Tag version 0.14.0

1.3.0rc1 is not compatible with salib

CHANGELOG.md

@@ -3,6 +3,28 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.14.0]
+### Added
+* Loading configuration from template definitions in the yaml, in preparation for SALib support.
+The definition of the variables and their possible values (i.e., a problem in SALib terms), as well as a sampler function, can be provided.
+Soil uses this definition and the template to generate a set of configurations.
+* Simulation group names, to link related simulations. For now, they are only used to group all simulations in the same group under the same folder.
+* Exporters unify exporting/dumping results and other files to disk. If `dry_run` is set to `True`, exporters will write to stdout instead of a file (useful for testing/debugging).
+* Distribution exporter, to write statistics about values and value_counts in every simulation. The results are dumped to two CSV files.
+
+### Changed
+* `dir_path` is now the directory for resources (modules, files)
+* Environments and simulations do not export or write anything by default. That task is delegated to Exporters
+
+### Removed
+* The output dir for environments and simulations (see Exporters)
+* DrawingAgent, because it wrote to disk and was not being used. We provide a partial alternative in the form of the GraphDrawing exporter. A complete alternative will be provided once the network at each state can be accessed by exporters.
+
+## Fixed
+* Modules with custom agents/environments failed to load when they were run from outside the directory of the definition file. Modules are now loaded from the directory of the simulation file in addition to the working directory
+* Memory databases (in history) can now be shared between threads.
+* Testing all examples, not just subdirectories
+
 ## [0.13.8]
 ### Changed
 * Moved TerroristNetworkModel to examples

Makefile

@@ -1,4 +1,7 @@
-test:
+quick-test:
 	docker-compose exec dev python -m pytest -s -v
 
-.PHONY: test
+test:
+	docker run -t -v $$PWD:/usr/src/app -w /usr/src/app python:3.7 python setup.py test
+
+.PHONY: test

examples/complete.yml

@@ -1,12 +1,11 @@
 ---
 name: simple
+group: tests
 dir_path: "/tmp/"
 num_trials: 3
-dry_run: True
 max_time: 100
 interval: 1
 seed: "CompleteSeed!"
-dump: false
 network_params:
   generator: complete_graph
   n: 10

examples/custom_generator/custom_generator.yml

@@ -2,7 +2,6 @@
 name: custom-generator
 description: Using a custom generator for the network
 num_trials: 3
-dry_run: True
 max_time: 100
 interval: 1
 network_params:
@@ -14,4 +13,4 @@ network_agents:
   - agent_type: CounterModel
     weight: 1
     state:
-      id: 0
+      id: 0

examples/custom_timeouts/custom_timeouts.py

@@ -29,8 +29,7 @@ if __name__ == '__main__':
     from soil import Simulation
     s = Simulation(network_agents=[{'ids': [0], 'agent_type': Fibonacci},
                                    {'ids': [1], 'agent_type': Odds}],
-                   dry_run=True,
                    network_params={"generator": "complete_graph", "n": 2},
                    max_time=100,
                    )
-    s.run()
+    s.run(dry_run=True)

examples/template.yml

@@ -0,0 +1,29 @@
+---
+vars:
+  bounds:
+    x1: [0, 1]
+    x2: [1, 2]
+  fixed:
+    x3: ["a", "b", "c"]
+sampler: "SALib.sample.morris.sample"
+samples: 10
+template: |
+  group: simple
+  num_trials: 1
+  interval: 1
+  max_time: 2
+  seed: "CompleteSeed!"
+  dump: false
+  network_params:
+    generator: complete_graph
+    n: 10
+  network_agents:
+    - agent_type: CounterModel
+      weight: {{ x1 }}
+      state:
+        id: 0
+    - agent_type: AggregatedCounter
+      weight: {{ 1 - x1 }}
+  environment_params:
+    name: {{ x3 }}
+  skip_test: true

