Release 0.20.6

First iteration to achieve MESA compatibility.
As a side effect, we have removed `simpy`.

For a full list of changes, see `CHANGELOG.md`.

.gitignore

@@ -8,3 +8,4 @@ soil_output
 docs/_build*
 build/*
 dist/*
+prof

.gitlab-ci.yml

@@ -1,9 +1,10 @@
 stages:
   - test
-  - build
+  - publish
+  - check_published
 
-build:
+docker:
-  stage: build
+  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 +3,85 @@ 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]
+## [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.
+## [0.20.0]
+### Added
+* Integration with MESA
+* `not_agent_ids` parameter to get sql in history
+### Changed
+* `soil.Environment` now also inherits from `mesa.Model`
+* `soil.Agent` now also inherits from `mesa.Agent`
+* `soil.time` to replace `simpy` events, delays, duration, etc.
+* `agent.id` is not `agent.unique_id` to be compatible with `mesa`. A property `BaseAgent.id` has been added for compatibility.
+* `agent.environment` is now `agent.model`, for the same reason as above. The parameter name in `BaseAgent.__init__` has also been renamed.
+### Removed
+* `simpy` dependency and compatibility. Each agent used to be a simpy generator, but that made debugging and error handling more complex. That has been replaced by a scheduler within the `soil.Environment` class, similar to how `mesa` does it.
+* `soil.history` is now a separate package named `tsih`. The keys namedtuple uses `dict_id` instead of `agent_id`.
+### Added
+* An option to choose whether a database should be used for history 
+## [0.15.2]
+### Fixed
+* Pass the right known_modules and parameters to stats discovery in simulation
+* The configuration file must exist when launching through the CLI. If it doesn't, an error will be logged
+* Minor changes in the documentation of the CLI arguments
+### Changed
+* Stats are now exported by default
+## [0.15.1]
+### Added
+* read-only `History`
+### Fixed
+* Serialization problem with the `Environment` on parallel mode.
+* Analysis functions now work as they should in the tutorial
+## [0.15.0]
+### Added
+* Control logging level in CLI and simulation
+* `Stats` to calculate trial and simulation-wide statistics
+* Simulation statistics are stored in a separate table in history (see `History.get_stats` and `History.save_stats`, as well as `soil.stats`)
+* Aliased `NetworkAgent.G` to `NetworkAgent.topology`.
+### Changed
+* Templates in config files can be given as dictionaries in addition to strings
+* Samplers are used more explicitly
+* Removed nxsim dependency. We had already made a lot of changes, and nxsim has not been updated in 5 years.
+* Exporter methods renamed to `trial` and `end`. Added `start`.
+* `Distribution` exporter now a stats class
+* `global_topology` renamed to `topology`
+* Moved topology-related methods to `NetworkAgent`
+### Fixed
+* Temporary files used for history in dry_run mode are not longer left open 
+
 ## [0.14.9]
 ### Changed
 * Seed random before environment initialization

README.md

@@ -5,6 +5,9 @@ Learn how to run your own simulations with our [documentation](http://soilsim.re
 
 Follow our [tutorial](examples/tutorial/soil_tutorial.ipynb) to develop your own agent models.
 
+## Citation 
+
+
 If you use Soil in your research, don't forget to cite this paper:
 
 ```bibtex
@@ -28,7 +31,24 @@ If you use Soil in your research, don't forget to cite this paper:
 
 ```
 
-@Copyright GSI - Universidad Politécnica de Madrid 2017
+## Mesa compatibility
+
+Soil is in the process of becoming fully compatible with MESA.
+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`:
+  - [x] `Soil.Environment` inherits from `mesa.Model`
+  - [x] `Soil.Environment` includes a Mesa-like Scheduler (see the `soil.time` module.
+- [ ] Integrate `soil.Agent` with `mesa.Agent`:
+  - [x] Rename agent.id to unique_id?
+  - [x] mesa agents can be used in soil simulations (see `examples/mesa`)
+- [ ] Document the new APIs and usage
+
+@Copyright GSI - Universidad Politécnica de Madrid 2017-2021
 
 [![SOIL](logo_gsi.png)](https://www.gsi.upm.es)
-

docs/conf.py

@@ -31,7 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = []
+extensions = ['IPython.sphinxext.ipython_console_highlighting']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -69,7 +69,7 @@ language = None
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

docs/configuration.rst

@@ -218,3 +218,24 @@ These agents are programmed in much the same way as network agents, the only dif
 
 You may use environment agents to model events that a normal agent cannot control, such as natural disasters or chance.
 They are also useful to add behavior that has little to do with the network and the interactions within that network.
+
+Templating
+==========
+
+Sometimes, it is useful to parameterize a simulation and run it over a range of values in order to compare each run and measure the effect of those parameters in the simulation.
+For instance, you may want to run a simulation with different agent distributions.
+
+This can be done in Soil using **templates**.
+A template is a configuration where some of the values are specified with a variable.
+e.g.,  ``weight: "{{ var1 }}"`` instead of ``weight: 1``.
+There are two types of variables, depending on how their values are decided:
+
+* Fixed. A list of values is provided, and a new simulation is run for each possible value. If more than a variable is given, a new simulation will be run per combination of values.
+* Bounded/Sampled. The bounds of the variable are provided, along with a sampler method, which will be used to compute all the configuration combinations.
+
+When fixed and bounded variables are mixed, Soil generates a new configuration per combination of fixed values and bounded values.
+
+Here is an example with a single fixed variable and two bounded variable:
+
+.. literalinclude:: ../examples/template.yml
+   :language: yaml

docs/requirements.txt

@@ -0,0 +1 @@
+ipython==7.31.1

docs/soil_tutorial.rst

@@ -47,12 +47,6 @@ There are three main elements in a soil simulation:
 -  The environment. It assigns agents to nodes in the network, and
    stores the environment parameters (shared state for all agents).
 
-Soil is based on ``simpy``, which is an event-based network simulation
-library. Soil provides several abstractions over events to make
-developing agents easier. This means you can use events (timeouts,
-delays) in soil, but for the most part we will assume your models will
-be step-based.
-
 Modeling behaviour
 ------------------
 

examples/NewsSpread.ipynb

@@ -500,7 +500,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.5"
   },
   "toc": {
    "colors": {

examples/Untitled.ipynb

@@ -80800,7 +80800,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,

examples/complete.yml

@@ -13,7 +13,7 @@ network_agents:
   - agent_type: CounterModel
     weight: 1
     state:
-      id: 0
+      state_id: 0
   - agent_type: AggregatedCounter
     weight: 0.2
 environment_agents: []

examples/custom_generator/custom_generator.yml

@@ -13,4 +13,4 @@ network_agents:
   - agent_type: CounterModel
     weight: 1
     state:
-      id: 0
+      state_id: 0

examples/mesa/mesa.yml

@@ -0,0 +1,21 @@
+---
+name: mesa_sim
+group: tests
+dir_path: "/tmp"
+num_trials: 3
+max_time: 100
+interval: 1
+seed: '1'
+network_params:
+  generator: social_wealth.graph_generator
+  n: 5
+network_agents:
+  - agent_type: social_wealth.SocialMoneyAgent
+    weight: 1
+environment_class: social_wealth.MoneyEnv
+environment_params:
+  num_mesa_agents: 5
+  mesa_agent_type: social_wealth.MoneyAgent
+  N: 10
+  width: 50
+  height: 50

examples/mesa/server.py

@@ -0,0 +1,105 @@
+from mesa.visualization.ModularVisualization import ModularServer
+from soil.visualization import UserSettableParameter
+from mesa.visualization.modules import ChartModule, NetworkModule, CanvasGrid
+from social_wealth import MoneyEnv, graph_generator, SocialMoneyAgent
+
+
+class MyNetwork(NetworkModule):
+    def render(self, model):
+        return self.portrayal_method(model)
+
+
+def network_portrayal(env):
+    # The model ensures there is 0 or 1 agent per node
+
+    portrayal = dict()
+    portrayal["nodes"] = [
+        {
+            "id": agent_id,
+            "size": env.get_agent(agent_id).wealth,
+            # "color": "#CC0000" if not agents or agents[0].wealth == 0 else "#007959",
+            "color": "#CC0000",
+            "label": f"{agent_id}: {env.get_agent(agent_id).wealth}",
+        }
+        for (agent_id) in env.G.nodes
+    ]
+
+    portrayal["edges"] = [
+        {"id": edge_id, "source": source, "target": target, "color": "#000000"}
+        for edge_id, (source, target) in enumerate(env.G.edges)
+    ]
+
+
+    return portrayal
+
+
+def gridPortrayal(agent):
+    """
+    This function is registered with the visualization server to be called
+    each tick to indicate how to draw the agent in its current state.
+    :param agent:  the agent in the simulation
+    :return: the portrayal dictionary
+    """
+    color = max(10, min(agent.wealth*10, 100))
+    return {
+        "Shape": "rect",
+        "w": 1,
+        "h": 1,
+        "Filled": "true",
+        "Layer": 0,
+        "Label": agent.unique_id,
+        "Text": agent.unique_id,
+        "x": agent.pos[0],
+        "y": agent.pos[1],
+        "Color": f"rgba(31, 10, 255, 0.{color})"
+    }
+
+
+grid = MyNetwork(network_portrayal, 500, 500, library="sigma")
+chart = ChartModule(
+    [{"Label": "Gini", "Color": "Black"}], data_collector_name="datacollector"
+)
+
+model_params = {
+    "N": UserSettableParameter(
+        "slider",
+        "N",
+        5,
+        1,
+        10,
+        1,
+        description="Choose how many agents to include in the model",
+    ),
+    "network_agents": [{"agent_type": SocialMoneyAgent}],
+    "height": UserSettableParameter(
+        "slider",
+        "height",
+        5,
+        5,
+        10,
+        1,
+        description="Grid height",
+        ),
+    "width": UserSettableParameter(
+        "slider",
+        "width",
+        5,
+        5,
+        10,
+        1,
+        description="Grid width",
+        ),
+    "network_params": {
+        'generator': graph_generator
+    },
+}
+
+canvas_element = CanvasGrid(gridPortrayal, model_params["width"].value, model_params["height"].value, 500, 500)
+
+
+server = ModularServer(
+    MoneyEnv, [grid, chart, canvas_element], "Money Model", model_params
+)
+server.port = 8521
+
+server.launch(open_browser=False)

examples/mesa/social_wealth.py

@@ -0,0 +1,120 @@
+'''
+This is an example that adds soil agents and environment in a normal
+mesa workflow.
+'''
+from mesa import Agent as MesaAgent
+from mesa.space import MultiGrid
+# from mesa.time import RandomActivation
+from mesa.datacollection import DataCollector
+from mesa.batchrunner import BatchRunner
+
+import networkx as nx
+
+from soil import NetworkAgent, Environment
+
+def compute_gini(model):
+    agent_wealths = [agent.wealth for agent in model.agents]
+    x = sorted(agent_wealths)
+    N = len(list(model.agents))
+    B = sum( xi * (N-i) for i,xi in enumerate(x) ) / (N*sum(x))
+    return (1 + (1/N) - 2*B)
+
+class MoneyAgent(MesaAgent):
+    """
+    A MESA agent with fixed initial wealth.
+    It will only share wealth with neighbors based on grid proximity
+    """
+
+    def __init__(self, unique_id, model):
+        super().__init__(unique_id=unique_id, model=model)
+        self.wealth = 1
+
+    def move(self):
+        possible_steps = self.model.grid.get_neighborhood(
+            self.pos,
+            moore=True,
+            include_center=False)
+        new_position = self.random.choice(possible_steps)
+        self.model.grid.move_agent(self, new_position)
+
+    def give_money(self):
+        cellmates = self.model.grid.get_cell_list_contents([self.pos])
+        if len(cellmates) > 1:
+            other = self.random.choice(cellmates)
+            other.wealth += 1
+            self.wealth -= 1
+
+    def step(self):
+        self.info("Crying wolf", self.pos)
+        self.move()
+        if self.wealth > 0:
+            self.give_money()
+
+
+class SocialMoneyAgent(NetworkAgent, MoneyAgent):
+    wealth = 1
+
+    def give_money(self):
+        cellmates = set(self.model.grid.get_cell_list_contents([self.pos]))
+        friends = set(self.get_neighboring_agents())
+        self.info("Trying to give money")
+        self.debug("Cellmates: ", cellmates)
+        self.debug("Friends: ", friends)
+
+        nearby_friends = list(cellmates & friends)
+
+        if len(nearby_friends):
+            other = self.random.choice(nearby_friends)
+            other.wealth += 1
+            self.wealth -= 1
+
+
+class MoneyEnv(Environment):
+    """A model with some number of agents."""
+    def __init__(self, N, width, height, *args, network_params, **kwargs):
+
+        network_params['n'] = N
+        super().__init__(*args, network_params=network_params, **kwargs)
+        self.grid = MultiGrid(width, height, False)
+
+        # Create agents
+        for agent in self.agents:
+            x = self.random.randrange(self.grid.width)
+            y = self.random.randrange(self.grid.height)
+            self.grid.place_agent(agent, (x, y))
+
+        self.datacollector = DataCollector(
+            model_reporters={"Gini": compute_gini},
+            agent_reporters={"Wealth": "wealth"})
+
+
+def graph_generator(n=5):
+    G = nx.Graph()
+    for ix in range(n):
+        G.add_edge(0, ix)
+    return G
+
+if __name__ == '__main__':
+
+
+    G = graph_generator()
+    fixed_params = {"topology": G,
+                    "width": 10,
+                    "network_agents": [{"agent_type": SocialMoneyAgent,
+                                       'weight': 1}],
+                    "height": 10}
+
+    variable_params = {"N": range(10, 100, 10)}
+
+    batch_run = BatchRunner(MoneyEnv,
+                            variable_parameters=variable_params,
+                            fixed_parameters=fixed_params,
+                            iterations=5,
+                            max_steps=100,
+                            model_reporters={"Gini": compute_gini})
+    batch_run.run_all()
+
+    run_data = batch_run.get_model_vars_dataframe()
+    run_data.head()
+    print(run_data.Gini)
+

