Improve exporters

Documentation needs some improvement

The API has been simplified to only allow for ONE topology per
NetworkEnvironment.
This covers the main use case, and simplifies the code.

CHANGELOG.md

@@ -5,14 +5,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [0.3 UNRELEASED]
 ### Added
-* Simple debugging capabilities, with a custom `pdb.Debugger` subclass that exposes commands to list agents and their status and set breakpoints on states (for FSM agents)
+* Simple debugging capabilities in `soil.debugging`, with a custom `pdb.Debugger` subclass that exposes commands to list agents and their status and set breakpoints on states (for FSM agents). Try it with `soil --debug <simulation file>`
+* Ability to run 
+* Ability to 
+* The `soil.exporters` module to export the results of datacollectors (model.datacollector) into files at the end of trials/simulations
+* A modular set of classes for environments/models. Now the ability to configure the agents through an agent definition and a topology through a network configuration is split into two classes (`soil.agents.BaseEnvironment` for agents, `soil.agents.NetworkEnvironment` to add topology).
+* FSM agents can now have generators as states. They work similar to normal states, with one caveat. Only `time` values can be yielded, not a state. This is because the state will not change, it will be resumed after the yield, at the appropriate time. The return value *can* be a state, or a `(state, time)` tuple, just like in normal states.
 ### Changed
 * Configuration schema is very different now. Check `soil.config` for more information. We are also using Pydantic for (de)serialization.
 * There may be more than one topology/network in the simulation
-* Agents are split into groups now. Each group may be assigned a given set of agents or an agent distribution, and a network topology to be assigned to.
+* Ability
 ### Removed
 * Any `tsih` and `History` integration in the main classes. To record the state of environments/agents, just use a datacollector. In some cases this may be slower or consume more memory than the previous system. However, few cases actually used the full potential of the history, and it came at the cost of unnecessary complexity and worse performance for the majority of cases.
 
+
 ## [0.20.7]
 ### Changed
 * Creating a `time.When` from another `time.When` does not nest them anymore (it returns the argument)

examples/complete.yml

@@ -10,19 +10,14 @@ seed: "CompleteSeed!"
 model_class: Environment
 model_params:
   am_i_complete: true
-  topologies:
-    default:
-      params:
-        generator: complete_graph
-        n: 10
-    another_graph:
-      params:
-        generator: complete_graph
-        n: 2
+  topology:
+    params:
+      generator: complete_graph
+      n: 12
   environment:
   agents:
     agent_class: CounterModel
-    topology: default
+    topology: true
     state:
       times: 1
       # In this group we are not specifying any topology
@@ -30,25 +25,23 @@ model_params:
       - name: 'Environment Agent 1'
         agent_class: BaseAgent
         group: environment
-        topology: null
+        topology: false
         hidden: true
         state:
           times: 10
       - agent_class: CounterModel
         id: 0
-        group: other_counters
-        topology: another_graph
+        group: fixed_counters
         state:
           times: 1
           total: 0
       - agent_class: CounterModel
-        topology: another_graph
-        group: other_counters
+        group: fixed_counters
         id: 1
     distribution:
       - agent_class: CounterModel
         weight: 1
-        group: general_counters
+        group: distro_counters
         state:
           times: 3
       - agent_class: AggregatedCounter

examples/complete_opt2.yml

@@ -1,63 +0,0 @@
----
-version: '2'
-id: simple
-group: tests
-dir_path: "/tmp/"
-num_trials: 3
-max_steps: 100
-interval: 1
-seed: "CompleteSeed!"
-model_class: "soil.Environment"
-model_params:
-  topologies:
-    default:
-      params:
-        generator: complete_graph
-        n: 10
-    another_graph:
-      params:
-        generator: complete_graph
-        n: 2
-  agents:
-    # The values here will be used as default values for any agent
-    agent_class: CounterModel
-    topology: default
-    state:
-      times: 1
-    # This specifies a distribution of agents, each with a `weight` or an explicit number of agents
-    distribution:
-      - agent_class: CounterModel
-        weight: 1
-        # This is inherited from the default settings
-        #topology: default
-        state:
-          times: 3
-      - agent_class: AggregatedCounter
-        topology: default
-        weight: 0.2
-    fixed:
-      - name: 'Environment Agent 1'
-        # All the other agents will assigned to the 'default' group
-        group: environment
-        # Do not count this agent towards total limits
-        hidden: true
-        agent_class: soil.BaseAgent
-        topology: null
-        state:
-          times: 10
-      - agent_class: CounterModel
-        topology: another_graph
-        id: 0
-        state:
-          times: 1
-          total: 0
-      - agent_class: CounterModel
-        topology: another_graph
-        id: 1
-    override:
-      # 2 agents that match this filter will be updated to match the state {times: 5}
-      - filter:
-          agent_class: AggregatedCounter
-        n: 2
-        state:
-            times: 5

examples/custom_timeouts/custom_timeouts.py

@@ -15,6 +15,7 @@ class Fibonacci(FSM):
         prev, self['prev'] = self['prev'], max([self.now, self['prev']])
         return None, self.env.timeout(prev)
 
+
 class Odds(FSM):
     '''Agent that only executes in odd t_steps'''
     @default_state
@@ -23,9 +24,8 @@ class Odds(FSM):
         self.log('Stopping at {}'.format(self.now))
         return None, self.env.timeout(1+self.now%2)
 
+
 if __name__ == '__main__':
-    import logging
-    logging.basicConfig(level=logging.INFO)
     from soil import Simulation
     s = Simulation(network_agents=[{'ids': [0], 'agent_class': Fibonacci},
                                    {'ids': [1], 'agent_class': Odds}],

examples/mesa/mesa.yml

@@ -8,17 +8,12 @@ interval: 1
 seed: '1'
 model_class: social_wealth.MoneyEnv
 model_params:
-  topologies:
-    default: 
-      params:
-        generator: social_wealth.graph_generator
-        n: 5
+  generator: social_wealth.graph_generator
   agents:
+    topology: true
     distribution:
       - agent_class: social_wealth.SocialMoneyAgent
-        topology: default
         weight: 1
-  mesa_agent_class: social_wealth.MoneyAgent
   N: 10
   width: 50
   height: 50

examples/mesa/server.py

@@ -2,6 +2,7 @@ from mesa.visualization.ModularVisualization import ModularServer
 from soil.visualization import UserSettableParameter
 from mesa.visualization.modules import ChartModule, NetworkModule, CanvasGrid
 from social_wealth import MoneyEnv, graph_generator, SocialMoneyAgent
+import networkx as nx
 
 
 class MyNetwork(NetworkModule):
@@ -13,15 +14,16 @@ def network_portrayal(env):
     # The model ensures there is 0 or 1 agent per node
 
     portrayal = dict()
+    wealths = {node_id: data['agent'].wealth for (node_id, data) in env.G.nodes(data=True)}
     portrayal["nodes"] = [
         {
-            "id": agent_id,
-            "size": env.get_agent(agent_id).wealth,
-            # "color": "#CC0000" if not agents or agents[0].wealth == 0 else "#007959",
-            "color": "#CC0000",
-            "label": f"{agent_id}: {env.get_agent(agent_id).wealth}",
-        }
-        for (agent_id) in env.G.nodes
+            "id": node_id,
+            "size": 2*(wealth+1),
+            "color": "#CC0000" if wealth == 0 else "#007959",
+            # "color": "#CC0000",
+            "label": f"{node_id}: {wealth}",
+        } for (node_id, wealth) in wealths.items()
+
     ]
 
     portrayal["edges"] = [
@@ -29,7 +31,6 @@ def network_portrayal(env):
         for edge_id, (source, target) in enumerate(env.G.edges)
     ]
 
-
     return portrayal
 
 
@@ -55,7 +56,7 @@ def gridPortrayal(agent):
     }
 
 
-grid = MyNetwork(network_portrayal, 500, 500, library="sigma")
+grid = MyNetwork(network_portrayal, 500, 500)
 chart = ChartModule(
     [{"Label": "Gini", "Color": "Black"}], data_collector_name="datacollector"
 )
@@ -70,7 +71,6 @@ model_params = {
         1,
         description="Choose how many agents to include in the model",
     ),
-    "network_agents": [{"agent_class": SocialMoneyAgent}],
     "height": UserSettableParameter(
         "slider",
         "height",
@@ -89,12 +89,15 @@ model_params = {
         1,
         description="Grid width",
         ),
-    "network_params": {
-        'generator': graph_generator
-    },
+    "agent_class": UserSettableParameter('choice', 'Agent class', value='MoneyAgent',
+                                         choices=['MoneyAgent', 'SocialMoneyAgent']),
+    "generator": graph_generator,
 }
 
-canvas_element = CanvasGrid(gridPortrayal, model_params["width"].value, model_params["height"].value, 500, 500)
+
+canvas_element = CanvasGrid(gridPortrayal,
+                            model_params["width"].value,
+                            model_params["height"].value, 500, 500)
 
 
 server = ModularServer(

examples/mesa/social_wealth.py

@@ -10,7 +10,7 @@ from mesa.batchrunner import BatchRunner
 
 import networkx as nx
 
-from soil import NetworkAgent, Environment
+from soil import NetworkAgent, Environment, serialization
 
 def compute_gini(model):
     agent_wealths = [agent.wealth for agent in model.agents]
@@ -19,15 +19,16 @@ def compute_gini(model):
     B = sum( xi * (N-i) for i,xi in enumerate(x) ) / (N*sum(x))
     return (1 + (1/N) - 2*B)
 
+
 class MoneyAgent(MesaAgent):
     """
     A MESA agent with fixed initial wealth.
     It will only share wealth with neighbors based on grid proximity
     """
 
-    def __init__(self, unique_id, model):
+    def __init__(self, unique_id, model, wealth=1):
         super().__init__(unique_id=unique_id, model=model)
-        self.wealth = 1
+        self.wealth = wealth
 
     def move(self):
         possible_steps = self.model.grid.get_neighborhood(
@@ -45,7 +46,7 @@ class MoneyAgent(MesaAgent):
             self.wealth -= 1
 
     def step(self):
-        self.info("Crying wolf", self.pos)
+        print("Crying wolf", self.pos)
         self.move()
         if self.wealth > 0:
             self.give_money()
@@ -58,8 +59,8 @@ class SocialMoneyAgent(NetworkAgent, MoneyAgent):
         cellmates = set(self.model.grid.get_cell_list_contents([self.pos]))
         friends = set(self.get_neighboring_agents())
         self.info("Trying to give money")
-        self.debug("Cellmates: ", cellmates)
-        self.debug("Friends: ", friends)
+        self.info("Cellmates: ", cellmates)
+        self.info("Friends: ", friends)
 
         nearby_friends = list(cellmates & friends)
 
@@ -68,14 +69,29 @@ class SocialMoneyAgent(NetworkAgent, MoneyAgent):
             other.wealth += 1
             self.wealth -= 1
 
+def graph_generator(n=5):
+    G = nx.Graph()
+    for ix in range(n):
+        G.add_edge(0, ix)
+    return G
+
 
 class MoneyEnv(Environment):
     """A model with some number of agents."""
-    def __init__(self, width, height, *args, topologies, **kwargs):
+    def __init__(self, width, height, N, generator=graph_generator,
+                 agent_class=SocialMoneyAgent,
+                 topology=None, **kwargs):
 
-        super().__init__(*args, topologies=topologies, **kwargs)
+        generator = serialization.deserialize(generator)
+        agent_class = serialization.deserialize(agent_class, globs=globals())
+        topology = generator(n=N)
+        super().__init__(topology=topology,
+                         N=N,
+                         **kwargs)
         self.grid = MultiGrid(width, height, False)
 
+        self.populate_network(agent_class=agent_class)
+
         # Create agents
         for agent in self.agents:
             x = self.random.randrange(self.grid.width)
@@ -87,17 +103,9 @@ class MoneyEnv(Environment):
             agent_reporters={"Wealth": "wealth"})
 
 
-def graph_generator(n=5):
-    G = nx.Graph()
-    for ix in range(n):
-        G.add_edge(0, ix)
-    return G
-
 if __name__ == '__main__':
 
-
-    G = graph_generator()
-    fixed_params = {"topology": G,
+    fixed_params = {"generator": nx.complete_graph,
                     "width": 10,
                     "network_agents": [{"agent_class": SocialMoneyAgent,
                                        'weight': 1}],
@@ -116,4 +124,3 @@ if __name__ == '__main__':
     run_data = batch_run.get_model_vars_dataframe()
     run_data.head()
     print(run_data.Gini)
-

examples/pubcrawl/pubcrawl.py

@@ -126,7 +126,7 @@ class Patron(FSM, NetworkAgent):
         success depend on both agents' openness.
         '''
         if force or self['openness'] > self.random.random():
-            self.model.add_edge(self, other_agent)
+            self.add_edge(self, other_agent)
             self.info('Made some friend {}'.format(other_agent))
             return True
         return False

examples/rabbits/basic/rabbit_agents.py

@@ -1,4 +1,4 @@
-from soil.agents import FSM, state, default_state, BaseAgent, NetworkAgent
+from soil import FSM, state, default_state, BaseAgent, NetworkAgent, Environment
 from soil.time import Delta
 from enum import Enum
 from collections import Counter
@@ -6,7 +6,23 @@ import logging
 import math
 
 
-class RabbitModel(FSM, NetworkAgent):
+class RabbitEnv(Environment):
+
+    @property
+    def num_rabbits(self):
+        return self.count_agents(agent_class=Rabbit)
+
+    @property
+    def num_males(self):
+        return self.count_agents(agent_class=Male)
+
+    @property
+    def num_females(self):
+        return self.count_agents(agent_class=Female)
+
+
+
+class Rabbit(FSM, NetworkAgent):
 
     sexual_maturity = 30
     life_expectancy = 300
@@ -35,7 +51,7 @@ class RabbitModel(FSM, NetworkAgent):
         self.die()
 
 
-class Male(RabbitModel):
+class Male(Rabbit):
     max_females = 5
     mating_prob = 0.001
 
@@ -56,8 +72,8 @@ class Male(RabbitModel):
                 break  # Take a break
 
 
-class Female(RabbitModel):
-    gestation = 100
+class Female(Rabbit):
+    gestation = 30
 
     @state
     def fertile(self):
@@ -72,10 +88,10 @@ class Female(RabbitModel):
         self.pregnancy = -1
         self.set_state(self.pregnant, when=self.now)
         self.number_of_babies = int(8+4*self.random.random())
-        self.debug('I am pregnant')
 
     @state
     def pregnant(self):
+        self.debug('I am pregnant')
         self.age += 1
         self.pregnancy += 1
 
@@ -88,7 +104,6 @@ class Female(RabbitModel):
                 state = {}
                 agent_class = self.random.choice([Male, Female])
                 child = self.model.add_node(agent_class=agent_class,
-                                            topology=self.topology,
                                             **state)
                 child.add_edge(self)
                 try:
@@ -113,18 +128,23 @@ class RandomAccident(BaseAgent):
     level = logging.INFO
 
     def step(self):
-        rabbits_alive = self.model.topology.number_of_nodes()
+        rabbits_alive = self.model.G.number_of_nodes()
 
         if not rabbits_alive:
             return self.die()
 
         prob_death = self.model.get('prob_death', 1e-100)*math.floor(math.log10(max(1, rabbits_alive)))
         self.debug('Killing some rabbits with prob={}!'.format(prob_death))
-        for i in self.iter_agents(agent_class=RabbitModel):
-            if i.state.id == i.dead.id:
+        for i in self.iter_agents(agent_class=Rabbit):
+            if i.state_id == i.dead.id:
                 continue
             if self.prob(prob_death):
                 self.info('I killed a rabbit: {}'.format(i.id))
                 rabbits_alive -= 1
                 i.set_state(i.dead)
         self.debug('Rabbits alive: {}'.format(rabbits_alive))
+
+if __name__ == '__main__':
+    from soil import easy
+    sim = easy('rabbits.yml')
+    sim.run()

examples/rabbits/basic/rabbits.yml

@@ -7,21 +7,18 @@ description: null
 group: null
 interval: 1.0
 max_time: 100
-model_class: soil.environment.Environment
+model_class: rabbit_agents.RabbitEnv
 model_params:
   agents:
-    topology: default
-    agent_class: rabbit_agents.RabbitModel
+    topology: true
     distribution:
     - agent_class: rabbit_agents.Male
-      topology: default
       weight: 1
     - agent_class: rabbit_agents.Female
-      topology: default
       weight: 1
     fixed:
     - agent_class: rabbit_agents.RandomAccident
-      topology: null
+      topology: false
       hidden: true
       state:
         group: environment
@@ -29,13 +26,17 @@ model_params:
       group: network
       mating_prob: 0.1
   prob_death: 0.001
-  topologies:
-    default:
-      topology:
-        directed: true
-        links: []
-        nodes:
-        - id: 1
-        - id: 0
+  topology:
+    fixed:
+      directed: true
+      links: []
+      nodes:
+      - id: 1
+      - id: 0
+  model_reporters:
+    num_males: 'num_males'
+    num_females: 'num_females'
+    num_rabbits: |
+      py:lambda env: env.num_males + env.num_females
 extra:
   visualization_params: {}

examples/rabbits/improved/rabbits.yml

@@ -10,18 +10,16 @@ max_time: 100
 model_class: soil.environment.Environment
 model_params:
   agents:
-    topology: default
+    topology: true
     agent_class: rabbit_agents.RabbitModel
     distribution:
     - agent_class: rabbit_agents.Male
-      topology: default
       weight: 1
     - agent_class: rabbit_agents.Female
-      topology: default
       weight: 1
     fixed:
     - agent_class: rabbit_agents.RandomAccident
-      topology: null
+      topology: false
       hidden: true
       state:
         group: environment
@@ -29,13 +27,12 @@ model_params:
       group: network
       mating_prob: 0.1
   prob_death: 0.001
-  topologies:
-    default:
-      topology:
-        directed: true
-        links: []
-        nodes:
-        - id: 1
-        - id: 0
+  topology:
+    fixed:
+      directed: true
+      links: []
+      nodes:
+      - id: 1
+      - id: 0
 extra:
   visualization_params: {}

examples/random_delays/random_delays.py

@@ -4,7 +4,6 @@ Example of a fully programmatic simulation, without definition files.
 '''
 from soil import Simulation, agents
 from soil.time import Delta
-import logging
 
 
 
@@ -40,5 +39,4 @@ s = Simulation(name='Programmatic',
                dry_run=True)
 
 
-logging.basicConfig(level=logging.INFO)
 envs = s.run()

requirements.txt

@@ -5,6 +5,6 @@ pyyaml>=5.1
 pandas>=1
 SALib>=1.3
 Jinja2
-Mesa>=1
+Mesa>=1.1
 pydantic>=1.9
 sqlalchemy>=1.4

setup.py

@@ -53,6 +53,6 @@ setup(
     include_package_data=True,
     entry_points={
         'console_scripts':
-        ['soil = soil.__init__:main',
+        ['soil = soil.__main__:main',
         'soil-web = soil.web.__init__:main']
     })

soil/__init__.py

@@ -21,93 +21,165 @@ from . import serialization
 from .utils import logger
 from .time import *
 
-def main(cfg='simulation.yml', **kwargs):
+
+def main(
+    cfg="simulation.yml",
+    exporters=None,
+    parallel=None,
+    output="soil_output",
+    *,
+    do_run=False,
+    debug=False,
+    **kwargs,
+):
     import argparse
     from . import simulation
 
-    logger.info('Running SOIL version: {}'.format(__version__))
+    logger.info("Running SOIL version: {}".format(__version__))
 
-    parser = argparse.ArgumentParser(description='Run a SOIL simulation')
-    parser.add_argument('file', type=str,
-                        nargs="?",
-                        default=cfg,
-                        help='Configuration file for the simulation (e.g., YAML or JSON)')
-    parser.add_argument('--version', action='store_true',
-                        help='Show version info and exit')
-    parser.add_argument('--module', '-m', type=str,
-                        help='file containing the code of any custom agents.')
-    parser.add_argument('--dry-run', '--dry', action='store_true',
-                        help='Do not store the results of the simulation to disk, show in terminal instead.')
-    parser.add_argument('--pdb', action='store_true',
-                        help='Use a pdb console in case of exception.')
-    parser.add_argument('--debug', action='store_true',
-                        help='Run a customized version of a pdb console to debug a simulation.')
-    parser.add_argument('--graph', '-g', action='store_true',
-                        help='Dump each trial\'s network topology as a GEXF graph. Defaults to false.')
-    parser.add_argument('--csv', action='store_true',
-                        help='Dump all data collected in CSV format. Defaults to false.')
-    parser.add_argument('--level', type=str,
-                        help='Logging level')
-    parser.add_argument('--output', '-o', type=str, default="soil_output",
-                        help='folder to write results to. It defaults to the current directory.')
-    parser.add_argument('--synchronous', action='store_true',
-                        help='Run trials serially and synchronously instead of in parallel. Defaults to false.')
-    parser.add_argument('-e', '--exporter', action='append',
-                        help='Export environment and/or simulations using this exporter')
-    parser.add_argument('--only-convert', '--convert', action='store_true',
-                        help='Do not run the simulation, only convert the configuration file(s) and output them.')
+    parser = argparse.ArgumentParser(description="Run a SOIL simulation")
+    parser.add_argument(
+        "file",
+        type=str,
+        nargs="?",
+        default=cfg,
+        help="Configuration file for the simulation (e.g., YAML or JSON)",
+    )
+    parser.add_argument(
+        "--version", action="store_true", help="Show version info and exit"
+    )
+    parser.add_argument(
+        "--module",
+        "-m",
+        type=str,
+        help="file containing the code of any custom agents.",
+    )
+    parser.add_argument(
+        "--dry-run",
+        "--dry",
+        action="store_true",
+        help="Do not store the results of the simulation to disk, show in terminal instead.",
+    )
+    parser.add_argument(
+        "--pdb", action="store_true", help="Use a pdb console in case of exception."
+    )
+    parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Run a customized version of a pdb console to debug a simulation.",
+    )
+    parser.add_argument(
+        "--graph",
+        "-g",
+        action="store_true",
+        help="Dump each trial's network topology as a GEXF graph. Defaults to false.",
+    )
+    parser.add_argument(
+        "--csv",
+        action="store_true",
+        help="Dump all data collected in CSV format. Defaults to false.",
+    )
+    parser.add_argument("--level", type=str, help="Logging level")
+    parser.add_argument(
+        "--output",
+        "-o",
+        type=str,
+        default=output or "soil_output",
+        help="folder to write results to. It defaults to the current directory.",
+    )
+    if parallel is None:
+        parser.add_argument(
+            "--synchronous",
+            action="store_true",
+            help="Run trials serially and synchronously instead of in parallel. Defaults to false.",
+        )
 
+    parser.add_argument(
+        "-e",
+        "--exporter",
+        action="append",
+        default=[],
+        help="Export environment and/or simulations using this exporter",
+    )
 
-    parser.add_argument("--set",
-                        metavar="KEY=VALUE",
-                        action='append',
-                        help="Set a number of parameters that will be passed to the simulation."
-                        "(do not put spaces before or after the = sign). "
-                        "If a value contains spaces, you should define "
-                        "it with double quotes: "
-                        'foo="this is a sentence". Note that '
-                        "values are always treated as strings.")
+    parser.add_argument(
+        "--only-convert",
+        "--convert",
+        action="store_true",
+        help="Do not run the simulation, only convert the configuration file(s) and output them.",
+    )
+
+    parser.add_argument(
+        "--set",
+        metavar="KEY=VALUE",
+        action="append",
+        help="Set a number of parameters that will be passed to the simulation."
+        "(do not put spaces before or after the = sign). "
+        "If a value contains spaces, you should define "
+        "it with double quotes: "
+        'foo="this is a sentence". Note that '
+        "values are always treated as strings.",
+    )
 
     args = parser.parse_args()
-    logger.setLevel(getattr(logging, (args.level or 'INFO').upper()))
+    logger.setLevel(getattr(logging, (args.level or "INFO").upper()))
 
     if args.version:
         return
 
+    if parallel is None:
+        parallel = not args.synchronous
+
+    exporters = exporters or [
+        "default",
+    ]
+    for exp in args.exporter:
+        if exp not in exporters:
+            exporters.append(exp)
+    if args.csv:
+        exporters.append("csv")
+    if args.graph:
+        exporters.append("gexf")
+
     if os.getcwd() not in sys.path:
         sys.path.append(os.getcwd())
     if args.module:
         importlib.import_module(args.module)
+    if output is None:
+        output = args.output
 
-    logger.info('Loading config file: {}'.format(args.file))
+    logger.info("Loading config file: {}".format(args.file))
 
-    if args.pdb or args.debug:
+    debug = debug or args.debug
+
+    if args.pdb or debug:
         args.synchronous = True
-    if args.debug:
-        os.environ['SOIL_DEBUG'] = 'true'
 
