.py             | 12 ++++++------
 tests/test_continuous_space.py                       | 12 ++++++------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 76cb80cc363..cf4cea05216 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -124,14 +124,14 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         self._agents[index] = agent
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
-        self._update_stuff()
+        self.active_agents = self._agents[self._positions_in_use]
 
         return index
 
-    def _update_stuff(self):
-        """Fixme: Needs a better name."""
-        self.agent_positions = self._agent_positions[self._positions_in_use]
-        self.active_agents = self._agents[self._positions_in_use]
+    @property
+    def agent_positions(self):
+        """Return the positions of the agents in the space."""
+        return self._agent_positions[self._positions_in_use]
 
     def _remove_agent(self, agent: Agent) -> None:
         """Remove an agent from the space."""
@@ -140,7 +140,7 @@ def _remove_agent(self, agent: Agent) -> None:
         self._index_to_agent.pop(index, None)
         self._positions_in_use[index] = False
         self._agents[index] = None
-        self._update_stuff()
+        self.active_agents = self._agents[self._positions_in_use]
 
     def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
         """Calculate the difference vector between the point and all agents."""
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 52fdd895fe7..a28de53351e 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -68,9 +68,9 @@ def test_continuous_agent():
 
     assert space.agent_positions.shape == (10, 2)
     for agent in space.agents:
-        assert np.all(
-            agent.position == space.agent_positions[space._get_index_for_agent(agent)]
-        )
+        a = agent.position
+        b = space._agent_positions[space._get_index_for_agent(agent)]
+        assert np.all(a == b)
 
     # add more agents, triggering a resizeing of the array
     for _ in range(100):
@@ -79,9 +79,9 @@ def test_continuous_agent():
 
     assert space.agent_positions.shape == (110, 2)
     for agent in space.agents:
-        assert np.all(
-            agent.position == space.agent_positions[space._get_index_for_agent(agent)]
-        )
+        a = agent.position
+        b = space._agent_positions[space._get_index_for_agent(agent)]
+        assert np.all(a == b)
 
     # remove all agents and check if the view is updated throughout correctly
     for i, agent in enumerate(space.agents):

From b7bdd82c6a1b972f9d1b590b2aacb0277df36bd2 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 11:45:57 +0100
Subject: [PATCH 44/84] make new continous spaces work with existing space
 drawing

---
 mesa/visualization/mpl_space_drawing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/visualization/mpl_space_drawing.py b/mesa/visualization/mpl_space_drawing.py
index 784d370eba0..815adbaa4e6 100644
--- a/mesa/visualization/mpl_space_drawing.py
+++ b/mesa/visualization/mpl_space_drawing.py
@@ -143,7 +143,7 @@ def draw_space(
             draw_orthogonal_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, **space_drawing_kwargs)
-        case mesa.space.ContinuousSpace():
+        case mesa.space.ContinuousSpace() | mesa.experimental.continuous_space.ContinuousSpace():
             draw_continuous_space(space, agent_portrayal, ax=ax)
         case VoronoiGrid():
             draw_voronoi_grid(space, agent_portrayal, ax=ax)

From 0db0a6fcc98acd6eb95558c74e46b6ab337029cd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Jan 2025 10:46:57 +0000
Subject: [PATCH 45/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/visualization/mpl_space_drawing.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/mesa/visualization/mpl_space_drawing.py b/mesa/visualization/mpl_space_drawing.py
index 815adbaa4e6..6e7fa9a05d5 100644
--- a/mesa/visualization/mpl_space_drawing.py
+++ b/mesa/visualization/mpl_space_drawing.py
@@ -143,7 +143,10 @@ def draw_space(
             draw_orthogonal_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, **space_drawing_kwargs)
-        case mesa.space.ContinuousSpace() | mesa.experimental.continuous_space.ContinuousSpace():
+        case (
+            mesa.space.ContinuousSpace()
+            | mesa.experimental.continuous_space.ContinuousSpace()
+        ):
             draw_continuous_space(space, agent_portrayal, ax=ax)
         case VoronoiGrid():
             draw_voronoi_grid(space, agent_portrayal, ax=ax)

From 625069c7524220764f753be85b6201578e97131b Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 11:51:17 +0100
Subject: [PATCH 46/84] ruff related

---
 mesa/experimental/continuous_space/__init__.py                | 2 ++
 mesa/experimental/continuous_space/continuous_space_agents.py | 4 ++--
 mesa/experimental/continuous_space/for_development.py         | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/mesa/experimental/continuous_space/__init__.py b/mesa/experimental/continuous_space/__init__.py
index 56dab0ef693..f9abc541413 100644
--- a/mesa/experimental/continuous_space/__init__.py
+++ b/mesa/experimental/continuous_space/__init__.py
@@ -1,3 +1,5 @@
+"""Continous space support."""
+
 from mesa.experimental.continuous_space.continuous_space import ContinuousSpace
 from mesa.experimental.continuous_space.continuous_space_agents import (
     ContinuousSpaceAgent,
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 5c0aea15b58..f86b6b79b09 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -43,12 +43,12 @@ def position(self, value: np.ndarray) -> None:
         self.space._agent_positions[self._mesa_index] = value
 
     @property
-    def pos(self):
+    def pos(self):  # noqa: D102
         # just here for compatability with solara_viz.
         return self.position
 
     @pos.setter
-    def pos(self, value):
+    def pos(self, value):  # noqa: D102
         # just here for compatability solara_viz.
         pass
 
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index 2ec046dab18..3e42959172c 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,4 +1,4 @@
-"""to be removed once further into the development"""
+"""to be removed once further into the development."""
 
 from random import Random
 

From b56a970958818b833619f10710481bf54ba3c693 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Jan 2025 10:51:32 +0000
Subject: [PATCH 47/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index f86b6b79b09..9a85bd0568f 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -48,7 +48,7 @@ def pos(self):  # noqa: D102
         return self.position
 
     @pos.setter
-    def pos(self, value):  # noqa: D102
+    def pos(self, value):
         # just here for compatability solara_viz.
         pass
 

From eb5abd6b884d978795c8648f9a889207fcf71e4d Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 13:00:00 +0100
Subject: [PATCH 48/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index cf4cea05216..1bfc3559236 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -151,7 +151,7 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
             else self._agent_positions[[self._agent_to_index[a] for a in agents]]
         )
 
-        delta = positions - point[np.newaxis, :]
+        delta = positions - point
 
         if self.torus:
             inverse_delta = delta - np.sign(delta) * self.size
@@ -179,7 +179,7 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             agents = np.asarray(agents)
 
         if self.torus:
-            delta = np.abs(point[np.newaxis, :] - positions)
+            delta = np.abs(positions - point)
             delta = np.minimum(delta, self.size - delta, out=delta)
             dists = np.linalg.norm(delta, axis=1)
         else:

From 53ffa3069849a82295822935987b06fa7101b78f Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 17:09:20 +0100
Subject: [PATCH 49/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 1bfc3559236..8e2b68509a7 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -1,4 +1,4 @@
-"""A Continyous Space class."""
+"""A Continuous Space class."""
 
 import warnings
 from collections.abc import Sequence

From 99bb9def2708d14fe61b2175e78d773e212b1874 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 3 Jan 2025 18:50:10 +0100
Subject: [PATCH 50/84] profiling

---
 mesa/experimental/continuous_space/continuous_space.py   | 9 ++++++++-
 .../continuous_space/continuous_space_agents.py          | 2 ++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 8e2b68509a7..180aefebc59 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -9,6 +9,7 @@
 
 from mesa.agent import Agent, AgentSet
 
+from line_profiler_pycharm import profile
 
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
@@ -125,12 +126,16 @@ def _get_index_for_agent(self, agent: Agent) -> int:
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
         self.active_agents = self._agents[self._positions_in_use]
+        self._is_full = bool(np.all(self._positions_in_use))
 
         return index
 
     @property
     def agent_positions(self):
         """Return the positions of the agents in the space."""
+        if self._is_full:
+            return self._agent_positions
+
         return self._agent_positions[self._positions_in_use]
 
     def _remove_agent(self, agent: Agent) -> None:
@@ -141,6 +146,7 @@ def _remove_agent(self, agent: Agent) -> None:
         self._positions_in_use[index] = False
         self._agents[index] = None
         self.active_agents = self._agents[self._positions_in_use]
+        self._is_full = False
 
     def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
         """Calculate the difference vector between the point and all agents."""
@@ -167,12 +173,13 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
 
         return delta
 
+    @profile
     def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarray]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
 
         if agents is None:
-            positions = self.agent_positions
+            positions = self._agent_positions
             agents = self.active_agents
         else:
             positions = self._agent_positions[[self._agent_to_index[a] for a in agents]]
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 9a85bd0568f..fd5fd71763c 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -9,6 +9,7 @@
 from mesa.agent import Agent
 from mesa.experimental.continuous_space import ContinuousSpace
 
+from line_profiler_pycharm import profile
 
 class HasPositionProtocol(Protocol):
     """Protocol for continuous space position holders."""
@@ -82,6 +83,7 @@ def get_neighbors_in_radius(
         self, radius=1, include_distance: bool = True
     ) -> tuple[np.ndarray[ContinuousSpaceAgent], np.ndarray[float]]: ...
 
+    @profile
     def get_neighbors_in_radius(self, radius=1, include_distance=False):
         """Get neighbors within radius.
 

From a1cb4cb46423efc8ad7c7e65a46eb7680f396b07 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sat, 4 Jan 2025 12:32:22 +0100
Subject: [PATCH 51/84] onging

---
 mesa/experimental/continuous_space/continuous_space.py | 10 ++++++++--
 .../continuous_space/continuous_space_agents.py        |  4 ++--
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 180aefebc59..ea258ccbed3 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -7,6 +7,7 @@
 import numpy as np
 from scipy.spatial.distance import cdist
 
+
 from mesa.agent import Agent, AgentSet
 
 from line_profiler_pycharm import profile
@@ -179,7 +180,7 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
         point = np.asanyarray(point)
 
         if agents is None:
-            positions = self._agent_positions
+            positions = self.agent_positions
             agents = self.active_agents
         else:
             positions = self._agent_positions[[self._agent_to_index[a] for a in agents]]
@@ -188,7 +189,12 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
         if self.torus:
             delta = np.abs(positions - point)
             delta = np.minimum(delta, self.size - delta, out=delta)
-            dists = np.linalg.norm(delta, axis=1)
+            # this is obscure: see https://stackoverflow.com/questions/7741878/how-to-apply-numpy-linalg-norm-to-each-row-of-a-matrix
+            # Also, this might be highly numpy version dependent and even cpu architecture dependent.
+            # would be good to test again once numpy 2.x is default in anaconda.
+            # dists = np.linalg.norm(delta, axis=1)
+            delta_T = delta.T
+            dists = np.sqrt(np.einsum('ij,ij->j', delta_T, delta_T))
         else:
             dists = cdist(point[np.newaxis, :], positions)[:, 0]
         return dists, agents
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index fd5fd71763c..a2898676864 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -9,7 +9,7 @@
 from mesa.agent import Agent
 from mesa.experimental.continuous_space import ContinuousSpace
 
-from line_profiler_pycharm import profile
+# from line_profiler_pycharm import profile
 
 class HasPositionProtocol(Protocol):
     """Protocol for continuous space position holders."""
@@ -83,7 +83,7 @@ def get_neighbors_in_radius(
         self, radius=1, include_distance: bool = True
     ) -> tuple[np.ndarray[ContinuousSpaceAgent], np.ndarray[float]]: ...
 
-    @profile
+    # @profile
     def get_neighbors_in_radius(self, radius=1, include_distance=False):
         """Get neighbors within radius.
 

From f7bdb8bc61863ec58c896fc3d03a53ec3dffc756 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sat, 4 Jan 2025 13:50:49 +0100
Subject: [PATCH 52/84] cleanup

---
 .../continuous_space/continuous_space.py      | 23 ++++++++++++-------
 .../continuous_space_agents.py                | 22 +++++++-----------
 2 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index ea258ccbed3..cab13e6791d 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -7,10 +7,8 @@
 import numpy as np
 from scipy.spatial.distance import cdist
 
-
 from mesa.agent import Agent, AgentSet
 
-from line_profiler_pycharm import profile
 
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
@@ -85,11 +83,6 @@ def agents(self) -> AgentSet:
         """Return an AgentSet with the agents in the space."""
         return AgentSet(self._agents[self._positions_in_use], random=self.random)
 
-    # @property
-    # def agent_positions(self) -> np.ndarray:
-    #     """Return the positions of the agents in the space."""
-    #     return self._agent_positions[self._positions_in_use]
-
     def _get_index_for_agent(self, agent: Agent) -> int:
         """Helper method to get the index for the agent.
 
