Fix history bug

Now the environment does not deal with history directly, it delegates it to a
specific class. The analysis also uses history instances instead of either
using the database directly or creating a proxy environment.

This should make it easier to change the implementation in the future.

In fact, the change was motivated by the large size of the csv files in previous
versions. This new implementation only stores results in deltas, and it fills
any necessary values when needed.

README.md

@@ -3,7 +3,7 @@
 Soil is an extensible and user-friendly Agent-based Social Simulator for Social Networks.
 Learn how to run your own simulations with our [documentation](http://soilsim.readthedocs.io).
 
-Follow our [tutorial](notebooks/soil_tutorial.ipynb) to develop your own agent models.
+Follow our [tutorial](examples/tutorial/soil_tutorial.ipynb) to develop your own agent models.
 
 If you use Soil in your research, don't forget to cite this paper:
 

docker-compose.yml

@@ -0,0 +1,8 @@
+version: '3'
+services:
+  dev:
+    build: .
+    volumes:
+      - .:/usr/src/app
+    tty: true
+    entrypoint: /bin/bash

docs/index.rst

@@ -34,13 +34,14 @@ If you use Soil in your research, do not forget to cite this paper:
 
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 0
    :caption: Learn more about soil:
 
    installation
    quickstart
-   Tutorial - Spreading news
+   Tutorial <soil_tutorial>
 
+..
 
 
 .. Indices and tables

docs/quickstart.rst

@@ -13,7 +13,7 @@ Here's an example (``example.yml``).
     name: MyExampleSimulation
     max_time: 50
     num_trials: 3
-    timeout: 2
+    interval: 2
     network_params:
         network_type: barabasi_albert_graph
         n: 100
@@ -34,6 +34,12 @@ Here's an example (``example.yml``).
     environment_params:
         prob_infect: 0.075
 
+
+This example configuration will run three trials of a simulation containing a randomly generated network.
+The 100 nodes in the network will be SISaModel agents, 10% of them will start in the content state, 10% in the discontent state, and the remaining 80% in the neutral state.
+All agents will have access to the environment, which only contains one variable, ``prob_infected``.
+The state of the agents will be updated every 2 seconds (``interval``).
+
 Now run the simulation with the command line tool:
 
 .. code:: bash
@@ -41,7 +47,7 @@ Now run the simulation with the command line tool:
    soil example.yml
 
 Once the simulation finishes, its results will be stored in a folder named ``MyExampleSimulation``.
-Four types of objects are saved by default: a pickle of the simulation, a ``YAML`` representation of the simulation (to re-launch it), for every trial, a csv file with the content of the state of every network node and the environment parameters at every step of the simulation as well as the network in gephi format (``gexf``).
+Four types of objects are saved by default: a pickle of the simulation; a ``YAML`` representation of the simulation (which can be used to re-launch it); and for every trial, a csv file with the content of the state of every network node and the environment parameters at every step of the simulation, as well as the network in gephi format (``gexf``).
 
 
 .. code::
@@ -54,12 +60,6 @@ Four types of objects are saved by default: a pickle of the simulation, a ``YAML
     │   └── Sim_prob_0_trial_0.gexf
 
 
-This example configuration will run three trials of a simulation containing a randomly generated network.
-The 100 nodes in the network will be SISaModel agents, 10% of them will start in the content state, 10% in the discontent state, and the remaining 80% in the neutral state.
-All agents will have access to the environment, which only contains one variable, ``prob_infected``.
-The state of the agents will be updated every 2 seconds (``timeout``).
-
-
 Network
 =======
 
@@ -94,7 +94,7 @@ For example, the following configuration is equivalent to :code:`nx.complete_gra
 Environment
 ============
 The environment is the place where the shared state of the simulation is stored.
-For instance, the probability of certain events.
+For instance, the probability of disease outbreak.
 The configuration file may specify the initial value of the environment parameters:
 
 .. code:: yaml
@@ -103,14 +103,17 @@ The configuration file may specify the initial value of the environment paramete
         daily_probability_of_earthquake: 0.001
         number_of_earthquakes: 0
 
+Any agent has unrestricted access to the environment.
+However, for the sake of simplicity, we recommend limiting environment updates to environment agents.
+
 Agents
 ======
 Agents are a way of modelling behavior.
 Agents can be characterized with two variables: an agent type (``agent_type``) and its state.
-Only one agent is executed at a time (generally, every ``timeout`` seconds), and it has access to its state and the environment parameters.
+Only one agent is executed at a time (generally, every ``interval`` seconds), and it has access to its state and the environment parameters.
 Through the environment, it can access the network topology and the state of other agents.
 
-There are three three types of agents according to how they are added to the simulation: network agents, environment agent, and other agents.
+There are three three types of agents according to how they are added to the simulation: network agents and environment agent.
 
 Network Agents
 ##############
@@ -118,13 +121,13 @@ Network agents are attached to a node in the topology.
 The configuration file allows you to specify how agents will be mapped to topology nodes.
 
 The simplest way is to specify a single type of agent.
-Hence, every node in the network will have an associated agent of that type.
+Hence, every node in the network will be associated to an agent of that type.
 
 .. code:: yaml
 
    agent_type: SISaModel
 
-It is also possible to add more than one type of agent to the simulation, and to control the ratio of each type (``weight``).
+It is also possible to add more than one type of agent to the simulation, and to control the ratio of each type (using the ``weight`` property).
 For instance, with following configuration, it is five times more likely for a node to be assigned a CounterModel type than a SISaModel type.
 
 .. code:: yaml

examples/complete.yml

@@ -4,6 +4,8 @@ dir_path: "/tmp/"
 num_trials: 3
 max_time: 100
 interval: 1
+seed: "CompleteSeed!"
+dump: false
 network_params:
   generator: complete_graph
   n: 10
@@ -21,4 +23,4 @@ default_state:
   incidents: 0
 states:
   - name: 'The first node'
-  - name: 'The second node'
+  - name: 'The second node'

examples/custom-agents/UnnamedSimulation.dumped.yml

@@ -1,17 +0,0 @@
-default_state: {}
-environment_agents: []
-environment_params: {prob_neighbor_spread: 0.0, prob_tv_spread: 0.01}
-interval: 1
-max_time: 20
-name: Sim_prob_0
-network_agents:
-- agent_type: NewsSpread
-  state: {has_tv: false}
-  weight: 1
-- agent_type: NewsSpread
-  state: {has_tv: true}
-  weight: 2
-network_params: {generator: erdos_renyi_graph, n: 500, p: 0.1}
-num_trials: 1
-states:
-- {has_tv: true}

examples/custom-agents/agent.py

@@ -1,20 +0,0 @@
-import soil
-import random
-
-class NewsSpread(soil.agents.FSM):
-    @soil.agents.default_state
-    @soil.agents.state
-    def neutral(self):
-        r = random.random()
-        if self['has_tv'] and r < self.env['prob_tv_spread']:
-                return self.infected
-        return
-
-    @soil.agents.state
-    def infected(self):
-        prob_infect = self.env['prob_neighbor_spread']
-        for neighbor in self.get_neighboring_agents(state_id=self.neutral.id):
-            r = random.random()
-            if r < prob_infect:
-                neighbor.state['id'] = self.infected.id
-        return

examples/newsspread/NewsSpread.yml

@@ -0,0 +1,138 @@
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+interval: 1
+max_time: 30
+name: Sim_all_dumb
+network_agents:
+- agent_type: DumbViewer
+  state:
+    has_tv: false
+  weight: 1
+- agent_type: DumbViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+interval: 1
+max_time: 30
+name: Sim_half_herd
+network_agents:
+- agent_type: DumbViewer
+  state:
+    has_tv: false
+  weight: 1
+- agent_type: DumbViewer
+  state:
+    has_tv: true
+  weight: 1
+- agent_type: HerdViewer
+  state:
+    has_tv: false
+  weight: 1
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+interval: 1
+max_time: 30
+name: Sim_all_herd
+network_agents:
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+    id: neutral
+  weight: 1
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+    id: neutral
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+  prob_neighbor_cure: 0.1
+interval: 1
+max_time: 30
+name: Sim_wise_herd
+network_agents:
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+    id: neutral
+  weight: 1
+- agent_type: WiseViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+  prob_neighbor_cure: 0.1
+interval: 1
+max_time: 30
+name: Sim_all_wise
+network_agents:
+- agent_type: WiseViewer
+  state:
+    has_tv: true
+    id: neutral
+  weight: 1
+- agent_type: WiseViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50

