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Code Issues Releases Wiki Activity

Large set of changes for v0.30

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The examples weren't being properly tested in the last commit. When we fixed
that a lot of bugs in the new implementation of environment and agent were
found, which accounts for most of these changes.

The main difference is the mechanism to load simulations from a configuration
file. For that to work, we had to rework our module loading code in
`serialization` and add a `source_file` attribute to configurations (and
simulations, for that matter).
This commit is contained in:
J. Fernando Sánchez
2023-04-14 19:41:24 +02:00
parent 73282530fd
commit feab0ba79e
36 changed files with 739 additions and 875 deletions
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162
soil/environment.py
View File

@@ -19,8 +19,7 @@ from mesa import Model, Agent
from . import agents as agentmod, datacollection, serialization, utils, time, network, events
# TODO: add metaclass to read attributes of a model
# TODO: read "report" attributes from the model
# TODO: maybe add metaclass to read attributes of a model
class BaseEnvironment(Model):
"""
@@ -35,10 +34,31 @@ class BaseEnvironment(Model):
:meth:`soil.environment.Environment.get` method.
"""
def __new__(cls, *args: Any, seed="default", dir_path=None, **kwargs: Any) -> Any:
def __new__(cls,
*args: Any,
seed="default",
dir_path=None,
collector_class: type = datacollection.SoilCollector,
agent_reporters: Optional[Any] = None,
model_reporters: Optional[Any] = None,
tables: Optional[Any] = None,
**kwargs: Any) -> Any:
"""Create a new model with a default seed value"""
self = super().__new__(cls, *args, seed=seed, **kwargs)
self.dir_path = dir_path or os.getcwd()
collector_class = serialization.deserialize(collector_class)
self.datacollector = collector_class(
model_reporters=model_reporters,
agent_reporters=agent_reporters,
tables=tables,
)
for k in dir(cls):
v = getattr(cls, k)
if isinstance(v, property):
v = v.fget
if getattr(v, "add_to_report", False):
self.add_model_reporter(k, v)
return self
def __init__(
@@ -69,18 +89,12 @@ class BaseEnvironment(Model):
schedule_class = time.TimedActivation
else:
schedule_class = serialization.deserialize(schedule_class)
self.schedule = schedule_class(self)
self.interval = interval
self.schedule = schedule_class(self)
self.logger = utils.logger.getChild(self.id)
collector_class = serialization.deserialize(collector_class)
self.datacollector = collector_class(
model_reporters=model_reporters,
agent_reporters=agent_reporters,
tables=tables,
)
for (k, v) in env_params.items():
self[k] = v
@@ -96,7 +110,7 @@ class BaseEnvironment(Model):
def agents(self):
return agentmod.AgentView(self.schedule._agents)
def find_one(self, *args, **kwargs):
def agent(self, *args, **kwargs):
return agentmod.AgentView(self.schedule._agents).one(*args, **kwargs)
def count_agents(self, *args, **kwargs):
@@ -109,6 +123,8 @@ class BaseEnvironment(Model):
raise Exception(
"The environment has not been scheduled, so it has no sense of time"
)
def init_agents(self):
pass
def add_agent(self, agent_class, unique_id=None, **agent):
if unique_id is None:
@@ -127,6 +143,8 @@ class BaseEnvironment(Model):
return a
def add_agents(self, agent_classes: List[type], k, weights: Optional[List[float]] = None, **kwargs):
if isinstance(agent_classes, type):
agent_classes = [agent_classes]
if weights is None:
weights = [1] * len(agent_classes)
@@ -150,12 +168,27 @@ class BaseEnvironment(Model):
Advance one step in the simulation, and update the data collection and scheduler appropriately
"""
super().step()
# self.logger.info(
# "--- Step: {:^5} - Time: {now:^5} ---", steps=self.schedule.steps, now=self.now
# )
self.schedule.step()
self.datacollector.collect(self)
msg = "Model data:\n"
max_width = max(len(k) for k in self.datacollector.model_vars.keys())
for (k, v) in self.datacollector.model_vars.items():
msg += f"\t{k:<{max_width}}: {v[-1]:>6}\n"
self.logger.info(f"--- Steps: {self.schedule.steps:^5} - Time: {self.now:^5} --- " + msg)
def add_model_reporter(self, name, func=None):
if not func:
func = lambda env: getattr(env, name)
self.datacollector._new_model_reporter(name, func)
def add_agent_reporter(self, name, agent_type=None):
if agent_type:
reporter = lambda a: getattr(a, name) if isinstance(a, agent_type) else None
else:
reporter = name
self.datacollector._new_agent_reporter(name, reporter)
def __getitem__(self, key):
try:
return getattr(self, key)
@@ -192,18 +225,19 @@ class NetworkEnvironment(BaseEnvironment):
and methods to associate agents to nodes and vice versa.
"""
def __init__(
self, *args,
topology: Optional[Union[nx.Graph, str]] = None,
agent_class: Optional[Type[agentmod.Agent]] = None,
network_generator: Optional[Callable] = None,
network_params: Optional[Dict] = None, **kwargs
):
def __init__(self,
*args,
topology: Optional[Union[nx.Graph, str]] = None,
agent_class: Optional[Type[agentmod.Agent]] = None,
network_generator: Optional[Callable] = None,
network_params: Optional[Dict] = {},
init=True,
**kwargs):
self.topology = topology
self.network_generator = network_generator
self.network_params = network_params
if topology or network_params or network_generator:
