examples/virus: Restructure

- VirusAgent in agents.py
- Flatten structure
- Remove old visualisation code

examples/basic/virus_on_network/README.md

@@ -43,9 +43,9 @@ Directly run the file ``run.py`` in the terminal. e.g.
 
 ## Files
 
-* ``run.py``: Launches a model visualization server.
 * ``model.py``: Contains the agent class, and the overall model class.
-* ``server.py``: Defines classes for visualizing the model (network layout) in the browser via Mesa's modular server, and instantiates a visualization server.
+* ``agents.py``: Contains the agent class.
+* ``app.py``: Contains the code for the interactive Solara visualization.
 
 ## Further Reading
 

examples/basic/virus_on_network/agents.py

@@ -0,0 +1,70 @@
+from mesa import Agent
+from enum import Enum
+
+
+class State(Enum):
+    SUSCEPTIBLE = 0
+    INFECTED = 1
+    RESISTANT = 2
+
+
+class VirusAgent(Agent):
+    """
+    Individual Agent definition and its properties/interaction methods
+    """
+
+    def __init__(
+        self,
+        model,
+        initial_state,
+        virus_spread_chance,
+        virus_check_frequency,
+        recovery_chance,
+        gain_resistance_chance,
+    ):
+        super().__init__(model)
+
+        self.state = initial_state
+
+        self.virus_spread_chance = virus_spread_chance
+        self.virus_check_frequency = virus_check_frequency
+        self.recovery_chance = recovery_chance
+        self.gain_resistance_chance = gain_resistance_chance
+
+    def try_to_infect_neighbors(self):
+        neighbors_nodes = self.model.grid.get_neighborhood(
+            self.pos, include_center=False
+        )
+        susceptible_neighbors = [
+            agent
+            for agent in self.model.grid.get_cell_list_contents(neighbors_nodes)
+            if agent.state is State.SUSCEPTIBLE
+        ]
+        for a in susceptible_neighbors:
+            if self.random.random() < self.virus_spread_chance:
+                a.state = State.INFECTED
+
+    def try_gain_resistance(self):
+        if self.random.random() < self.gain_resistance_chance:
+            self.state = State.RESISTANT
+
+    def try_remove_infection(self):
+        # Try to remove
+        if self.random.random() < self.recovery_chance:
+            # Success
+            self.state = State.SUSCEPTIBLE
+            self.try_gain_resistance()
+        else:
+            # Failed
+            self.state = State.INFECTED
+
+    def try_check_situation(self):
+        if (self.random.random() < self.virus_check_frequency) and (
+            self.state is State.INFECTED
+        ):
+            self.try_remove_infection()
+
+    def step(self):
+        if self.state is State.INFECTED:
+            self.try_to_infect_neighbors()
+        self.try_check_situation()

examples/basic/virus_on_network/app.py

@@ -4,7 +4,7 @@
 from matplotlib.figure import Figure
 from matplotlib.ticker import MaxNLocator
 from mesa.visualization import SolaraViz, Slider, make_space_matplotlib
-from virus_on_network.model import State, VirusOnNetwork, number_infected
+from model import State, VirusOnNetwork, number_infected
 
 
 def agent_portrayal(graph):

examples/basic/virus_on_network/virus_on_network/model.py → examples/basic/virus_on_network/model.py

@@ -1,14 +1,10 @@
 import math
-from enum import Enum
 
 import mesa
+from mesa import Model
 import networkx as nx
 
-
-class State(Enum):
-    SUSCEPTIBLE = 0
-    INFECTED = 1
-    RESISTANT = 2
+from agents import VirusAgent, State
 
 
 def number_state(model, state):
@@ -27,7 +23,7 @@ def number_resistant(model):
     return number_state(model, State.RESISTANT)
 
 
-class VirusOnNetwork(mesa.Model):
+class VirusOnNetwork(Model):
     """
     A virus model with some number of agents
     """
@@ -102,65 +98,3 @@ def step(self):
     def run_model(self, n):
         for i in range(n):
             self.step()
-
-
-class VirusAgent(mesa.Agent):
-    """
-    Individual Agent definition and its properties/interaction methods
-    """
-
-    def __init__(
-        self,
-        model,
-        initial_state,
-        virus_spread_chance,
-        virus_check_frequency,
-        recovery_chance,
-        gain_resistance_chance,
-    ):
-        super().__init__(model)
-
-        self.state = initial_state
-
-        self.virus_spread_chance = virus_spread_chance
-        self.virus_check_frequency = virus_check_frequency
-        self.recovery_chance = recovery_chance
-        self.gain_resistance_chance = gain_resistance_chance
-
-    def try_to_infect_neighbors(self):
-        neighbors_nodes = self.model.grid.get_neighborhood(
-            self.pos, include_center=False
-        )
-        susceptible_neighbors = [
-            agent
-            for agent in self.model.grid.get_cell_list_contents(neighbors_nodes)
-            if agent.state is State.SUSCEPTIBLE
-        ]
-        for a in susceptible_neighbors:
-            if self.random.random() < self.virus_spread_chance:
-                a.state = State.INFECTED
-
-    def try_gain_resistance(self):
-        if self.random.random() < self.gain_resistance_chance:
-            self.state = State.RESISTANT
-
-    def try_remove_infection(self):
-        # Try to remove
-        if self.random.random() < self.recovery_chance:
-            # Success
-            self.state = State.SUSCEPTIBLE
-            self.try_gain_resistance()
-        else:
-            # Failed
-            self.state = State.INFECTED
-
-    def try_check_situation(self):
-        if (self.random.random() < self.virus_check_frequency) and (
-            self.state is State.INFECTED
-        ):
-            self.try_remove_infection()
-
-    def step(self):
-        if self.state is State.INFECTED:
-            self.try_to_infect_neighbors()
-        self.try_check_situation()