examples/newsspread/newsspread.py

@@ -0,0 +1,81 @@
+from soil.agents import FSM, state, default_state, prob
+import logging
+
+
+class DumbViewer(FSM):
+    '''
+    A viewer that gets infected via TV (if it has one) and tries to infect
+    its neighbors once it's infected.
+    '''
+    defaults = {
+        'prob_neighbor_spread': 0.5,
+        'prob_tv_spread': 0.1,
+    }
+
+    @default_state
+    @state
+    def neutral(self):
+        if self['has_tv']:
+            if prob(self.env['prob_tv_spread']):
+                self.set_state(self.infected)
+
+    @state
+    def infected(self):
+        for neighbor in self.get_neighboring_agents(state_id=self.neutral.id):
+            if prob(self.env['prob_neighbor_spread']):
+                neighbor.infect()
+
+    def infect(self):
+        self.set_state(self.infected)
+
+
+class HerdViewer(DumbViewer):
+    '''
+    A viewer whose probability of infection depends on the state of its neighbors.
+    '''
+
+    level = logging.DEBUG
+
+    def infect(self):
+        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)
+
+
+class WiseViewer(HerdViewer):
+    '''
+    A viewer that can change its mind.
+    '''
+
+    defaults = {
+        'prob_neighbor_spread': 0.5,
+        'prob_neighbor_cure': 0.25,
+        'prob_tv_spread': 0.1,
+    }
+
+    @state
+    def cured(self):
+        prob_cure = self.env['prob_neighbor_cure']
+        for neighbor in self.get_neighboring_agents(state_id=self.infected.id):
+            if prob(prob_cure):
+                try:
+                    neighbor.cure()
+                except AttributeError:
+                    self.debug('Viewer {} cannot be cured'.format(neighbor.id))
+
+    def cure(self):
+        self.set_state(self.cured.id)
+
+    @state
+    def infected(self):
+        cured = max(self.count_neighboring_agents(self.cured.id),
+                    1.0)
+        infected = max(self.count_neighboring_agents(self.infected.id),
+                       1.0)
+        prob_cure = self.env['prob_neighbor_cure'] * (cured/infected)
+        if prob(prob_cure):
+            return self.cure()
+        return self.set_state(super().infected)

examples/rabbits/rabbit_agents.py

@@ -0,0 +1,120 @@
+from soil.agents import FSM, state, default_state, BaseAgent
+from enum import Enum
+from random import random, choice
+from itertools import islice
+import logging
+import math
+
+
+class Genders(Enum):
+    male = 'male'
+    female = 'female'
+
+
+class RabbitModel(FSM):
+
+    level = logging.INFO
+
+    defaults = {
+        'age': 0,
+        'gender': Genders.male.value,
+        'mating_prob': 0.001,
+        'offspring': 0,
+    }
+
+    sexual_maturity = 4*30
+    life_expectancy = 365 * 3
+    gestation = 33
+    pregnancy = -1
+    max_females = 5
+
+    @default_state
+    @state
+    def newborn(self):
+        self['age'] += 1
+
+        if self['age'] >= self.sexual_maturity:
+            return self.fertile
+
+    @state
+    def fertile(self):
+        self['age'] += 1
+        if self['age'] > self.life_expectancy:
+            return self.dead
+
+        if self['gender'] == Genders.female.value:
+            return
+
+        # Males try to mate
+        females = self.get_agents(state_id=self.fertile.id, gender=Genders.female.value, limit_neighbors=False)
+        for f in islice(females, 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))
+
+    @state
+    def pregnant(self):
+        self['age'] += 1
+        if self['age'] > self.life_expectancy:
+            return self.dead
+
+        self['pregnancy'] += 1
+        self.debug('Pregnancy: {}'.format(self['pregnancy']))
+        if self['pregnancy'] >= self.gestation:
+            number_of_babies = int(8+4*random())
+            self.info('Having {} babies'.format(number_of_babies))
+            for i in range(number_of_babies):
+                state = {}
+                state['gender'] = choice(list(Genders)).value
+                child = self.env.add_node(self.__class__, state)
+                self.env.add_edge(self.id, child.id)
+                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.debug('Rabbits alive: {}'.format(self.env['rabbits_alive']))
+                self['offspring'] += 1
+                self.env.get_agent(self['mate'])['offspring'] += 1
+            del self['mate']
+            self['pregnancy'] = -1
+            return self.fertile
+
+    @state
+    def dead(self):
+        self.info('Agent {} is dying'.format(self.id))
+        if 'pregnancy' in self and self['pregnancy'] > -1:
+            self.info('A mother has died carrying a baby!!')
+        self.die()
+        return
+
+
+class RandomAccident(BaseAgent):
+
+    level = logging.DEBUG
+
+    def step(self):
+        rabbits_total = self.global_topology.number_of_nodes()
+        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))
+        for i in self.env.network_agents:
+            if i.state['id'] == i.dead.id:
+                continue
+            r = random()
+            if r < prob_death:
+                self.debug('I killed a rabbit: {}'.format(i.id))
+                rabbits_alive = self.env['rabbits_alive'] = rabbits_alive -1
+                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():
+            self.die()

examples/rabbits/rabbits.yml

@@ -0,0 +1,23 @@
+---
+load_module: rabbit_agents
+name: rabbits_example
+max_time: 1200
+interval: 1
+seed: MySeed
+agent_type: RabbitModel
+environment_agents:
+    - agent_type: RandomAccident
+environment_params:
+  prob_death: 0.001
+default_state:
+  mating_prob: 0.01
+topology:
+  nodes:
+    - id: 1
+      state:
+        gender: female
+    - id: 0
+      state:
+        gender: male
+  directed: true
+  links: []

examples/torvalds.yml

@@ -1,6 +1,6 @@
 ---
 name: torvalds_example
-max_time: 1
+max_time: 10
 interval: 2
 agent_type: CounterModel
 default_state:
@@ -11,4 +11,4 @@ states:
   Torvalds:
     skill_level: 'God'
   balkian:
-    skill_level: 'developer'
+    skill_level: 'developer'

requirements.txt

@@ -1,6 +1,7 @@
 nxsim
 simpy
-networkx
+networkx>=2.0
 numpy
 matplotlib
 pyyaml
+pandas

setup.py

@@ -1,20 +1,21 @@
-import pip
+import os
 from setuptools import setup
-# parse_requirements() returns generator of pip.req.InstallRequirement objects
-from pip.req import parse_requirements
-from soil import __version__
 
-try:
-    install_reqs = parse_requirements(
-        "requirements.txt", session=pip.download.PipSession())
-    test_reqs = parse_requirements(
-        "test-requirements.txt", session=pip.download.PipSession())
-except AttributeError:
-    install_reqs = parse_requirements("requirements.txt")
-    test_reqs = parse_requirements("test-requirements.txt")
 
-install_reqs = [str(ir.req) for ir in install_reqs]
-test_reqs = [str(ir.req) for ir in test_reqs]
+with open(os.path.join('soil', 'VERSION')) as f:
+    __version__ = f.readlines()[0].strip()
+    assert __version__
+
+
+def parse_requirements(filename):
+    """ load requirements from a pip requirements file """
+    with open(filename, 'r') as f:
+        lineiter = list(line.strip() for line in f)
+    return [line for line in lineiter if line and not line.startswith("#")]
+
+
+install_reqs = parse_requirements("requirements.txt")
+test_reqs = parse_requirements("test-requirements.txt")
 
 
 setup(

simulation.yml

@@ -1,61 +0,0 @@
----
-name: ControlModelM2_sim
-max_time: 50
-num_trials: 1
-network_params:
-  generator: barabasi_albert_graph
-  n: 100
-  m: 2
-network_agents:
-  - agent_type: ControlModelM2
-    weight: 0.1
-    state:
-      id: 1
-  - agent_type: ControlModelM2
-    weight: 0.9
-    state:
-      id: 0
-environment_params:
-  prob_neutral_making_denier: 0.035
-  prob_infect: 0.075
-  prob_cured_healing_infected: 0.035
-  prob_cured_vaccinate_neutral: 0.035
-  prob_vaccinated_healing_infected: 0.035
-  prob_vaccinated_vaccinate_neutral: 0.035
-  prob_generate_anti_rumor: 0.035
-  standard_variance: 0.055
----
-name: SISA_sm
-max_time: 50
-num_trials: 2
-network_params:
-  generator: erdos_renyi_graph
-  n: 1000
-  p: 0.05
-#other_agents:
-#  - agent_type: DrawingAgent
-network_agents:
-  - agent_type: SISaModel
-    weight: 1
-    state:
-      id: content
-  - agent_type: SISaModel
-    weight: 1
-    state:
-      id: neutral
-  - agent_type: SISaModel
-    weight: 1
-    state:
-      id: discontent
-environment_params:
-  neutral_discontent_spon_prob: 0.04
-  neutral_discontent_infected_prob: 0.04
-  neutral_content_spon_prob: 0.18
-  neutral_content_infected_prob: 0.02
-  discontent_neutral: 0.13
-  discontent_content: 0.07
-  variance_d_c: 0.02
-  content_discontent: 0.009
-  variance_c_d: 0.003
-  content_neutral: 0.088
-  standard_variance: 0.055

soil/VERSION

@@ -0,0 +1 @@
+0.11.1

soil/__init__.py

@@ -1,19 +1,23 @@
 import importlib
 import sys
 import os
+import pdb
+import logging
 
-__version__ = "0.9.7"
+from .version import __version__
 
 try:
     basestring
 except NameError:
     basestring = str
 
+logging.basicConfig()
+
 from . import agents
 from . import simulation
 from . import environment
 from . import utils
-from . import settings
+from . import analysis
 
 
 def main():
@@ -29,8 +33,16 @@ def main():
                         help='file containing the code of any custom agents.')
     parser.add_argument('--dry-run', '--dry', action='store_true',
                         help='Do not store the results of the simulation.')
-    parser.add_argument('--output', '-o', type=str,
+    parser.add_argument('--pdb', action='store_true',
+                        help='Use a pdb console in case of exception.')
+    parser.add_argument('--graph', '-g', action='store_true',
+                        help='Dump GEXF graph. Defaults to false.')
+    parser.add_argument('--csv', action='store_true',
+                        help='Dump history in CSV format. Defaults to false.')
+    parser.add_argument('--output', '-o', type=str, default="soil_output",
                         help='folder to write results to. It defaults to the current directory.')
+    parser.add_argument('--synchronous', action='store_true',
+                        help='Run trials serially and synchronously instead of in parallel. Defaults to false.')
 