examples/mesa/wealth.py

@@ -0,0 +1,83 @@
+from mesa import Agent, Model
+from mesa.space import MultiGrid
+from mesa.time import RandomActivation
+from mesa.datacollection import DataCollector
+from mesa.batchrunner import BatchRunner
+
+def compute_gini(model):
+    agent_wealths = [agent.wealth for agent in model.schedule.agents]
+    x = sorted(agent_wealths)
+    N = model.num_agents
+    B = sum( xi * (N-i) for i,xi in enumerate(x) ) / (N*sum(x))
+    return (1 + (1/N) - 2*B)
+
+class MoneyAgent(Agent):
+    """ An agent with fixed initial wealth."""
+    def __init__(self, unique_id, model):
+        super().__init__(unique_id, model)
+        self.wealth = 1
+
+    def move(self):
+        possible_steps = self.model.grid.get_neighborhood(
+            self.pos,
+            moore=True,
+            include_center=False)
+        new_position = self.random.choice(possible_steps)
+        self.model.grid.move_agent(self, new_position)
+
+    def give_money(self):
+        cellmates = self.model.grid.get_cell_list_contents([self.pos])
+        if len(cellmates) > 1:
+            other = self.random.choice(cellmates)
+            other.wealth += 1
+            self.wealth -= 1
+
+    def step(self):
+        self.move()
+        if self.wealth > 0:
+            self.give_money()
+
+class MoneyModel(Model):
+    """A model with some number of agents."""
+    def __init__(self, N, width, height):
+        self.num_agents = N
+        self.grid = MultiGrid(width, height, True)
+        self.schedule = RandomActivation(self)
+        self.running = True
+
+        # Create agents
+        for i in range(self.num_agents):
+            a = MoneyAgent(i, self)
+            self.schedule.add(a)
+            # Add the agent to a random grid cell
+            x = self.random.randrange(self.grid.width)
+            y = self.random.randrange(self.grid.height)
+            self.grid.place_agent(a, (x, y))
+
+        self.datacollector = DataCollector(
+            model_reporters={"Gini": compute_gini},
+            agent_reporters={"Wealth": "wealth"})
+
+    def step(self):
+        self.datacollector.collect(self)
+        self.schedule.step()
+
+
+if __name__ == '__main__':
+
+    fixed_params = {"width": 10,
+                    "height": 10}
+    variable_params = {"N": range(10, 500, 10)}
+
+    batch_run = BatchRunner(MoneyModel,
+                            variable_params,
+                            fixed_params,
+                            iterations=5,
+                            max_steps=100,
+                            model_reporters={"Gini": compute_gini})
+    batch_run.run_all()
+
+    run_data = batch_run.get_model_vars_dataframe()
+    run_data.head()
+    print(run_data.Gini)
+

examples/newsspread/NewsSpread.yml

@@ -68,12 +68,12 @@ network_agents:
 - agent_type: HerdViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 - agent_type: HerdViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 network_params:
   generator: barabasi_albert_graph
@@ -95,7 +95,7 @@ network_agents:
 - agent_type: HerdViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 - agent_type: WiseViewer
   state:
@@ -121,7 +121,7 @@ network_agents:
 - agent_type: WiseViewer
   state:
     has_tv: true
-    id: neutral
+    state_id: neutral
   weight: 1
 - agent_type: WiseViewer
   state:

examples/newsspread/newsspread.py

@@ -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)
 
 
@@ -34,15 +40,14 @@ class HerdViewer(DumbViewer):
     A viewer whose probability of infection depends on the state of its neighbors.
     '''
 
-    level = logging.DEBUG
-
     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):
@@ -77,5 +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()
+# Uncomment this to output the simulation to a YAML file
-
+# s.dump_yaml('simulation.yaml')
-for env in envs:
-    env.dump_csv()

examples/rabbits/rabbit_agents.py

@@ -1,7 +1,6 @@
-from soil.agents import FSM, state, default_state, BaseAgent
+from soil.agents import FSM, state, default_state, BaseAgent, NetworkAgent
 from enum import Enum
 from random import random, choice
-from itertools import islice
 import logging
 import math
 
@@ -13,8 +12,6 @@ class Genders(Enum):
 
 class RabbitModel(FSM):
 
-    level = logging.INFO
-
     defaults = {
         'age': 0,
         'gender': Genders.male.value,
@@ -22,7 +19,7 @@ class RabbitModel(FSM):
         'offspring': 0,
     }
 
-    sexual_maturity = 4*30
+    sexual_maturity = 3 #4*30
     life_expectancy = 365 * 3
     gestation = 33
     pregnancy = -1
@@ -31,10 +28,23 @@ class RabbitModel(FSM):
     @default_state
     @state
     def newborn(self):
+        self.debug(f'I am a newborn at age {self["age"]}')
         self['age'] += 1
 
         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):
@@ -46,21 +56,26 @@ class RabbitModel(FSM):
             return
 
         # Males try to mate
-        females = self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False)
+        for f in self.get_agents(state_id=Female.fertile.id,
-        for f in islice(females, self.max_females):
+                                 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
@@ -80,7 +95,7 @@ class RabbitModel(FSM):
                 self.env.add_edge(self['mate'], child.id)
                 # self.add_edge()
                 self.debug('A BABY IS COMING TO LIFE')
-                self.env['rabbits_alive'] = self.env.get('rabbits_alive', self.global_topology.number_of_nodes())+1
+                self.env['rabbits_alive'] = self.env.get('rabbits_alive', self.topology.number_of_nodes())+1
                 self.debug('Rabbits alive: {}'.format(self.env['rabbits_alive']))
                 self['offspring'] += 1
                 self.env.get_agent(self['mate'])['offspring'] += 1
@@ -90,19 +105,19 @@ 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(BaseAgent):
+class RandomAccident(NetworkAgent):
 
     level = logging.DEBUG
 
     def step(self):
-        rabbits_total = self.global_topology.number_of_nodes()
+        rabbits_total = self.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)
         prob_death = self.env.get('prob_death', 1e-100)*math.floor(math.log10(max(1, rabbits_alive)))
         self.debug('Killing some rabbits with prob={}!'.format(prob_death))
@@ -116,5 +131,5 @@ class RandomAccident(BaseAgent):
                 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.global_topology.number_of_nodes():
+        if self.count_agents(state_id=RabbitModel.dead.id) == self.topology.number_of_nodes():
             self.die()

examples/rabbits/rabbits.yml

@@ -1,23 +1,21 @@
 ---
 load_module: rabbit_agents
 name: rabbits_example
-max_time: 500
+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:
+      agent_type: rabbit_agents.Male
-        gender: female
     - id: 0
-      state:
+      agent_type: rabbit_agents.Female
-        gender: male
   directed: true
   links: []

examples/random_delays/random_delays.py

@@ -0,0 +1,45 @@
+'''
+Example of setting a 
+Example of a fully programmatic simulation, without definition files.
+'''
+from soil import Simulation, agents
+from soil.time import Delta
+from random import expovariate
+import logging
+
+
+
+class MyAgent(agents.FSM):
+    '''
+    An agent that first does a ping
+    '''
+
+    defaults = {'pong_counts': 2}
+
+    @agents.default_state
+    @agents.state
+    def ping(self):
+        self.info('Ping')
+        return self.pong, Delta(expovariate(1/16))
+
+    @agents.state
+    def pong(self):
+        self.info('Pong')
+        self.pong_counts -= 1
+        self.info(str(self.pong_counts))
+        if self.pong_counts < 1:
+            return self.die()
+        return None, Delta(expovariate(1/16))
+
+
+s = Simulation(name='Programmatic',
+               network_agents=[{'agent_type': MyAgent, 'id': 0}],
+               topology={'nodes': [{'id': 0}], 'links': []},
+               num_trials=1,
+               max_time=100,
+               agent_type=MyAgent,
+               dry_run=True)
+
+
+logging.basicConfig(level=logging.INFO)
+envs = s.run()

examples/template.yml

@@ -1,13 +1,8 @@
 ---
-vars:
+sampler:
-  bounds:
+  method: "SALib.sample.morris.sample"
-    x1: [0, 1]
+  N: 10
-    x2: [1, 2]
+template:
-  fixed:
-    x3: ["a", "b", "c"]
-sampler: "SALib.sample.morris.sample"
-samples: 10
-template: |
   group: simple
   num_trials: 1
   interval: 1
@@ -19,11 +14,17 @@ template: |
     n: 10
   network_agents:
     - agent_type: CounterModel
-      weight: {{ x1 }}
+      weight: "{{ x1 }}"
       state:
-        id: 0
+        state_id: 0
     - agent_type: AggregatedCounter
-      weight: {{ 1 - x1 }}
+      weight: "{{ 1 - x1 }}"
   environment_params:
-    name: {{ x3 }}
+    name: "{{ x3 }}"
   skip_test: true
+vars:
+  bounds:
+    x1: [0, 1]
+    x2: [1, 2]
+  fixed:
+    x3: ["a", "b", "c"]

examples/terrorism/TerroristNetworkModel.py

@@ -18,12 +18,12 @@ class TerroristSpreadModel(FSM, Geo):
         prob_interaction
     """
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, model=None, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=model, unique_id=unique_id, state=state)
 
-        self.information_spread_intensity = environment.environment_params['information_spread_intensity']
+        self.information_spread_intensity = model.environment_params['information_spread_intensity']
-        self.terrorist_additional_influence = environment.environment_params['terrorist_additional_influence']
+        self.terrorist_additional_influence = model.environment_params['terrorist_additional_influence']
-        self.prob_interaction = environment.environment_params['prob_interaction']
+        self.prob_interaction = model.environment_params['prob_interaction']
 
         if self['id'] == self.civilian.id:       # Civilian
             self.mean_belief = random.uniform(0.00, 0.5)
@@ -34,10 +34,10 @@ class TerroristSpreadModel(FSM, Geo):
         else:
             raise Exception('Invalid state id: {}'.format(self['id']))
 
-        if 'min_vulnerability' in environment.environment_params:
+        if 'min_vulnerability' in model.environment_params:
-            self.vulnerability = random.uniform( environment.environment_params['min_vulnerability'], environment.environment_params['max_vulnerability'] )
+            self.vulnerability = random.uniform( model.environment_params['min_vulnerability'], model.environment_params['max_vulnerability'] )
         else :
-            self.vulnerability = random.uniform( 0, environment.environment_params['max_vulnerability'] )
+            self.vulnerability = random.uniform( 0, model.environment_params['max_vulnerability'] )
 
 
     @state
@@ -93,11 +93,11 @@ class TrainingAreaModel(FSM, Geo):
     Requires TerroristSpreadModel.
     """
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, model=None, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=model, unique_id=unique_id, state=state)
-        self.training_influence = environment.environment_params['training_influence']
+        self.training_influence = model.environment_params['training_influence']
-        if 'min_vulnerability' in environment.environment_params:
+        if 'min_vulnerability' in model.environment_params:
-            self.min_vulnerability = environment.environment_params['min_vulnerability']
+            self.min_vulnerability = model.environment_params['min_vulnerability']
         else: self.min_vulnerability = 0
 
     @default_state
@@ -120,13 +120,13 @@ class HavenModel(FSM, Geo):
     Requires TerroristSpreadModel.
     """
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, model=None, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=model, unique_id=unique_id, state=state)
-        self.haven_influence = environment.environment_params['haven_influence']
+        self.haven_influence = model.environment_params['haven_influence']
-        if 'min_vulnerability' in environment.environment_params:
+        if 'min_vulnerability' in model.environment_params:
-            self.min_vulnerability = environment.environment_params['min_vulnerability']
+            self.min_vulnerability = model.environment_params['min_vulnerability']
         else: self.min_vulnerability = 0
-        self.max_vulnerability = environment.environment_params['max_vulnerability']
+        self.max_vulnerability = model.environment_params['max_vulnerability']
 
     def get_occupants(self, **kwargs):
         return self.get_neighboring_agents(agent_type=TerroristSpreadModel, **kwargs)
@@ -162,13 +162,13 @@ class TerroristNetworkModel(TerroristSpreadModel):
         weight_link_distance
     """
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, model=None, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=model, unique_id=unique_id, state=state)
 
-        self.vision_range = environment.environment_params['vision_range']
+        self.vision_range = model.environment_params['vision_range']
-        self.sphere_influence = environment.environment_params['sphere_influence']
+        self.sphere_influence = model.environment_params['sphere_influence']
-        self.weight_social_distance = environment.environment_params['weight_social_distance']
+        self.weight_social_distance = model.environment_params['weight_social_distance']
-        self.weight_link_distance = environment.environment_params['weight_link_distance']
+        self.weight_link_distance = model.environment_params['weight_link_distance']
 
     @state
     def terrorist(self):
@@ -195,14 +195,14 @@ class TerroristNetworkModel(TerroristSpreadModel):
                     break
 
     def get_distance(self, target):
-        source_x, source_y = nx.get_node_attributes(self.global_topology, 'pos')[self.id]
+        source_x, source_y = nx.get_node_attributes(self.topology, 'pos')[self.id]
-        target_x, target_y = nx.get_node_attributes(self.global_topology, 'pos')[target]
+        target_x, target_y = nx.get_node_attributes(self.topology, 'pos')[target]
         dx = abs( source_x - target_x )
         dy = abs( source_y - target_y )
         return ( dx ** 2 + dy ** 2 ) ** ( 1 / 2 )
 
     def shortest_path_length(self, target):
         try:
-            return nx.shortest_path_length(self.global_topology, self.id, target)
+            return nx.shortest_path_length(self.topology, self.id, target)
         except nx.NetworkXNoPath:
             return float('inf')

requirements.txt

@@ -1,10 +1,9 @@
-nxsim>=0.1.2
+networkx>=2.5
-simpy
-networkx>=2.0,<2.4
 numpy
 matplotlib
 pyyaml>=5.1
 pandas>=0.23
-scipy>=1.3
 SALib>=1.3
 Jinja2
+Mesa>=0.8
+tsih>=0.1.5

setup.py

@@ -16,6 +16,12 @@ def parse_requirements(filename):
 
 install_reqs = parse_requirements("requirements.txt")
 test_reqs = parse_requirements("test-requirements.txt")
+extras_require={
+    'mesa': ['mesa>=0.8.9'],
+    'geo': ['scipy>=1.3'],
+    'web': ['tornado']
+}
+extras_require['all'] = [dep for package in extras_require.values() for dep in package]
 
 
 setup(
@@ -40,10 +46,7 @@ setup(
         'Operating System :: POSIX',
         'Programming Language :: Python :: 3'],
     install_requires=install_reqs,
-    extras_require={
+    extras_require=extras_require,
-        'web': ['tornado']
-
-    },
     tests_require=test_reqs,
     setup_requires=['pytest-runner', ],
     include_package_data=True,

soil/VERSION

@@ -1 +1 @@
-0.14.9
+0.20.5

soil/__init__.py

@@ -11,25 +11,28 @@ try:
 except NameError:
     basestring = str
 
+from .agents import *
 from . import agents
 from .simulation import *
 from .environment import Environment
-from .history import History
 from . import serialization
 from . import analysis
+from .utils import logger
+from .time import *
 
 def main():
     import argparse
     from . import simulation
 
-    logging.basicConfig(level=logging.INFO)
+    logger.info('Running SOIL version: {}'.format(__version__))
-    logging.info('Running SOIL version: {}'.format(__version__))
 
     parser = argparse.ArgumentParser(description='Run a SOIL simulation')
     parser.add_argument('file', type=str,
                         nargs="?",
                         default='simulation.yml',
-                        help='python module containing the simulation configuration.')
+                        help='Configuration file for the simulation (e.g., YAML or JSON)')
+    parser.add_argument('--version', action='store_true',
+                        help='Show version info and exit')
     parser.add_argument('--module', '-m', type=str,
                         help='file containing the code of any custom agents.')
     parser.add_argument('--dry-run', '--dry', action='store_true',
@@ -40,6 +43,8 @@ def main():
                         help='Dump GEXF graph. Defaults to false.')
     parser.add_argument('--csv', action='store_true',
                         help='Dump history in CSV format. Defaults to false.')
+    parser.add_argument('--level', type=str,
+                        help='Logging level')
     parser.add_argument('--output', '-o', type=str, default="soil_output",
                         help='folder to write results to. It defaults to the current directory.')
     parser.add_argument('--synchronous', action='store_true',
@@ -48,13 +53,21 @@ def main():
                         help='Export environment and/or simulations using this exporter')
 
     args = parser.parse_args()
+    logging.basicConfig(level=getattr(logging, (args.level or 'INFO').upper()))
+
+    if args.version:
+        return
 
     if os.getcwd() not in sys.path:
         sys.path.append(os.getcwd())
     if args.module:
         importlib.import_module(args.module)
 
