Refactoring v0.15.1

See CHANGELOG.md for a full list of changes

* Removed nxsim
* Refactored `agents.NetworkAgent` and `agents.BaseAgent`
* Refactored exporters
* Added stats to history

examples/NewsSpread.ipynb

@@ -500,7 +500,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.5"
   },
   "toc": {
    "colors": {

examples/Untitled.ipynb

@@ -80800,7 +80800,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,

examples/rabbits/rabbit_agents.py

@@ -1,4 +1,4 @@
-from soil.agents import FSM, state, default_state, BaseAgent
+from soil.agents import FSM, state, default_state, BaseAgent, NetworkAgent
 from enum import Enum
 from random import random, choice
 from itertools import islice
@@ -80,7 +80,7 @@ class RabbitModel(FSM):
                 self.env.add_edge(self['mate'], child.id)
                 # self.add_edge()
                 self.debug('A BABY IS COMING TO LIFE')
-                self.env['rabbits_alive'] = self.env.get('rabbits_alive', self.global_topology.number_of_nodes())+1
+                self.env['rabbits_alive'] = self.env.get('rabbits_alive', self.topology.number_of_nodes())+1
                 self.debug('Rabbits alive: {}'.format(self.env['rabbits_alive']))
                 self['offspring'] += 1
                 self.env.get_agent(self['mate'])['offspring'] += 1
@@ -97,12 +97,14 @@ class RabbitModel(FSM):
         return
 
 
-class RandomAccident(BaseAgent):
+class RandomAccident(NetworkAgent):
 
     level = logging.DEBUG
 
     def step(self):
-        rabbits_total = self.global_topology.number_of_nodes()
+        rabbits_total = self.topology.number_of_nodes()
+        if 'rabbits_alive' not in self.env:
+            self.env['rabbits_alive'] = 0
         rabbits_alive = self.env.get('rabbits_alive', rabbits_total)
         prob_death = self.env.get('prob_death', 1e-100)*math.floor(math.log10(max(1, rabbits_alive)))
         self.debug('Killing some rabbits with prob={}!'.format(prob_death))
@@ -116,5 +118,5 @@ class RandomAccident(BaseAgent):
                 self.log('Rabbits alive: {}'.format(self.env['rabbits_alive']))
                 i.set_state(i.dead)
         self.log('Rabbits alive: {}/{}'.format(rabbits_alive, rabbits_total))
-        if self.count_agents(state_id=RabbitModel.dead.id) == self.global_topology.number_of_nodes():
+        if self.count_agents(state_id=RabbitModel.dead.id) == self.topology.number_of_nodes():
             self.die()

examples/template.yml

@@ -1,13 +1,8 @@
 ---
-vars:
-  bounds:
-    x1: [0, 1]
-    x2: [1, 2]
-  fixed:
-    x3: ["a", "b", "c"]
-sampler: "SALib.sample.morris.sample"
-samples: 10
-template: |
+sampler:
+  method: "SALib.sample.morris.sample"
+  N: 10
+template:
   group: simple
   num_trials: 1
   interval: 1
@@ -19,11 +14,17 @@ template: |
     n: 10
   network_agents:
     - agent_type: CounterModel
-      weight: {{ x1 }}
+      weight: "{{ x1 }}"
       state:
         id: 0
     - agent_type: AggregatedCounter
-      weight: {{ 1 - x1 }}
+      weight: "{{ 1 - x1 }}"
   environment_params:
-    name: {{ x3 }}
+    name: "{{ x3 }}"
   skip_test: true
+vars:
+  bounds:
+    x1: [0, 1]
+    x2: [1, 2]
+  fixed:
+    x3: ["a", "b", "c"]

examples/terrorism/TerroristNetworkModel.py

@@ -195,14 +195,14 @@ class TerroristNetworkModel(TerroristSpreadModel):
                     break
 
     def get_distance(self, target):
-        source_x, source_y = nx.get_node_attributes(self.global_topology, 'pos')[self.id]
-        target_x, target_y = nx.get_node_attributes(self.global_topology, 'pos')[target]
+        source_x, source_y = nx.get_node_attributes(self.topology, 'pos')[self.id]
+        target_x, target_y = nx.get_node_attributes(self.topology, 'pos')[target]
         dx = abs( source_x - target_x )
         dy = abs( source_y - target_y )
         return ( dx ** 2 + dy ** 2 ) ** ( 1 / 2 )
 
     def shortest_path_length(self, target):
         try:
-            return nx.shortest_path_length(self.global_topology, self.id, target)
+            return nx.shortest_path_length(self.topology, self.id, target)
         except nx.NetworkXNoPath:
             return float('inf')