requirements.txt

@@ -1,8 +1,10 @@
-nxsim
+nxsim>=0.1.2
 simpy
 networkx>=2.0
 numpy
 matplotlib
-pyyaml
-pandas
-scipy
+pyyaml>=5.1
+pandas>=0.23
+scipy==1.2.1 # scipy 1.3.0rc1 is not compatible with salib
+SALib>=1.3
+Jinja2

soil/VERSION

@@ -1 +1 @@
-0.13.8
+0.14.0

soil/__init__.py

@@ -15,7 +15,7 @@ from . import agents
 from .simulation import *
 from .environment import Environment
 from .history import History
-from . import utils
+from . import serialization
 from . import analysis
 
 def main():
@@ -44,6 +44,8 @@ def main():
                         help='folder to write results to. It defaults to the current directory.')
     parser.add_argument('--synchronous', action='store_true',
                         help='Run trials serially and synchronously instead of in parallel. Defaults to false.')
+    parser.add_argument('-e', '--exporter', action='append',
+                        help='Export environment and/or simulations using this exporter')
 
     args = parser.parse_args()
 
@@ -55,17 +57,20 @@ def main():
     logging.info('Loading config file: {}'.format(args.file))
 
     try:
-        dump = []
-        if not args.dry_run:
-            if args.csv:
-                dump.append('csv')
-            if args.graph:
-                dump.append('gexf')
+        exporters = list(args.exporter or [])
+        if args.csv:
+            exporters.append('CSV')
+        if args.graph:
+            exporters.append('Gexf')
+        exp_params = {}
+        if args.dry_run:
+            exp_params['copy_to'] = sys.stdout
         simulation.run_from_config(args.file,
                                    dry_run=args.dry_run,
-                                   dump=dump,
+                                   exporters=exporters,
                                    parallel=(not args.synchronous),
-                                   results_dir=args.output)
+                                   outdir=args.output,
+                                   exporter_params=exp_params)
     except Exception:
         if args.pdb:
             pdb.post_mortem()

soil/agents/DrawingAgent.py

@@ -1,18 +0,0 @@
-from . import BaseAgent
-
-import os.path
-import matplotlib
-import matplotlib.pyplot as plt
-import networkx as nx
-
-
-class DrawingAgent(BaseAgent):
-    """
-    Agent that draws the state of the network.
-    """
-
-    def step(self):
-        # 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.get_path(), "graph-"+str(self.env.now)+".png"))

soil/agents/__init__.py

@@ -15,7 +15,7 @@ import json
 
 from functools import wraps
 
-from .. import utils, history
+from .. import serialization, history
 
 
 def as_node(agent):
@@ -388,7 +388,7 @@ def serialize_type(agent_type, known_modules=[], **kwargs):
     if isinstance(agent_type, str):
         return agent_type
     known_modules += ['soil.agents']
-    return utils.serialize(agent_type, known_modules=known_modules, **kwargs)[1] # Get the name of the class
+    return serialization.serialize(agent_type, known_modules=known_modules, **kwargs)[1] # Get the name of the class
 
 
 def serialize_distribution(network_agents, known_modules=[]):
@@ -409,7 +409,7 @@ def deserialize_type(agent_type, known_modules=[]):
     if not isinstance(agent_type, str):
         return agent_type
     known = known_modules + ['soil.agents', 'soil.agents.custom' ]
-    agent_type = utils.deserializer(agent_type, known_modules=known)
+    agent_type = serialization.deserializer(agent_type, known_modules=known)
     return agent_type
 
 
@@ -515,4 +515,3 @@ from .ModelM2 import *
 from .SentimentCorrelationModel import *
 from .SISaModel import *
 from .CounterModel import *
-from .DrawingAgent import *

soil/analysis.py

@@ -4,7 +4,7 @@ import glob
 import yaml
 from os.path import join
 
-from . import utils, history
+from . import serialization, history
 
 
 def read_data(*args, group=False, **kwargs):
@@ -34,7 +34,7 @@ def _read_data(pattern, *args, from_csv=False, process_args=None, **kwargs):
 
 
 def read_sql(db, *args, **kwargs):
-    h = history.History(db, backup=False)
+    h = history.History(db_path=db, backup=False)
     df = h.read_sql(*args, **kwargs)
     return df
 