@@ -174,7 +167,6 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
 
         return delta
 
-    @profile
     def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarray]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
@@ -199,6 +191,21 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             dists = cdist(point[np.newaxis, :], positions)[:, 0]
         return dists, agents
 
+    def get_agents_in_radius(self, point, radius=1) -> tuple[np.ndarray, np.ndarray]:
+        """Return the agents and their distances within a radius for the point."""
+        distances, agents = self.calculate_distances(point)
+        logical = distances <= radius
+
+        return distances[logical], agents[logical]
+
+    def get_k_nearest_agents(self, point, k=1) -> tuple[np.ndarray, np.ndarray]:
+        """Return the k nearest agents and their distances to the point."""
+        dists, agents = self.calculate_distances(point)
+
+        k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
+        indices = np.argpartition(dists, k)[:k]
+        return dists[indices], agents[indices]
+
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
         return bool(
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index a2898676864..aea76752174 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -9,8 +9,6 @@
 from mesa.agent import Agent
 from mesa.experimental.continuous_space import ContinuousSpace
 
-# from line_profiler_pycharm import profile
-
 class HasPositionProtocol(Protocol):
     """Protocol for continuous space position holders."""
 
@@ -92,14 +90,13 @@ def get_neighbors_in_radius(self, radius=1, include_distance=False):
             include_distance: include the distance information for each neighbor
 
         """
-        dists, agents = self.space.calculate_distances(self.position)
-        indices = np.where(dists <= radius)[0]
-        indices = indices[indices != self._mesa_index]
+        dists, agents = self.space.get_agents_in_radius(self.position, radius=radius)
+        logical = agents != self
 
         if include_distance:
-            return agents[indices], dists[indices]
+            return agents[logical], dists[logical]
         else:
-            return agents[indices]
+            return agents[logical]
 
     @overload
     def get_nearest_neighbors(
@@ -119,13 +116,10 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
             include_distance: include the distance information for each neighbor
 
         """
-        dists, agents = self.space.calculate_distances(self.position)
-
-        k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
-        indices = np.argpartition(dists, k)[:k]
-        indices = indices[indices != self._mesa_index]
+        dists, agents = self.space.get_k_nearest_agents(self.position, k=k)
+        logical = agents != self
 
         if include_distance:
-            return agents[indices], dists[indices]
+            return agents[logical], dists[logical]
         else:
-            return agents[indices]
+            return agents[logical]

From e2ae60ec63d07dc30931b3d4f5b95477776c0c46 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 4 Jan 2025 12:51:27 +0000
Subject: [PATCH 53/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/continuous_space/continuous_space.py        | 2 +-
 mesa/experimental/continuous_space/continuous_space_agents.py | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index cab13e6791d..f5cff1bfa48 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -186,7 +186,7 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             # would be good to test again once numpy 2.x is default in anaconda.
             # dists = np.linalg.norm(delta, axis=1)
             delta_T = delta.T
-            dists = np.sqrt(np.einsum('ij,ij->j', delta_T, delta_T))
+            dists = np.sqrt(np.einsum("ij,ij->j", delta_T, delta_T))
         else:
             dists = cdist(point[np.newaxis, :], positions)[:, 0]
         return dists, agents
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index aea76752174..c0d01256230 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -9,6 +9,7 @@
 from mesa.agent import Agent
 from mesa.experimental.continuous_space import ContinuousSpace
 
+
 class HasPositionProtocol(Protocol):
     """Protocol for continuous space position holders."""
 

From 45d5744a8bd0c705adbf7984131f0f710a69e794 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sat, 4 Jan 2025 13:51:33 +0100
Subject: [PATCH 54/84] ruff

---
 mesa/experimental/continuous_space/__init__.py                | 2 +-
 mesa/experimental/continuous_space/continuous_space_agents.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/mesa/experimental/continuous_space/__init__.py b/mesa/experimental/continuous_space/__init__.py
index f9abc541413..13425cc0b8c 100644
--- a/mesa/experimental/continuous_space/__init__.py
+++ b/mesa/experimental/continuous_space/__init__.py
@@ -1,4 +1,4 @@
-"""Continous space support."""
+"""Continuous space support."""
 
 from mesa.experimental.continuous_space.continuous_space import ContinuousSpace
 from mesa.experimental.continuous_space.continuous_space_agents import (
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index c0d01256230..82eefc8a896 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -44,12 +44,12 @@ def position(self, value: np.ndarray) -> None:
 
     @property
     def pos(self):  # noqa: D102
-        # just here for compatability with solara_viz.
+        # just here for compatibility with solara_viz.
         return self.position
 
     @pos.setter
     def pos(self, value):
-        # just here for compatability solara_viz.
+        # just here for compatibility solara_viz.
         pass
 
     def __init__(self, space: ContinuousSpace, model):

From cf94c46c599064a8a89413bd77d811b28a762896 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sat, 4 Jan 2025 13:57:37 +0100
Subject: [PATCH 55/84] cleaning

---
 mesa/experimental/continuous_space/continuous_space.py      | 6 +++---
 .../continuous_space/continuous_space_agents.py             | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index f5cff1bfa48..f3588304de9 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -67,7 +67,7 @@ def __init__(
 
         self.torus: bool = torus
 
-        self._agent_positions: np.array = np.zeros(
+        self._agent_positions: np.array = np.empty(
             (n_agents, self.dimensions.shape[0]), dtype=float
         )
         self._agents: np.array = np.zeros((n_agents,), dtype=object)
@@ -104,7 +104,7 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 self._agent_positions = np.vstack(
                     [
                         self._agent_positions,
-                        np.zeros(
+                        np.empty(
                             (n, self.dimensions.shape[0]),
                         ),
                     ]
@@ -185,7 +185,7 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             # Also, this might be highly numpy version dependent and even cpu architecture dependent.
             # would be good to test again once numpy 2.x is default in anaconda.
             # dists = np.linalg.norm(delta, axis=1)
-            delta_T = delta.T
+            delta_T = delta.T  # noqa: N806
             dists = np.sqrt(np.einsum("ij,ij->j", delta_T, delta_T))
         else:
             dists = cdist(point[np.newaxis, :], positions)[:, 0]
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 82eefc8a896..977f35a5902 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -63,7 +63,7 @@ def __init__(self, space: ContinuousSpace, model):
         super().__init__(model)
         self.space: ContinuousSpace = space
         self._mesa_index = self.space._get_index_for_agent(self)
-        self.position[:] = np.nan
+        # self.position[:] = np.nan
 
     def remove(self) -> None:
         """Remove and delete the agent from the model."""

From c5a53c6d1935026965eef290c91fcdc1d88b6328 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 5 Jan 2025 11:24:36 +0100
Subject: [PATCH 56/84] fine tuning

---
 mesa/examples/basic/boid_flockers/agents.py   |  3 +-
 .../continuous_space/continuous_space.py      | 13 +++---
 .../continuous_space_agents.py                | 36 +++-------------
 .../continuous_space/for_development.py       | 42 +++++++++++--------
 mesa/space.py                                 |  2 +
 5 files changed, 38 insertions(+), 58 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 58151d442a0..24f57840c10 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -62,8 +62,7 @@ def __init__(
     def step(self):
         """Get the Boid's neighbors, compute the new vector, and move accordingly."""
         neighbors, distances = self.get_neighbors_in_radius(
-            radius=self.vision, include_distance=True
-        )
+            radius=self.vision)
         self.neighbors = neighbors
 
         # If no neighbors, maintain current direction
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index f3588304de9..4ecdb3519a4 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -9,7 +9,6 @@
 
 from mesa.agent import Agent, AgentSet
 
-
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
 
@@ -181,14 +180,12 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
         if self.torus:
             delta = np.abs(positions - point)
             delta = np.minimum(delta, self.size - delta, out=delta)
-            # this is obscure: see https://stackoverflow.com/questions/7741878/how-to-apply-numpy-linalg-norm-to-each-row-of-a-matrix
-            # Also, this might be highly numpy version dependent and even cpu architecture dependent.
-            # would be good to test again once numpy 2.x is default in anaconda.
-            # dists = np.linalg.norm(delta, axis=1)
-            delta_T = delta.T  # noqa: N806
-            dists = np.sqrt(np.einsum("ij,ij->j", delta_T, delta_T))
+            dists = delta[:, 0]**2
+            for i in range(1, self.ndims):
+                dists += delta[:,i]**2
+            dists = np.sqrt(dists)
         else:
-            dists = cdist(point[np.newaxis, :], positions)[:, 0]
+            dists = cdist(point[np.newaxis, :], positions)[0, :]
         return dists, agents
 
     def get_agents_in_radius(self, point, radius=1) -> tuple[np.ndarray, np.ndarray]:
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 977f35a5902..b6dc696d18b 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -72,18 +72,7 @@ def remove(self) -> None:
         self._mesa_index = None
         self.space = None
 
-    @overload
-    def get_neighbors_in_radius(
-        self, radius: int = 1, include_distance: bool = False
-    ) -> np.ndarray[ContinuousSpaceAgent]: ...
-
-    @overload
-    def get_neighbors_in_radius(
-        self, radius=1, include_distance: bool = True
-    ) -> tuple[np.ndarray[ContinuousSpaceAgent], np.ndarray[float]]: ...
-
-    # @profile
-    def get_neighbors_in_radius(self, radius=1, include_distance=False):
+    def get_neighbors_in_radius(self, radius=1):
         """Get neighbors within radius.
 
         Args:
@@ -94,22 +83,9 @@ def get_neighbors_in_radius(self, radius=1, include_distance=False):
         dists, agents = self.space.get_agents_in_radius(self.position, radius=radius)
         logical = agents != self
 
-        if include_distance:
-            return agents[logical], dists[logical]
-        else:
-            return agents[logical]
+        return agents[logical], dists[logical]
 
-    @overload
-    def get_nearest_neighbors(
-        self, k: int = 1, include_distance: bool = False
-    ) -> list[ContinuousSpaceAgent]: ...
-
-    @overload
-    def get_nearest_neighbors(
-        self, k=1, include_distance: bool = True
-    ) -> list[tuple[ContinuousSpaceAgent, float]]: ...
-
-    def get_nearest_neighbors(self, k=1, include_distance=False):
+    def get_nearest_neighbors(self, k=1):
         """Get neighbors within radius.
 
         Args:
@@ -120,7 +96,5 @@ def get_nearest_neighbors(self, k=1, include_distance=False):
         dists, agents = self.space.get_k_nearest_agents(self.position, k=k)
         logical = agents != self
 
-        if include_distance:
-            return agents[logical], dists[logical]
-        else:
-            return agents[logical]
+        return agents[logical], dists[logical]
+
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index 3e42959172c..b51fc84d593 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,26 +1,34 @@
 """to be removed once further into the development."""
 
-from random import Random
 
-import numpy as np
-from continuous_space import ContinuousSpace
-from continuous_space_agents import ContinuousSpaceAgent
+if __name__ == "__main__":
+    from mesa import Model, Agent
+    from mesa.space import ContinuousSpace as OldStyleSpace
 
-from mesa import Model
+    from mesa.experimental.continuous_space import ContinuousSpace as NewStyleSpace
+    from mesa.experimental.continuous_space import ContinuousSpaceAgent
 
-if __name__ == "__main__":
-    dimensions = [[0, 1], [0, 1]]
+    n = 400
+
+    model = Model(rng=42)
+    space = OldStyleSpace(100, 100, torus=True)
+
+    positions = model.rng.random((n, 2)) * n
+    for pos in positions:
+        agent = Agent(model)
+        space.place_agent(agent, pos)
+
+    for _ in range(100):
+        space.get_neighbors([50,50], radius=5, include_center=False)
 
-    model = Model(seed=42)
-    space = ContinuousSpace(dimensions, random=Random(42), torus=True)
 
-    for _ in range(2):
-        agent = ContinuousSpaceAgent(
-            space,
-            model,
-        )
-        agent.position = [agent.random.random(), agent.random.random()]
+    model = Model(rng=42)
+    space = NewStyleSpace([[0,100], [0,100]], torus=True, random=model.random, n_agents=n)
 
-    distances = space.calculate_distances(np.asarray([0.5, 0.5]))
+    positions = model.rng.random((n, 2)) * n
+    for pos in positions:
+        agent = ContinuousSpaceAgent(space, model)
+        agent.position = pos
 
-    print("blaat")
+    for _ in range(100):
+        space.get_agents_in_radius([50, 50], radius=5)
\ No newline at end of file
diff --git a/mesa/space.py b/mesa/space.py
index 6e15426bf34..401181d1e5a 100644
--- a/mesa/space.py
+++ b/mesa/space.py
@@ -25,6 +25,7 @@
 # Remove this __future__ import once the oldest supported Python is 3.10
 from __future__ import annotations
 
+
 import collections
 import contextlib
 import inspect
@@ -1403,6 +1404,7 @@ def remove_agent(self, agent: Agent) -> None:
         self._invalidate_agent_cache()
         agent.pos = None
 
+
     def get_neighbors(
         self, pos: FloatCoordinate, radius: float, include_center: bool = True
     ) -> list[Agent]:

