WIP soil

* Pandas integration
* Improved environment
* Logging and data dumps
* Tests
* Added Finite State Machine models
* Rewritten ipython notebook and documentation

examples/complete.yml

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+---
+name: simple
+dir_path: "/tmp/"
+num_trials: 3
+max_time: 100
+interval: 1
+network_params:
+  generator: complete_graph
+  n: 10
+network_agents:
+  - agent_type: CounterModel
+    weight: 1
+    state:
+      id: 0
+  - agent_type: AggregatedCounter
+    weight: 0.2
+environment_agents: []
+environment_params:
+  am_i_complete: true
+default_state:
+  incidents: 0
+states:
+  - name: 'The first node'
+  - name: 'The second node'

examples/custom-agents/UnnamedSimulation.dumped.yml

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+default_state: {}
+environment_agents: []
+environment_params: {prob_neighbor_spread: 0.0, prob_tv_spread: 0.01}
+interval: 1
+max_time: 20
+name: Sim_prob_0
+network_agents:
+- agent_type: NewsSpread
+  state: {has_tv: false}
+  weight: 1
+- agent_type: NewsSpread
+  state: {has_tv: true}
+  weight: 2
+network_params: {generator: erdos_renyi_graph, n: 500, p: 0.1}
+num_trials: 1
+states:
+- {has_tv: true}

examples/custom-agents/agent.py

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+import soil
+import random
+
+class NewsSpread(soil.agents.FSM):
+    @soil.agents.default_state
+    @soil.agents.state
+    def neutral(self):
+        r = random.random()
+        if self['has_tv'] and r < self.env['prob_tv_spread']:
+                return self.infected
+        return
+
+    @soil.agents.state
+    def infected(self):
+        prob_infect = self.env['prob_neighbor_spread']
+        for neighbor in self.get_neighboring_agents(state_id=self.neutral.id):
+            r = random.random()
+            if r < prob_infect:
+                neighbor.state['id'] = self.infected.id
+        return

examples/torvalds.edgelist

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+balkian Torvalds {}
+anonymous Torvalds {}

examples/torvalds.yml

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+---
+name: torvalds_example
+max_time: 1
+interval: 2
+agent_type: CounterModel
+default_state:
+  skill_level: 'beginner'
+network_params:
+  path: 'torvalds.edgelist'
+states:
+  Torvalds:
+    skill_level: 'God'
+  balkian:
+    skill_level: 'developer'