+    res = []
     try:
-        exporters = list(args.exporter or ['default', ])
-        if args.csv:
-            exporters.append('csv')
-        if args.graph:
-            exporters.append('gexf')
         exp_params = {}
-        if args.dry_run:
-            exp_params['copy_to'] = sys.stdout
 
         if not os.path.exists(args.file):
-            logger.error('Please, input a valid file')
+            logger.error("Please, input a valid file")
             return
-        for sim in simulation.iter_from_config(args.file):
+
+        for sim in simulation.iter_from_config(
+            args.file,
+            dry_run=args.dry_run,
+            exporters=exporters,
+            parallel=parallel,
+            outdir=output,
+            exporter_params=exp_params,
+            **kwargs,
+        ):
             if args.set:
                 for s in args.set:
-                    k, v = s.split('=', 1)[:2]
+                    k, v = s.split("=", 1)[:2]
                     v = eval(v)
-                    tail, *head = k.rsplit('.', 1)[::-1]
+                    tail, *head = k.rsplit(".", 1)[::-1]
                     target = sim
                     if head:
-                        for part in head[0].split('.'):
+                        for part in head[0].split("."):
                             try:
                                 target = getattr(target, part)
                             except AttributeError:
@@ -117,30 +189,34 @@ def main(cfg='simulation.yml', **kwargs):
                     except AttributeError:
                         target[tail] = v
 
-                if args.only_convert:
-                    print(sim.to_yaml())
-                    continue
-
-            sim.run_simulation(dry_run=args.dry_run,
-                               exporters=exporters,
-                               parallel=(not args.synchronous),
-                               outdir=args.output,
-                               exporter_params=exp_params,
-                               **kwargs)
+            if args.only_convert:
+                print(sim.to_yaml())
+                continue
+            if do_run:
+                res.append(sim.run())
+            else:
+                print("not running")
+                res.append(sim)
 
     except Exception as ex:
         if args.pdb:
             from .debugging import post_mortem
+
             print(traceback.format_exc())
             post_mortem()
         else:
             raise
+    if debug:
+        from .debugging import set_trace
 
-def easy(cfg, debug=False):
-    sim = simulation.from_config(cfg)
-    if debug or os.environ.get('SOIL_DEBUG'):
-        from .debugging import setup
-        setup(sys._getframe().f_back)
-    return sim
-if __name__ == '__main__':
-    main()
+        os.environ["SOIL_DEBUG"] = "true"
+        set_trace()
+    return res
+
+
+def easy(cfg, debug=False, **kwargs):
+    return main(cfg, **kwargs)[0]
+
+
+if __name__ == "__main__":
+    main(do_run=True)

soil/__main__.py

@@ -1,4 +1,9 @@
-from . import main
+from . import main as init_main
 
-if __name__ == '__main__':
-    main()
+
+def main():
+    init_main(do_run=True)
+
+
+if __name__ == "__main__":
+    init_main(do_run=True)

soil/agents/BassModel.py

@@ -7,6 +7,7 @@ class BassModel(FSM):
         innovation_prob
         imitation_prob
     """
+
     sentimentCorrelation = 0
 
     def step(self):
@@ -21,7 +22,7 @@ class BassModel(FSM):
         else:
             aware_neighbors = self.get_neighboring_agents(state_id=self.aware.id)
             num_neighbors_aware = len(aware_neighbors)
-            if self.prob((self['imitation_prob']*num_neighbors_aware)):
+            if self.prob((self["imitation_prob"] * num_neighbors_aware)):
                 self.sentimentCorrelation = 1
                 return self.aware
 

soil/agents/BigMarketModel.py

@@ -6,42 +6,54 @@ class BigMarketModel(FSM):
     Settings:
         Names:
             enterprises [Array]
-            
+
             tweet_probability_enterprises [Array]
         Users:
             tweet_probability_users
-            
+
             tweet_relevant_probability
-            
+
             tweet_probability_about [Array]
-            
+
             sentiment_about [Array]
     """
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.enterprises = self.env.environment_params['enterprises']
+        self.enterprises = self.env.environment_params["enterprises"]
         self.type = ""
 
         if self.id < len(self.enterprises):  # Enterprises
             self.set_state(self.enterprise.id)
             self.type = "Enterprise"
-            self.tweet_probability = environment.environment_params['tweet_probability_enterprises'][self.id]
+            self.tweet_probability = environment.environment_params[
+                "tweet_probability_enterprises"
+            ][self.id]
         else:  # normal users
             self.type = "User"
             self.set_state(self.user.id)
-            self.tweet_probability = environment.environment_params['tweet_probability_users']
-            self.tweet_relevant_probability = environment.environment_params['tweet_relevant_probability']
-            self.tweet_probability_about = environment.environment_params['tweet_probability_about']  # List
-            self.sentiment_about = environment.environment_params['sentiment_about']  # List
+            self.tweet_probability = environment.environment_params[
+                "tweet_probability_users"
+            ]
+            self.tweet_relevant_probability = environment.environment_params[
+                "tweet_relevant_probability"
+            ]
+            self.tweet_probability_about = environment.environment_params[
+                "tweet_probability_about"
+            ]  # List
+            self.sentiment_about = environment.environment_params[
+                "sentiment_about"
+            ]  # List
 
     @state
     def enterprise(self):
 
         if self.random.random() < self.tweet_probability:  # Tweets
-            aware_neighbors = self.get_neighboring_agents(state_id=self.number_of_enterprises)  # Nodes neighbour users
+            aware_neighbors = self.get_neighboring_agents(
+                state_id=self.number_of_enterprises
+            )  # Nodes neighbour users
             for x in aware_neighbors:
-                if self.random.uniform(0,10) < 5:
+                if self.random.uniform(0, 10) < 5:
                     x.sentiment_about[self.id] += 0.1  # Increments for enterprise
                 else:
                     x.sentiment_about[self.id] -= 0.1  # Decrements for enterprise
@@ -49,15 +61,19 @@ class BigMarketModel(FSM):
                 # Establecemos limites
                 if x.sentiment_about[self.id] > 1:
                     x.sentiment_about[self.id] = 1
-                if x.sentiment_about[self.id]< -1:
+                if x.sentiment_about[self.id] < -1:
                     x.sentiment_about[self.id] = -1
 
-                x.attrs['sentiment_enterprise_%s'% self.enterprises[self.id]] = x.sentiment_about[self.id]
+                x.attrs[
+                    "sentiment_enterprise_%s" % self.enterprises[self.id]
+                ] = x.sentiment_about[self.id]
 
     @state
     def user(self):
         if self.random.random() < self.tweet_probability:  # Tweets
-            if self.random.random() < self.tweet_relevant_probability:  # Tweets something relevant
+            if (
+                self.random.random() < self.tweet_relevant_probability
+            ):  # Tweets something relevant
                 # Tweet probability per enterprise
                 for i in range(len(self.enterprises)):
                     random_num = self.random.random()
@@ -65,23 +81,29 @@ class BigMarketModel(FSM):
                         # The condition is fulfilled, sentiments are evaluated towards that enterprise
                         if self.sentiment_about[i] < 0:
                             # NEGATIVO
-                            self.userTweets("negative",i)
+                            self.userTweets("negative", i)
                         elif self.sentiment_about[i] == 0:
                             # NEUTRO
                             pass
                         else:
                             # POSITIVO
-                            self.userTweets("positive",i)
-        for i in range(len(self.enterprises)):  # So that it never is set to 0 if there are not changes (logs)
-            self.attrs['sentiment_enterprise_%s'% self.enterprises[i]] = self.sentiment_about[i]
+                            self.userTweets("positive", i)
+        for i in range(
+            len(self.enterprises)
+        ):  # So that it never is set to 0 if there are not changes (logs)
+            self.attrs[
+                "sentiment_enterprise_%s" % self.enterprises[i]
+            ] = self.sentiment_about[i]
 
-    def userTweets(self, sentiment,enterprise):
-        aware_neighbors = self.get_neighboring_agents(state_id=self.number_of_enterprises)  # Nodes neighbours users
+    def userTweets(self, sentiment, enterprise):
+        aware_neighbors = self.get_neighboring_agents(
+            state_id=self.number_of_enterprises
+        )  # Nodes neighbours users
         for x in aware_neighbors:
             if sentiment == "positive":
-                x.sentiment_about[enterprise] +=0.003
+                x.sentiment_about[enterprise] += 0.003
             elif sentiment == "negative":
-                x.sentiment_about[enterprise] -=0.003
+                x.sentiment_about[enterprise] -= 0.003
             else:
                 pass
 
@@ -91,4 +113,6 @@ class BigMarketModel(FSM):
             if x.sentiment_about[enterprise] < -1:
                 x.sentiment_about[enterprise] = -1
 
-            x.attrs['sentiment_enterprise_%s'% self.enterprises[enterprise]] = x.sentiment_about[enterprise]
+            x.attrs[
+                "sentiment_enterprise_%s" % self.enterprises[enterprise]
+            ] = x.sentiment_about[enterprise]

soil/agents/CounterModel.py

@@ -15,9 +15,9 @@ class CounterModel(NetworkAgent):
         # Outside effects
         total = len(list(self.model.schedule._agents))
         neighbors = len(list(self.get_neighboring_agents()))
-        self['times'] = self.get('times', 0) + 1
-        self['neighbors'] = neighbors
-        self['total'] = total
+        self["times"] = self.get("times", 0) + 1
+        self["neighbors"] = neighbors
+        self["total"] = total
 
 
 class AggregatedCounter(NetworkAgent):
@@ -32,9 +32,9 @@ class AggregatedCounter(NetworkAgent):
 
     def step(self):
         # Outside effects
-        self['times'] += 1
+        self["times"] += 1
         neighbors = len(list(self.get_neighboring_agents()))
-        self['neighbors'] += neighbors
+        self["neighbors"] += neighbors
         total = len(list(self.model.schedule.agents))
-        self['total'] += total
-        self.debug('Running for step: {}. Total: {}'.format(self.now, total))
+        self["total"] += total
+        self.debug("Running for step: {}. Total: {}".format(self.now, total))

soil/agents/Geo.py

@@ -2,20 +2,20 @@ from scipy.spatial import cKDTree as KDTree
 import networkx as nx
 from . import NetworkAgent, as_node
 
+
 class Geo(NetworkAgent):
-    '''In this type of network, nodes have a "pos" attribute.'''
+    """In this type of network, nodes have a "pos" attribute."""
 
     def geo_search(self, radius, node=None, center=False, **kwargs):
-        '''Get a list of nodes whose coordinates are closer than *radius* to *node*.'''
+        """Get a list of nodes whose coordinates are closer than *radius* to *node*."""
         node = as_node(node if node is not None else self)
 
         G = self.subgraph(**kwargs)
 
-        pos = nx.get_node_attributes(G, 'pos')
+        pos = nx.get_node_attributes(G, "pos")
         if not pos:
             return []
         nodes, coords = list(zip(*pos.items()))
         kdtree = KDTree(coords)  # Cannot provide generator.
         indices = kdtree.query_ball_point(pos[node], radius)
         return [nodes[i] for i in indices if center or (nodes[i] != node)]
-

soil/agents/IndependentCascadeModel.py

@@ -11,10 +11,10 @@ class IndependentCascadeModel(BaseAgent):
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.innovation_prob = self.env.environment_params['innovation_prob']
-        self.imitation_prob = self.env.environment_params['imitation_prob']
-        self.state['time_awareness'] = 0
-        self.state['sentimentCorrelation'] = 0
+        self.innovation_prob = self.env.environment_params["innovation_prob"]
+        self.imitation_prob = self.env.environment_params["imitation_prob"]
+        self.state["time_awareness"] = 0
+        self.state["sentimentCorrelation"] = 0
 
     def step(self):
         self.behaviour()
@@ -23,25 +23,27 @@ class IndependentCascadeModel(BaseAgent):
         aware_neighbors_1_time_step = []
         # Outside effects
         if self.prob(self.innovation_prob):
-            if self.state['id'] == 0:
-                self.state['id'] = 1
-                self.state['sentimentCorrelation'] = 1
-                self.state['time_awareness'] = self.env.now  # To know when they have been infected
+            if self.state["id"] == 0:
+                self.state["id"] = 1
+                self.state["sentimentCorrelation"] = 1
+                self.state[
+                    "time_awareness"
+                ] = self.env.now  # To know when they have been infected
             else:
                 pass
 
             return
 
         # Imitation effects
-        if self.state['id'] == 0:
+        if self.state["id"] == 0:
             aware_neighbors = self.get_neighboring_agents(state_id=1)
             for x in aware_neighbors:
-                if x.state['time_awareness'] == (self.env.now-1):
+                if x.state["time_awareness"] == (self.env.now - 1):
                     aware_neighbors_1_time_step.append(x)
             num_neighbors_aware = len(aware_neighbors_1_time_step)
-            if self.prob(self.imitation_prob*num_neighbors_aware):
-                self.state['id'] = 1
-                self.state['sentimentCorrelation'] = 1
+            if self.prob(self.imitation_prob * num_neighbors_aware):
+                self.state["id"] = 1
+                self.state["sentimentCorrelation"] = 1
             else:
                 pass
 

soil/agents/ModelM2.py

@@ -23,36 +23,49 @@ class SpreadModelM2(BaseAgent):
     def __init__(self, model=None, unique_id=0, state=()):
         super().__init__(model=environment, unique_id=unique_id, state=state)
 
-
         # Use a single generator with the same seed as `self.random`
         random = np.random.default_rng(seed=self._seed)
-        self.prob_neutral_making_denier = random.normal(environment.environment_params['prob_neutral_making_denier'],
-                                                        environment.environment_params['standard_variance'])
+        self.prob_neutral_making_denier = random.normal(
+            environment.environment_params["prob_neutral_making_denier"],
+            environment.environment_params["standard_variance"],
+        )
 
-        self.prob_infect = random.normal(environment.environment_params['prob_infect'],
-                                         environment.environment_params['standard_variance'])
+        self.prob_infect = random.normal(
+            environment.environment_params["prob_infect"],
+            environment.environment_params["standard_variance"],
+        )
 
-        self.prob_cured_healing_infected = random.normal(environment.environment_params['prob_cured_healing_infected'],
-                                                         environment.environment_params['standard_variance'])
-        self.prob_cured_vaccinate_neutral = random.normal(environment.environment_params['prob_cured_vaccinate_neutral'],
-                                                          environment.environment_params['standard_variance'])
+        self.prob_cured_healing_infected = random.normal(
+            environment.environment_params["prob_cured_healing_infected"],
+            environment.environment_params["standard_variance"],
+        )
+        self.prob_cured_vaccinate_neutral = random.normal(
+            environment.environment_params["prob_cured_vaccinate_neutral"],
+            environment.environment_params["standard_variance"],
+        )
 
-        self.prob_vaccinated_healing_infected = random.normal(environment.environment_params['prob_vaccinated_healing_infected'],
-                                                              environment.environment_params['standard_variance'])
-        self.prob_vaccinated_vaccinate_neutral = random.normal(environment.environment_params['prob_vaccinated_vaccinate_neutral'],
-                                                               environment.environment_params['standard_variance'])
-        self.prob_generate_anti_rumor = random.normal(environment.environment_params['prob_generate_anti_rumor'],
-                                                      environment.environment_params['standard_variance'])
+        self.prob_vaccinated_healing_infected = random.normal(
+            environment.environment_params["prob_vaccinated_healing_infected"],
+            environment.environment_params["standard_variance"],
+        )
+        self.prob_vaccinated_vaccinate_neutral = random.normal(
+            environment.environment_params["prob_vaccinated_vaccinate_neutral"],
+            environment.environment_params["standard_variance"],
+        )
+        self.prob_generate_anti_rumor = random.normal(
+            environment.environment_params["prob_generate_anti_rumor"],
+            environment.environment_params["standard_variance"],
+        )
 
     def step(self):
 
-        if self.state['id'] == 0:  # Neutral
+        if self.state["id"] == 0:  # Neutral
             self.neutral_behaviour()
-        elif self.state['id'] == 1:  # Infected
+        elif self.state["id"] == 1:  # Infected
             self.infected_behaviour()
-        elif self.state['id'] == 2:  # Cured
+        elif self.state["id"] == 2:  # Cured
             self.cured_behaviour()
-        elif self.state['id'] == 3:  # Vaccinated
+        elif self.state["id"] == 3:  # Vaccinated
             self.vaccinated_behaviour()
 
     def neutral_behaviour(self):
@@ -61,7 +74,7 @@ class SpreadModelM2(BaseAgent):
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         if len(infected_neighbors) > 0:
             if self.prob(self.prob_neutral_making_denier):
-                self.state['id'] = 3   # Vaccinated making denier
+                self.state["id"] = 3  # Vaccinated making denier
 
     def infected_behaviour(self):
 
@@ -69,7 +82,7 @@ class SpreadModelM2(BaseAgent):
         neutral_neighbors = self.get_neighboring_agents(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_infect):
-                neighbor.state['id'] = 1  # Infected
+                neighbor.state["id"] = 1  # Infected
 
     def cured_behaviour(self):
 
@@ -77,13 +90,13 @@ class SpreadModelM2(BaseAgent):
         neutral_neighbors = self.get_neighboring_agents(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
-                neighbor.state['id'] = 3  # Vaccinated
+                neighbor.state["id"] = 3  # Vaccinated
 
         # Cure
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
-                neighbor.state['id'] = 2  # Cured
+                neighbor.state["id"] = 2  # Cured
 
     def vaccinated_behaviour(self):
 
@@ -91,19 +104,19 @@ class SpreadModelM2(BaseAgent):
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
-                neighbor.state['id'] = 2  # Cured
+                neighbor.state["id"] = 2  # Cured
 
         # Vaccinate
         neutral_neighbors = self.get_neighboring_agents(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
-                neighbor.state['id'] = 3  # Vaccinated
+                neighbor.state["id"] = 3  # Vaccinated
 
         # Generate anti-rumor
         infected_neighbors_2 = self.get_neighboring_agents(state_id=1)
         for neighbor in infected_neighbors_2:
             if self.prob(self.prob_generate_anti_rumor):
-                neighbor.state['id'] = 2  # Cured
+                neighbor.state["id"] = 2  # Cured
 
 
 class ControlModelM2(BaseAgent):
@@ -112,63 +125,76 @@ class ControlModelM2(BaseAgent):
         prob_neutral_making_denier
 
         prob_infect
-        
+
         prob_cured_healing_infected
-        
+
         prob_cured_vaccinate_neutral
-        
+
         prob_vaccinated_healing_infected
-        
+
         prob_vaccinated_vaccinate_neutral
-        
+
         prob_generate_anti_rumor
     """
 
-
     def __init__(self, model=None, unique_id=0, state=()):
         super().__init__(model=environment, unique_id=unique_id, state=state)
 
-        self.prob_neutral_making_denier = np.random.normal(environment.environment_params['prob_neutral_making_denier'],
-                                                           environment.environment_params['standard_variance'])
+        self.prob_neutral_making_denier = np.random.normal(
+            environment.environment_params["prob_neutral_making_denier"],
+            environment.environment_params["standard_variance"],
+        )
 
-        self.prob_infect = np.random.normal(environment.environment_params['prob_infect'],
-                                            environment.environment_params['standard_variance'])
+        self.prob_infect = np.random.normal(
+            environment.environment_params["prob_infect"],
+            environment.environment_params["standard_variance"],
+        )
 
-        self.prob_cured_healing_infected = np.random.normal(environment.environment_params['prob_cured_healing_infected'],
-                                                            environment.environment_params['standard_variance'])
-        self.prob_cured_vaccinate_neutral = np.random.normal(environment.environment_params['prob_cured_vaccinate_neutral'],
-                                                             environment.environment_params['standard_variance'])
+        self.prob_cured_healing_infected = np.random.normal(
+            environment.environment_params["prob_cured_healing_infected"],
+            environment.environment_params["standard_variance"],
+        )
+        self.prob_cured_vaccinate_neutral = np.random.normal(
+            environment.environment_params["prob_cured_vaccinate_neutral"],
+            environment.environment_params["standard_variance"],
+        )
 
-        self.prob_vaccinated_healing_infected = np.random.normal(environment.environment_params['prob_vaccinated_healing_infected'],
-                                                                 environment.environment_params['standard_variance'])
-        self.prob_vaccinated_vaccinate_neutral = np.random.normal(environment.environment_params['prob_vaccinated_vaccinate_neutral'],
-                                                                  environment.environment_params['standard_variance'])
-        self.prob_generate_anti_rumor = np.random.normal(environment.environment_params['prob_generate_anti_rumor'],
-                                                         environment.environment_params['standard_variance'])
+        self.prob_vaccinated_healing_infected = np.random.normal(
+            environment.environment_params["prob_vaccinated_healing_infected"],
+            environment.environment_params["standard_variance"],
+        )
+        self.prob_vaccinated_vaccinate_neutral = np.random.normal(
+            environment.environment_params["prob_vaccinated_vaccinate_neutral"],
+            environment.environment_params["standard_variance"],
+        )
+        self.prob_generate_anti_rumor = np.random.normal(
+            environment.environment_params["prob_generate_anti_rumor"],
+            environment.environment_params["standard_variance"],
+        )
 
     def step(self):
 
-        if self.state['id'] == 0:  # Neutral
+        if self.state["id"] == 0:  # Neutral
             self.neutral_behaviour()
-        elif self.state['id'] == 1:  # Infected
+        elif self.state["id"] == 1:  # Infected
             self.infected_behaviour()
-        elif self.state['id'] == 2:  # Cured
+        elif self.state["id"] == 2:  # Cured
             self.cured_behaviour()
-        elif self.state['id'] == 3:  # Vaccinated
+        elif self.state["id"] == 3:  # Vaccinated
             self.vaccinated_behaviour()
-        elif self.state['id'] == 4:  # Beacon-off
+        elif self.state["id"] == 4:  # Beacon-off
             self.beacon_off_behaviour()
-        elif self.state['id'] == 5:  # Beacon-on
+        elif self.state["id"] == 5:  # Beacon-on
             self.beacon_on_behaviour()
 
     def neutral_behaviour(self):
-        self.state['visible'] = False
+        self.state["visible"] = False
 
         # Infected
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         if len(infected_neighbors) > 0:
             if self.random(self.prob_neutral_making_denier):
-                self.state['id'] = 3   # Vaccinated making denier
+                self.state["id"] = 3  # Vaccinated making denier
 
     def infected_behaviour(self):
 
@@ -176,69 +202,69 @@ class ControlModelM2(BaseAgent):
         neutral_neighbors = self.get_neighboring_agents(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_infect):
-                neighbor.state['id'] = 1  # Infected
-        self.state['visible'] = False
+                neighbor.state["id"] = 1  # Infected
+        self.state["visible"] = False
 
     def cured_behaviour(self):
 
-        self.state['visible'] = True
+        self.state["visible"] = True
         # Vaccinate
         neutral_neighbors = self.get_neighboring_agents(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
-                neighbor.state['id'] = 3  # Vaccinated
+                neighbor.state["id"] = 3  # Vaccinated
 
         # Cure
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
-                neighbor.state['id'] = 2  # Cured
+                neighbor.state["id"] = 2  # Cured
 
     def vaccinated_behaviour(self):
-        self.state['visible'] = True
+        self.state["visible"] = True
 
         # Cure
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_cured_healing_infected):
-                neighbor.state['id'] = 2  # Cured
+                neighbor.state["id"] = 2  # Cured
 
         # Vaccinate
         neutral_neighbors = self.get_neighboring_agents(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
-                neighbor.state['id'] = 3  # Vaccinated
+                neighbor.state["id"] = 3  # Vaccinated
 
         # Generate anti-rumor
         infected_neighbors_2 = self.get_neighboring_agents(state_id=1)
         for neighbor in infected_neighbors_2:
             if self.prob(self.prob_generate_anti_rumor):
-                neighbor.state['id'] = 2  # Cured
+                neighbor.state["id"] = 2  # Cured
 
     def beacon_off_behaviour(self):
-        self.state['visible'] = False
+        self.state["visible"] = False
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         if len(infected_neighbors) > 0:
-            self.state['id'] == 5  # Beacon on
+            self.state["id"] == 5  # Beacon on
 
     def beacon_on_behaviour(self):
-        self.state['visible'] = False
+        self.state["visible"] = False
         # Cure (M2 feature added)
         infected_neighbors = self.get_neighboring_agents(state_id=1)
         for neighbor in infected_neighbors:
             if self.prob(self.prob_generate_anti_rumor):
-                neighbor.state['id'] = 2  # Cured
+                neighbor.state["id"] = 2  # Cured
             neutral_neighbors_infected = neighbor.get_neighboring_agents(state_id=0)
             for neighbor in neutral_neighbors_infected:
                 if self.prob(self.prob_generate_anti_rumor):
-                    neighbor.state['id'] = 3  # Vaccinated
+                    neighbor.state["id"] = 3  # Vaccinated
             infected_neighbors_infected = neighbor.get_neighboring_agents(state_id=1)
             for neighbor in infected_neighbors_infected:
                 if self.prob(self.prob_generate_anti_rumor):
-                    neighbor.state['id'] = 2  # Cured
+                    neighbor.state["id"] = 2  # Cured
 
         # Vaccinate
         neutral_neighbors = self.get_neighboring_agents(state_id=0)
         for neighbor in neutral_neighbors:
             if self.prob(self.prob_cured_vaccinate_neutral):
-                neighbor.state['id'] = 3  # Vaccinated
+                neighbor.state["id"] = 3  # Vaccinated

soil/agents/SISaModel.py

@@ -6,25 +6,25 @@ class SISaModel(FSM):
     """
     Settings:
         neutral_discontent_spon_prob
-        
+
         neutral_discontent_infected_prob
-        
+
         neutral_content_spon_prob
-        
+
         neutral_content_infected_prob
-        
+
         discontent_neutral
-        
+
         discontent_content
-        
+
         variance_d_c
-        
+
         content_discontent
-        
+
         variance_c_d
-        
+
         content_neutral
-        
+
         standard_variance
     """
 
@@ -33,24 +33,32 @@ class SISaModel(FSM):
 
         random = np.random.default_rng(seed=self._seed)
 