     args = parser.parse_args()
 
@@ -38,8 +50,25 @@ def main():
         sys.path.append(os.getcwd())
         importlib.import_module(args.module)
 
-    print('Loading config file: {}'.format(args.file, args.output))
-    simulation.run_from_config(args.file, dump=(not args.dry_run), results_dir=args.output)
+    logging.info('Loading config file: {}'.format(args.file, args.output))
+
+    try:
+        dump = []
+        if not args.dry_run:
+            if args.csv:
+                dump.append('csv')
+            if args.graph:
+                dump.append('gexf')
+        simulation.run_from_config(args.file,
+                                   dry_run=args.dry_run,
+                                   dump=dump,
+                                   parallel=(not args.synchronous and not args.pdb),
+                                   results_dir=args.output)
+    except Exception as ex:
+        if args.pdb:
+            pdb.post_mortem()
+        else:
+            raise
 
 
 if __name__ == '__main__':

soil/__main__.py

@@ -1,32 +1,4 @@
-import importlib
-import sys
-import argparse
-from . import simulation
-
-
-def main():
-
-    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.')
-    parser.add_argument('--module', '-m', type=str,
-                        help='file containing the code of any custom agents.')
-    parser.add_argument('--dry-run', '--dry', action='store_true',
-                        help='Do not store the results of the simulation.')
-    parser.add_argument('--output', '-o', type=str,
-                        help='folder to write results to. It defaults to the current directory.')
-
-    args = parser.parse_args()
-
-    if args.module:
-        sys.path.append(os.getcwd())
-        importlib.import_module(args.module)
-
-    print('Loading config file: {}'.format(args.file, args.output))
-    simulation.run_from_config(args.file, dump=not args.dry_run, results_dir=args.output)
-
+from . import main
 
 if __name__ == '__main__':
     main()

soil/agents/BassModel.py

@@ -1,8 +1,8 @@
 import random
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class BassModel(NetworkAgent):
+class BassModel(BaseAgent):
     """
     Settings:
         innovation_prob

soil/agents/BigMarketModel.py

@@ -1,8 +1,8 @@
 import random
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class BigMarketModel(NetworkAgent):
+class BigMarketModel(BaseAgent):
     """
     Settings:
         Names:

soil/agents/CounterModel.py

@@ -1,7 +1,7 @@
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class CounterModel(NetworkAgent):
+class CounterModel(BaseAgent):
     """
     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(NetworkAgent):
 
     def step(self):
         # Outside effects
-        total = len(self.get_all_agents())
-        neighbors = len(self.get_neighboring_agents())
-        self.state['times'] = self.state.get('times', 0) + 1
-        self.state['neighbors'] = neighbors
-        self.state['total'] = total
+        total = len(list(self.get_all_agents()))
+        neighbors = len(list(self.get_neighboring_agents()))
+        self['times'] = self.get('times', 0) + 1
+        self['neighbors'] = neighbors
+        self['total'] = total
 
 
-class AggregatedCounter(NetworkAgent):
+class AggregatedCounter(BaseAgent):
     """
     Dummy behaviour. It counts the number of nodes in the network and neighbors
     in each step and adds it to its state.
@@ -24,8 +24,9 @@ class AggregatedCounter(NetworkAgent):
 
     def step(self):
         # Outside effects
-        total = len(self.get_all_agents())
-        neighbors = len(self.get_neighboring_agents())
-        self.state['times'] = self.state.get('times', 0) + 1
-        self.state['neighbors'] = self.state.get('neighbors', 0) + neighbors
-        self.state['total'] = self.state.get('total', 0) + total
+        total = len(list(self.get_all_agents()))
+        neighbors = len(list(self.get_neighboring_agents()))
+        self['times'] = self.get('times', 0) + 1
+        self['neighbors'] = self.get('neighbors', 0) + neighbors
+        self['total'] = total = self.get('total', 0) + total
+        self.debug('Running for step: {}. Total: {}'.format(self.now, total))

soil/agents/DrawingAgent.py

@@ -15,4 +15,4 @@ class DrawingAgent(BaseAgent):
         # Outside effects
         f = plt.figure()
         nx.draw(self.env.G, node_size=10, width=0.2, pos=nx.spring_layout(self.env.G, scale=100), ax=f.add_subplot(111))
-        f.savefig(os.path.join(self.env.sim().dir_path, "graph-"+str(self.env.now)+".png"))
+        f.savefig(os.path.join(self.env.get_path(), "graph-"+str(self.env.now)+".png"))

soil/agents/ModelM2.py

@@ -1,9 +1,9 @@
 import random
 import numpy as np
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class SpreadModelM2(NetworkAgent):
+class SpreadModelM2(BaseAgent):
     """
     Settings:
         prob_neutral_making_denier
@@ -104,7 +104,7 @@ class SpreadModelM2(NetworkAgent):
                 neighbor.state['id'] = 2  # Cured
 
 
-class ControlModelM2(NetworkAgent):
+class ControlModelM2(BaseAgent):
     """
     Settings:
         prob_neutral_making_denier

soil/agents/SISaModel.py

@@ -1,9 +1,9 @@
 import random
 import numpy as np
-from . import FSM, NetworkAgent, state
+from . import FSM, state
 
 
-class SISaModel(FSM, NetworkAgent):
+class SISaModel(FSM):
     """
     Settings:
         neutral_discontent_spon_prob

soil/agents/SentimentCorrelationModel.py

@@ -1,8 +1,8 @@
 import random
-from . import NetworkAgent
+from . import BaseAgent
 
 
-class SentimentCorrelationModel(NetworkAgent):
+class SentimentCorrelationModel(BaseAgent):
     """
     Settings:
         outside_effects_prob

soil/agents/__init__.py

@@ -6,12 +6,15 @@
     
 
 import nxsim
+import logging
 from collections import OrderedDict
 from copy import deepcopy
+from functools import partial
 import json
 
 from functools import wraps
 
+from .. import utils, history
 
 agent_types = {}
 
@@ -27,28 +30,72 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
     A special simpy BaseAgent that keeps track of its state history.
     """
 
-    def __init__(self, *args, **kwargs):
-        self._history = OrderedDict()
+    defaults = {}
+
+    def __init__(self, environment=None, agent_id=None, state=None,
+                 name='network_process', interval=None, **state_params):
+        # 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
+        self.name = name
+        self.state_params = state_params
+
+        # Global parameters
+        self.global_topology = environment.G
+        self.environment_params = environment.environment_params
+
+        # Register agent to environment
+        self.env = environment
+
         self._neighbors = None
-        super().__init__(*args, **kwargs)
+        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.level = logging.DEBUG
+        self.logger = logging.getLogger('{}-Agent-{}'.format(self.env.name,
+                                                             self.id))
+        self.logger.setLevel(self.level)
+
+        # initialize every time an instance of the agent is created
+        self.action = self.env.process(self.run())
+
+    @property
+    def state(self):
+        return self._state
+
+    @state.setter
+    def state(self, value):
+        for k, v in value.items():
+            self[k] = v
 
     def __getitem__(self, key):
         if isinstance(key, tuple):
-            k, t_step = key
-            if k is not None:
-                if t_step is not None:
-                    return self._history[t_step][k]
-                else:
-                    return {tt: tv.get(k, None) for tt, tv in self._history.items()}
-            else:
-                return self._history[t_step]
-        return self.state[key]
+            key, t_step = key
+            k = history.Key(key=key, t_step=t_step, agent_id=self.id)
+            return self.env[k]
+        return self.state.get(key, None)
+
+    def __delitem__(self, key):
+        self.state[key] = None
+
+    def __contains__(self, key):
+        return key in self.state
 
     def __setitem__(self, key, value):
         self.state[key] = value
+        k = history.Key(t_step=self.now,
+                        agent_id=self.id,
+                        key=key)
+        self.env[k] = value
 
-    def save_state(self):
-        self._history[self.now] = deepcopy(self.state)
+    def get(self, key, default=None):
+        return self[key] if key in self else default
 
     @property
     def now(self):
@@ -59,18 +106,26 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
             return None
 
     def run(self):
-        while True:
+        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(self.env.interval)
+            yield res or self.env.timeout(interval)
+
+    def die(self, remove=False):
+        self.alive = False
+        if remove:
+            super().die()
 
     def step(self):
         pass
 
     def to_json(self):
-        return json.dumps(self._history)
-
-
-class NetworkAgent(BaseAgent, nxsim.BaseNetworkAgent):
+        return json.dumps(self.state)
 
     def count_agents(self, state_id=None, limit_neighbors=False):
         if limit_neighbors:
@@ -79,30 +134,69 @@ class NetworkAgent(BaseAgent, nxsim.BaseNetworkAgent):
             agents = self.global_topology.nodes()
         count = 0
         for agent in agents:
-            if state_id and state_id != self.global_topology.node[agent]['agent'].state['id']:
+            if state_id and state_id != self.global_topology.node[agent]['agent']['id']:
                 continue
             count += 1
         return count
 
     def count_neighboring_agents(self, state_id=None):
-        return self.count_agents(state_id, limit_neighbors=True)
+        return len(super().get_agents(state_id, limit_neighbors=True))
+
+    def get_agents(self, state_id=None, limit_neighbors=False, iterator=False, **kwargs):
+        if limit_neighbors:
+            agents = super().get_agents(state_id, limit_neighbors)
+        else:
+            agents = filter(lambda x: state_id is None or x.state.get('id', None) == state_id,
+                            self.env.agents)
+
+        def matches_all(agent):
+            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 iterator:
+            return f
+        return list(f)
+
+    def log(self, message, *args, level=logging.INFO, **kwargs):
+        message = message + " ".join(str(i) for i in args)
+        message = "\t@{:>5}:\t{}".format(self.now, message)
+        for k, v in kwargs:
+            message += " {k}={v} ".format(k, v)
+        extra = {}
+        extra['now'] = self.now
+        extra['id'] = self.id
+        return self.logger.log(level, message, extra=extra)
+
+    def debug(self, *args, **kwargs):
+        return self.log(*args, level=logging.DEBUG, **kwargs)
+
+    def info(self, *args, **kwargs):
+        return self.log(*args, level=logging.INFO, **kwargs)
 
 
 def state(func):
+    '''
+    A state function should return either a state id, or a tuple (state_id, when)
+    The default value for state_id is the current state id.
+    The default value for when is the interval defined in the nevironment.
+    '''
 
