WIP: removed stats

.gitlab-ci.yml

@@ -1,9 +1,10 @@
 stages:
   - test
-  - build
+  - publish
+  - check_published
 
-build:
-  stage: build
+docker:
+  stage: publish
   image:
     name: gcr.io/kaniko-project/executor:debug
     entrypoint: [""]
@@ -16,13 +17,37 @@ build:
   only:
     - tags
 
-
 test:
-  except:
-    - tags  # Avoid running tests for tags, because they are already run for the branch
   tags:
     - docker
   image: python:3.7
   stage: test
   script:
-    - python setup.py test
+    - pip install -r requirements.txt -r test-requirements.txt
+    - python setup.py test
+
+push_pypi:
+  only:
+    - tags
+  tags:
+    - docker
+  image: python:3.7
+  stage: publish
+  script:
+    - echo $CI_COMMIT_TAG > soil/VERSION
+    - pip install twine
+    - python setup.py sdist bdist_wheel
+    - TWINE_PASSWORD=$PYPI_PASSWORD TWINE_USERNAME=$PYPI_USERNAME python -m twine upload dist/*
+
+check_pypi:
+  only:
+    - tags
+  tags:
+    - docker
+  image: python:3.7
+  stage: check_published
+  script:
+    - pip install soil==$CI_COMMIT_TAG
+  # Allow PYPI to update its index before we try to install 
+  when: delayed
+  start_in: 2 minutes

CHANGELOG.md

@@ -3,6 +3,48 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [UNRELEASED]
+### Changed
+* Configuration schema is very different now. Check `soil.config` for more information. We are 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.
+### 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)
+### Fixed
+* Bug with time.NEVER/time.INFINITY
+## [0.20.6]
+### Fixed
+* Agents now return `time.INFINITY` when dead, instead of 'inf'
+* `soil.__init__` does not re-export built-in time (change in `soil.simulation`. It used to create subtle import conflicts when importing soil.time.
+* Parallel simulations were broken because lambdas cannot be pickled properly, which is needed for multiprocessing.
+### Changed
+* Some internal simulation methods do not accept `*args` anymore, to avoid ambiguity and bugs.
+## [0.20.5]
+### Changed
+* Defaults are now set in the agent __init__, not in the environment. This decouples both classes a bit more, and it is more intuitive 
+## [0.20.4]
+### Added
+* Agents can now be given any kwargs, which will be used to set their state
+* Environments have a default logger `self.logger` and a log method, just like agents
+## [0.20.3]
+### Fixed
+* Default state values are now deepcopied again.
+* Seeds for environments only concatenate the trial id (i.e., a number), to provide repeatable results.
+* `Environment.run` now calls `Environment.step`, to allow for easy overloading of the environment step
+### Removed
+* Datacollectors are not being used for now.
+* `time.TimedActivation.step` does not use an `until` parameter anymore.
+### Changed
+* Simulations now run right up to `until` (open interval)
+* Time instants (`time.When`) don't need to be floats anymore. Now we can avoid precision issues with big numbers by using ints.
+* Rabbits simulation is more idiomatic (using subclasses)
+
+## [0.20.2]
+### Fixed
+* CI/CD testing issues
 ## [0.20.1]
 ### Fixed
 * Agents would run another step after dying.

README.md

@@ -39,6 +39,7 @@ As of this writing,
 This is a non-exhaustive list of tasks to achieve compatibility:
 
 * Environments.agents and mesa.Agent.agents are not the same. env is a property, and it only takes into account network and environment agents. Might rename environment_agents to other_agents or sth like that
+
 - [ ] Integrate `soil.Simulation` with mesa's runners:
   - [ ] `soil.Simulation` could mimic/become a `mesa.batchrunner`
 - [ ] Integrate `soil.Environment` with `mesa.Model`:

docs/configuration.rst

@@ -88,9 +88,18 @@ For example, the following configuration is equivalent to :code:`nx.complete_gra
 
 Environment
 ============
+
 The environment is the place where the shared state of the simulation is stored.
-For instance, the probability of disease outbreak.
-The configuration file may specify the initial value of the environment parameters:
+That means both global parameters, such as the probability of disease outbreak.
+But it also means other data, such as a map, or a network topology that connects multiple agents.
+As a result, it is also typical to add custom functions in an environment that help agents interact with each other and with the state of the simulation.
+
+Last but not least, an environment controls when and how its agents will be executed.
+By default, soil environments incorporate a ``soil.time.TimedActivation`` model for agent execution (more on this on the following section).
+
+Soil environments are very similar, and often interchangeable with, mesa models (``mesa.Model``).
+
+A configuration may specify the initial value of the environment parameters:
 
 .. code:: yaml
 
@@ -98,23 +107,33 @@ The configuration file may specify the initial value of the environment paramete
         daily_probability_of_earthquake: 0.001
         number_of_earthquakes: 0
 
-All agents have access to the environment parameters.
+All agents have access to the environment (and its parameters).
 
 In some scenarios, it is useful to have a custom environment, to provide additional methods or to control the way agents update environment state.
 For example, if our agents play the lottery, the environment could provide a method to decide whether the agent wins, instead of leaving it to the agent.
 
-
 Agents
 ======
+
 Agents are a way of modelling behavior.
 Agents can be characterized with two variables: agent type (``agent_type``) and state.
-Only one agent is executed at a time (generally, every ``interval`` seconds), and it has access to its state and the environment parameters.
+The agent type is a ``soil.Agent`` class, which contains the code that encapsulates the behavior of the agent.
+The state is a set of variables, which may change during the simulation, and that the code may use to control the behavior.
+All agents provide a ``step`` method either explicitly or implicitly (by inheriting it from a superclass), which controls how the agent will behave in each step of the simulation.
+
+When and how agent steps are executed in a simulation depends entirely on the ``environment``.
+Most environments will internally use a scheduler (``mesa.time.BaseScheduler``), which controls the activation of agents.
+
+In soil, we generally used the ``soil.time.TimedActivation`` scheduler, which allows agents to specify when their next activation will happen, defaulting to a 
+
+When an agent's step is executed (generally, every ``interval`` seconds), the agent has access to its state and the environment.
 Through the environment, it can access the network topology and the state of other agents.
 
-There are three three types of agents according to how they are added to the simulation: network agents and environment agent.
+There are two types of agents according to how they are added to the simulation: network agents and environment agent.
 
 Network Agents
 ##############
+
 Network agents are attached to a node in the topology.
 The configuration file allows you to specify how agents will be mapped to topology nodes.
 
@@ -125,7 +144,9 @@ Hence, every node in the network will be associated to an agent of that type.
 
    agent_type: SISaModel
 
-It is also possible to add more than one type of agent to the simulation, and to control the ratio of each type (using the ``weight`` property).
+It is also possible to add more than one type of agent to the simulation.
+
+To control the ratio of each type (using the ``weight`` property).
 For instance, with following configuration, it is five times more likely for a node to be assigned a CounterModel type than a SISaModel type.
 
 .. code:: yaml

docs/requirements.txt

@@ -1 +1 @@
-ipython==7.23
+ipython>=7.31.1

examples/complete.yml

@@ -1,27 +1,65 @@
 ---
-name: simple
-group: tests
-dir_path: "/tmp/"
-num_trials: 3
-max_time: 100
-interval: 1
-seed: "CompleteSeed!"
-network_params:
-  generator: complete_graph
-  n: 10
-network_agents:
-  - agent_type: CounterModel
-    weight: 1
+version: '2'
+general:
+  id: simple
+  group: tests
+  dir_path: "/tmp/"
+  num_trials: 3
+  max_time: 100
+  interval: 1
+  seed: "CompleteSeed!"
+topologies:
+  default:
+    params:
+      generator: complete_graph
+      n: 10
+  another_graph:
+    params:
+      generator: complete_graph
+      n: 2
+environment:
+  environment_class: Environment
+  params:
+    am_i_complete: true
+agents:
+# Agents are split several groups, each with its own definition
+  default: # This is a special group. Its values will be used as default values for the rest of the groups
+    agent_class: CounterModel
+    topology: default
     state:
-      state_id: 0
-  - agent_type: AggregatedCounter
-    weight: 0.2
-environment_agents: []
-environment_class: Environment
-environment_params:
-  am_i_complete: true
-default_state:
-  incidents: 0
-states:
-  - name: 'The first node'
-  - name: 'The second node'
+      times: 1
+  environment:
+    # In this group we are not specifying any topology
+    fixed:
+      - name: 'Environment Agent 1'
+        agent_class: CounterModel
+        state:
+          times: 10
+  general_counters:
+    topology: default
+    distribution:
+      - agent_class: CounterModel
+        weight: 1
+        state:
+          times: 3
+      - agent_class: AggregatedCounter
+        weight: 0.2
+    override:
+      - filter:
+          agent_class: AggregatedCounter
+        n: 2
+        state:
+          times: 5
+
+  other_counters:
+    topology: another_graph
+    fixed:
+      - agent_class: CounterModel
+        id: 0
+        state:
+          times: 1
+          total: 0
+      - agent_class: CounterModel
+        id: 1
+        # If not specified, it will use the state set in the default
+        # state:

examples/mesa/mesa.yml

@@ -14,7 +14,6 @@ network_agents:
     weight: 1
 environment_class: social_wealth.MoneyEnv
 environment_params:
-  num_mesa_agents: 5
   mesa_agent_type: social_wealth.MoneyAgent
   N: 10
   width: 50

examples/mesa/social_wealth.py

@@ -71,10 +71,9 @@ class SocialMoneyAgent(NetworkAgent, MoneyAgent):
 
 class MoneyEnv(Environment):
     """A model with some number of agents."""
-    def __init__(self, N, width, height, *args, network_params, **kwargs):
+    def __init__(self, width, height, *args, topologies, **kwargs):
 
-        network_params['n'] = N
-        super().__init__(*args, network_params=network_params, **kwargs)
+        super().__init__(*args, topologies=topologies, **kwargs)
         self.grid = MultiGrid(width, height, False)
 
         # Create agents

examples/newsspread/NewsSpread.yml

@@ -1,6 +1,5 @@
 ---
 default_state: {}
-load_module: newsspread
 environment_agents: []
 environment_params:
   prob_neighbor_spread: 0.0
@@ -9,11 +8,11 @@ interval: 1
 max_time: 300
 name: Sim_all_dumb
 network_agents:
-- agent_type: DumbViewer
+- agent_type: newsspread.DumbViewer
   state:
     has_tv: false
   weight: 1
-- agent_type: DumbViewer
+- agent_type: newsspread.DumbViewer
   state:
     has_tv: true
   weight: 1
@@ -24,7 +23,6 @@ network_params:
 num_trials: 50
 ---
 default_state: {}
-load_module: newsspread
 environment_agents: []
 environment_params:
   prob_neighbor_spread: 0.0
@@ -33,19 +31,19 @@ interval: 1
 max_time: 300
 name: Sim_half_herd
 network_agents:
-- agent_type: DumbViewer
+- agent_type: newsspread.DumbViewer
   state:
     has_tv: false
   weight: 1
-- agent_type: DumbViewer
+- agent_type: newsspread.DumbViewer
   state:
     has_tv: true
   weight: 1
-- agent_type: HerdViewer
+- agent_type: newsspread.HerdViewer
   state:
     has_tv: false
   weight: 1
-- agent_type: HerdViewer
+- agent_type: newsspread.HerdViewer
   state:
     has_tv: true
   weight: 1
@@ -56,7 +54,6 @@ network_params:
 num_trials: 50
 ---
 default_state: {}
-load_module: newsspread
 environment_agents: []
 environment_params:
   prob_neighbor_spread: 0.0
@@ -65,12 +62,12 @@ interval: 1
 max_time: 300
 name: Sim_all_herd
 network_agents:
-- agent_type: HerdViewer
+- agent_type: newsspread.HerdViewer
   state:
     has_tv: true
     state_id: neutral
   weight: 1
-- agent_type: HerdViewer
+- agent_type: newsspread.HerdViewer
   state:
     has_tv: true
     state_id: neutral
@@ -82,7 +79,6 @@ network_params:
 num_trials: 50
 ---
 default_state: {}
-load_module: newsspread
 environment_agents: []
 environment_params:
   prob_neighbor_spread: 0.0
@@ -92,12 +88,12 @@ interval: 1
 max_time: 300
 name: Sim_wise_herd
 network_agents:
-- agent_type: HerdViewer
+- agent_type: newsspread.HerdViewer
   state:
     has_tv: true
     state_id: neutral
   weight: 1
-- agent_type: WiseViewer
+- agent_type: newsspread.WiseViewer
   state:
     has_tv: true
   weight: 1
@@ -108,7 +104,6 @@ network_params:
 num_trials: 50
 ---
 default_state: {}
-load_module: newsspread
 environment_agents: []
 environment_params:
   prob_neighbor_spread: 0.0
@@ -118,12 +113,12 @@ interval: 1
 max_time: 300
 name: Sim_all_wise
 network_agents:
-- agent_type: WiseViewer
+- agent_type: newsspread.WiseViewer
   state:
     has_tv: true
     state_id: neutral
   weight: 1
-- agent_type: WiseViewer
+- agent_type: newsspread.WiseViewer
   state:
     has_tv: true
   weight: 1

examples/newsspread/newsspread.py

@@ -1,8 +1,8 @@
-from soil.agents import FSM, state, default_state, prob
+from soil.agents import FSM, NetworkAgent, state, default_state, prob
 import logging
 
 
-class DumbViewer(FSM):
+class DumbViewer(FSM, NetworkAgent):
     '''
     A viewer that gets infected via TV (if it has one) and tries to infect
     its neighbors once it's infected.
@@ -17,7 +17,7 @@ class DumbViewer(FSM):
     def neutral(self):
         if self['has_tv']:
             if prob(self.env['prob_tv_spread']):
-                self.set_state(self.infected)
+                return self.infected
 
     @state
     def infected(self):
@@ -26,6 +26,12 @@ class DumbViewer(FSM):
                 neighbor.infect()
 
     def infect(self):
+        '''
+        This is not a state. It is a function that other agents can use to try to
+        infect this agent. DumbViewer always gets infected, but other agents like
+        HerdViewer might not become infected right away
+        '''
+
         self.set_state(self.infected)
 
 
@@ -35,12 +41,13 @@ class HerdViewer(DumbViewer):
     '''
 
     def infect(self):
+        '''Notice again that this is NOT a state. See DumbViewer.infect for reference'''
         infected = self.count_neighboring_agents(state_id=self.infected.id)
         total = self.count_neighboring_agents()
         prob_infect = self.env['prob_neighbor_spread'] * infected/total
         self.debug('prob_infect', prob_infect)
         if prob(prob_infect):
-            self.set_state(self.infected.id)
+            self.set_state(self.infected)
 
 
 class WiseViewer(HerdViewer):
@@ -75,5 +82,5 @@ class WiseViewer(HerdViewer):
                        1.0)
         prob_cure = self.env['prob_neighbor_cure'] * (cured/infected)
         if prob(prob_cure):
-            return self.cure()
+            return self.cured
         return self.set_state(super().infected)

examples/programmatic/programmatic.py

@@ -18,7 +18,9 @@ class MyAgent(agents.FSM):
     @agents.default_state
     @agents.state
     def neutral(self):
-        self.info('I am running')
+        self.debug('I am running')
+        if agents.prob(0.2):
+            self.info('This runs 2/10 times on average')
 
 
 s = Simulation(name='Programmatic',
@@ -29,10 +31,10 @@ s = Simulation(name='Programmatic',
                dry_run=True)
 