-    logging.info('Loading config file: {}'.format(args.file))
+    logger.info('Loading config file: {}'.format(args.file))
+
+    if args.pdb:
+        args.synchronous = True
+
 
     try:
         exporters = list(args.exporter or ['default', ])
@@ -65,6 +78,10 @@ def main():
         exp_params = {}
         if args.dry_run:
             exp_params['copy_to'] = sys.stdout
+
+        if not os.path.exists(args.file):
+            logger.error('Please, input a valid file')
+            return
         simulation.run_from_config(args.file,
                                    dry_run=args.dry_run,
                                    exporters=exporters,

soil/agents/BassModel.py

@@ -1,40 +1,31 @@
 import random
-from . import BaseAgent
+from . import FSM, state, default_state
 
 
-class BassModel(BaseAgent):
+class BassModel(FSM):
     """
     Settings:
         innovation_prob
         imitation_prob
     """
-
+    sentimentCorrelation = 0
-    def __init__(self, environment, agent_id, state):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
-        env_params = environment.environment_params
-        self.state['sentimentCorrelation'] = 0
 
     def step(self):
         self.behaviour()
 
-    def behaviour(self):
+    @default_state
-        # Outside effects
+    @state
-        if random.random() < self.state_params['innovation_prob']:
+    def innovation(self):
-            if self.state['id'] == 0:
+        if random.random() < self.innovation_prob:
-                self.state['id'] = 1
+            self.sentimentCorrelation = 1
-                self.state['sentimentCorrelation'] = 1
+            return self.aware
-            else:
+        else:
-                pass
+            aware_neighbors = self.get_neighboring_agents(state_id=self.aware.id)
-
-            return
-
-        # Imitation effects
-        if self.state['id'] == 0:
-            aware_neighbors = self.get_neighboring_agents(state_id=1)
             num_neighbors_aware = len(aware_neighbors)
-            if random.random() < (self.state_params['imitation_prob']*num_neighbors_aware):
+            if random.random() < (self['imitation_prob']*num_neighbors_aware):
-                self.state['id'] = 1
+                self.sentimentCorrelation = 1
-                self.state['sentimentCorrelation'] = 1
+                return self.aware
 
-            else:
+    @state
-                pass
+    def aware(self):
+        self.die()

soil/agents/BigMarketModel.py

@@ -1,8 +1,8 @@
 import random
-from . import BaseAgent
+from . import FSM, state, default_state
 
 
-class BigMarketModel(BaseAgent):
+class BigMarketModel(FSM):
     """
     Settings:
         Names:
@@ -19,34 +19,25 @@ class BigMarketModel(BaseAgent):
             sentiment_about [Array]
     """
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, *args, **kwargs):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(*args, **kwargs)
-        self.enterprises = environment.environment_params['enterprises']
+        self.enterprises = self.env.environment_params['enterprises']
         self.type = ""
-        self.number_of_enterprises = len(environment.environment_params['enterprises'])
 
-        if self.id < self.number_of_enterprises:  # Enterprises
+        if self.id < len(self.enterprises):  # Enterprises
-            self.state['id'] = self.id
+            self.set_state(self.enterprise.id)
             self.type = "Enterprise"
             self.tweet_probability = environment.environment_params['tweet_probability_enterprises'][self.id]
         else:  # normal users
-            self.state['id'] = self.number_of_enterprises
             self.type = "User"
+            self.set_state(self.user.id)
             self.tweet_probability = environment.environment_params['tweet_probability_users']
             self.tweet_relevant_probability = environment.environment_params['tweet_relevant_probability']
             self.tweet_probability_about = environment.environment_params['tweet_probability_about']  # List
             self.sentiment_about = environment.environment_params['sentiment_about']  # List
 
-    def step(self):
+    @state
-
+    def enterprise(self):
-        if self.id < self.number_of_enterprises:  # Enterprise
-            self.enterpriseBehaviour()
-        else:  # Usuario
-            self.userBehaviour()
-            for i in range(self.number_of_enterprises):  # So that it never is set to 0 if there are not changes (logs)
-                self.attrs['sentiment_enterprise_%s'% self.enterprises[i]] = self.sentiment_about[i]
-
-    def enterpriseBehaviour(self):
 
         if random.random() < self.tweet_probability:  # Tweets
             aware_neighbors = self.get_neighboring_agents(state_id=self.number_of_enterprises)  # Nodes neighbour users
@@ -64,12 +55,12 @@ class BigMarketModel(BaseAgent):
 
                 x.attrs['sentiment_enterprise_%s'% self.enterprises[self.id]] = x.sentiment_about[self.id]
 
-    def userBehaviour(self):
+    @state
-
+    def user(self):
         if random.random() < self.tweet_probability:  # Tweets
             if random.random() < self.tweet_relevant_probability:  # Tweets something relevant
                 # Tweet probability per enterprise
-                for i in range(self.number_of_enterprises):
+                for i in range(len(self.enterprises)):
                     random_num = random.random()
                     if random_num < self.tweet_probability_about[i]:
                         # The condition is fulfilled, sentiments are evaluated towards that enterprise
@@ -82,8 +73,10 @@ class BigMarketModel(BaseAgent):
                         else:
                             # POSITIVO
                             self.userTweets("positive",i)
+        for i in range(len(self.enterprises)):  # So that it never is set to 0 if there are not changes (logs)
+            self.attrs['sentiment_enterprise_%s'% self.enterprises[i]] = self.sentiment_about[i]
 
-    def userTweets(self,sentiment,enterprise):
+    def userTweets(self, sentiment,enterprise):
         aware_neighbors = self.get_neighboring_agents(state_id=self.number_of_enterprises)  # Nodes neighbours users
         for x in aware_neighbors:
             if sentiment == "positive":

soil/agents/CounterModel.py

@@ -1,7 +1,7 @@
-from . import BaseAgent
+from . import NetworkAgent
 
 
-class CounterModel(BaseAgent):
+class CounterModel(NetworkAgent):
     """
     Dummy behaviour. It counts the number of nodes in the network and neighbors
     in each step and adds it to its state.
@@ -9,14 +9,14 @@ class CounterModel(BaseAgent):
 
     def step(self):
         # Outside effects
-        total = len(list(self.get_all_agents()))
+        total = len(list(self.get_agents()))
         neighbors = len(list(self.get_neighboring_agents()))
         self['times'] = self.get('times', 0) + 1
         self['neighbors'] = neighbors
         self['total'] = total
 
 
-class AggregatedCounter(BaseAgent):
+class AggregatedCounter(NetworkAgent):
     """
     Dummy behaviour. It counts the number of nodes in the network and neighbors
     in each step and adds it to its state.
@@ -33,6 +33,6 @@ class AggregatedCounter(BaseAgent):
         self['times'] += 1
         neighbors = len(list(self.get_neighboring_agents()))
         self['neighbors'] += neighbors
-        total = len(list(self.get_all_agents()))
+        total = len(list(self.get_agents()))
         self['total'] += total
         self.debug('Running for step: {}. Total: {}'.format(self.now, total))

soil/agents/Geo.py

@@ -0,0 +1,21 @@
+from scipy.spatial import cKDTree as KDTree
+import networkx as nx
+from . import NetworkAgent, as_node
+
+class Geo(NetworkAgent):
+    '''In this type of network, nodes have a "pos" attribute.'''
+
+    def geo_search(self, radius, node=None, center=False, **kwargs):
+        '''Get a list of nodes whose coordinates are closer than *radius* to *node*.'''
+        node = as_node(node if node is not None else self)
+
+        G = self.subgraph(**kwargs)
+
+        pos = nx.get_node_attributes(G, 'pos')
+        if not pos:
+            return []
+        nodes, coords = list(zip(*pos.items()))
+        kdtree = KDTree(coords)  # Cannot provide generator.
+        indices = kdtree.query_ball_point(pos[node], radius)
+        return [nodes[i] for i in indices if center or (nodes[i] != node)]
+

soil/agents/IndependentCascadeModel.py

@@ -10,10 +10,10 @@ class IndependentCascadeModel(BaseAgent):
         imitation_prob
     """
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, *args, **kwargs):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(*args, **kwargs)
-        self.innovation_prob = environment.environment_params['innovation_prob']
+        self.innovation_prob = self.env.environment_params['innovation_prob']
-        self.imitation_prob = environment.environment_params['imitation_prob']
+        self.imitation_prob = self.env.environment_params['imitation_prob']
         self.state['time_awareness'] = 0
         self.state['sentimentCorrelation'] = 0
 

soil/agents/ModelM2.py

@@ -21,8 +21,8 @@ class SpreadModelM2(BaseAgent):
         prob_generate_anti_rumor
     """
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, model=None, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=environment, unique_id=unique_id, state=state)
 
         self.prob_neutral_making_denier = np.random.normal(environment.environment_params['prob_neutral_making_denier'],
                                                            environment.environment_params['standard_variance'])
@@ -123,8 +123,8 @@ class ControlModelM2(BaseAgent):
     """
 
 
-    def __init__(self, environment=None, agent_id=0, state=()):
+    def __init__(self, model=None, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=environment, unique_id=unique_id, state=state)
 
         self.prob_neutral_making_denier = np.random.normal(environment.environment_params['prob_neutral_making_denier'],
                                                            environment.environment_params['standard_variance'])

soil/agents/SISaModel.py

@@ -29,8 +29,8 @@ class SISaModel(FSM):
         standard_variance
     """
 
-    def __init__(self, environment, agent_id=0, state=()):
+    def __init__(self, environment, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=environment, unique_id=unique_id, state=state)
 
         self.neutral_discontent_spon_prob = np.random.normal(self.env['neutral_discontent_spon_prob'],
                                                              self.env['standard_variance'])

soil/agents/SentimentCorrelationModel.py

@@ -16,8 +16,8 @@ class SentimentCorrelationModel(BaseAgent):
         disgust_prob
     """
 
-    def __init__(self, environment, agent_id=0, state=()):
+    def __init__(self, environment, unique_id=0, state=()):
-        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        super().__init__(model=environment, unique_id=unique_id, state=state)
         self.outside_effects_prob = environment.environment_params['outside_effects_prob']
         self.anger_prob = environment.environment_params['anger_prob']
         self.joy_prob = environment.environment_params['joy_prob']

soil/agents/__init__.py

@@ -1,21 +1,16 @@
-# networkStatus = {}  # Dict that will contain the status of every agent in the network
-# sentimentCorrelationNodeArray = []
-# for x in range(0, settings.network_params["number_of_nodes"]):
-#     sentimentCorrelationNodeArray.append({'id': x})
-# Initialize agent states. Let's assume everyone is normal.
-    
-
-import nxsim
 import logging
-from collections import OrderedDict
+from collections import OrderedDict, defaultdict
 from copy import deepcopy
-from functools import partial
+from functools import partial, wraps
-from scipy.spatial import cKDTree as KDTree
+from itertools import islice
 import json
+import networkx as nx
 
-from functools import wraps
+from .. import serialization, utils, time
 
-from .. import serialization, history
+from tsih import Key
+
+from mesa import Agent
 
 
 def as_node(agent):
@@ -23,41 +18,62 @@ def as_node(agent):
         return agent.id
     return agent
 
+IGNORED_FIELDS = ('model', 'logger')
 
-class BaseAgent(nxsim.BaseAgent):
+
+class DeadAgent(Exception):
+    pass
+
+class BaseAgent(Agent):
     """
-    A special simpy BaseAgent that keeps track of its state history.
+    A special Agent that keeps track of its state history.
     """
 
     defaults = {}
 
-    def __init__(self, environment, agent_id, state=None,
+    def __init__(self,
-                 name=None, interval=None, **state_params):
+                 unique_id,
+                 model,
+                 name=None,
+                 interval=None,
+                 **kwargs
+    ):
         # Check for REQUIRED arguments
-        assert environment is not None, TypeError('__init__ missing 1 required keyword argument: \'environment\'. '
-                                                  'Cannot be NoneType.')
         # Initialize agent parameters
-        self.id = agent_id
+        if isinstance(unique_id, Agent):
-        self.name = name or '{}[{}]'.format(type(self).__name__, self.id)
+            raise Exception()
-        self.state_params = state_params
+        self._saved = set()
-
+        super().__init__(unique_id=unique_id, model=model)
-        # Register agent to environment
+        self.name = name or '{}[{}]'.format(type(self).__name__, self.unique_id)
-        self.env = environment
 
         self._neighbors = None
         self.alive = True
-        real_state = deepcopy(self.defaults)
-        real_state.update(state or {})
-        self.state = real_state
-        self.interval = interval
 
-        if not hasattr(self, 'level'):
+        self.interval = interval or self.get('interval', 1)
-            self.level = logging.DEBUG
+        self.logger = logging.getLogger(self.model.name).getChild(self.name)
-        self.logger = logging.getLogger(self.env.name)
-        self.logger.setLevel(self.level)
 
-        # initialize every time an instance of the agent is created
+        if hasattr(self, 'level'):
-        self.action = self.env.process(self.run())
+            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)
+
+
+    # TODO: refactor to clean up mesa compatibility
+    @property
+    def id(self):
+        return self.unique_id
+
+    @property
+    def env(self):
+        return self.model
+
+    @env.setter
+    def env(self, model):
+        self.model = model
 
     @property
     def state(self):
@@ -71,44 +87,47 @@ class BaseAgent(nxsim.BaseAgent):
 
     @state.setter
     def state(self, value):
-        self._state = {}
         for k, v in value.items():
             self[k] = v
 
-    @property
-    def global_topology(self):
-        return self.env.G
-    
     @property
     def environment_params(self):
-        return self.env.environment_params
+        return self.model.environment_params
-    
+
     @environment_params.setter
     def environment_params(self, value):
-        self.env.environment_params = 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 = history.Key(key=key, t_step=t_step, agent_id=self.id)
+            k = Key(key=key, t_step=t_step, dict_id=self.unique_id)
-            return self.env[k]
+            return self.model[k]
-        return self._state.get(key, None)
+        return getattr(self, key)
 
     def __delitem__(self, key):
-        self._state[key] = None
+        return delattr(self, key)
 
     def __contains__(self, key):
-        return key in self._state
+        return hasattr(self, key)
 
     def __setitem__(self, key, value):
-        self._state[key] = value
+        setattr(self, key, value)
-        k = history.Key(t_step=self.now,
-                        agent_id=self.id,
-                        key=key)
-        self.env[k] = value
 
     def items(self):
-        return self._state.items()
+        return ((k, getattr(self, k)) for k in self._saved)
 
     def get(self, key, default=None):
         return self[key] if key in self else default
@@ -116,54 +135,34 @@ class BaseAgent(nxsim.BaseAgent):
     @property
     def now(self):
         try:
-            return self.env.now
+            return self.model.now
         except AttributeError:
             # No environment
             return None
 