     @wraps(func)
     def func_wrapper(self):
-        when = None
         next_state = func(self)
+        when = None
+        if next_state is None:
+            return when
         try:
             next_state, when = next_state
-        except TypeError:
+        except (ValueError, TypeError):
             pass
         if next_state:
-            try:
-                self.state['id'] = next_state.id
-            except AttributeError:
-                raise NotImplemented('State id %s is not valid.' % next_state)
+            self.set_state(next_state)
         return when
 
     func_wrapper.id = func.__name__
@@ -142,11 +236,13 @@ class FSM(BaseAgent, metaclass=MetaFSM):
     def __init__(self, *args, **kwargs):
         super(FSM, self).__init__(*args, **kwargs)
         if 'id' not in self.state:
-            self.state['id'] = self.default_state.id
+            if not self.default_state:
+                raise ValueError('No default state specified for {}'.format(self.id))
+            self['id'] = self.default_state.id
 
     def step(self):
         if 'id' in self.state:
-            next_state = self.state['id']
+            next_state = self['id']
         elif self.default_state:
             next_state = self.default_state.id
         else:
@@ -155,6 +251,123 @@ class FSM(BaseAgent, metaclass=MetaFSM):
             raise Exception('{} is not a valid id for {}'.format(next_state, self))
         self.states[next_state](self)
 
+    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
+        return state
+
+
+def prob(prob=1):
+    '''
+    A true/False uniform distribution with a given probability.
+    To be used like this:
+
+    .. code-block:: python
+          
+          if prob(0.3):
+              do_something()
+
+    '''
+    r = random.random()
+    return r < prob
+
+
+def calculate_distribution(network_agents=None,
+                           agent_type=None):
+    '''
+    Calculate the threshold values (thresholds for a uniform distribution)
+    of an agent distribution given the weights of each agent type.
+
+    The input has this form: ::
+
+            [
+            {'agent_type': 'agent_type_1',
+                'weight': 0.2,
+                'state': {
+                    'id': 0
+                }
+            },
+            {'agent_type': 'agent_type_2',
+                'weight': 0.8,
+                'state': {
+                    'id': 1
+                }
+            }
+            ]
+
+    In this example, 20% of the nodes will be marked as type
+    'agent_type_1'.
+    '''
+    if network_agents:
+        network_agents = deepcopy(network_agents)
+    elif agent_type:
+        network_agents = [{'agent_type': agent_type}]
+    else:
+        return []
+
+    # Calculate the thresholds
+    total = sum(x.get('weight', 1) for x in network_agents)
+    acc = 0
+    for v in network_agents:
+        upper = acc + (v.get('weight', 1)/total)
+        v['threshold'] = [acc, upper]
+        acc = upper
+    return network_agents
+
+
+def _serialize_distribution(network_agents):
+    d = _convert_agent_types(network_agents,
+                             to_string=True)
+    '''
+    When serializing an agent distribution, remove the thresholds, in order
+    to avoid cluttering the YAML definition file.
+    '''
+    for v in d:
+        if 'threshold' in v:
+            del v['threshold']
+    return d
+
+
+def _validate_states(states, topology):
+    '''Validate states to avoid ignoring states during initialization'''
+    states = states or []
+    if isinstance(states, dict):
+        for x in states:
+            assert x in topology.node
+    else:
+        assert len(states) <= len(topology)
+    return states
+
+
+def _convert_agent_types(ind, to_string=False):
+    '''Convenience method to allow specifying agents by class or class name.'''
+    d = deepcopy(ind)
+    for v in d:
+        agent_type = v['agent_type']
+        if to_string and not isinstance(agent_type, str):
+            v['agent_type'] = str(agent_type.__name__)
+        elif not to_string and isinstance(agent_type, str):
+            v['agent_type'] = agent_types[agent_type]
+    return d
+
+
+def _agent_from_distribution(distribution, value=-1):
+    """Used in the initialization of agents given an agent distribution."""
+    if value < 0:
+        value = random.random()
+    for d in distribution:
+        threshold = d['threshold']
+        if value >= threshold[0] and value < threshold[1]:
+            state = {}
+            if 'state' in d:
+                state = deepcopy(d['state'])
+            return d['agent_type'], state
+
+    raise Exception('Distribution for value {} not found in: {}'.format(value, distribution))
+
 
 from .BassModel import *
 from .BigMarketModel import *

soil/analysis.py

@@ -4,20 +4,163 @@ import glob
 import yaml
 from os.path import join
 
+from . import utils, history
 
-def get_data(pattern, process=True, attributes=None):
+
+def read_data(*args, group=False, **kwargs):
+    iterable = _read_data(*args, **kwargs)
+    if group:
+        return group_trials(iterable)
+    else:
+        return list(iterable)
+
+
+def _read_data(pattern, *args, from_csv=False, process_args=None, **kwargs):
+    if not process_args:
+        process_args = {}
     for folder in glob.glob(pattern):
         config_file = glob.glob(join(folder, '*.yml'))[0]
         config = yaml.load(open(config_file))
-        for trial_data in sorted(glob.glob(join(folder, '*.environment.csv'))):
-            df = pd.read_csv(trial_data)
-            if process:
-                if attributes is not None:
-                    df = df[df['attribute'].isin(attributes)]
-                df = df.pivot_table(values='attribute', index='tstep', columns=['value'], aggfunc='count').fillna(0)
-            yield config_file, df, config
+        df = None
+        if from_csv:
+            for trial_data in sorted(glob.glob(join(folder,
+                                                    '*.environment.csv'))):
+                df = read_csv(trial_data, **kwargs)
+                yield config_file, df, config
+        else:
+            for trial_data in sorted(glob.glob(join(folder, '*.db.sqlite'))):
+                df = read_sql(trial_data, **kwargs)
+                yield config_file, df, config
+
+
+def read_sql(db, *args, **kwargs):
+    h = history.History(db, backup=False)
+    df = h.read_sql(*args, **kwargs)
+    return df
+
+
+def read_csv(filename, keys=None, convert_types=False, **kwargs):
+    '''
+    Read a CSV in canonical form: ::
+
+        <agent_id, t_step, key, value, value_type>
+
+    '''
+    df = pd.read_csv(filename)
+    if convert_types:
+        df = convert_types_slow(df)
+    if keys:
+        df = df[df['key'].isin(keys)]
+    df = process_one(df)
+    return df
+
+
+def convert_row(row):
+    row['value'] = utils.convert(row['value'], row['value_type'])
+    return row
+
+
+def convert_types_slow(df):
+    '''This is a slow operation.'''
+    dtypes = get_types(df)
+    for k, v in dtypes.items():
+        t = df[df['key']==k]
+        t['value'] = t['value'].astype(v)
+    df = df.apply(convert_row, axis=1)
+    return df
+
+def split_df(df):
+    '''
+    Split a dataframe in two dataframes: one with the history of agents,
+    and one with the environment history
+    '''
+    envmask = (df['agent_id'] == 'env')
+    n_env = envmask.sum()
+    if n_env == len(df):
+        return df, None
+    elif n_env == 0:
+        return None, df
+    agents, env = [x for _, x in df.groupby(envmask)]
+    return env, agents
+
+
+def process(df, **kwargs):
+    '''
+    Process a dataframe in canonical form ``(t_step, agent_id, key, value, value_type)`` into
+    two dataframes with a column per key: one with the history of the agents, and one for the
+    history of the environment.
+    '''
+    env, agents = split_df(df)
+    return process_one(env, **kwargs), process_one(agents, **kwargs)
+
+
+def get_types(df):
+    dtypes = df.groupby(by=['key'])['value_type'].unique()
+    return {k:v[0] for k,v in dtypes.iteritems()}
+
+
+def process_one(df, *keys, columns=['key', 'agent_id'], values='value',
+                fill=True, index=['t_step',],
+                aggfunc='first', **kwargs):
+    '''
+    Process a dataframe in canonical form ``(t_step, agent_id, key, value, value_type)`` into
+    a dataframe with a column per key
+    '''
+    if df is None:
+        return df
+    if keys:
+        df = df[df['key'].isin(keys)]
+
+    df = df.pivot_table(values=values, index=index, columns=columns,
+                        aggfunc=aggfunc, **kwargs)
+    if fill:
+        df = fillna(df)
+    return df
+
+
+def get_count(df, *keys):
+    if keys:
+        df = df[list(keys)]
+    counts = pd.DataFrame()
+    for key in df.columns.levels[0]:
+        g = df[key].apply(pd.Series.value_counts, axis=1).fillna(0)
+        for value, series in g.iteritems():
+            counts[key, value] = series
+    counts.columns = pd.MultiIndex.from_tuples(counts.columns)
+    return counts
+
+
+def get_value(df, *keys, aggfunc='sum'):
+    if keys:
+        df = df[list(keys)]
+    return df.groupby(axis=1, level=0).agg(aggfunc, axis=1)
 