 
+# By default, logging will only print WARNING logs (and above).
+# You need to choose a lower logging level to get INFO/DEBUG traces
 logging.basicConfig(level=logging.INFO)
 envs = s.run()
 
-s.dump_yaml()
-
-for env in envs:
-    env.dump_csv()
+# Uncomment this to output the simulation to a YAML file
+# s.dump_yaml('simulation.yaml')

examples/pubcrawl/pubcrawl.py

@@ -1,4 +1,4 @@
-from soil.agents import FSM, state, default_state
+from soil.agents import FSM, NetworkAgent, state, default_state
 from soil import Environment
 from random import random, shuffle
 from itertools import islice
@@ -53,7 +53,7 @@ class CityPubs(Environment):
                 pub['occupancy'] -= 1
 
 
-class Patron(FSM):
+class Patron(FSM, NetworkAgent):
     '''Agent that looks for friends to drink with. It will do three things:
         1) Look for other patrons to drink with
         2) Look for a bar where the agent and other agents in the same group can get in.
@@ -151,7 +151,7 @@ class Patron(FSM):
         return befriended
 
 
-class Police(FSM):
+class Police(FSM, NetworkAgent):
     '''Simple agent to take drunk people out of pubs.'''
     level = logging.INFO
 

examples/rabbits/rabbit_agents.py

@@ -10,9 +10,7 @@ class Genders(Enum):
     female = 'female'
 
 
-class RabbitModel(FSM):
-
-    level = logging.INFO
+class RabbitModel(FSM, NetworkAgent):
 
     defaults = {
         'age': 0,
@@ -36,6 +34,17 @@ class RabbitModel(FSM):
         if self['age'] >= self.sexual_maturity:
             self.debug('I am fertile!')
             return self.fertile
+    @state
+    def fertile(self):
+        raise Exception("Each subclass should define its fertile state")
+
+    @state
+    def dead(self):
+        self.info('Agent {} is dying'.format(self.id))
+        self.die()
+
+
+class Male(RabbitModel):
 
     @state
     def fertile(self):
@@ -47,20 +56,26 @@ class RabbitModel(FSM):
             return
 
         # Males try to mate
-        for f in self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False, limit=self.max_females):
+        for f in self.get_agents(state_id=Female.fertile.id,
+                                 agent_type=Female,
+                                 limit_neighbors=False,
+                                 limit=self.max_females):
             r = random()
             if r < self['mating_prob']:
                 self.impregnate(f)
                 break # Take a break
-
     def impregnate(self, whom):
-        if self['gender'] == Genders.female.value:
-            raise NotImplementedError('Females cannot impregnate')
         whom['pregnancy'] = 0
         whom['mate'] = self.id
         whom.set_state(whom.pregnant)
         self.debug('{} impregnating: {}. {}'.format(self.id, whom.id, whom.state))
 
+class Female(RabbitModel):
+    @state
+    def fertile(self):
+        # Just wait for a Male
+        pass
+
     @state
     def pregnant(self):
         self['age'] += 1
@@ -90,19 +105,17 @@ class RabbitModel(FSM):
 
     @state
     def dead(self):
-        self.info('Agent {} is dying'.format(self.id))
+        super().dead()
         if 'pregnancy' in self and self['pregnancy'] > -1:
             self.info('A mother has died carrying a baby!!')
-        self.die()
-        return
 
 
-class RandomAccident(NetworkAgent):
+class RandomAccident(BaseAgent):
 
     level = logging.DEBUG
 
     def step(self):
-        rabbits_total = self.topology.number_of_nodes()
+        rabbits_total = self.env.topology.number_of_nodes()
         if 'rabbits_alive' not in self.env:
             self.env['rabbits_alive'] = 0
         rabbits_alive = self.env.get('rabbits_alive', rabbits_total)
@@ -118,5 +131,5 @@ class RandomAccident(NetworkAgent):
                 self.log('Rabbits alive: {}'.format(self.env['rabbits_alive']))
                 i.set_state(i.dead)
         self.log('Rabbits alive: {}/{}'.format(rabbits_alive, rabbits_total))
-        if self.count_agents(state_id=RabbitModel.dead.id) == self.topology.number_of_nodes():
+        if self.env.count_agents(state_id=RabbitModel.dead.id) == self.env.topology.number_of_nodes():
             self.die()

examples/rabbits/rabbits.yml

@@ -1,23 +1,20 @@
 ---
-load_module: rabbit_agents
 name: rabbits_example
-max_time: 150
+max_time: 100
 interval: 1
 seed: MySeed
-agent_type: RabbitModel
+agent_type: rabbit_agents.RabbitModel
 environment_agents:
-    - agent_type: RandomAccident
+    - agent_type: rabbit_agents.RandomAccident
 environment_params:
   prob_death: 0.001
 default_state:
-  mating_prob: 0.01
+  mating_prob: 0.1
 topology:
   nodes:
     - id: 1
-      state:
-        gender: female
+      agent_type: rabbit_agents.Male
     - id: 0
-      state:
-        gender: male
+      agent_type: rabbit_agents.Female
   directed: true
   links: []

examples/terrorism/TerroristNetworkModel.yml

@@ -1,5 +1,4 @@
 name: TerroristNetworkModel_sim
-load_module: TerroristNetworkModel
 max_time: 150 
 num_trials: 1
 network_params:
@@ -9,19 +8,19 @@ network_params:
   # theta: 20
   n: 100
 network_agents:
-  - agent_type: TerroristNetworkModel
+  - agent_type: TerroristNetworkModel.TerroristNetworkModel
     weight: 0.8
     state:
       id: civilian  # Civilians
-  - agent_type: TerroristNetworkModel
+  - agent_type: TerroristNetworkModel.TerroristNetworkModel
     weight: 0.1
     state:
       id: leader    # Leaders
-  - agent_type: TrainingAreaModel
+  - agent_type: TerroristNetworkModel.TrainingAreaModel
     weight: 0.05
     state:
       id: terrorist # Terrorism
-  - agent_type: HavenModel
+  - agent_type: TerroristNetworkModel.HavenModel
     weight: 0.05
     state:
       id: civilian  # Civilian

requirements.txt

@@ -5,5 +5,5 @@ pyyaml>=5.1
 pandas>=0.23
 SALib>=1.3
 Jinja2
-Mesa>=0.8
-tsih>=0.1.5
+Mesa>=0.8.9
+pydantic>=1.9

setup.py

@@ -49,6 +49,7 @@ setup(
     extras_require=extras_require,
     tests_require=test_reqs,
     setup_requires=['pytest-runner', ],
+    pytest_plugins = ['pytest_profiling'],
     include_package_data=True,
     entry_points={
         'console_scripts':

soil/VERSION

@@ -1 +1 @@
-0.20.1
+0.20.7

soil/__init__.py

@@ -36,13 +36,13 @@ def main():
     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.')
+                        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('--graph', '-g', action='store_true',
-                        help='Dump GEXF graph. Defaults to false.')
+                        help='Dump each trial\'s network topology as a GEXF graph. Defaults to false.')
     parser.add_argument('--csv', action='store_true',
-                        help='Dump history in CSV format. Defaults to false.')
+                        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",
@@ -65,6 +65,10 @@ def main():
 
     logger.info('Loading config file: {}'.format(args.file))
 
+    if args.pdb:
+        args.synchronous = True
+
+
     try:
         exporters = list(args.exporter or ['default', ])
         if args.csv:

soil/agents/CounterModel.py

@@ -7,9 +7,15 @@ class CounterModel(NetworkAgent):
     in each step and adds it to its state.
     """
 
+    defaults = {
+        'times': 0,
+        'neighbors': 0,
+        'total': 0
+    }
+
     def step(self):
         # Outside effects
-        total = len(list(self.get_agents()))
+        total = len(list(self.env.agents))
         neighbors = len(list(self.get_neighboring_agents()))
         self['times'] = self.get('times', 0) + 1
         self['neighbors'] = neighbors
@@ -33,6 +39,6 @@ class AggregatedCounter(NetworkAgent):
         self['times'] += 1
         neighbors = len(list(self.get_neighboring_agents()))
         self['neighbors'] += neighbors
-        total = len(list(self.get_agents()))
+        total = len(list(self.env.agents))
         self['total'] += total
         self.debug('Running for step: {}. Total: {}'.format(self.now, total))

soil/agents/__init__.py

@@ -1,16 +1,20 @@
 import logging
 from collections import OrderedDict, defaultdict
+from collections.abc import MutableMapping, Mapping, Set
+from abc import ABCMeta
 from copy import deepcopy
 from functools import partial, wraps
-from itertools import islice
+from itertools import islice, chain
 import json
 import networkx as nx
 
-from .. import serialization, utils, time
+from mesa import Agent as MesaAgent
+from typing import Dict, List
 
-from tsih import Key
+from random import shuffle
+
+from .. import serialization, utils, time, config
 
-from mesa import Agent
 
 
 def as_node(agent):
@@ -24,9 +28,16 @@ IGNORED_FIELDS = ('model', 'logger')
 class DeadAgent(Exception):
     pass
 
-class BaseAgent(Agent):
+class BaseAgent(MesaAgent, MutableMapping):
     """
-    A special Agent that keeps track of its state history.
+    A special type of Mesa Agent that:
+
+    * Can be used as a dictionary to access its state.
+    * Has logging built-in
+    * Can be given default arguments through a defaults class attribute,
+    which will be used on construction to initialize each agent's state
+
+    Any attribute that is not preceded by an underscore (`_`) will also be added to its state.
     """
 
     defaults = {}
@@ -35,24 +46,41 @@ class BaseAgent(Agent):
                  unique_id,
                  model,
                  name=None,
-                 interval=None):
+                 interval=None,
+                 **kwargs
+    ):
         # Check for REQUIRED arguments
         # Initialize agent parameters
-        if isinstance(unique_id, Agent):
+        if isinstance(unique_id, MesaAgent):
             raise Exception()
-        self._saved = set()
+        assert isinstance(unique_id, int)
         super().__init__(unique_id=unique_id, model=model)
-        self.name = name or '{}[{}]'.format(type(self).__name__, self.unique_id)
+
+        self.name = str(name) if name else'{}[{}]'.format(type(self).__name__, self.unique_id)
+
 
         self._neighbors = None
         self.alive = True
 
         self.interval = interval or self.get('interval', 1)
-        self.logger = logging.getLogger(self.model.name).getChild(self.name)
+        self.logger = logging.getLogger(self.model.id).getChild(self.name)
 
         if hasattr(self, 'level'):
             self.logger.setLevel(self.level)
+        for (k, v) in self.defaults.items():
+            if not hasattr(self, k) or getattr(self, k) is None:
+                setattr(self, k, deepcopy(v))
 
+        for (k, v) in kwargs.items():
+
+            setattr(self, k, v)
+
+        for (k, v) in getattr(self, 'defaults', {}).items():
+            if not hasattr(self, k) or getattr(self, k) is None:
+                setattr(self, k, v)
+
+    def __hash__(self):
+        return hash(self.unique_id)
 
     # TODO: refactor to clean up mesa compatibility
     @property
@@ -71,7 +99,6 @@ class BaseAgent(Agent):
     def state(self):
         '''
         Return the agent itself, which behaves as a dictionary.
-        Changes made to `agent.state` will be reflected in the history.
 
         This method shouldn't be used, but is kept here for backwards compatibility.
         '''
@@ -90,23 +117,7 @@ class BaseAgent(Agent):
     def environment_params(self, value):
         self.model.environment_params = value
 
-    def __setattr__(self, key, value):
-        if not key.startswith('_') and key not in IGNORED_FIELDS:
-            try:
-                k = Key(t_step=self.now,
-                        dict_id=self.unique_id,
-                        key=key)
-                self._saved.add(key)
-                self.model[k] = value
-            except AttributeError:
-                pass
-        super().__setattr__(key, value)
-
     def __getitem__(self, key):
-        if isinstance(key, tuple):
-            key, t_step = key
-            k = Key(key=key, t_step=t_step, dict_id=self.unique_id)
-            return self.model[k]
         return getattr(self, key)
 
     def __delitem__(self, key):
@@ -118,8 +129,17 @@ class BaseAgent(Agent):
     def __setitem__(self, key, value):
         setattr(self, key, value)
 
+    def __len__(self):
+        return sum(1 for n in self.keys())
+
+    def __iter__(self):
+        return self.items()
+
+    def keys(self):
+        return (k for k in self.__dict__ if k[0] != '_')
+
     def items(self):
-        return ((k, getattr(self, k)) for k in self._saved)
+        return ((k, v) for (k, v) in self.__dict__.items() if k[0] != '_')
 
     def get(self, key, default=None):
         return self[key] if key in self else default
@@ -137,6 +157,7 @@ class BaseAgent(Agent):
         self.alive = False
         if remove:
             self.remove_node(self.id)
+        return time.NEVER
 
     def step(self):
         if not self.alive:
@@ -156,22 +177,30 @@ class BaseAgent(Agent):
         extra['agent_name'] = self.name
         return self.logger.log(level, message, extra=extra)
 
+
+
     def debug(self, *args, **kwargs):
         return self.log(*args, level=logging.DEBUG, **kwargs)
 
     def info(self, *args, **kwargs):
         return self.log(*args, level=logging.INFO, **kwargs)
 
+# Alias
+# Agent = BaseAgent
 
 class NetworkAgent(BaseAgent):
 
     @property
     def topology(self):
-        return self.model.G
+        return self.env.topology_for(self.unique_id)
+
+    @property
+    def node_id(self):
+        return self.env.node_id_for(self.unique_id)
 
     @property
     def G(self):
-        return self.model.G
+        return self.model.topologies[self._topology]
 
     def count_agents(self, **kwargs):
         return len(list(self.get_agents(**kwargs)))
@@ -188,16 +217,19 @@ class NetworkAgent(BaseAgent):
             it = islice(it, limit)
         return list(it)
 
-    def iter_agents(self, agents=None, limit_neighbors=False, **kwargs):
+    def iter_agents(self, unique_id=None, limit_neighbors=False, **kwargs):
         if limit_neighbors:
-            agents = self.topology.neighbors(self.unique_id)
+            unique_id = [self.topology.nodes[node]['agent_id'] for node in self.topology.neighbors(self.node_id)]
+            if not unique_id:
+                return
+
+        yield from self.model.agents(unique_id=unique_id, **kwargs)
 
-        agents = self.model.get_agents(agents)
-        return select(agents, **kwargs)
 
     def subgraph(self, center=True, **kwargs):
         include = [self] if center else []
-        return self.topology.subgraph(n.unique_id for n in list(self.get_agents(**kwargs))+include)
+        G = self.topology.subgraph(n.node_id for n in list(self.get_agents(**kwargs)+include))
+        return G
 
     def remove_node(self, unique_id):
         self.topology.remove_node(unique_id)
@@ -211,7 +243,6 @@ class NetworkAgent(BaseAgent):
 
         self.topology.add_edge(self.unique_id, other.unique_id, edge_attr_dict=edge_attr_dict, *edge_attrs)
 