From a64ac3874155267c739717d2b8bcd422dd4ad222 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 5 Jan 2025 10:24:51 +0000
Subject: [PATCH 57/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/basic/boid_flockers/agents.py       |  3 +--
 .../continuous_space/continuous_space.py          |  5 +++--
 .../continuous_space/continuous_space_agents.py   |  3 +--
 .../continuous_space/for_development.py           | 15 +++++++--------
 mesa/space.py                                     |  2 --
 5 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 24f57840c10..901d822d859 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -61,8 +61,7 @@ def __init__(
 
     def step(self):
         """Get the Boid's neighbors, compute the new vector, and move accordingly."""
-        neighbors, distances = self.get_neighbors_in_radius(
-            radius=self.vision)
+        neighbors, distances = self.get_neighbors_in_radius(radius=self.vision)
         self.neighbors = neighbors
 
         # If no neighbors, maintain current direction
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 4ecdb3519a4..bce944f2b05 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -9,6 +9,7 @@
 
 from mesa.agent import Agent, AgentSet
 
+
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
 
@@ -180,9 +181,9 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
         if self.torus:
             delta = np.abs(positions - point)
             delta = np.minimum(delta, self.size - delta, out=delta)
-            dists = delta[:, 0]**2
+            dists = delta[:, 0] ** 2
             for i in range(1, self.ndims):
-                dists += delta[:,i]**2
+                dists += delta[:, i] ** 2
             dists = np.sqrt(dists)
         else:
             dists = cdist(point[np.newaxis, :], positions)[0, :]
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index b6dc696d18b..20977ec74ec 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import Protocol, overload
+from typing import Protocol
 
 import numpy as np
 
@@ -97,4 +97,3 @@ def get_nearest_neighbors(self, k=1):
         logical = agents != self
 
         return agents[logical], dists[logical]
-
diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
index b51fc84d593..525d3246641 100644
--- a/mesa/experimental/continuous_space/for_development.py
+++ b/mesa/experimental/continuous_space/for_development.py
@@ -1,12 +1,10 @@
 """to be removed once further into the development."""
 
-
 if __name__ == "__main__":
-    from mesa import Model, Agent
-    from mesa.space import ContinuousSpace as OldStyleSpace
-
+    from mesa import Agent, Model
     from mesa.experimental.continuous_space import ContinuousSpace as NewStyleSpace
     from mesa.experimental.continuous_space import ContinuousSpaceAgent
+    from mesa.space import ContinuousSpace as OldStyleSpace
 
     n = 400
 
@@ -19,11 +17,12 @@
         space.place_agent(agent, pos)
 
     for _ in range(100):
-        space.get_neighbors([50,50], radius=5, include_center=False)
-
+        space.get_neighbors([50, 50], radius=5, include_center=False)
 
     model = Model(rng=42)
-    space = NewStyleSpace([[0,100], [0,100]], torus=True, random=model.random, n_agents=n)
+    space = NewStyleSpace(
+        [[0, 100], [0, 100]], torus=True, random=model.random, n_agents=n
+    )
 
     positions = model.rng.random((n, 2)) * n
     for pos in positions:
@@ -31,4 +30,4 @@
         agent.position = pos
 
     for _ in range(100):
-        space.get_agents_in_radius([50, 50], radius=5)
\ No newline at end of file
+        space.get_agents_in_radius([50, 50], radius=5)
diff --git a/mesa/space.py b/mesa/space.py
index 401181d1e5a..6e15426bf34 100644
--- a/mesa/space.py
+++ b/mesa/space.py
@@ -25,7 +25,6 @@
 # Remove this __future__ import once the oldest supported Python is 3.10
 from __future__ import annotations
 
-
 import collections
 import contextlib
 import inspect
@@ -1404,7 +1403,6 @@ def remove_agent(self, agent: Agent) -> None:
         self._invalidate_agent_cache()
         agent.pos = None
 
-
     def get_neighbors(
         self, pos: FloatCoordinate, radius: float, include_center: bool = True
     ) -> list[Agent]:

From 6303863394eead8321dc3abb37ba43ce73a6f7d2 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 5 Jan 2025 17:16:32 +0100
Subject: [PATCH 58/84] tweak

---
 mesa/examples/basic/boid_flockers/agents.py           |  6 +++---
 .../experimental/continuous_space/continuous_space.py |  8 ++++++--
 .../continuous_space/continuous_space_agents.py       | 11 ++++++-----
 3 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 901d822d859..2473d1f8410 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -71,14 +71,14 @@ def step(self):
 
         delta = self.space.calculate_difference_vector(self.position, agents=neighbors)
 
-        cohere_vector = np.sum(delta, axis=0) * self.cohere_factor
+        cohere_vector = delta.sum(axis=0) * self.cohere_factor
         separation_vector = (
             -1
-            * np.sum(delta[distances < self.separation], axis=0)
+            * delta[distances < self.separation].sum(axis=0)
             * self.separate_factor
         )
         match_vector = (
-            np.sum(np.asarray([n.direction for n in neighbors]), axis=0)
+            np.asarray([n.direction for n in neighbors]).sum(axis=0)
             * self.match_factor
         )
 
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index bce944f2b05..9a93aedcae8 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -74,6 +74,7 @@ def __init__(
         self._positions_in_use: np.array = np.zeros(
             (n_agents,), dtype=bool
         )  # effectively a mask over _agent_positions
+        self._is_full = False
 
         self._index_to_agent: dict[int, Agent] = {}
         self._agent_to_index: dict[Agent, int | None] = {}
@@ -116,9 +117,11 @@ def _get_index_for_agent(self, agent: Agent) -> int:
                 index = np.where(~self._positions_in_use)[0][0]
 
         self._positions_in_use[index] = True
+
         self._agents[index] = agent
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
+
         self.active_agents = self._agents[self._positions_in_use]
         self._is_full = bool(np.all(self._positions_in_use))
 
@@ -179,8 +182,10 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             agents = np.asarray(agents)
 
         if self.torus:
-            delta = np.abs(positions - point)
+            delta = np.abs(point-positions)
             delta = np.minimum(delta, self.size - delta, out=delta)
+
+            # + is much faster than np.sum or array.sum
             dists = delta[:, 0] ** 2
             for i in range(1, self.ndims):
                 dists += delta[:, i] ** 2
@@ -193,7 +198,6 @@ def get_agents_in_radius(self, point, radius=1) -> tuple[np.ndarray, np.ndarray]
         """Return the agents and their distances within a radius for the point."""
         distances, agents = self.calculate_distances(point)
         logical = distances <= radius
-
         return distances[logical], agents[logical]
 
     def get_k_nearest_agents(self, point, k=1) -> tuple[np.ndarray, np.ndarray]:
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 20977ec74ec..a0ba7a370d1 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -72,25 +72,26 @@ def remove(self) -> None:
         self._mesa_index = None
         self.space = None
 
-    def get_neighbors_in_radius(self, radius=1):
+    def get_neighbors_in_radius(self, radius:float=1) -> tuple[np.ndarray, np.ndarray]:
         """Get neighbors within radius.
 
         Args:
             radius: radius within which to look for neighbors
-            include_distance: include the distance information for each neighbor
 
         """
         dists, agents = self.space.get_agents_in_radius(self.position, radius=radius)
-        logical = agents != self
 
+        if dists.size == 0:
+            return dists, agents
+
+        logical = np.asarray([True if agent is not self else False for agent in agents])
         return agents[logical], dists[logical]
 
-    def get_nearest_neighbors(self, k=1):
+    def get_nearest_neighbors(self, k:int=1) -> tuple[np.ndarray, np.ndarray]:
         """Get neighbors within radius.
 
         Args:
             k: the number of nearest neighbors to return
-            include_distance: include the distance information for each neighbor
 
         """
         dists, agents = self.space.get_k_nearest_agents(self.position, k=k)

From 2b8ed2b11bb59b6f8b2bf8bfdeaa84df720c5f4a Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 5 Jan 2025 20:03:26 +0100
Subject: [PATCH 59/84] substantial update

---
 .../continuous_space/continuous_space.py      | 87 +++++++++----------
 .../continuous_space_agents.py                |  6 +-
 tests/test_continuous_space.py                |  4 +-
 3 files changed, 45 insertions(+), 52 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 9a93aedcae8..60c6e0e18b7 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -71,79 +71,72 @@ def __init__(
             (n_agents, self.dimensions.shape[0]), dtype=float
         )
         self._agents: np.array = np.zeros((n_agents,), dtype=object)
-        self._positions_in_use: np.array = np.zeros(
-            (n_agents,), dtype=bool
-        )  # effectively a mask over _agent_positions
-        self._is_full = False
+
+        self.active_agents: np.array  # a view on _agents containing all active agents
+        self.agent_positions: np.array  # a view on _agent_positions containing all active positions
+
+        self._n_agents = 0
 
         self._index_to_agent: dict[int, Agent] = {}
         self._agent_to_index: dict[Agent, int | None] = {}
 
+
     @property
     def agents(self) -> AgentSet:
         """Return an AgentSet with the agents in the space."""
-        return AgentSet(self._agents[self._positions_in_use], random=self.random)
+        return AgentSet(self.active_agents, random=self.random)
 
-    def _get_index_for_agent(self, agent: Agent) -> int:
+
+    def _add_agent(self, agent: Agent) -> int:
         """Helper method to get the index for the agent.
 
         This method manages the numpy array with the agent positions and ensuring it is
         enlarged if and when needed.
 
         """
-        try:
-            return self._agent_to_index[agent]
-        except KeyError:
-            indices = np.where(~self._positions_in_use)[0]
-
-            if indices.size > 0:
-                index = indices[0]
-            else:
-                # we are out of space
-                fraction = 0.2  # we add 20%  Fixme
-                n = int(round(fraction * self._agent_positions.shape[0]))
-                self._agent_positions = np.vstack(
-                    [
-                        self._agent_positions,
-                        np.empty(
-                            (n, self.dimensions.shape[0]),
-                        ),
-                    ]
-                )
-                self._positions_in_use = np.hstack(
-                    [self._positions_in_use, np.zeros((n,), dtype=bool)]
-                )
-                self._agents = np.hstack([self._agents, np.zeros((n,), dtype=object)])
-                index = np.where(~self._positions_in_use)[0][0]
-
-        self._positions_in_use[index] = True
+        index = self._n_agents
+        self._n_agents += 1
+
+        if self._agent_positions.shape[0] <= index:
+            # we are out of space
+            fraction = 0.2  # we add 20%  Fixme
+            n = int(round(fraction * self._n_agents))
+            self._agent_positions = np.vstack(
+                [
+                    self._agent_positions,
+                    np.empty(
+                        (n, self.dimensions.shape[0]),
+                    ),
+                ]
+            )
+            self._agents = np.hstack([self._agents, np.zeros((n,), dtype=object)])
 
         self._agents[index] = agent
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
 
-        self.active_agents = self._agents[self._positions_in_use]
-        self._is_full = bool(np.all(self._positions_in_use))
+        # we want to maintain a view rather than a copy on the active agents and positions
+        # this is essential for the performance of the rest of this code
+        self.active_agents = self._agents[0:self._n_agents]
+        self.agent_positions = self._agent_positions[0:self._n_agents]
 
         return index
 
-    @property
-    def agent_positions(self):
-        """Return the positions of the agents in the space."""
-        if self._is_full:
-            return self._agent_positions
-
-        return self._agent_positions[self._positions_in_use]
-
     def _remove_agent(self, agent: Agent) -> None:
         """Remove an agent from the space."""
-        index = self._get_index_for_agent(agent)
+        index = self._agent_to_index[agent]
         self._agent_to_index.pop(agent, None)
         self._index_to_agent.pop(index, None)
-        self._positions_in_use[index] = False
-        self._agents[index] = None
-        self.active_agents = self._agents[self._positions_in_use]
-        self._is_full = False
+
+        for i in range(index, self._n_agents):
+            self._agent_to_index[agent] = i
+            self._index_to_agent[i] = agent
+
+        # we move all data below the removed agent one row up
+        self._agent_positions[index:self._n_agents-1] = self._agent_positions[index+1:self._n_agents]
+        self._n_agents -= 1
+        self.active_agents = self._agents[0:self._n_agents]
+        self.agent_positions = self._agent_positions[0:self._n_agents]
 
     def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
         """Calculate the difference vector between the point and all agents."""
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index a0ba7a370d1..a9de73bf42d 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -30,7 +30,7 @@ class ContinuousSpaceAgent(Agent):
     @property
     def position(self) -> np.ndarray:
         """Position of the agent."""
-        return self.space._agent_positions[self._mesa_index]
+        return self.space.agent_positions[self.space._agent_to_index[self]]
 
     @position.setter
     def position(self, value: np.ndarray) -> None:
@@ -40,7 +40,7 @@ def position(self, value: np.ndarray) -> None:
             else:
                 raise ValueError(f"point {value} is outside the bounds of the space")
 