 
 def plot_all(*args, **kwargs):
-    for config_file, df, config in sorted(get_data(*args, **kwargs)):
+    '''
+    Read all the trial data and plot the result of applying a function on them.
+    '''
+    dfs = do_all(*args, **kwargs)
+    ps = []
+    for line in dfs:
+        f, df, config = line
         df.plot(title=config['name'])
+        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):
+        p = func(df, *keys, **kwargs)
+        p.plot(title=config['name'])
+        yield config_file, p, config
+
+
+def group_trials(trials, aggfunc=['mean', 'min', 'max', 'std']):
+    trials = list(trials)
+    trials = list(map(lambda x: x[1] if isinstance(x, tuple) else x, trials))
+    return pd.concat(trials).groupby(level=0).agg(aggfunc).reorder_levels([2, 0,1] ,axis=1)
+
+
+def fillna(df):
+    new_df = df.ffill(axis=0)
+    return new_df

soil/environment.py

@@ -1,14 +1,30 @@
 import os
+import sqlite3
+import time
 import csv
-import weakref
-from random import random
+import random
+import simpy
+import tempfile
+import pandas as pd
 from copy import deepcopy
+from networkx.readwrite import json_graph
 
 import networkx as nx
 import nxsim
 
+from . import utils, agents, analysis, history
+
 
 class SoilEnvironment(nxsim.NetworkEnvironment):
+    """
+    The environment is key in a simulation. It contains the network topology,
+    a reference to network and environment agents, as well as the environment
+    params, which are used as shared state between agents.
+
+    The environment parameters and the state of every agent can be accessed
+    both by using the environment as a dictionary or with the environment's 
+    :meth:`soil.environment.SoilEnvironment.get` method.
+    """
 
     def __init__(self, name=None,
                  network_agents=None,
@@ -16,20 +32,32 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
                  states=None,
                  default_state=None,
                  interval=1,
+                 seed=None,
+                 dry_run=False,
+                 dir_path=None,
+                 topology=None,
                  *args, **kwargs):
         self.name = name or 'UnnamedEnvironment'
-        self.states = deepcopy(states) or {}
+        if isinstance(states, list):
+            states = dict(enumerate(states))
+        self.states = deepcopy(states) if states else {}
         self.default_state = deepcopy(default_state) or {}
-        super().__init__(*args, **kwargs)
+        if not topology:
+            topology = nx.Graph()
+        super().__init__(*args, topology=topology, **kwargs)
         self._env_agents = {}
-        self._history = {}
+        self.dry_run = dry_run
         self.interval = interval
-        self.logger = None
+        self.dir_path = dir_path or tempfile.mkdtemp('soil-env')
+        self.get_path()
+        self._history = history.History(name=self.name if not dry_run else None,
+                                        dir_path=self.dir_path)
         # Add environment agents first, so their events get
         # executed before network agents
         self.environment_agents = environment_agents or []
         self.network_agents = network_agents or []
-        self.process(self.save_state())
+        self['SEED'] = seed or time.time()
+        random.seed(self['SEED'])
 
     @property
     def agents(self):
@@ -39,7 +67,7 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
     @property
     def environment_agents(self):
         for ref in self._env_agents.values():
-            yield ref()
+            yield ref
 
     @environment_agents.setter
     def environment_agents(self, environment_agents):
@@ -51,7 +79,7 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
             kwargs['agent_id'] = kwargs.get('agent_id', atype.__name__)
             kwargs['state'] = kwargs.get('state', {})
             a = atype(environment=self, **kwargs)
-            self._env_agents[a.id] = weakref.ref(a)
+            self._env_agents[a.id] = a
 
     @property
     def network_agents(self):
@@ -62,60 +90,104 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
 
     @network_agents.setter
     def network_agents(self, network_agents):
+        if not network_agents:
+            return
         for ix in self.G.nodes():
-            i = ix
-            node = self.G.node[i]
-            v = random()
-            found = False
-            for d in network_agents:
-                threshold = d['threshold']
-                if v >= threshold[0] and v < threshold[1]:
-                    agent = d['agent_type']
-                    state = None
-                    if 'state' in d:
-                        state = deepcopy(d['state'])
-                    else:
-                        try:
-                            state = self.states[i]
-                        except (IndexError, KeyError):
-                            state = deepcopy(self.default_state)
-                    node['agent'] = agent(environment=self,
-                                          agent_id=i,
-                                          state=state)
-                    found = True
-                    break
-            assert found
+            agent, state = agents._agent_from_distribution(network_agents)
+            self.set_agent(ix, agent_type=agent, state=state)
+
+    def set_agent(self, agent_id, agent_type, state=None):
+        node = self.G.nodes[agent_id]
+        defstate = deepcopy(self.default_state)
+        defstate.update(self.states.get(agent_id, {}))
+        if state:
+            defstate.update(state)
+        state = defstate
+        state.update(node.get('state', {}))
+        a = agent_type(environment=self,
+                       agent_id=agent_id,
+                       state=state)
+        node['agent'] = a
+        return a
+
+    def add_node(self, agent_type, state=None):
+        agent_id = int(len(self.G.nodes()))
+        self.G.add_node(agent_id)
+        a = self.set_agent(agent_id, agent_type, state)
+        a['visible'] = True
+        return a
+
+    def add_edge(self, agent1, agent2, attrs=None):
+        return self.G.add_edge(agent1, agent2)
 
     def run(self, *args, **kwargs):
         self._save_state()
         super().run(*args, **kwargs)
-        self._save_state()
+        self._history.flush_cache()
 
-    def _save_state(self):
-        for agent in self.agents:
-            agent.save_state()
-        self._history[self.now] = deepcopy(self.environment_params)
+    def _save_state(self, now=None):
+        # for agent in self.agents:
+        #     agent.save_state()
+        utils.logger.debug('Saving state @{}'.format(self.now))
+        self._history.save_records(self.state_to_tuples(now=now))
 
     def save_state(self):
-        while True:
+        '''
+        :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)
+            utils.logger.debug('Step: {}'.format(self.now))
             ev = self.event()
             ev._ok = True
             # Schedule the event with minimum priority so
-            # that it executes after all agents are done
-            self.schedule(ev, -1, self.interval)
+            # 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()
+            return self._history[key]
+
         return self.environment_params[key]
 
     def __setitem__(self, key, value):
+        if isinstance(key, tuple):
+            k = history.Key(*key)
+            self._history.save_record(*k,
+                                      value=value)
+            return
         self.environment_params[key] = value
+        self._history.save_record(agent_id='env',
+                                  t_step=self.now,
+                                  key=key,
+                                  value=value)
+
+    def __contains__(self, key):
+        return key in self.environment_params
+
+    def get(self, key, default=None):
+        '''
+        Get the value of an environment attribute in a
+        given point in the simulation (history).
+        If key is an attribute name, this method returns
+        the current value.
+        To get values at other times, use a
+        :meth: `soil.history.Key` tuple.
+        '''
+        return self[key] if key in self else default
 
     def get_path(self, dir_path=None):
-        dir_path = dir_path or self.sim().dir_path
+        dir_path = dir_path or self.dir_path
         if not os.path.exists(dir_path):
-            os.makedirs(dir_path)
+            try:
+                os.makedirs(dir_path)
+            except FileExistsError:
+                pass
         return dir_path
 
     def get_agent(self, agent_id):
@@ -130,7 +202,7 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
 
         with open(csv_name, 'w') as f:
             cr = csv.writer(f)
-            cr.writerow(('agent_id', 'tstep', 'attribute', 'value'))
+            cr.writerow(('agent_id', 't_step', 'key', 'value', 'value_type'))
             for i in self.history_to_tuples():
                 cr.writerow(i)
 
@@ -138,28 +210,60 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
         G = self.history_to_graph()
         graph_path = os.path.join(self.get_path(dir_path),
                                   self.name+".gexf")
+        # Workaround for geometric models
+        # See soil/soil#4
+        for node in G.nodes():
+            if 'pos' in G.node[node]:
+                G.node[node]['viz'] = {"position": {"x": G.node[node]['pos'][0], "y": G.node[node]['pos'][1], "z": 0.0}}
+                del (G.node[node]['pos'])
+
         nx.write_gexf(G, graph_path, version="1.2draft")
 
-    def history_to_tuples(self):
-        for tstep, state in self._history.items():
-            for attribute, value in state.items():
-                yield ('env', tstep, attribute, value)
+    def dump(self, dir_path=None, formats=None):
+        if not formats:
+            return
+        functions = {
+            'csv': self.dump_csv,
+            'gexf': self.dump_gexf
+        }
+        for f in formats:
+            if f in functions:
+                functions[f](dir_path)
+            else:
+                raise ValueError('Unknown format: {}'.format(f))
+
+    def state_to_tuples(self, now=None):
+        if now is None:
+            now = self.now
+        for k, v in self.environment_params.items():
+            yield history.Record(agent_id='env',
+                                 t_step=now,
+                                 key=k,
+                                 value=v)
         for agent in self.agents:
-            for tstep, state in agent._history.items():
-                for attribute, value in state.items():
-                    yield (agent.id, tstep, attribute, value)
+            for k, v in agent.state.items():
+                yield history.Record(agent_id=agent.id,
+                                     t_step=now,
+                                     key=k,
+                                     value=v)
+
+    def history_to_tuples(self):
+        return self._history.to_tuples()
 
     def history_to_graph(self):
         G = nx.Graph(self.G)
 