-
     def ego_search(self, steps=1, center=False, node=None, **kwargs):
         '''Get a list of nodes in the ego network of *node* of radius *steps*'''
         node = as_node(node if node is not None else self)
@@ -270,7 +301,7 @@ def default_state(func):
     return func
 
 
-class MetaFSM(type):
+class MetaFSM(ABCMeta):
     def __init__(cls, name, bases, nmspc):
         super(MetaFSM, cls).__init__(name, bases, nmspc)
         states = {}
@@ -293,7 +324,7 @@ class MetaFSM(type):
         cls.states = states
 
 
-class FSM(NetworkAgent, metaclass=MetaFSM):
+class FSM(BaseAgent, metaclass=MetaFSM):
     def __init__(self, *args, **kwargs):
         super(FSM, self).__init__(*args, **kwargs)
         if not hasattr(self, 'state_id'):
@@ -305,18 +336,16 @@ class FSM(NetworkAgent, metaclass=MetaFSM):
 
     def step(self):
         self.debug(f'Agent {self.unique_id} @ state {self.state_id}')
-        try:
-            interval = super().step()
-        except DeadAgent:
-            return time.When('inf')
+        interval = super().step()
         if 'id' not in self.state:
-            # if 'id' in self.state:
-            #     self.set_state(self.state['id'])
             if self.default_state:
                 self.set_state(self.default_state.id)
             else:
                 raise Exception('{} has no valid state id or default state'.format(self))
-        return self.states[self.state_id](self) or interval
+        interval = self.states[self.state_id](self) or interval
+        if not self.alive:
+            return time.NEVER
+        return interval
 
     def set_state(self, state):
         if hasattr(state, 'id'):
@@ -343,7 +372,7 @@ def prob(prob=1):
 
 
 def calculate_distribution(network_agents=None,
-                           agent_type=None):
+                           agent_class=None):
     '''
     Calculate the threshold values (thresholds for a uniform distribution)
     of an agent distribution given the weights of each agent type.
@@ -351,13 +380,13 @@ def calculate_distribution(network_agents=None,
     The input has this form: ::
 
             [
-            {'agent_type': 'agent_type_1',
+            {'agent_class': 'agent_class_1',
                 'weight': 0.2,
                 'state': {
                     'id': 0
                 }
             },
-            {'agent_type': 'agent_type_2',
+            {'agent_class': 'agent_class_2',
                 'weight': 0.8,
                 'state': {
                     'id': 1
@@ -366,12 +395,12 @@ def calculate_distribution(network_agents=None,
             ]
 
     In this example, 20% of the nodes will be marked as type
-    'agent_type_1'.
+    'agent_class_1'.
     '''
     if network_agents:
         network_agents = [deepcopy(agent) for agent in network_agents if not hasattr(agent, 'id')]
-    elif agent_type:
-        network_agents = [{'agent_type': agent_type}]
+    elif agent_class:
+        network_agents = [{'agent_class': agent_class}]
     else:
         raise ValueError('Specify a distribution or a default agent type')
 
@@ -391,11 +420,11 @@ def calculate_distribution(network_agents=None,
     return network_agents
 
 
-def serialize_type(agent_type, known_modules=[], **kwargs):
-    if isinstance(agent_type, str):
-        return agent_type
+def serialize_type(agent_class, known_modules=[], **kwargs):
+    if isinstance(agent_class, str):
+        return agent_class
     known_modules += ['soil.agents']
-    return serialization.serialize(agent_type, known_modules=known_modules, **kwargs)[1] # Get the name of the class
+    return serialization.serialize(agent_class, known_modules=known_modules, **kwargs)[1] # Get the name of the class
 
 
 def serialize_definition(network_agents, known_modules=[]):
@@ -407,23 +436,23 @@ def serialize_definition(network_agents, known_modules=[]):
     for v in d:
         if 'threshold' in v:
             del v['threshold']
-        v['agent_type'] = serialize_type(v['agent_type'],
+        v['agent_class'] = serialize_type(v['agent_class'],
                                          known_modules=known_modules)
     return d
 
 
-def deserialize_type(agent_type, known_modules=[]):
-    if not isinstance(agent_type, str):
-        return agent_type
+def deserialize_type(agent_class, known_modules=[]):
+    if not isinstance(agent_class, str):
+        return agent_class
     known = known_modules + ['soil.agents', 'soil.agents.custom' ]
-    agent_type = serialization.deserializer(agent_type, known_modules=known)
-    return agent_type
+    agent_class = serialization.deserializer(agent_class, known_modules=known)
+    return agent_class
 
 
 def deserialize_definition(ind, **kwargs):
     d = deepcopy(ind)
     for v in d:
-        v['agent_type'] = deserialize_type(v['agent_type'], **kwargs)
+        v['agent_class'] = deserialize_type(v['agent_class'], **kwargs)
     return d
 
 
@@ -438,7 +467,7 @@ def _validate_states(states, topology):
     return states
 
 
-def _convert_agent_types(ind, to_string=False, **kwargs):
+def _convert_agent_classs(ind, to_string=False, **kwargs):
     '''Convenience method to allow specifying agents by class or class name.'''
     if to_string:
         return serialize_definition(ind, **kwargs)
@@ -457,7 +486,7 @@ def _agent_from_definition(definition, value=-1, unique_id=None):
             state = {}
             if 'state' in d:
                 state = deepcopy(d['state'])
-            return d['agent_type'], state
+            return d['agent_class'], state
 
     raise Exception('Definition for value {} not found in: {}'.format(value, definition))
 
@@ -474,14 +503,15 @@ def _definition_to_dict(definition, size=None, default_state=None):
 
     distro = sorted([item for item in definition if 'weight' in item])
 
-    ix = 0
+    id = 0
+
     def init_agent(item, id=ix):
         while id in agents:
             id += 1
 
         agent = remaining[id]
         agent['state'].update(copy(item.get('state', {})))
-        agents[id] = agent
+        agents[agent.unique_id] = agent
         del remaining[id]
         return agent
 
@@ -521,32 +551,237 @@ def _definition_to_dict(definition, size=None, default_state=None):
     return agents
 
 
-def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False, **kwargs):
+class AgentView(Mapping, Set):
+    """A lazy-loaded list of agents.
+    """
+
+    __slots__ = ("_agents",)
+
+
+    def __init__(self, agents):
+        self._agents = agents
+
+    def __getstate__(self):
+        return {"_agents": self._agents}
+
+    def __setstate__(self, state):
+        self._agents = state["_agents"]
+
+    # Mapping methods
+    def __len__(self):
+        return sum(len(x) for x in self._agents.values())
+
+    def __iter__(self):
+        yield from iter(chain.from_iterable(g.values() for g in self._agents.values()))
+
+    def __getitem__(self, agent_id):
+        if isinstance(agent_id, slice):
+            raise ValueError(f"Slicing is not supported")
+        for group in self._agents.values():
+            if agent_id in group:
+                return group[agent_id]
+        raise ValueError(f"Agent {agent_id} not found")
+
+    def filter(self, *args, **kwargs):
+        yield from filter_groups(self._agents, *args, **kwargs)
+
+    def one(self, *args, **kwargs):
+        return next(filter_groups(self._agents, *args, **kwargs))
+
+    def __call__(self, *args, **kwargs):
+        return list(self.filter(*args, **kwargs))
+
+    def __contains__(self, agent_id):
+        return any(agent_id in g for g in self._agents)
+
+    def __str__(self):
+        return str(list(a.unique_id for a in self))
+
+    def __repr__(self):
+        return f"{self.__class__.__name__}({self})"
+
+
+def filter_groups(groups, *, group=None, **kwargs):
+    assert isinstance(groups, dict)
+
+    if group is not None and not isinstance(group, list):
+        group = [group]
+
+    if group:
+        groups = list(groups[g] for g in group if g in groups)
+    else:
+        groups = list(groups.values())
+
+    agents = chain.from_iterable(filter_group(g, **kwargs) for g in groups)
+
+    yield from agents
+
+
+def filter_group(group, *id_args, unique_id=None, state_id=None, agent_class=None, ignore=None, state=None, **kwargs):
+    '''
+    Filter agents given as a dict, by the criteria given as arguments (e.g., certain type or state id).
+    '''
+    assert isinstance(group, dict)
+
+    ids = []
+
+    if unique_id is not None:
+        if isinstance(unique_id, list):
+            ids += unique_id
+        else:
+            ids.append(unique_id)
+
+    if id_args:
+        ids += id_args
 
     if state_id is not None and not isinstance(state_id, (tuple, list)):
         state_id = tuple([state_id])
-    if agent_type is not None:
+
+    if agent_class is not None:
+        agent_class = deserialize_type(agent_class)
         try:
-            agent_type = tuple(agent_type)
+            agent_class = tuple(agent_class)
         except TypeError:
-            agent_type = tuple([agent_type])
+            agent_class = tuple([agent_class])
+
+    if ids:
+        agents = (group[aid] for aid in ids if aid in group)
+    else:
+        agents = (a for a in group.values())
 
     f = agents
-
     if ignore:
         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)
 
-    if agent_type is not None:
-        f = filter(lambda agent: isinstance(agent, agent_type), f)
-    for k, v in kwargs.items():
+    if agent_class is not None:
+        f = filter(lambda agent: isinstance(agent, agent_class), f)
+
+    state = state or dict()
+    state.update(kwargs)
+
+    for k, v in state.items():
         f = filter(lambda agent: agent.state.get(k, None) == v, f)
 
-    if iterator:
-        return f
-    return f
+    yield from f
+
+
+def from_config(cfg: Dict[str, config.AgentConfig], env):
+    '''
+    Agents are specified in groups.
+    Each group can be specified in two ways, either through a fixed list in which each item has
+    has the agent type, number of agents to create, and the other parameters, or through what we call
+    an `agent distribution`, which is similar but instead of number of agents, it specifies the weight
+    of each agent type.
+    '''
+    default = cfg.get('default', None)
+    return {k: _group_from_config(c, default=default, env=env) for (k, c)  in cfg.items() if k is not 'default'}
+
+
+def _group_from_config(cfg: config.AgentConfig, default: config.SingleAgentConfig, env):
+    agents = {}
+    if cfg.fixed is not None:
+        agents = _from_fixed(cfg.fixed, topology=cfg.topology, default=default, env=env)
+    if cfg.distribution:
+        n = cfg.n or len(env.topologies[cfg.topology or default.topology])
+        target = n - len(agents)
+        agents.update(_from_distro(cfg.distribution, target,
+                                   topology=cfg.topology or default.topology,
+                                   default=default,
+                                   env=env))
+        assert len(agents) == n
+    if cfg.override:
+        for attrs in cfg.override:
+            if attrs.filter:
+                filtered = list(filter_group(agents, **attrs.filter))
+            else:
+                filtered = list(agents)
+
+            if attrs.n > len(filtered):
+                raise ValueError(f'Not enough agents to sample. Got {len(filtered)}, expected >= {attrs.n}')
+            for agent in random.sample(filtered, attrs.n):
+                agent.state.update(attrs.state)
+
+    return agents
+
+
+def _from_fixed(lst: List[config.FixedAgentConfig], topology: str, default: config.SingleAgentConfig, env):
+    agents = {}
+
+    for fixed in lst:
+        agent_id = fixed.agent_id
+        if agent_id is None:
+            agent_id = env.next_id()
+
+        cls = serialization.deserialize(fixed.agent_class or default.agent_class)
+        state = fixed.state.copy()
+        state.update(default.state)
+        agent = cls(unique_id=agent_id,
+                    model=env,
+                    **state)
+        topology = fixed.topology if (fixed.topology is not None) else (topology or default.topology)
+        if topology:
+            env.agent_to_node(agent_id, topology, fixed.node_id)
+        agents[agent.unique_id] = agent
+
+    return agents
+
+
+def _from_distro(distro: List[config.AgentDistro],
+                 n: int,
+                 topology: str,
+                 default: config.SingleAgentConfig,
+                 env):
+
+    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')
+        n = sum(dist.n for dist in distro)
+
+    weights = list(dist.weight if dist.weight is not None else 1 for dist in distro)
+    minw = min(weights)
+    norm = list(weight / minw for weight in weights)
+    total = sum(norm)
+    chunk = n // total
+
+    # random.choices would be enough to get a weighted distribution. But it can vary a lot for smaller k
+    # 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)))
+
+    # 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))
+
+    # Deserialize classes for efficiency
+    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]
+        cls = classes[idx]
+        agent_id = env.next_id()
+        state = d.state.copy()
+        if default:
+            state.update(default.state)
+        agent = cls(unique_id=agent_id, model=env, **state)
+        topology = d.topology if (d.topology is not None) else topology or default.topology
+        if topology:
+            env.agent_to_node(agent.unique_id, topology)
+        assert agent.name is not None
+        assert agent.name != 'None'
+        assert agent.name
+        agents[agent.unique_id] = agent
+
+    return agents
 