-        self.neutral_discontent_spon_prob = random.normal(self.env['neutral_discontent_spon_prob'],
-                                                             self.env['standard_variance'])
-        self.neutral_discontent_infected_prob = random.normal(self.env['neutral_discontent_infected_prob'],
-                                                                 self.env['standard_variance'])
-        self.neutral_content_spon_prob = random.normal(self.env['neutral_content_spon_prob'],
-                                                          self.env['standard_variance'])
-        self.neutral_content_infected_prob = random.normal(self.env['neutral_content_infected_prob'],
-                                                              self.env['standard_variance'])
+        self.neutral_discontent_spon_prob = random.normal(
+            self.env["neutral_discontent_spon_prob"], self.env["standard_variance"]
+        )
+        self.neutral_discontent_infected_prob = random.normal(
+            self.env["neutral_discontent_infected_prob"], self.env["standard_variance"]
+        )
+        self.neutral_content_spon_prob = random.normal(
+            self.env["neutral_content_spon_prob"], self.env["standard_variance"]
+        )
+        self.neutral_content_infected_prob = random.normal(
+            self.env["neutral_content_infected_prob"], self.env["standard_variance"]
+        )
 
-        self.discontent_neutral = random.normal(self.env['discontent_neutral'],
-                                                   self.env['standard_variance'])
-        self.discontent_content = random.normal(self.env['discontent_content'],
-                                                   self.env['variance_d_c'])
+        self.discontent_neutral = random.normal(
+            self.env["discontent_neutral"], self.env["standard_variance"]
+        )
+        self.discontent_content = random.normal(
+            self.env["discontent_content"], self.env["variance_d_c"]
+        )
 
-        self.content_discontent = random.normal(self.env['content_discontent'],
-                                                   self.env['variance_c_d'])
-        self.content_neutral = random.normal(self.env['content_neutral'],
-                                                self.env['standard_variance'])
+        self.content_discontent = random.normal(
+            self.env["content_discontent"], self.env["variance_c_d"]
+        )
+        self.content_neutral = random.normal(
+            self.env["content_neutral"], self.env["standard_variance"]
+        )
 
     @state
     def neutral(self):
@@ -88,7 +96,9 @@ class SISaModel(FSM):
             return self.neutral
 
         # Superinfected
-        discontent_neighbors = self.count_neighboring_agents(state_id=self.discontent.id)
+        discontent_neighbors = self.count_neighboring_agents(
+            state_id=self.discontent.id
+        )
         if self.prob(scontent_neighbors * self.content_discontent):
             self.discontent
         return self.content

soil/agents/SentimentCorrelationModel.py

@@ -5,27 +5,31 @@ class SentimentCorrelationModel(BaseAgent):
     """
     Settings:
         outside_effects_prob
-        
+
         anger_prob
-        
+
         joy_prob
-        
+
         sadness_prob
-        
+
         disgust_prob
     """
 
     def __init__(self, environment, unique_id=0, state=()):
         super().__init__(model=environment, unique_id=unique_id, state=state)
-        self.outside_effects_prob = environment.environment_params['outside_effects_prob']
-        self.anger_prob = environment.environment_params['anger_prob']
-        self.joy_prob = environment.environment_params['joy_prob']
-        self.sadness_prob = environment.environment_params['sadness_prob']
-        self.disgust_prob = environment.environment_params['disgust_prob']
-        self.state['time_awareness'] = []
+        self.outside_effects_prob = environment.environment_params[
+            "outside_effects_prob"
+        ]
+        self.anger_prob = environment.environment_params["anger_prob"]
+        self.joy_prob = environment.environment_params["joy_prob"]
+        self.sadness_prob = environment.environment_params["sadness_prob"]
+        self.disgust_prob = environment.environment_params["disgust_prob"]
+        self.state["time_awareness"] = []
         for i in range(4):  # In this model we have 4 sentiments
-            self.state['time_awareness'].append(0)  # 0-> Anger, 1-> joy, 2->sadness, 3 -> disgust
-        self.state['sentimentCorrelation'] = 0
+            self.state["time_awareness"].append(
+                0
+            )  # 0-> Anger, 1-> joy, 2->sadness, 3 -> disgust
+        self.state["sentimentCorrelation"] = 0
 
     def step(self):
         self.behaviour()
@@ -39,63 +43,73 @@ class SentimentCorrelationModel(BaseAgent):
 
         angry_neighbors = self.get_neighboring_agents(state_id=1)
         for x in angry_neighbors:
-            if x.state['time_awareness'][0] > (self.env.now-500):
+            if x.state["time_awareness"][0] > (self.env.now - 500):
                 angry_neighbors_1_time_step.append(x)
         num_neighbors_angry = len(angry_neighbors_1_time_step)
 
         joyful_neighbors = self.get_neighboring_agents(state_id=2)
         for x in joyful_neighbors:
-            if x.state['time_awareness'][1] > (self.env.now-500):
+            if x.state["time_awareness"][1] > (self.env.now - 500):
                 joyful_neighbors_1_time_step.append(x)
         num_neighbors_joyful = len(joyful_neighbors_1_time_step)
 
         sad_neighbors = self.get_neighboring_agents(state_id=3)
         for x in sad_neighbors:
-            if x.state['time_awareness'][2] > (self.env.now-500):
+            if x.state["time_awareness"][2] > (self.env.now - 500):
                 sad_neighbors_1_time_step.append(x)
         num_neighbors_sad = len(sad_neighbors_1_time_step)
 
         disgusted_neighbors = self.get_neighboring_agents(state_id=4)
         for x in disgusted_neighbors:
-            if x.state['time_awareness'][3] > (self.env.now-500):
+            if x.state["time_awareness"][3] > (self.env.now - 500):
                 disgusted_neighbors_1_time_step.append(x)
         num_neighbors_disgusted = len(disgusted_neighbors_1_time_step)
 
-        anger_prob = self.anger_prob+(len(angry_neighbors_1_time_step)*self.anger_prob)
-        joy_prob = self.joy_prob+(len(joyful_neighbors_1_time_step)*self.joy_prob)
-        sadness_prob = self.sadness_prob+(len(sad_neighbors_1_time_step)*self.sadness_prob)
-        disgust_prob = self.disgust_prob+(len(disgusted_neighbors_1_time_step)*self.disgust_prob)
+        anger_prob = self.anger_prob + (
+            len(angry_neighbors_1_time_step) * self.anger_prob
+        )
+        joy_prob = self.joy_prob + (len(joyful_neighbors_1_time_step) * self.joy_prob)
+        sadness_prob = self.sadness_prob + (
+            len(sad_neighbors_1_time_step) * self.sadness_prob
+        )
+        disgust_prob = self.disgust_prob + (
+            len(disgusted_neighbors_1_time_step) * self.disgust_prob
+        )
         outside_effects_prob = self.outside_effects_prob
 
         num = self.random.random()
 
-        if num<outside_effects_prob:
-            self.state['id'] = self.random.randint(1, 4)
+        if num < outside_effects_prob:
+            self.state["id"] = self.random.randint(1, 4)
 
-            self.state['sentimentCorrelation'] = self.state['id'] # It is stored when it has been infected for the dynamic network
-            self.state['time_awareness'][self.state['id']-1] = self.env.now
-            self.state['sentiment'] = self.state['id']
+            self.state["sentimentCorrelation"] = self.state[
+                "id"
+            ]  # It is stored when it has been infected for the dynamic network
+            self.state["time_awareness"][self.state["id"] - 1] = self.env.now
+            self.state["sentiment"] = self.state["id"]
 
+        if num < anger_prob:
 
-        if(num<anger_prob):
+            self.state["id"] = 1
+            self.state["sentimentCorrelation"] = 1
+            self.state["time_awareness"][self.state["id"] - 1] = self.env.now
+        elif num < joy_prob + anger_prob and num > anger_prob:
 
-            self.state['id'] = 1
-            self.state['sentimentCorrelation'] = 1
-            self.state['time_awareness'][self.state['id']-1] = self.env.now
-        elif (num<joy_prob+anger_prob and num>anger_prob):
+            self.state["id"] = 2
+            self.state["sentimentCorrelation"] = 2
+            self.state["time_awareness"][self.state["id"] - 1] = self.env.now
+        elif num < sadness_prob + anger_prob + joy_prob and num > joy_prob + anger_prob:
 
-            self.state['id'] = 2
-            self.state['sentimentCorrelation'] = 2
-            self.state['time_awareness'][self.state['id']-1] = self.env.now
-        elif (num<sadness_prob+anger_prob+joy_prob and num>joy_prob+anger_prob):
+            self.state["id"] = 3
+            self.state["sentimentCorrelation"] = 3
+            self.state["time_awareness"][self.state["id"] - 1] = self.env.now
+        elif (
+            num < disgust_prob + sadness_prob + anger_prob + joy_prob
+            and num > sadness_prob + anger_prob + joy_prob
+        ):
 
-            self.state['id'] = 3
-            self.state['sentimentCorrelation'] = 3
-            self.state['time_awareness'][self.state['id']-1] = self.env.now
-        elif (num<disgust_prob+sadness_prob+anger_prob+joy_prob and num>sadness_prob+anger_prob+joy_prob):
+            self.state["id"] = 4
+            self.state["sentimentCorrelation"] = 4
+            self.state["time_awareness"][self.state["id"] - 1] = self.env.now
 
-            self.state['id'] = 4
-            self.state['sentimentCorrelation'] = 4
-            self.state['time_awareness'][self.state['id']-1] = self.env.now
-
-        self.state['sentiment'] = self.state['id']
+        self.state["sentiment"] = self.state["id"]

soil/agents/__init__.py

@@ -20,13 +20,13 @@ from typing import Dict, List
 from .. import serialization, utils, time, config
 
 
-
 def as_node(agent):
     if isinstance(agent, BaseAgent):
         return agent.id
     return agent
 
-IGNORED_FIELDS = ('model', 'logger')
+
+IGNORED_FIELDS = ("model", "logger")
 
 
 class DeadAgent(Exception):
@@ -43,13 +43,18 @@ class MetaAgent(ABCMeta):
                 defaults.update(i._defaults)
 
         new_nmspc = {
-            '_defaults': defaults,
+            "_defaults": defaults,
         }
 
         for attr, func in namespace.items():
-            if isinstance(func, types.FunctionType) or isinstance(func, property) or attr[0] == '_':
+            if (
+                isinstance(func, types.FunctionType)
+                or isinstance(func, property)
+                or isinstance(func, classmethod)
+                or attr[0] == "_"
+            ):
                 new_nmspc[attr] = func
-            elif attr == 'defaults':
+            elif attr == "defaults":
                 defaults.update(func)
             else:
                 defaults[attr] = copy(func)
@@ -69,12 +74,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
     Any attribute that is not preceded by an underscore (`_`) will also be added to its state.
     """
 
-    def __init__(self,
-                 unique_id,
-                 model,
-                 name=None,
-                 interval=None,
-                 **kwargs):
+    def __init__(self, unique_id, model, name=None, interval=None, **kwargs):
         # Check for REQUIRED arguments
         # Initialize agent parameters
         if isinstance(unique_id, MesaAgent):
@@ -82,16 +82,19 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         assert isinstance(unique_id, int)
         super().__init__(unique_id=unique_id, model=model)
 
-        self.name = str(name) if name else'{}[{}]'.format(type(self).__name__, self.unique_id)
-
+        self.name = (
+            str(name) if name else "{}[{}]".format(type(self).__name__, self.unique_id)
+        )
 
         self.alive = True
 
-        self.interval = interval or self.get('interval', 1)
-        logger = utils.logger.getChild(getattr(self.model, 'id', self.model)).getChild(self.name)
-        self.logger = logging.LoggerAdapter(logger, {'agent_name': self.name})
+        self.interval = interval or self.get("interval", 1)
+        logger = utils.logger.getChild(getattr(self.model, "id", self.model)).getChild(
+            self.name
+        )
+        self.logger = logging.LoggerAdapter(logger, {"agent_name": self.name})
 
-        if hasattr(self, 'level'):
+        if hasattr(self, "level"):
             self.logger.setLevel(self.level)
 
         for (k, v) in self._defaults.items():
@@ -113,27 +116,26 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
     def id(self):
         return self.unique_id
 
-    @property
-    def state(self):
-        '''
-        Return the agent itself, which behaves as a dictionary.
-
-        This method shouldn't be used, but is kept here for backwards compatibility.
-        '''
-        return self
-
-    @state.setter
-    def state(self, value):
-        if not value:
-            return
-        for k, v in value.items():
-            self[k] = v
+    @classmethod
+    def from_dict(cls, model, attrs, warn_extra=True):
+        ignored = {}
+        args = {}
+        for k, v in attrs.items():
+            if k in inspect.signature(cls).parameters:
+                args[k] = v
+            else:
+                ignored[k] = v
+        if ignored and warn_extra:
+            utils.logger.info(
+                f"Ignoring the following arguments for agent class { agent_class.__name__ }: { ignored }"
+            )
+        return cls(model=model, **args)
 
     def __getitem__(self, key):
         try:
             return getattr(self, key)
         except AttributeError:
-            raise KeyError(f'key {key}  not found in agent')
+            raise KeyError(f"key {key}  not found in agent")
 
     def __delitem__(self, key):
         return delattr(self, key)
@@ -151,7 +153,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         return self.items()
 
     def keys(self):
-        return (k for k in self.__dict__ if k[0] != '_' and k not in IGNORED_FIELDS)
+        return (k for k in self.__dict__ if k[0] != "_" and k not in IGNORED_FIELDS)
 
     def items(self, keys=None, skip=None):
         keys = keys if keys is not None else self.keys()
@@ -159,7 +161,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         if skip:
             return filter(lambda x: x[0] not in skip, it)
         return it
-        
+
     def get(self, key, default=None):
         return self[key] if key in self else default
 
@@ -172,7 +174,7 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
             return None
 
     def die(self):
-        self.info(f'agent dying')
+        self.info(f"agent dying")
         self.alive = False
         return time.NEVER
 
@@ -189,9 +191,9 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         for k, v in kwargs:
             message += " {k}={v} ".format(k, v)
         extra = {}
-        extra['now'] = self.now
-        extra['unique_id'] = self.unique_id
-        extra['agent_name'] = self.name
+        extra["now"] = self.now
+        extra["unique_id"] = self.unique_id
+        extra["agent_name"] = self.name
         return self.logger.log(level, message, extra=extra)
 
     def debug(self, *args, **kwargs):
@@ -217,10 +219,10 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
         content = dict(self.items(keys=keys))
         if pretty and content:
             d = content
-            content = '\n'
+            content = "\n"
             for k, v in d.items():
-                content += f'- {k}: {v}\n'
-            content = textwrap.indent(content, '    ')
+                content += f"- {k}: {v}\n"
+            content = textwrap.indent(content, "    ")
         return f"{repr(self)}{content}"
 
     def __repr__(self):
@@ -228,32 +230,43 @@ class BaseAgent(MesaAgent, MutableMapping, metaclass=MetaAgent):
 
 
 class NetworkAgent(BaseAgent):
-
     def __init__(self, *args, topology, node_id, **kwargs):
         super().__init__(*args, **kwargs)
 
-        self.topology = topology
-        self.node_id = node_id
-        self.G = self.model.topologies[topology]
+        assert topology is not None
+        assert node_id is not None
+        self.G = topology
         assert self.G
+        self.node_id = node_id
 
     def count_neighboring_agents(self, state_id=None, **kwargs):
         return len(self.get_neighboring_agents(state_id=state_id, **kwargs))
 
-    def get_neighboring_agents(self, state_id=None, **kwargs):
-        return self.get_agents(limit_neighbors=True, state_id=state_id, **kwargs)
+    def get_neighboring_agents(self, **kwargs):
+        return list(self.iter_agents(limit_neighbors=True, **kwargs))
 
-    def iter_agents(self, unique_id=None, limit_neighbors=False, **kwargs):
+    def add_edge(self, other):
+        self.topology.add_edge(self.node_id, other.node_id)
+
+    @property
+    def node(self):
+        return self.topology.nodes[self.node_id]
+
+    def iter_agents(self, unique_id=None, *, limit_neighbors=False, **kwargs):
         unique_ids = None
         if isinstance(unique_id, list):
             unique_ids = set(unique_id)
         elif unique_id is not None:
-            unique_ids = set([unique_id,])
+            unique_ids = set(
+                [
+                    unique_id,
+                ]
+            )
 
         if limit_neighbors:
             neighbor_ids = set()
             for node_id in self.G.neighbors(self.node_id):
-                if self.G.nodes[node_id].get('agent_id') is not None:
+                if self.G.nodes[node_id].get("agent") is not None:
                     neighbor_ids.add(node_id)
             if unique_ids:
                 unique_ids = unique_ids & neighbor_ids
@@ -266,7 +279,9 @@ class NetworkAgent(BaseAgent):
 
     def subgraph(self, center=True, **kwargs):
         include = [self] if center else []
-        G = self.G.subgraph(n.node_id for n in list(self.get_agents(**kwargs)+include))
+        G = self.G.subgraph(
+            n.node_id for n in list(self.get_agents(**kwargs) + include)
+        )
         return G
 
     def remove_node(self):
@@ -274,11 +289,19 @@ class NetworkAgent(BaseAgent):
 
     def add_edge(self, other, edge_attr_dict=None, *edge_attrs):
         if self.node_id not in self.G.nodes(data=False):
-            raise ValueError('{} not in list of existing agents in the network'.format(self.unique_id))
+            raise ValueError(
+                "{} not in list of existing agents in the network".format(
+                    self.unique_id
+                )
+            )
         if other.node_id not in self.G.nodes(data=False):
-            raise ValueError('{} not in list of existing agents in the network'.format(other))
+            raise ValueError(
+                "{} not in list of existing agents in the network".format(other)
+            )
 
-        self.G.add_edge(self.node_id, other.node_id, edge_attr_dict=edge_attr_dict, *edge_attrs)
+        self.G.add_edge(
+            self.node_id, other.node_id, edge_attr_dict=edge_attr_dict, *edge_attrs
+        )
 
     def die(self, remove=True):
         if remove:
@@ -288,11 +311,11 @@ class NetworkAgent(BaseAgent):
 
 def state(name=None):
     def decorator(func, name=None):
-        '''
+        """
         A state function should return either a state id, or a tuple (state_id, when)
         The default value for state_id is the current state id.
         The default value for when is the interval defined in the environment.
-        '''
+        """
         if inspect.isgeneratorfunction(func):
             orig_func = func
 
@@ -342,32 +365,38 @@ class MetaFSM(MetaAgent):
 
         # Add new states
         for attr, func in namespace.items():
-            if hasattr(func, 'id'):
+            if hasattr(func, "id"):
                 if func.is_default:
                     default_state = func
                 states[func.id] = func
 
-        namespace.update({
-            '_default_state': default_state,
-            '_states': states,
-        })
+        namespace.update(
+            {
+                "_default_state": default_state,
+                "_states": states,
+            }
+        )
 
-        return super(MetaFSM, mcls).__new__(mcls=mcls, name=name, bases=bases, namespace=namespace)
+        return super(MetaFSM, mcls).__new__(
+            mcls=mcls, name=name, bases=bases, namespace=namespace
+        )
 
 
 class FSM(BaseAgent, metaclass=MetaFSM):
     def __init__(self, *args, **kwargs):
         super(FSM, self).__init__(*args, **kwargs)
-        if not hasattr(self, 'state_id'):
+        if not hasattr(self, "state_id"):
             if not self._default_state:
-                raise ValueError('No default state specified for {}'.format(self.unique_id))
+                raise ValueError(
+                    "No default state specified for {}".format(self.unique_id)
+                )
             self.state_id = self._default_state.id
 
         self._coroutine = None
         self.set_state(self.state_id)
 
     def step(self):
-        self.debug(f'Agent {self.unique_id} @ state {self.state_id}')
+        self.debug(f"Agent {self.unique_id} @ state {self.state_id}")
         default_interval = super().step()
 
         next_state = self._states[self.state_id](self)
@@ -380,7 +409,9 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             elif len(when) == 1:
                 when = when[0]
             else:
-                raise ValueError('Too many values returned. Only state (and time) allowed')
+                raise ValueError(
+                    "Too many values returned. Only state (and time) allowed"
+                )
         except TypeError:
             pass
 
@@ -390,10 +421,10 @@ class FSM(BaseAgent, metaclass=MetaFSM):
         return when or default_interval
 
     def set_state(self, state, when=None):
-        if hasattr(state, 'id'):
+        if hasattr(state, "id"):
             state = state.id
         if state not in self._states:
-            raise ValueError('{} is not a valid state'.format(state))
+            raise ValueError("{} is not a valid state".format(state))
         self.state_id = state
         if when is not None:
             self.model.schedule.add(self, when=when)
@@ -408,23 +439,22 @@ class FSM(BaseAgent, metaclass=MetaFSM):
 
 
 def prob(prob, random):
-    '''
+    """
     A true/False uniform distribution with a given probability.
     To be used like this:
 
     .. code-block:: python
-          
+
           if prob(0.3):
               do_something()
 
-    '''
+    """
     r = random.random()
     return r < prob
 
 
-def calculate_distribution(network_agents=None,
-                           agent_class=None):
-    '''
+def calculate_distribution(network_agents=None, agent_class=None):
+    """
     Calculate the threshold values (thresholds for a uniform distribution)
     of an agent distribution given the weights of each agent type.
 
@@ -447,26 +477,28 @@ def calculate_distribution(network_agents=None,
 
     In this example, 20% of the nodes will be marked as type
     'agent_class_1'.
-    '''
+    """
     if network_agents:
-        network_agents = [deepcopy(agent) for agent in network_agents if not hasattr(agent, 'id')]
+        network_agents = [
+            deepcopy(agent) for agent in network_agents if not hasattr(agent, "id")
+        ]
     elif agent_class:
-        network_agents = [{'agent_class': agent_class}]
+        network_agents = [{"agent_class": agent_class}]
     else:
-        raise ValueError('Specify a distribution or a default agent type')
+        raise ValueError("Specify a distribution or a default agent type")
 
     # Fix missing weights and incompatible types
     for x in network_agents:
-        x['weight'] = float(x.get('weight', 1))
+        x["weight"] = float(x.get("weight", 1))
 
     # Calculate the thresholds
-    total = sum(x['weight'] for x in network_agents)
+    total = sum(x["weight"] for x in network_agents)
     acc = 0
     for v in network_agents:
-        if 'ids' in v:
+        if "ids" in v:
             continue
-        upper = acc + (v['weight']/total)
-        v['threshold'] = [acc, upper]
+        upper = acc + (v["weight"] / total)
+        v["threshold"] = [acc, upper]
         acc = upper
     return network_agents
 
@@ -474,28 +506,29 @@ def calculate_distribution(network_agents=None,
 def serialize_type(agent_class, known_modules=[], **kwargs):
     if isinstance(agent_class, str):
         return agent_class
-    known_modules += ['soil.agents']
-    return serialization.serialize(agent_class, known_modules=known_modules, **kwargs)[1] # Get the name of the class
+    known_modules += ["soil.agents"]
+    return serialization.serialize(agent_class, known_modules=known_modules, **kwargs)[
+        1
+    ]  # Get the name of the class
 
 
 def serialize_definition(network_agents, known_modules=[]):
-    '''
+    """
     When serializing an agent distribution, remove the thresholds, in order
     to avoid cluttering the YAML definition file.
-    '''
+    """
     d = deepcopy(list(network_agents))
     for v in d:
-        if 'threshold' in v:
-            del v['threshold']
-        v['agent_class'] = serialize_type(v['agent_class'],
-                                         known_modules=known_modules)
+        if "threshold" in v:
+            del v["threshold"]
+        v["agent_class"] = serialize_type(v["agent_class"], known_modules=known_modules)
     return d
 
 
 def deserialize_type(agent_class, known_modules=[]):
     if not isinstance(agent_class, str):
         return agent_class
-    known = known_modules + ['soil.agents', 'soil.agents.custom' ]
+    known = known_modules + ["soil.agents", "soil.agents.custom"]
     agent_class = serialization.deserializer(agent_class, known_modules=known)
     return agent_class
 
@@ -503,12 +536,12 @@ def deserialize_type(agent_class, known_modules=[]):
 def deserialize_definition(ind, **kwargs):
     d = deepcopy(ind)
     for v in d:
-        v['agent_class'] = deserialize_type(v['agent_class'], **kwargs)
+        v["agent_class"] = deserialize_type(v["agent_class"], **kwargs)
     return d
 
 
 def _validate_states(states, topology):
-    '''Validate states to avoid ignoring states during initialization'''
+    """Validate states to avoid ignoring states during initialization"""
     states = states or []
     if isinstance(states, dict):
         for x in states:
@@ -519,7 +552,7 @@ def _validate_states(states, topology):
 
 
 def _convert_agent_classs(ind, to_string=False, **kwargs):
-    '''Convenience method to allow specifying agents by class or class name.'''
+    """Convenience method to allow specifying agents by class or class name."""
     if to_string:
         return serialize_definition(ind, **kwargs)
     return deserialize_definition(ind, **kwargs)
@@ -603,12 +636,10 @@ def _convert_agent_classs(ind, to_string=False, **kwargs):
 
 
 class AgentView(Mapping, Set):
-    """A lazy-loaded list of agents.
-    """
+    """A lazy-loaded list of agents."""
 