-        self.space._agent_positions[self._mesa_index] = value
+        self.space.agent_positions[self.space._agent_to_index[self]] = value
 
     @property
     def pos(self):  # noqa: D102
@@ -62,7 +62,7 @@ def __init__(self, space: ContinuousSpace, model):
         """
         super().__init__(model)
         self.space: ContinuousSpace = space
-        self._mesa_index = self.space._get_index_for_agent(self)
+        self.space._add_agent(self)
         # self.position[:] = np.nan
 
     def remove(self) -> None:
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index a28de53351e..55193c2c33e 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -69,7 +69,7 @@ def test_continuous_agent():
     assert space.agent_positions.shape == (10, 2)
     for agent in space.agents:
         a = agent.position
-        b = space._agent_positions[space._get_index_for_agent(agent)]
+        b = space._agent_positions[space._agent_to_index[agent]]
         assert np.all(a == b)
 
     # add more agents, triggering a resizeing of the array
@@ -80,7 +80,7 @@ def test_continuous_agent():
     assert space.agent_positions.shape == (110, 2)
     for agent in space.agents:
         a = agent.position
-        b = space._agent_positions[space._get_index_for_agent(agent)]
+        b = space._agent_positions[space._agent_to_index[agent]]
         assert np.all(a == b)
 
     # remove all agents and check if the view is updated throughout correctly

From 4e9a39ba688673b0d55cdc44c0687899a21085fc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 5 Jan 2025 19:03:34 +0000
Subject: [PATCH 60/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/examples/basic/boid_flockers/agents.py   |  7 ++-----
 .../continuous_space/continuous_space.py      | 20 ++++++++++---------
 .../continuous_space_agents.py                |  6 ++++--
 3 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 2473d1f8410..008bc516666 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -73,13 +73,10 @@ def step(self):
 
         cohere_vector = delta.sum(axis=0) * self.cohere_factor
         separation_vector = (
-            -1
-            * delta[distances < self.separation].sum(axis=0)
-            * self.separate_factor
+            -1 * delta[distances < self.separation].sum(axis=0) * self.separate_factor
         )
         match_vector = (
-            np.asarray([n.direction for n in neighbors]).sum(axis=0)
-            * self.match_factor
+            np.asarray([n.direction for n in neighbors]).sum(axis=0) * self.match_factor
         )
 
         # Update direction based on the three behaviors
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 60c6e0e18b7..e2991f4114a 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -73,20 +73,20 @@ def __init__(
         self._agents: np.array = np.zeros((n_agents,), dtype=object)
 
         self.active_agents: np.array  # a view on _agents containing all active agents
-        self.agent_positions: np.array  # a view on _agent_positions containing all active positions
+        self.agent_positions: (
+            np.array
+        )  # a view on _agent_positions containing all active positions
 
         self._n_agents = 0
 
         self._index_to_agent: dict[int, Agent] = {}
         self._agent_to_index: dict[Agent, int | None] = {}
 
-
     @property
     def agents(self) -> AgentSet:
         """Return an AgentSet with the agents in the space."""
         return AgentSet(self.active_agents, random=self.random)
 
-
     def _add_agent(self, agent: Agent) -> int:
         """Helper method to get the index for the agent.
 
@@ -117,8 +117,8 @@ def _add_agent(self, agent: Agent) -> int:
 
         # we want to maintain a view rather than a copy on the active agents and positions
         # this is essential for the performance of the rest of this code
-        self.active_agents = self._agents[0:self._n_agents]
-        self.agent_positions = self._agent_positions[0:self._n_agents]
+        self.active_agents = self._agents[0 : self._n_agents]
+        self.agent_positions = self._agent_positions[0 : self._n_agents]
 
         return index
 
@@ -133,10 +133,12 @@ def _remove_agent(self, agent: Agent) -> None:
             self._index_to_agent[i] = agent
 
         # we move all data below the removed agent one row up
-        self._agent_positions[index:self._n_agents-1] = self._agent_positions[index+1:self._n_agents]
+        self._agent_positions[index : self._n_agents - 1] = self._agent_positions[
+            index + 1 : self._n_agents
+        ]
         self._n_agents -= 1
-        self.active_agents = self._agents[0:self._n_agents]
-        self.agent_positions = self._agent_positions[0:self._n_agents]
+        self.active_agents = self._agents[0 : self._n_agents]
+        self.agent_positions = self._agent_positions[0 : self._n_agents]
 
     def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
         """Calculate the difference vector between the point and all agents."""
@@ -175,7 +177,7 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             agents = np.asarray(agents)
 
         if self.torus:
-            delta = np.abs(point-positions)
+            delta = np.abs(point - positions)
             delta = np.minimum(delta, self.size - delta, out=delta)
 
             # + is much faster than np.sum or array.sum
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index a9de73bf42d..34c372bf725 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -72,7 +72,9 @@ def remove(self) -> None:
         self._mesa_index = None
         self.space = None
 
-    def get_neighbors_in_radius(self, radius:float=1) -> tuple[np.ndarray, np.ndarray]:
+    def get_neighbors_in_radius(
+        self, radius: float = 1
+    ) -> tuple[np.ndarray, np.ndarray]:
         """Get neighbors within radius.
 
         Args:
@@ -87,7 +89,7 @@ def get_neighbors_in_radius(self, radius:float=1) -> tuple[np.ndarray, np.ndarra
         logical = np.asarray([True if agent is not self else False for agent in agents])
         return agents[logical], dists[logical]
 
-    def get_nearest_neighbors(self, k:int=1) -> tuple[np.ndarray, np.ndarray]:
+    def get_nearest_neighbors(self, k: int = 1) -> tuple[np.ndarray, np.ndarray]:
         """Get neighbors within radius.
 
         Args:

From 102492a8c37d6e153f14a43f5eeb5c65f46db8b2 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 5 Jan 2025 21:38:50 +0100
Subject: [PATCH 61/84] switch active agents to list

---
 mesa/examples/basic/boid_flockers/agents.py   |  2 +-
 .../continuous_space/continuous_space.py      | 35 +++++++++++--------
 .../continuous_space_agents.py                | 15 ++++----
 3 files changed, 31 insertions(+), 21 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index 008bc516666..a7f2edffe49 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -65,7 +65,7 @@ def step(self):
         self.neighbors = neighbors
 
         # If no neighbors, maintain current direction
-        if neighbors.size == 0:
+        if not neighbors:
             self.position += self.direction * self.speed
             return
 
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index e2991f4114a..2320777e33c 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -3,6 +3,7 @@
 import warnings
 from collections.abc import Sequence
 from random import Random
+from itertools import compress
 
 import numpy as np
 from scipy.spatial.distance import cdist
@@ -70,9 +71,9 @@ def __init__(
         self._agent_positions: np.array = np.empty(
             (n_agents, self.dimensions.shape[0]), dtype=float
         )
-        self._agents: np.array = np.zeros((n_agents,), dtype=object)
+        # self._agents: np.array = np.zeros((n_agents,), dtype=object)
 
-        self.active_agents: np.array  # a view on _agents containing all active agents
+        self.active_agents = []
         self.agent_positions: (
             np.array
         )  # a view on _agent_positions containing all active positions
@@ -109,15 +110,14 @@ def _add_agent(self, agent: Agent) -> int:
                     ),
                 ]
             )
-            self._agents = np.hstack([self._agents, np.zeros((n,), dtype=object)])
 
-        self._agents[index] = agent
+
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
 
         # we want to maintain a view rather than a copy on the active agents and positions
         # this is essential for the performance of the rest of this code
-        self.active_agents = self._agents[0 : self._n_agents]
+        self.active_agents.append(agent)
         self.agent_positions = self._agent_positions[0 : self._n_agents]
 
         return index
@@ -127,17 +127,22 @@ def _remove_agent(self, agent: Agent) -> None:
         index = self._agent_to_index[agent]
         self._agent_to_index.pop(agent, None)
         self._index_to_agent.pop(index, None)
+        try:
+            del self.active_agents[index]
+        except IndexError as e:
+            raise e
 
-        for i in range(index, self._n_agents):
-            self._agent_to_index[agent] = i
-            self._index_to_agent[i] = agent
+        # we update all indices
+        for agent in self.active_agents[index::]:
+            old_index = self._agent_to_index[agent]
+            self._agent_to_index[agent] = old_index-1
+            self._index_to_agent[old_index-1] = agent
 
         # we move all data below the removed agent one row up
         self._agent_positions[index : self._n_agents - 1] = self._agent_positions[
             index + 1 : self._n_agents
         ]
         self._n_agents -= 1
-        self.active_agents = self._agents[0 : self._n_agents]
         self.agent_positions = self._agent_positions[0 : self._n_agents]
 
     def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
@@ -165,7 +170,7 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
 
         return delta
 
-    def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarray]:
+    def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, list]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
 
@@ -189,19 +194,21 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, np.ndarra
             dists = cdist(point[np.newaxis, :], positions)[0, :]
         return dists, agents
 
-    def get_agents_in_radius(self, point, radius=1) -> tuple[np.ndarray, np.ndarray]:
+    def get_agents_in_radius(self, point, radius=1) -> tuple[np.ndarray, list]:
         """Return the agents and their distances within a radius for the point."""
         distances, agents = self.calculate_distances(point)
         logical = distances <= radius
-        return distances[logical], agents[logical]
+        agents = list(compress(agents, logical))
+        return distances[logical], agents
 
-    def get_k_nearest_agents(self, point, k=1) -> tuple[np.ndarray, np.ndarray]:
+    def get_k_nearest_agents(self, point, k=1) -> tuple[np.ndarray,list]:
         """Return the k nearest agents and their distances to the point."""
         dists, agents = self.calculate_distances(point)
 
         k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
         indices = np.argpartition(dists, k)[:k]
-        return dists[indices], agents[indices]
+        agents = [agents[i] for i in indices]
+        return dists[indices], agents
 
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 34c372bf725..a15f699d20f 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+from itertools import compress
+
 from typing import Protocol
 
 import numpy as np
@@ -74,7 +76,7 @@ def remove(self) -> None:
 
     def get_neighbors_in_radius(
         self, radius: float = 1
-    ) -> tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[list, np.ndarray]:
         """Get neighbors within radius.
 
         Args:
@@ -87,9 +89,10 @@ def get_neighbors_in_radius(
             return dists, agents
 
         logical = np.asarray([True if agent is not self else False for agent in agents])
-        return agents[logical], dists[logical]
+        agents = list(compress(agents, logical))
+        return agents, dists[logical]
 
-    def get_nearest_neighbors(self, k: int = 1) -> tuple[np.ndarray, np.ndarray]:
+    def get_nearest_neighbors(self, k: int = 1) -> tuple[list, np.ndarray]:
         """Get neighbors within radius.
 
         Args:
@@ -97,6 +100,6 @@ def get_nearest_neighbors(self, k: int = 1) -> tuple[np.ndarray, np.ndarray]:
 
         """
         dists, agents = self.space.get_k_nearest_agents(self.position, k=k)
-        logical = agents != self
-
-        return agents[logical], dists[logical]
+        logical = np.asarray([True if agent is not self else False for agent in agents])
+        agents = list(compress(agents, logical))
+        return agents, dists[logical]

From 037bc3bd765ef7af95131e471000b45860a7604c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 5 Jan 2025 20:38:59 +0000
Subject: [PATCH 62/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mesa/experimental/continuous_space/continuous_space.py   | 9 ++++-----
 .../continuous_space/continuous_space_agents.py          | 5 +----
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 2320777e33c..548cb873fc9 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -2,8 +2,8 @@
 
 import warnings
 from collections.abc import Sequence
-from random import Random
 from itertools import compress
+from random import Random
 
 import numpy as np
 from scipy.spatial.distance import cdist
@@ -111,7 +111,6 @@ def _add_agent(self, agent: Agent) -> int:
                 ]
             )
 
-
         self._agent_to_index[agent] = index
         self._index_to_agent[index] = agent
 
@@ -135,8 +134,8 @@ def _remove_agent(self, agent: Agent) -> None:
         # we update all indices
         for agent in self.active_agents[index::]:
             old_index = self._agent_to_index[agent]
-            self._agent_to_index[agent] = old_index-1
-            self._index_to_agent[old_index-1] = agent
+            self._agent_to_index[agent] = old_index - 1
+            self._index_to_agent[old_index - 1] = agent
 
         # we move all data below the removed agent one row up
         self._agent_positions[index : self._n_agents - 1] = self._agent_positions[
@@ -201,7 +200,7 @@ def get_agents_in_radius(self, point, radius=1) -> tuple[np.ndarray, list]:
         agents = list(compress(agents, logical))
         return distances[logical], agents
 
-    def get_k_nearest_agents(self, point, k=1) -> tuple[np.ndarray,list]:
+    def get_k_nearest_agents(self, point, k=1) -> tuple[np.ndarray, list]:
         """Return the k nearest agents and their distances to the point."""
         dists, agents = self.calculate_distances(point)
 
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index a15f699d20f..3533b56c917 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 from itertools import compress
-
 from typing import Protocol
 
 import numpy as np
@@ -74,9 +73,7 @@ def remove(self) -> None:
         self._mesa_index = None
         self.space = None
 
-    def get_neighbors_in_radius(
-        self, radius: float = 1
-    ) -> tuple[list, np.ndarray]:
+    def get_neighbors_in_radius(self, radius: float = 1) -> tuple[list, np.ndarray]:
         """Get neighbors within radius.
 