-    def run(self):
-        if self.interval is not None:
-            interval = self.interval
-        elif 'interval' in self:
-            interval = self['interval']
-        else:
-            interval = self.env.interval
-        while self.alive:
-            res = self.step()
-            yield res or self.env.timeout(interval)
-
     def die(self, remove=False):
+        self.info(f'agent {self.unique_id}  is dying')
         self.alive = False
         if remove:
-            super().die()
+            self.remove_node(self.id)
+        return time.INFINITY
 
     def step(self):
-        pass
+        if not self.alive:
-
+            raise DeadAgent(self.unique_id)
-    def count_agents(self, **kwargs):
+        return super().step() or time.Delta(self.interval)
-        return len(list(self.get_agents(**kwargs)))
-
-    def count_neighboring_agents(self, state_id=None, **kwargs):
-        return len(super().get_neighboring_agents(state_id=state_id, **kwargs))
-
-    def get_neighboring_agents(self, state_id=None, **kwargs):
-        return self.get_agents(limit_neighbors=True, state_id=state_id, **kwargs)
-
-    def get_agents(self, agents=None, limit_neighbors=False, **kwargs):
-        if limit_neighbors:
-            agents = super().get_agents(limit_neighbors=limit_neighbors)
-        else:
-            agents = self.env.get_agents(agents)
-        return select(agents, **kwargs)
 
     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 = "\t{:10}@{:>5}:\t{}".format(self.name, self.now, message)
+        message = " @{:>3}: {}".format(self.now, message)
         for k, v in kwargs:
             message += " {k}={v} ".format(k, v)
         extra = {}
         extra['now'] = self.now
-        extra['id'] = self.id
+        extra['unique_id'] = self.unique_id
+        extra['agent_name'] = self.name
         return self.logger.log(level, message, extra=extra)
 
     def debug(self, *args, **kwargs):
@@ -172,44 +171,55 @@ class BaseAgent(nxsim.BaseAgent):
     def info(self, *args, **kwargs):
         return self.log(*args, level=logging.INFO, **kwargs)
 
-    def __getstate__(self):
-        '''
-        Serializing an agent will lose all its running information (you cannot
-        serialize an iterator), but it keeps the state and link to the environment,
-        so it can be used for inspection and dumping to a file
-        '''
-        state = {}
-        state['id'] = self.id
-        state['environment'] = self.env
-        state['_state'] = self._state
-        return state
-
-    def __setstate__(self, state):
-        '''
-        Get back a serialized agent and try to re-compose it
-        '''
-        self.id = state['id']
-        self._state = state['_state']
-        self.env = state['environment']
-
-    def add_edge(self, node1, node2, **attrs):
-        node1 = as_node(node1)
-        node2 = as_node(node2)
-
-        for n in [node1, node2]:
-            if n not in self.global_topology.nodes(data=False):
-                raise ValueError('"{}" not in the graph'.format(n))
-        return self.global_topology.add_edge(node1, node2, **attrs)
-
-    def subgraph(self, center=True, **kwargs):
-        include = [self] if center else []
-        return self.global_topology.subgraph(n.id for n in self.get_agents(**kwargs)+include)
-
 
 class NetworkAgent(BaseAgent):
 
-    def add_edge(self, other, **kwargs):
+    @property
-        return super(NetworkAgent, self).add_edge(node1=self.id, node2=other, **kwargs)
+    def topology(self):
+        return self.model.G
+
+    @property
+    def G(self):
+        return self.model.G
+
+    def count_agents(self, **kwargs):
+        return len(list(self.get_agents(**kwargs)))
+
+    def count_neighboring_agents(self, state_id=None, **kwargs):
+        return len(self.get_neighboring_agents(state_id=state_id, **kwargs))
+
+    def get_neighboring_agents(self, state_id=None, **kwargs):
+        return self.get_agents(limit_neighbors=True, state_id=state_id, **kwargs)
+
+    def get_agents(self, *args, limit=None, **kwargs):
+        it = self.iter_agents(*args, **kwargs)
+        if limit is not None:
+            it = islice(it, limit)
+        return list(it)
+
+    def iter_agents(self, agents=None, limit_neighbors=False, **kwargs):
+        if limit_neighbors:
+            agents = self.topology.neighbors(self.unique_id)
+
+        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)
+
+    def remove_node(self, unique_id):
+        self.topology.remove_node(unique_id)
+
+    def add_edge(self, other, edge_attr_dict=None, *edge_attrs):
+        # return super(NetworkAgent, self).add_edge(node1=self.id, node2=other, **kwargs)
+        if self.unique_id not in self.topology.nodes(data=False):
+            raise ValueError('{} not in list of existing agents in the network'.format(self.unique_id))
+        if other.unique_id not in self.topology.nodes(data=False):
+            raise ValueError('{} not in list of existing agents in the network'.format(other))
+
+        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*'''
@@ -219,17 +229,17 @@ class NetworkAgent(BaseAgent):
 
     def degree(self, node, force=False):
         node = as_node(node)
-        if force or (not hasattr(self.env, '_degree')) or getattr(self.env, '_last_step', 0) < self.now:
+        if force or (not hasattr(self.model, '_degree')) or getattr(self.model, '_last_step', 0) < self.now:
-            self.env._degree = nx.degree_centrality(self.global_topology)
+            self.model._degree = nx.degree_centrality(self.topology)
-            self.env._last_step = self.now
+            self.model._last_step = self.now
-        return self.env._degree[node]
+        return self.model._degree[node]
 
     def betweenness(self, node, force=False):
         node = as_node(node)
-        if force or (not hasattr(self.env, '_betweenness')) or getattr(self.env, '_last_step', 0) < self.now:
+        if force or (not hasattr(self.model, '_betweenness')) or getattr(self.model, '_last_step', 0) < self.now:
-            self.env._betweenness = nx.betweenness_centrality(self.global_topology)
+            self.model._betweenness = nx.betweenness_centrality(self.topology)
-            self.env._last_step = self.now
+            self.model._last_step = self.now
-        return self.env._betweenness[node]
+        return self.model._betweenness[node]
 
 
 def state(name=None):
@@ -292,31 +302,35 @@ class MetaFSM(type):
         cls.states = states
 
 
-class FSM(BaseAgent, metaclass=MetaFSM):
+class FSM(NetworkAgent, metaclass=MetaFSM):
     def __init__(self, *args, **kwargs):
         super(FSM, self).__init__(*args, **kwargs)
-        if 'id' not in self.state:
+        if not hasattr(self, 'state_id'):
             if not self.default_state:
-                raise ValueError('No default state specified for {}'.format(self.id))
+                raise ValueError('No default state specified for {}'.format(self.unique_id))
-            self['id'] = self.default_state.id
+            self.state_id = self.default_state.id
+
+        self.set_state(self.state_id)
 
     def step(self):
-        if 'id' in self.state:
+        self.debug(f'Agent {self.unique_id} @ state {self.state_id}')
-            next_state = self['id']
+        interval = super().step()
-        elif self.default_state:
+        if 'id' not in self.state:
-            next_state = self.default_state.id
+            if self.default_state:
-        else:
+                self.set_state(self.default_state.id)
-            raise Exception('{} has no valid state id or default state'.format(self))
+            else:
-        if next_state not in self.states:
+                raise Exception('{} has no valid state id or default state'.format(self))
-            raise Exception('{} is not a valid id for {}'.format(next_state, self))
+        interval = self.states[self.state_id](self) or interval
-        return self.states[next_state](self)
+        if not self.alive:
+            return time.NEVER
+        return interval
 
     def set_state(self, state):
         if hasattr(state, 'id'):
             state = state.id
         if state not in self.states:
             raise ValueError('{} is not a valid state'.format(state))
-        self['id'] = state
+        self.state_id = state
         return state
 
 
@@ -335,9 +349,6 @@ def prob(prob=1):
     return r < prob
 
 
-STATIC_THRESHOLD = (-1, -1)
-
-
 def calculate_distribution(network_agents=None,
                            agent_type=None):
     '''
@@ -365,20 +376,23 @@ def calculate_distribution(network_agents=None,
     'agent_type_1'.
     '''
     if network_agents:
-        network_agents = deepcopy(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}]
     else:
         raise ValueError('Specify a distribution or a default agent type')
 
+    # Fix missing weights and incompatible types
+    for x in network_agents:
+        x['weight'] = float(x.get('weight', 1))
+
     # Calculate the thresholds
-    total = sum(x.get('weight', 1) for x in network_agents)
+    total = sum(x['weight'] for x in network_agents)
     acc = 0
     for v in network_agents:
         if 'ids' in v:
-            v['threshold'] = STATIC_THRESHOLD
             continue
-        upper = acc + (v.get('weight', 1)/total)
+        upper = acc + (v['weight']/total)
         v['threshold'] = [acc, upper]
         acc = upper
     return network_agents
@@ -391,7 +405,7 @@ def serialize_type(agent_type, known_modules=[], **kwargs):
     return serialization.serialize(agent_type, known_modules=known_modules, **kwargs)[1] # Get the name of the class
 
 
-def serialize_distribution(network_agents, known_modules=[]):
+def serialize_definition(network_agents, known_modules=[]):
     '''
     When serializing an agent distribution, remove the thresholds, in order
     to avoid cluttering the YAML definition file.
@@ -413,7 +427,7 @@ def deserialize_type(agent_type, known_modules=[]):
     return agent_type
 
 
-def deserialize_distribution(ind, **kwargs):
+def deserialize_definition(ind, **kwargs):
     d = deepcopy(ind)
     for v in d:
         v['agent_type'] = deserialize_type(v['agent_type'], **kwargs)
@@ -425,7 +439,7 @@ def _validate_states(states, topology):
     states = states or []
     if isinstance(states, dict):
         for x in states:
-            assert x in topology.node
+            assert x in topology.nodes
     else:
         assert len(states) <= len(topology)
     return states
@@ -434,44 +448,84 @@ def _validate_states(states, topology):
 def _convert_agent_types(ind, to_string=False, **kwargs):
     '''Convenience method to allow specifying agents by class or class name.'''
     if to_string:
-        return serialize_distribution(ind, **kwargs)
+        return serialize_definition(ind, **kwargs)
-    return deserialize_distribution(ind, **kwargs)
+    return deserialize_definition(ind, **kwargs)
 
 
-def _agent_from_distribution(distribution, value=-1, agent_id=None):
+def _agent_from_definition(definition, value=-1, unique_id=None):
     """Used in the initialization of agents given an agent distribution."""
     if value < 0:
         value = random.random()
-    for d in sorted(distribution, key=lambda x: x['threshold']):
+    for d in sorted(definition, key=lambda x: x.get('threshold')):
-        threshold = d['threshold']
+        threshold = d.get('threshold', (-1, -1))
         # Check if the definition matches by id (first) or by threshold
-        if not ((agent_id is not None and threshold == STATIC_THRESHOLD and agent_id in d['ids']) or \
+        if (unique_id is not None and unique_id in d.get('ids', [])) or \
-                (value >= threshold[0] and value < threshold[1])):
+           (value >= threshold[0] and value < threshold[1]):
-            continue
+            state = {}
-        state = {}
+            if 'state' in d:
-        if 'state' in d:
+                state = deepcopy(d['state'])
-            state = deepcopy(d['state'])
+            return d['agent_type'], state
-        return d['agent_type'], state
 
-    raise Exception('Distribution for value {} not found in: {}'.format(value, distribution))
+    raise Exception('Definition for value {} not found in: {}'.format(value, definition))
 
 
-class Geo(NetworkAgent):
+def _definition_to_dict(definition, size=None, default_state=None):
-    '''In this type of network, nodes have a "pos" attribute.'''
+    state = default_state or {}
+    agents = {}
+    remaining = {}
+    if size:
+        for ix in range(size):
+            remaining[ix] = copy(state)
+    else:
+        remaining = defaultdict(lambda x: copy(state))
 
-    def geo_search(self, radius, node=None, center=False, **kwargs):
+    distro = sorted([item for item in definition if 'weight' in item])
-        '''Get a list of nodes whose coordinates are closer than *radius* to *node*.'''
-        node = as_node(node if node is not None else self)
 
-        G = self.subgraph(**kwargs)
+    ix = 0
+    def init_agent(item, id=ix):
+        while id in agents:
+            id += 1
 
-        pos = nx.get_node_attributes(G, 'pos')
+        agent = remaining[id]
-        if not pos:
+        agent['state'].update(copy(item.get('state', {})))
-            return []
+        agents[id] = agent
-        nodes, coords = list(zip(*pos.items()))
+        del remaining[id]
-        kdtree = KDTree(coords)  # Cannot provide generator.
+        return agent
-        indices = kdtree.query_ball_point(pos[node], radius)
+
-        return [nodes[i] for i in indices if center or (nodes[i] != node)]
+    for item in definition:
+        if 'ids' in item:
+            ids = item['ids']
+            del item['ids']
+            for id in ids:
+                agent = init_agent(item, id)
+
+    for item in definition:
+        if 'number' in item:
+            times = item['number']
+            del item['number']
+            for times in range(times):
+                if size:
+                    ix = random.choice(remaining.keys())
+                    agent = init_agent(item, id)
+                else:
+                    agent = init_agent(item)
+    if not size:
+        return agents
+
+    if len(remaining) < 0:
+        raise Exception('Invalid definition. Too many agents to add')
+
+
+    total_weight = float(sum(s['weight'] for s in distro))
+    unit = size / total_weight
+
+    for item in distro:
+        times = unit * item['weight']
+        del item['weight']
+        for times in range(times):
+            ix = random.choice(remaining.keys())
+            agent = init_agent(item, id)
+    return agents
 
 
 def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False, **kwargs):
@@ -484,25 +538,22 @@ def select(agents, state_id=None, agent_type=None, ignore=None, iterator=False,
         except TypeError:
             agent_type = tuple([agent_type])
 
-    def matches_all(agent):
+    f = agents
-        if state_id is not None:
-            if agent.state.get('id', None) not in state_id:
-                return False
-        if agent_type is not None:
-            if not isinstance(agent, agent_type):
-                return False
-        state = agent.state
-        for k, v in kwargs.items():
-            if state.get(k, None) != v:
-                return False
-        return True
 