     __slots__ = ("_agents",)
 
-
     def __init__(self, agents):
         self._agents = agents
 
@@ -651,11 +682,20 @@ class AgentView(Mapping, Set):
         return f"{self.__class__.__name__}({self})"
 
 
-def filter_agents(agents, *id_args, unique_id=None, state_id=None, agent_class=None, ignore=None, state=None,
-                  limit=None, **kwargs):
-    '''
+def filter_agents(
+    agents,
+    *id_args,
+    unique_id=None,
+    state_id=None,
+    agent_class=None,
+    ignore=None,
+    state=None,
+    limit=None,
+    **kwargs,
+):
+    """
     Filter agents given as a dict, by the criteria given as arguments (e.g., certain type or state id).
-    '''
+    """
     assert isinstance(agents, dict)
 
     ids = []
@@ -688,7 +728,7 @@ def filter_agents(agents, *id_args, unique_id=None, state_id=None, agent_class=N
         f = filter(lambda x: x not in ignore, f)
 
     if state_id is not None:
-        f = filter(lambda agent: agent.get('state_id', None) in state_id, f)
+        f = filter(lambda agent: agent.get("state_id", None) in state_id, f)
 
     if agent_class is not None:
         f = filter(lambda agent: isinstance(agent, agent_class), f)
@@ -697,7 +737,7 @@ def filter_agents(agents, *id_args, unique_id=None, state_id=None, agent_class=N
     state.update(kwargs)
 
     for k, v in state.items():
-        f = filter(lambda agent: agent.state.get(k, None) == v, f)
+        f = filter(lambda agent: getattr(agent, k, None) == v, f)
 
     if limit is not None:
         f = islice(f, limit)
@@ -705,123 +745,143 @@ def filter_agents(agents, *id_args, unique_id=None, state_id=None, agent_class=N
     yield from f
 
 
-def from_config(cfg: config.AgentConfig, random, topologies: Dict[str, nx.Graph] = None) -> List[Dict[str, Any]]:
-    '''
+def from_config(
+    cfg: config.AgentConfig, random, topology: nx.Graph = None
+) -> List[Dict[str, Any]]:
+    """
     This function turns an agentconfig into a list of individual "agent specifications", which are just a dictionary
     with the parameters that the environment will use to construct each agent.
 
     This function does NOT return a list of agents, mostly because some attributes to the agent are not known at the
     time of calling this function, such as `unique_id`.
-    '''
+    """
     default = cfg or config.AgentConfig()
     if not isinstance(cfg, config.AgentConfig):
         cfg = config.AgentConfig(**cfg)
-    return _agents_from_config(cfg, topologies=topologies, random=random)
+    return _agents_from_config(cfg, topology=topology, random=random)
 
 
-def _agents_from_config(cfg: config.AgentConfig,
-                        topologies: Dict[str, nx.Graph],
-                        random) -> List[Dict[str, Any]]:
+def _agents_from_config(
+    cfg: config.AgentConfig, topology: nx.Graph, random
+) -> List[Dict[str, Any]]:
     if cfg and not isinstance(cfg, config.AgentConfig):
         cfg = config.AgentConfig(**cfg)
 
     agents = []
 
-    assigned = defaultdict(int)
+    assigned_total = 0
+    assigned_network = 0
 
     if cfg.fixed is not None:
-        agents, counts = _from_fixed(cfg.fixed, topology=cfg.topology, default=cfg)
-        assigned.update(counts)
+        agents, assigned_total, assigned_network = _from_fixed(
+            cfg.fixed, topology=cfg.topology, default=cfg
+        )
 
     n = cfg.n
 
     if cfg.distribution:
-        topo_size = {top: len(topologies[top]) for top in topologies}
+        topo_size = len(topology) if topology else 0
 
-        grouped = defaultdict(list)
+        networked = []
         total = []
 
         for d in cfg.distribution:
             if d.strategy == config.Strategy.topology:
-                topology = d.topology if ('topology' in d.__fields_set__) else cfg.topology
-                if not topology:
-                    raise ValueError('The "topology" strategy only works if the topology parameter is specified')
-                if topology not in topo_size:
-                    raise ValueError(f'Unknown topology selected: { topology }. Make sure the topology has been defined')
+                topo = d.topology if ("topology" in d.__fields_set__) else cfg.topology
+                if not topo:
+                    raise ValueError(
+                        'The "topology" strategy only works if the topology parameter is set to True'
+                    )
+                if not topo_size:
+                    raise ValueError(
+                        f"Topology does not have enough free nodes to assign one to the agent"
+                    )
 
-                grouped[topology].append(d)
+                networked.append(d)
 
             if d.strategy == config.Strategy.total:
                 if not cfg.n:
-                    raise ValueError('Cannot use the "total" strategy without providing the total number of agents')
+                    raise ValueError(
+                        'Cannot use the "total" strategy without providing the total number of agents'
+                    )
                 total.append(d)
 
-        
-        for (topo, distro) in grouped.items():
-            if not topologies or topo not in topo_size:
-                raise ValueError(
-                    'You need to specify a target number of agents for the distribution \
-                    or a configuration with a topology, along with a dictionary with \
-                    all the available topologies')
-            n = len(topologies[topo])
-            target = topo_size[topo] - assigned[topo]
-            new_agents = _from_distro(cfg.distribution, target,
-                                      topology=topo,
-                                      default=cfg,
-                                      random=random)
-            assigned[topo] += len(new_agents)
+        if networked:
+            new_agents = _from_distro(
+                networked,
+                n=topo_size - assigned_network,
+                topology=topo,
+                default=cfg,
+                random=random,
+            )
+            assigned_total += len(new_agents)
+            assigned_network += len(new_agents)
             agents += new_agents
 
         if total:
-          remaining = n - sum(assigned.values())
-          agents += _from_distro(total, remaining,
-                                topology='',  # DO NOT assign to any topology
-                                default=cfg,
-                                random=random)
+            remaining = n - assigned_total
+            agents += _from_distro(total, n=remaining, default=cfg, random=random)
 
-
-        if sum(assigned.values()) != sum(topo_size.values()):
-            utils.logger.warn(f'The total number of agents does not match the total number of nodes in '
-                              'every topology. This may be due to a definition error: assigned: '
-                              f'{ assigned } total sizes: { topo_size }')
+        if assigned_network < topo_size:
+            utils.logger.warn(
+                f"The total number of agents does not match the total number of nodes in "
+                "every topology. This may be due to a definition error: assigned: "
+                f"{ assigned } total size: { topo_size }"
+            )
 
     return agents
 
 
-def _from_fixed(lst: List[config.FixedAgentConfig], topology: str, default: config.SingleAgentConfig) -> List[Dict[str, Any]]:
+def _from_fixed(
+    lst: List[config.FixedAgentConfig],
+    topology: bool,
+    default: config.SingleAgentConfig,
+) -> List[Dict[str, Any]]:
     agents = []
 
-    counts = {}
+    counts_total = 0
+    counts_network = 0
 
     for fixed in lst:
         agent = {}
         if default:
             agent = default.state.copy()
         agent.update(fixed.state)
-        cls = serialization.deserialize(fixed.agent_class or (default and default.agent_class))
-        agent['agent_class'] = cls
-        topo = fixed.topology if ('topology' in fixed.__fields_set__) else topology or default.topology
+        cls = serialization.deserialize(
+            fixed.agent_class or (default and default.agent_class)
+        )
+        agent["agent_class"] = cls
+        topo = (
+            fixed.topology
+            if ("topology" in fixed.__fields_set__)
+            else topology or default.topology
+        )
 
         if topo:
-            agent['topology'] = topo
+            agent["topology"] = True
+            counts_network += 1
         if not fixed.hidden:
-            counts[topo] = counts.get(topo, 0) + 1
+            counts_total += 1
         agents.append(agent)
 
-    return agents, counts
+    return agents, counts_total, counts_network
 
 
-def _from_distro(distro: List[config.AgentDistro],
-                 n: int,
-                 topology: str,
-                 default: config.SingleAgentConfig,
-                 random) -> List[Dict[str, Any]]:
+def _from_distro(
+    distro: List[config.AgentDistro],
+    n: int,
+    topology: str,
+    default: config.SingleAgentConfig,
+    random,
+) -> List[Dict[str, Any]]:
 
     agents = []
 
     if n is None:
         if any(lambda dist: dist.n is None, distro):
-            raise ValueError('You must provide a total number of agents, or the number of each type')
+            raise ValueError(
+                "You must provide a total number of agents, or the number of each type"
+            )
         n = sum(dist.n for dist in distro)
 
     weights = list(dist.weight if dist.weight is not None else 1 for dist in distro)
@@ -834,30 +894,40 @@ def _from_distro(distro: List[config.AgentDistro],
     # So instead we calculate our own distribution to make sure the actual ratios are close to what we would expect
 
     # Calculate how many times each has to appear
-    indices = list(chain.from_iterable([idx] * int(n*chunk) for (idx, n) in enumerate(norm)))
+    indices = list(
+        chain.from_iterable([idx] * int(n * chunk) for (idx, n) in enumerate(norm))
+    )
 
     # Complete with random agents following the original weight distribution
     if len(indices) < n:
-        indices += random.choices(list(range(len(distro))), weights=[d.weight for d in distro], k=n-len(indices))
+        indices += random.choices(
+            list(range(len(distro))),
+            weights=[d.weight for d in distro],
+            k=n - len(indices),
+        )
 
     # Deserialize classes for efficiency
-    classes = list(serialization.deserialize(i.agent_class or default.agent_class) for i in distro)
+    classes = list(
+        serialization.deserialize(i.agent_class or default.agent_class) for i in distro
+    )
 
     # Add them in random order
     random.shuffle(indices)
 
-
     for idx in indices:
         d = distro[idx]
         agent = d.state.copy()
         cls = classes[idx]
-        agent['agent_class'] = cls
+        agent["agent_class"] = cls
         if default:
             agent.update(default.state)
-        # agent = cls(unique_id=agent_id, model=env, **state)
-        topology = d.topology if ('topology' in d.__fields_set__) else topology or default.topology
+        topology = (
+            d.topology
+            if ("topology" in d.__fields_set__)
+            else topology or default.topology
+        )
         if topology:
-            agent['topology'] = topology
+            agent["topology"] = topology
         agents.append(agent)
 
     return agents
@@ -876,4 +946,5 @@ try:
     from .Geo import Geo
 except ImportError:
     import sys
-    print('Could not load the Geo Agent, scipy is not installed', file=sys.stderr)
+
+    print("Could not load the Geo Agent, scipy is not installed", file=sys.stderr)

soil/config.py

@@ -19,6 +19,7 @@ import networkx as nx
 # Could use TypeAlias in python >= 3.10
 nodeId = int
 
+
 class Node(BaseModel):
     id: nodeId
     state: Optional[Dict[str, Any]] = {}
@@ -38,12 +39,12 @@ class Topology(BaseModel):
 
 class NetParams(BaseModel, extra=Extra.allow):
     generator: Union[Callable, str]
-    n: int 
+    n: int
 
 
 class NetConfig(BaseModel):
     params: Optional[NetParams]
-    topology: Optional[Union[Topology, nx.Graph]]
+    fixed: Optional[Union[Topology, nx.Graph]]
     path: Optional[str]
 
     class Config:
@@ -54,14 +55,15 @@ class NetConfig(BaseModel):
         return NetConfig(topology=None, params=None)
 
     @root_validator
-    def validate_all(cls,  values):
-        if 'params' not in values and 'topology' not in values:
-            raise ValueError('You must specify either a topology or the parameters to generate a graph')
+    def validate_all(cls, values):
+        if "params" not in values and "topology" not in values:
+            raise ValueError(
+                "You must specify either a topology or the parameters to generate a graph"
+            )
         return values
 
 
 class EnvConfig(BaseModel):
-
     @staticmethod
     def default():
         return EnvConfig()
@@ -70,7 +72,7 @@ class EnvConfig(BaseModel):
 class SingleAgentConfig(BaseModel):
     agent_class: Optional[Union[Type, str]] = None
     unique_id: Optional[int] = None
-    topology: Optional[str] = None
+    topology: Optional[bool] = False
     node_id: Optional[Union[int, str]] = None
     state: Optional[Dict[str, Any]] = {}
 
@@ -80,9 +82,11 @@ class FixedAgentConfig(SingleAgentConfig):
     hidden: Optional[bool] = False  # Do not count this agent towards total agent count
 
     @root_validator
-    def validate_all(cls,  values):
-        if values.get('agent_id', None) is not None and values.get('n', 1) > 1:
-            raise ValueError(f"An agent_id can only be provided when there is only one agent ({values.get('n')} given)")
+    def validate_all(cls, values):
+        if values.get("unique_id", None) is not None and values.get("n", 1) > 1:
+            raise ValueError(
+                f"An unique_id can only be provided when there is only one agent ({values.get('n')} given)"
+            )
         return values
 
 
@@ -91,8 +95,8 @@ class OverrideAgentConfig(FixedAgentConfig):
 
 
 class Strategy(Enum):
-    topology = 'topology'
-    total = 'total'
+    topology = "topology"
+    total = "total"
 
 
 class AgentDistro(SingleAgentConfig):
@@ -102,7 +106,6 @@ class AgentDistro(SingleAgentConfig):
 
 class AgentConfig(SingleAgentConfig):
     n: Optional[int] = None
-    topology: Optional[str]
     distribution: Optional[List[AgentDistro]] = None
     fixed: Optional[List[FixedAgentConfig]] = None
     override: Optional[List[OverrideAgentConfig]] = None
@@ -112,16 +115,20 @@ class AgentConfig(SingleAgentConfig):
         return AgentConfig()
 
     @root_validator
-    def validate_all(cls,  values):
-        if 'distribution' in values and ('n' not in values and 'topology' not in values):
-            raise ValueError("You need to provide the number of agents or a topology to extract the value from.")
+    def validate_all(cls, values):
+        if "distribution" in values and (
+            "n" not in values and "topology" not in values
+        ):
+            raise ValueError(
+                "You need to provide the number of agents or a topology to extract the value from."
+            )
         return values
 
 
 class Config(BaseModel, extra=Extra.allow):
-    version: Optional[str] = '1'
+    version: Optional[str] = "1"
 
-    name: str = 'Unnamed Simulation'
+    name: str = "Unnamed Simulation"
     description: Optional[str] = None
     group: str = None
     dir_path: Optional[str] = None
@@ -141,45 +148,48 @@ class Config(BaseModel, extra=Extra.allow):
     def from_raw(cls, cfg):
         if isinstance(cfg, Config):
             return cfg
-        if cfg.get('version', '1') == '1' and any(k in cfg for k in ['agents', 'agent_class', 'topology', 'environment_class']):
+        if cfg.get("version", "1") == "1" and any(
+            k in cfg for k in ["agents", "agent_class", "topology", "environment_class"]
+        ):
             return convert_old(cfg)
         return Config(**cfg)
 
 
 def convert_old(old, strict=True):
-    '''
+    """
     Try to convert old style configs into the new format.
 
     This is still a work in progress and might not work in many cases.
-    '''
+    """
 
-    utils.logger.warning('The old configuration format is deprecated. The converted file MAY NOT yield the right results')
+    utils.logger.warning(
+        "The old configuration format is deprecated. The converted file MAY NOT yield the right results"
+    )
 
     new = old.copy()
 
     network = {}
 
-    if 'topology' in old:
-        del new['topology']
-        network['topology'] = old['topology']
+    if "topology" in old:
+        del new["topology"]
+        network["topology"] = old["topology"]
 
-    if 'network_params' in old and old['network_params']:
-        del new['network_params']
-        for (k, v) in old['network_params'].items():
-            if k == 'path':
-                network['path'] = v
+    if "network_params" in old and old["network_params"]:
+        del new["network_params"]
+        for (k, v) in old["network_params"].items():
+            if k == "path":
+                network["path"] = v
             else:
-                network.setdefault('params', {})[k] = v
+                network.setdefault("params", {})[k] = v
 
-    topologies = {}
+    topology = None
     if network:
-        topologies['default'] = network
+        topology = network
 
-
-    agents = {'fixed': [], 'distribution': []}
+    agents = {"fixed": [], "distribution": []}
 
     def updated_agent(agent):
-        '''Convert an agent definition'''
+        """Convert an agent definition"""
         newagent = dict(agent)
         return newagent
 
@@ -187,80 +197,74 @@ def convert_old(old, strict=True):
     fixed = []
     override = []
 
-    if 'environment_agents' in new:
+    if "environment_agents" in new:
 
-        for agent in new['environment_agents']:
-            agent.setdefault('state', {})['group'] = 'environment'
-            if 'agent_id' in agent:
-                agent['state']['name'] = agent['agent_id']
-                del agent['agent_id']
-            agent['hidden'] = True
-            agent['topology'] = None
+        for agent in new["environment_agents"]:
+            agent.setdefault("state", {})["group"] = "environment"
+            if "agent_id" in agent:
+                agent["state"]["name"] = agent["agent_id"]
+                del agent["agent_id"]
+            agent["hidden"] = True
+            agent["topology"] = False
             fixed.append(updated_agent(agent))
-        del new['environment_agents']
+        del new["environment_agents"]
 
+    if "agent_class" in old:
+        del new["agent_class"]
+        agents["agent_class"] = old["agent_class"]
 
-    if 'agent_class' in old:
-        del new['agent_class']
-        agents['agent_class'] = old['agent_class']
+    if "default_state" in old:
+        del new["default_state"]
+        agents["state"] = old["default_state"]
 
-    if 'default_state' in old:
-        del new['default_state']
-        agents['state'] = old['default_state']
+    if "network_agents" in old:
+        agents["topology"] = True
 
-    if 'network_agents' in old:
-        agents['topology'] = 'default'
+        agents.setdefault("state", {})["group"] = "network"
 
-        agents.setdefault('state', {})['group'] = 'network'
-
-        for agent in new['network_agents']:
+        for agent in new["network_agents"]:
             agent = updated_agent(agent)
-            if 'agent_id' in agent:
-                agent['state']['name'] = agent['agent_id']
-                del agent['agent_id']
+            if "agent_id" in agent:
+                agent["state"]["name"] = agent["agent_id"]
+                del agent["agent_id"]
                 fixed.append(agent)
             else:
                 by_weight.append(agent)
-        del new['network_agents']
+        del new["network_agents"]
 
-    if 'agent_class' in old and (not fixed and not by_weight):
-        agents['topology'] = 'default'
-        by_weight = [{'agent_class': old['agent_class'], 'weight': 1}]
+    if "agent_class" in old and (not fixed and not by_weight):
+        agents["topology"] = True
+        by_weight = [{"agent_class": old["agent_class"], "weight": 1}]
 
-    
     # TODO: translate states properly
-    if 'states' in old:
-        del new['states']
-        states = old['states']
+    if "states" in old:
+        del new["states"]
+        states = old["states"]
         if isinstance(states, dict):
             states = states.items()
         else:
             states = enumerate(states)
         for (k, v) in states:
-            override.append({'filter': {'node_id': k},
-                             'state': v})
-
-    agents['override'] = override
-    agents['fixed'] = fixed
-    agents['distribution'] = by_weight
+            override.append({"filter": {"node_id": k}, "state": v})
 
+    agents["override"] = override
+    agents["fixed"] = fixed
+    agents["distribution"] = by_weight
 
     model_params = {}
-    if 'environment_params' in new:
-        del new['environment_params']
-        model_params = dict(old['environment_params'])
+    if "environment_params" in new:
+        del new["environment_params"]
+        model_params = dict(old["environment_params"])
 
-    if 'environment_class' in old:
-        del new['environment_class']
-        new['model_class'] = old['environment_class']
+    if "environment_class" in old:
+        del new["environment_class"]
+        new["model_class"] = old["environment_class"]
 
-    if 'dump' in old:
-        del new['dump']
-        new['dry_run'] = not old['dump']
+    if "dump" in old:
+        del new["dump"]
+        new["dry_run"] = not old["dump"]
 
-    model_params['topologies'] = topologies
-    model_params['agents'] = agents
+    model_params["topology"] = topology
+    model_params["agents"] = agents
 
-    return Config(version='2',
-                  model_params=model_params,
-                  **new)
+    return Config(version="2", model_params=model_params, **new)

soil/datacollection.py

@@ -1,6 +1,6 @@
 from mesa import DataCollector as MDC
 
-class SoilDataCollector(MDC):
 
+class SoilDataCollector(MDC):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)

soil/debugging.py

@@ -18,9 +18,9 @@ def wrapcmd(func):
         known = globals()
         known.update(self.curframe.f_globals)
         known.update(self.curframe.f_locals)
-        known['agent'] = known.get('self', None)
-        known['model'] = known.get('self', {}).get('model')
-        known['attrs'] = arg.strip().split()
+        known["agent"] = known.get("self", None)
+        known["model"] = known.get("self", {}).get("model")
+        known["attrs"] = arg.strip().split()
 
         exec(func.__code__, known, known)
 
@@ -29,10 +29,12 @@ def wrapcmd(func):
 
 class Debug(pdb.Pdb):
     def __init__(self, *args, skip_soil=False, **kwargs):
-        skip = kwargs.get('skip', [])
+        skip = kwargs.get("skip", [])
+        skip.append("soil")
         if skip_soil:
-            skip.append('soil.*')
-            skip.append('mesa.*')
+            skip.append("soil")
+            skip.append("soil.*")
+            skip.append("mesa.*")
         super(Debug, self).__init__(*args, skip=skip, **kwargs)
         self.prompt = "[soil-pdb] "
 
@@ -40,7 +42,7 @@ class Debug(pdb.Pdb):
     def _soil_agents(model, attrs=None, pretty=True, **kwargs):
         for agent in model.agents(**kwargs):
             d = agent
-            print(' - ' + indent(agent.to_str(keys=attrs, pretty=pretty), '  '))
+            print(" - " + indent(agent.to_str(keys=attrs, pretty=pretty), "  "))
 
     @wrapcmd
     def do_soil_agents():
@@ -50,14 +52,20 @@ class Debug(pdb.Pdb):
 
     @wrapcmd
     def do_soil_list():
-        return Debug._soil_agents(model, attrs=['state_id'], pretty=False)
+        return Debug._soil_agents(model, attrs=["state_id"], pretty=False)
 
     do_sl = do_soil_list
 
+    def do_continue_state(self, arg):
+        self.do_break_state(arg, temporary=True)
+        return self.do_continue("")
+
+    do_cs = do_continue_state
+
     @wrapcmd
-    def do_soil_self():
+    def do_soil_agent():
         if not agent:
-            print('No agent available')
+            print("No agent available")
             return
 
         keys = None
@@ -70,46 +78,56 @@ class Debug(pdb.Pdb):
 
         print(agent.to_str(pretty=True, keys=keys))
 
-    do_ss = do_soil_self
+    do_aa = do_soil_agent
 
-    def do_break_state(self, arg: str, temporary=False):
-        '''
+    def do_break_state(self, arg: str, instances=None, temporary=False):
+        """
         Break before a specified state is stepped into.
-        '''
+        """
 
         klass = None
-        state = arg.strip()
+        state = arg
         if not state:
             self.error("Specify at least a state name")
             return
 
-        comma = arg.find(':')
-        if comma > 0:
-            state = arg[comma+1:].lstrip()
-            klass = arg[:comma].rstrip()
-            klass = eval(klass,
-                         self.curframe.f_globals,
-                         self.curframe_locals)
+        state, *tokens = state.lstrip().split()
+        if tokens:
+            instances = list(eval(token) for token in tokens)
+
+        colon = state.find(":")
+
+        if colon > 0:
+            klass = state[:colon].rstrip()
+            state = state[colon + 1 :].strip()
+
+            print(klass, state, tokens)
+            klass = eval(klass, self.curframe.f_globals, self.curframe_locals)
 
         if klass:
             klasses = [klass]
         else:
-            klasses = [k for k in self.curframe.f_globals.values() if isinstance(k, type) and issubclass(k, FSM)]
-            print(klasses)
-            if not klasses:
-                self.error('No agent classes found')
-        
+            klasses = [
+                k
+                for k in self.curframe.f_globals.values()
+                if isinstance(k, type) and issubclass(k, FSM)
+            ]
+
+        if not klasses:
+            self.error("No agent classes found")
+
         for klass in klasses:
             try:
                 func = getattr(klass, state)
             except AttributeError:
+                self.error(f"State {state} not found in class {klass}")
                 continue
-            if hasattr(func, '__func__'):
+            if hasattr(func, "__func__"):
                 func = func.__func__
 
             code = func.__code__
-            #use co_name to identify the bkpt (function names
-            #could be aliased, but co_name is invariant)
+            # use co_name to identify the bkpt (function names
+            # could be aliased, but co_name is invariant)
             funcname = code.co_name
             lineno = code.co_firstlineno
             filename = code.co_filename
@@ -117,35 +135,56 @@ class Debug(pdb.Pdb):
             # Check for reasonable breakpoint
             line = self.checkline(filename, lineno)
             if not line:
-                raise ValueError('no line found')
+                raise ValueError("no line found")
                 # now set the break point
             cond = None
+            if instances:
+                cond = f"self.unique_id in { repr(instances) }"
+
             existing = self.get_breaks(filename, line)
             if existing:
-                self.message("Breakpoint already exists at %s:%d" %
-                              (filename, line))
+                self.message("Breakpoint already exists at %s:%d" % (filename, line))
                 continue
             err = self.set_break(filename, line, temporary, cond, funcname)
             if err:
                 self.error(err)
             else:
                 bp = self.get_breaks(filename, line)[-1]
-                self.message("Breakpoint %d at %s:%d" %
-                              (bp.number, bp.file, bp.line))
+                self.message("Breakpoint %d at %s:%d" % (bp.number, bp.file, bp.line))
+
     do_bs = do_break_state
 
