Add generator and programmatic examples

soil/VERSION

@@ -1 +1 @@
-0.13.4
+0.13.6

soil/simulation.py

@@ -88,14 +88,8 @@ class Simulation(NetworkSimulation):
                  environment_agents=None, environment_params=None,
                  environment_class=None, **kwargs):
 
-        if topology is None:
-            topology = utils.load_network(network_params,
-                                          dir_path=dir_path)
-        elif isinstance(topology, basestring) or isinstance(topology, dict):
-            topology = json_graph.node_link_graph(topology)
-
+        self.seed = str(seed) or str(time.time())
         self.load_module = load_module
-        self.topology = nx.Graph(topology)
         self.network_params = network_params
         self.name = name or 'UnnamedSimulation'
         self.num_trials = num_trials
@@ -103,12 +97,19 @@ class Simulation(NetworkSimulation):
         self.default_state = default_state or {}
         self.dir_path = dir_path or os.getcwd()
         self.interval = interval
-        self.seed = str(seed) or str(time.time())
         self.dump = dump
         self.dry_run = dry_run
 
         sys.path += [self.dir_path, os.getcwd()]
 
+        if topology is None:
+            topology = utils.load_network(network_params,
+                                          dir_path=self.dir_path)
+        elif isinstance(topology, basestring) or isinstance(topology, dict):
+            topology = json_graph.node_link_graph(topology)
+        self.topology = nx.Graph(topology)
+
+
         self.environment_params = environment_params or {}
         self.environment_class = utils.deserialize(environment_class,
                                                    known_modules=['soil.environment', ]) or Environment

soil/utils.py

@@ -1,5 +1,6 @@
 import os
 import ast
+import sys
 import yaml
 import logging
 import importlib
@@ -36,9 +37,14 @@ def load_network(network_params, dir_path=None):
         return method(path, **kwargs)
 
     net_args = network_params.copy()
-    net_type = net_args.pop('generator')
+    net_gen = net_args.pop('generator')
+
+    if dir_path not in sys.path:
+        sys.path.append(dir_path)
+
+    method = deserializer(net_gen,
+                          known_modules=['networkx.generators',])
 
-    method = getattr(nx.generators, net_type)
     return method(**net_args)
 
 
@@ -114,6 +120,8 @@ def serialize(v, known_modules=[]):
     return func(v), tname
 
 def deserializer(type_, known_modules=[]):
+    if type(type_) != str:  # Already deserialized
+        return type_
     if type_ == 'str':
         return lambda x='': x
     if type_ == 'None':