         Args:

From 3a4fa51c053625e89f612a12caf9b36264c10376 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 5 Jan 2025 21:54:21 +0100
Subject: [PATCH 63/84] an additional test

---
 tests/test_continuous_space.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 55193c2c33e..7cc7dfe44f6 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -64,27 +64,34 @@ def test_continuous_agent():
 
     for _ in range(10):
         agent = ContinuousSpaceAgent(space, model)
-        agent.position = [agent.random.random(), agent.random.random()]
+        position = [agent.random.random(), agent.random.random()]
+        agent.position = position
+        agent.coordinate = position
 
     assert space.agent_positions.shape == (10, 2)
     for agent in space.agents:
         a = agent.position
         b = space._agent_positions[space._agent_to_index[agent]]
         assert np.all(a == b)
+        assert np.all(agent.position == agent.coordinate)
 
     # add more agents, triggering a resizeing of the array
     for _ in range(100):
         agent = ContinuousSpaceAgent(space, model)
-        agent.position = [agent.random.random(), agent.random.random()]
+        position = [agent.random.random(), agent.random.random()]
+        agent.position = position
+        agent.coordinate = position
 
     assert space.agent_positions.shape == (110, 2)
     for agent in space.agents:
         a = agent.position
         b = space._agent_positions[space._agent_to_index[agent]]
         assert np.all(a == b)
+        assert np.all(agent.position == agent.coordinate)
 
     # remove all agents and check if the view is updated throughout correctly
     for i, agent in enumerate(space.agents):
+        assert np.all(agent.position == agent.coordinate) ## check if updates of indices is correctly done
         agent.remove()
         assert space.agent_positions.shape == (110 - 1 - i, 2)
 

From 06a8c348b0ce79c3f79b6331c72fa3e3c7d44588 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 5 Jan 2025 20:55:03 +0000
Subject: [PATCH 64/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 7cc7dfe44f6..4d618fa5f7d 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -91,7 +91,9 @@ def test_continuous_agent():
 
     # remove all agents and check if the view is updated throughout correctly
     for i, agent in enumerate(space.agents):
-        assert np.all(agent.position == agent.coordinate) ## check if updates of indices is correctly done
+        assert np.all(
+            agent.position == agent.coordinate
+        )  ## check if updates of indices is correctly done
         agent.remove()
         assert space.agent_positions.shape == (110 - 1 - i, 2)
 

From 73b8777610ff02e85d7a37ec960aaf305e4180ba Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Sun, 5 Jan 2025 21:58:58 +0100
Subject: [PATCH 65/84] Update continuous_space_agents.py

---
 mesa/experimental/continuous_space/continuous_space_agents.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 3533b56c917..274ccfc3819 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -85,7 +85,7 @@ def get_neighbors_in_radius(self, radius: float = 1) -> tuple[list, np.ndarray]:
         if dists.size == 0:
             return dists, agents
 
-        logical = np.asarray([True if agent is not self else False for agent in agents])
+        logical = np.asarray([agent is not self for agent in agents])
         agents = list(compress(agents, logical))
         return agents, dists[logical]
 
@@ -97,6 +97,6 @@ def get_nearest_neighbors(self, k: int = 1) -> tuple[list, np.ndarray]:
 
         """
         dists, agents = self.space.get_k_nearest_agents(self.position, k=k)
-        logical = np.asarray([True if agent is not self else False for agent in agents])
+        logical = np.asarray([agent is not self for agent in agents])
         agents = list(compress(agents, logical))
         return agents, dists[logical]

From a23b98287eb9f64b7a8ab217978dde1e59b3e2b1 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 6 Jan 2025 11:06:36 +0100
Subject: [PATCH 66/84] additional test

---
 .../continuous_space/continuous_space.py      |  5 +--
 tests/test_continuous_space.py                | 39 +++++++++++++++++++
 2 files changed, 40 insertions(+), 4 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 548cb873fc9..bbd42bbf8f9 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -126,10 +126,7 @@ def _remove_agent(self, agent: Agent) -> None:
         index = self._agent_to_index[agent]
         self._agent_to_index.pop(agent, None)
         self._index_to_agent.pop(index, None)
-        try:
-            del self.active_agents[index]
-        except IndexError as e:
-            raise e
+        del self.active_agents[index]
 
         # we update all indices
         for agent in self.active_agents[index::]:
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 4d618fa5f7d..fb8f17855fb 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -193,6 +193,45 @@ def test_distances():
     )
 
 
+def test_difference_vector():
+    """Test ContinuousSpace.distance method."""
+    # non torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.1, 0.1]
+
+    vector = space.calculate_difference_vector([0.1, 0.9])
+    assert np.all(
+        vector
+        == [0, -0.8]
+    )
+
+    vector = space.calculate_difference_vector([0.9, 0.1])
+    assert np.all(
+        vector
+        == [-0.8, 0]
+    )
+
+    # torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=True, random=model.random)
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.1, 0.1]
+
+    vector = space.calculate_difference_vector([0.1, 0.9])
+    assert np.allclose(vector, [0, 0.2])
+
+    vector = space.calculate_difference_vector([0.9, 0.1])
+    assert np.allclose(vector, [0.2, 0])
+
+    vector = space.calculate_difference_vector([0.9, 0.9])
+    assert np.allclose(vector, [0.2, 0.2])
+
 # class TestSpaceToroidal(unittest.TestCase):
 #     """Testing a toroidal continuous space."""
 #

From b625e239e7d6d8a67070c0639f348cc5b73cc974 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jan 2025 10:08:13 +0000
Subject: [PATCH 67/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_continuous_space.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index fb8f17855fb..b758e7e4cfe 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -204,16 +204,10 @@ def test_difference_vector():
     agent.position = [0.1, 0.1]
 
     vector = space.calculate_difference_vector([0.1, 0.9])
-    assert np.all(
-        vector
-        == [0, -0.8]
-    )
+    assert np.all(vector == [0, -0.8])
 
     vector = space.calculate_difference_vector([0.9, 0.1])
-    assert np.all(
-        vector
-        == [-0.8, 0]
-    )
+    assert np.all(vector == [-0.8, 0])
 
     # torus
     model = Model(seed=42)
@@ -232,6 +226,7 @@ def test_difference_vector():
     vector = space.calculate_difference_vector([0.9, 0.9])
     assert np.allclose(vector, [0.2, 0.2])
 
+
 # class TestSpaceToroidal(unittest.TestCase):
 #     """Testing a toroidal continuous space."""
 #

From ce0c311f703ac57a55eef5480a748886c4b196ae Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 6 Jan 2025 11:45:27 +0100
Subject: [PATCH 68/84] additional tests

---
 .../continuous_space/continuous_space.py      | 16 +++--
 .../continuous_space_agents.py                |  5 +-
 tests/test_continuous_space.py                | 58 ++++++++++++++++++-
 3 files changed, 69 insertions(+), 10 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index bbd42bbf8f9..4f9604e4191 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -190,21 +190,25 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, list]:
             dists = cdist(point[np.newaxis, :], positions)[0, :]
         return dists, agents
 
-    def get_agents_in_radius(self, point, radius=1) -> tuple[np.ndarray, list]:
+    def get_agents_in_radius(self, point, radius=1) -> tuple[list, np.ndarray]:
         """Return the agents and their distances within a radius for the point."""
         distances, agents = self.calculate_distances(point)
         logical = distances <= radius
         agents = list(compress(agents, logical))
-        return distances[logical], agents
+        return agents, distances[logical],
 
-    def get_k_nearest_agents(self, point, k=1) -> tuple[np.ndarray, list]:
-        """Return the k nearest agents and their distances to the point."""
+    def get_k_nearest_agents(self, point, k=1) -> tuple[list, np.ndarray]:
+        """Return the k nearest agents and their distances to the point.
+
+        Notes:
+            This method returns the k nearest agents and ignores ties.
+
+        """
         dists, agents = self.calculate_distances(point)
 
-        k += 1  # the distance calculation includes self, with a distance of 0, so we remove this later
         indices = np.argpartition(dists, k)[:k]
         agents = [agents[i] for i in indices]
-        return dists[indices], agents
+        return agents, dists[indices]
 
     def in_bounds(self, point) -> bool:
         """Check if point is inside the bounds of the space."""
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 274ccfc3819..9fadcff0352 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -80,7 +80,7 @@ def get_neighbors_in_radius(self, radius: float = 1) -> tuple[list, np.ndarray]:
             radius: radius within which to look for neighbors
 
         """
-        dists, agents = self.space.get_agents_in_radius(self.position, radius=radius)
+        agents, dists = self.space.get_agents_in_radius(self.position, radius=radius)
 
         if dists.size == 0:
             return dists, agents
@@ -96,7 +96,8 @@ def get_nearest_neighbors(self, k: int = 1) -> tuple[list, np.ndarray]:
             k: the number of nearest neighbors to return
 
         """
-        dists, agents = self.space.get_k_nearest_agents(self.position, k=k)
+        # return includes self, so we need to get k+1
+        agents, dists = self.space.get_k_nearest_agents(self.position, k=k+1)
         logical = np.asarray([agent is not self for agent in agents])
         agents = list(compress(agents, logical))
         return agents, dists[logical]
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index b758e7e4cfe..892e1dc0dc2 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -98,7 +98,7 @@ def test_continuous_agent():
         assert space.agent_positions.shape == (110 - 1 - i, 2)
 
 
-def test_distances():
+def test_continous_space_calculate_distances():
     """Test ContinuousSpace.distance method."""
     # non torus
     model = Model(seed=42)
@@ -193,7 +193,7 @@ def test_distances():
     )
 
 
-def test_difference_vector():
+def test_continous_space_difference_vector():
     """Test ContinuousSpace.distance method."""
     # non torus
     model = Model(seed=42)
@@ -227,6 +227,60 @@ def test_difference_vector():
     assert np.allclose(vector, [0.2, 0.2])
 
 
+def test_continuous_space_get_k_nearest_agents():
+    # non torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.1, 0.1]
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.1, 0.9]
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.9, 0.1]
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.9, 0.9]
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.5, 0.5]
+
+    agents, distances = space.get_k_nearest_agents([0.1, 0.1], k=1)
+    assert len(agents)==1
+    assert np.allclose(distances, [0,])
+
+    agents, distances = space.get_k_nearest_agents([0.5, 0.1], k=1)
+    assert len(agents)==1
+    assert np.allclose(distances, [0.4, 0.4])
+
+    agents, distances = space.get_k_nearest_agents([0.5, 0.1], k=2)
+    assert len(agents)==2
+    assert np.allclose(distances, [0.4, 0.4])
+
+    # torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=True, random=model.random)
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.1, 0.1]
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.9, 0.1]
+
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position = [0.9, 0.9]
+
+    agents, distances = space.get_k_nearest_agents([0.0, 0.1], k=2)
+    assert len(agents)==2
+    assert np.allclose(distances, [0.1, 0.1])
+
+def test_continuous_space_get_agents_in_radius():
+    pass
+
 # class TestSpaceToroidal(unittest.TestCase):
 #     """Testing a toroidal continuous space."""
 #

From 21c01ad835f574e4eb20fabcf3228e9325e7a17d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jan 2025 10:45:36 +0000
Subject: [PATCH 69/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../continuous_space/continuous_space.py        |  5 ++++-
 .../continuous_space/continuous_space_agents.py |  2 +-
 tests/test_continuous_space.py                  | 17 ++++++++++++-----
 3 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 4f9604e4191..96519edb10f 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -195,7 +195,10 @@ def get_agents_in_radius(self, point, radius=1) -> tuple[list, np.ndarray]:
         distances, agents = self.calculate_distances(point)
         logical = distances <= radius
         agents = list(compress(agents, logical))
-        return agents, distances[logical],
+        return (
+            agents,
+            distances[logical],
+        )
 
     def get_k_nearest_agents(self, point, k=1) -> tuple[list, np.ndarray]:
         """Return the k nearest agents and their distances to the point.
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 9fadcff0352..b828a3bee86 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -97,7 +97,7 @@ def get_nearest_neighbors(self, k: int = 1) -> tuple[list, np.ndarray]:
 