+    def do_break_state_self(self, arg: str, temporary=False):
+        """
+        Break before a specified state is stepped into, for the current agent
+        """
+        agent = self.curframe.f_locals.get("self")
+        if not agent:
+            self.error("No current agent.")
+            self.error("Try this again when the debugger is stopped inside an agent")
+            return
 
-def setup(frame=None):
-    debugger = Debug()
+        arg = f"{agent.__class__.__name__}:{ arg } {agent.unique_id}"
+        return self.do_break_state(arg)
+
+    do_bss = do_break_state_self
+
+
+debugger = None
+
+
+def set_trace(frame=None, **kwargs):
+    global debugger
+    if debugger is None:
+        debugger = Debug(**kwargs)
     frame = frame or sys._getframe().f_back
     debugger.set_trace(frame)
 
-def debug_env():
-    if os.environ.get('SOIL_DEBUG'):
-        return setup(frame=sys._getframe().f_back)
 
 def post_mortem(traceback=None):
-    p = Debug()
+    global debugger
+    if debugger is None:
+        debugger = Debug(**kwargs)
     t = sys.exc_info()[2]
-    p.reset()
-    p.interaction(None, t)
+    debugger.reset()
+    debugger.interaction(None, t)

soil/environment.py

@@ -5,6 +5,7 @@ import sqlite3
 import math
 import random
 import logging
+import inspect
 
 from typing import Any, Dict, Optional, Union
 from collections import namedtuple
@@ -21,9 +22,6 @@ from mesa.datacollection import DataCollector
 from . import agents as agentmod, config, serialization, utils, time, network
 
 
-Record = namedtuple('Record', 'dict_id t_step key value')
-
-
 class BaseEnvironment(Model):
     """
     The environment is key in a simulation. It controls how agents interact,
@@ -37,20 +35,24 @@ class BaseEnvironment(Model):
     :meth:`soil.environment.Environment.get` method.
     """
 
-    def __init__(self,
-                 id='unnamed_env',
-                 seed='default',
-                 schedule=None,
-                 dir_path=None,
-                 interval=1,
-                 agent_class=None,
-                 agents: [tuple[type, Dict[str, Any]]] = {},
-                 agent_reporters: Optional[Any] = None,
-                 model_reporters: Optional[Any] = None,
-                 tables: Optional[Any] = None,
-                 **env_params):
+    def __init__(
+        self,
+        id="unnamed_env",
+        seed="default",
+        schedule=None,
+        dir_path=None,
+        interval=1,
+        agent_class=None,
+        agents: [tuple[type, Dict[str, Any]]] = {},
+        agent_reporters: Optional[Any] = None,
+        model_reporters: Optional[Any] = None,
+        tables: Optional[Any] = None,
+        **env_params,
+    ):
 
         super().__init__(seed=seed)
+        self.env_params = env_params or {}
+
         self.current_id = -1
 
         self.id = id
@@ -63,11 +65,8 @@ class BaseEnvironment(Model):
 
         self.agent_class = agent_class or agentmod.BaseAgent
 
-        self.init_agents(agents)
-
-        self.env_params = env_params or {}
-
         self.interval = interval
+        self.init_agents(agents)
 
         self.logger = utils.logger.getChild(self.id)
 
@@ -77,17 +76,27 @@ class BaseEnvironment(Model):
             tables=tables,
         )
 
-    def _read_single_agent(self, agent):
+    def _agent_from_dict(self, agent):
+        """
+        Translate an agent dictionary into an agent
+        """
         agent = dict(**agent)
-        cls = agent.pop('agent_class', None) or self.agent_class
-        unique_id = agent.pop('unique_id', None)
+        cls = agent.pop("agent_class", None) or self.agent_class
+        unique_id = agent.pop("unique_id", None)
         if unique_id is None:
             unique_id = self.next_id()
 
-        return serialization.deserialize(cls)(unique_id=unique_id,
-                                              model=self, **agent)
+        return serialization.deserialize(cls)(unique_id=unique_id, model=self, **agent)
 
     def init_agents(self, agents: Union[config.AgentConfig, [Dict[str, Any]]] = {}):
+        """
+        Initialize the agents in the model from either a `soil.config.AgentConfig` or a list of
+        dictionaries that each describes an agent.
+
+        If given a list of dictionaries, an agent will be created for each dictionary. The agent
+        class can be specified through the `agent_class` key. The rest of the items will be used
+        as parameters to the agent.
+        """
         if not agents:
             return
 
@@ -98,14 +107,11 @@ class BaseEnvironment(Model):
                 lst = config.AgentConfig(**agents)
             if lst.override:
                 override = lst.override
-            lst = agentmod.from_config(lst,
-                                       topologies=getattr(self, 'topologies', None),
-                                       random=self.random)
+            lst = self._agent_dict_from_config(lst)
 
-        #TODO: check override is working again. It cannot (easily) be part of agents.from_config anymore, 
+        # TODO: check override is working again. It cannot (easily) be part of agents.from_config anymore,
         # because it needs attribute such as unique_id, which are only present after init
-        new_agents = [self._read_single_agent(agent) for agent in lst]
-
+        new_agents = [self._agent_from_dict(agent) for agent in lst]
 
         for a in new_agents:
             self.schedule.add(a)
@@ -115,6 +121,8 @@ class BaseEnvironment(Model):
                 for attr, value in rule.state.items():
                     setattr(agent, attr, value)
 
+    def _agent_dict_from_config(self, cfg):
+        return agentmod.from_config(cfg, random=self.random)
 
     @property
     def agents(self):
@@ -122,7 +130,7 @@ class BaseEnvironment(Model):
 
     def find_one(self, *args, **kwargs):
         return agentmod.AgentView(self.schedule._agents).one(*args, **kwargs)
-    
+
     def count_agents(self, *args, **kwargs):
         return sum(1 for i in self.agents(*args, **kwargs))
 
@@ -130,15 +138,16 @@ class BaseEnvironment(Model):
     def now(self):
         if self.schedule:
             return self.schedule.time
-        raise Exception('The environment has not been scheduled, so it has no sense of time')
+        raise Exception(
+            "The environment has not been scheduled, so it has no sense of time"
+        )
 
-
-    def add_agent(self, agent_id, agent_class, **kwargs):
+    def add_agent(self, agent_class, unique_id=None, **kwargs):
         a = None
-        if agent_class:
-            a = agent_class(model=self,
-                            unique_id=agent_id,
-                            **kwargs)
+        if unique_id is None:
+            unique_id = self.next_id()
+
+        a = agent_class(model=self, unique_id=unique_id, **args)
 
         self.schedule.add(a)
         return a
@@ -151,16 +160,16 @@ class BaseEnvironment(Model):
         for k, v in kwargs:
             message += " {k}={v} ".format(k, v)
         extra = {}
-        extra['now'] = self.now
-        extra['id'] = self.id
+        extra["now"] = self.now
+        extra["id"] = self.id
         return self.logger.log(level, message, extra=extra)
 
     def step(self):
-        '''
+        """
         Advance one step in the simulation, and update the data collection and scheduler appropriately
-        '''
+        """
         super().step()
-        self.logger.info(f'--- Step {self.now:^5} ---')
+        self.logger.info(f"--- Step {self.now:^5} ---")
         self.schedule.step()
         self.datacollector.collect(self)
 
@@ -168,10 +177,10 @@ class BaseEnvironment(Model):
         return key in self.env_params
 
     def get(self, key, default=None):
-        '''
+        """
         Get the value of an environment attribute.
         Return `default` if the value is not set.
-        '''
+        """
         return self.env_params.get(key, default)
 
     def __getitem__(self, key):
@@ -180,123 +189,110 @@ class BaseEnvironment(Model):
     def __setitem__(self, key, value):
         return self.env_params.__setitem__(key, value)
 
-    def _agent_to_tuples(self, agent, now=None):
-        if now is None:
-            now = self.now
-        for k, v in agent.state.items():
-            yield Record(dict_id=agent.id,
-                          t_step=now,
-                          key=k,
-                          value=v)
-
-    def state_to_tuples(self, agent_id=None, now=None):
-        if now is None:
-            now = self.now
-
-        if agent_id:
-            agent = self.agents[agent_id]
-            yield from self._agent_to_tuples(agent, now)
-            return
-
-        for k, v in self.env_params.items():
-            yield Record(dict_id='env',
-                         t_step=now,
-                         key=k,
-                         value=v)
-        for agent in self.agents:
-            yield from self._agent_to_tuples(agent, now)
+    def __str__(self):
+        return str(self.env_params)
 
 
 class NetworkEnvironment(BaseEnvironment):
+    """
+    The NetworkEnvironment is an environment that includes one or more networkx.Graph intances
+    and methods to associate agents to nodes and vice versa.
+    """
 
-    def __init__(self, *args, topology: nx.Graph = None, topologies: Dict[str, config.NetConfig] = {}, **kwargs):
-        agents = kwargs.pop('agents', None)
+    def __init__(
+        self, *args, topology: Union[config.NetConfig, nx.Graph] = None, **kwargs
+    ):
+        agents = kwargs.pop("agents", None)
         super().__init__(*args, agents=None, **kwargs)
-        self._node_ids = {}
-        assert not hasattr(self, 'topologies')
-        if topology is not None:
-            if topologies:
-                raise ValueError('Please, provide either a single topology or a dictionary of them')
-            topologies = {'default': topology}
 
-        self.topologies = {}
-        for (name, cfg) in topologies.items():
-            self.set_topology(cfg=cfg, graph=name)
+        self._set_topology(topology)
 
         self.init_agents(agents)
 
+    def init_agents(self, *args, **kwargs):
+        """Initialize the agents from a"""
+        super().init_agents(*args, **kwargs)
+        for agent in self.schedule._agents.values():
+            if hasattr(agent, "node_id"):
+                self._init_node(agent)
 
-    def _read_single_agent(self, agent, unique_id=None):
+    def _init_node(self, agent):
+        """
+        Make sure the node for a given agent has the proper attributes.
+        """
+        self.G.nodes[agent.node_id]["agent"] = agent
+
+    def _agent_dict_from_config(self, cfg):
+        return agentmod.from_config(cfg, topology=self.G, random=self.random)
+
+    def _agent_from_dict(self, agent, unique_id=None):
         agent = dict(agent)
 
-        if agent.get('topology', None) is not None:
-            topology = agent.get('topology')
-            if unique_id is None:
-                unique_id = self.next_id()
-            if topology:
-                node_id = self.agent_to_node(unique_id, graph_name=topology, node_id=agent.get('node_id'))
-                agent['node_id'] = node_id
-                agent['topology'] = topology
-            agent['unique_id'] = unique_id
+        if not agent.get("topology", False):
+            return super()._agent_from_dict(agent)
 
-        return super()._read_single_agent(agent)
-        
+        if unique_id is None:
+            unique_id = self.next_id()
+        node_id = agent.get("node_id", None)
+        if node_id is None:
+            node_id = network.find_unassigned(self.G, random=self.random)
+        agent["node_id"] = node_id
+        agent["unique_id"] = unique_id
+        agent["topology"] = self.G
+        node_attrs = self.G.nodes[node_id]
+        node_attrs.update(agent)
+        agent = node_attrs
 
-    @property
-    def topology(self):
-        return self.topologies['default']
+        a = super()._agent_from_dict(agent)
+        self._init_node(a)
 
-    def set_topology(self, cfg=None, dir_path=None, graph='default'):
-        topology = cfg
-        if not isinstance(cfg, nx.Graph):
-            topology = network.from_config(cfg, dir_path=dir_path or self.dir_path)
+        return a
 
-        self.topologies[graph] = topology
+    def _set_topology(self, cfg=None, dir_path=None):
+        if cfg is None:
+            cfg = nx.Graph()
+        elif not isinstance(cfg, nx.Graph):
+            cfg = network.from_config(cfg, dir_path=dir_path or self.dir_path)
 
-    def topology_for(self, unique_id):
-        return self.topologies[self._node_ids[unique_id][0]]
+        self.G = cfg
 
     @property
     def network_agents(self):
-        yield from self.agents(agent_class=agentmod.NetworkAgent)
+        for a in self.schedule._agents:
+            if isinstance(a, agentmod.NetworkAgent):
+                yield a
 
-    def agent_to_node(self, unique_id, graph_name='default',
-                      node_id=None, shuffle=False):
-        node_id = network.agent_to_node(G=self.topologies[graph_name],
-                                        agent_id=unique_id,
-                                        node_id=node_id,
-                                        shuffle=shuffle,
-                                        random=self.random)
+    def add_node(self, agent_class, unique_id=None, node_id=None, **kwargs):
+        if unique_id is None:
+            unique_id = self.next_id()
+        if node_id is None:
+            node_id = network.find_unassigned(
+                G=self.G, shuffle=True, random=self.random
+            )
 
-        self._node_ids[unique_id] = (graph_name, node_id)
-        return node_id
+        if node_id in G.nodes:
+            self.G.nodes[node_id]["agent"] = None  # Reserve
+        else:
+            self.G.add_node(node_id)
 
-    def add_node(self, agent_class, topology, **kwargs):
-        unique_id = self.next_id()
-        self.topologies[topology].add_node(unique_id)
-        node_id = self.agent_to_node(unique_id=unique_id, node_id=unique_id, graph_name=topology)
-
-        a = self.add_agent(unique_id=unique_id, agent_class=agent_class, node_id=node_id, topology=topology, **kwargs)
-        a['visible'] = True
+        a = self.add_agent(
+            unique_id=unique_id, agent_class=agent_class, node_id=node_id, **kwargs
+        )
+        a["visible"] = True
         return a
 
-    def add_edge(self, agent1, agent2, start=None, graph='default', **attrs):
-        agent1 = agent1.node_id
-        agent2 = agent2.node_id
-        return self.topologies[graph].add_edge(agent1, agent2, start=start)
+    def agent_for_node_id(self, node_id):
+        return self.G.nodes[node_id].get("agent")
 
-    def add_agent(self, unique_id, state=None, graph='default', **kwargs):
-        node = self.topologies[graph].nodes[unique_id]
-        node_state = node.get('state', {})
-        if node_state:
-            node_state.update(state or {})
-            state = node_state
-        a = super().add_agent(unique_id, state=state, **kwargs)
-        node['agent'] = a
-        return a
-
-    def node_id_for(self, agent_id):
-        return self._node_ids[agent_id][1]
+    def populate_network(self, agent_class, weights=None, **agent_params):
+        if not hasattr(agent_class, "len"):
+            agent_class = [agent_class]
+            weights = None
+        for (node_id, node) in self.G.nodes(data=True):
+            if "agent" in node:
+                continue
+            a_class = self.random.choices(agent_class, weights)[0]
+            self.add_agent(node_id=node_id, agent_class=a_class, **agent_params)
 
 
 Environment = NetworkEnvironment

soil/exporters.py

@@ -1,4 +1,5 @@
 import os
+import sys
 from time import time as current_time
 from io import BytesIO
 from sqlalchemy import create_engine
@@ -9,7 +10,7 @@ import networkx as nx
 
 
 from .serialization import deserialize
-from .utils import open_or_reuse, logger, timer
+from .utils import try_backup, open_or_reuse, logger, timer
 
 
 from . import utils, network
@@ -23,54 +24,58 @@ class DryRunner(BytesIO):
 
     def write(self, txt):
         if self.__copy_to:
-            self.__copy_to.write('{}:::{}'.format(self.__fname, txt))
+            self.__copy_to.write("{}:::{}".format(self.__fname, txt))
         try:
             super().write(txt)
         except TypeError:
-            super().write(bytes(txt, 'utf-8'))
+            super().write(bytes(txt, "utf-8"))
 
     def close(self):
-        content = '(binary data not shown)'
+        content = "(binary data not shown)"
         try:
             content = self.getvalue().decode()
         except UnicodeDecodeError:
             pass
-        logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname, content))
+        logger.info(
+            "**Not** written to {} (dry run mode):\n\n{}\n\n".format(
+                self.__fname, content
+            )
+        )
         super().close()
 
 
 class Exporter:
-    '''
+    """
     Interface for all exporters. It is not necessary, but it is useful
     if you don't plan to implement all the methods.
-    '''
+    """
 
     def __init__(self, simulation, outdir=None, dry_run=None, copy_to=None):
         self.simulation = simulation
-        outdir = outdir or os.path.join(os.getcwd(), 'soil_output')
-        self.outdir = os.path.join(outdir,
-                                   simulation.group or '',
-                                   simulation.name)
+        outdir = outdir or os.path.join(os.getcwd(), "soil_output")
+        self.outdir = os.path.join(outdir, simulation.group or "", simulation.name)
         self.dry_run = dry_run
+        if copy_to is None and dry_run:
+            copy_to = sys.stdout
         self.copy_to = copy_to
 
     def sim_start(self):
-        '''Method to call when the simulation starts'''
+        """Method to call when the simulation starts"""
         pass
 
     def sim_end(self):
-        '''Method to call when the simulation ends'''
+        """Method to call when the simulation ends"""
         pass
 
     def trial_start(self, env):
-        '''Method to call when a trial start'''
+        """Method to call when a trial start"""
         pass
 
     def trial_end(self, env):
-        '''Method to call when a trial ends'''
+        """Method to call when a trial ends"""
         pass
 
-    def output(self, f, mode='w', **kwargs):
+    def output(self, f, mode="w", **kwargs):
         if self.dry_run:
             f = DryRunner(f, copy_to=self.copy_to)
         else:
@@ -83,97 +88,121 @@ class Exporter:
 
 
 class default(Exporter):
-    '''Default exporter. Writes sqlite results, as well as the simulation YAML'''
+    """Default exporter. Writes sqlite results, as well as the simulation YAML"""
 
     def sim_start(self):
-        if not self.dry_run:
-            logger.info('Dumping results to %s', self.outdir)
-            with self.output(self.simulation.name + '.dumped.yml') as f:
-                f.write(self.simulation.to_yaml())
-        else:
-            logger.info('NOT dumping results')
+        if self.dry_run:
+            logger.info("NOT dumping results")
+            return
+        logger.info("Dumping results to %s", self.outdir)
+        with self.output(self.simulation.name + ".dumped.yml") as f:
+            f.write(self.simulation.to_yaml())
+        self.dbpath = os.path.join(self.outdir, f"{self.simulation.name}.sqlite")
+        try_backup(self.dbpath, move=True)
 
     def trial_end(self, env):
-        if not self.dry_run:
-            with timer('Dumping simulation {} trial {}'.format(self.simulation.name,
-                                                               env.id)):
-                engine = create_engine('sqlite:///{}.sqlite'.format(env.id), echo=False)
+        if self.dry_run:
+            logger.info("Running in DRY_RUN mode, the database will NOT be created")
+            return
 
-                dc = env.datacollector
-                for (t, df) in get_dc_dfs(dc):
-                    df.to_sql(t, con=engine, if_exists='append')
+        with timer(
+            "Dumping simulation {} trial {}".format(self.simulation.name, env.id)
+        ):
+
+            engine = create_engine(f"sqlite:///{self.dbpath}", echo=False)
+
+            dc = env.datacollector
+            for (t, df) in get_dc_dfs(dc, trial_id=env.id):
+                df.to_sql(t, con=engine, if_exists="append")
 
 
-def get_dc_dfs(dc):
-    dfs = {'env': dc.get_model_vars_dataframe(),
-           'agents': dc.get_agent_vars_dataframe() }
+def get_dc_dfs(dc, trial_id=None):
+    dfs = {
+        "env": dc.get_model_vars_dataframe(),
+        "agents": dc.get_agent_vars_dataframe(),
+    }
     for table_name in dc.tables:
         dfs[table_name] = dc.get_table_dataframe(table_name)
-    yield from dfs.items() 
+    if trial_id:
+        for (name, df) in dfs.items():
+            df['trial_id'] = trial_id
+    yield from dfs.items()
 
 
 class csv(Exporter):
 
-    '''Export the state of each environment (and its agents) in a separate CSV file'''
+    """Export the state of each environment (and its agents) in a separate CSV file"""
+
     def trial_end(self, env):
-        with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.simulation.name,
-                                                                          env.id,
-                                                                          self.outdir)):
-            for (df_name, df) in get_dc_dfs(env.datacollector):
-                with self.output('{}.{}.csv'.format(env.id, df_name)) as f:
+        with timer(
+            "[CSV] Dumping simulation {} trial {} @ dir {}".format(
+                self.simulation.name, env.id, self.outdir
+            )
+        ):
+            for (df_name, df) in get_dc_dfs(env.datacollector, trial_id=env.id):
+                with self.output("{}.{}.csv".format(env.id, df_name)) as f:
                     df.to_csv(f)
 
 
-#TODO: reimplement GEXF exporting without history
+# TODO: reimplement GEXF exporting without history
 class gexf(Exporter):
     def trial_end(self, env):
         if self.dry_run:
-            logger.info('Not dumping GEXF in dry_run mode')
+            logger.info("Not dumping GEXF in dry_run mode")
             return
 
-        with timer('[GEXF] Dumping simulation {} trial {}'.format(self.simulation.name,
-                                                                  env.id)):
-            with self.output('{}.gexf'.format(env.id), mode='wb') as f:
+        with timer(
+            "[GEXF] Dumping simulation {} trial {}".format(self.simulation.name, env.id)
+        ):
+            with self.output("{}.gexf".format(env.id), mode="wb") as f:
                 network.dump_gexf(env.history_to_graph(), f)
                 self.dump_gexf(env, f)
 
 
 class dummy(Exporter):
-
     def sim_start(self):
-        with self.output('dummy', 'w') as f:
-            f.write('simulation started @ {}\n'.format(current_time()))
+        with self.output("dummy", "w") as f:
+            f.write("simulation started @ {}\n".format(current_time()))
 
     def trial_start(self, env):
-        with self.output('dummy', 'w') as f:
-            f.write('trial started@ {}\n'.format(current_time()))
+        with self.output("dummy", "w") as f:
+            f.write("trial started@ {}\n".format(current_time()))
 
     def trial_end(self, env):
-        with self.output('dummy', 'w') as f:
-            f.write('trial ended@ {}\n'.format(current_time()))
+        with self.output("dummy", "w") as f:
+            f.write("trial ended@ {}\n".format(current_time()))
 
     def sim_end(self):
-        with self.output('dummy', 'a') as f:
-            f.write('simulation ended @ {}\n'.format(current_time()))
+        with self.output("dummy", "a") as f:
+            f.write("simulation ended @ {}\n".format(current_time()))
+
 
 class graphdrawing(Exporter):
-
     def trial_end(self, env):
         # Outside effects
         f = plt.figure()
-        nx.draw(env.G, node_size=10, width=0.2, pos=nx.spring_layout(env.G, scale=100), ax=f.add_subplot(111))
-        with open('graph-{}.png'.format(env.id)) as f:
+        nx.draw(
+            env.G,
+            node_size=10,
+            width=0.2,
+            pos=nx.spring_layout(env.G, scale=100),
+            ax=f.add_subplot(111),
+        )
+        with open("graph-{}.png".format(env.id)) as f:
             f.savefig(f)
 
-'''
+
+"""
 Convert an environment into a NetworkX graph
-'''
+"""
+
+
 def env_to_graph(env, history=None):
     G = nx.Graph(env.G)
 
     for agent in env.network_agents:
 
-        attributes = {'agent': str(agent.__class__)}
+        attributes = {"agent": str(agent.__class__)}
         lastattributes = {}
         spells = []
         lastvisible = False
@@ -181,7 +210,7 @@ def env_to_graph(env, history=None):
         if not history:
             history = sorted(list(env.state_to_tuples()))
         for _, t_step, attribute, value in history:
-            if attribute == 'visible':
+            if attribute == "visible":
                 nowvisible = value
                 if nowvisible and not lastvisible:
                     laststep = t_step
@@ -190,7 +219,7 @@ def env_to_graph(env, history=None):
 
                 lastvisible = nowvisible
                 continue
-            key = 'attr_' + attribute
+            key = "attr_" + attribute
             if key not in attributes:
                 attributes[key] = list()
             if key not in lastattributes:

soil/network.py

@@ -9,6 +9,7 @@ import networkx as nx
 
 from . import config, serialization, basestring
 
+
 def from_config(cfg: config.NetConfig, dir_path: str = None):
     if not isinstance(cfg, config.NetConfig):
         cfg = config.NetConfig(**cfg)
@@ -19,60 +20,67 @@ def from_config(cfg: config.NetConfig, dir_path: str = None):
             path = os.path.join(dir_path, path)
         extension = os.path.splitext(path)[1][1:]
         kwargs = {}
-        if extension == 'gexf':
-            kwargs['version'] = '1.2draft'
-            kwargs['node_type'] = int
+        if extension == "gexf":
+            kwargs["version"] = "1.2draft"
+            kwargs["node_type"] = int
         try:
-            method = getattr(nx.readwrite, 'read_' + extension)
+            method = getattr(nx.readwrite, "read_" + extension)
         except AttributeError:
-            raise AttributeError('Unknown format')
+            raise AttributeError("Unknown format")
         return method(path, **kwargs)
 
     if cfg.params:
         net_args = cfg.params.dict()
-        net_gen = net_args.pop('generator')
+        net_gen = net_args.pop("generator")
 
         if dir_path not in sys.path:
             sys.path.append(dir_path)
 
-        method = serialization.deserializer(net_gen,
-                                            known_modules=['networkx.generators',])
+        method = serialization.deserializer(
+            net_gen,
+            known_modules=[
+                "networkx.generators",
+            ],
+        )
         return method(**net_args)
 
-    if isinstance(cfg.topology, config.Topology):
-        cfg = cfg.topology.dict()
+    if isinstance(cfg.fixed, config.Topology):
+        cfg = cfg.fixed.dict()
+
     if isinstance(cfg, str) or isinstance(cfg, dict):
         return nx.json_graph.node_link_graph(cfg)
 
     return nx.Graph()
 
 
-def agent_to_node(G, agent_id, node_id=None, shuffle=False, random=random):
-    '''
+def find_unassigned(G, shuffle=False, random=random):
+    """
     Link an agent to a node in a topology.
 