@@ -56,7 +56,7 @@ def read_csv(filename, keys=None, convert_types=False, **kwargs):
 
 
 def convert_row(row):
-    row['value'] = utils.deserialize(row['value_type'], row['value'])
+    row['value'] = serialization.deserialize(row['value_type'], row['value'])
     return row
 
 

soil/environment.py

@@ -14,15 +14,13 @@ from networkx.readwrite import json_graph
 import networkx as nx
 import nxsim
 
-from . import utils, agents, analysis, history
+from . import serialization, agents, analysis, history, utils
 
 # These properties will be copied when pickling/unpickling the environment
 _CONFIG_PROPS = [ 'name',
                  'states',
                  'default_state',
                  'interval',
-                 'dry_run',
-                 'dir_path',
                  ]
 
 class Environment(nxsim.NetworkEnvironment):
@@ -43,8 +41,6 @@ class Environment(nxsim.NetworkEnvironment):
                  default_state=None,
                  interval=1,
                  seed=None,
-                 dry_run=False,
-                 dir_path=None,
                  topology=None,
                  *args, **kwargs):
         self.name = name or 'UnnamedEnvironment'
@@ -56,13 +52,8 @@ class Environment(nxsim.NetworkEnvironment):
             topology = nx.Graph()
         super().__init__(*args, topology=topology, **kwargs)
         self._env_agents = {}
-        self.dry_run = dry_run
         self.interval = interval
-        self.dir_path = dir_path or tempfile.mkdtemp('soil-env')
-        if not dry_run:
-            self.get_path()
-        self._history = history.History(name=self.name if not dry_run else None,
-                                        dir_path=self.dir_path,
+        self._history = history.History(name=self.name,
                                         backup=True)
         # Add environment agents first, so their events get
         # executed before network agents
@@ -124,7 +115,7 @@ class Environment(nxsim.NetworkEnvironment):
         elif agent_distribution:
             agent_type, state = agents._agent_from_distribution(agent_distribution, agent_id=agent_id)
         else:
-            utils.logger.debug('Skipping node {}'.format(agent_id))
+            serialization.logger.debug('Skipping node {}'.format(agent_id))
             return
         return self.set_agent(agent_id, agent_type, state)
 
@@ -167,9 +158,7 @@ class Environment(nxsim.NetworkEnvironment):
         self.log_stats()
 
     def _save_state(self, now=None):
-        # for agent in self.agents:
-        #     agent.save_state()
-        utils.logger.debug('Saving state @{}'.format(self.now))
+        serialization.logger.debug('Saving state @{}'.format(self.now))
         self._history.save_records(self.state_to_tuples(now=now))
 
     def save_state(self):
@@ -180,7 +169,7 @@ class Environment(nxsim.NetworkEnvironment):
         self._save_state()
         while self.peek() != simpy.core.Infinity:
             delay = max(self.peek() - self.now, self.interval)
-            utils.logger.debug('Step: {}'.format(self.now))
+            serialization.logger.debug('Step: {}'.format(self.now))
             ev = self.event()
             ev._ok = True
             # Schedule the event with minimum priority so
@@ -222,15 +211,6 @@ class Environment(nxsim.NetworkEnvironment):
         '''
         return self[key] if key in self else default
 
-    def get_path(self, dir_path=None):
-        dir_path = dir_path or self.dir_path
-        if not os.path.exists(dir_path):
-            try:
-                os.makedirs(dir_path)
-            except FileExistsError:
-                pass
-        return dir_path
-
     def get_agent(self, agent_id):
         return self.G.node[agent_id]['agent']
 
@@ -239,20 +219,15 @@ class Environment(nxsim.NetworkEnvironment):
             return list(self.agents)
         return [self.G.node[i]['agent'] for i in nodes]
 