 
 from .BassModel import *

soil/config.py

@@ -0,0 +1,242 @@
+from __future__ import annotations
+from pydantic import BaseModel, ValidationError, validator, root_validator
+
+import yaml
+import os
+import sys
+
+from typing import Any, Callable, Dict, List, Optional, Union, Type
+from pydantic import BaseModel, Extra
+import networkx as nx
+
+class General(BaseModel):
+    id: str = 'Unnamed Simulation'
+    group: str = None
+    dir_path: Optional[str] = None
+    num_trials: int = 1
+    max_time: float = 100
+    interval: float = 1
+    seed: str = ""
+
+    @staticmethod
+    def default():
+        return General()
+
+
+# Could use TypeAlias in python >= 3.10
+nodeId = int
+
+class Node(BaseModel):
+    id: nodeId
+    state: Optional[Dict[str, Any]] = {}
+
+
+class Edge(BaseModel):
+    source: nodeId
+    target: nodeId
+    value: Optional[float] = 1
+
+
+class Topology(BaseModel):
+    nodes: List[Node]
+    directed: bool
+    links: List[Edge]
+
+
+class NetParams(BaseModel, extra=Extra.allow):
+    generator: Union[Callable, str]
+    n: int 
+
+
+class NetConfig(BaseModel):
+    group: str = 'network'
+    params: Optional[NetParams]
+    topology: Optional[Union[Topology, nx.Graph]]
+    path: Optional[str]
+
+    class Config:
+        arbitrary_types_allowed = True
+
+    @staticmethod
+    def default():
+        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')
+        return values
+
+
+class EnvConfig(BaseModel):
+    environment_class: Union[Type, str] = 'soil.Environment'
+    params: Dict[str, Any] = {}
+    schedule: Union[Type, str] = 'soil.time.TimedActivation'
+
+    @staticmethod
+    def default():
+        return EnvConfig()
+
+
+class SingleAgentConfig(BaseModel):
+    agent_class: Optional[Union[Type, str]] = None
+    agent_id: Optional[int] = None
+    topology: Optional[str] = None
+    node_id: Optional[Union[int, str]] = None
+    name: Optional[str] = None
+    state: Optional[Dict[str, Any]] = {}
+
+class FixedAgentConfig(SingleAgentConfig):
+    n: Optional[int] = 1
+
+    @root_validator
+    def validate_all(cls,  values):
+        if values.get('agent_id', None) is not None and values.get('n', 1) > 1:
+            print(values)
+            raise ValueError(f"An agent_id can only be provided when there is only one agent ({values.get('n')} given)")
+        return values
+
+
+class OverrideAgentConfig(FixedAgentConfig):
+    filter: Optional[Dict[str, Any]] = None
+
+
+class AgentDistro(SingleAgentConfig):
+    weight: Optional[float] = 1
+
+
+class AgentConfig(SingleAgentConfig):
+    n: Optional[int] = None
+    topology: Optional[str] = None
+    distribution: Optional[List[AgentDistro]] = None
+    fixed: Optional[List[FixedAgentConfig]] = None
+    override: Optional[List[OverrideAgentConfig]] = None
+
+    @staticmethod
+    def default():
+        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.")
+        return values
+
+
+class Config(BaseModel, extra=Extra.forbid):
+    version: Optional[str] = '1'
+    general: General = General.default()
+    topologies: Optional[Dict[str, NetConfig]] = {}
+    environment: EnvConfig = EnvConfig.default()
+    agents: Optional[Dict[str, AgentConfig]] = {}
+
+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.
+    '''
+
+
+    new = {}
+
+
+    general = {}
+    for k in ['id', 
+              'group',
+              'dir_path',
+              'num_trials',
+              'max_time',
+              'interval',
+              'seed']:
+        if k in old:
+            general[k] = old[k]
+
+    if 'name' in old:
+        general['id'] = old['name']
+
+    network = {}
+
+
+    if 'network_params' in old and old['network_params']:
+        for (k, v) in old['network_params'].items():
+            if k == 'path':
+                network['path'] = v
+            else:
+                network.setdefault('params', {})[k] = v
+
+    if 'topology' in old:
+        network['topology'] = old['topology']
+
+    agents = {
+        'network': {},
+        'default': {},
+    }
+
+    if 'agent_type' in old:
+        agents['default']['agent_class'] = old['agent_type']
+
+    if 'default_state' in old:
+        agents['default']['state'] = old['default_state']
+
+
+    def updated_agent(agent):
+        newagent = dict(agent)
+        newagent['agent_class'] = newagent['agent_type']
+        del newagent['agent_type']
+        return newagent
+
+    for agent in old.get('environment_agents', []):
+        agents['environment'] = {'distribution': [], 'fixed': []}
+        if 'agent_id' in agent:
+            agent['name'] = agent['agent_id']
+            del agent['agent_id']
+        agents['environment']['fixed'].append(updated_agent(agent))
+
+    by_weight = []
+    fixed = []
+    override = []
+
+    if 'network_agents' in old:
+        agents['network']['topology'] = 'default'
+
+        for agent in old['network_agents']:
+            agent = updated_agent(agent)
+            if 'agent_id' in agent:
+                fixed.append(agent)
+            else:
+                by_weight.append(agent)
+
+    if 'agent_type' in old and (not fixed and not by_weight):
+        agents['network']['topology'] = 'default'
+        by_weight = [{'agent_class': old['agent_type']}]
+
+    
+    # TODO: translate states properly
+    if 'states' in old:
+        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['network']['override'] = override
+    agents['network']['fixed'] = fixed
+    agents['network']['distribution'] = by_weight
+
+    environment = {'params': {}}
+    if 'environment_class' in old:
+        environment['environment_class'] = old['environment_class']
+
+    for (k, v) in old.get('environment_params', {}).items():
+        environment['params'][k] = v
+
+    return Config(version='2',
+                  general=general,
+                  topologies={'default': network},
+                  environment=environment,
+                  agents=agents)

soil/datacollection.py

@@ -8,19 +8,17 @@ class SoilDataCollector(MDC):
         # Populate model and env reporters so they have a key per 
         # So they can be shown in the web interface
         self.environment = environment
-
+        raise NotImplementedError()
 
     @property
     def model_vars(self):
-        pass
+        raise NotImplementedError()
 
     @model_vars.setter
     def model_vars(self, value):
-        pass
+        raise NotImplementedError()
 
     @property
     def agent_reporters(self):
-        self.model._history._
-
-        pass
+        raise NotImplementedError()
 

soil/environment.py

@@ -1,29 +1,27 @@
+from __future__ import annotations
 import os
 import sqlite3
-import csv
 import math
 import random
-import yaml
-import tempfile
-import pandas as pd
+import logging
+
+from typing import Dict
+from collections import namedtuple
 from time import time as current_time
 from copy import deepcopy
 from networkx.readwrite import json_graph
 
+
 import networkx as nx
 
-from tsih import History, Record, Key, NoHistory
-
 from mesa import Model
+from mesa.datacollection import DataCollector
 
-from . import serialization, agents, analysis, utils, time
+from . import serialization, agents, analysis, utils, time, config, network
+
+
+Record = namedtuple('Record', 'dict_id t_step key value')
 
-# These properties will be copied when pickling/unpickling the environment
-_CONFIG_PROPS = [ 'name',
-                  'states',
-                  'default_state',
-                  'interval',
-                 ]
 
 class Environment(Model):
     """
@@ -32,74 +30,77 @@ class Environment(Model):
     params, which are used as shared state between agents.
 
     The environment parameters and the state of every agent can be accessed
-    both by using the environment as a dictionary or with the environment's 
+    both by using the environment as a dictionary or with the environment's
     :meth:`soil.environment.Environment.get` method.
     """
 
-    def __init__(self, name=None,
-                 network_agents=None,
-                 environment_agents=None,
-                 states=None,
-                 default_state=None,
-                 interval=1,
-                 network_params=None,
-                 seed=None,
-                 topology=None,
+    def __init__(self,
+                 env_id='unnamed_env',
+                 seed='default',
                  schedule=None,
-                 initial_time=0,
-                 environment_params=None,
-                 history=True,
                  dir_path=None,
-                 **kwargs):
-
+                 interval=1,
+                 agents: Dict[str, config.AgentConfig] = {},
+                 topologies: Dict[str, config.NetConfig] = {},
+                 agent_reporters: Optional[Any] = None,
+                 model_reporters: Optional[Any] = None,
+                 tables: Optional[Any] = None,
+                 **env_params):
 
         super().__init__()
+        self.current_id = -1
+
+        self.seed = '{}_{}'.format(seed, env_id)
+        self.id = env_id
+
+        self.dir_path = dir_path or os.getcwd()
 
-        self.schedule = schedule
         if schedule is None:
-            self.schedule = time.TimedActivation()
+            schedule = time.TimedActivation()
+        self.schedule = schedule
 
-        self.name = name or 'UnnamedEnvironment'
         seed = seed or current_time()
+
         random.seed(seed)
-        if isinstance(states, list):
-            states = dict(enumerate(states))
-        self.states = deepcopy(states) if states else {}
-        self.default_state = deepcopy(default_state) or {}
-
-        if topology is None:
-            network_params = network_params or {}
-            topology = serialization.load_network(network_params,
-                                                  dir_path=dir_path)
-        if not topology:
-            topology = nx.Graph()
-        self.G = nx.Graph(topology) 
 
 
-        self.environment_params = environment_params or {}
-        self.environment_params.update(kwargs)
+        self.topologies = {}
+        self._node_ids = {}
+        for (name, cfg) in topologies.items():
+            self.set_topology(cfg=cfg,
+                              graph=name)
+        self.agents = agents or {}
+
+        self.env_params = env_params or {}
 
-        self._env_agents = {}
         self.interval = interval
-        if history:
-            history = History
-        else:
-            history = NoHistory
-        self._history = history(name=self.name,
-                                backup=True)
         self['SEED'] = seed
 
-        if network_agents:
-            distro = agents.calculate_distribution(network_agents)
-            self.network_agents = agents._convert_agent_types(distro)
-        else:
-            self.network_agents = []
+        self.logger = utils.logger.getChild(self.id)
+        self.datacollector = DataCollector(model_reporters, agent_reporters, tables)
 
-        environment_agents = environment_agents or []
-        if environment_agents:
-            distro = agents.calculate_distribution(environment_agents)
-            environment_agents = agents._convert_agent_types(distro)
-        self.environment_agents = environment_agents
+    @property
+    def topology(self):
+        return self.topologies['default']
+
+    @property
+    def network_agents(self):
+        yield from self.agents(agent_class=agents.NetworkAgent)
+
+    @staticmethod
+    def from_config(conf: config.Config, trial_id, **kwargs) -> Environment:
+        '''Create an environment for a trial of the simulation'''
+        conf = conf
+        if kwargs:
+            conf = config.Config(**conf.dict(exclude_defaults=True), **kwargs)
+        seed = '{}_{}'.format(conf.general.seed, trial_id)
+        id = '{}_trial_{}'.format(conf.general.id, trial_id).replace('.', '-')
+        opts = conf.environment.params.copy()
+        dir_path = conf.general.dir_path
+        opts.update(conf)
+        opts.update(kwargs)
+        env = serialization.deserialize(conf.environment.environment_class)(env_id=id, seed=seed, dir_path=dir_path, **opts)
+        return env
 
     @property
     def now(self):
@@ -107,73 +108,93 @@ class Environment(Model):
             return self.schedule.time
         raise Exception('The environment has not been scheduled, so it has no sense of time')
 
+
+    def topology_for(self, agent_id):
+        return self.topologies[self._node_ids[agent_id][0]]
+
+    def node_id_for(self, agent_id):
+        return self._node_ids[agent_id][1]
+
+    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)
+
+        self.topologies[graph] = topology
+
     @property
     def agents(self):
-        yield from self.environment_agents
-        yield from self.network_agents
+        return agents.AgentView(self._agents)
+    
+    def count_agents(self, *args, **kwargs):
+        return sum(1 for i in self.find_all(*args, **kwargs))
 
-    @property
-    def environment_agents(self):
-        for ref in self._env_agents.values():
-            yield ref
+    def find_all(self, *args, **kwargs):
+        return agents.AgentView(self._agents).filter(*args, **kwargs)
 
-    @environment_agents.setter
-    def environment_agents(self, environment_agents):
-        self._environment_agents = environment_agents
+    def find_one(self, *args, **kwargs):
+        return agents.AgentView(self._agents).one(*args, **kwargs)
 
-        self._env_agents = agents._definition_to_dict(definition=environment_agents)
+    @agents.setter
+    def agents(self, agents_def: Dict[str, config.AgentConfig]):
+        self._agents = agents.from_config(agents_def, env=self)
+        for d in self._agents.values():
+            for a in d.values():
+                self.schedule.add(a)
 
-    @property
-    def network_agents(self):
-        for i in self.G.nodes():
-            node = self.G.nodes[i]
-            if 'agent' in node:
-                yield node['agent']
-
-    @network_agents.setter
-    def network_agents(self, network_agents):
-        self._network_agents = network_agents
-        for ix in self.G.nodes():
-            self.init_agent(ix, agent_definitions=network_agents)
-
-    def init_agent(self, agent_id, agent_definitions):
-        node = self.G.nodes[agent_id]
+    def init_agent(self, agent_id, agent_definitions, graph='default'):
+        node = self.topologies[graph].nodes[agent_id]
         init = False
         state = dict(node)
 
-        agent_type = None
-        if 'agent_type' in self.states.get(agent_id, {}):
-            agent_type = self.states[agent_id]['agent_type']
-        elif 'agent_type' in node:
-            agent_type = node['agent_type']
-        elif 'agent_type' in self.default_state:
-            agent_type = self.default_state['agent_type']
+        agent_class = None
+        if 'agent_class' in self.states.get(agent_id, {}):
+            agent_class = self.states[agent_id]['agent_class']
+        elif 'agent_class' in node:
+            agent_class = node['agent_class']
+        elif 'agent_class' in self.default_state:
+            agent_class = self.default_state['agent_class']
 
-        if agent_type:
-            agent_type = agents.deserialize_type(agent_type)
+        if agent_class:
+            agent_class = agents.deserialize_type(agent_class)
         elif agent_definitions:
-            agent_type, state = agents._agent_from_definition(agent_definitions, unique_id=agent_id)
+            agent_class, state = agents._agent_from_definition(agent_definitions, unique_id=agent_id)
         else:
             serialization.logger.debug('Skipping node {}'.format(agent_id))
             return
-        return self.set_agent(agent_id, agent_type, state)
+        return self.set_agent(agent_id, agent_class, state)
 
-    def set_agent(self, agent_id, agent_type, state=None):
-        node = self.G.nodes[agent_id]
+    def agent_to_node(self, agent_id, graph_name='default', node_id=None, shuffle=False):
+        #TODO: test
+        if node_id is None:
+            G = self.topologies[graph_name]
+            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
+                    data['agent_id'] = agent_id
+                    break
+                    
+
+        self._node_ids[agent_id] = (graph_name, node_id)
+        print(self._node_ids)
+
+
+    def set_agent(self, agent_id, agent_class, state=None, graph='default'):
+        node = self.topologies[graph].nodes[agent_id]
         defstate = deepcopy(self.default_state) or {}
         defstate.update(self.states.get(agent_id, {}))
         defstate.update(node.get('state', {}))
         if state:
             defstate.update(state)
         a = None
-        if agent_type:
+        if agent_class:
             state = defstate
-            a = agent_type(model=self,
-                           unique_id=agent_id)
-
-        for (k, v) in getattr(a, 'defaults', {}).items():
-            if not hasattr(a, k) or getattr(a, k) is None:
-                setattr(a, k, v)
+            a = agent_class(model=self,
+                           unique_id=agent_id
+            )
 
         for (k, v) in state.items():
             setattr(a, k, v)
@@ -182,196 +203,91 @@ class Environment(Model):
         self.schedule.add(a)
         return a
 
-    def add_node(self, agent_type, state=None):
-        agent_id = int(len(self.G.nodes()))
-        self.G.add_node(agent_id)
-        a = self.set_agent(agent_id, agent_type, state)
+    def add_node(self, agent_class, state=None, graph='default'):
+        agent_id = int(len(self.topologies[graph].nodes()))
+        self.topologies[graph].add_node(agent_id)
+        a = self.set_agent(agent_id, agent_class, state, graph=graph)
         a['visible'] = True
         return a
 
-    def add_edge(self, agent1, agent2, start=None, **attrs):
+    def add_edge(self, agent1, agent2, start=None, graph='default', **attrs):
         if hasattr(agent1, 'id'):
             agent1 = agent1.id
         if hasattr(agent2, 'id'):
             agent2 = agent2.id
         start = start or self.now
-        return self.G.add_edge(agent1, agent2, **attrs)
+        return self.topologies[graph].add_edge(agent1, agent2, **attrs)
+
+    def log(self, message, *args, level=logging.INFO, **kwargs):
+        if not self.logger.isEnabledFor(level):
+            return
+        message = message + " ".join(str(i) for i in args)
+        message = " @{:>3}: {}".format(self.now, message)
+        for k, v in kwargs:
+            message += " {k}={v} ".format(k, v)
+        extra = {}
+        extra['now'] = self.now
+        extra['unique_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.datacollector.collect(self)
         self.schedule.step()
+        self.datacollector.collect(self)
 
     def run(self, until, *args, **kwargs):
-        self._save_state()
+        until = until or float('inf')
 