     If node_id is None, a node without an agent_id will be found.
-    '''
-    #TODO: test
-    if node_id is None:
-        candidates = list(G.nodes(data=True))
-        if shuffle:
-            random.shuffle(candidates)
-        for next_id, data in candidates:
-            if data.get('agent_id', None) is None:
-                node_id = next_id
-                break
+    """
+    # TODO: test
+    candidates = list(G.nodes(data=True))
+    if shuffle:
+        random.shuffle(candidates)
+    for next_id, data in candidates:
+        if "agent" not in data:
+            node_id = next_id
+            break
 
-    if node_id is None:
-        raise ValueError(f"Not enough nodes in topology to assign one to agent {agent_id}")
-    G.nodes[node_id]['agent_id'] = agent_id
     return node_id
 
 
 def dump_gexf(G, f):
     for node in G.nodes():
-        if 'pos' in G.nodes[node]:
-            G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
-            del (G.nodes[node]['pos'])
+        if "pos" in G.nodes[node]:
+            G.nodes[node]["viz"] = {
+                "position": {
+                    "x": G.nodes[node]["pos"][0],
+                    "y": G.nodes[node]["pos"][1],
+                    "z": 0.0,
+                }
+            }
+            del G.nodes[node]["pos"]
 
     nx.write_gexf(G, f, version="1.2draft")

soil/serialization.py

@@ -15,49 +15,14 @@ import networkx as nx
 from jinja2 import Template
 
 
-logger = logging.getLogger('soil')
-
-
-# def load_network(network_params, dir_path=None):
-#     G = nx.Graph()
-
-#     if not network_params:
-#         return G
-
-#     if 'path' in network_params:
-#         path = network_params['path']
-#         if dir_path and not os.path.isabs(path):
-#             path = os.path.join(dir_path, path)
-#         extension = os.path.splitext(path)[1][1:]
-#         kwargs = {}
-#         if extension == 'gexf':
-#             kwargs['version'] = '1.2draft'
-#             kwargs['node_type'] = int
-#         try:
-#             method = getattr(nx.readwrite, 'read_' + extension)
-#         except AttributeError:
-#             raise AttributeError('Unknown format')
-#         G = method(path, **kwargs)
-
-#     elif 'generator' in network_params:
-#         net_args = network_params.copy()
-#         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',])
-#         G = method(**net_args)
-
-#     return G
+logger = logging.getLogger("soil")
 
 
 def load_file(infile):
     folder = os.path.dirname(infile)
     if folder not in sys.path:
         sys.path.append(folder)
-    with open(infile, 'r') as f:
+    with open(infile, "r") as f:
         return list(chain.from_iterable(map(expand_template, load_string(f))))
 
 
@@ -66,14 +31,15 @@ def load_string(string):
 
 
 def expand_template(config):
-    if 'template' not in config:
+    if "template" not in config:
         yield config
         return
-    if 'vars' not in config:
-        raise ValueError(('You must provide a definition of variables'
-                          ' for the template.'))
+    if "vars" not in config:
+        raise ValueError(
+            ("You must provide a definition of variables" " for the template.")
+        )
 
-    template = config['template']
+    template = config["template"]
 
     if not isinstance(template, str):
         template = yaml.dump(template)
@@ -85,9 +51,9 @@ def expand_template(config):
     blank_str = template.render({k: 0 for k in params[0].keys()})
     blank = list(load_string(blank_str))
     if len(blank) > 1:
-        raise ValueError('Templates must not return more than one configuration')
-    if 'name' in blank[0]:
-        raise ValueError('Templates cannot be named, use group instead')
+        raise ValueError("Templates must not return more than one configuration")
+    if "name" in blank[0]:
+        raise ValueError("Templates cannot be named, use group instead")
 
     for ps in params:
         string = template.render(ps)
@@ -96,32 +62,32 @@ def expand_template(config):
 
 
 def params_for_template(config):
-    sampler_config = config.get('sampler', {'N': 100})
-    sampler = sampler_config.pop('method', 'SALib.sample.morris.sample')
+    sampler_config = config.get("sampler", {"N": 100})
+    sampler = sampler_config.pop("method", "SALib.sample.morris.sample")
     sampler = deserializer(sampler)
-    bounds = config['vars']['bounds']
+    bounds = config["vars"]["bounds"]
 
     problem = {
-        'num_vars': len(bounds),
-        'names': list(bounds.keys()),
-        'bounds': list(v for v in bounds.values())
+        "num_vars": len(bounds),
+        "names": list(bounds.keys()),
+        "bounds": list(v for v in bounds.values()),
     }
     samples = sampler(problem, **sampler_config)
 
-    lists = config['vars'].get('lists', {})
+    lists = config["vars"].get("lists", {})
     names = list(lists.keys())
     values = list(lists.values())
     combs = list(product(*values))
 
-    allnames = names + problem['names']
-    allvalues = [(list(i[0])+list(i[1])) for i in product(combs, samples)]
+    allnames = names + problem["names"]
+    allvalues = [(list(i[0]) + list(i[1])) for i in product(combs, samples)]
     params = list(map(lambda x: dict(zip(allnames, x)), allvalues))
     return params
 
 
 def load_files(*patterns, **kwargs):
     for pattern in patterns:
-        for i in glob(pattern, **kwargs):
+        for i in glob(pattern, **kwargs, recursive=True):
             for cfg in load_file(i):
                 path = os.path.abspath(i)
                 yield Config.from_raw(cfg), path
@@ -136,22 +102,24 @@ def load_config(cfg):
         yield from load_files(cfg)
 
 
-builtins = importlib.import_module('builtins')
+builtins = importlib.import_module("builtins")
 
-KNOWN_MODULES = ['soil', ]
+KNOWN_MODULES = [
+    "soil",
+]
 
 
 def name(value, known_modules=KNOWN_MODULES):
-    '''Return a name that can be imported, to serialize/deserialize an object'''
+    """Return a name that can be imported, to serialize/deserialize an object"""
     if value is None:
-        return 'None'
+        return "None"
     if not isinstance(value, type):  # Get the class name first
         value = type(value)
     tname = value.__name__
     if hasattr(builtins, tname):
         return tname
     modname = value.__module__
-    if modname == '__main__':
+    if modname == "__main__":
         return tname
     if known_modules and modname in known_modules:
         return tname
@@ -161,17 +129,17 @@ def name(value, known_modules=KNOWN_MODULES):
         module = importlib.import_module(kmod)
         if hasattr(module, tname):
             return tname
-    return '{}.{}'.format(modname, tname)
+    return "{}.{}".format(modname, tname)
 
 
 def serializer(type_):
-    if type_ != 'str' and hasattr(builtins, type_):
+    if type_ != "str" and hasattr(builtins, type_):
         return repr
     return lambda x: x
 
 
 def serialize(v, known_modules=KNOWN_MODULES):
-    '''Get a text representation of an object.'''
+    """Get a text representation of an object."""
     tname = name(v, known_modules=known_modules)
     func = serializer(tname)
     return func(v), tname
@@ -196,9 +164,9 @@ IS_CLASS = re.compile(r"<class '(.*)'>")
 def deserializer(type_, known_modules=KNOWN_MODULES):
     if type(type_) != str:  # Already deserialized
         return type_
-    if type_ == 'str':
-        return lambda x='': x
-    if type_ == 'None':
+    if type_ == "str":
+        return lambda x="": x
+    if type_ == "None":
         return lambda x=None: None
     if hasattr(builtins, type_):  # Check if it's a builtin type
         cls = getattr(builtins, type_)
@@ -208,8 +176,8 @@ def deserializer(type_, known_modules=KNOWN_MODULES):
         modname, tname = match.group(1).rsplit(".", 1)
         module = importlib.import_module(modname)
         cls = getattr(module, tname)
-        return getattr(cls, 'deserialize', cls)
-        
+        return getattr(cls, "deserialize", cls)
+
     # Otherwise, see if we can find the module and the class
     options = []
 
@@ -217,7 +185,7 @@ def deserializer(type_, known_modules=KNOWN_MODULES):
         if mod:
             options.append((mod, type_))
 
-    if '.' in type_:  # Fully qualified module
+    if "." in type_:  # Fully qualified module
         module, type_ = type_.rsplit(".", 1)
         options.append((module, type_))
 
@@ -226,27 +194,37 @@ def deserializer(type_, known_modules=KNOWN_MODULES):
         try:
             module = importlib.import_module(modname)
             cls = getattr(module, tname)
-            return getattr(cls, 'deserialize', cls)
+            return getattr(cls, "deserialize", cls)
         except (ImportError, AttributeError) as ex:
             errors.append((modname, tname, ex))
-    raise Exception('Could not find type {}. Tried: {}'.format(type_, errors))
+    raise ValueError('Could not find type "{}". Tried: {}'.format(type_, errors))
 
 
-def deserialize(type_, value=None, **kwargs):
-    '''Get an object from a text representation'''
+def deserialize(type_, value=None, globs=None, **kwargs):
+    """Get an object from a text representation"""
     if not isinstance(type_, str):
         return type_
-    des = deserializer(type_, **kwargs)
+    if globs and type_ in globs:
+        des = globs[type_]
+    else:
+        try:
+            des = deserializer(type_, **kwargs)
+        except ValueError as ex:
+            try:
+                des = eval(type_)
+            except Exception:
+                raise ex
     if value is None:
         return des
     return des(value)
 
 
 def deserialize_all(names, *args, known_modules=KNOWN_MODULES, **kwargs):
-    '''Return the list of deserialized objects'''
+    """Return the list of deserialized objects"""
+    # TODO: remove
+    print("SERIALIZATION", kwargs)
     objects = []
     for name in names:
         mod = deserialize(name, known_modules=known_modules)
         objects.append(mod(*args, **kwargs))
     return objects
-

soil/simulation.py

@@ -1,5 +1,5 @@
 import os
-from time import time as current_time, strftime 
+from time import time as current_time, strftime
 import importlib
 import sys
 import yaml
@@ -11,22 +11,21 @@ import networkx as nx
 from textwrap import dedent
 
 from dataclasses import dataclass, field, asdict
-from typing import Any, Dict, Union, Optional
+from typing import Any, Dict, Union, Optional, List
 
 
 from networkx.readwrite import json_graph
 from functools import partial
 import pickle
 
-from . import serialization, utils, basestring, agents
+from . import serialization, exporters, utils, basestring, agents
 from .environment import Environment
 from .utils import logger, run_and_return_exceptions
-from .exporters import default
 from .time import INFINITY
 from .config import Config, convert_old
 
 
-#TODO: change documentation for simulation
+# TODO: change documentation for simulation
 @dataclass
 class Simulation:
     """
@@ -35,74 +34,105 @@ class Simulation:
     config (optional): :class:`config.Config`
         name of the Simulation
 
-    kwargs: parameters to use to initialize a new configuration, if one has not been provided.
+    kwargs: parameters to use to initialize a new configuration, if one not been provided.
     """
-    version: str = '2'
-    name: str = 'Unnamed simulation'
-    description: Optional[str] = ''
+
+    version: str = "2"
+    name: str = "Unnamed simulation"
+    description: Optional[str] = ""
     group: str = None
-    model_class: Union[str, type] = 'soil.Environment'
+    model_class: Union[str, type] = "soil.Environment"
     model_params: dict = field(default_factory=dict)
     seed: str = field(default_factory=lambda: current_time())
     dir_path: str = field(default_factory=lambda: os.getcwd())
-    max_time: float = float('inf')
+    max_time: float = float("inf")
     max_steps: int = -1
     interval: int = 1
     num_trials: int = 3
+    parallel: Optional[bool] = None
+    exporters: Optional[List[str]] = field(default_factory=list)
+    outdir: Optional[str] = None
+    exporter_params: Optional[Dict[str, Any]] = field(default_factory=dict)
     dry_run: bool = False
     extra: Dict[str, Any] = field(default_factory=dict)
 
     @classmethod
-    def from_dict(cls, env):      
+    def from_dict(cls, env, **kwargs):
 
-        ignored = {k: v for k, v in env.items() 
-                   if k not in inspect.signature(cls).parameters}
+        ignored = {
+            k: v for k, v in env.items() if k not in inspect.signature(cls).parameters
+        }
 
-        kwargs = {k:v for k, v in env.items() if k not in ignored}
+        d = {k: v for k, v in env.items() if k not in ignored}
         if ignored:
-            kwargs.setdefault('extra', {}).update(ignored)
+            d.setdefault("extra", {}).update(ignored)
         if ignored:
             print(f'Warning: Ignoring these parameters (added to "extra"): { ignored }')
+        d.update(kwargs)
 
-        return cls(**kwargs)
+        return cls(**d)
 
     def run_simulation(self, *args, **kwargs):
         return self.run(*args, **kwargs)
 
     def run(self, *args, **kwargs):
-        '''Run the simulation and return the list of resulting environments'''
-        logger.info(dedent('''
+        """Run the simulation and return the list of resulting environments"""
+        logger.info(
+            dedent(
+                """
         Simulation:
         ---
-        ''') +
-        self.to_yaml())
+        """
+            )
+            + self.to_yaml()
+        )
         return list(self.run_gen(*args, **kwargs))
 
-    def run_gen(self, parallel=False, dry_run=False,
-                exporters=[default, ], outdir=None, exporter_params={},
-                log_level=None,
-                **kwargs):
-        '''Run the simulation and yield the resulting environments.'''
+    def run_gen(
+        self,
+        parallel=False,
+        dry_run=None,
+        exporters=None,
+        outdir=None,
+        exporter_params={},
+        log_level=None,
+        **kwargs,
+    ):
+        """Run the simulation and yield the resulting environments."""
         if log_level:
             logger.setLevel(log_level)
-        logger.info('Using exporters: %s', exporters or [])
-        logger.info('Output directory: %s', outdir)
-        exporters = serialization.deserialize_all(exporters,
-                                                  simulation=self,
-                                                  known_modules=['soil.exporters', ],
-                                                  dry_run=dry_run,
-                                                  outdir=outdir,
-                                                  **exporter_params)
+        outdir = outdir or self.outdir
+        logger.info("Using exporters: %s", exporters or [])
+        logger.info("Output directory: %s", outdir)
+        if dry_run is None:
+            dry_run = self.dry_run
+        if exporters is None:
+            exporters = self.exporters
+        if not exporter_params:
+            exporter_params = self.exporter_params
 
-        with utils.timer('simulation {}'.format(self.name)):
+        exporters = serialization.deserialize_all(
+            exporters,
+            simulation=self,
+            known_modules=[
+                "soil.exporters",
+            ],
+            dry_run=dry_run,
+            outdir=outdir,
+            **exporter_params,
+        )
+
+        with utils.timer("simulation {}".format(self.name)):
             for exporter in exporters:
                 exporter.sim_start()
 
-            for env in utils.run_parallel(func=self.run_trial,
-                                          iterable=range(int(self.num_trials)),
-                                          parallel=parallel,
-                                          log_level=log_level,
-                                          **kwargs):
+            for env in utils.run_parallel(
+                func=self.run_trial,
+                iterable=range(int(self.num_trials)),
+                parallel=parallel,
+                log_level=log_level,
+                **kwargs,
+            ):
 
                 for exporter in exporters:
                     exporter.trial_start(env)
@@ -115,28 +145,36 @@ class Simulation:
             for exporter in exporters:
                 exporter.sim_end()
 
-    def get_env(self, trial_id=0, **kwargs):
-        '''Create an environment for a trial of the simulation'''
+    def get_env(self, trial_id=0, model_params=None, **kwargs):
+        """Create an environment for a trial of the simulation"""
+
         def deserialize_reporters(reporters):
             for (k, v) in reporters.items():
-                if isinstance(v, str) and v.startswith('py:'):
-                    reporters[k] = serialization.deserialize(value.lsplit(':', 1)[1])
+                if isinstance(v, str) and v.startswith("py:"):
+                    reporters[k] = serialization.deserialize(v.split(":", 1)[1])
+            return reporters
 
-        model_params = self.model_params.copy()
-        model_params.update(kwargs)
+        params = self.model_params.copy()
+        if model_params:
+            params.update(model_params)
+        params.update(kwargs)
 
-        agent_reporters = deserialize_reporters(model_params.pop('agent_reporters', {}))
-        model_reporters = deserialize_reporters(model_params.pop('model_reporters', {}))
+        agent_reporters = deserialize_reporters(params.pop("agent_reporters", {}))
+        model_reporters = deserialize_reporters(params.pop("model_reporters", {}))
 
-        env =  serialization.deserialize(self.model_class)
-        return env(id=f'{self.name}_trial_{trial_id}',
-                   seed=f'{self.seed}_trial_{trial_id}',
-                   dir_path=self.dir_path,
-                   agent_reporters=agent_reporters,
-                   model_reporters=model_reporters,
-                   **model_params)
+        env = serialization.deserialize(self.model_class)
+        return env(
+            id=f"{self.name}_trial_{trial_id}",
+            seed=f"{self.seed}_trial_{trial_id}",
+            dir_path=self.dir_path,
+            agent_reporters=agent_reporters,
+            model_reporters=model_reporters,
+            **params,
+        )
 
-    def run_trial(self, trial_id=None, until=None, log_file=False, log_level=logging.INFO, **opts):
+    def run_trial(
+        self, trial_id=None, until=None, log_file=False, log_level=logging.INFO, **opts
+    ):
         """
         Run a single trial of the simulation
 
@@ -145,73 +183,78 @@ class Simulation:
             logger.setLevel(log_level)
         model = self.get_env(trial_id, **opts)
         trial_id = trial_id if trial_id is not None else current_time()
-        with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
-            return self.run_model(model=model, trial_id=trial_id, until=until, log_level=log_level)
+        with utils.timer("Simulation {} trial {}".format(self.name, trial_id)):
+            return self.run_model(
+                model=model, trial_id=trial_id, until=until, log_level=log_level
+            )
 
     def run_model(self, model, until=None, **opts):
         # Set-up trial environment and graph
-        until = float(until or self.max_time or 'inf')
+        until = float(until or self.max_time or "inf")
 
         # Set up agents on nodes
         def is_done():
             return False
 
-        if until and hasattr(model.schedule, 'time'):
+        if until and hasattr(model.schedule, "time"):
             prev = is_done
 
             def is_done():
                 return prev() or model.schedule.time >= until
 
-        if self.max_steps and self.max_steps > 0 and hasattr(model.schedule, 'steps'):
+        if self.max_steps and self.max_steps > 0 and hasattr(model.schedule, "steps"):
             prev_steps = is_done
 
             def is_done():
                 return prev_steps() or model.schedule.steps >= self.max_steps
 
-        newline = '\n'
-        logger.info(dedent(f'''
+        newline = "\n"
+        logger.info(
+            dedent(
+                f"""
 Model stats:
   Agents (total: { model.schedule.get_agent_count() }):
-      - { (newline + '      - ').join(str(a) for a in model.schedule.agents) }'''
-f'''
+      - { (newline + '      - ').join(str(a) for a in model.schedule.agents) }
 
-  Topologies (size):
-      -  { dict( (k, len(v)) for (k, v) in model.topologies.items())  }
-''' if getattr(model, "topologies", None) else ''
-))
+  Topology size: { len(model.G) if hasattr(model, "G") else 0 }
+        """
+            )
+        )
 
         while not is_done():
-            utils.logger.debug(f'Simulation time {model.schedule.time}/{until}. Next: {getattr(model.schedule, "next_time", model.schedule.time + self.interval)}')
+            utils.logger.debug(
+                f'Simulation time {model.schedule.time}/{until}. Next: {getattr(model.schedule, "next_time", model.schedule.time + self.interval)}'
+            )
             model.step()
         return model
 
     def to_dict(self):
         d = asdict(self)
-        if not isinstance(d['model_class'], str):
-            d['model_class'] = serialization.name(d['model_class'])
-        d['model_params'] = serialization.serialize_dict(d['model_params'])
-        d['dir_path'] = str(d['dir_path'])
-        d['version'] = '2'
+        if not isinstance(d["model_class"], str):
+            d["model_class"] = serialization.name(d["model_class"])
+        d["model_params"] = serialization.serialize_dict(d["model_params"])
+        d["dir_path"] = str(d["dir_path"])
+        d["version"] = "2"
         return d
 
     def to_yaml(self):
         return yaml.dump(self.to_dict())
 
 
-def iter_from_config(*cfgs):
+def iter_from_config(*cfgs, **kwargs):
     for config in cfgs:
         configs = list(serialization.load_config(config))
         for config, path in configs:
             d = dict(config)
-            if 'dir_path' not in d:
-                d['dir_path'] = os.path.dirname(path)
-            yield Simulation.from_dict(d)
+            if "dir_path" not in d:
+                d["dir_path"] = os.path.dirname(path)
+            yield Simulation.from_dict(d, **kwargs)
 
 
 def from_config(conf_or_path):
     lst = list(iter_from_config(conf_or_path))
     if len(lst) > 1:
-        raise AttributeError('Provide only one configuration')
+        raise AttributeError("Provide only one configuration")
     return lst[0]
 
 

soil/time.py

@@ -6,7 +6,8 @@ from .utils import logger
 from mesa import Agent as MesaAgent
 
 
-INFINITY = float('inf')
+INFINITY = float("inf")
+
 
 class When:
     def __init__(self, time):
@@ -42,7 +43,7 @@ class TimedActivation(BaseScheduler):
         self._next = {}
         self._queue = []
         self.next_time = 0
-        self.logger = logger.getChild(f'time_{ self.model }')
+        self.logger = logger.getChild(f"time_{ self.model }")
 
     def add(self, agent: MesaAgent, when=None):
         if when is None:
@@ -51,7 +52,7 @@ class TimedActivation(BaseScheduler):
             self._queue.remove((self._next[agent.unique_id], agent.unique_id))
             del self._agents[agent.unique_id]
             heapify(self._queue)
-        
+
         heappush(self._queue, (when, agent.unique_id))
         self._next[agent.unique_id] = when
         super().add(agent)
@@ -62,7 +63,7 @@ class TimedActivation(BaseScheduler):
         an agent will signal when it wants to be scheduled next.
         """
 
-        self.logger.debug(f'Simulation step {self.next_time}')
+        self.logger.debug(f"Simulation step {self.next_time}")
         if not self.model.running:
             return
 
@@ -71,18 +72,22 @@ class TimedActivation(BaseScheduler):
 
         while self._queue and self._queue[0][0] == self.time:
             (when, agent_id) = heappop(self._queue)
-            self.logger.debug(f'Stepping agent {agent_id}')
+            self.logger.debug(f"Stepping agent {agent_id}")
 
             agent = self._agents[agent_id]
             returned = agent.step()
 
-            if not agent.alive:
+            if not getattr(agent, "alive", True):
                 self.remove(agent)
                 continue
 
             when = (returned or Delta(1)).abs(self.time)
             if when < self.time:
-                raise Exception("Cannot schedule an agent for a time in the past ({} < {})".format(when, self.time))
+                raise Exception(
+                    "Cannot schedule an agent for a time in the past ({} < {})".format(
+                        when, self.time
+                    )
+                )
 
             self._next[agent_id] = when
             heappush(self._queue, (when, agent_id))
@@ -96,4 +101,4 @@ class TimedActivation(BaseScheduler):
             return self.time
 
         self.next_time = self._queue[0][0]
-        self.logger.debug(f'Next step: {self.next_time}')
+        self.logger.debug(f"Next step: {self.next_time}")

soil/utils.py

@@ -4,57 +4,77 @@ import os
 import traceback
 
 from functools import partial
-from shutil import copyfile
+from shutil import copyfile, move
 from multiprocessing import Pool
 
 from contextlib import contextmanager
 
-logger = logging.getLogger('soil')
+logger = logging.getLogger("soil")
 logger.setLevel(logging.INFO)
 
 timeformat = "%H:%M:%S"
 
-if os.environ.get('SOIL_VERBOSE', ''):
+if os.environ.get("SOIL_VERBOSE", ""):
     logformat = "[%(levelname)-5.5s][%(asctime)s][%(name)s]:  %(message)s"
 else:
     logformat = "[%(levelname)-5.5s][%(asctime)s] %(message)s"
 
 logFormatter = logging.Formatter(logformat, timeformat)
-
 consoleHandler = logging.StreamHandler()
 consoleHandler.setFormatter(logFormatter)
-logger.addHandler(consoleHandler)
+
+logging.basicConfig(
+    level=logging.INFO,
+    handlers=[
+        consoleHandler,
+    ],
+)
 
 
 @contextmanager
-def timer(name='task', pre="", function=logger.info, to_object=None):
+def timer(name="task", pre="", function=logger.info, to_object=None):
     start = current_time()
-    function('{}Starting {} at {}.'.format(pre, name,
-                                           strftime("%X", gmtime(start))))
+    function("{}Starting {} at {}.".format(pre, name, strftime("%X", gmtime(start))))
     yield start
     end = current_time()
-    function('{}Finished {} at {} in {} seconds'.format(pre, name,
-                                                        strftime("%X", gmtime(end)),
-                                                        str(end-start)))
+    function(
+        "{}Finished {} at {} in {} seconds".format(
+            pre, name, strftime("%X", gmtime(end)), str(end - start)
+        )
+    )
     if to_object:
         to_object.start = start
         to_object.end = end
 