         """
         # return includes self, so we need to get k+1
-        agents, dists = self.space.get_k_nearest_agents(self.position, k=k+1)
+        agents, dists = self.space.get_k_nearest_agents(self.position, k=k + 1)
         logical = np.asarray([agent is not self for agent in agents])
         agents = list(compress(agents, logical))
         return agents, dists[logical]
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 892e1dc0dc2..c18a2ed5a6c 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -249,15 +249,20 @@ def test_continuous_space_get_k_nearest_agents():
     agent.position = [0.5, 0.5]
 
     agents, distances = space.get_k_nearest_agents([0.1, 0.1], k=1)
-    assert len(agents)==1
-    assert np.allclose(distances, [0,])
+    assert len(agents) == 1
+    assert np.allclose(
+        distances,
+        [
+            0,
+        ],
+    )
 
     agents, distances = space.get_k_nearest_agents([0.5, 0.1], k=1)
-    assert len(agents)==1
+    assert len(agents) == 1
     assert np.allclose(distances, [0.4, 0.4])
 
     agents, distances = space.get_k_nearest_agents([0.5, 0.1], k=2)
-    assert len(agents)==2
+    assert len(agents) == 2
     assert np.allclose(distances, [0.4, 0.4])
 
     # torus
@@ -275,12 +280,14 @@ def test_continuous_space_get_k_nearest_agents():
     agent.position = [0.9, 0.9]
 
     agents, distances = space.get_k_nearest_agents([0.0, 0.1], k=2)
-    assert len(agents)==2
+    assert len(agents) == 2
     assert np.allclose(distances, [0.1, 0.1])
 
+
 def test_continuous_space_get_agents_in_radius():
     pass
 
+
 # class TestSpaceToroidal(unittest.TestCase):
 #     """Testing a toroidal continuous space."""
 #

From c7df9bedefb1b7e2030612eca8afe50c410b9aee Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 6 Jan 2025 14:40:26 +0100
Subject: [PATCH 70/84] Update test_continuous_space.py

---
 tests/test_continuous_space.py | 113 ++++++++++++++-------------------
 1 file changed, 49 insertions(+), 64 deletions(-)

diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index c18a2ed5a6c..ce63e7a1db3 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -285,67 +285,52 @@ def test_continuous_space_get_k_nearest_agents():
 
 
 def test_continuous_space_get_agents_in_radius():
-    pass
-
-
-# class TestSpaceToroidal(unittest.TestCase):
-#     """Testing a toroidal continuous space."""
-#
-#     def setUp(self):
-#         """Create a test space and populate with Mock Agents."""
-#         self.space = ContinuousSpace(70, 20, True, -30, -30)
-#         self.agents = []
-#         for i, pos in enumerate(TEST_AGENTS):
-#             a = MockAgent(i)
-#             self.agents.append(a)
-#             self.space.place_agent(a, pos)
-#
-#     def test_agent_positions(self):
-#         """Ensure that the agents are all placed properly."""
-#         for i, pos in enumerate(TEST_AGENTS):
-#             a = self.agents[i]
-#             assert a.pos == pos
-#
-#     def test_agent_matching(self):
-#         """Ensure that the agents are all placed and indexed properly."""
-#         for i, agent in self.space._index_to_agent.items():
-#             assert agent.pos == tuple(self.space._agent_points[i, :])
-#             assert i == self.space._agent_to_index[agent]
-#
-#     def test_distance_calculations(self):
-#         """Test toroidal distance calculations."""
-#         pos_1 = (-30, -30)
-#         pos_2 = (70, 20)
-#         assert self.space.get_distance(pos_1, pos_2) == 0
-#
-#         pos_3 = (-30, -20)
-#         assert self.space.get_distance(pos_1, pos_3) == 10
-#
-#         pos_4 = (20, -5)
-#         pos_5 = (20, -15)
-#         assert self.space.get_distance(pos_4, pos_5) == 10
-#
-#         pos_6 = (-30, -29)
-#         pos_7 = (21, -5)
-#         assert self.space.get_distance(pos_6, pos_7) == np.sqrt(49**2 + 24**2)
-#
-#     def test_heading(self):
-#         pos_1 = (-30, -30)
-#         pos_2 = (70, 20)
-#         self.assertEqual((0, 0), self.space.get_heading(pos_1, pos_2))
-#
-#         pos_1 = (65, -25)
-#         pos_2 = (-25, -25)
-#         self.assertEqual((10, 0), self.space.get_heading(pos_1, pos_2))
-#
-#     def test_neighborhood_retrieval(self):
-#         """Test neighborhood retrieval."""
-#         neighbors_1 = self.space.get_neighbors((-20, -20), 1)
-#         assert len(neighbors_1) == 2
-#
-#         neighbors_2 = self.space.get_neighbors((40, -10), 10)
-#         assert len(neighbors_2) == 0
-#
-#         neighbors_3 = self.space.get_neighbors((-30, -30), 10)
-#         assert len(neighbors_3) == 1
-#
+    # non torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    positions = [[0.1, 0.1],
+                 [0.1, 0.9],
+                 [0.9, 0.1],
+                 [0.9, 0.9],
+                 [0.5, 0.5],]
+
+    for position in positions:
+        agent = ContinuousSpaceAgent(space, model)
+        agent.position = position
+
+    agents, distances = space.get_agents_in_radius([0.1, 0.1], radius=0.1)
+    assert len(agents) == 1
+    assert np.allclose(
+        distances,
+        [
+            0,
+        ],
+    )
+
+    agents, distances = space.get_agents_in_radius([0.5, 0.1], radius=0.4)
+    assert len(agents) == 3
+    assert np.allclose(distances, [0.4, 0.4, 0.4])
+
+    agents, distances = space.get_agents_in_radius([0.5, 0.5], radius=1)
+    assert len(agents) == 5
+
+    # torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=True, random=model.random)
+
+    positions = [[0.1, 0.1],
+                 [0.1, 0.9],
+                 [0.9, 0.1],
+                 [0.9, 0.9],
+                 [0.5, 0.5],]
+
+    for position in positions:
+        agent = ContinuousSpaceAgent(space, model)
+        agent.position = position
+
+    agents, distances = space.get_agents_in_radius([0.0, 0.1], radius=0.1)
+    assert len(agents) == 2
+    assert np.allclose(distances, [0.1, 0.1])
\ No newline at end of file

From c0782ab86e31fa838c6fa7997837d14085d5c3da Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jan 2025 13:40:35 +0000
Subject: [PATCH 71/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_continuous_space.py | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index ce63e7a1db3..1546e83c161 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -290,11 +290,13 @@ def test_continuous_space_get_agents_in_radius():
     dimensions = np.asarray([[0, 1], [0, 1]])
     space = ContinuousSpace(dimensions, torus=False, random=model.random)
 
-    positions = [[0.1, 0.1],
-                 [0.1, 0.9],
-                 [0.9, 0.1],
-                 [0.9, 0.9],
-                 [0.5, 0.5],]
+    positions = [
+        [0.1, 0.1],
+        [0.1, 0.9],
+        [0.9, 0.1],
+        [0.9, 0.9],
+        [0.5, 0.5],
+    ]
 
     for position in positions:
         agent = ContinuousSpaceAgent(space, model)
@@ -321,11 +323,13 @@ def test_continuous_space_get_agents_in_radius():
     dimensions = np.asarray([[0, 1], [0, 1]])
     space = ContinuousSpace(dimensions, torus=True, random=model.random)
 
-    positions = [[0.1, 0.1],
-                 [0.1, 0.9],
-                 [0.9, 0.1],
-                 [0.9, 0.9],
-                 [0.5, 0.5],]
+    positions = [
+        [0.1, 0.1],
+        [0.1, 0.9],
+        [0.9, 0.1],
+        [0.9, 0.9],
+        [0.5, 0.5],
+    ]
 
     for position in positions:
         agent = ContinuousSpaceAgent(space, model)
@@ -333,4 +337,4 @@ def test_continuous_space_get_agents_in_radius():
 
     agents, distances = space.get_agents_in_radius([0.0, 0.1], radius=0.1)
     assert len(agents) == 2
-    assert np.allclose(distances, [0.1, 0.1])
\ No newline at end of file
+    assert np.allclose(distances, [0.1, 0.1])

From 6f0a46a19e344b26d00939e998cf0f8c06219404 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Mon, 6 Jan 2025 16:58:55 +0100
Subject: [PATCH 72/84] merge related fixes

---
 mesa/examples/basic/boid_flockers/agents.py                   | 2 +-
 mesa/experimental/continuous_space/continuous_space_agents.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/agents.py b/mesa/examples/basic/boid_flockers/agents.py
index d5258747545..10f31cdc530 100644
--- a/mesa/examples/basic/boid_flockers/agents.py
+++ b/mesa/examples/basic/boid_flockers/agents.py
@@ -61,7 +61,7 @@ def __init__(
 
     def step(self):
         """Get the Boid's neighbors, compute the new vector, and move accordingly."""
-        neighbors = self.model.space.get_neighbors(self.pos, self.vision, True)
+        neighbors, distances = self.get_neighbors_in_radius(radius=self.vision)
         self.neighbors = [n for n in neighbors if n is not self]
 
         # If no neighbors, maintain current direction
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index b828a3bee86..cc4f780f1ce 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -83,7 +83,7 @@ def get_neighbors_in_radius(self, radius: float = 1) -> tuple[list, np.ndarray]:
         agents, dists = self.space.get_agents_in_radius(self.position, radius=radius)
 
         if dists.size == 0:
-            return dists, agents
+            return agents, dists
 
         logical = np.asarray([agent is not self for agent in agents])
         agents = list(compress(agents, logical))

From 7780b3a3bfd4025fe67b1ec423beaa05e3fb765a Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 8 Jan 2025 15:48:02 +0100
Subject: [PATCH 73/84] typing and tests

---
 mesa/examples/basic/boid_flockers/model.py      |  2 +-
 .../continuous_space/continuous_space.py        | 10 ++++++----
 tests/test_continuous_space.py                  | 17 +++++++++++++++++
 3 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index 497a69e9b06..b9e126a70eb 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -101,5 +101,5 @@ def step(self):
 if __name__ == "__main__":
     model = BoidFlockers(population_size=200, width=100, height=100, vision=5, seed=42)
 
-    for _i in range(100):
+    for _i in range(20):
         model.step()
diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 96519edb10f..e05dfd0e843 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -10,6 +10,8 @@
 
 from mesa.agent import Agent, AgentSet
 
+from typing import Iterable, Sequence
+from numpy.typing import ArrayLike
 
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
@@ -166,7 +168,7 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
 
         return delta
 
-    def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, list]:
+    def calculate_distances(self, point:ArrayLike, agents:Iterable[Agent]|None=None) -> tuple[np.ndarray, list]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
 
@@ -190,7 +192,7 @@ def calculate_distances(self, point, agents=None) -> tuple[np.ndarray, list]:
             dists = cdist(point[np.newaxis, :], positions)[0, :]
         return dists, agents
 
-    def get_agents_in_radius(self, point, radius=1) -> tuple[list, np.ndarray]:
+    def get_agents_in_radius(self, point:ArrayLike, radius:float|int=1) -> tuple[list, np.ndarray]:
         """Return the agents and their distances within a radius for the point."""
         distances, agents = self.calculate_distances(point)
         logical = distances <= radius
@@ -200,11 +202,11 @@ def get_agents_in_radius(self, point, radius=1) -> tuple[list, np.ndarray]:
             distances[logical],
         )
 
-    def get_k_nearest_agents(self, point, k=1) -> tuple[list, np.ndarray]:
+    def get_k_nearest_agents(self, point:ArrayLike, k:int=1) -> tuple[list, np.ndarray]:
         """Return the k nearest agents and their distances to the point.
 