-        while self.schedule.next_time <= until and not math.isinf(self.schedule.next_time):
-            self.schedule.step(until=until)
+        while self.schedule.next_time < until:
+            self.step()
             utils.logger.debug(f'Simulation step {self.schedule.time}/{until}. Next: {self.schedule.next_time}')
-        self._history.flush_cache()
-
-    def _save_state(self, now=None):
-        serialization.logger.debug('Saving state @{}'.format(self.now))
-        self._history.save_records(self.state_to_tuples(now=now))
-
-    def __getitem__(self, key):
-        if isinstance(key, tuple):
-            self._history.flush_cache()
-            return self._history[key]
-
-        return self.environment_params[key]
-
-    def __setitem__(self, key, value):
-        if isinstance(key, tuple):
-            k = Key(*key)
-            self._history.save_record(*k,
-                                      value=value)
-            return
-        self.environment_params[key] = value
-        self._history.save_record(dict_id='env',
-                                  t_step=self.now,
-                                  key=key,
-                                  value=value)
+        self.schedule.time = until
 
     def __contains__(self, key):
-        return key in self.environment_params
+        return key in self.env_params
 
     def get(self, key, default=None):
         '''
-        Get the value of an environment attribute in a
-        given point in the simulation (history).
-        If key is an attribute name, this method returns
-        the current value.
-        To get values at other times, use a
-        :meth: `soil.history.Key` tuple.
+        Get the value of an environment attribute.
+        Return `default` if the value is not set.
         '''
-        return self[key] if key in self else default
+        return self.env_params.get(key, default)
 
-    def get_agent(self, agent_id):
-        return self.G.nodes[agent_id]['agent']
+    def __getitem__(self, key):
+        return self.env_params.get(key)
 
-    def get_agents(self, nodes=None):
-        if nodes is None:
-            return self.agents
-        return (self.G.nodes[i]['agent'] for i in nodes)
+    def __setitem__(self, key, value):
+        return self.env_params.__setitem__(key, value)
 
-    def dump_csv(self, f):
-        with utils.open_or_reuse(f, 'w') as f:
-            cr = csv.writer(f)
-            cr.writerow(('agent_id', 't_step', 'key', 'value'))
-            for i in self.history_to_tuples():
-                cr.writerow(i)
-
-    def dump_gexf(self, f):
-        G = self.history_to_graph()
-        # Workaround for geometric models
-        # See soil/soil#4
-        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'])
-
-        nx.write_gexf(G, f, version="1.2draft")
-
-    def dump(self, *args, formats=None, **kwargs):
-        if not formats:
-            return
-        functions = {
-            'csv': self.dump_csv,
-            'gexf': self.dump_gexf
-        }
-        for f in formats:
-            if f in functions:
-                functions[f](*args, **kwargs)
-            else:
-                raise ValueError('Unknown format: {}'.format(f))
-
-    def dump_sqlite(self, f):
-        return self._history.dump(f)
-
-    def state_to_tuples(self, now=None):
+    def _agent_to_tuples(self, agent, now=None):
         if now is None:
             now = self.now
-        for k, v in self.environment_params.items():
+        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:
-            for k, v in agent.state.items():
-                yield Record(dict_id=agent.id,
-                             t_step=now,
-                             key=k,
-                             value=v)
+            yield from self._agent_to_tuples(agent, now)
 
-    def history_to_tuples(self):
-        return self._history.to_tuples()
-
-    def history_to_graph(self):
-        G = nx.Graph(self.G)
-
-        for agent in self.network_agents:
-
-            attributes = {'agent': str(agent.__class__)}
-            lastattributes = {}
-            spells = []
-            lastvisible = False
-            laststep = None
-            history = self[agent.id, None, None]
-            if not history:
-                continue
-            for t_step, attribute, value in sorted(list(history)):
-                if attribute == 'visible':
-                    nowvisible = value
-                    if nowvisible and not lastvisible:
-                        laststep = t_step
-                    if not nowvisible and lastvisible:
-                        spells.append((laststep, t_step))
-
-                    lastvisible = nowvisible
-                    continue
-                key = 'attr_' + attribute
-                if key not in attributes:
-                    attributes[key] = list()
-                if key not in lastattributes:
-                    lastattributes[key] = (value, t_step)
-                elif lastattributes[key][0] != value:
-                    last_value, laststep = lastattributes[key]
-                    commit_value = (last_value, laststep, t_step)
-                    if key not in attributes:
-                        attributes[key] = list()
-                    attributes[key].append(commit_value)
-                    lastattributes[key] = (value, t_step)
-            for k, v in lastattributes.items():
-                attributes[k].append((v[0], v[1], None))
-            if lastvisible:
-                spells.append((laststep, None))
-            if spells:
-                G.add_node(agent.id, spells=spells, **attributes)
-            else:
-                G.add_node(agent.id, **attributes)
-
-        return G
-
-    def __getstate__(self):
-        state = {}
-        for prop in _CONFIG_PROPS:
-            state[prop] = self.__dict__[prop]
-        state['G'] = json_graph.node_link_data(self.G)
-        state['environment_agents'] = self._env_agents
-        state['history'] = self._history
-        state['schedule'] = self.schedule
-        return state
-
-    def __setstate__(self, state):
-        for prop in _CONFIG_PROPS:
-            self.__dict__[prop] = state[prop]
-        self._env_agents = state['environment_agents']
-        self.G = json_graph.node_link_graph(state['G'])
-        self._history = state['history']
-        # self._env = None
-        self.schedule = state['schedule']
-        self._queue = []
 
 
 SoilEnvironment = Environment

soil/exporters.py

@@ -1,7 +1,8 @@
 import os
-import csv as csvlib
-import time
+from time import time as current_time
 from io import BytesIO
+from sqlalchemy import create_engine
+
 
 import matplotlib.pyplot as plt
 import networkx as nx
@@ -48,20 +49,24 @@ class Exporter:
         self.simulation = simulation
         outdir = outdir or os.path.join(os.getcwd(), 'soil_output')
         self.outdir = os.path.join(outdir,
-                                   simulation.group or '',
-                                   simulation.name)
+                                   simulation.config.general.group or '',
+                                   simulation.config.general.id)
         self.dry_run = dry_run
         self.copy_to = copy_to
 
-    def start(self):
+    def sim_start(self):
         '''Method to call when the simulation starts'''
         pass
 
-    def end(self, stats):
+    def sim_end(self):
         '''Method to call when the simulation ends'''
         pass
 
-    def trial(self, env, stats):
+    def trial_start(self, env):
+        '''Method to call when a trial start'''
+        pass
+
+    def trial_end(self, env):
         '''Method to call when a trial ends'''
         pass
 
@@ -80,79 +85,148 @@ class Exporter:
 class default(Exporter):
     '''Default exporter. Writes sqlite results, as well as the simulation YAML'''
 
-    def start(self):
-        if not self.dry_run:
-            logger.info('Dumping results to %s', self.outdir)
-            self.simulation.dump_yaml(outdir=self.outdir)
-        else:
-            logger.info('NOT dumping results')
+    # def sim_start(self):
+    #     if not self.dry_run:
+    #         logger.info('Dumping results to %s', self.outdir)
+    #         self.simulation.dump_yaml(outdir=self.outdir)
+    #     else:
+    #         logger.info('NOT dumping results')
 
-    def trial(self, env, stats):
-        if not self.dry_run:
-            with timer('Dumping simulation {} trial {}'.format(self.simulation.name,
-                                                               env.name)):
-                with self.output('{}.sqlite'.format(env.name), mode='wb') as f:
-                    env.dump_sqlite(f)
+    # def trial_start(self, env, stats):
+    #     if not self.dry_run:
+    #         with timer('Dumping simulation {} trial {}'.format(self.simulation.name,
+    #                                                            env.name)):
+    #             engine = create_engine('sqlite:///{}.sqlite'.format(env.name), echo=False)
 
-    def end(self, stats):
-          with timer('Dumping simulation {}\'s stats'.format(self.simulation.name)):
-              with self.output('{}.sqlite'.format(self.simulation.name), mode='wb') as f:
-                  self.simulation.dump_sqlite(f)
+    #             dc = env.datacollector
+    #             tables = {'env': dc.get_model_vars_dataframe(),
+    #                       'agents': dc.get_agent_vars_dataframe(),
+    #                       'agents': dc.get_agent_vars_dataframe()}
+    #             for table in dc.tables:
+    #                 tables[table] = dc.get_table_dataframe(table)
+    #             for (t, df) in tables.items():
+    #                 df.to_sql(t, con=engine)
 
+    # def sim_end(self, stats):
+    #       with timer('Dumping simulation {}\'s stats'.format(self.simulation.name)):
+    #           engine = create_engine('sqlite:///{}.sqlite'.format(self.simulation.name), echo=False)
+    #           with self.output('{}.sqlite'.format(self.simulation.name), mode='wb') as f:
+    #               self.simulation.dump_sqlite(f)
+
+
+def get_dc_dfs(dc):
+    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() 
 
 
 class csv(Exporter):
+
     '''Export the state of each environment (and its agents) in a separate CSV file'''
-    def trial(self, env, stats):
+    def trial_end(self, env):
         with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.simulation.name,
-                                                                          env.name,
+                                                                          env.id,
                                                                           self.outdir)):
-            with self.output('{}.csv'.format(env.name)) as f:
-                env.dump_csv(f)
-
-            with self.output('{}.stats.csv'.format(env.name)) as f:
-                statwriter = csvlib.writer(f, delimiter='\t', quotechar='"', quoting=csvlib.QUOTE_ALL)
-
-                for stat in stats:
-                    statwriter.writerow(stat)
+            for (df_name, df) in get_dc_dfs(env.datacollector):
+                with self.output('{}.stats.{}.csv'.format(env.id, df_name)) as f:
+                    df.to_csv(f)
 
 
 class gexf(Exporter):
-    def trial(self, env, stats):
+    def trial_end(self, env):
         if self.dry_run:
             logger.info('Not dumping GEXF in dry_run mode')
             return
 
         with timer('[GEXF] Dumping simulation {} trial {}'.format(self.simulation.name,
-                                                                  env.name)):
-            with self.output('{}.gexf'.format(env.name), mode='wb') as f:
-                env.dump_gexf(f)
+                                                                  env.id)):
+            with self.output('{}.gexf'.format(env.id), mode='wb') as f:
+                self.dump_gexf(env, f)
 
+    def dump_gexf(self, env, f):
+        G = env.history_to_graph()
+        # Workaround for geometric models
+        # See soil/soil#4
+        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'])
+
+        nx.write_gexf(G, f, version="1.2draft")
 
 class dummy(Exporter):
 
-    def start(self):
+    def sim_start(self):
         with self.output('dummy', 'w') as f:
-            f.write('simulation started @ {}\n'.format(time.time()))
+            f.write('simulation started @ {}\n'.format(current_time()))
 
-    def trial(self, env, stats):
+    def trial_start(self, env):
         with self.output('dummy', 'w') as f:
-            for i in env.history_to_tuples():
-                f.write(','.join(map(str, i)))
-                f.write('\n')
+            f.write('trial started@ {}\n'.format(current_time()))
 
-    def sim(self, stats):
+    def trial_end(self, env):
+        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(time.time()))
-
-
+            f.write('simulation ended @ {}\n'.format(current_time()))
 
 class graphdrawing(Exporter):
 
-    def trial(self, env, stats):
+    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.name)) as f:
+        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__)}
+        lastattributes = {}
+        spells = []
+        lastvisible = False
+        laststep = None
+        if not history:
+            history = sorted(list(env.state_to_tuples()))
+        for _, t_step, attribute, value in history:
+            if attribute == 'visible':
+                nowvisible = value
+                if nowvisible and not lastvisible:
+                    laststep = t_step
+                if not nowvisible and lastvisible:
+                    spells.append((laststep, t_step))
+
+                lastvisible = nowvisible
+                continue
+            key = 'attr_' + attribute
+            if key not in attributes:
+                attributes[key] = list()
+            if key not in lastattributes:
+                lastattributes[key] = (value, t_step)
+            elif lastattributes[key][0] != value:
+                last_value, laststep = lastattributes[key]
+                commit_value = (last_value, laststep, t_step)
+                if key not in attributes:
+                    attributes[key] = list()
+                attributes[key].append(commit_value)
+                lastattributes[key] = (value, t_step)
+        for k, v in lastattributes.items():
+            attributes[k].append((v[0], v[1], None))
+        if lastvisible:
+            spells.append((laststep, None))
+        if spells:
+            G.add_node(agent.id, spells=spells, **attributes)
+        else:
+            G.add_node(agent.id, **attributes)
+
+    return G

soil/network.py

@@ -0,0 +1,42 @@
+from typing import Dict
+import os
+import sys
+
+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)
+
+    if cfg.path:
+        path = cfg.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')
+        return method(path, **kwargs)
+
+    if cfg.params:
+        net_args = cfg.params.dict()
+        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',])
+        return method(**net_args)
+
+    if isinstance(cfg.topology, basestring) or isinstance(cfg.topology, dict):
+        return nx.json_graph.node_link_graph(cfg.topology)
+
+    return nx.Graph()

soil/serialization.py

@@ -2,6 +2,7 @@ import os
 import logging
 import ast
 import sys
+import re
 import importlib
 from glob import glob
 from itertools import product, chain
@@ -15,38 +16,39 @@ from jinja2 import Template
 logger = logging.getLogger('soil')
 
 
-def load_network(network_params, dir_path=None):
-    G = nx.Graph()
+# def load_network(network_params, dir_path=None):
+#     G = nx.Graph()
 
-    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)
+#     if not network_params:
+#         return G
 
-    elif 'generator' in network_params:
-        net_args = network_params.copy()
-        net_gen = net_args.pop('generator')
+#     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)
 
-        if dir_path not in sys.path:
-            sys.path.append(dir_path)
+#     elif 'generator' in network_params:
+#         net_args = network_params.copy()
+#         net_gen = net_args.pop('generator')
 
-        method = deserializer(net_gen,
-                              known_modules=['networkx.generators',])
-        G = method(**net_args)
-
-    return G
+#         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
 
 
 def load_file(infile):
@@ -120,8 +122,8 @@ def load_files(*patterns, **kwargs):
         for i in glob(pattern, **kwargs):
             for config in load_file(i):
                 path = os.path.abspath(i)
-                if 'dir_path' not in config:
-                    config['dir_path'] = os.path.dirname(path)
+                if 'general' in config and 'dir_path' not in config['general']:
+                    config['general']['dir_path'] = os.path.dirname(path)
                 yield config, path
 
 
@@ -134,7 +136,9 @@ def load_config(config):
 
 builtins = importlib.import_module('builtins')
 
-def name(value, known_modules=[]):
+KNOWN_MODULES = ['soil', ]
+
+def name(value, known_modules=KNOWN_MODULES):
     '''Return a name that can be imported, to serialize/deserialize an object'''
     if value is None:
         return 'None'
@@ -163,13 +167,16 @@ def serializer(type_):
     return lambda x: x
 
 
-def serialize(v, known_modules=[]):
+def serialize(v, known_modules=KNOWN_MODULES):
     '''Get a text representation of an object.'''
     tname = name(v, known_modules=known_modules)
     func = serializer(tname)
     return func(v), tname
 