self.create_network(topology, network_params=network_params, network_generator=network_generator)
self.create_network(topology, generator=network_generator, **network_params)
else:
self.G = nx.Graph()
super().__init__(*args, **kwargs, init=False)
@@ -211,23 +245,35 @@ class NetworkEnvironment(BaseEnvironment):
self.agent_class = agent_class
if agent_class:
self.agent_class = serialization.deserialize(agent_class)
self.init()
if self.agent_class:
self.populate_network(self.agent_class)
self._check_agent_nodes()
if init:
self.init()
def add_agent(self, agent_class, *args, node_id=None, topology=None, **kwargs):
if node_id is None and topology is None:
return super().add_agent(agent_class, *args, **kwargs)
try:
a = super().add_agent(agent_class, *args, node_id=node_id, **kwargs)
except TypeError:
self.logger.warning(f"Agent constructor for {agent_class} does not have a node_id attribute. Might be a bug.")
a = super().add_agent(agent_class, *args, **kwargs)
self.G.nodes[node_id]["agent"] = a
return a
def add_agents(self, *args, k=None, **kwargs):
if not k and not self.G:
raise ValueError("Cannot add agents to an empty network")
super().add_agents(*args, k=k or len(self.G), **kwargs)
def create_network(self, topology=None, network_generator=None, path=None, network_params=None):
def create_network(self, topology=None, generator=None, path=None, **network_params):
if topology is not None:
topology = network.from_topology(topology, dir_path=self.dir_path)
elif path is not None:
topology = network.from_topology(path, dir_path=self.dir_path)
elif network_generator is not None:
topology = network.from_params(network_generator, dir_path=self.dir_path, **network_params)
elif generator is not None:
topology = network.from_params(generator=generator, dir_path=self.dir_path, **network_params)
else:
raise ValueError("topology must be a networkx.Graph or a string, or network_generator must be provided")
self.G = topology
@@ -235,21 +281,15 @@ class NetworkEnvironment(BaseEnvironment):
def init_agents(self, *args, **kwargs):
"""Initialize the agents from a"""
super().init_agents(*args, **kwargs)
for agent in self.schedule._agents.values():
self._assign_node(agent)
def _assign_node(self, agent):
"""
Make sure the node for a given agent has the proper attributes.
"""
if hasattr(agent, "node_id"):
self.G.nodes[agent.node_id]["agent"] = agent
@property
def network_agents(self):
for a in self.schedule._agents.values():
if isinstance(a, agentmod.NetworkAgent):
yield a
"""Return agents still alive and assigned to a node in the network."""
for (id, data) in self.G.nodes(data=True):
if "agent" in data:
agent = data["agent"]
if getattr(agent, "alive", True):
yield agent
def add_node(self, agent_class, unique_id=None, node_id=None, **kwargs):
if unique_id is None:
@@ -265,7 +305,6 @@ class NetworkEnvironment(BaseEnvironment):
self.G.add_node(node_id)
assert "agent" not in self.G.nodes[node_id]
self.G.nodes[node_id]["agent"] = None # Reserve
a = self.add_agent(
unique_id=unique_id,
@@ -277,17 +316,32 @@ class NetworkEnvironment(BaseEnvironment):
a["visible"] = True
return a
def add_agent(self, agent_class, *args, **kwargs):
if issubclass(agent_class, agentmod.NetworkAgent) and "node_id" not in kwargs:
return self.add_node(agent_class, *args, **kwargs)
a = super().add_agent(agent_class, *args, **kwargs)
if hasattr(a, "node_id"):
assigned = self.G.nodes[a.node_id].get("agent")
if not assigned:
self.G.nodes[a.node_id]["agent"] = a
elif assigned != a:
raise ValueError(f"Node {a.node_id} already has an agent assigned: {assigned}")
return a
def _check_agent_nodes(self):
"""
Detect nodes that have agents assigned to them.
"""
for (id, data) in self.G.nodes(data=True):
if "agent_id" in data:
agent = self.agents(data["agent_id"])
self.G.nodes[id]["agent"] = agent
assert not getattr(agent, "node_id", None) or agent.node_id == id
agent.node_id = id
for agent in self.agents():
if hasattr(agent, "node_id"):
node_id = agent["node_id"]
if node_id not in self.G.nodes:
raise ValueError(f"Agent {agent} is assigned to node {agent.node_id} which is not in the network")
node = self.G.nodes[node_id]
if node.get("agent") is not None and node["agent"] != agent:
raise ValueError(f"Node {node_id} already has a different agent assigned to it")
self.G.nodes[node_id]["agent"] = agent
def add_agents(self, agent_classes: List[type], k=None, weights: Optional[List[float]] = None, **kwargs):
if k is None:
k = len(self.G)
if not k:
raise ValueError("Cannot add agents to an empty network")
super().add_agents(agent_classes, k=k, weights=weights, **kwargs)
def agent_for_node_id(self, node_id):
return self.G.nodes[node_id].get("agent")
@@ -301,11 +355,15 @@ class NetworkEnvironment(BaseEnvironment):
weights = [1] * len(agent_class)
assert len(self.G)
classes = self.random.choices(agent_class, weights, k=len(self.G))
toadd = []
for (cls, (node_id, node)) in zip(classes, self.G.nodes(data=True)):
if "agent" in node:
continue
a = self.add_agent(node_id=node_id, topology=self.G, agent_class=cls, **agent_params)
node["agent"] = a
node["agent"] = None # Reserve
toadd.append(dict(node_id=node_id, topology=self.G, agent_class=cls, **agent_params))
for d in toadd:
a = self.add_agent(**d)
self.G.nodes[d["node_id"]]["agent"] = a
assert all("agent" in node for (_, node) in self.G.nodes(data=True))
assert len(list(self.network_agents))