-    f = filter(matches_all, 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():
+        f = filter(lambda agent: agent.state.get(k, None) == v, f)
+
     if iterator:
         return f
-    return list(f)
+    return f
 
 
 from .BassModel import *
@@ -512,3 +563,10 @@ from .ModelM2 import *
 from .SentimentCorrelationModel import *
 from .SISaModel import *
 from .CounterModel import *
+
+try:
+    import scipy
+    from .Geo import Geo
+except ImportError:
+    import sys
+    print('Could not load the Geo Agent, scipy is not installed', file=sys.stderr)

soil/analysis.py

@@ -4,7 +4,8 @@ import glob
 import yaml
 from os.path import join
 
-from . import serialization, history
+from . import serialization
+from tsih import History
 
 
 def read_data(*args, group=False, **kwargs):
@@ -28,13 +29,13 @@ def _read_data(pattern, *args, from_csv=False, process_args=None, **kwargs):
                 df = read_csv(trial_data, **kwargs)
                 yield config_file, df, config
         else:
-            for trial_data in sorted(glob.glob(join(folder, '*.db.sqlite'))):
+            for trial_data in sorted(glob.glob(join(folder, '*.sqlite'))):
                 df = read_sql(trial_data, **kwargs)
                 yield config_file, df, config
 
 
 def read_sql(db, *args, **kwargs):
-    h = history.History(db_path=db, backup=False)
+    h = History(db_path=db, backup=False, readonly=True)
     df = h.read_sql(*args, **kwargs)
     return df
 
@@ -61,7 +62,12 @@ def convert_row(row):
 
 
 def convert_types_slow(df):
-    '''This is a slow operation.'''
+    '''
+    Go over every column in a dataframe and convert it to the type determined by the `get_types`
+    function.
+
+    This is a slow operation.
+    '''
     dtypes = get_types(df)
     for k, v in dtypes.items():
         t = df[df['key']==k]
@@ -69,6 +75,13 @@ def convert_types_slow(df):
     df = df.apply(convert_row, axis=1)
     return df
 
+
+def split_processed(df):
+    env = df.loc[:, df.columns.get_level_values(1).isin(['env', 'stats'])]
+    agents = df.loc[:, ~df.columns.get_level_values(1).isin(['env', 'stats'])]
+    return env, agents
+
+
 def split_df(df):
     '''
     Split a dataframe in two dataframes: one with the history of agents,
@@ -95,6 +108,9 @@ def process(df, **kwargs):
 
 
 def get_types(df):
+    '''
+    Get the value type for every key stored in a raw history dataframe.
+    '''
     dtypes = df.groupby(by=['key'])['value_type'].unique()
     return {k:v[0] for k,v in dtypes.iteritems()}
 
@@ -119,8 +135,14 @@ def process_one(df, *keys, columns=['key', 'agent_id'], values='value',
 
 
 def get_count(df, *keys):
+    '''
+    For every t_step and key, get the value count.
+
+    The result is a dataframe with `t_step` as index, an a multiindex column based on `key` and the values found for each `key`.
+    '''
     if keys:
         df = df[list(keys)]
+        df.columns = df.columns.remove_unused_levels()
     counts = pd.DataFrame()
     for key in df.columns.levels[0]:
         g = df[[key]].apply(pd.Series.value_counts, axis=1).fillna(0)
@@ -130,13 +152,28 @@ def get_count(df, *keys):
     return counts
 
 
+def get_majority(df, *keys):
+    '''
+    For every t_step and key, get the value of the majority of agents
+
+    The result is a dataframe with `t_step` as index, and columns based on `key`.
+    '''
+    df = get_count(df, *keys)
+    return df.stack(level=0).idxmax(axis=1).unstack()
+
+
 def get_value(df, *keys, aggfunc='sum'):
+    '''
+    For every t_step and key, get the value of *numeric columns*, aggregated using a specific function.
+    '''
     if keys:
         df = df[list(keys)]
-    return df.groupby(axis=1, level=0).agg(aggfunc)
+        df.columns = df.columns.remove_unused_levels()
+    df = df.select_dtypes('number')
+    return df.groupby(level='key', axis=1).agg(aggfunc)
 
 
-def plot_all(*args, **kwargs):
+def plot_all(*args, plot_args={}, **kwargs):
     '''
     Read all the trial data and plot the result of applying a function on them.
     '''
@@ -144,14 +181,17 @@ def plot_all(*args, **kwargs):
     ps = []
     for line in dfs:
         f, df, config = line
-        df.plot(title=config['name'])
+        if len(df) < 1:
+            continue
+        df.plot(title=config['name'], **plot_args)
         ps.append(df)
     return ps
 
 def do_all(pattern, func, *keys, include_env=False, **kwargs):
     for config_file, df, config in read_data(pattern, keys=keys):
+        if len(df) < 1:
+            continue
         p = func(df, *keys, **kwargs)
-        p.plot(title=config['name'])
         yield config_file, p, config
 
 

soil/datacollection.py

@@ -0,0 +1,26 @@
+from mesa import DataCollector as MDC
+
+class SoilDataCollector(MDC):
+
+
+    def __init__(self, environment, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        # Populate model and env reporters so they have a key per 
+        # So they can be shown in the web interface
+        self.environment = environment
+
+
+    @property
+    def model_vars(self):
+        pass
+
+    @model_vars.setter
+    def model_vars(self, value):
+        pass
+
+    @property
+    def agent_reporters(self):
+        self.model._history._
+
+        pass
+

soil/environment.py

@@ -1,29 +1,32 @@
 import os
 import sqlite3
-import time
 import csv
+import math
 import random
-import simpy
 import yaml
 import tempfile
+import logging
 import pandas as pd
+from time import time as current_time
 from copy import deepcopy
-from collections import Counter
 from networkx.readwrite import json_graph
 
 import networkx as nx
-import nxsim
 
-from . import serialization, agents, analysis, history, utils
+from tsih import History, Record, Key, NoHistory
+
+from mesa import Model
+
+from . import serialization, agents, analysis, utils, time
 
 # These properties will be copied when pickling/unpickling the environment
 _CONFIG_PROPS = [ 'name',
-                 'states',
+                  'states',
-                 'default_state',
+                  'default_state',
-                 'interval',
+                  'interval',
                  ]
 
-class Environment(nxsim.NetworkEnvironment):
+class Environment(Model):
     """
     The environment is key in a simulation. It contains the network topology,
     a reference to network and environment agents, as well as the environment
@@ -40,28 +43,72 @@ class Environment(nxsim.NetworkEnvironment):
                  states=None,
                  default_state=None,
                  interval=1,
+                 network_params=None,
                  seed=None,
                  topology=None,
-                 *args, **kwargs):
+                 schedule=None,
+                 initial_time=0,
+                 environment_params=None,
+                 history=True,
+                 dir_path=None,
+                 **kwargs):
+
+
+        super().__init__()
+
+        self.schedule = schedule
+        if schedule is None:
+            self.schedule = time.TimedActivation()
+
         self.name = name or 'UnnamedEnvironment'
-        seed = seed or time.time()
+        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()
-        super().__init__(*args, topology=topology, **kwargs)
+        self.G = nx.Graph(topology) 
+
+
+        self.environment_params = environment_params or {}
+        self.environment_params.update(kwargs)
+
         self._env_agents = {}
         self.interval = interval
-        self._history = history.History(name=self.name,
+        if history:
-                                        backup=True)
+            history = History
+        else:
+            history = NoHistory
+        self._history = history(name=self.name,
+                                backup=True)
         self['SEED'] = seed
-        # Add environment agents first, so their events get
+
-        # executed before network agents
+        if network_agents:
-        self.environment_agents = environment_agents or []
+            distro = agents.calculate_distribution(network_agents)
-        self.network_agents = network_agents or []
+            self.network_agents = agents._convert_agent_types(distro)
+        else:
+            self.network_agents = []
+
+        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
+
+        self.logger = utils.logger.getChild(self.name)
+
+    @property
+    def now(self):
+        if self.schedule:
+            return self.schedule.time
+        raise Exception('The environment has not been scheduled, so it has no sense of time')
 
     @property
     def agents(self):
@@ -75,15 +122,9 @@ class Environment(nxsim.NetworkEnvironment):
 
     @environment_agents.setter
     def environment_agents(self, environment_agents):
-        # Set up environmental agent
+        self._environment_agents = environment_agents
-        self._env_agents = {}
+
-        for item in environment_agents:
+        self._env_agents = agents._definition_to_dict(definition=environment_agents)
-            kwargs = deepcopy(item)
-            atype = kwargs.pop('agent_type')
-            kwargs['agent_id'] = kwargs.get('agent_id', atype.__name__)
-            kwargs['state'] = kwargs.get('state', {})
-            a = atype(environment=self, **kwargs)
-            self._env_agents[a.id] = a
 
     @property
     def network_agents(self):
@@ -96,9 +137,9 @@ class Environment(nxsim.NetworkEnvironment):
     def network_agents(self, network_agents):
         self._network_agents = network_agents
         for ix in self.G.nodes():
-            self.init_agent(ix, agent_distribution=network_agents)
+            self.init_agent(ix, agent_definitions=network_agents)
 
-    def init_agent(self, agent_id, agent_distribution):
+    def init_agent(self, agent_id, agent_definitions):
         node = self.G.nodes[agent_id]
         init = False
         state = dict(node)
@@ -113,8 +154,8 @@ class Environment(nxsim.NetworkEnvironment):
 
         if agent_type:
             agent_type = agents.deserialize_type(agent_type)
-        elif agent_distribution:
+        elif agent_definitions:
-            agent_type, state = agents._agent_from_distribution(agent_distribution, agent_id=agent_id)
+            agent_type, state = agents._agent_from_definition(agent_definitions, unique_id=agent_id)
         else:
             serialization.logger.debug('Skipping node {}'.format(agent_id))
             return
@@ -130,10 +171,15 @@ class Environment(nxsim.NetworkEnvironment):
         a = None
         if agent_type:
             state = defstate
-            a = agent_type(environment=self,
+            a = agent_type(model=self,
-                           agent_id=agent_id,
+                           unique_id=agent_id
-                           state=state)
+            )
+
+        for (k, v) in state.items():
+            setattr(a, k, v)
+
         node['agent'] = a
+        self.schedule.add(a)
         return a
 
     def add_node(self, agent_type, state=None):
@@ -151,34 +197,35 @@ class Environment(nxsim.NetworkEnvironment):
         start = start or self.now
         return self.G.add_edge(agent1, agent2, **attrs)
 
-    def run(self, *args, **kwargs):
+    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.name
+        return self.logger.log(level, message, extra=extra)
+
+    def step(self):
+        super().step()
+        self.schedule.step()
+
+    def run(self, until, *args, **kwargs):
         self._save_state()
-        self.log_stats()
+
-        super().run(*args, **kwargs)
+        while self.schedule.next_time < until:
+            self.step()
+            utils.logger.debug(f'Simulation step {self.schedule.time}/{until}. Next: {self.schedule.next_time}')
+        self.schedule.time = until
         self._history.flush_cache()
-        self.log_stats()
 
     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 save_state(self):
-        '''
-        :DEPRECATED:
-        Periodically save the state of the environment and the agents.
-        '''
-        self._save_state()
-        while self.peek() != simpy.core.Infinity:
-            delay = max(self.peek() - self.now, self.interval)
-            serialization.logger.debug('Step: {}'.format(self.now))
-            ev = self.event()
-            ev._ok = True
-            # Schedule the event with minimum priority so
-            # that it executes before all agents
-            self.schedule(ev, -999, delay)
-            yield ev
-            self._save_state()
-
     def __getitem__(self, key):
         if isinstance(key, tuple):
             self._history.flush_cache()
@@ -188,12 +235,12 @@ class Environment(nxsim.NetworkEnvironment):
 
     def __setitem__(self, key, value):
         if isinstance(key, tuple):
-            k = history.Key(*key)
+            k = Key(*key)
             self._history.save_record(*k,
                                       value=value)
             return
         self.environment_params[key] = value
-        self._history.save_record(agent_id='env',
+        self._history.save_record(dict_id='env',
                                   t_step=self.now,
                                   key=key,
                                   value=value)
@@ -217,8 +264,8 @@ class Environment(nxsim.NetworkEnvironment):
 
     def get_agents(self, nodes=None):
         if nodes is None:
-            return list(self.agents)
+            return self.agents
-        return [self.G.nodes[i]['agent'] for i in nodes]
+        return (self.G.nodes[i]['agent'] for i in nodes)
 
     def dump_csv(self, f):
         with utils.open_or_reuse(f, 'w') as f:
@@ -258,16 +305,16 @@ class Environment(nxsim.NetworkEnvironment):
         if now is None:
             now = self.now
         for k, v in self.environment_params.items():
-            yield history.Record(agent_id='env',
+            yield Record(dict_id='env',
-                                 t_step=now,
+                         t_step=now,
-                                 key=k,
+                         key=k,
-                                 value=v)
+                         value=v)
         for agent in self.agents:
             for k, v in agent.state.items():
-                yield history.Record(agent_id=agent.id,
+                yield Record(dict_id=agent.id,
-                                     t_step=now,
+                             t_step=now,
-                                     key=k,
+                             key=k,
-                                     value=v)
+                             value=v)
 
     def history_to_tuples(self):
         return self._history.to_tuples()
@@ -318,25 +365,6 @@ class Environment(nxsim.NetworkEnvironment):
 
         return G
 
-    def stats(self):
-        stats = {}
-        stats['network'] = {}
-        stats['network']['n_nodes'] = self.G.number_of_nodes()
-        stats['network']['n_edges'] = self.G.number_of_edges()
-        c = Counter()
-        c.update(a.__class__.__name__ for a in self.network_agents)
-        stats['agents'] = {}
-        stats['agents']['model_count'] = dict(c)
-        c2 = Counter()
-        c2.update(a['id'] for a in self.network_agents)
-        stats['agents']['state_count'] = dict(c2)
-        stats['params'] = self.environment_params
-        return stats
-
-    def log_stats(self):
-        stats = self.stats()
-        serialization.logger.info('Environment stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
-    
     def __getstate__(self):
         state = {}
         for prop in _CONFIG_PROPS:
@@ -344,6 +372,7 @@ class Environment(nxsim.NetworkEnvironment):
         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):
@@ -352,6 +381,9 @@ class Environment(nxsim.NetworkEnvironment):
         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

@@ -1,10 +1,11 @@
 import os
+import csv as csvlib
 import time
 from io import BytesIO
 
 import matplotlib.pyplot as plt
 import networkx as nx
-import pandas as pd
+
 
 from .serialization import deserialize
 from .utils import open_or_reuse, logger, timer
@@ -13,15 +14,6 @@ from .utils import open_or_reuse, logger, timer
 from . import utils
 
 
-def for_sim(simulation, names, *args, **kwargs):
-    '''Return the set of exporters for a simulation, given the exporter names'''
-    exporters = []
-    for name in names:
-        mod = deserialize(name, known_modules=['soil.exporters'])
-        exporters.append(mod(simulation, *args, **kwargs))
-    return exporters
-
-
 class DryRunner(BytesIO):
     def __init__(self, fname, *args, copy_to=None, **kwargs):
         super().__init__(*args, **kwargs)
@@ -37,8 +29,12 @@ class DryRunner(BytesIO):
             super().write(bytes(txt, 'utf-8'))
 
     def close(self):
-        logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname,
+        content = '(binary data not shown)'
-                                                                       self.getvalue().decode()))
+        try:
+            content = self.getvalue().decode()
+        except UnicodeDecodeError:
+            pass
+        logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname, content))
         super().close()
 