-    def dump_csv(self, dir_path=None):
-        csv_name = os.path.join(self.get_path(dir_path),
-                                '{}.environment.csv'.format(self.name))
-
-        with open(csv_name, 'w') as f:
+    def dump_csv(self, f):
+        with utils.open_or_reuse(f, 'w') as f:
             cr = csv.writer(f)
             cr.writerow(('agent_id', 't_step', 'key', 'value'))
             for i in self.history_to_tuples():
                 cr.writerow(i)
 
-    def dump_gexf(self, dir_path=None):
+    def dump_gexf(self, f):
         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():
@@ -260,9 +235,9 @@ class Environment(nxsim.NetworkEnvironment):
                 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")
+        nx.write_gexf(G, f, version="1.2draft")
 
-    def dump(self, dir_path=None, formats=None):
+    def dump(self, *args, formats=None, **kwargs):
         if not formats:
             return
         functions = {
@@ -271,10 +246,13 @@ class Environment(nxsim.NetworkEnvironment):
         }
         for f in formats:
             if f in functions:
-                functions[f](dir_path)
+                functions[f](*args, **kwargs)
             else:
                 raise ValueError('Unknown format: {}'.format(f))
 
+    def dump_sqlite(self, f):
+        return self._history.dump(f)
+
     def state_to_tuples(self, now=None):
         if now is None:
             now = self.now
@@ -338,7 +316,7 @@ class Environment(nxsim.NetworkEnvironment):
                 G.add_node(agent.id, **attributes)
 
         return G
-    
+
     def stats(self):
         stats = {}
         stats['network'] = {}
@@ -356,7 +334,7 @@ class Environment(nxsim.NetworkEnvironment):
 
     def log_stats(self):
         stats = self.stats()
-        utils.logger.info('Environment stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
+        serialization.logger.info('Environment stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
     