-        for agent in self.agents:
+        for agent in self.network_agents:
 
             attributes = {'agent': str(agent.__class__)}
             lastattributes = {}
             spells = []
             lastvisible = False
             laststep = None
-            for t_step, state in reversed(list(agent._history.items())):
+            history = self[agent.id, None, None]
+            if not history:
+                continue
+            for t_step, state in reversed(sorted(list(history.items()))):
                 for attribute, value in state.items():
                     if attribute == 'visible':
                         nowvisible = state[attribute]
@@ -170,15 +274,20 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
 
                         lastvisible = nowvisible
                     else:
-                        if attribute not in lastattributes or lastattributes[attribute][0] != value:
-                            laststep = lastattributes.get(attribute,
-                                                          (None, None))[1]
-                            value = (state[attribute], t_step, laststep)
-                            key = 'attr_' + attribute
+                        key = 'attr_' + attribute
+                        if key not in attributes:
+                            attributes[key] = list()
+                        if key not in lastattributes:
+                            lastattributes[key] = (state[attribute], t_step)
+                        elif lastattributes[key][0] != value:
+                            last_value, laststep = lastattributes[key]
+                            value = (last_value, t_step, laststep)
                             if key not in attributes:
                                 attributes[key] = list()
                             attributes[key].append(value)
-                            lastattributes[attribute] = (state[attribute], t_step)
+                            lastattributes[key] = (state[attribute], t_step)
+            for k, v in lastattributes.items():
+                attributes[k].append((v[0], 0, v[1]))
             if lastvisible:
                 spells.append((laststep, None))
             if spells:
@@ -187,3 +296,19 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
                 G.add_node(agent.id, **attributes)
 
         return G
+
+    def __getstate__(self):
+        state = self.__dict__.copy()
+        state['G'] = json_graph.node_link_data(self.G)
+        state['network_agents'] = agents._serialize_distribution(self.network_agents)
+        state['environment_agents'] = agents._convert_agent_types(self.environment_agents,
+                                                                 to_string=True)
+        del state['_queue']
+        return state
+
+    def __setstate__(self, state):
+        self.__dict__ = state
+        self.G = json_graph.node_link_graph(state['G'])
+        self.network_agents = self.calculate_distribution(self._convert_agent_types(self.network_agents))
+        self.environment_agents = self._convert_agent_types(self.environment_agents)
+        return state

soil/history.py

@@ -0,0 +1,231 @@
+import time
+import os
+import pandas as pd
+import sqlite3
+import copy
+from collections import UserDict, Iterable, namedtuple
+
+from . import utils
+
+
+class History:
+    """
+    Store and retrieve values from a sqlite database.
+    """
+
+    def __init__(self, db_path=None, name=None, dir_path=None, backup=True):
+        if db_path is None and name:
+            db_path = os.path.join(dir_path or os.getcwd(),
+                                   '{}.db.sqlite'.format(name))
+        if db_path is None:
+            db_path = ":memory:"
+        else:
+            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
+        if isinstance(db_path, str):
+            self._db = sqlite3.connect(db_path)
+        else:
+            self._db = db_path
+
+        with self._db:
+            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 = []
+
+    def conversors(self, key):
+        """Get the serializer and deserializer for a given key."""
+        if key not in self._dtypes:
+            self.read_types()
+        return self._dtypes[key]
+
+    @property
+    def dtypes(self):
+        return {k:v[0] for k, v in self._dtypes.items()}
+
+    def save_tuples(self, tuples):
+        self.save_records(Record(*tup) for tup in tuples)
+
+    def save_records(self, records):
+        with self._db:
+            for rec in records:
+                if not isinstance(rec, Record):
+                    rec = Record(*rec)
+                if rec.key not in self._dtypes:
+                    name = utils.name(rec.value)
+                    serializer = utils.serializer(name)
+                    deserializer = utils.deserializer(name)
+                    self._dtypes[rec.key] = (name, serializer, deserializer)
+                    self._db.execute("replace into value_types (key, value_type) values (?, ?)", (rec.key, name))
+                self._db.execute("replace into history(agent_id, t_step, key, value) values (?, ?, ?, ?)", (rec.agent_id, rec.t_step, rec.key, rec.value))
+
+    def save_record(self, *args, **kwargs):
+        self._tups.append(Record(*args, **kwargs))
+        if len(self._tups) > 100:
+            self.flush_cache()
+
+    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.
+        '''
+        self.save_records(self._tups)
+        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
+                _, _ , des = self.conversors(key)
+                yield agent_id, t_step, key, des(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 = utils.serializer(v)
+                deserializer = utils.deserializer(v)
+                self._dtypes[k] = (v, serializer, deserializer)
+
+    def __getitem__(self, key):
+        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)
+        return r.value()
+
+
+
+    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').fillna(deserial()).astype(dtype)
+        if t_steps:
+            df_p = df_p.reindex(t_steps, method='ffill')
+        return df_p.ffill()
+
+
+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:
+                return self.dtypes[f.key][2]()
+        return self
+
+    def __getitem__(self, k):
+        n = copy.copy(self)
+        n.filter(k)
+        return n.value()
+
+    def __len__(self):
+        return len(self._df)
+
+
+Key = namedtuple('Key', ['agent_id', 't_step', 'key'])
+Record = namedtuple('Record', 'agent_id t_step key value')

soil/simulation.py

@@ -1,27 +1,26 @@
-import weakref
 import os
-import csv
 import time
+import imp
+import sys
 import yaml
 import networkx as nx
 from networkx.readwrite import json_graph
-
-from copy import deepcopy
-from random import random
-from matplotlib import pyplot as plt
+from multiprocessing import Pool
+from functools import partial
 
 import pickle
 
 from nxsim import NetworkSimulation
 
-from . import agents, utils, environment, basestring
+from . import utils, environment, basestring, agents
+from .utils import logger
 
 
 class SoilSimulation(NetworkSimulation):
     """
     Subclass of nsim.NetworkSimulation with three main differences:
         1) agent type can be specified by name or by class.
-        2) instead of just one type, an network_agents can be used.
+        2) instead of just one type, a network agents distribution can be used.
            The distribution specifies the weight (or probability) of each
            agent type in the topology. This is an example distribution: ::
 
@@ -47,9 +46,9 @@ class SoilSimulation(NetworkSimulation):
     """
     def __init__(self, name=None, topology=None, network_params=None,
                  network_agents=None, agent_type=None, states=None,
-                 default_state=None, interval=1,
-                 dir_path=None, num_trials=3, max_time=100,
-                 agent_module=None,
+                 default_state=None, interval=1, dump=None, dry_run=False,
+                 dir_path=None, num_trials=1, max_time=100,
+                 agent_module=None, load_module=None, seed=None,
                  environment_agents=None, environment_params=None):
 
         if topology is None:
@@ -58,6 +57,7 @@ class SoilSimulation(NetworkSimulation):
         elif isinstance(topology, basestring) or isinstance(topology, dict):
             topology = json_graph.node_link_graph(topology)
 
+        self.load_module = load_module
         self.topology = nx.Graph(topology)
         self.network_params = network_params
         self.name = name or 'UnnamedSimulation'
@@ -66,78 +66,72 @@ class SoilSimulation(NetworkSimulation):
         self.default_state = default_state or {}
         self.dir_path = dir_path or os.getcwd()
         self.interval = interval
+        self.seed = str(seed) or str(time.time())
+        self.dump = dump
+        self.dry_run = dry_run
         self.environment_params = environment_params or {}
 
+        if load_module:
+            path = sys.path + [self.dir_path, os.getcwd()]
+            f, fp, desc = imp.find_module(load_module, path)
+            imp.load_module('soil.agents.custom', f, fp, desc)
+
         environment_agents = environment_agents or []
-        self.environment_agents = self._convert_agent_types(environment_agents)
+        self.environment_agents = agents._convert_agent_types(environment_agents)
 
-        distro = self.calculate_distribution(network_agents,
-                                             agent_type)
-        self.network_agents = self._convert_agent_types(distro)
+        distro = agents.calculate_distribution(network_agents,
+                                               agent_type)
+        self.network_agents = agents._convert_agent_types(distro)
 
-        self.states = self.validate_states(states,
-                                           topology)
+        self.states = agents._validate_states(states,
+                                              self.topology)
 
-    def calculate_distribution(self,
-                               network_agents=None,
-                               agent_type=None):
-        if network_agents:
-            network_agents = deepcopy(network_agents)
-        elif agent_type:
-            network_agents = [{'agent_type': agent_type}]
-        else:
-            return []
+    def run_simulation(self, *args, **kwargs):
+        return self.run(*args, **kwargs)
 
-        # Calculate the thresholds
-        total = sum(x.get('weight', 1) for x in network_agents)
-        acc = 0
-        for v in network_agents:
-            upper = acc + (v.get('weight', 1)/total)
-            v['threshold'] = [acc, upper]
-            acc = upper
-        return network_agents
+    def run(self, *args, **kwargs):
+        return list(self.run_simulation_gen(*args, **kwargs))
 