-def deserializer(type_, known_modules=[]):
+
+IS_CLASS = re.compile(r"<class '(.*)'>")
+
+def deserializer(type_, known_modules=KNOWN_MODULES):
     if type(type_) != str:  # Already deserialized
         return type_
     if type_ == 'str':
@@ -179,17 +186,23 @@ def deserializer(type_, known_modules=[]):
     if hasattr(builtins, type_):  # Check if it's a builtin type
         cls = getattr(builtins, type_)
         return lambda x=None: ast.literal_eval(x) if x is not None else cls()
+    match = IS_CLASS.match(type_)
+    if match:
+        modname, tname = match.group(1).rsplit(".", 1)
+        module = importlib.import_module(modname)
+        cls = getattr(module, tname)
+        return getattr(cls, 'deserialize', cls)
+        
     # Otherwise, see if we can find the module and the class
-    modules = known_modules or []
     options = []
 
-    for mod in modules:
+    for mod in known_modules:
         if mod:
             options.append((mod, type_))
 
     if '.' in type_:  # Fully qualified module
         module, type_ = type_.rsplit(".", 1)
-        options.append ((module, type_))
+        options.append((module, type_))
 
     errors = []
     for modname, tname in options:
@@ -212,11 +225,11 @@ def deserialize(type_, value=None, **kwargs):
     return des(value)
 
 
-def deserialize_all(names, *args, known_modules=['soil'], **kwargs):
-    '''Return the set of exporters for a simulation, given the exporter names'''
-    exporters = []
+def deserialize_all(names, *args, known_modules=KNOWN_MODULES, **kwargs):
+    '''Return the list of deserialized objects'''
+    objects = []
     for name in names:
         mod = deserialize(name, known_modules=known_modules)
-        exporters.append(mod(*args, **kwargs))
-    return exporters
+        objects.append(mod(*args, **kwargs))
+    return objects
 

soil/simulation.py

@@ -1,139 +1,52 @@
 import os
-import time
+from time import time as current_time, strftime 
 import importlib
 import sys
 import yaml
 import traceback
 import logging
 import networkx as nx
+
 from networkx.readwrite import json_graph
 from multiprocessing import Pool
 from functools import partial
-from tsih import History
-
 import pickle
 
 from . import serialization, utils, basestring, agents
 from .environment import Environment
 from .utils import logger
 from .exporters import default
-from .stats import defaultStats
+
+from .config import Config, convert_old
 
 
 #TODO: change documentation for simulation
-
 class Simulation:
     """
-    Similar to nsim.NetworkSimulation with three main differences:
-        1) agent type can be specified by name or by class.
-        2) instead of just one type, a network agents distribution can be used.
-           The distribution specifies the weight (or probability) of each
-           agent type in the topology. This is an example distribution: ::
-
-                  [
-                    {'agent_type': 'agent_type_1',
-                     'weight': 0.2,
-                     'state': {
-                         'id': 0
-                      }
-                    },
-                    {'agent_type': 'agent_type_2',
-                     'weight': 0.8,
-                     'state': {
-                         'id': 1
-                      }
-                    }
-                  ]
-
-          In this example, 20% of the nodes will be marked as type
-          'agent_type_1'.
-        3) if no initial state is given, each node's state will be set
-           to `{'id': 0}`.
-
     Parameters
     ---------
-    name : str, optional
+    config (optional): :class:`config.Config`
         name of the Simulation
-    group : str, optional
-        a group name can be used to link simulations
-    topology : networkx.Graph instance, optional
-    network_params : dict
-        parameters used to create a topology with networkx, if no topology is given
-    network_agents : dict
-        definition of agents to populate the topology with
-    agent_type : NetworkAgent subclass, optional
-        Default type of NetworkAgent to use for nodes not specified in network_agents
-    states : list, optional
-        List of initial states corresponding to the nodes in the topology. Basic form is a list of integers
-        whose value indicates the state
-    dir_path: str, optional
-        Directory path to load simulation assets (files, modules...)
-    seed : str, optional
-        Seed to use for the random generator
-    num_trials : int, optional
-        Number of independent simulation runs
-    max_time : int, optional
-        Time how long the simulation should run
-    environment_params : dict, optional
-        Dictionary of globally-shared environmental parameters
-    environment_agents: dict, optional
-        Similar to network_agents. Distribution of Agents that control the environment
-    environment_class: soil.environment.Environment subclass, optional
-        Class for the environment. It defailts to soil.environment.Environment
-    load_module : str, module name, deprecated
-        If specified, soil will load the content of this module under 'soil.agents.custom'
-
 
+    kwargs: parameters to use to initialize a new configuration, if one has not been provided.
     """
 
-    def __init__(self, name=None, group=None, topology=None, network_params=None,
-                 network_agents=None, agent_type=None, states=None,
-                 default_state=None, interval=1, num_trials=1,
-                 max_time=100, load_module=None, seed=None,
-                 dir_path=None, environment_agents=None,
-                 environment_params=None, environment_class=None,
+    def __init__(self, config=None,
                  **kwargs):
-
-        self.load_module = load_module
-        self.network_params = network_params
-        self.name = name or 'Unnamed'
-        self.seed = str(seed or name)
-        self._id = '{}_{}'.format(self.name, time.strftime("%Y-%m-%d_%H.%M.%S"))
-        self.group = group or ''
-        self.num_trials = num_trials
-        self.max_time = max_time
-        self.default_state = default_state or {}
-        self.dir_path = dir_path or os.getcwd()
-        self.interval = interval
-
-        sys.path += list(x for x in [os.getcwd(), self.dir_path] if x not in sys.path)
-
-        if topology is None:
-            topology = serialization.load_network(network_params,
-                                                  dir_path=self.dir_path)
-        elif isinstance(topology, basestring) or isinstance(topology, dict):
-            topology = json_graph.node_link_graph(topology)
-        self.topology = nx.Graph(topology)
+        if kwargs:
+            cfg = {}
+            if config:
+                cfg.update(config.dict(include_defaults=False))
+            cfg.update(kwargs)
+            config = Config(**cfg)
+        if not config:
+            raise ValueError("You need to specify a simulation configuration")
+        self.config = config
 
 
-        self.environment_params = environment_params or {}
-        self.environment_class = serialization.deserialize(environment_class,
-                                                   known_modules=['soil.environment', ]) or Environment
-
-        environment_agents = environment_agents or []
-        self.environment_agents = agents._convert_agent_types(environment_agents,
-                                                              known_modules=[self.load_module])
-
-        distro = agents.calculate_distribution(network_agents,
-                                               agent_type)
-        self.network_agents = agents._convert_agent_types(distro,
-                                                          known_modules=[self.load_module])
-
-        self.states = agents._validate_states(states,
-                                              self.topology)
-
-        self._history = History(name=self.name,
-                                backup=False)
+    @property
+    def name(self) -> str:
+        return self.config.general.id
 
     def run_simulation(self, *args, **kwargs):
         return self.run(*args, **kwargs)
@@ -142,25 +55,23 @@ class Simulation:
         '''Run the simulation and return the list of resulting environments'''
         return list(self.run_gen(*args, **kwargs))
 
-    def _run_sync_or_async(self, parallel=False, *args, **kwargs):
+    def _run_sync_or_async(self, parallel=False, **kwargs):
         if parallel and not os.environ.get('SENPY_DEBUG', None):
             p = Pool()
-            func = partial(self.run_trial_exceptions,
-                           *args,
-                           **kwargs)
-            for i in p.imap_unordered(func, range(self.num_trials)):
+            func = partial(self.run_trial_exceptions, **kwargs)
+            for i in p.imap_unordered(func, range(self.config.general.num_trials)):
                 if isinstance(i, Exception):
                     logger.error('Trial failed:\n\t%s', i.message)
                     continue
                 yield i
         else:
-            for i in range(self.num_trials):
-                yield self.run_trial(*args,
+            for i in range(self.config.general.num_trials):
+                yield self.run_trial(trial_id=i,
                                      **kwargs)
 
-    def run_gen(self, *args, parallel=False, dry_run=False,
-                exporters=[default, ], stats=[], outdir=None, exporter_params={},
-                stats_params={}, log_level=None,
+    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.'''
         if log_level:
@@ -173,87 +84,63 @@ class Simulation:
                                                   dry_run=dry_run,
                                                   outdir=outdir,
                                                   **exporter_params)
-        stats = serialization.deserialize_all(simulation=self,
-                                              names=stats,
-                                              known_modules=['soil.stats',],
-                                              **stats_params)
-
-        with utils.timer('simulation {}'.format(self.name)):
-            for stat in stats:
-                stat.start()
 
+        with utils.timer('simulation {}'.format(self.config.general.id)):
             for exporter in exporters:
-                exporter.start()
-            for env in self._run_sync_or_async(*args,
-                                               parallel=parallel,
+                exporter.sim_start()
+
+            for env in self._run_sync_or_async(parallel=parallel,
                                                log_level=log_level,
                                                **kwargs):
 
-                collected = list(stat.trial(env) for stat in stats)
-
-                saved = self.save_stats(collected, t_step=env.now, trial_id=env.name)
+                for exporter in exporters:
+                    exporter.trial_start(env)
 
                 for exporter in exporters:
-                    exporter.trial(env, saved)
+                    exporter.trial_end(env)
 
                 yield env
 
-
-            collected = list(stat.end() for stat in stats)
-            saved = self.save_stats(collected)
-
             for exporter in exporters:
-                exporter.end(saved)
-
-
-    def save_stats(self, collection, **kwargs):
-        stats = dict(kwargs)
-        for stat in collection:
-            stats.update(stat)
-        self._history.save_stats(utils.flatten_dict(stats))
-        return stats
-
-    def get_stats(self, **kwargs):
-        return self._history.get_stats(**kwargs)
-
-    def log_stats(self, stats):
-        logger.info('Stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
-    
+                exporter.sim_end()
 
     def get_env(self, trial_id=0, **kwargs):
         '''Create an environment for a trial of the simulation'''
-        opts = self.environment_params.copy()
-        opts.update({
-            'name': trial_id,
-            'topology': self.topology.copy(),
-            'network_params': self.network_params,
-            'seed': '{}_trial_{}'.format(self.seed, trial_id),
-            'initial_time': 0,
-            'interval': self.interval,
-            'network_agents': self.network_agents,
-            'initial_time': 0,
-            'states': self.states,
-            'dir_path': self.dir_path,
-            'default_state': self.default_state,
-            'environment_agents': self.environment_agents,
-        })
-        opts.update(kwargs)
-        env = self.environment_class(**opts)
+        # opts = self.environment_params.copy()
+        # opts.update({
+        #     'name': '{}_trial_{}'.format(self.name, trial_id),
+        #     'topology': self.topology.copy(),
+        #     'network_params': self.network_params,
+        #     'seed': '{}_trial_{}'.format(self.seed, trial_id),
+        #     'initial_time': 0,
+        #     'interval': self.interval,
+        #     'network_agents': self.network_agents,
+        #     'initial_time': 0,
+        #     'states': self.states,
+        #     'dir_path': self.dir_path,
+        #     'default_state': self.default_state,
+        #     'history': bool(self._history),
+        #     'environment_agents': self.environment_agents,
+        # })
+        # opts.update(kwargs)
+        print(self.config)
+        env = Environment.from_config(self.config, trial_id=trial_id, **kwargs)
         return env
 
-    def run_trial(self, until=None, log_level=logging.INFO, **opts):
+    def run_trial(self, trial_id=None, until=None, log_level=logging.INFO, **opts):
         """
         Run a single trial of the simulation
 
         """
-        trial_id = '{}_trial_{}'.format(self.name, time.time()).replace('.', '-')
+        trial_id = trial_id if trial_id is not None else current_time()
         if log_level:
             logger.setLevel(log_level)
         # Set-up trial environment and graph
-        until = until or self.max_time
-        env = self.get_env(trial_id=trial_id, **opts)
+        until = until or self.config.general.max_time
+
+        env = self.get_env(trial_id, **opts)
         # Set up agents on nodes
-        with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
+        with utils.timer('Simulation {} trial {}'.format(self.config.general.id, trial_id)):
             env.run(until)
         return env
 
@@ -271,88 +158,41 @@ class Simulation:
             return ex
 
     def to_dict(self):
-        return self.__getstate__()
+        return self.config.dict()
 
     def to_yaml(self):
-        return yaml.dump(self.to_dict())
-
-
-    def dump_yaml(self, f=None, outdir=None):
-        if not f and not outdir:
-            raise ValueError('specify a file or an output directory')
-
-        if not f:
-            f = os.path.join(outdir, '{}.dumped.yml'.format(self.name))
-
-        with utils.open_or_reuse(f, 'w') as f:
-            f.write(self.to_yaml())
-
-    def dump_pickle(self, f=None, outdir=None):
-        if not outdir and not f:
-            raise ValueError('specify a file or an output directory')
-
-        if not f:
-            f = os.path.join(outdir,
-                             '{}.simulation.pickle'.format(self.name))
-        with utils.open_or_reuse(f, 'wb') as f:
-            pickle.dump(self, f)
-
-    def dump_sqlite(self, f):
-        return self._history.dump(f)
-
-    def __getstate__(self):
-        state={}
-        for k, v in self.__dict__.items():
-            if k[0] != '_':
-                state[k] = v
-                state['topology'] = json_graph.node_link_data(self.topology)
-                state['network_agents'] = agents.serialize_definition(self.network_agents,
-                                                                      known_modules = [])
-                state['environment_agents'] = agents.serialize_definition(self.environment_agents,
-                                                                          known_modules = [])
-                state['environment_class'] = serialization.serialize(self.environment_class,
-                                                                     known_modules=['soil.environment'])[1]  # func, name
-        if state['load_module'] is None:
-            del state['load_module']
-        return state
-
-    def __setstate__(self, state):
-        self.__dict__ = state
-        self.load_module = getattr(self, 'load_module', None)
-        if self.dir_path not in sys.path:
-            sys.path += [self.dir_path, os.getcwd()]
-        self.topology = json_graph.node_link_graph(state['topology'])
-        self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
-        self.environment_agents = agents._convert_agent_types(self.environment_agents,
-                                                              known_modules=[self.load_module])
-        self.environment_class = serialization.deserialize(self.environment_class,
-                                                   known_modules=[self.load_module, 'soil.environment', ])  # func, name
+        return yaml.dump(self.config.dict())
 
 
 def all_from_config(config):
     configs = list(serialization.load_config(config))
-    for config, _ in configs:
-        sim = Simulation(**config)
+    for config, path in configs:
+        if config.get('version', '1') == '1':
+            config = convert_old(config)
+        if not isinstance(config, Config):
+            config = Config(**config)
+        if not config.general.dir_path:
+            config.general.dir_path = os.path.dirname(path)
+        sim = Simulation(config=config)
         yield sim
 
 
 def from_config(conf_or_path):
+    lst = list(all_from_config(conf_or_path))
+    if len(lst) > 1:
+        raise AttributeError('Provide only one configuration')
+    return lst[0]
+
+def from_old_config(conf_or_path):
     config = list(serialization.load_config(conf_or_path))
     if len(config) > 1:
         raise AttributeError('Provide only one configuration')
-    config = config[0][0]
-    sim = Simulation(**config)
-    return sim
+    config = convert_old(config[0][0])
+    return Simulation(config)
 
