restructured files into package and used seeded RNG also whilst updating README

Author: Syn-Eon

examples/pathogen_outbreak/README.md

@@ -22,7 +22,7 @@ analyzing changes in infection, death and immunity rates.
 
 ## How It Works
 
-1. **Initialization** — citizens are placed randomly on a MultiGrid.
+1. **Initialization** — citizens are placed randomly on a Grid(OrthogonalMooreGrid).
    A configurable number are set initially as infected.
 2. **Disease Spread** — each step, healthy agents check their neighbours including diagonals.
    If any are infected, there is a configurable chance of transmission.
@@ -37,7 +37,7 @@ analyzing changes in infection, death and immunity rates.
    - Infected agents - compliant ones, freeze in place, simulating isolation or a lockdowned zone
 5. **Recovery** — after 10 steps of infection, agents recover to full
    immunity or die with the probability of 10%. Dead agents remain
-   on the grid as red circles/squares(this is an intentional mechanic) as a visual indicator to assess how compliance affects the compliant as well as non-compliant groups.
+   on the grid as red circles/squares(this is an intentional mechanic) as a visual indicator to assess how compliance affects the compliant as well as non-compliant groups.It is to be noted that dead agents block movement as well.
 
 ## Interesting Cases to Observe
 

examples/pathogen_outbreak/app.py

@@ -1,5 +1,5 @@
 from mesa.visualization import SolaraViz, make_plot_component, make_space_component
-from model import PathogenModel
+from pathogen_outbreak.model import PathogenModel
 
 
 def make_agent(agent):

examples/pathogen_outbreak/pathogen_outbreak/__init__.py

@@ -1,5 +1,3 @@
-import random
-
 from mesa.discrete_space import CellAgent
 
 
@@ -9,7 +7,7 @@ def __init__(self, model):
 
         self.state = "healthy"
         self.stage = 0
-        self.compliant = random.random() < self.model.compliance_rate
+        self.compliant = self.random.random() < self.model.compliance_rate
 
     def step(self):
         if self.model.quarantine_status and self.compliant:
@@ -20,7 +18,7 @@ def step(self):
         if self.state == "infected":
             self.stage += 1
             if self.stage > 9:
-                chance_of_death = random.random()
+                chance_of_death = self.random.random()
 
                 if chance_of_death < 0.1:
                     self.state = "dead"
@@ -36,7 +34,7 @@ def step(self):
                         for a in cell.agents]
             for i in neighbors:
                 if i.state == "infected":
-                    if random.random() > 0.40:
+                    if self.random.random() > 0.40:
                         self.state = "infected"
                     break
 

examples/pathogen_outbreak/agents.py …gen_outbreak/pathogen_outbreak/agents.pyexamples/pathogen_outbreak/agents.py renamed to examples/pathogen_outbreak/pathogen_outbreak/agents.py examples/pathogen_outbreak/agents.py renamed to examples/pathogen_outbreak/pathogen_outbreak/agents.py

@@ -1,5 +1,4 @@
-
-from agents import Citizen
+from pathogen_outbreak.agents import Citizen
 from mesa import DataCollector, Model
 from mesa.discrete_space import OrthogonalMooreGrid
 
@@ -58,6 +57,8 @@ def __init__(
         for i in range(infn):
             self.agents[i].state = "infected"
 
+        self.datacollector.collect(self)
+ 
     def step(self):
         self.infected_count = c_infected(self)