 
@@ -49,7 +45,7 @@ class Exporter:
     '''
 
     def __init__(self, simulation, outdir=None, dry_run=None, copy_to=None):
-        self.sim = simulation
+        self.simulation = simulation
         outdir = outdir or os.path.join(os.getcwd(), 'soil_output')
         self.outdir = os.path.join(outdir,
                                    simulation.group or '',
@@ -59,12 +55,15 @@ class Exporter:
 
     def start(self):
         '''Method to call when the simulation starts'''
+        pass
 
-    def end(self):
+    def end(self, stats):
         '''Method to call when the simulation ends'''
+        pass
 
-    def trial_end(self, env):
+    def trial(self, env, stats):
         '''Method to call when a trial ends'''
+        pass
 
     def output(self, f, mode='w', **kwargs):
         if self.dry_run:
@@ -84,35 +83,47 @@ class default(Exporter):
     def start(self):
         if not self.dry_run:
             logger.info('Dumping results to %s', self.outdir)
-            self.sim.dump_yaml(outdir=self.outdir)
+            self.simulation.dump_yaml(outdir=self.outdir)
         else:
             logger.info('NOT dumping results')
 
-    def trial_end(self, env):
+    def trial(self, env, stats):
         if not self.dry_run:
-            with timer('Dumping simulation {} trial {}'.format(self.sim.name,
+            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 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)
+
+
 
 class csv(Exporter):
     '''Export the state of each environment (and its agents) in a separate CSV file'''
-    def trial_end(self, env):
+    def trial(self, env, stats):
-        with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.sim.name,
+        with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.simulation.name,
                                                                           env.name,
                                                                           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)
+
 
 class gexf(Exporter):
-    def trial_end(self, env):
+    def trial(self, env, stats):
         if self.dry_run:
             logger.info('Not dumping GEXF in dry_run mode')
             return
 
-        with timer('[GEXF] Dumping simulation {} trial {}'.format(self.sim.name,
+        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)
@@ -124,56 +135,24 @@ class dummy(Exporter):
         with self.output('dummy', 'w') as f:
             f.write('simulation started @ {}\n'.format(time.time()))
 
-    def trial_end(self, env):
+    def trial(self, env, stats):
         with self.output('dummy', 'w') as f:
             for i in env.history_to_tuples():
                 f.write(','.join(map(str, i)))
                 f.write('\n')
 
-    def end(self):
+    def sim(self, stats):
         with self.output('dummy', 'a') as f:
             f.write('simulation ended @ {}\n'.format(time.time()))
 
 
-class distribution(Exporter):
-    '''
-    Write 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_end(self, env):
-        df = env[None, None, None].df()
-        ix = df.index[-1]
-        attrs = df.columns.levels[0]
-        vc = {}
-        stats = {}
-        for a in attrs:
-            t = df.loc[(ix, a)]
-            try:
-                self.means.append(('mean', a, t.mean()))
-            except TypeError:
-                for name, count in t.value_counts().iteritems():
-                    self.counts.append(('count', a, name, count))
-
-    def end(self):
-        dfm = pd.DataFrame(self.means, columns=['metric', 'key', 'value'])
-        dfc = pd.DataFrame(self.counts, columns=['metric', 'key', 'value', 'count'])
-        dfm = dfm.groupby(by=['key']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
-        dfc = dfc.groupby(by=['key', 'value']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
-        with self.output('counts.csv') as f:
-            dfc.to_csv(f)
-        with self.output('metrics.csv') as f:
-            dfm.to_csv(f)
 
 class graphdrawing(Exporter):
 
-    def trial_end(self, env):
+    def trial(self, env, stats):
         # 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:
             f.savefig(f)
+

soil/history.py

@@ -1,315 +0,0 @@
-import time
-import os
-import pandas as pd
-import sqlite3
-import copy
-import logging
-import tempfile
-
-logger = logging.getLogger(__name__)
-
-from collections import UserDict, namedtuple
-
-from . import serialization
-from .utils import open_or_reuse
-
-
-class History:
-    """
-    Store and retrieve values from a sqlite database.
-    """
-
-    def __init__(self, name=None, db_path=None, backup=False):
-        self._db = None
-
-        if db_path is None:
-            if not name:
-                name = time.time()
-            _, db_path = tempfile.mkstemp(suffix='{}.sqlite'.format(name))
-
-        if backup and os.path.exists(db_path):
-            newname = db_path + '.backup{}.sqlite'.format(time.time())
-            os.rename(db_path, newname)
-
-        self.db_path = db_path
-
-        self.db = db_path
-
-        with self.db:
-            logger.debug('Creating database {}'.format(self.db_path))
-            self.db.execute('''CREATE TABLE IF NOT EXISTS history (agent_id text, t_step int, key text, value text text)''')
-            self.db.execute('''CREATE TABLE IF NOT EXISTS value_types (key text, value_type text)''')
-            self.db.execute('''CREATE UNIQUE INDEX IF NOT EXISTS idx_history ON history (agent_id, t_step, key);''')
-        self._dtypes = {}
-        self._tups = []
-
-    @property
-    def db(self):
-        try:
-            self._db.cursor()
-        except (sqlite3.ProgrammingError, AttributeError):
-            self.db = None  # Reset the database
-        return self._db
-
-    @db.setter
-    def db(self, db_path=None):
-        self._close()
-        db_path = db_path or self.db_path
-        if isinstance(db_path, str):
-            logger.debug('Connecting to database {}'.format(db_path))
-            self._db = sqlite3.connect(db_path)
-        else:
-            self._db = db_path
-
-    def _close(self):
-        if self._db is None:
-            return
-        self.flush_cache()
-        self._db.close()
-        self._db = None
-
-    @property
-    def dtypes(self):
-        self.read_types()
-        return {k:v[0] for k, v in self._dtypes.items()}
-
-    def save_tuples(self, tuples):
-        '''
-        Save a series of tuples, converting them to records if necessary
-        '''
-        self.save_records(Record(*tup) for tup in tuples)
-
-    def save_records(self, records):
-        '''
-        Save a collection of records
-        '''
-        for record in records:
-            if not isinstance(record, Record):
-                record = Record(*record)
-            self.save_record(*record)
-
-    def save_record(self, agent_id, t_step, key, value):
-        '''
-        Save a collection of records to the database.
-        Database writes are cached.
-        '''
-        value = self.convert(key, value)
-        self._tups.append(Record(agent_id=agent_id,
-                                 t_step=t_step,
-                                 key=key,
-                                 value=value))
-        if len(self._tups) > 100:
-            self.flush_cache()
-
-    def convert(self, key, value):
-        """Get the serialized value for a given key."""
-        if key not in self._dtypes:
-            self.read_types()
-            if key not in self._dtypes:
-                name = serialization.name(value)
-                serializer = serialization.serializer(name)
-                deserializer = serialization.deserializer(name)
-                self._dtypes[key] = (name, serializer, deserializer)
-                with self.db:
-                    self.db.execute("replace into value_types (key, value_type) values (?, ?)", (key, name))
-        return self._dtypes[key][1](value)
-
-    def recover(self, key, value):
-        """Get the deserialized value for a given key, and the serialized version."""
-        if key not in self._dtypes:
-            self.read_types()
-        if key not in self._dtypes:
-            raise ValueError("Unknown datatype for {} and {}".format(key, value))
-        return self._dtypes[key][2](value)
-
-    def flush_cache(self):
-        '''
-        Use a cache to save state changes to avoid opening a session for every change.
-        The cache will be flushed at the end of the simulation, and when history is accessed.
-        '''
-        logger.debug('Flushing cache {}'.format(self.db_path))
-        with self.db:
-            for rec in self._tups:
-                self.db.execute("replace into history(agent_id, t_step, key, value) values (?, ?, ?, ?)", (rec.agent_id, rec.t_step, rec.key, rec.value))
-        self._tups = list()
-
-    def to_tuples(self):
-        self.flush_cache()
-        with self.db:
-            res = self.db.execute("select agent_id, t_step, key, value from history ").fetchall()
-        for r in res:
-            agent_id, t_step, key, value = r
-            value = self.recover(key, value)
-            yield agent_id, t_step, key, value
-
-    def read_types(self):
-        with self.db:
-            res = self.db.execute("select key, value_type from value_types ").fetchall()
-        for k, v in res:
-            serializer = serialization.serializer(v)
-            deserializer = serialization.deserializer(v)
-            self._dtypes[k] = (v, serializer, deserializer)
-
-    def __getitem__(self, key):
-        self.flush_cache()
-        key = Key(*key)
-        agent_ids = [key.agent_id] if key.agent_id is not None else []
-        t_steps = [key.t_step] if key.t_step is not None else []
-        keys = [key.key] if key.key is not None else []
-
-        df = self.read_sql(agent_ids=agent_ids,
-                           t_steps=t_steps,
-                           keys=keys)
-        r = Records(df, filter=key, dtypes=self._dtypes)
-        if r.resolved:
-            return r.value()
-        return r
-
-    def read_sql(self, keys=None, agent_ids=None, t_steps=None, convert_types=False, limit=-1):
-
-        self.read_types()
-
-        def escape_and_join(v):
-            if v is None:
-                return
-            return ",".join(map(lambda x: "\'{}\'".format(x), v))
-
-        filters = [("key in ({})".format(escape_and_join(keys)), keys),
-                   ("agent_id in ({})".format(escape_and_join(agent_ids)), agent_ids)
-        ]
-        filters = list(k[0] for k in filters if k[1])
-
-        last_df = None
-        if t_steps:
-            # Look for the last value before the minimum step in the query
-            min_step = min(t_steps)
-            last_filters = ['t_step < {}'.format(min_step),]
-            last_filters = last_filters + filters
-            condition = ' and '.join(last_filters)
-
-            last_query = '''
-            select h1.*
-            from history h1
-            inner join (
-            select agent_id, key, max(t_step) as t_step
-            from history
-            where {condition}
-            group by agent_id, key
-            ) h2
-            on h1.agent_id = h2.agent_id  and
-               h1.key      = h2.key       and
-               h1.t_step   = h2.t_step
-            '''.format(condition=condition)
-            last_df = pd.read_sql_query(last_query, self.db)
-
-            filters.append("t_step >= '{}' and t_step <= '{}'".format(min_step, max(t_steps)))
-
-        condition = ''
-        if filters:
-            condition = 'where {} '.format(' and '.join(filters))
-        query = 'select * from history {} limit {}'.format(condition, limit)
-        df = pd.read_sql_query(query, self.db)
-        if last_df is not None:
-            df = pd.concat([df, last_df])
-
-        df_p = df.pivot_table(values='value', index=['t_step'],
-                              columns=['key', 'agent_id'],
-                              aggfunc='first')
-
-        for k, v in self._dtypes.items():
-            if k in df_p:
-                dtype, _, deserial = v
-                df_p[k] = df_p[k].fillna(method='ffill').astype(dtype)
-        if t_steps:
-            df_p = df_p.reindex(t_steps, method='ffill')
-        return df_p.ffill()
-
-    def __getstate__(self):
-        state = dict(**self.__dict__)
-        del state['_db']
-        del state['_dtypes']
-        return state
-
-    def __setstate__(self, state):
-        self.__dict__ = state
-        self._dtypes = {}
-        self._db = None
-
-    def dump(self, f):
-        self._close()
-        for line in open_or_reuse(self.db_path, 'rb'):
-            f.write(line)
-
-
-class Records():
-
-    def __init__(self, df, filter=None, dtypes=None):
-        if not filter:
-            filter = Key(agent_id=None,
-                         t_step=None,
-                         key=None)
-        self._df = df
-        self._filter = filter
-        self.dtypes = dtypes or {}
-        super().__init__()
-
-    def mask(self, tup):
-        res = ()
-        for i, k in zip(tup[:-1], self._filter):
-            if k is None:
-                res = res + (i,)
-        res = res + (tup[-1],)
-        return res
-
-    def filter(self, newKey):
-        f = list(self._filter)
-        for ix, i in enumerate(f):
-            if i is None:
-                f[ix] = newKey
-        self._filter = Key(*f)
-
-    @property
-    def resolved(self):
-        return sum(1 for i in self._filter if i is not None) == 3
-
-    def __iter__(self):
-        for column, series in self._df.iteritems():
-            key, agent_id = column
-            for t_step, value in series.iteritems():
-                r = Record(t_step=t_step,
-                           agent_id=agent_id,
-                           key=key,
-                           value=value)
-                yield self.mask(r)
-
-    def value(self):
-        if self.resolved:
-            f = self._filter
-            try:
-                i = self._df[f.key][str(f.agent_id)]
-                ix = i.index.get_loc(f.t_step, method='ffill')
-                return i.iloc[ix]
-            except KeyError as ex:
-                return self.dtypes[f.key][2]()
-        return list(self)
-
-    def df(self):
-        return self._df
-
-    def __getitem__(self, k):
-        n = copy.copy(self)
-        n.filter(k)
-        if n.resolved:
-            return n.value()
-        return n
-
-    def __len__(self):
-        return len(self._df)
-
-    def __str__(self):
-        if self.resolved:
-            return str(self.value())
-        return '<Records for [{}]>'.format(self._filter)
-
-Key = namedtuple('Key', ['agent_id', 't_step', 'key'])
-Record = namedtuple('Record', 'agent_id t_step key value')

soil/serialization.py

@@ -13,14 +13,13 @@ from jinja2 import Template
 
 
 logger = logging.getLogger('soil')
-logger.setLevel(logging.INFO)
 
 
 def load_network(network_params, dir_path=None):
-    if network_params is None:
+    G = nx.Graph()
-        return nx.Graph()
+
-    path = network_params.get('path', None)
+    if 'path' in network_params:
-    if path:
+        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:]
@@ -32,24 +31,28 @@ def load_network(network_params, dir_path=None):
             method = getattr(nx.readwrite, 'read_' + extension)
         except AttributeError:
             raise AttributeError('Unknown format')
-        return method(path, **kwargs)
+        G = method(path, **kwargs)
 
-    net_args = network_params.copy()
+    elif 'generator' in network_params:
-    if 'generator' not in net_args:
+        net_args = network_params.copy()
-        return nx.Graph()
+        net_gen = net_args.pop('generator')
 
-    net_gen = net_args.pop('generator')
+        if dir_path not in sys.path:
+            sys.path.append(dir_path)
 
-    if dir_path not in sys.path:
+        method = deserializer(net_gen,
-        sys.path.append(dir_path)
+                              known_modules=['networkx.generators',])
+        G = method(**net_args)
+
+    return G
 
-    method = deserializer(net_gen,
-                          known_modules=['networkx.generators',])
 
-    return method(**net_args)
 
 
 def load_file(infile):
+    folder = os.path.dirname(infile)
+    if folder not in sys.path:
+        sys.path.append(folder)
     with open(infile, 'r') as f:
         return list(chain.from_iterable(map(expand_template, load_string(f))))
 
@@ -66,11 +69,32 @@ def expand_template(config):
         raise ValueError(('You must provide a definition of variables'
                           ' for the template.'))
 