 
 def run_from_config(*configs, **kwargs):
-    for config_def in configs:
-        # logger.info("Found {} config(s)".format(len(ls)))
-        for config, path in serialization.load_config(config_def):
-            name = config.get('name', 'unnamed')
-            logger.info("Using config(s): {name}".format(name=name))
-
-            dir_path = config.pop('dir_path', os.path.dirname(path))
-            sim = Simulation(dir_path=dir_path,
-                             **config)
-            sim.run_simulation(**kwargs)
+    for sim in all_from_config(configs):
+        name = config.general.id
+        logger.info("Using config(s): {name}".format(name=name))
+        sim.run_simulation(**kwargs)

soil/stats.py

@@ -1,106 +0,0 @@
-import pandas as pd
-
-from collections import Counter
-
-class Stats:
-    '''
-    Interface for all stats. It is not necessary, but it is useful
-    if you don't plan to implement all the methods.
-    '''
-
-    def __init__(self, simulation):
-        self.simulation = simulation
-
-    def start(self):
-        '''Method to call when the simulation starts'''
-        pass
-
-    def end(self):
-        '''Method to call when the simulation ends'''
-        return {}
-
-    def trial(self, env):
-        '''Method to call when a trial ends'''
-        return {}
-
-
-class distribution(Stats):
-    '''
-    Calculate the distribution of agent states at the end of each trial,
-    the mean value, and its deviation.
-    '''
-
-    def start(self):
-        self.means = []
-        self.counts = []
-
-    def trial(self, env):
-        df = env[None, None, None].df()
-        df = df.drop('SEED', axis=1)
-        ix = df.index[-1]
-        attrs = df.columns.get_level_values(0)
-        vc = {}
-        stats = {
-            'mean': {},
-            'count': {},
-        }
-        for a in attrs:
-            t = df.loc[(ix, a)]
-            try:
-                stats['mean'][a] = t.mean()
-                self.means.append(('mean', a, t.mean()))
-            except TypeError:
-                pass
-
-            for name, count in t.value_counts().iteritems():
-                if a not in stats['count']:
-                    stats['count'][a] = {}
-                stats['count'][a][name] = count
-                self.counts.append(('count', a, name, count))
-
-        return stats
-
-    def end(self):
-        dfm = pd.DataFrame(self.means, columns=['metric', 'key', 'value'])
-        dfc = pd.DataFrame(self.counts, columns=['metric', 'key', 'value', 'count'])
-
-        count = {}
-        mean = {}
-
-        if self.means:
-            res = dfm.groupby(by=['key']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
-            mean = res['value'].to_dict()
-        if self.counts:
-            res = dfc.groupby(by=['key', 'value']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
-            for k,v in res['count'].to_dict().items():
-                if k not in count:
-                    count[k] = {}
-                for tup, times in v.items():
-                    subkey, subcount = tup
-                    if subkey not in count[k]:
-                        count[k][subkey] = {}
-                    count[k][subkey][subcount] = times
-
-
-        return {'count': count, 'mean': mean}
-
-
-class defaultStats(Stats):
-
-    def trial(self, env):
-        c = Counter()
-        c.update(a.__class__.__name__ for a in env.network_agents)
-
-        c2 = Counter()
-        c2.update(a['id'] for a in env.network_agents)
-
-        return {
-            'network ': {
-                'n_nodes': env.G.number_of_nodes(),
-                'n_edges': env.G.number_of_edges(),
-            },
-            'agents': {
-                'model_count': dict(c),
-                'state_count': dict(c2),
-            }
-        }

soil/time.py

@@ -3,18 +3,24 @@ from queue import Empty
 from heapq import heappush, heappop
 import math
 from .utils import logger
-from mesa import Agent
+from mesa import Agent as MesaAgent
 
 
+INFINITY = float('inf')
+
 class When:
     def __init__(self, time):
-        self._time = float(time)
+        if isinstance(time, When):
+            return time
+        self._time = time
 
     def abs(self, time):
         return self._time
 
+NEVER = When(INFINITY)
 
-class Delta:
+
+class Delta(When):
     def __init__(self, delta):
         self._delta = delta
 
@@ -35,53 +41,40 @@ class TimedActivation(BaseScheduler):
         self._queue = []
         self.next_time = 0
 
-    def add(self, agent: Agent):
+    def add(self, agent: MesaAgent):
         if agent.unique_id not in self._agents:
             heappush(self._queue, (self.time, agent.unique_id))
             super().add(agent)
 
-    def step(self, until: float =float('inf')) -> None:
+    def step(self) -> None:
         """
         Executes agents in order, one at a time. After each step,
         an agent will signal when it wants to be scheduled next.
         """
 
-        when = None
-        agent_id = None
-        unsched = []
-        until = until or float('inf')
+        if self.next_time == INFINITY:
+            return
+
+        self.time = self.next_time
+        when = self.time
+
+        while self._queue and self._queue[0][0] == self.time:
+            (when, agent_id) = heappop(self._queue)
+            logger.debug(f'Stepping agent {agent_id}')
+
+            returned = self._agents[agent_id].step()
+            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))
+
+            heappush(self._queue, (when, agent_id))
+
+        self.steps += 1
 
         if not self._queue:
-            self.time = until
-            self.next_time = float('inf')
+            self.time = INFINITY
+            self.next_time = INFINITY
             return
 
-        (when, agent_id) = self._queue[0]
+        self.next_time = self._queue[0][0]
 
-        if until and when > until:
-            self.time = until
-            self.next_time = when
-            return
-
-        self.time = when
-        next_time = float("inf")
-
-        while when == self.time:
-            heappop(self._queue)
-            logger.debug(f'Stepping agent {agent_id}')
-            when = (self._agents[agent_id].step() or Delta(1)).abs(self.time)
-            heappush(self._queue, (when, agent_id))
-            if when < next_time:
-                next_time = when
-
-            if not self._queue or self._queue[0][0] > self.time:
-                agent_id = None
-                break
-            else:
-                (when, agent_id) = self._queue[0]
-
-        if when and when < self.time:
-            raise Exception("Invalid scheduling time")
-
-        self.next_time = next_time
-        self.steps += 1

soil/utils.py

@@ -1,5 +1,5 @@
 import logging
-import time
+from time import time as current_time, strftime, gmtime, localtime
 import os
 
 from shutil import copyfile
@@ -13,13 +13,13 @@ logger = logging.getLogger('soil')
 
 @contextmanager
 def timer(name='task', pre="", function=logger.info, to_object=None):
-    start = time.time()
+    start = current_time()
     function('{}Starting {} at {}.'.format(pre, name,
-                                           time.strftime("%X", time.gmtime(start))))
+                                           strftime("%X", gmtime(start))))
     yield start
-    end = time.time()
+    end = current_time()
     function('{}Finished {} at {} in {} seconds'.format(pre, name,
-                                                        time.strftime("%X", time.gmtime(end)),
+                                                        strftime("%X", gmtime(end)),
                                                         str(end-start)))
     if to_object:
         to_object.start = start
@@ -34,7 +34,7 @@ def safe_open(path, mode='r', backup=True, **kwargs):
         os.makedirs(outdir)
     if backup and 'w' in mode and os.path.exists(path):
         creation = os.path.getctime(path)
-        stamp = time.strftime('%Y-%m-%d_%H.%M.%S', time.localtime(creation))
+        stamp = strftime('%Y-%m-%d_%H.%M.%S', localtime(creation))
 
         backup_dir = os.path.join(outdir, 'backup')
         if not os.path.exists(backup_dir):
@@ -45,11 +45,13 @@ def safe_open(path, mode='r', backup=True, **kwargs):
     return open(path, mode=mode, **kwargs)
 
 
+@contextmanager
 def open_or_reuse(f, *args, **kwargs):
     try:
-        return safe_open(f, *args, **kwargs)
+        with safe_open(f, *args, **kwargs) as f:
+            yield f
     except (AttributeError, TypeError):
-        return f
+        yield f
 
 def flatten_dict(d):
     if not isinstance(d, dict):

test-requirements.txt

@@ -1,4 +1,4 @@
 pytest
-mesa>=0.8.9
+pytest-profiling
 scipy>=1.3
 tornado

tests/complete_converted.yml

@@ -0,0 +1,49 @@
+---
+version: '2'
+general:
+  id: simple
+  group: tests
+  dir_path: "/tmp/"
+  num_trials: 3
+  max_time: 100
+  interval: 1
+  seed: "CompleteSeed!"
+topologies:
+  default:
+    params:
+      generator: complete_graph
+      n: 10
+agents:
+  default:
+    agent_class: CounterModel
+    state:
+      times: 1
+  network:
+    topology: 'default'
+    distribution:
+      - agent_class: CounterModel
+        weight: 0.4
+        state:
+          state_id: 0
+      - agent_class: AggregatedCounter
+        weight: 0.6
+    override:
+      - filter:
+          node_id: 0
+        state:
+          name: 'The first node'
+      - filter:
+          node_id: 1
+        state:
+          name: 'The second node'
+
+  environment:
+    fixed:
+      - name: 'Environment Agent 1'
+        agent_class: CounterModel
+        state:
+          times: 10
+environment:
+  environment_class: Environment
+  params:
+    am_i_complete: true

tests/old_complete.yml

@@ -0,0 +1,32 @@
+---
+name: simple
+group: tests
+dir_path: "/tmp/"
+num_trials: 3
+max_time: 100
+interval: 1
+seed: "CompleteSeed!"
+network_params:
+  generator: complete_graph
+  n: 10
+network_agents:
+  - agent_type: CounterModel
+    weight: 0.4
+    state:
+      state_id: 0
+  - agent_type: AggregatedCounter
+    weight: 0.6
+environment_agents:
+  - agent_id: 'Environment Agent 1'
+    agent_type: CounterModel
+    state:
+      times: 10
+environment_class: Environment
+environment_params:
+  am_i_complete: true
+agent_type: CounterModel
+default_state:
+  times: 1
+states:
+  - name: 'The first node'
+  - name: 'The second node'

tests/test_agents.py

@@ -0,0 +1,22 @@
+from unittest import TestCase
+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):
+        self.die()
+
+class TestMain(TestCase):
+    def test_die_raises_exception(self):
+        d = Dead(unique_id=0, model=environment.Environment())
+        d.step()
+        with pytest.raises(agents.DeadAgent):
+            d.step()
+
+    def test_die_returns_infinity(self):
+        d = Dead(unique_id=0, model=environment.Environment())
+        assert d.step().abs(0) == stime.INFINITY

tests/test_analysis.py

@@ -50,6 +50,7 @@ class TestAnalysis(TestCase):
             'states': [{'interval': 1}, {'interval': 2}],
             'max_time': 30,
             'num_trials': 1,
+            'history': True,
             'environment_params': {
             }
         }

tests/test_config.py

@@ -0,0 +1,119 @@
+from unittest import TestCase
+import os
+from os.path import join
+
+from soil import simulation, serialization, config, network, agents
+
+ROOT = os.path.abspath(os.path.dirname(__file__))
+EXAMPLES = join(ROOT, '..', 'examples')
+
+FORCE_TESTS = os.environ.get('FORCE_TESTS', '')
+
+
+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]
+        converted_defaults = config.convert_old(old, strict=False)
+        converted = converted_defaults.dict(skip_defaults=True)
+
+        def isequal(a, b):
+            if isinstance(a, dict):
+                for (k, v) in a.items():
+                    if v:
+                        isequal(a[k], b[k])
+                    else:
+                        assert not b.get(k, None)
+                return
+            assert a == b
+
+        isequal(converted, expected)
+
+    def test_topology_config(self):
+        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
+
+    def test_env_from_config(self):
+        """
+        Simple configuration that tests that the graph is loaded, and that
+        network agents are initialized properly.
+        """
+        config = {
+            'name': 'CounterAgent',
+            'network_params': {
+                'path': join(ROOT, 'test.gexf')
+            },
+            'agent_type': 'CounterModel',
+            # 'states': [{'times': 10}, {'times': 20}],
+            'max_time': 2,
+            'dry_run': True,
+            'num_trials': 1,
+            'environment_params': {
+            }
+        }
+        s = simulation.from_old_config(config)
+        env = s.get_env()
+        assert len(env.topologies['default'].nodes) == 2
+        assert len(env.topologies['default'].edges) == 1
+        assert len(env.agents) == 2
+        assert env.agents[0].topology == env.topologies['default']
+
+
+    def test_agents_from_config(self):
+        '''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) == 10
+        assert len(env.agents(group='network')) == 10
+        assert len(env.agents(group='environment')) == 1
+        
+        assert sum(1 for a in env.agents(group='network', agent_type=agents.CounterModel)) == 4
+        assert sum(1 for a in env.agents(group='network', agent_type=agents.AggregatedCounter)) == 6
+
+def make_example_test(path, cfg):
+    def wrapped(self):
+        root = os.getcwd()
+        print(path)
+        s = simulation.from_config(cfg)
+        # for s in simulation.all_from_config(path):
+        #     iterations = s.config.max_time * s.config.num_trials
+        #     if iterations > 1000:
+        #         s.config.max_time = 100
+        #         s.config.num_trials = 1
+        #     if config.get('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 = config['network_params']['n']
+        #             assert len(list(env.network_agents)) == n
+        #             assert env.now > 0  # It has run
+        #             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'),
+    ):
+        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
+        setattr(TestConfig, p.__name__, p)
+        del p
+
+
+add_example_tests()

tests/test_examples.py

@@ -18,10 +18,10 @@ def make_example_test(path, config):
     def wrapped(self):
         root = os.getcwd()
         for s in simulation.all_from_config(path):
-            iterations = s.max_time * s.num_trials
+            iterations = s.config.general.max_time * s.config.general.num_trials
             if iterations > 1000:
-                s.max_time = 100
-                s.num_trials = 1
+                s.config.general.max_time = 100
+                s.config.general.num_trials = 1
             if config.get('skip_test', False) and not FORCE_TESTS:
                 self.skipTest('Example ignored.')
             envs = s.run_simulation(dry_run=True)

tests/test_exporters.py

@@ -2,14 +2,11 @@ import os
 import io
 import tempfile
 import shutil
-from time import time
 
 from unittest import TestCase
 from soil import exporters
 from soil import simulation
 
-from soil.stats import distribution
-
 class Dummy(exporters.Exporter):
     started = False
     trials = 0
@@ -19,17 +16,17 @@ class Dummy(exporters.Exporter):
     called_trial = 0
     called_end = 0
 
-    def start(self):
+    def sim_start(self):
         self.__class__.called_start += 1
         self.__class__.started = True
 
-    def trial(self, env, stats):
+    def trial_end(self, env):
         assert env
         self.__class__.trials += 1
         self.__class__.total_time += env.now
         self.__class__.called_trial += 1
 
-    def end(self, stats):
+    def sim_end(self):
         self.__class__.ended = True
         self.__class__.called_end += 1
 