         Notes:
-            This method returns the k nearest agents and ignores ties.
+            This method returns exactly k agents, ignoring ties
 
         """
         dists, agents = self.calculate_distances(point)
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 1546e83c161..78e043e4d71 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -192,6 +192,22 @@ def test_continous_space_calculate_distances():
         ]
     )
 
+    distances, agents = space.calculate_distances([0.9, 0.9], agents=[agent,])
+    assert np.all(
+        np.isclose(
+            distances,
+            [
+                0.2 * 2**0.5,
+            ],
+        )
+    )
+    assert np.all(
+        agents
+        == [
+            agent,
+        ]
+    )
+
 
 def test_continous_space_difference_vector():
     """Test ContinuousSpace.distance method."""
@@ -318,6 +334,7 @@ def test_continuous_space_get_agents_in_radius():
     agents, distances = space.get_agents_in_radius([0.5, 0.5], radius=1)
     assert len(agents) == 5
 
+
     # torus
     model = Model(seed=42)
     dimensions = np.asarray([[0, 1], [0, 1]])

From c2aa0f2205ed3f95d7ae78716cf4546c0ef3c0ae Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 8 Jan 2025 14:48:12 +0000
Subject: [PATCH 74/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../continuous_space/continuous_space.py        | 17 +++++++++++------
 tests/test_continuous_space.py                  |  8 ++++++--
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index e05dfd0e843..c358893b4dc 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -1,17 +1,16 @@
 """A Continuous Space class."""
 
 import warnings
-from collections.abc import Sequence
+from collections.abc import Iterable, Sequence
 from itertools import compress
 from random import Random
 
 import numpy as np
+from numpy.typing import ArrayLike
 from scipy.spatial.distance import cdist
 
 from mesa.agent import Agent, AgentSet
 
-from typing import Iterable, Sequence
-from numpy.typing import ArrayLike
 
 class ContinuousSpace:
     """Continuous space where each agent can have an arbitrary position."""
@@ -168,7 +167,9 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
 
         return delta
 
-    def calculate_distances(self, point:ArrayLike, agents:Iterable[Agent]|None=None) -> tuple[np.ndarray, list]:
+    def calculate_distances(
+        self, point: ArrayLike, agents: Iterable[Agent] | None = None
+    ) -> tuple[np.ndarray, list]:
         """Calculate the distance between the point and all agents."""
         point = np.asanyarray(point)
 
@@ -192,7 +193,9 @@ def calculate_distances(self, point:ArrayLike, agents:Iterable[Agent]|None=None)
             dists = cdist(point[np.newaxis, :], positions)[0, :]
         return dists, agents
 
-    def get_agents_in_radius(self, point:ArrayLike, radius:float|int=1) -> tuple[list, np.ndarray]:
+    def get_agents_in_radius(
+        self, point: ArrayLike, radius: float | int = 1
+    ) -> tuple[list, np.ndarray]:
         """Return the agents and their distances within a radius for the point."""
         distances, agents = self.calculate_distances(point)
         logical = distances <= radius
@@ -202,7 +205,9 @@ def get_agents_in_radius(self, point:ArrayLike, radius:float|int=1) -> tuple[lis
             distances[logical],
         )
 
-    def get_k_nearest_agents(self, point:ArrayLike, k:int=1) -> tuple[list, np.ndarray]:
+    def get_k_nearest_agents(
+        self, point: ArrayLike, k: int = 1
+    ) -> tuple[list, np.ndarray]:
         """Return the k nearest agents and their distances to the point.
 
         Notes:
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 78e043e4d71..85c8b36e115 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -192,7 +192,12 @@ def test_continous_space_calculate_distances():
         ]
     )
 
-    distances, agents = space.calculate_distances([0.9, 0.9], agents=[agent,])
+    distances, agents = space.calculate_distances(
+        [0.9, 0.9],
+        agents=[
+            agent,
+        ],
+    )
     assert np.all(
         np.isclose(
             distances,
@@ -334,7 +339,6 @@ def test_continuous_space_get_agents_in_radius():
     agents, distances = space.get_agents_in_radius([0.5, 0.5], radius=1)
     assert len(agents) == 5
 
-
     # torus
     model = Model(seed=42)
     dimensions = np.asarray([[0, 1], [0, 1]])

From 528aab52bd50827bc419e562c943b4628f48fc6f Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 8 Jan 2025 17:17:08 +0100
Subject: [PATCH 75/84] more tests

---
 .../continuous_space_agents.py                |  4 -
 tests/test_continuous_space.py                | 78 ++++++++++++++++++-
 2 files changed, 75 insertions(+), 7 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index cc4f780f1ce..3f2167e0ef2 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -81,10 +81,6 @@ def get_neighbors_in_radius(self, radius: float = 1) -> tuple[list, np.ndarray]:
 
         """
         agents, dists = self.space.get_agents_in_radius(self.position, radius=radius)
-
-        if dists.size == 0:
-            return agents, dists
-
         logical = np.asarray([agent is not self for agent in agents])
         agents = list(compress(agents, logical))
         return agents, dists[logical]
diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 85c8b36e115..4184aa15ec3 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -1,6 +1,7 @@
 """Tests for continuous space."""
 
 import numpy as np
+import pytest
 
 from mesa import Model
 from mesa.experimental.continuous_space import ContinuousSpace, ContinuousSpaceAgent
@@ -97,6 +98,21 @@ def test_continuous_agent():
         agent.remove()
         assert space.agent_positions.shape == (110 - 1 - i, 2)
 
+    model = Model(seed=42)
+
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=True, random=model.random)
+    agent = ContinuousSpaceAgent(space, model)
+    agent.position =[1.1, 1.1]
+    assert np.allclose(agent.position, [0.1, 0.1])
+
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+    agent = ContinuousSpaceAgent(space, model)
+    with pytest.raises(ValueError):
+        agent.position =[1.1, 1.1]
+
+
 
 def test_continous_space_calculate_distances():
     """Test ContinuousSpace.distance method."""
@@ -215,7 +231,7 @@ def test_continous_space_calculate_distances():
 
 
 def test_continous_space_difference_vector():
-    """Test ContinuousSpace.distance method."""
+    """Test ContinuousSpace.get_difference_vector method."""
     # non torus
     model = Model(seed=42)
     dimensions = np.asarray([[0, 1], [0, 1]])
@@ -248,7 +264,7 @@ def test_continous_space_difference_vector():
     assert np.allclose(vector, [0.2, 0.2])
 
 
-def test_continuous_space_get_k_nearest_agents():
+def test_continuous_space_get_k_nearest_agents():  # noqa: D103
     # non torus
     model = Model(seed=42)
     dimensions = np.asarray([[0, 1], [0, 1]])
@@ -305,7 +321,7 @@ def test_continuous_space_get_k_nearest_agents():
     assert np.allclose(distances, [0.1, 0.1])
 
 
-def test_continuous_space_get_agents_in_radius():
+def test_continuous_space_get_agents_in_radius():  # noqa: D103
     # non torus
     model = Model(seed=42)
     dimensions = np.asarray([[0, 1], [0, 1]])
@@ -359,3 +375,59 @@ def test_continuous_space_get_agents_in_radius():
     agents, distances = space.get_agents_in_radius([0.0, 0.1], radius=0.1)
     assert len(agents) == 2
     assert np.allclose(distances, [0.1, 0.1])
+
+
+def test_get_neighbor_methos():  # noqa: D103
+    # non torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=False, random=model.random)
+
+    positions = [
+        [0.1, 0.1],
+        [0.1, 0.9],
+        [0.9, 0.1],
+        [0.9, 0.9],
+        [0.5, 0.5],
+    ]
+
+    for position in positions:
+        agent = ContinuousSpaceAgent(space, model)
+        agent.position = position
+
+    agent: ContinuousSpaceAgent = model.agents[-1]  # 0.5, 0.5
+    agents, distances = agent.get_neighbors_in_radius(1)
+    assert len(agents) == 4
+
+    agents, distances = agent.get_neighbors_in_radius(0.1)
+    assert len(agents) == 0
+
+    agent: ContinuousSpaceAgent = model.agents[0]  # 0.1, 0.1
+    agents, distances = agent.get_nearest_neighbors(k=2)
+    assert len(agents) == 2
+
+    # torus
+    model = Model(seed=42)
+    dimensions = np.asarray([[0, 1], [0, 1]])
+    space = ContinuousSpace(dimensions, torus=True, random=model.random)
+
+    positions = [
+        [0.1, 0.1],
+        [0.1, 0.9],
+        [0.9, 0.1],
+        [0.9, 0.9],
+        [0.5, 0.5],
+    ]
+
+    for position in positions:
+        agent = ContinuousSpaceAgent(space, model)
+        agent.position = position
+
+    agent: ContinuousSpaceAgent = model.agents[-1]  # 0.5, 0.5
+    agents, distances = agent.get_neighbors_in_radius(1)
+    assert len(agents) == 4
+
+    agent: ContinuousSpaceAgent = model.agents[0]  # 0.1, 0.1
+    agents, distances = agent.get_nearest_neighbors(k=2)
+    assert len(agents) == 2
+    assert np.allclose(distances, [0.2, 0.2])
\ No newline at end of file

From e98eadf48d393545de2254530b268e494d654a09 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 8 Jan 2025 17:17:36 +0100
Subject: [PATCH 76/84] Delete for_development.py

---
 .../continuous_space/for_development.py       | 33 -------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 mesa/experimental/continuous_space/for_development.py

diff --git a/mesa/experimental/continuous_space/for_development.py b/mesa/experimental/continuous_space/for_development.py
deleted file mode 100644
index 525d3246641..00000000000
--- a/mesa/experimental/continuous_space/for_development.py
+++ /dev/null
@@ -1,33 +0,0 @@
-"""to be removed once further into the development."""
-
-if __name__ == "__main__":
-    from mesa import Agent, Model
-    from mesa.experimental.continuous_space import ContinuousSpace as NewStyleSpace
-    from mesa.experimental.continuous_space import ContinuousSpaceAgent
-    from mesa.space import ContinuousSpace as OldStyleSpace
-
-    n = 400
-
-    model = Model(rng=42)
-    space = OldStyleSpace(100, 100, torus=True)
-
-    positions = model.rng.random((n, 2)) * n
-    for pos in positions:
-        agent = Agent(model)
-        space.place_agent(agent, pos)
-
-    for _ in range(100):
-        space.get_neighbors([50, 50], radius=5, include_center=False)
-
-    model = Model(rng=42)
-    space = NewStyleSpace(
-        [[0, 100], [0, 100]], torus=True, random=model.random, n_agents=n
-    )
-
-    positions = model.rng.random((n, 2)) * n
-    for pos in positions:
-        agent = ContinuousSpaceAgent(space, model)
-        agent.position = pos
-
-    for _ in range(100):
-        space.get_agents_in_radius([50, 50], radius=5)

From 983fbb9eecfad1b452fbee81ae071c66c0c2b9a3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 8 Jan 2025 16:17:47 +0000
Subject: [PATCH 77/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_continuous_space.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/test_continuous_space.py b/tests/test_continuous_space.py
index 4184aa15ec3..41d7ca33186 100644
--- a/tests/test_continuous_space.py
+++ b/tests/test_continuous_space.py
@@ -103,15 +103,14 @@ def test_continuous_agent():
     dimensions = np.asarray([[0, 1], [0, 1]])
     space = ContinuousSpace(dimensions, torus=True, random=model.random)
     agent = ContinuousSpaceAgent(space, model)
-    agent.position =[1.1, 1.1]
+    agent.position = [1.1, 1.1]
     assert np.allclose(agent.position, [0.1, 0.1])
 
     dimensions = np.asarray([[0, 1], [0, 1]])
     space = ContinuousSpace(dimensions, torus=False, random=model.random)
     agent = ContinuousSpaceAgent(space, model)
     with pytest.raises(ValueError):
-        agent.position =[1.1, 1.1]
-
+        agent.position = [1.1, 1.1]
 
 
 def test_continous_space_calculate_distances():
@@ -430,4 +429,4 @@ def test_get_neighbor_methos():  # noqa: D103
     agent: ContinuousSpaceAgent = model.agents[0]  # 0.1, 0.1
     agents, distances = agent.get_nearest_neighbors(k=2)
     assert len(agents) == 2
-    assert np.allclose(distances, [0.2, 0.2])
\ No newline at end of file
+    assert np.allclose(distances, [0.2, 0.2])

From c4de8de45aae6e07988d7a202a961968ee6fdb74 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 8 Jan 2025 18:45:14 +0100
Subject: [PATCH 78/84] Update mesa/examples/basic/boid_flockers/model.py

Co-authored-by: Ewout ter Hoeven <E.M.terHoeven@student.tudelft.nl>
---
 mesa/examples/basic/boid_flockers/model.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index b9e126a70eb..cc7cfaa85e7 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -59,14 +59,14 @@ def __init__(
         )
 
         # Create and place the Boid agents
-        position = self.rng.random(size=(population_size, 2)) * self.space.size
-        direction = self.rng.uniform(-1, 1, size=(population_size, 2))
+        positions = self.rng.random(size=(population_size, 2)) * self.space.size
+        directions = self.rng.uniform(-1, 1, size=(population_size, 2))
         Boid.create_agents(
             self,
             population_size,
             self.space,
-            position=position,
-            direction=direction,
+            position=positions,
+            direction=directions,
             cohere=cohere,
             separate=separate,
             match=match,

From 23159bf450b0ea8efdf5c9e3ad0732022e25f9a5 Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 8 Jan 2025 18:47:23 +0100
Subject: [PATCH 79/84] Update mesa/examples/basic/boid_flockers/model.py

Co-authored-by: Ewout ter Hoeven <E.M.terHoeven@student.tudelft.nl>
---
 mesa/examples/basic/boid_flockers/model.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/mesa/examples/basic/boid_flockers/model.py b/mesa/examples/basic/boid_flockers/model.py
index cc7cfaa85e7..c5d46a12b85 100644
--- a/mesa/examples/basic/boid_flockers/model.py
+++ b/mesa/examples/basic/boid_flockers/model.py
@@ -96,10 +96,3 @@ def step(self):
         """
         self.agents.shuffle_do("step")
         self.update_average_heading()
-
-
-if __name__ == "__main__":
-    model = BoidFlockers(population_size=200, width=100, height=100, vision=5, seed=42)
-
-    for _i in range(20):
-        model.step()