     def __getstate__(self):
         state = {}

soil/exporters.py

@@ -0,0 +1,175 @@
+import os
+import time
+from io import BytesIO
+
+import matplotlib.pyplot as plt
+import networkx as nx
+import pandas as pd
+
+from .serialization import deserialize
+from .utils import open_or_reuse, logger, timer
+
+
+from . import utils
+
+
+def for_sim(simulation, names, *args, **kwargs):
+    '''Return the set of exporters for a simulation, given the exporter names'''
+    exporters = []
+    for name in names:
+        mod = deserialize(name, known_modules=['soil.exporters'])
+        exporters.append(mod(simulation, *args, **kwargs))
+    return exporters
+
+
+class DryRunner(BytesIO):
+    def __init__(self, fname, *args, copy_to=None, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.__fname = fname
+        self.__copy_to = copy_to
+
+    def write(self, txt):
+        if self.__copy_to:
+            self.__copy_to.write('{}:::{}'.format(self.__fname, txt))
+        try:
+            super().write(txt)
+        except TypeError:
+            super().write(bytes(txt, 'utf-8'))
+
+    def close(self):
+        logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname,
+                                                                       self.getvalue().decode()))
+        super().close()
+
+
+class Exporter:
+    '''
+    Interface for all exporters. It is not necessary, but it is useful
+    if you don't plan to implement all the methods.
+    '''
+
+    def __init__(self, simulation, outdir=None, dry_run=None, copy_to=None):
+        self.sim = simulation
+        outdir = outdir or os.getcwd()
+        self.outdir = os.path.join(outdir,
+                                   simulation.group or '',
+                                   simulation.name)
+        self.dry_run = dry_run
+        self.copy_to = copy_to
+
+    def start(self):
+        '''Method to call when the simulation starts'''
+
+    def end(self):
+        '''Method to call when the simulation ends'''
+
+    def trial_end(self, env):
+        '''Method to call when a trial ends'''
+
+    def output(self, f, mode='w', **kwargs):
+        if self.dry_run:
+            f = DryRunner(f, copy_to=self.copy_to)
+        else:
+            try:
+                if not os.path.isabs(f):
+                    f = os.path.join(self.outdir, f)
+            except TypeError:
+                pass
+        return open_or_reuse(f, mode=mode, **kwargs)
+
+
+class Default(Exporter):
+    '''Default exporter. Writes CSV and sqlite results, as well as the simulation YAML'''
+
+    def start(self):
+        if not self.dry_run:
+            logger.info('Dumping results to %s', self.outdir)
+            self.sim.dump_yaml(outdir=self.outdir)
+        else:
+            logger.info('NOT dumping results')
+
+    def trial_end(self, env):
+        if not self.dry_run:
+            with timer('Dumping simulation {} trial {}'.format(self.sim.name,
+                                                               env.name)):
+                with self.output('{}.sqlite'.format(env.name), mode='wb') as f:
+                    env.dump_sqlite(f)
+
+
+class CSV(Exporter):
+    def trial_end(self, env):
+        if not self.dry_run:
+            with timer('[CSV] Dumping simulation {} trial {}'.format(self.sim.name,
+                                                               env.name)):
+                with self.output('{}.csv'.format(env.name)) as f:
+                    env.dump_csv(f)
+
+
+class Gexf(Exporter):
+    def trial_end(self, env):
+        if not self.dry_run:
+            with timer('[CSV] Dumping simulation {} trial {}'.format(self.sim.name,
+                                                                     env.name)):
+                with self.output('{}.gexf'.format(env.name), mode='wb') as f:
+                    env.dump_gexf(f)
+
+
+class Dummy(Exporter):
+
+    def start(self):
+        with self.output('dummy', 'w') as f:
+            f.write('simulation started @ {}\n'.format(time.time()))
+
+    def trial_end(self, env):
+        with self.output('dummy', 'w') as f:
+            for i in env.history_to_tuples():
+                f.write(','.join(map(str, i)))
+                f.write('\n')
+
+    def end(self):
+        with self.output('dummy', 'a') as f:
+            f.write('simulation ended @ {}\n'.format(time.time()))
+
+
+class Distribution(Exporter):
+    '''
+    Write the distribution of agent states at the end of each trial,
+    the mean value, and its deviation.
+    '''
+
+    def start(self):
+        self.means = []
+        self.counts = []
+
+    def trial_end(self, env):
+        df = env[None, None, None].df()
+        ix = df.index[-1]
+        attrs = df.columns.levels[0]
+        vc = {}
+        stats = {}
+        for a in attrs:
+            t = df.loc[(ix, a)]
+            try:
+                self.means.append(('mean', a, t.mean()))
+            except TypeError:
+                for name, count in t.value_counts().iteritems():
+                    self.counts.append(('count', a, name, count))
+
+    def end(self):
+        dfm = pd.DataFrame(self.means, columns=['metric', 'key', 'value'])
+        dfc = pd.DataFrame(self.counts, columns=['metric', 'key', 'value', 'count'])
+        dfm = dfm.groupby(by=['key']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
+        dfc = dfc.groupby(by=['key', 'value']).agg(['mean', 'std', 'count', 'median', 'max', 'min'])
+        with self.output('counts.csv') as f:
+            dfc.to_csv(f)
+        with self.output('metrics.csv') as f:
+            dfm.to_csv(f)
+
+class GraphDrawing(Exporter):
+
+    def trial_end(self, env):
+        # Outside effects
+        f = plt.figure()
+        nx.draw(env.G, node_size=10, width=0.2, pos=nx.spring_layout(env.G, scale=100), ax=f.add_subplot(111))
+        with open('graph-{}.png'.format(env.name)) as f:
+            f.savefig(f)

soil/history.py

@@ -4,12 +4,13 @@ import pandas as pd
 import sqlite3
 import copy
 import logging
+import tempfile
 
 logger = logging.getLogger(__name__)
 
 from collections import UserDict, namedtuple
 
-from . import utils
+from . import serialization
 
 
 class History:
@@ -17,16 +18,18 @@ class History:
     Store and retrieve values from a sqlite database.
     """
 