-    template = Template(config['template'])
+    template = config['template']
 
-    sampler_name = config.get('sampler', 'SALib.sample.morris.sample')
+    if not isinstance(template, str):
-    n_samples = int(config.get('samples', 100))
+        template = yaml.dump(template)
-    sampler = deserializer(sampler_name)
+
+    template = Template(template)
+
+    params = params_for_template(config)
+
+    blank_str = template.render({k: 0 for k in params[0].keys()})
+    blank = list(load_string(blank_str))
+    if len(blank) > 1:
+        raise ValueError('Templates must not return more than one configuration')
+    if 'name' in blank[0]:
+        raise ValueError('Templates cannot be named, use group instead')
+
+    for ps in params:
+        string = template.render(ps)
+        for c in load_string(string):
+            yield c
+
+
+def params_for_template(config):
+    sampler_config = config.get('sampler', {'N': 100})
+    sampler = sampler_config.pop('method', 'SALib.sample.morris.sample')
+    sampler = deserializer(sampler)
     bounds = config['vars']['bounds']
 
     problem = {
@@ -78,7 +102,7 @@ def expand_template(config):
         'names': list(bounds.keys()),
         'bounds': list(v for v in bounds.values())
     }
-    samples = sampler(problem, n_samples)
+    samples = sampler(problem, **sampler_config)
 
     lists = config['vars'].get('lists', {})
     names = list(lists.keys())
@@ -88,20 +112,7 @@ def expand_template(config):
     allnames = names + problem['names']
     allvalues = [(list(i[0])+list(i[1])) for i in product(combs, samples)]
     params = list(map(lambda x: dict(zip(allnames, x)), allvalues))
-
+    return params
-
-    blank_str = template.render({k: 0 for k in allnames})
-    blank = list(load_string(blank_str))
-    if len(blank) > 1:
-        raise ValueError('Templates must not return more than one configuration')
-    if 'name' in blank[0]:
-        raise ValueError('Templates cannot be named, use group instead')
-
-    confs = []
-    for ps in params:
-        string = template.render(ps)
-        for c in load_string(string):
-            yield c
 
 
 def load_files(*patterns, **kwargs):
@@ -116,7 +127,7 @@ def load_files(*patterns, **kwargs):
 
 def load_config(config):
     if isinstance(config, dict):
-        yield config, None
+        yield config, os.getcwd()
     else:
         yield from load_files(config)
 
@@ -199,3 +210,13 @@ def deserialize(type_, value=None, **kwargs):
     if value is None:
         return des
     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 = []
+    for name in names:
+        mod = deserialize(name, known_modules=known_modules)
+        exporters.append(mod(*args, **kwargs))
+    return exporters
+

soil/simulation.py

@@ -1,27 +1,31 @@
 import os
-import time
 import importlib
 import sys
 import yaml
 import traceback
+import logging
 import networkx as nx
+
+from time import strftime
 from networkx.readwrite import json_graph
 from multiprocessing import Pool
 from functools import partial
+from tsih import History
 
 import pickle
 
-from nxsim import NetworkSimulation
-
 from . import serialization, utils, basestring, agents
 from .environment import Environment
 from .utils import logger
-from .exporters import for_sim as exporters_for_sim
+from .exporters import default
+from .stats import defaultStats
 
 
-class Simulation(NetworkSimulation):
+#TODO: change documentation for simulation
+
+class Simulation:
     """
-    Subclass of nsim.NetworkSimulation with three main differences:
+    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
@@ -91,11 +95,12 @@ class Simulation(NetworkSimulation):
                  environment_params=None, environment_class=None,
                  **kwargs):
 
-        self.seed = str(seed) or str(time.time())
         self.load_module = load_module
         self.network_params = network_params
-        self.name = name or 'Unnamed_' + time.strftime("%Y-%m-%d_%H.%M.%S")
+        self.name = name or 'Unnamed'
-        self.group = group or None
+        self.seed = str(seed or name)
+        self._id = '{}_{}'.format(self.name, 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 {}
@@ -128,19 +133,20 @@ class Simulation(NetworkSimulation):
         self.states = agents._validate_states(states,
                                               self.topology)
 
+        self._history = History(name=self.name,
+                                backup=False)
+
     def run_simulation(self, *args, **kwargs):
         return self.run(*args, **kwargs)
 
     def run(self, *args, **kwargs):
         '''Run the simulation and return the list of resulting environments'''
-        return list(self._run_simulation_gen(*args, **kwargs))
+        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:
+        if parallel and not os.environ.get('SENPY_DEBUG', None):
             p = Pool()
-            func = partial(self.run_trial_exceptions,
+            func = partial(self.run_trial_exceptions, **kwargs)
-                           *args,
-                           **kwargs)
             for i in p.imap_unordered(func, range(self.num_trials)):
                 if isinstance(i, Exception):
                     logger.error('Trial failed:\n\t%s', i.message)
@@ -148,45 +154,84 @@ class Simulation(NetworkSimulation):
                 yield i
         else:
             for i in range(self.num_trials):
-                yield self.run_trial(i,
+                yield self.run_trial(trial_id=i,
-                                     *args,
                                      **kwargs)
 
-    def _run_simulation_gen(self, *args, parallel=False, dry_run=False,
+    def run_gen(self, parallel=False, dry_run=False,
-                            exporters=['default', ], outdir=None, exporter_params={}, **kwargs):
+                exporters=[default, ], stats=[], outdir=None, exporter_params={},
+                stats_params={}, log_level=None,
+                **kwargs):
+        '''Run the simulation and yield the resulting environments.'''
+        if log_level:
+            logger.setLevel(log_level)
         logger.info('Using exporters: %s', exporters or [])
         logger.info('Output directory: %s', outdir)
-        exporters = exporters_for_sim(self,
+        exporters = serialization.deserialize_all(exporters,
-                                      exporters,
+                                                  simulation=self,
-                                      dry_run=dry_run,
+                                                  known_modules=['soil.exporters',],
-                                      outdir=outdir,
+                                                  dry_run=dry_run,
-                                      **exporter_params)
+                                                  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()
+
             for exporter in exporters:
                 exporter.start()
-
+            for env in self._run_sync_or_async(parallel=parallel,
-            for env in self._run_sync_or_async(*args, 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_end(env)
+                    exporter.trial(env, saved)
+
                 yield env
 
-            for exporter in exporters:
-                exporter.end()
 
-    def get_env(self, trial_id = 0, **kwargs):
+            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)))
+    
+
+    def get_env(self, trial_id=0, **kwargs):
         '''Create an environment for a trial of the simulation'''
         opts = self.environment_params.copy()
-        env_name = '{}_trial_{}'.format(self.name, trial_id)
         opts.update({
-            'name': env_name,
+            'name': '{}_trial_{}'.format(self.name, trial_id),
             'topology': self.topology.copy(),
-            'seed': self.seed+env_name,
+            '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,
         })
@@ -194,20 +239,21 @@ class Simulation(NetworkSimulation):
         env = self.environment_class(**opts)
         return env
 
-    def run_trial(self, trial_id=0, until=None, **opts):
+    def run_trial(self, trial_id=0, until=None, log_level=logging.INFO, **opts):
-        """Run a single trial of the simulation
-
-        Parameters
-        ----------
-        trial_id : int
         """
+        Run a single trial of the simulation
+
+        """
+        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)
+        env = self.get_env(trial_id=trial_id, **opts)
         # Set up agents on nodes
         with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
             env.run(until)
         return env
+
     def run_trial_exceptions(self, *args, **kwargs):
         '''
         A wrapper for run_trial that catches exceptions and returns them.
@@ -248,16 +294,19 @@ class Simulation(NetworkSimulation):
         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_distribution(self.network_agents,
+                state['network_agents'] = agents.serialize_definition(self.network_agents,
-                                                                        known_modules = [])
+                                                                      known_modules = [])
-                state['environment_agents'] = agents.serialize_distribution(self.environment_agents,
+                state['environment_agents'] = agents.serialize_definition(self.environment_agents,
-                                                                            known_modules = [])
+                                                                          known_modules = [])
                 state['environment_class'] = serialization.serialize(self.environment_class,
                                                                      known_modules=['soil.environment'])[1]  # func, name
         if state['load_module'] is None:
@@ -275,7 +324,6 @@ class Simulation(NetworkSimulation):
                                                               known_modules=[self.load_module])
         self.environment_class = serialization.deserialize(self.environment_class,
                                                    known_modules=[self.load_module, 'soil.environment', ])  # func, name
-        return state
 
 
 def all_from_config(config):

soil/stats.py

@@ -0,0 +1,106 @@
+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

@@ -0,0 +1,77 @@
+from mesa.time import BaseScheduler
+from queue import Empty
+from heapq import heappush, heappop
+import math
+from .utils import logger
+from mesa import Agent
+
+
+INFINITY = float('inf')
+
+class When:
+    def __init__(self, time):
+        self._time = time
+
+    def abs(self, time):
+        return self._time
+
+NEVER = When(INFINITY)
+
+
+class Delta:
+    def __init__(self, delta):
+        self._delta = delta
+
+    def __eq__(self, other):
+        return self._delta == other._delta
+
+    def abs(self, time):
+        return time + self._delta
+
+
+class TimedActivation(BaseScheduler):
+    """A scheduler which activates each agent when the agent requests.
+    In each activation, each agent will update its 'next_time'.
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(self)
+        self._queue = []
+        self.next_time = 0
+
+    def add(self, agent: Agent):
+        if agent.unique_id not in self._agents:
+            heappush(self._queue, (self.time, agent.unique_id))
+            super().add(agent)
+
+    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.
+        """
+
+        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}')
+
+            when = (self._agents[agent_id].step() 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 = INFINITY
+            self.next_time = INFINITY
+            return
+
+        self.next_time = self._queue[0][0]
+

soil/utils.py

@@ -7,7 +7,8 @@ from shutil import copyfile
 from contextlib import contextmanager
 
 logger = logging.getLogger('soil')
-logger.setLevel(logging.INFO)
+# logging.basicConfig()
+# logger.setLevel(logging.INFO)
 
 
 @contextmanager
@@ -25,20 +26,21 @@ def timer(name='task', pre="", function=logger.info, to_object=None):
         to_object.end = end
 
 
+
+
 def safe_open(path, mode='r', backup=True, **kwargs):
     outdir = os.path.dirname(path)
     if outdir and not os.path.exists(outdir):
         os.makedirs(outdir)
     if backup and 'w' in mode and os.path.exists(path):
         creation = os.path.getctime(path)
-        stamp = time.strftime('%Y-%m-%d_%H.%M', time.localtime(creation))
+        stamp = time.strftime('%Y-%m-%d_%H.%M.%S', time.localtime(creation))
 
-        backup_dir = os.path.join(outdir, stamp)
+        backup_dir = os.path.join(outdir, 'backup')
         if not os.path.exists(backup_dir):
             os.makedirs(backup_dir)
-        newpath = os.path.join(backup_dir, os.path.basename(path))
+        newpath = os.path.join(backup_dir, '{}@{}'.format(os.path.basename(path),
-        if os.path.exists(newpath):
+                                                               stamp))
-            newpath = '{}@{}'.format(newpath, time.time())
         copyfile(path, newpath)
     return open(path, mode=mode, **kwargs)
 
@@ -48,3 +50,40 @@ def open_or_reuse(f, *args, **kwargs):
         return safe_open(f, *args, **kwargs)
     except (AttributeError, TypeError):
         return f
+
+def flatten_dict(d):
+    if not isinstance(d, dict):
+        return d
+    return dict(_flatten_dict(d))
+
+def _flatten_dict(d, prefix=''):
+    if not isinstance(d, dict):
+        # print('END:', prefix, d)
+        yield prefix, d
+        return
+    if prefix:
+        prefix = prefix + '.'
+    for k, v in d.items():
+        # print(k, v)
+        res = list(_flatten_dict(v, prefix='{}{}'.format(prefix, k)))
+        # print('RES:', res)
+        yield from res
+
+
+def unflatten_dict(d):
+    out = {}
+    for k, v in d.items():
+        target = out
+        if not isinstance(k, str):
+            target[k] = v
+            continue
+        tokens = k.split('.')
+        if len(tokens) < 2:
+            target[k] = v
+            continue
+        for token in tokens[:-1]:
+            if token not in target:
+                target[token] = {}
+            target = target[token]
+        target[tokens[-1]] = v
+    return out

soil/visualization.py

@@ -0,0 +1,5 @@
+from mesa.visualization.UserParam import UserSettableParameter
+
+class UserSettableParameter(UserSettableParameter):
+    def __str__(self):
+        return self.value

test-requirements.txt

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

tests/test_agents.py

@@ -0,0 +1,24 @@
+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

@@ -21,11 +21,13 @@ class Ping(agents.FSM):
     @agents.default_state
     @agents.state
     def even(self):
+        self.debug(f'Even {self["count"]}')
         self['count'] += 1
         return self.odd
 
     @agents.state
     def odd(self):
+        self.debug(f'Odd {self["count"]}')
         self['count'] += 1
         return self.even
 
@@ -65,25 +67,24 @@ class TestAnalysis(TestCase):
     def test_count(self):
         env = self.env
         df = analysis.read_sql(env._history.db_path)
-        res = analysis.get_count(df, 'SEED', 'id')
+        res = analysis.get_count(df, 'SEED', 'state_id')
-        assert res['SEED']['seedanalysis_trial_0'].iloc[0] == 1
+        assert res['SEED'][self.env['SEED']].iloc[0] == 1
-        assert res['SEED']['seedanalysis_trial_0'].iloc[-1] == 1
+        assert res['SEED'][self.env['SEED']].iloc[-1] == 1
-        assert res['id']['odd'].iloc[0] == 2
+        assert res['state_id']['odd'].iloc[0] == 2
-        assert res['id']['even'].iloc[0] == 0
+        assert res['state_id']['even'].iloc[0] == 0
-        assert res['id']['odd'].iloc[-1] == 1
+        assert res['state_id']['odd'].iloc[-1] == 1
-        assert res['id']['even'].iloc[-1] == 1
+        assert res['state_id']['even'].iloc[-1] == 1
 
     def test_value(self):
         env = self.env
-        df = analysis.read_sql(env._history._db)
+        df = analysis.read_sql(env._history.db_path)
         res_sum = analysis.get_value(df, 'count')
 
         assert res_sum['count'].iloc[0] == 2
 
         import numpy as np
         res_mean = analysis.get_value(df, 'count', aggfunc=np.mean)
-        assert res_mean['count'].iloc[0] == 1
+        assert res_mean['count'].iloc[15] == (16+8)/2
 
-        res_total = analysis.get_value(df)
+        res_total = analysis.get_majority(df)
-
+        res_total['SEED'].iloc[0] == self.env['SEED']
-        res_total['SEED'].iloc[0] == 'seedanalysis_trial_0'

tests/test_examples.py

@@ -31,7 +31,7 @@ def make_example_test(path, config):
                 try:
                     n = config['network_params']['n']
                     assert len(list(env.network_agents)) == n
-                    assert env.now > 2  # It has run
+                    assert env.now > 0  # It has run
                     assert env.now <= config['max_time']  # But not further than allowed
                 except KeyError:
                     pass

tests/test_exporters.py

@@ -6,26 +6,32 @@ from time import time
 
 from unittest import TestCase
 from soil import exporters
-from soil.utils import safe_open
 from soil import simulation
 