From 0706667f30e730000e292db2c5a8e90d0a08bbfb Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 8 Jan 2025 19:20:11 +0100
Subject: [PATCH 80/84] expanded docstring and comments

---
 .../continuous_space/continuous_space.py      | 70 ++++++++++++++-----
 .../continuous_space_agents.py                |  4 +-
 2 files changed, 55 insertions(+), 19 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index c358893b4dc..caac339ba84 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -47,12 +47,24 @@ def height(self):  # noqa: D102
 
     def __init__(
         self,
-        dimensions: Sequence[Sequence[float]],
+        dimensions: ArrayLike,
         torus: bool = False,
         random: Random | None = None,
         n_agents: int = 100,
     ) -> None:
-        """Create a new continuous space."""
+        """Create a new continuous space.
+
+        Args:
+            dimensions: a numpy array like object where eahc row specifies the minimum and maximum value of that dimesnion
+            torus: boolean for whether the space wraps around or not
+            random: a seeded stdlib random.Random instance
+            n_agents: the expected number of agents in the space
+
+        Internally, a numpy array is used to store the positions of all agents. This is resized if needed,
+        but you can control the initial size explicitly by passing n_agents.
+
+
+        """
         if random is None:
             warnings.warn(
                 "Random number generator not specified, this can make models non-reproducible. Please pass a random number generator explicitly",
@@ -62,25 +74,29 @@ def __init__(
             random = Random()
         self.random = random
 
-        self.dimensions: np.array = np.asarray(dimensions)
+        self.dimensions: np.array = np.asanarray(dimensions)
         self.ndims: int = self.dimensions.shape[0]
         self.size: np.array = self.dimensions[:, 1] - self.dimensions[:, 0]
         self.center: np.array = np.sum(self.dimensions, axis=1) / 2
 
         self.torus: bool = torus
 
+
+        # self._agent_positions is the array containing all agent positions
+        # plus potential extra empty rows
+        # agent_positions is a view into _agent_positions containing only the filled rows
         self._agent_positions: np.array = np.empty(
             (n_agents, self.dimensions.shape[0]), dtype=float
         )
-        # self._agents: np.array = np.zeros((n_agents,), dtype=object)
-
-        self.active_agents = []
         self.agent_positions: (
             np.array
         )  # a view on _agent_positions containing all active positions
 
-        self._n_agents = 0
+        # the list of agents in the space
+        self.active_agents = []
+        self._n_agents = 0  # the number of active agents in the space
 
+        #  a mapping from agents to index and vice versa
         self._index_to_agent: dict[int, Agent] = {}
         self._agent_to_index: dict[Agent, int | None] = {}
 
@@ -90,10 +106,10 @@ def agents(self) -> AgentSet:
         return AgentSet(self.active_agents, random=self.random)
 
     def _add_agent(self, agent: Agent) -> int:
-        """Helper method to get the index for the agent.
+        """Helper method for adding an agent to the space.
 
         This method manages the numpy array with the agent positions and ensuring it is
-        enlarged if and when needed.
+        enlarged if and when needed. It is called automatically by ContinousSpaceAgent when created.
 
         """
         index = self._n_agents
@@ -123,7 +139,11 @@ def _add_agent(self, agent: Agent) -> int:
         return index
 
     def _remove_agent(self, agent: Agent) -> None:
-        """Remove an agent from the space."""
+        """Remove an agent from the space.
+
+        This method is automatically called by ContinuousSpaceAgent.remove.
+
+        """
         index = self._agent_to_index[agent]
         self._agent_to_index.pop(agent, None)
         self._index_to_agent.pop(index, None)
@@ -143,7 +163,15 @@ def _remove_agent(self, agent: Agent) -> None:
         self.agent_positions = self._agent_positions[0 : self._n_agents]
 
     def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndarray:
-        """Calculate the difference vector between the point and all agents."""
+        """Calculate the difference vector between the point and all agenents.
+
+        Args:
+            point: the point to calculate the difference vector for
+            agents: the agents to calculate the difference vector of point with. By default,
+                    all agents are considered.
+
+
+        """
         point = np.asanyarray(point)
         positions = (
             self.agent_positions
@@ -170,7 +198,14 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
     def calculate_distances(
         self, point: ArrayLike, agents: Iterable[Agent] | None = None
     ) -> tuple[np.ndarray, list]:
-        """Calculate the distance between the point and all agents."""
+        """Calculate the distance between the point and all agents.
+
+        Args:
+            point: the point to calculate the difference vector for
+            agents: the agents to calculate the difference vector of point with. By default,
+                    all agents are considered.
+
+        """
         point = np.asanyarray(point)
 
         if agents is None:
@@ -211,7 +246,8 @@ def get_k_nearest_agents(
         """Return the k nearest agents and their distances to the point.
 
         Notes:
-            This method returns exactly k agents, ignoring ties
+            This method returns exactly k agents, ignoring ties. In case of ties, the
+            earlier an agent is inserted the higher it will rank.
 
         """
         dists, agents = self.calculate_distances(point)
@@ -220,12 +256,12 @@ def get_k_nearest_agents(
         agents = [agents[i] for i in indices]
         return agents, dists[indices]
 
-    def in_bounds(self, point) -> bool:
+    def in_bounds(self, point:ArrayLike) -> bool:
         """Check if point is inside the bounds of the space."""
         return bool(
-            ((point >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])).all()
+            ((np.asanyarray(point) >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])).all()
         )
 
-    def torus_correct(self, point) -> np.ndarray:
+    def torus_correct(self, point:ArrayLike) -> np.ndarray:
         """Apply a torus correction to the point."""
-        return self.dimensions[:, 0] + np.mod(point - self.dimensions[:, 0], self.size)
+        return self.dimensions[:, 0] + np.mod(np.asanyarray(point) - self.dimensions[:, 0], self.size)
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 3f2167e0ef2..155fa275ff3 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -67,13 +67,13 @@ def __init__(self, space: ContinuousSpace, model):
         # self.position[:] = np.nan
 
     def remove(self) -> None:
-        """Remove and delete the agent from the model."""
+        """Remove and delete the agent from the model and continuous space"""
         super().remove()
         self.space._remove_agent(self)
         self._mesa_index = None
         self.space = None
 
-    def get_neighbors_in_radius(self, radius: float = 1) -> tuple[list, np.ndarray]:
+    def get_neighbors_in_radius(self, radius: float|int = 1) -> tuple[list, np.ndarray]:
         """Get neighbors within radius.
 
         Args:

From 0cbbbb504b4a61c8e52e42532db9bdd8940634cf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 8 Jan 2025 18:20:26 +0000
Subject: [PATCH 81/84] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../continuous_space/continuous_space.py         | 16 ++++++++++------
 .../continuous_space/continuous_space_agents.py  |  4 +++-
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index caac339ba84..6efb2a1ba53 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -1,7 +1,7 @@
 """A Continuous Space class."""
 
 import warnings
-from collections.abc import Iterable, Sequence
+from collections.abc import Iterable
 from itertools import compress
 from random import Random
 
@@ -81,7 +81,6 @@ def __init__(
 
         self.torus: bool = torus
 
-
         # self._agent_positions is the array containing all agent positions
         # plus potential extra empty rows
         # agent_positions is a view into _agent_positions containing only the filled rows
@@ -256,12 +255,17 @@ def get_k_nearest_agents(
         agents = [agents[i] for i in indices]
         return agents, dists[indices]
 
-    def in_bounds(self, point:ArrayLike) -> bool:
+    def in_bounds(self, point: ArrayLike) -> bool:
         """Check if point is inside the bounds of the space."""
         return bool(
-            ((np.asanyarray(point) >= self.dimensions[:, 0]) & (point <= self.dimensions[:, 1])).all()
+            (
+                (np.asanyarray(point) >= self.dimensions[:, 0])
+                & (point <= self.dimensions[:, 1])
+            ).all()
         )
 
-    def torus_correct(self, point:ArrayLike) -> np.ndarray:
+    def torus_correct(self, point: ArrayLike) -> np.ndarray:
         """Apply a torus correction to the point."""
-        return self.dimensions[:, 0] + np.mod(np.asanyarray(point) - self.dimensions[:, 0], self.size)
+        return self.dimensions[:, 0] + np.mod(
+            np.asanyarray(point) - self.dimensions[:, 0], self.size
+        )
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 155fa275ff3..02a7305bed4 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -73,7 +73,9 @@ def remove(self) -> None:
         self._mesa_index = None
         self.space = None
 
-    def get_neighbors_in_radius(self, radius: float|int = 1) -> tuple[list, np.ndarray]:
+    def get_neighbors_in_radius(
+        self, radius: float | int = 1
+    ) -> tuple[list, np.ndarray]:
         """Get neighbors within radius.
 
         Args:

From 418778651030b9e4c233b3cde301c55558fd2a9d Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Wed, 8 Jan 2025 19:25:11 +0100
Subject: [PATCH 82/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index 6efb2a1ba53..d847ef23ce7 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -74,7 +74,7 @@ def __init__(
             random = Random()
         self.random = random
 
-        self.dimensions: np.array = np.asanarray(dimensions)
+        self.dimensions: np.array = np.asanyarray(dimensions)
         self.ndims: int = self.dimensions.shape[0]
         self.size: np.array = self.dimensions[:, 1] - self.dimensions[:, 0]
         self.center: np.array = np.sum(self.dimensions, axis=1) / 2

From 1b8937f1de6bb21e01398193691d1ea36dffab8e Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 10 Jan 2025 08:20:53 +0100
Subject: [PATCH 83/84] final tweaks

---
 mesa/experimental/continuous_space/continuous_space.py      | 6 ++++--
 .../continuous_space/continuous_space_agents.py             | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index d847ef23ce7..a88733fcb1c 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -195,7 +195,7 @@ def calculate_difference_vector(self, point: np.ndarray, agents=None) -> np.ndar
         return delta
 
     def calculate_distances(
-        self, point: ArrayLike, agents: Iterable[Agent] | None = None
+        self, point: ArrayLike, agents: Iterable[Agent] | None = None, **kwargs
     ) -> tuple[np.ndarray, list]:
         """Calculate the distance between the point and all agents.
 
@@ -203,6 +203,8 @@ def calculate_distances(
             point: the point to calculate the difference vector for
             agents: the agents to calculate the difference vector of point with. By default,
                     all agents are considered.
+            kwargs: any additional keyword arguments are passed to scipy's cdist, which is used
+                    only if torus is False. This allows for non-Euclidian distance measures.
 
         """
         point = np.asanyarray(point)
@@ -224,7 +226,7 @@ def calculate_distances(
                 dists += delta[:, i] ** 2
             dists = np.sqrt(dists)
         else:
-            dists = cdist(point[np.newaxis, :], positions)[0, :]
+            dists = cdist(point[np.newaxis, :], positions, **kwargs)[0, :]
         return dists, agents
 
     def get_agents_in_radius(
diff --git a/mesa/experimental/continuous_space/continuous_space_agents.py b/mesa/experimental/continuous_space/continuous_space_agents.py
index 02a7305bed4..f4ea9c2885f 100644
--- a/mesa/experimental/continuous_space/continuous_space_agents.py
+++ b/mesa/experimental/continuous_space/continuous_space_agents.py
@@ -67,7 +67,7 @@ def __init__(self, space: ContinuousSpace, model):
         # self.position[:] = np.nan
 
     def remove(self) -> None:
-        """Remove and delete the agent from the model and continuous space"""
+        """Remove and delete the agent from the model and continuous space."""
         super().remove()
         self.space._remove_agent(self)
         self._mesa_index = None

From 897d62e3b818dd232764d47cd1cd44bff39f812b Mon Sep 17 00:00:00 2001
From: Jan Kwakkel <j.h.kwakkel@tudelft.nl>
Date: Fri, 10 Jan 2025 08:23:20 +0100
Subject: [PATCH 84/84] Update continuous_space.py

---
 mesa/experimental/continuous_space/continuous_space.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mesa/experimental/continuous_space/continuous_space.py b/mesa/experimental/continuous_space/continuous_space.py
index a88733fcb1c..232eb38414b 100644
--- a/mesa/experimental/continuous_space/continuous_space.py
+++ b/mesa/experimental/continuous_space/continuous_space.py
@@ -55,7 +55,7 @@ def __init__(
         """Create a new continuous space.
 
         Args:
-            dimensions: a numpy array like object where eahc row specifies the minimum and maximum value of that dimesnion
+            dimensions: a numpy array like object where each row specifies the minimum and maximum value of that dimension.
             torus: boolean for whether the space wraps around or not
             random: a seeded stdlib random.Random instance
             n_agents: the expected number of agents in the space