 
-def safe_open(path, mode='r', backup=True, **kwargs):
+def try_backup(path, move=False):
+    if not os.path.exists(path):
+        return None
     outdir = os.path.dirname(path)
     if outdir and not os.path.exists(outdir):
         os.makedirs(outdir)
-    if backup and 'w' in mode and os.path.exists(path):
-        creation = os.path.getctime(path)
-        stamp = strftime('%Y-%m-%d_%H.%M.%S', localtime(creation))
+    creation = os.path.getctime(path)
+    stamp = strftime("%Y-%m-%d_%H.%M.%S", localtime(creation))
 
-        backup_dir = os.path.join(outdir, 'backup')
-        if not os.path.exists(backup_dir):
-            os.makedirs(backup_dir)
-        newpath = os.path.join(backup_dir, '{}@{}'.format(os.path.basename(path),
-                                                          stamp))
+    backup_dir = os.path.join(outdir, "backup")
+    if not os.path.exists(backup_dir):
+        os.makedirs(backup_dir)
+    newpath = os.path.join(
+        backup_dir, "{}@{}".format(os.path.basename(path), stamp)
+    )
+    if move:
+        move(path, newpath)
+    else:
         copyfile(path, newpath)
+    return newpath
+
+
+def safe_open(path, mode="r", backup=True, **kwargs):
+    outdir = os.path.dirname(path)
+    if outdir and not os.path.exists(outdir):
+        os.makedirs(outdir)
+    if backup and "w" in mode:
+        try_backup(path)
     return open(path, mode=mode, **kwargs)
 
 
@@ -63,24 +83,26 @@ def open_or_reuse(f, *args, **kwargs):
     try:
         with safe_open(f, *args, **kwargs) as f:
             yield f
-    except (AttributeError, TypeError):
+    except (AttributeError, TypeError) as ex:
         yield f
 
+
 def flatten_dict(d):
     if not isinstance(d, dict):
         return d
     return dict(_flatten_dict(d))
 
-def _flatten_dict(d, prefix=''):
+
+def _flatten_dict(d, prefix=""):
     if not isinstance(d, dict):
         # print('END:', prefix, d)
         yield prefix, d
         return
     if prefix:
-        prefix = prefix + '.'
+        prefix = prefix + "."
     for k, v in d.items():
         # print(k, v)
-        res = list(_flatten_dict(v, prefix='{}{}'.format(prefix, k)))
+        res = list(_flatten_dict(v, prefix="{}{}".format(prefix, k)))
         # print('RES:', res)
         yield from res
 
@@ -92,7 +114,7 @@ def unflatten_dict(d):
         if not isinstance(k, str):
             target[k] = v
             continue
-        tokens = k.split('.')
+        tokens = k.split(".")
         if len(tokens) < 2:
             target[k] = v
             continue
@@ -105,27 +127,28 @@ def unflatten_dict(d):
 
 
 def run_and_return_exceptions(func, *args, **kwargs):
-    '''
+    """
     A wrapper for run_trial that catches exceptions and returns them.
     It is meant for async simulations.
-    '''
+    """
     try:
         return func(*args, **kwargs)
     except Exception as ex:
         if ex.__cause__ is not None:
             ex = ex.__cause__
-        ex.message = ''.join(traceback.format_exception(type(ex), ex, ex.__traceback__)[:])
+        ex.message = "".join(
+            traceback.format_exception(type(ex), ex, ex.__traceback__)[:]
+        )
         return ex
 
 
 def run_parallel(func, iterable, parallel=False, **kwargs):
-    if parallel and not os.environ.get('SOIL_DEBUG', None):
+    if parallel and not os.environ.get("SOIL_DEBUG", None):
         p = Pool()
-        wrapped_func = partial(run_and_return_exceptions,
-                               func, **kwargs)
+        wrapped_func = partial(run_and_return_exceptions, func, **kwargs)
         for i in p.imap_unordered(wrapped_func, iterable):
             if isinstance(i, Exception):
-                logger.error('Trial failed:\n\t%s', i.message)
+                logger.error("Trial failed:\n\t%s", i.message)
                 continue
             yield i
     else:

soil/version.py

@@ -4,7 +4,7 @@ import logging
 logger = logging.getLogger(__name__)
 
 ROOT = os.path.dirname(__file__)
-DEFAULT_FILE = os.path.join(ROOT, 'VERSION')
+DEFAULT_FILE = os.path.join(ROOT, "VERSION")
 
 
 def read_version(versionfile=DEFAULT_FILE):
@@ -12,9 +12,10 @@ def read_version(versionfile=DEFAULT_FILE):
         with open(versionfile) as f:
             return f.read().strip()
     except IOError:  # pragma: no cover
-        logger.error(('Running an unknown version of {}.'
-                      'Be careful!.').format(__name__))
-        return '0.0'
+        logger.error(
+            ("Running an unknown version of {}." "Be careful!.").format(__name__)
+        )
+        return "0.0"
 
 
 __version__ = read_version()

soil/visualization.py

@@ -1,5 +1,6 @@
 from mesa.visualization.UserParam import UserSettableParameter
 
+
 class UserSettableParameter(UserSettableParameter):
     def __str__(self):
         return self.value

soil/web/__init__.py

@@ -20,6 +20,7 @@ from tornado.concurrent import run_on_executor
 from concurrent.futures import ThreadPoolExecutor
 
 from ..simulation import Simulation
+
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
@@ -31,140 +32,183 @@ LOGGING_INTERVAL = 0.5
 # Workaround to let Soil load the required modules
 sys.path.append(ROOT)
 
+
 class PageHandler(tornado.web.RequestHandler):
-    """ Handler for the HTML template which holds the visualization. """
+    """Handler for the HTML template which holds the visualization."""
 
     def get(self):
-        self.render('index.html', port=self.application.port,
-                    name=self.application.name)
+        self.render(
+            "index.html", port=self.application.port, name=self.application.name
+        )
 
 
 class SocketHandler(tornado.websocket.WebSocketHandler):
-    """ Handler for websocket. """
+    """Handler for websocket."""
+
     executor = ThreadPoolExecutor(max_workers=MAX_WORKERS)
 
     def open(self):
         if self.application.verbose:
-            logger.info('Socket opened!')
+            logger.info("Socket opened!")
 
     def check_origin(self, origin):
         return True
 
     def on_message(self, message):
-        """ Receiving a message from the websocket, parse, and act accordingly. """
+        """Receiving a message from the websocket, parse, and act accordingly."""
 
         msg = tornado.escape.json_decode(message)
 
-        if msg['type'] == 'config_file':
+        if msg["type"] == "config_file":
 
             if self.application.verbose:
-                print(msg['data'])
+                print(msg["data"])
 
-            self.config = list(yaml.load_all(msg['data']))
+            self.config = list(yaml.load_all(msg["data"]))
 
             if len(self.config) > 1:
-                error = 'Please, provide only one configuration.'
+                error = "Please, provide only one configuration."
                 if self.application.verbose:
                     logger.error(error)
-                self.write_message({'type': 'error',
-                    'error': error})
+                self.write_message({"type": "error", "error": error})
                 return
 
             self.config = self.config[0]
-            self.send_log('INFO.' + self.simulation_name,
-                          'Using config: {name}'.format(name=self.config['name']))
+            self.send_log(
+                "INFO." + self.simulation_name,
+                "Using config: {name}".format(name=self.config["name"]),
+            )
 
-            if 'visualization_params' in self.config:
-                self.write_message({'type': 'visualization_params',
-                    'data': self.config['visualization_params']})
-            self.name = self.config['name']
+            if "visualization_params" in self.config:
+                self.write_message(
+                    {
+                        "type": "visualization_params",
+                        "data": self.config["visualization_params"],
+                    }
+                )
+            self.name = self.config["name"]
             self.run_simulation()
 
             settings = []
-            for key in self.config['environment_params']: 
-                if type(self.config['environment_params'][key]) == float or type(self.config['environment_params'][key]) == int:
-                    if self.config['environment_params'][key] <= 1:
-                        setting_type = 'number'
+            for key in self.config["environment_params"]:
+                if (
+                    type(self.config["environment_params"][key]) == float
+                    or type(self.config["environment_params"][key]) == int
+                ):
+                    if self.config["environment_params"][key] <= 1:
+                        setting_type = "number"
                     else:
-                        setting_type = 'great_number'
-                elif type(self.config['environment_params'][key]) == bool:
-                    setting_type = 'boolean'
+                        setting_type = "great_number"
+                elif type(self.config["environment_params"][key]) == bool:
+                    setting_type = "boolean"
                 else:
-                    setting_type = 'undefined'
+                    setting_type = "undefined"
 
-                settings.append({
-                    'label': key,
-                    'type': setting_type,
-                    'value': self.config['environment_params'][key]
-                })
+                settings.append(
+                    {
+                        "label": key,
+                        "type": setting_type,
+                        "value": self.config["environment_params"][key],
+                    }
+                )
 
-            self.write_message({'type': 'settings',
-                'data': settings})
+            self.write_message({"type": "settings", "data": settings})
 
-        elif msg['type'] == 'get_trial':
+        elif msg["type"] == "get_trial":
             if self.application.verbose:
-                logger.info('Trial {} requested!'.format(msg['data']))
-            self.send_log('INFO.' + __name__, 'Trial {} requested!'.format(msg['data']))
-            self.write_message({'type': 'get_trial',
-                                'data': self.get_trial(int(msg['data']))})
+                logger.info("Trial {} requested!".format(msg["data"]))
+            self.send_log("INFO." + __name__, "Trial {} requested!".format(msg["data"]))
+            self.write_message(
+                {"type": "get_trial", "data": self.get_trial(int(msg["data"]))}
+            )
 
-        elif msg['type'] == 'run_simulation':
+        elif msg["type"] == "run_simulation":
             if self.application.verbose:
-                logger.info('Running new simulation for {name}'.format(name=self.config['name']))
-            self.send_log('INFO.' + self.simulation_name, 'Running new simulation for {name}'.format(name=self.config['name']))
-            self.config['environment_params'] = msg['data']
+                logger.info(
+                    "Running new simulation for {name}".format(name=self.config["name"])
+                )
+            self.send_log(
+                "INFO." + self.simulation_name,
+                "Running new simulation for {name}".format(name=self.config["name"]),
+            )
+            self.config["environment_params"] = msg["data"]
             self.run_simulation()
 
-        elif msg['type'] == 'download_gexf':
-            G = self.trials[ int(msg['data']) ].history_to_graph()
+        elif msg["type"] == "download_gexf":
+            G = self.trials[int(msg["data"])].history_to_graph()
             for node in G.nodes():
-                if 'pos' in G.nodes[node]:
-                    G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
-                    del (G.nodes[node]['pos'])
-            writer = nx.readwrite.gexf.GEXFWriter(version='1.2draft')
+                if "pos" in G.nodes[node]:
+                    G.nodes[node]["viz"] = {
+                        "position": {
+                            "x": G.nodes[node]["pos"][0],
+                            "y": G.nodes[node]["pos"][1],
+                            "z": 0.0,
+                        }
+                    }
+                    del G.nodes[node]["pos"]
+            writer = nx.readwrite.gexf.GEXFWriter(version="1.2draft")
             writer.add_graph(G)
-            self.write_message({'type': 'download_gexf',
-                'filename': self.config['name'] + '_trial_' + str(msg['data']),
-                'data': tostring(writer.xml).decode(writer.encoding) })
+            self.write_message(
+                {
+                    "type": "download_gexf",
+                    "filename": self.config["name"] + "_trial_" + str(msg["data"]),
+                    "data": tostring(writer.xml).decode(writer.encoding),
+                }
+            )
 
-        elif msg['type'] == 'download_json':
-            G = self.trials[ int(msg['data']) ].history_to_graph()
+        elif msg["type"] == "download_json":
+            G = self.trials[int(msg["data"])].history_to_graph()
             for node in G.nodes():
-                if 'pos' in G.nodes[node]:
-                    G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
-                    del (G.nodes[node]['pos'])
-            self.write_message({'type': 'download_json',
-                'filename': self.config['name'] + '_trial_' + str(msg['data']),
-                'data': nx.node_link_data(G) })
+                if "pos" in G.nodes[node]:
+                    G.nodes[node]["viz"] = {
+                        "position": {
+                            "x": G.nodes[node]["pos"][0],
+                            "y": G.nodes[node]["pos"][1],
+                            "z": 0.0,
+                        }
+                    }
+                    del G.nodes[node]["pos"]
+            self.write_message(
+                {
+                    "type": "download_json",
+                    "filename": self.config["name"] + "_trial_" + str(msg["data"]),
+                    "data": nx.node_link_data(G),
+                }
+            )
 
         else:
             if self.application.verbose:
-                logger.info('Unexpected message!')
+                logger.info("Unexpected message!")
 
     def update_logging(self):
         try:
-            if (not self.log_capture_string.closed and self.log_capture_string.getvalue()):
-                for i in range(len(self.log_capture_string.getvalue().split('\n')) - 1):
-                    self.send_log('INFO.' + self.simulation_name, self.log_capture_string.getvalue().split('\n')[i])
+            if (
+                not self.log_capture_string.closed
+                and self.log_capture_string.getvalue()
+            ):
+                for i in range(len(self.log_capture_string.getvalue().split("\n")) - 1):
+                    self.send_log(
+                        "INFO." + self.simulation_name,
+                        self.log_capture_string.getvalue().split("\n")[i],
+                    )
                 self.log_capture_string.truncate(0)
                 self.log_capture_string.seek(0)
         finally:
             if self.capture_logging:
-                tornado.ioloop.IOLoop.current().call_later(LOGGING_INTERVAL, self.update_logging)
-
+                tornado.ioloop.IOLoop.current().call_later(
+                    LOGGING_INTERVAL, self.update_logging
+                )
 
     def on_close(self):
         if self.application.verbose:
-            logger.info('Socket closed!')
+            logger.info("Socket closed!")
 
     def send_log(self, logger, logging):
-        self.write_message({'type': 'log',
-                            'logger': logger,
-                            'logging': logging})
+        self.write_message({"type": "log", "logger": logger, "logging": logging})
 
     @property
     def simulation_name(self):
-        return self.config.get('name', 'NoSimulationRunning')
+        return self.config.get("name", "NoSimulationRunning")
 
     @run_on_executor
     def nonblocking(self, config):
@@ -174,28 +218,31 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
     @tornado.gen.coroutine
     def run_simulation(self):
         # Run simulation and capture logs
-        logger.info('Running simulation!')
-        if 'visualization_params' in self.config:
-            del self.config['visualization_params']
+        logger.info("Running simulation!")
+        if "visualization_params" in self.config:
+            del self.config["visualization_params"]
         with self.logging(self.simulation_name):
             try:
                 config = dict(**self.config)
-                config['outdir'] = os.path.join(self.application.outdir, config['name'])
-                config['dump'] = self.application.dump
+                config["outdir"] = os.path.join(self.application.outdir, config["name"])
+                config["dump"] = self.application.dump
                 self.trials = yield self.nonblocking(config)
 
-                self.write_message({'type': 'trials',
-                    'data': list(trial.name for trial in self.trials) })
+                self.write_message(
+                    {
+                        "type": "trials",
+                        "data": list(trial.name for trial in self.trials),
+                    }
+                )
             except Exception as ex:
-                error = 'Something went wrong:\n\t{}'.format(ex)
+                error = "Something went wrong:\n\t{}".format(ex)
                 logging.info(error)
-                self.write_message({'type': 'error',
-                                    'error': error})
-                self.send_log('ERROR.' + self.simulation_name, error)
+                self.write_message({"type": "error", "error": error})
+                self.send_log("ERROR." + self.simulation_name, error)
 
     def get_trial(self, trial):
-        logger.info('Available trials: %s ' % len(self.trials))
-        logger.info('Ask for : %s' % trial)
+        logger.info("Available trials: %s " % len(self.trials))
+        logger.info("Ask for : %s" % trial)
         trial = self.trials[trial]
         G = trial.history_to_graph()
         return nx.node_link_data(G)
@@ -215,25 +262,28 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
         self.logger_application.removeHandler(ch)
         self.capture_logging = False
         return self.capture_logging
-    
+
 
 class ModularServer(tornado.web.Application):
-    """ Main visualization application. """
+    """Main visualization application."""
 
     port = 8001
-    page_handler = (r'/', PageHandler)
-    socket_handler = (r'/ws', SocketHandler)
-    static_handler = (r'/(.*)', tornado.web.StaticFileHandler,
-                      {'path': os.path.join(ROOT, 'static')})
-    local_handler = (r'/local/(.*)', tornado.web.StaticFileHandler,
-                     {'path': ''})
+    page_handler = (r"/", PageHandler)
+    socket_handler = (r"/ws", SocketHandler)
+    static_handler = (
+        r"/(.*)",
+        tornado.web.StaticFileHandler,
+        {"path": os.path.join(ROOT, "static")},
+    )
+    local_handler = (r"/local/(.*)", tornado.web.StaticFileHandler, {"path": ""})
 
     handlers = [page_handler, socket_handler, static_handler, local_handler]
-    settings = {'debug': True,
-                'template_path': ROOT + '/templates'}
+    settings = {"debug": True, "template_path": ROOT + "/templates"}
+
+    def __init__(
+        self, dump=False, outdir="output", name="SOIL", verbose=True, *args, **kwargs
+    ):
 
-    def __init__(self, dump=False, outdir='output', name='SOIL', verbose=True, *args, **kwargs):
-        
         self.verbose = verbose
         self.name = name
         self.dump = dump
@@ -243,12 +293,12 @@ class ModularServer(tornado.web.Application):
         super().__init__(self.handlers, **self.settings)
 
     def launch(self, port=None):
-        """ Run the app. """
-        
+        """Run the app."""
+
         if port is not None:
             self.port = port
-        url = 'http://127.0.0.1:{PORT}'.format(PORT=self.port)
-        print('Interface starting at {url}'.format(url=url))
+        url = "http://127.0.0.1:{PORT}".format(PORT=self.port)
+        print("Interface starting at {url}".format(url=url))
         self.listen(self.port)
         # webbrowser.open(url)
         tornado.ioloop.IOLoop.instance().start()
@@ -263,12 +313,22 @@ def run(*args, **kwargs):
 def main():
     import argparse
 
-    parser = argparse.ArgumentParser(description='Visualization of a Graph Model')
+    parser = argparse.ArgumentParser(description="Visualization of a Graph Model")
 
-    parser.add_argument('--name', '-n', nargs=1, default='SOIL', help='name of the simulation')
-    parser.add_argument('--dump', '-d', help='dumping results in folder output', action='store_true')
-    parser.add_argument('--port', '-p', nargs=1, default=8001, help='port for launching the server')
-    parser.add_argument('--verbose', '-v', help='verbose mode', action='store_true')
+    parser.add_argument(
+        "--name", "-n", nargs=1, default="SOIL", help="name of the simulation"
+    )
+    parser.add_argument(
+        "--dump", "-d", help="dumping results in folder output", action="store_true"
+    )
+    parser.add_argument(
+        "--port", "-p", nargs=1, default=8001, help="port for launching the server"
+    )
+    parser.add_argument("--verbose", "-v", help="verbose mode", action="store_true")
     args = parser.parse_args()
 
-    run(name=args.name, port=(args.port[0] if isinstance(args.port, list) else args.port), verbose=args.verbose)
+    run(
+        name=args.name,
+        port=(args.port[0] if isinstance(args.port, list) else args.port),
+        verbose=args.verbose,
+    )

soil/web/__main__.py

@@ -2,4 +2,4 @@ from . import main
 
 
 if __name__ == "__main__":
-    main()
+    main()

soil/web/run.py

@@ -4,20 +4,33 @@ from simulator import Simulator
 
 
 def run(simulator, name="SOIL", port=8001, verbose=False):
-    server = ModularServer(simulator, name=(name[0] if isinstance(name, list) else name), verbose=verbose)
+    server = ModularServer(
+        simulator, name=(name[0] if isinstance(name, list) else name), verbose=verbose
+    )
     server.port = port
     server.launch()
 
 
 if __name__ == "__main__":
 
-    parser = argparse.ArgumentParser(description='Visualization of a Graph Model')
+    parser = argparse.ArgumentParser(description="Visualization of a Graph Model")
 
-    parser.add_argument('--name', '-n', nargs=1, default='SOIL', help='name of the simulation')
-    parser.add_argument('--dump', '-d', help='dumping results in folder output', action='store_true')
-    parser.add_argument('--port', '-p', nargs=1, default=8001, help='port for launching the server')
-    parser.add_argument('--verbose', '-v', help='verbose mode', action='store_true')
+    parser.add_argument(
+        "--name", "-n", nargs=1, default="SOIL", help="name of the simulation"
+    )
+    parser.add_argument(
+        "--dump", "-d", help="dumping results in folder output", action="store_true"
+    )
+    parser.add_argument(
+        "--port", "-p", nargs=1, default=8001, help="port for launching the server"
+    )
+    parser.add_argument("--verbose", "-v", help="verbose mode", action="store_true")
     args = parser.parse_args()
 
     soil = Simulator(dump=args.dump)
-    run(soil, name=args.name, port=(args.port[0] if isinstance(args.port, list) else args.port), verbose=args.verbose)
+    run(
+        soil,
+        name=args.name,
+        port=(args.port[0] if isinstance(args.port, list) else args.port),
+        verbose=args.verbose,
+    )

tests/complete_converted.yml

@@ -9,17 +9,16 @@ interval: 1
 seed: "CompleteSeed!"
 model_class: Environment
 model_params:
-  topologies:
-    default:
-      params:
-        generator: complete_graph
-        n: 4
+  topology:
+    params:
+      generator: complete_graph
+      n: 4
   agents:
     agent_class: CounterModel
     state:
       group: network
       times: 1
-    topology: 'default'
+    topology: true
     distribution:
       - agent_class: CounterModel
         weight: 0.25
@@ -42,7 +41,7 @@ model_params:
     fixed:
       - agent_class: BaseAgent
         hidden: true
-        topology: null
+        topology: false
         state:
           name: 'Environment Agent 1'
           times: 10

tests/test_agents.py

@@ -4,12 +4,14 @@ import pytest
 from soil import agents, environment
 from soil import time as stime
 
+
 class Dead(agents.FSM):
     @agents.default_state
     @agents.state
     def only(self):
         return self.die()
 
+
 class TestMain(TestCase):
     def test_die_raises_exception(self):
         d = Dead(unique_id=0, model=environment.Environment())
@@ -20,5 +22,5 @@ class TestMain(TestCase):
     def test_die_returns_infinity(self):
         d = Dead(unique_id=0, model=environment.Environment())
         ret = d.step().abs(0)
-        print(ret, 'next')
+        print(ret, "next")
         assert ret == stime.INFINITY

tests/test_config.py

@@ -7,9 +7,9 @@ from os.path import join
 from soil import simulation, serialization, config, network, agents, utils
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
-EXAMPLES = join(ROOT, '..', 'examples')
+EXAMPLES = join(ROOT, "..", "examples")
 
-FORCE_TESTS = os.environ.get('FORCE_TESTS', '')
+FORCE_TESTS = os.environ.get("FORCE_TESTS", "")
 
 
 def isequal(a, b):
@@ -24,7 +24,6 @@ def isequal(a, b):
 
 
 class TestConfig(TestCase):
-
     def test_conversion(self):
         expected = serialization.load_file(join(ROOT, "complete_converted.yml"))[0]
         old = serialization.load_file(join(ROOT, "old_complete.yml"))[0]
@@ -38,7 +37,7 @@ class TestConfig(TestCase):
         The configuration should not change after running
          the simulation.
         """
-        config = serialization.load_file(join(EXAMPLES, 'complete.yml'))[0]
+        config = serialization.load_file(join(EXAMPLES, "complete.yml"))[0]
         s = simulation.from_config(config)
         init_config = copy.copy(s.to_dict())
 
@@ -47,11 +46,8 @@ class TestConfig(TestCase):
         # del nconfig['to
         isequal(init_config, nconfig)
 