+from soil.stats import distribution
 
 class Dummy(exporters.Exporter):
     started = False
     trials = 0
     ended = False
     total_time = 0
+    called_start = 0
+    called_trial = 0
+    called_end = 0
 
     def start(self):
+        self.__class__.called_start += 1
         self.__class__.started = True
 
-    def trial_end(self, env):
+    def trial(self, env, stats):
         assert env
         self.__class__.trials += 1
         self.__class__.total_time += env.now
+        self.__class__.called_trial += 1
 
-    def end(self):
+    def end(self, stats):
         self.__class__.ended = True
+        self.__class__.called_end += 1
 
 
 class Exporters(TestCase):
@@ -39,32 +45,17 @@ class Exporters(TestCase):
             'environment_params': {}
         }
         s = simulation.from_config(config)
-        s.run_simulation(exporters=[Dummy], dry_run=True)
+        for env in s.run_simulation(exporters=[Dummy], dry_run=True):
+            assert env.now <= 2
+
         assert Dummy.started
         assert Dummy.ended
+        assert Dummy.called_start == 1
+        assert Dummy.called_end == 1
+        assert Dummy.called_trial == 5
         assert Dummy.trials == 5
         assert Dummy.total_time == 2*5
 
-    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': {}
-        }
-        output = io.StringIO()
-        s = simulation.from_config(config)
-        s.run_simulation(exporters=[exporters.distribution], dry_run=True, exporter_params={'copy_to': output})
-        result = output.getvalue()
-        assert 'count' in result
-        assert 'SEED,Noneexporter_sim_trial_3,1,,1,1,1,1' in result
-
     def test_writing(self):
         '''Try to write CSV, GEXF, sqlite and YAML (without dry_run)'''
         n_trials = 5
@@ -83,11 +74,11 @@ class Exporters(TestCase):
         s = simulation.from_config(config)
         tmpdir = tempfile.mkdtemp()
         envs = s.run_simulation(exporters=[
-            exporters.default,
+                                    exporters.default,
-            exporters.csv,
+                                    exporters.csv,
-            exporters.gexf,
+                                    exporters.gexf,
-            exporters.distribution,
+                                ],
-        ],
+                                stats=[distribution,],
                                 outdir=tmpdir,
                                 exporter_params={'copy_to': output})
         result = output.getvalue()

tests/test_history.py

@@ -1,156 +0,0 @@
-from unittest import TestCase
-
-import os
-import shutil
-from glob import glob
-
-from soil import history
-
-
-ROOT = os.path.abspath(os.path.dirname(__file__))
-DBROOT = os.path.join(ROOT, 'testdb')
-
-
-class TestHistory(TestCase):
-
-    def setUp(self):
-        if not os.path.exists(DBROOT):
-            os.makedirs(DBROOT)
-
-    def tearDown(self):
-        if os.path.exists(DBROOT):
-            shutil.rmtree(DBROOT)
-
-    def test_history(self):
-        """
-        """
-        tuples = (
-            ('a_0', 0, 'id', 'h'),
-            ('a_0', 1, 'id', 'e'),
-            ('a_0', 2, 'id', 'l'),
-            ('a_0', 3, 'id', 'l'),
-            ('a_0', 4, 'id', 'o'),
-            ('a_1', 0, 'id', 'v'),
-            ('a_1', 1, 'id', 'a'),
-            ('a_1', 2, 'id', 'l'),
-            ('a_1', 3, 'id', 'u'),
-            ('a_1', 4, 'id', 'e'),
-            ('env', 1, 'prob', 1),
-            ('env', 3, 'prob', 2),
-            ('env', 5, 'prob', 3),
-            ('a_2', 7, 'finished', True),
-        )
-        h = history.History()
-        h.save_tuples(tuples)
-        # assert h['env', 0, 'prob'] == 0
-        for i in range(1, 7):
-            assert h['env', i, 'prob'] == ((i-1)//2)+1
-
-
-        for i, k in zip(range(5), 'hello'):
-            assert h['a_0', i, 'id'] == k
-        for record, value in zip(h['a_0', None, 'id'], 'hello'):
-            t_step, val = record
-            assert val == value
-
-        for i, k in zip(range(5), 'value'):
-            assert h['a_1', i, 'id'] == k
-        for i in range(5, 8):
-            assert h['a_1', i, 'id'] == 'e'
-        for i in range(7):
-            assert h['a_2', i, 'finished'] == False
-        assert h['a_2', 7, 'finished']
-
-    def test_history_gen(self):
-        """
-        """
-        tuples = (
-            ('a_1', 0, 'id', 'v'),
-            ('a_1', 1, 'id', 'a'),
-            ('a_1', 2, 'id', 'l'),
-            ('a_1', 3, 'id', 'u'),
-            ('a_1', 4, 'id', 'e'),
-            ('env', 1, 'prob', 1),
-            ('env', 2, 'prob', 2),
-            ('env', 3, 'prob', 3),
-            ('a_2', 7, 'finished', True),
-        )
-        h = history.History()
-        h.save_tuples(tuples)
-        for t_step, key, value in h['env', None, None]:
-            assert t_step == value
-            assert key == 'prob'
-
-        records = list(h[None, 7, None])
-        assert len(records) == 3
-        for i in records:
-            agent_id, key, value = i
-            if agent_id == 'a_1':
-                assert key == 'id'
-                assert value == 'e'
-            elif agent_id == 'a_2':
-                assert key == 'finished'
-                assert value
-            else:
-                assert key == 'prob'
-                assert value == 3
-
-        records = h['a_1', 7, None]
-        assert records['id'] == 'e'
-
-    def test_history_file(self):
-        """
-        History should be saved to a file
-        """
-        tuples = (
-            ('a_1', 0, 'id', 'v'),
-            ('a_1', 1, 'id', 'a'),
-            ('a_1', 2, 'id', 'l'),
-            ('a_1', 3, 'id', 'u'),
-            ('a_1', 4, 'id', 'e'),
-            ('env', 1, 'prob', 1),
-            ('env', 2, 'prob', 2),
-            ('env', 3, 'prob', 3),
-            ('a_2', 7, 'finished', True),
-        )
-        db_path = os.path.join(DBROOT, 'test')
-        h = history.History(db_path=db_path)
-        h.save_tuples(tuples)
-        h.flush_cache()
-        assert os.path.exists(db_path)
-
-        # Recover the data
-        recovered = history.History(db_path=db_path)
-        assert recovered['a_1', 0, 'id'] == 'v'
-        assert recovered['a_1', 4, 'id'] == 'e'
-
-        # Using backup=True should create a backup copy, and initialize an empty history
-        newhistory = history.History(db_path=db_path, backup=True)
-        backuppaths = glob(db_path + '.backup*.sqlite')
-        assert len(backuppaths) == 1
-        backuppath = backuppaths[0]
-        assert newhistory.db_path == h.db_path
-        assert os.path.exists(backuppath)
-        assert len(newhistory[None, None, None]) == 0
-
-    def test_history_tuples(self):
-        """
-        The data recovered should be equal to the one recorded.
-        """
-        tuples = (
-            ('a_1', 0, 'id', 'v'),
-            ('a_1', 1, 'id', 'a'),
-            ('a_1', 2, 'id', 'l'),
-            ('a_1', 3, 'id', 'u'),
-            ('a_1', 4, 'id', 'e'),
-            ('env', 1, 'prob', 1),
-            ('env', 2, 'prob', 2),
-            ('env', 3, 'prob', 3),
-            ('a_2', 7, 'finished', True),
-        )
-        h = history.History()
-        h.save_tuples(tuples)
-        recovered = list(h.to_tuples())
-        assert recovered
-        for i in recovered:
-            assert i in tuples

tests/test_main.py

@@ -9,7 +9,8 @@ from functools import partial
 
 from os.path import join
 from soil import (simulation, Environment, agents, serialization,
-                  history, utils)
+                  utils)
+from soil.time import Delta
 
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -20,8 +21,8 @@ class CustomAgent(agents.FSM):
     @agents.default_state
     @agents.state
     def normal(self):
-        self.state['neighbors'] = self.count_agents(state_id='normal',
+        self.neighbors = self.count_agents(state_id='normal',
-                                                    limit_neighbors=True)
+                                           limit_neighbors=True)
     @agents.state
     def unreachable(self):
         return
@@ -115,7 +116,7 @@ class TestMain(TestCase):
             'network_agents': [{
                 'agent_type': 'AggregatedCounter',
                 'weight': 1,
-                'state': {'id': 0}
+                'state': {'state_id': 0}
 
             }],
             'max_time': 10,
@@ -148,10 +149,9 @@ class TestMain(TestCase):
         }
         s = simulation.from_config(config)
         env = s.run_simulation(dry_run=True)[0]
-        assert env.get_agent(0).state['neighbors'] == 1
-        assert env.get_agent(0).state['neighbors'] == 1
         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
 
     def test_torvalds_example(self):
         """A complete example from a documentation should work."""
@@ -198,11 +198,11 @@ class TestMain(TestCase):
         """
         config = serialization.load_file(join(EXAMPLES, 'complete.yml'))[0]
         s = simulation.from_config(config)
-        for i in range(5):
+
-            s.run_simulation(dry_run=True)
+        s.run_simulation(dry_run=True)
-            nconfig = s.to_dict()
+        nconfig = s.to_dict()
-            del nconfig['topology']
+        del nconfig['topology']
-            assert config == nconfig
+        assert config == nconfig
 
     def test_row_conversion(self):
         env = Environment()
@@ -211,7 +211,7 @@ class TestMain(TestCase):
         res = list(env.history_to_tuples())
         assert len(res) == len(env.environment_params)
 
-        env._now = 1
+        env.schedule.time = 1
         env['test'] = 'second_value'
         res = list(env.history_to_tuples())
 
@@ -281,7 +281,7 @@ class TestMain(TestCase):
                 'weight': 2
             },
         ]
-        converted = agents.deserialize_distribution(agent_distro)
+        converted = agents.deserialize_definition(agent_distro)
         assert converted[0]['agent_type'] == agents.CounterModel
         assert converted[1]['agent_type'] == CustomAgent
         pickle.dumps(converted)
@@ -297,14 +297,14 @@ class TestMain(TestCase):
                 'weight': 2
             },
         ]
-        converted = agents.serialize_distribution(agent_distro)
+        converted = agents.serialize_definition(agent_distro)
         assert converted[0]['agent_type'] == 'CounterModel'
         assert converted[1]['agent_type'] == 'test_main.CustomAgent'
         pickle.dumps(converted)
 
     def test_pickle_agent_environment(self):
         env = Environment(name='Test')
-        a = agents.BaseAgent(environment=env, agent_id=25)
+        a = agents.BaseAgent(model=env, unique_id=25)
 
         a['key'] = 'test'
 
@@ -316,12 +316,6 @@ class TestMain(TestCase):
         assert recovered['key', 0] == 'test'
         assert recovered['key'] == 'test'
 
-    def test_history(self):
-        '''Test storing in and retrieving from history (sqlite)'''
-        h = history.History()
-        h.save_record(agent_id=0, t_step=0, key="test", value="hello")
-        assert h[0, 0, "test"] == "hello"
-
     def test_subgraph(self):
         '''An agent should be able to subgraph the global topology'''
         G = nx.Graph()
@@ -343,4 +337,55 @@ class TestMain(TestCase):
         configs = serialization.load_file(join(EXAMPLES, 'template.yml'))
         assert len(configs) > 0
 
+    def test_until(self):
+        config = {
+            'name': 'until_sim',
+            'network_params': {},
+            'agent_type': 'CounterModel',
+            'max_time': 2,
+            'num_trials': 50,
+            'environment_params': {}
+        }
+        s = simulation.from_config(config)
+        runs = list(s.run_simulation(dry_run=True))
+        over = list(x.now for x in runs if x.now>2)
+        assert len(runs) == config['num_trials']
+        assert len(over) == 0
 
+
+    def test_fsm(self):
+        '''Basic state change'''
+        class ToggleAgent(agents.FSM):
+            @agents.default_state
+            @agents.state
+            def ping(self):
+                return self.pong
+
+            @agents.state
+            def pong(self):
+                return self.ping
+
+        a = ToggleAgent(unique_id=1, model=Environment())
+        assert a.state_id == a.ping.id
+        a.step()
+        assert a.state_id == a.pong.id
+        a.step()
+        assert a.state_id == a.ping.id
+
+    def test_fsm_when(self):
+        '''Basic state change'''
+        class ToggleAgent(agents.FSM):
+            @agents.default_state
+            @agents.state
+            def ping(self):
+                return self.pong, 2
+
+            @agents.state
+            def pong(self):
+                return self.ping
+
+        a = ToggleAgent(unique_id=1, model=Environment())
+        when = a.step()
+        assert when == 2
+        when = a.step()
+        assert when == Delta(a.interval)

tests/test_mesa.py

@@ -0,0 +1,69 @@
+'''
+Mesa-SOIL integration tests
+
+We have to test that:
+- Mesa agents can be used in SOIL
+- Simplified soil agents can be used in mesa simulations
+- Mesa and soil agents can interact in a simulation
+
+- Mesa visualizations work with SOIL simulations
+
+'''
+from mesa import Agent, Model
+from mesa.time import RandomActivation
+from mesa.space import MultiGrid
+
+class MoneyAgent(Agent):
+    """ An agent with fixed initial wealth."""
+    def __init__(self, unique_id, model):
+        super().__init__(unique_id, model)
+        self.wealth = 1
+
+    def step(self):
+        self.move()
+        if self.wealth > 0:
+            self.give_money()
+
+    def give_money(self):
+        cellmates = self.model.grid.get_cell_list_contents([self.pos])
+        if len(cellmates) > 1:
+            other = self.random.choice(cellmates)
+            other.wealth += 1
+            self.wealth -= 1
+
+    def move(self):
+        possible_steps = self.model.grid.get_neighborhood(
+            self.pos,
+            moore=True,
+            include_center=False)
+        new_position = self.random.choice(possible_steps)
+        self.model.grid.move_agent(self, new_position)
+
+
+class MoneyModel(Model):
+    """A model with some number of agents."""
+    def __init__(self, N, width, height):
+        self.num_agents = N
+        self.grid = MultiGrid(width, height, True)
+        self.schedule = RandomActivation(self)
+
+        # Create agents
+        for i in range(self.num_agents):
+            a = MoneyAgent(i, self)
+            self.schedule.add(a)
+
+            # Add the agent to a random grid cell
+            x = self.random.randrange(self.grid.width)
+            y = self.random.randrange(self.grid.height)
+            self.grid.place_agent(a, (x, y))
+
+    def step(self):
+        '''Advance the model by one step.'''
+        self.schedule.step()
+
+
+# model = MoneyModel(10)
+# for i in range(10):
+#     model.step()
+
+# agent_wealth = [a.wealth for a in model.schedule.agents]

tests/test_stats.py

@@ -0,0 +1,34 @@
+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']