-    def serialize_distribution(self):
-        d = self._convert_agent_types(self.network_agents,
-                                      to_string=True)
-        for v in d:
-            if 'threshold' in v:
-                del v['threshold']
-        return d
+    def run_simulation_gen(self, *args, parallel=False, dry_run=False,
+                           **kwargs):
+        p = Pool()
+        with utils.timer('simulation {}'.format(self.name)):
+            if parallel:
+                func = partial(self.run_trial, dry_run=dry_run or self.dry_run,
+                               return_env=not parallel, **kwargs)
+                for i in p.imap_unordered(func, range(self.num_trials)):
+                    yield i
+            else:
+                for i in range(self.num_trials):
+                    yield self.run_trial(i, dry_run=dry_run or self.dry_run, **kwargs)
+            if not (dry_run or self.dry_run):
+                logger.info('Dumping results to {}'.format(self.dir_path))
+                self.dump_pickle(self.dir_path)
+                self.dump_yaml(self.dir_path)
+            else:
+                logger.info('NOT dumping results')
 
-    def _convert_agent_types(self, ind, to_string=False):
-        d = deepcopy(ind)
-        for v in d:
-            agent_type = v['agent_type']
-            if to_string and not isinstance(agent_type, str):
-                v['agent_type'] = str(agent_type.__name__)
-            elif not to_string and isinstance(agent_type, str):
-                v['agent_type'] = agents.agent_types[agent_type]
-        return d
+    def get_env(self, trial_id=0, **kwargs):
+        opts = self.environment_params.copy()
+        env_name = '{}_trial_{}'.format(self.name, trial_id)
+        opts.update({
+            'name': env_name,
+            'topology': self.topology.copy(),
+            'seed': self.seed+env_name,
+            'initial_time': 0,
+            'dry_run': self.dry_run,
+            'interval': self.interval,
+            'network_agents': self.network_agents,
+            'states': self.states,
+            'default_state': self.default_state,
+            'environment_agents': self.environment_agents,
+            'dir_path': self.dir_path,
+        })
+        opts.update(kwargs)
+        env = environment.SoilEnvironment(**opts)
+        return env
 
-    def validate_states(self, states, topology):
-        states = states or []
-        # Validate states to avoid ignoring states during
-        # initialization
-        if isinstance(states, dict):
-            for x in states:
-                assert x in self.topology.node
-        else:
-            assert len(states) <= len(self.topology)
-        return states
-
-    def run_simulation(self):
-        return self.run()
-
-    def run(self):
-        return list(self.run_simulation_gen())
-
-    def run_simulation_gen(self):
-        with utils.timer('simulation'):
-            for i in range(self.num_trials):
-                yield self.run_trial(i)
-
-    def run_trial(self, trial_id=0):
+    def run_trial(self, trial_id=0, until=None, return_env=True, **opts):
         """Run a single trial of the simulation
 
         Parameters
@@ -145,24 +139,16 @@ class SoilSimulation(NetworkSimulation):
         trial_id : int
         """
         # Set-up trial environment and graph
-        print('Trial: {}'.format(trial_id))
-        env_name = '{}_trial_{}'.format(self.name, trial_id)
-        env = environment.SoilEnvironment(name=env_name,
-                                          topology=self.topology.copy(),
-                                          initial_time=0,
-                                          interval=self.interval,
-                                          network_agents=self.network_agents,
-                                          states=self.states,
-                                          default_state=self.default_state,
-                                          environment_agents=self.environment_agents,
-                                          **self.environment_params)
-
-        env.sim = weakref.ref(self)
+        until = until or self.max_time
+        env = self.get_env(trial_id=trial_id, **opts)
         # Set up agents on nodes
-        print('\tRunning')
-        with utils.timer('trial'):
-            env.run(until=self.max_time)
-        return env
+        with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
+            env.run(until)
+        if self.dump and not self.dry_run:
+            with utils.timer('Dumping simulation {} trial {}'.format(self.name, trial_id)):
+                env.dump(formats=self.dump)
+        if return_env:
+            return env
 
     def to_dict(self):
         return self.__getstate__()
@@ -193,20 +179,20 @@ class SoilSimulation(NetworkSimulation):
     def __getstate__(self):
         state = self.__dict__.copy()
         state['topology'] = json_graph.node_link_data(self.topology)
-        state['network_agents'] = self.serialize_distribution()
-        state['environment_agents'] = self._convert_agent_types(self.environment_agents,
-                                                          to_string=True)
+        state['network_agents'] = agents._serialize_distribution(self.network_agents)
+        state['environment_agents'] = agents._convert_agent_types(self.environment_agents,
+                                                                 to_string=True)
         return state
 
     def __setstate__(self, state):
         self.__dict__ = state
         self.topology = json_graph.node_link_graph(state['topology'])
-        self.network_agents = self._convert_agent_types(self.network_agents)
-        self.environment_agents = self._convert_agent_types(self.environment_agents)
+        self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
+        self.environment_agents = agents._convert_agent_types(self.environment_agents)
         return state
 
 
-def from_config(config, G=None):
+def from_config(config):
     config = list(utils.load_config(config))
     if len(config) > 1:
         raise AttributeError('Provide only one configuration')
@@ -215,27 +201,19 @@ def from_config(config, G=None):
     return sim
 
 
-def run_from_config(*configs, dump=True, results_dir=None, timestamp=False):
-    if not results_dir:
-        results_dir = 'soil_output'
+def run_from_config(*configs, results_dir='soil_output', dry_run=False, dump=None, timestamp=False,  **kwargs):
     for config_def in configs:
-        for config, cpath in utils.load_config(config_def):
+        # logger.info("Found {} config(s)".format(len(ls)))
+        for config, _ in utils.load_config(config_def):
             name = config.get('name', 'unnamed')
-            print("Using config(s): {name}".format(name=name))
+            logger.info("Using config(s): {name}".format(name=name))
 
-            sim = SoilSimulation(**config)
             if timestamp:
-                sim_folder = '{}_{}'.format(sim.name,
+                sim_folder = '{}_{}'.format(name,
                                             time.strftime("%Y-%m-%d_%H:%M:%S"))
             else:
-                sim_folder = sim.name
-            dir_path = os.path.join(results_dir,
-                                    sim_folder)
-            results = sim.run_simulation()
-
-            if dump:
-                sim.dump_pickle(dir_path)
-                sim.dump_yaml(dir_path)
-                for env in results:
-                    env.dump_gexf(dir_path)
-                    env.dump_csv(dir_path)
+                sim_folder = name
+            dir_path = os.path.join(results_dir, sim_folder)
+            sim = SoilSimulation(dir_path=dir_path, dump=dump, **config)
+            logger.info('Dumping results to {} : {}'.format(sim.dir_path, sim.dump))
+            sim.run_simulation(**kwargs)

soil/utils.py

@@ -1,14 +1,24 @@
 import os
 import yaml
+import logging
+import importlib
 from time import time
 from glob import glob
+from random import random
+from copy import deepcopy
 
 import networkx as nx
 
 from contextlib import contextmanager
 
 
+logger = logging.getLogger('soil')
+logger.setLevel(logging.INFO)
+
+
 def load_network(network_params, dir_path=None):
+    if network_params is None:
+        return nx.Graph()
     path = network_params.get('path', None)
     if path:
         if dir_path and not os.path.isabs(path):
@@ -51,11 +61,45 @@ def load_config(config):
 
 
 @contextmanager
-def timer(name='task', pre="", function=print, to_object=None):
+def timer(name='task', pre="", function=logger.info, to_object=None):
     start = time()
+    function('{}Starting {} at {}.'.format(pre, name, start))
     yield start
     end = time()
     function('{}Finished {} in {} seconds'.format(pre, name, str(end-start)))
     if to_object:
         to_object.start = start
         to_object.end = end
+
+
+def repr(v):
+    func = serializer(v)
+    tname = name(v)
+    return func(v), tname
+
+
+def name(v):
+    return type(v).__name__
+
+
+def serializer(type_):
+    if type_ == 'bool':
+        return lambda x:  "true" if x else ""
+    return lambda x: x
+
+
+def deserializer(type_):
+    try:
+        # Check if it's a builtin type
+        module = importlib.import_module('builtins')
+        cls = getattr(module, type_)
+    except AttributeError:
+        # if not, separate module and class
+        module, type_ = type_.rsplit(".", 1)
+        module = importlib.import_module(module)
+        cls = getattr(module, type_)
+    return cls
+
+
+def convert(value, type_):
+    return deserializer(type_)(value)

soil/version.py

@@ -0,0 +1,20 @@
+import os
+import logging
+
+logger = logging.getLogger(__name__)
+
+ROOT = os.path.dirname(__file__)
+DEFAULT_FILE = os.path.join(ROOT, 'VERSION')
+
+
+def read_version(versionfile=DEFAULT_FILE):
+    try:
+        with open(versionfile) as f:
+            return f.read().strip()
+    except IOError:  # pragma: no cover
+        logger.error(('Running an unknown version of {}.'
+                      'Be careful!.').format(__name__))
+        return '0.0'
+
+
+__version__ = read_version()

tests/test.csv

@@ -0,0 +1,16 @@
+agent_id,t_step,key,value,value_type
+a0,0,hello,w,str
+a0,1,hello,o,str
+a0,2,hello,r,str
+a0,3,hello,l,str
+a0,4,hello,d,str
+a0,5,hello,!,str
+env,1,started,,bool
+env,2,started,True,bool
+env,7,started,,bool
+a0,0,hello,w,str
+a0,1,hello,o,str
+a0,2,hello,r,str
+a0,3,hello,l,str
+a0,4,hello,d,str
+a0,5,hello,!,str