-
     def test_topology_config(self):
-        netconfig = config.NetConfig(**{
-            'path': join(ROOT, 'test.gexf')
-        })
+        netconfig = config.NetConfig(**{"path": join(ROOT, "test.gexf")})
         net = network.from_config(netconfig, dir_path=ROOT)
         assert len(net.nodes) == 2
         assert len(net.edges) == 1
@@ -62,36 +58,33 @@ class TestConfig(TestCase):
         network agents are initialized properly.
         """
         cfg = {
-            'name': 'CounterAgent',
-            'network_params': {
-                'path': join(ROOT, 'test.gexf')
-            },
-            'agent_class': 'CounterModel',
+            "name": "CounterAgent",
+            "network_params": {"path": join(ROOT, "test.gexf")},
+            "agent_class": "CounterModel",
             # 'states': [{'times': 10}, {'times': 20}],
-            'max_time': 2,
-            'dry_run': True,
-            'num_trials': 1,
-            'environment_params': {
-            }
+            "max_time": 2,
+            "dry_run": True,
+            "num_trials": 1,
+            "environment_params": {},
         }
         conf = config.convert_old(cfg)
         s = simulation.from_config(conf)
 
         env = s.get_env()
-        assert len(env.topologies['default'].nodes) == 2
-        assert len(env.topologies['default'].edges) == 1
+        assert len(env.G.nodes) == 2
+        assert len(env.G.edges) == 1
         assert len(env.agents) == 2
-        assert env.agents[0].G == env.topologies['default']
+        assert env.agents[0].G == env.G
 
     def test_agents_from_config(self):
-        '''We test that the known complete configuration produces
-        the right agents in the right groups'''
+        """We test that the known complete configuration produces
+        the right agents in the right groups"""
         cfg = serialization.load_file(join(ROOT, "complete_converted.yml"))[0]
         s = simulation.from_config(cfg)
         env = s.get_env()
-        assert len(env.topologies['default'].nodes) == 4
-        assert len(env.agents(group='network')) == 4
-        assert len(env.agents(group='environment')) == 1
+        assert len(env.G.nodes) == 4
+        assert len(env.agents(group="network")) == 4
+        assert len(env.agents(group="environment")) == 1
 
     def test_yaml(self):
         """
@@ -100,16 +93,17 @@ class TestConfig(TestCase):
         Values not present in the original config file should have reasonable
         defaults.
         """
-        with utils.timer('loading'):
-            config = serialization.load_file(join(EXAMPLES, 'complete.yml'))[0]
+        with utils.timer("loading"):
+            config = serialization.load_file(join(EXAMPLES, "complete.yml"))[0]
             s = simulation.from_config(config)
-        with utils.timer('serializing'):
+        with utils.timer("serializing"):
             serial = s.to_yaml()
-        with utils.timer('recovering'):
+        with utils.timer("recovering"):
             recovered = yaml.load(serial, Loader=yaml.SafeLoader)
         for (k, v) in config.items():
             assert recovered[k] == v
 
+
 def make_example_test(path, cfg):
     def wrapped(self):
         root = os.getcwd()
@@ -133,18 +127,19 @@ def make_example_test(path, cfg):
         #             assert env.now <= config['max_time']  # But not further than allowed
         #         except KeyError:
         #             pass
+
     return wrapped
 
 
 def add_example_tests():
     for config, path in serialization.load_files(
-            join(EXAMPLES, '*', '*.yml'),
-            join(EXAMPLES, '*.yml'),
+        join(EXAMPLES, "*", "*.yml"),
+        join(EXAMPLES, "*.yml"),
     ):
         p = make_example_test(path=path, cfg=config)
         fname = os.path.basename(path)
-        p.__name__ = 'test_example_file_%s' % fname
-        p.__doc__ = '%s should be a valid configuration' % fname
+        p.__name__ = "test_example_file_%s" % fname
+        p.__doc__ = "%s should be a valid configuration" % fname
         setattr(TestConfig, p.__name__, p)
         del p
 

tests/test_examples.py

@@ -5,9 +5,9 @@ from os.path import join
 from soil import serialization, simulation, config
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
-EXAMPLES = join(ROOT, '..', 'examples')
+EXAMPLES = join(ROOT, "..", "examples")
 
-FORCE_TESTS = os.environ.get('FORCE_TESTS', '')
+FORCE_TESTS = os.environ.get("FORCE_TESTS", "")
 
 
 class TestExamples(TestCase):
@@ -23,31 +23,31 @@ def make_example_test(path, cfg):
                 s.max_steps = 100
                 s.num_trials = 1
             assert isinstance(cfg, config.Config)
-            if getattr(cfg, 'skip_test', False) and not FORCE_TESTS:
-                self.skipTest('Example ignored.')
+            if getattr(cfg, "skip_test", False) and not FORCE_TESTS:
+                self.skipTest("Example ignored.")
             envs = s.run_simulation(dry_run=True)
             assert envs
             for env in envs:
                 assert env
                 try:
-                    n = cfg.model_params['network_params']['n']
+                    n = cfg.model_params["network_params"]["n"]
                     assert len(list(env.network_agents)) == n
                 except KeyError:
                     pass
                 assert env.schedule.steps > 0  # It has run
                 assert env.schedule.steps <= s.max_steps  # But not further than allowed
+
     return wrapped
 
 
 def add_example_tests():
     for cfg, path in serialization.load_files(
-            join(EXAMPLES, '*', '*.yml'),
-            join(EXAMPLES, '*.yml'),
+        join(EXAMPLES, "**", "*.yml"),
     ):
         p = make_example_test(path=path, cfg=config.Config.from_raw(cfg))
         fname = os.path.basename(path)
-        p.__name__ = 'test_example_file_%s' % fname
-        p.__doc__ = '%s should be a valid configuration' % fname
+        p.__name__ = "test_example_file_%s" % fname
+        p.__doc__ = "%s should be a valid configuration" % fname
         setattr(TestExamples, p.__name__, p)
         del p
 

tests/test_exporters.py

@@ -2,6 +2,7 @@ import os
 import io
 import tempfile
 import shutil
+import sqlite3
 
 from unittest import TestCase
 from soil import exporters
@@ -40,14 +41,10 @@ class Exporters(TestCase):
         num_trials = 5
         max_time = 2
         config = {
-            'name': 'exporter_sim',
-            'model_params': {
-                'agents': [{
-                    'agent_class': agents.BaseAgent
-                }]
-            },
-            'max_time': max_time,
-            'num_trials': num_trials,
+            "name": "exporter_sim",
+            "model_params": {"agents": [{"agent_class": agents.BaseAgent}]},
+            "max_time": max_time,
+            "num_trials": num_trials,
         }
         s = simulation.from_config(config)
 
@@ -64,40 +61,52 @@ class Exporters(TestCase):
         assert Dummy.total_time == max_time * num_trials
 
     def test_writing(self):
-        '''Try to write CSV, sqlite and YAML (without dry_run)'''
+        """Try to write CSV, sqlite and YAML (without dry_run)"""
         n_trials = 5
         config = {
-            'name': 'exporter_sim',
-            'network_params': {
-                'generator': 'complete_graph',
-                'n': 4
-            },
-            'agent_class': 'CounterModel',
-            'max_time': 2,
-            'num_trials': n_trials,
-            'dry_run': False,
-            'environment_params': {}
+            "name": "exporter_sim",
+            "network_params": {"generator": "complete_graph", "n": 4},
+            "agent_class": "CounterModel",
+            "max_time": 2,
+            "num_trials": n_trials,
+            "dry_run": False,
+            "environment_params": {},
         }
         output = io.StringIO()
         s = simulation.from_config(config)
         tmpdir = tempfile.mkdtemp()
-        envs = s.run_simulation(exporters=[
-                                    exporters.default,
-                                    exporters.csv,
-                                ],
-                                dry_run=False,
-                                outdir=tmpdir,
-                                exporter_params={'copy_to': output})
+        envs = s.run_simulation(
+            exporters=[
+                exporters.default,
+                exporters.csv,
+            ],
+            model_params={
+                "agent_reporters": {"times": "times"},
+                "model_reporters": {
+                    "constant": lambda x: 1,
+                },
+            },
+            dry_run=False,
+            outdir=tmpdir,
+            exporter_params={"copy_to": output},
+        )
         result = output.getvalue()
 
-        simdir = os.path.join(tmpdir, s.group or '', s.name)
-        with open(os.path.join(simdir, '{}.dumped.yml'.format(s.name))) as f:
+        simdir = os.path.join(tmpdir, s.group or "", s.name)
+        with open(os.path.join(simdir, "{}.dumped.yml".format(s.name))) as f:
             result = f.read()
             assert result
 
         try:
             for e in envs:
-                with open(os.path.join(simdir, '{}.env.csv'.format(e.id))) as f:
+                db = sqlite3.connect(os.path.join(simdir, f"{s.name}.sqlite"))
+                cur = db.cursor()
+                agent_entries = cur.execute("SELECT * from agents").fetchall()
+                env_entries = cur.execute("SELECT * from env").fetchall()
+                assert len(agent_entries) > 0
+                assert len(env_entries) > 0
+
+                with open(os.path.join(simdir, "{}.env.csv".format(e.id))) as f:
                     result = f.read()
                     assert result
         finally:

tests/test_main.py

@@ -6,60 +6,55 @@ import networkx as nx
 from functools import partial
 
 from os.path import join
-from soil import (simulation, Environment, agents, network, serialization,
-                  utils, config)
+from soil import simulation, Environment, agents, network, serialization, utils, config
 from soil.time import Delta
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
-EXAMPLES = join(ROOT, '..', 'examples')
+EXAMPLES = join(ROOT, "..", "examples")
 
 
 class CustomAgent(agents.FSM, agents.NetworkAgent):
     @agents.default_state
     @agents.state
     def normal(self):
-        self.neighbors = self.count_agents(state_id='normal',
-                                           limit_neighbors=True)
+        self.neighbors = self.count_agents(state_id="normal", limit_neighbors=True)
+
     @agents.state
     def unreachable(self):
         return
 
 
 class TestMain(TestCase):
-
     def test_empty_simulation(self):
         """A simulation with a base behaviour should do nothing"""
         config = {
-            'model_params': {
-              'network_params': {
-                  'path': join(ROOT, 'test.gexf')
-              },
-              'agent_class': 'BaseAgent',
+            "model_params": {
+                "network_params": {"path": join(ROOT, "test.gexf")},
+                "agent_class": "BaseAgent",
             }
         }
         s = simulation.from_config(config)
         s.run_simulation(dry_run=True)
 
-
     def test_network_agent(self):
         """
         The initial states should be applied to the agent and the
         agent should be able to update its state."""
         config = {
-            'name': 'CounterAgent',
-            'num_trials': 1,
-            'max_time': 2,
-            'model_params': {
-                'network_params': {
-                    'generator': nx.complete_graph,
-                    'n': 2,
+            "name": "CounterAgent",
+            "num_trials": 1,
+            "max_time": 2,
+            "model_params": {
+                "network_params": {
+                    "generator": nx.complete_graph,
+                    "n": 2,
                 },
-                'agent_class': 'CounterModel',
-                'states': {
-                    0: {'times': 10},
-                    1: {'times': 20},
+                "agent_class": "CounterModel",
+                "states": {
+                    0: {"times": 10},
+                    1: {"times": 20},
                 },
-            }
+            },
         }
         s = simulation.from_config(config)
 
@@ -68,48 +63,41 @@ class TestMain(TestCase):
         The initial states should be applied to the agent and the
         agent should be able to update its state."""
         config = {
-            'version': '2',
-            'name': 'CounterAgent',
-            'dry_run': True,
-            'num_trials': 1,
-            'max_time': 2,
-            'model_params': {
-                'topologies': {
-                    'default': {
-                        'path': join(ROOT, 'test.gexf')
-                    }
+            "version": "2",
+            "name": "CounterAgent",
+            "dry_run": True,
+            "num_trials": 1,
+            "max_time": 2,
+            "model_params": {
+                "topology": {"path": join(ROOT, "test.gexf")},
+                "agents": {
+                    "agent_class": "CounterModel",
+                    "topology": True,
+                    "fixed": [{"state": {"times": 10}}, {"state": {"times": 20}}],
                 },
-                'agents': {
-                    'agent_class': 'CounterModel',
-                    'topology': 'default',
-                    'fixed': [{'state': {'times': 10}}, {'state': {'times': 20}}],
-                }
-            }
+            },
         }
         s = simulation.from_config(config)
         env = s.get_env()
         assert isinstance(env.agents[0], agents.CounterModel)
-        assert env.agents[0].G == env.topologies['default']
-        assert env.agents[0]['times'] == 10
-        assert env.agents[0]['times'] == 10
+        assert env.agents[0].G == env.G
+        assert env.agents[0]["times"] == 10
+        assert env.agents[0]["times"] == 10
         env.step()
-        assert env.agents[0]['times'] == 11
-        assert env.agents[1]['times'] == 21
+        assert env.agents[0]["times"] == 11
+        assert env.agents[1]["times"] == 21
 
     def test_init_and_count_agents(self):
         """Agents should be properly initialized and counting should filter them properly"""
-        #TODO: separate this test into two or more test cases
+        # TODO: separate this test into two or more test cases
         config = {
-            'max_time': 10,
-            'model_params': {
-                'agents': [{'agent_class': CustomAgent, 'weight': 1, 'topology': 'default'},
-                           {'agent_class': CustomAgent, 'weight': 3, 'topology': 'default'},
+            "max_time": 10,
+            "model_params": {
+                "agents": [
+                    {"agent_class": CustomAgent, "weight": 1, "topology": True},
+                    {"agent_class": CustomAgent, "weight": 3, "topology": True},
                 ],
-                'topologies': {
-                    'default': {
-                        'path': join(ROOT, 'test.gexf')
-                    }
-                },
+                "topology": {"path": join(ROOT, "test.gexf")},
             },
         }
         s = simulation.from_config(config)
@@ -120,40 +108,45 @@ class TestMain(TestCase):
         assert env.count_agents(weight=3) == 1
         assert env.count_agents(agent_class=CustomAgent) == 2
 
-
     def test_torvalds_example(self):
         """A complete example from a documentation should work."""
-        config = serialization.load_file(join(EXAMPLES, 'torvalds.yml'))[0]
-        config['model_params']['network_params']['path'] = join(EXAMPLES,
-                                                config['model_params']['network_params']['path'])
+        config = serialization.load_file(join(EXAMPLES, "torvalds.yml"))[0]
+        config["model_params"]["network_params"]["path"] = join(
+            EXAMPLES, config["model_params"]["network_params"]["path"]
+        )
         s = simulation.from_config(config)
         env = s.run_simulation(dry_run=True)[0]
         for a in env.network_agents:
-            skill_level = a.state['skill_level']
-            if a.id == 'Torvalds':
-                assert skill_level == 'God'
-                assert a.state['total'] == 3
-                assert a.state['neighbors'] == 2
-            elif a.id == 'balkian':
-                assert skill_level == 'developer'
-                assert a.state['total'] == 3
-                assert a.state['neighbors'] == 1
+            skill_level = a.state["skill_level"]
+            if a.id == "Torvalds":
+                assert skill_level == "God"
+                assert a.state["total"] == 3
+                assert a.state["neighbors"] == 2
+            elif a.id == "balkian":
+                assert skill_level == "developer"
+                assert a.state["total"] == 3
+                assert a.state["neighbors"] == 1
             else:
-                assert skill_level == 'beginner'
-                assert a.state['total'] == 3
-                assert a.state['neighbors'] == 1
+                assert skill_level == "beginner"
+                assert a.state["total"] == 3
+                assert a.state["neighbors"] == 1
 
     def test_serialize_class(self):
         ser, name = serialization.serialize(agents.BaseAgent, known_modules=[])
-        assert name == 'soil.agents.BaseAgent'
+        assert name == "soil.agents.BaseAgent"
         assert ser == agents.BaseAgent
 
-        ser, name = serialization.serialize(agents.BaseAgent, known_modules=['soil', ])
-        assert name == 'BaseAgent'
+        ser, name = serialization.serialize(
+            agents.BaseAgent,
+            known_modules=[
+                "soil",
+            ],
+        )
+        assert name == "BaseAgent"
         assert ser == agents.BaseAgent
 
         ser, name = serialization.serialize(CustomAgent)
-        assert name == 'test_main.CustomAgent'
+        assert name == "test_main.CustomAgent"
         assert ser == CustomAgent
         pickle.dumps(ser)
 
@@ -166,72 +159,63 @@ class TestMain(TestCase):
             assert i == des
 
     def test_serialize_agent_class(self):
-        '''A class from soil.agents should be serialized without the module part'''
+        """A class from soil.agents should be serialized without the module part"""
         ser = agents.serialize_type(CustomAgent)
-        assert ser == 'test_main.CustomAgent'
+        assert ser == "test_main.CustomAgent"
         ser = agents.serialize_type(agents.BaseAgent)
-        assert ser == 'BaseAgent'
+        assert ser == "BaseAgent"
         pickle.dumps(ser)
-    
+
     def test_deserialize_agent_distribution(self):
         agent_distro = [
-            {
-                'agent_class': 'CounterModel',
-                'weight': 1
-            },
-            {
-                'agent_class': 'test_main.CustomAgent',
-                'weight': 2
-            },
+            {"agent_class": "CounterModel", "weight": 1},
+            {"agent_class": "test_main.CustomAgent", "weight": 2},
         ]
         converted = agents.deserialize_definition(agent_distro)
-        assert converted[0]['agent_class'] == agents.CounterModel
-        assert converted[1]['agent_class'] == CustomAgent
+        assert converted[0]["agent_class"] == agents.CounterModel
+        assert converted[1]["agent_class"] == CustomAgent
         pickle.dumps(converted)
 
     def test_serialize_agent_distribution(self):
         agent_distro = [
-            {
-                'agent_class': agents.CounterModel,
-                'weight': 1
-            },
-            {
-                'agent_class': CustomAgent,
-                'weight': 2
-            },
+            {"agent_class": agents.CounterModel, "weight": 1},
+            {"agent_class": CustomAgent, "weight": 2},
         ]
         converted = agents.serialize_definition(agent_distro)
-        assert converted[0]['agent_class'] == 'CounterModel'
-        assert converted[1]['agent_class'] == 'test_main.CustomAgent'
+        assert converted[0]["agent_class"] == "CounterModel"
+        assert converted[1]["agent_class"] == "test_main.CustomAgent"
         pickle.dumps(converted)
 
     def test_templates(self):
-        '''Loading a template should result in several configs'''
-        configs = serialization.load_file(join(EXAMPLES, 'template.yml'))
+        """Loading a template should result in several configs"""
+        configs = serialization.load_file(join(EXAMPLES, "template.yml"))
         assert len(configs) > 0
 
     def test_until(self):
         config = {
-            'name': 'until_sim',
-            'model_params': {
-                'network_params': {},
-                'agents': {
-                    'fixed': [{
-                        'agent_class': agents.BaseAgent,
-                    }]
+            "name": "until_sim",
+            "model_params": {
+                "network_params": {},
+                "agents": {
+                    "fixed": [
+                        {
+                            "agent_class": agents.BaseAgent,
+                        }
+                    ]
                 },
             },
-            'max_time': 2,
-            'num_trials': 50,
+            "max_time": 2,
+            "num_trials": 50,
         }
         s = simulation.from_config(config)
         runs = list(s.run_simulation(dry_run=True))
         over = list(x.now for x in runs if x.now > 2)
-        assert len(runs) == config['num_trials']
+        assert len(runs) == config["num_trials"]
         assert len(over) == 0
 
     def test_fsm(self):
-        '''Basic state change'''
+        """Basic state change"""
+
         class ToggleAgent(agents.FSM):
             @agents.default_state
             @agents.state
@@ -250,7 +234,8 @@ class TestMain(TestCase):
         assert a.state_id == a.ping.id
 
     def test_fsm_when(self):
-        '''Basic state change'''
+        """Basic state change"""
+
         class ToggleAgent(agents.FSM):
             @agents.default_state
             @agents.state

tests/test_mesa.py

@@ -1,4 +1,4 @@
-'''
+"""
 Mesa-SOIL integration tests
 
 We have to test that:
@@ -8,13 +8,15 @@ We have to test that:
 
 - Mesa visualizations work with SOIL simulations
 
-'''
+"""
 from mesa import Agent, Model
 from mesa.time import RandomActivation
 from mesa.space import MultiGrid
 
+
 class MoneyAgent(Agent):
-    """ An agent with fixed initial wealth."""
+    """An agent with fixed initial wealth."""
+
     def __init__(self, unique_id, model):
         super().__init__(unique_id, model)
         self.wealth = 1
@@ -33,15 +35,15 @@ class MoneyAgent(Agent):
 
     def move(self):
         possible_steps = self.model.grid.get_neighborhood(
-            self.pos,
-            moore=True,
-            include_center=False)
+            self.pos, moore=True, include_center=False
+        )
         new_position = self.random.choice(possible_steps)
         self.model.grid.move_agent(self, new_position)
 
 
 class MoneyModel(Model):
     """A model with some number of agents."""
+
     def __init__(self, N, width, height):
         self.num_agents = N
         self.grid = MultiGrid(width, height, True)
@@ -58,7 +60,7 @@ class MoneyModel(Model):
             self.grid.place_agent(a, (x, y))
 
     def step(self):
-        '''Advance the model by one step.'''
+        """Advance the model by one step."""
         self.schedule.step()
 
 

tests/test_network.py

@@ -10,7 +10,7 @@ from soil import config, network, environment, agents, simulation
 from test_main import CustomAgent
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
-EXAMPLES = join(ROOT, '..', 'examples')
+EXAMPLES = join(ROOT, "..", "examples")
 
 
 class TestNetwork(TestCase):
@@ -19,21 +19,13 @@ class TestNetwork(TestCase):
         Load a graph from file if the extension is known.
         Raise an exception otherwise.
         """
-        config = {
-            'network_params': {
-                'path': join(ROOT, 'test.gexf')
-            }
-        }
-        G = network.from_config(config['network_params'])
+        config = {"network_params": {"path": join(ROOT, "test.gexf")}}
+        G = network.from_config(config["network_params"])
         assert G
         assert len(G) == 2
         with self.assertRaises(AttributeError):
-            config = {
-                'network_params': {
-                    'path': join(ROOT, 'unknown.extension')
-                }
-            }
-            G = network.from_config(config['network_params'])
+            config = {"network_params": {"path": join(ROOT, "unknown.extension")}}
+            G = network.from_config(config["network_params"])
             print(G)
 
     def test_generate_barabasi(self):
@@ -41,88 +33,73 @@ class TestNetwork(TestCase):
         If no path is given, a generator and network parameters
         should be used to generate a network
         """
-        cfg = {
-            'params': {
-                'generator': 'barabasi_albert_graph'
-            }
-        }
+        cfg = {"params": {"generator": "barabasi_albert_graph"}}
         with self.assertRaises(Exception):
             G = network.from_config(cfg)
-        cfg['params']['n'] = 100
-        cfg['params']['m'] = 10
+        cfg["params"]["n"] = 100
+        cfg["params"]["m"] = 10
         G = network.from_config(cfg)
         assert len(G) == 100
 
     def test_save_geometric(self):
         """
-        There is a bug in networkx that prevents it from creating a GEXF file 
+        There is a bug in networkx that prevents it from creating a GEXF file
         from geometric models. We should work around it.
         """
         G = nx.random_geometric_graph(20, 0.1)
         env = environment.NetworkEnvironment(topology=G)
         f = io.BytesIO()
-        assert env.topologies['default']
-        network.dump_gexf(env.topologies['default'], f)
+        assert env.G
+        network.dump_gexf(env.G, f)
 
     def test_networkenvironment_creation(self):
         """Networkenvironment should accept netconfig as parameters"""
         model_params = {
-            'topologies': {
-                'default': {
-                    'path': join(ROOT, 'test.gexf')
-                }
+            "topology": {"path": join(ROOT, "test.gexf")},
+            "agents": {
+                "topology": True,
+                "distribution": [
+                    {
+                        "agent_class": CustomAgent,
+                    }
+                ],
             },
-            'agents': {
-                'topology': 'default',
-                'distribution': [{
-                    'agent_class': CustomAgent,
-                }]
-            }
         }
         env = environment.Environment(**model_params)
-        assert env.topologies
+        assert env.G
         env.step()
-        assert len(env.topologies['default']) == 2
+        assert len(env.G) == 2
         assert len(env.agents) == 2
-        assert env.agents[1].count_agents(state_id='normal') == 2
-        assert env.agents[1].count_agents(state_id='normal', limit_neighbors=True) == 1
+        assert env.agents[1].count_agents(state_id="normal") == 2
+        assert env.agents[1].count_agents(state_id="normal", limit_neighbors=True) == 1
         assert env.agents[0].neighbors == 1
 
     def test_custom_agent_neighbors(self):
         """Allow for search of neighbors with a certain state_id"""
         config = {
-            'model_params': {
-                'topologies': {
-                    'default': {
-                        'path': join(ROOT, 'test.gexf')
-                    }
-                 },
-                'agents': {
-                    'topology': 'default',
-                    'distribution': [
-                        {
-                            'weight': 1,
-                            'agent_class': CustomAgent
-                        }
-                    ]
-                }
+            "model_params": {
+                "topology": {"path": join(ROOT, "test.gexf")},
+                "agents": {
+                    "topology": True,
+                    "distribution": [{"weight": 1, "agent_class": CustomAgent}],
+                },
             },
-            'max_time': 10,
+            "max_time": 10,
         }
         s = simulation.from_config(config)
         env = s.run_simulation(dry_run=True)[0]
-        assert env.agents[1].count_agents(state_id='normal') == 2
-        assert env.agents[1].count_agents(state_id='normal', limit_neighbors=True) == 1
+        assert env.agents[1].count_agents(state_id="normal") == 2
+        assert env.agents[1].count_agents(state_id="normal", limit_neighbors=True) == 1
         assert env.agents[0].neighbors == 1
 
     def test_subgraph(self):
-        '''An agent should be able to subgraph the global topology'''
+        """An agent should be able to subgraph the global topology"""
         G = nx.Graph()
         G.add_node(3)
         G.add_edge(1, 2)
         distro = agents.calculate_distribution(agent_class=agents.NetworkAgent)
-        aconfig = config.AgentConfig(distribution=distro, topology='default')
-        env = environment.Environment(name='Test', topologies={'default': G}, agents=aconfig)
+        aconfig = config.AgentConfig(distribution=distro, topology=True)
+        env = environment.Environment(name="Test", topology=G, agents=aconfig)
         lst = list(env.network_agents)
 
         a2 = env.find_one(node_id=2)