@@ -68,6 +65,7 @@ class Exporters(TestCase):
             'agent_type': 'CounterModel',
             'max_time': 2,
             'num_trials': n_trials,
+            'dry_run': False,
             'environment_params': {}
         }
         output = io.StringIO()
@@ -78,7 +76,7 @@ class Exporters(TestCase):
                                     exporters.csv,
                                     exporters.gexf,
                                 ],
-                                stats=[distribution,],
+                                dry_run=False,
                                 outdir=tmpdir,
                                 exporter_params={'copy_to': output})
         result = output.getvalue()

tests/test_history.py

@@ -0,0 +1,128 @@
+from unittest import TestCase
+
+import os
+import io
+import yaml
+import copy
+import pickle
+import networkx as nx
+from functools import partial
+
+from os.path import join
+from soil import (simulation, Environment, agents, serialization,
+                  utils)
+from soil.time import Delta
+from tsih import NoHistory, History
+
+
+ROOT = os.path.abspath(os.path.dirname(__file__))
+EXAMPLES = join(ROOT, '..', 'examples')
+
+
+class CustomAgent(agents.FSM):
+    @agents.default_state
+    @agents.state
+    def normal(self):
+        self.neighbors = self.count_agents(state_id='normal',
+                                           limit_neighbors=True)
+    @agents.state
+    def unreachable(self):
+        return
+
+class TestHistory(TestCase):
+
+    def test_counter_agent_history(self):
+        """
+        The evolution of the state should be recorded in the logging agent
+        """
+        config = {
+            'name': 'CounterAgent',
+            'network_params': {
+                'path': join(ROOT, 'test.gexf')
+            },
+            'network_agents': [{
+                'agent_type': 'AggregatedCounter',
+                'weight': 1,
+                'state': {'state_id': 0}
+
+            }],
+            'max_time': 10,
+            'environment_params': {
+            }
+        }
+        s = simulation.from_config(config)
+        env = s.run_simulation(dry_run=True)[0]
+        for agent in env.network_agents:
+            last = 0
+            assert len(agent[None, None]) == 11
+            for step, total in sorted(agent['total', None]):
+                assert total == last + 2
+                last = total
+
+    def test_row_conversion(self):
+        env = Environment(history=True)
+        env['test'] = 'test_value'
+
+        res = list(env.history_to_tuples())
+        assert len(res) == len(env.environment_params)
+
+        env.schedule.time = 1
+        env['test'] = 'second_value'
+        res = list(env.history_to_tuples())
+
+        assert env['env', 0, 'test' ] == 'test_value'
+        assert env['env', 1, 'test' ] == 'second_value'
+
+    def test_nohistory(self):
+        '''
+        Make sure that no history(/sqlite) is used by default
+        '''
+        env = Environment(topology=nx.Graph(), network_agents=[])
+        assert isinstance(env._history, NoHistory)
+
+    def test_save_graph_history(self):
+        '''
+        The history_to_graph method should return a valid networkx graph.
+
+        The state of the agent should be encoded as intervals in the nx graph.
+        '''
+        G = nx.cycle_graph(5)
+        distribution = agents.calculate_distribution(None, agents.BaseAgent)
+        env = Environment(topology=G, network_agents=distribution, history=True)
+        env[0, 0, 'testvalue'] = 'start'
+        env[0, 10, 'testvalue'] = 'finish'
+        nG = env.history_to_graph()
+        values = nG.nodes[0]['attr_testvalue']
+        assert ('start', 0, 10) in values
+        assert ('finish', 10, None) in values
+
+    def test_save_graph_nohistory(self):
+        '''
+        The history_to_graph method should return a valid networkx graph.
+
+        When NoHistory is used, only the last known value is known
+        '''
+        G = nx.cycle_graph(5)
+        distribution = agents.calculate_distribution(None, agents.BaseAgent)
+        env = Environment(topology=G, network_agents=distribution, history=False)
+        env.get_agent(0)['testvalue'] = 'start'
+        env.schedule.time = 10
+        env.get_agent(0)['testvalue'] = 'finish'
+        nG = env.history_to_graph()
+        values = nG.nodes[0]['attr_testvalue']
+        assert ('start', 0, None) not in values
+        assert ('finish', 10, None) in values
+
+    def test_pickle_agent_environment(self):
+        env = Environment(name='Test', history=True)
+        a = agents.BaseAgent(model=env, unique_id=25)
+
+        a['key'] = 'test'
+
+        pickled = pickle.dumps(a)
+        recovered = pickle.loads(pickled)
+
+        assert recovered.env.name == 'Test'
+        assert list(recovered.env._history.to_tuples())
+        assert recovered['key', 0] == 'test'
+        assert recovered['key'] == 'test'

tests/test_main.py

@@ -3,21 +3,21 @@ from unittest import TestCase
 import os
 import io
 import yaml
+import copy
 import pickle
 import networkx as nx
 from functools import partial
 
 from os.path import join
-from soil import (simulation, Environment, agents, serialization,
-                  utils)
+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')
 
 
-class CustomAgent(agents.FSM):
+class CustomAgent(agents.FSM, agents.NetworkAgent):
     @agents.default_state
     @agents.state
     def normal(self):
@@ -39,7 +39,7 @@ class TestMain(TestCase):
                 'path': join(ROOT, 'test.gexf')
             }
         }
-        G = serialization.load_network(config['network_params'])
+        G = network.from_config(config['network_params'])
         assert G
         assert len(G) == 2
         with self.assertRaises(AttributeError):
@@ -48,7 +48,7 @@ class TestMain(TestCase):
                     'path': join(ROOT, 'unknown.extension')
                 }
             }
-            G = serialization.load_network(config['network_params'])
+            G = network.from_config(config['network_params'])
             print(G)
 
     def test_generate_barabasi(self):
@@ -56,16 +56,16 @@ class TestMain(TestCase):
         If no path is given, a generator and network parameters
         should be used to generate a network
         """
-        config = {
-            'network_params': {
+        cfg = {
+            'params': {
                 'generator': 'barabasi_albert_graph'
             }
         }
-        with self.assertRaises(TypeError):
-            G = serialization.load_network(config['network_params'])
-        config['network_params']['n'] = 100
-        config['network_params']['m'] = 10
-        G = serialization.load_network(config['network_params'])
+        with self.assertRaises(Exception):
+            G = network.from_config(cfg)
+        cfg['params']['n'] = 100
+        cfg['params']['m'] = 10
+        G = network.from_config(cfg)
         assert len(G) == 100
 
     def test_empty_simulation(self):
@@ -78,59 +78,68 @@ class TestMain(TestCase):
             'environment_params': {
             }
         }
-        s = simulation.from_config(config)
+        s = simulation.from_old_config(config)
         s.run_simulation(dry_run=True)
 
-    def test_counter_agent(self):
+
+    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',
             'network_params': {
-                'path': join(ROOT, 'test.gexf')
+                'generator': nx.complete_graph,
+                'n': 2,
             },
             'agent_type': 'CounterModel',
-            'states': [{'times': 10}, {'times': 20}],
+            'states': {
+                0: {'times': 10},
+                1: {'times': 20},
+            },
             'max_time': 2,
             'num_trials': 1,
             'environment_params': {
             }
         }
-        s = simulation.from_config(config)
-        env = s.run_simulation(dry_run=True)[0]
-        assert env.get_agent(0)['times', 0] == 11
-        assert env.get_agent(0)['times', 1] == 12
-        assert env.get_agent(1)['times', 0] == 21
-        assert env.get_agent(1)['times', 1] == 22
+        s = simulation.from_old_config(config)
 
-    def test_counter_agent_history(self):
-        """
-        The evolution of the state should be recorded in the logging agent
+    def test_counter_agent(self):
         """
+        The initial states should be applied to the agent and the
+        agent should be able to update its state."""
         config = {
-            'name': 'CounterAgent',
-            'network_params': {
-                'path': join(ROOT, 'test.gexf')
+            'version': '2',
+            'general': {
+                'name': 'CounterAgent',
+                'max_time': 2,
+                'dry_run': True,
+                'num_trials': 1,
             },
-            'network_agents': [{
-                'agent_type': 'AggregatedCounter',
-                'weight': 1,
-                'state': {'state_id': 0}
-
-            }],
-            'max_time': 10,
-            'environment_params': {
+            'topologies': {
+                'default': {
+                    'path': join(ROOT, 'test.gexf')
+                }
+            },
+            'agents': {
+                'default': {
+                    'agent_class': 'CounterModel',
+                },
+                'counters': {
+                    'topology': 'default',
+                    'fixed': [{'state': {'times': 10}}, {'state': {'times': 20}}],
+                }
             }
         }
         s = simulation.from_config(config)
-        env = s.run_simulation(dry_run=True)[0]
-        for agent in env.network_agents:
-            last = 0
-            assert len(agent[None, None]) == 11
-            for step, total in sorted(agent['total', None]):
-                assert total == last + 2
-                last = total
+        env = s.get_env()
+        assert isinstance(env.agents[0], agents.CounterModel)
+        assert env.agents[0].topology == env.topologies['default']
+        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
 
     def test_custom_agent(self):
         """Allow for search of neighbors with a certain state_id"""
@@ -147,18 +156,18 @@ class TestMain(TestCase):
             'environment_params': {
             }
         }
-        s = simulation.from_config(config)
+        s = simulation.from_old_config(config)
         env = s.run_simulation(dry_run=True)[0]
-        assert env.get_agent(1).count_agents(state_id='normal') == 2
-        assert env.get_agent(1).count_agents(state_id='normal', limit_neighbors=True) == 1
-        assert env.get_agent(0).neighbors == 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_torvalds_example(self):
         """A complete example from a documentation should work."""
         config = serialization.load_file(join(EXAMPLES, 'torvalds.yml'))[0]
         config['network_params']['path'] = join(EXAMPLES,
                                                 config['network_params']['path'])
-        s = simulation.from_config(config)
+        s = simulation.from_old_config(config)
         env = s.run_simulation(dry_run=True)[0]
         for a in env.network_agents:
             skill_level = a.state['skill_level']
@@ -177,19 +186,20 @@ class TestMain(TestCase):
 
     def test_yaml(self):
         """
-        The YAML version of a newly created simulation
-        should be equivalent to the configuration file used
+        The YAML version of a newly created configuration should be equivalent
+        to the configuration file used.
+        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]
-            s = simulation.from_config(config)
+            s = simulation.from_old_config(config)
         with utils.timer('serializing'):
             serial = s.to_yaml()
         with utils.timer('recovering'):
             recovered = yaml.load(serial, Loader=yaml.SafeLoader)
-        with utils.timer('deleting'):
-            del recovered['topology']
-        assert config == recovered
+        for (k, v) in config.items():
+            assert recovered[k] == v
 
     def test_configuration_changes(self):
         """
@@ -197,26 +207,13 @@ class TestMain(TestCase):
          the simulation.
         """
         config = serialization.load_file(join(EXAMPLES, 'complete.yml'))[0]
-        s = simulation.from_config(config)
+        s = simulation.from_old_config(config)
+        init_config = copy.copy(s.config)
 
         s.run_simulation(dry_run=True)
-        nconfig = s.to_dict()
-        del nconfig['topology']
-        assert config == nconfig
-
-    def test_row_conversion(self):
-        env = Environment()
-        env['test'] = 'test_value'
-
-        res = list(env.history_to_tuples())
-        assert len(res) == len(env.environment_params)
-
-        env.schedule.time = 1
-        env['test'] = 'second_value'
-        res = list(env.history_to_tuples())
-
-        assert env['env', 0, 'test' ] == 'test_value'
-        assert env['env', 1, 'test' ] == 'second_value'
+        nconfig = s.config
+        # del nconfig['to
+        assert init_config == nconfig
 
     def test_save_geometric(self):
         """
@@ -228,27 +225,15 @@ class TestMain(TestCase):
         f = io.BytesIO()
         env.dump_gexf(f)
 
-    def test_save_graph(self):
-        '''
-        The history_to_graph method should return a valid networkx graph.
-
-        The state of the agent should be encoded as intervals in the nx graph.
-        '''
-        G = nx.cycle_graph(5)
-        distribution = agents.calculate_distribution(None, agents.BaseAgent)
-        env = Environment(topology=G, network_agents=distribution)
-        env[0, 0, 'testvalue'] = 'start'
-        env[0, 10, 'testvalue'] = 'finish'
-        nG = env.history_to_graph()
-        values = nG.nodes[0]['attr_testvalue']
-        assert ('start', 0, 10) in values
-        assert ('finish', 10, None) in values
-
     def test_serialize_class(self):
-        ser, name = serialization.serialize(agents.BaseAgent)
+        ser, name = serialization.serialize(agents.BaseAgent, known_modules=[])
         assert name == 'soil.agents.BaseAgent'
         assert ser == agents.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 ser == CustomAgent
@@ -302,31 +287,19 @@ class TestMain(TestCase):
         assert converted[1]['agent_type'] == 'test_main.CustomAgent'
         pickle.dumps(converted)
 
-    def test_pickle_agent_environment(self):
-        env = Environment(name='Test')
-        a = agents.BaseAgent(model=env, unique_id=25)
-
-        a['key'] = 'test'
-
-        pickled = pickle.dumps(a)
-        recovered = pickle.loads(pickled)
-
-        assert recovered.env.name == 'Test'
-        assert list(recovered.env._history.to_tuples())
-        assert recovered['key', 0] == 'test'
-        assert recovered['key'] == 'test'
-
     def test_subgraph(self):
         '''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_type=agents.NetworkAgent)
-        env = Environment(name='Test', topology=G, network_agents=distro)
+        distro[0]['topology'] = 'default'
+        aconfig = config.AgentConfig(distribution=distro, topology='default')
+        env = Environment(name='Test', topologies={'default': G}, agents={'network': aconfig})
         lst = list(env.network_agents)
 
-        a2 = env.get_agent(2)
-        a3 = env.get_agent(3)
+        a2 = env.find_one(node_id=2)
+        a3 = env.find_one(node_id=3)
         assert len(a2.subgraph(limit_neighbors=True)) == 2
         assert len(a3.subgraph(limit_neighbors=True)) == 1
         assert len(a3.subgraph(limit_neighbors=True, center=False)) == 0
@@ -346,7 +319,7 @@ class TestMain(TestCase):
             'num_trials': 50,
             'environment_params': {}
         }
-        s = simulation.from_config(config)
+        s = simulation.from_old_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']

tests/test_stats.py

@@ -1,34 +0,0 @@
-from unittest import TestCase
-
-from soil import simulation, stats
-from soil.utils import unflatten_dict
-
-class Stats(TestCase):
-
-    def test_distribution(self):
-        '''The distribution exporter should write the number of agents in each state'''
-        config = {
-            'name': 'exporter_sim',
-            'network_params': {
-                'generator': 'complete_graph',
-                'n': 4
-            },
-            'agent_type': 'CounterModel',
-            'max_time': 2,
-            'num_trials': 5,
-            'environment_params': {}
-        }
-        s = simulation.from_config(config)
-        for env in s.run_simulation(stats=[stats.distribution]):
-            pass
-            # stats_res = unflatten_dict(dict(env._history['stats', -1, None]))
-        allstats = s.get_stats()
-        for stat in allstats:
-            assert 'count' in stat
-            assert 'mean' in stat
-            if 'trial_id' in stat:
-                assert stat['mean']['neighbors'] == 3
-                assert stat['count']['total']['4'] == 4
-            else:
-                assert stat['count']['count']['neighbors']['3'] == 20
-                assert stat['mean']['min']['neighbors'] == stat['mean']['max']['neighbors']