tests/test_analysis.py

@@ -0,0 +1,90 @@
+from unittest import TestCase
+
+import os
+import pandas as pd
+import yaml
+from functools import partial
+
+from os.path import join
+from soil import simulation, analysis, agents
+
+
+ROOT = os.path.abspath(os.path.dirname(__file__))
+
+
+class Ping(agents.FSM):
+
+    defaults = {
+        'count': 0,
+    }
+
+    @agents.default_state
+    @agents.state
+    def even(self):
+        self['count'] += 1
+        return self.odd
+
+    @agents.state
+    def odd(self):
+        self['count'] += 1
+        return self.even
+
+
+class TestAnalysis(TestCase):
+
+    # Code to generate a simple sqlite history
+    def setUp(self):
+        """
+        The initial states should be applied to the agent and the
+        agent should be able to update its state."""
+        config = {
+            'name': 'analysis',
+            'dry_run': True,
+            'seed': 'seed',
+            'network_params': {
+                'generator': 'complete_graph',
+                'n': 2
+            },
+            'agent_type': Ping,
+            'states': [{'interval': 1}, {'interval': 2}],
+            'max_time': 30,
+            'num_trials': 1,
+            'environment_params': {
+            }
+        }
+        s = simulation.from_config(config)
+        self.env = s.run_simulation()[0]
+
+    def test_saved(self):
+        env = self.env
+        assert env.get_agent(0)['count', 0] == 1
+        assert env.get_agent(0)['count', 29] == 30
+        assert env.get_agent(1)['count', 0] == 1
+        assert env.get_agent(1)['count', 29] == 15
+        assert env['env', 29, None]['SEED'] == env['env', 29, 'SEED']
+
+    def test_count(self):
+        env = self.env
+        df = analysis.read_sql(env._history._db)
+        res = analysis.get_count(df, 'SEED', 'id')
+        assert res['SEED']['seedanalysis_trial_0'].iloc[0] == 1
+        assert res['SEED']['seedanalysis_trial_0'].iloc[-1] == 1
+        assert res['id']['odd'].iloc[0] == 2
+        assert res['id']['even'].iloc[0] == 0
+        assert res['id']['odd'].iloc[-1] == 1
+        assert res['id']['even'].iloc[-1] == 1
+
+    def test_value(self):
+        env = self.env
+        df = analysis.read_sql(env._history._db)
+        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
+
+        res_total = analysis.get_value(df)
+
+        res_total['SEED'].iloc[0] == 'seedanalysis_trial_0'

tests/test_history.py

@@ -0,0 +1,133 @@
+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)
+        assert os.path.exists(db_path)
+
+        # Recover the data
+        recovered = history.History(db_path=db_path, backup=False)
+        assert recovered['a_1', 0, 'id'] == 'v'
+        assert recovered['a_1', 4, 'id'] == 'e'
+
+        # Using the same name should create a backup copy
+        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 not len(newhistory[None, None, None])

tests/test_main.py

@@ -2,10 +2,11 @@ from unittest import TestCase
 
 import os
 import yaml
+import networkx as nx
 from functools import partial
 
 from os.path import join
-from soil import simulation, agents, utils
+from soil import simulation, environment, agents, utils
 
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -21,6 +22,7 @@ class TestMain(TestCase):
         Raise an exception otherwise.
         """
         config = {
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             }
@@ -30,6 +32,7 @@ class TestMain(TestCase):
         assert len(G) == 2
         with self.assertRaises(AttributeError):
             config = {
+            'dry_run': True,
                 'network_params': {
                     'path': join(ROOT, 'unknown.extension')
                 }
@@ -43,6 +46,7 @@ class TestMain(TestCase):
         should be used to generate a network
         """
         config = {
+            'dry_run': True,
             'network_params': {
                 'generator': 'barabasi_albert_graph'
             }
@@ -57,43 +61,48 @@ class TestMain(TestCase):
     def test_empty_simulation(self):
         """A simulation with a base behaviour should do nothing"""
         config = {
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
-            'agent_type': 'NetworkAgent',
+            'agent_type': 'BaseAgent',
             'environment_params': {
             }
         }
         s = simulation.from_config(config)
-        s.run_simulation()
+        s.run_simulation(dry_run=True)
 
     def test_counter_agent(self):
         """
         The initial states should be applied to the agent and the
         agent should be able to update its state."""
         config = {
+            'name': 'CounterAgent',
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
             'agent_type': 'CounterModel',
-            'states': [{'neighbors': 10}, {'total': 12}],
+            'states': [{'times': 10}, {'times': 20}],
             'max_time': 2,
             'num_trials': 1,
             'environment_params': {
             }
         }
         s = simulation.from_config(config)
-        env = s.run_simulation()[0]
-        assert env.get_agent(0)['neighbors', 0] == 10
-        assert env.get_agent(0)['neighbors', 1] == 1
-        assert env.get_agent(1)['total', 0] == 12
-        assert env.get_agent(1)['neighbors', 1] == 1
+        env = s.run_simulation(dry_run=True)[0]
+        assert env.get_agent(0)['times', 0] == 11
+        assert env.get_agent(0)['times', 1] == 12
+        assert env.get_agent(1)['times', 0] == 21
+        assert env.get_agent(1)['times', 1] == 22
 
     def test_counter_agent_history(self):
         """
         The evolution of the state should be recorded in the logging agent
         """
         config = {
+            'name': 'CounterAgent',
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -108,22 +117,22 @@ class TestMain(TestCase):
             }
         }
         s = simulation.from_config(config)
-        env = s.run_simulation()[0]
+        env = s.run_simulation(dry_run=True)[0]
         for agent in env.network_agents:
             last = 0
-            assert len(agent._history) == 11
-            for step, total in agent['total', None].items():
-                if step > 0:
-                    assert total == last + 2
-                    last = total
+            assert len(agent[None, None]) == 10
+            for step, total in sorted(agent['total', None]):
+                assert total == last + 2
+                last = total
 
     def test_custom_agent(self):
         """Allow for search of neighbors with a certain state_id"""
-        class CustomAgent(agents.NetworkAgent):
+        class CustomAgent(agents.BaseAgent):
             def step(self):
                 self.state['neighbors'] = self.count_agents(state_id=0,
                                                             limit_neighbors=True)
         config = {
+            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -138,7 +147,7 @@ class TestMain(TestCase):
             }
         }
         s = simulation.from_config(config)
-        env = s.run_simulation()[0]
+        env = s.run_simulation(dry_run=True)[0]
         assert env.get_agent(0).state['neighbors'] == 1
 
     def test_torvalds_example(self):
@@ -147,6 +156,7 @@ class TestMain(TestCase):
         config['network_params']['path'] = join(EXAMPLES,
                                                 config['network_params']['path'])
         s = simulation.from_config(config)
+        s.dry_run = True
         env = s.run_simulation()[0]
         for a in env.network_agents:
             skill_level = a.state['skill_level']
@@ -171,12 +181,15 @@ class TestMain(TestCase):
         with utils.timer('loading'):
             config = utils.load_file(join(EXAMPLES, 'complete.yml'))[0]
             s = simulation.from_config(config)
+            s.dry_run = True
         with utils.timer('serializing'):
             serial = s.to_yaml()
         with utils.timer('recovering'):
             recovered = yaml.load(serial)
         with utils.timer('deleting'):
             del recovered['topology']
+            del recovered['load_module']
+            del recovered['dry_run']
         assert config == recovered
 
     def test_configuration_changes(self):
@@ -186,16 +199,43 @@ class TestMain(TestCase):
         """
         config = utils.load_file('examples/complete.yml')[0]
         s = simulation.from_config(config)
+        s.dry_run = True
         for i in range(5):
-            s.run_simulation()
+            s.run_simulation(dry_run=True)
             nconfig = s.to_dict()
             del nconfig['topology']
+            del nconfig['dry_run']
+            del nconfig['load_module']
             assert config == nconfig
 
     def test_examples(self):
         """
         Make sure all examples in the examples folder are correct
         """
+        pass
+
+    def test_row_conversion(self):
+        env = environment.SoilEnvironment(dry_run=True)
+        env['test'] = 'test_value'
+
+        res = list(env.history_to_tuples())
+        assert len(res) == len(env.environment_params)
+
+        env._now = 1
+        env['test'] = 'second_value'
+        res = list(env.history_to_tuples())
+
+        assert env['env', 0, 'test' ] == 'test_value'
+        assert env['env', 1, 'test' ] == 'second_value'
+
+    def test_save_geometric(self):
+        """
+        There is a bug in networkx that prevents it from creating a GEXF file 
+        from geometric models. We should work around it.
+        """
+        G = nx.random_geometric_graph(20,0.1)
+        env = environment.SoilEnvironment(topology=G, dry_run=True)
+        env.dump_gexf('/tmp/dump-gexf')
 
 
 def make_example_test(path, config):
@@ -203,11 +243,15 @@ def make_example_test(path, config):
         root = os.getcwd()
         os.chdir(os.path.dirname(path))
         s = simulation.from_config(config)
-        envs = s.run_simulation()
+        envs = s.run_simulation(dry_run=True)
+        assert envs
         for env in envs:
-            n = config['network_params'].get('n', None)
-            if n is not None:
+            assert env
+            try:
+                n = config['network_params']['n']
                 assert len(env.get_agents()) == n
+            except KeyError:
+                pass
         os.chdir(root)
     return wrapped