-    def __init__(self, db_path=None, name=None, dir_path=None, backup=False):
-        if db_path is None and name:
-            db_path = os.path.join(dir_path or os.getcwd(),
-                                   '{}.db.sqlite'.format(name))
-        if db_path:
-            if backup and os.path.exists(db_path):
-                newname = db_path + '.backup{}.sqlite'.format(time.time())
-                os.rename(db_path, newname)
-        else:
-            db_path = ":memory:"
+    def __init__(self, name=None, db_path=None, backup=False):
+        self._db = None
+
+        if db_path is None:
+            if not name:
+                name = time.time()
+            _, db_path = tempfile.mkstemp(suffix='{}.sqlite'.format(name))
+
+        if backup and os.path.exists(db_path):
+            newname = db_path + '.backup{}.sqlite'.format(time.time())
+            os.rename(db_path, newname)
+
         self.db_path = db_path
 
         self.db = db_path
@@ -49,6 +52,7 @@ class History:
 
     @db.setter
     def db(self, db_path=None):
+        self._close()
         db_path = db_path or self.db_path
         if isinstance(db_path, str):
             logger.debug('Connecting to database {}'.format(db_path))
@@ -56,6 +60,13 @@ class History:
         else:
             self._db = db_path
 
+    def _close(self):
+        if self._db is None:
+            return
+        self.flush_cache()
+        self._db.close()
+        self._db = None
+
     @property
     def dtypes(self):
         self.read_types()
@@ -94,9 +105,9 @@ class History:
         if key not in self._dtypes:
             self.read_types()
             if key not in self._dtypes:
-                name = utils.name(value)
-                serializer = utils.serializer(name)
-                deserializer = utils.deserializer(name)
+                name = serialization.name(value)
+                serializer = serialization.serializer(name)
+                deserializer = serialization.deserializer(name)
                 self._dtypes[key] = (name, serializer, deserializer)
                 with self.db:
                     self.db.execute("replace into value_types (key, value_type) values (?, ?)", (key, name))
@@ -110,7 +121,6 @@ class History:
             raise ValueError("Unknown datatype for {} and {}".format(key, value))
         return self._dtypes[key][2](value)
 
-
     def flush_cache(self):
         '''
         Use a cache to save state changes to avoid opening a session for every change.
@@ -135,8 +145,8 @@ class History:
         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)
+            serializer = serialization.serializer(v)
+            deserializer = serialization.deserializer(v)
             self._dtypes[k] = (v, serializer, deserializer)
 
     def __getitem__(self, key):
@@ -154,8 +164,6 @@ class History:
             return r.value()
         return r
 
-
-
     def read_sql(self, keys=None, agent_ids=None, t_steps=None, convert_types=False, limit=-1):
 
         self.read_types()
@@ -214,16 +222,22 @@ class History:
         if t_steps:
             df_p = df_p.reindex(t_steps, method='ffill')
         return df_p.ffill()
-    
+
     def __getstate__(self):
         state = dict(**self.__dict__)
         del state['_db']
         del state['_dtypes']
         return state
-    
+
     def __setstate__(self, state):
         self.__dict__ = state
         self._dtypes = {}
+        self._db = None
+
+    def dump(self, f):
+        self._close()
+        for line in open(self.db_path, 'rb'):
+            f.write(line)
 
 
 class Records():
@@ -274,10 +288,13 @@ class Records():
                 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:
+            except KeyError as ex:
                 return self.dtypes[f.key][2]()
         return list(self)
 
+    def df(self):
+        return self._df
+
     def __getitem__(self, k):
         n = copy.copy(self)
         n.filter(k)
@@ -293,6 +310,5 @@ class Records():
             return str(self.value())
         return '<Records for [{}]>'.format(self._filter)
 
-
 Key = namedtuple('Key', ['agent_id', 't_step', 'key'])
 Record = namedtuple('Record', 'agent_id t_step key value')

soil/serialization.py

@@ -0,0 +1,201 @@
+import os
+import logging
+import ast
+import sys
+import importlib
+from glob import glob
+from itertools import product, chain
+
+import yaml
+import networkx as nx
+
+from jinja2 import Template
+
+
+logger = logging.getLogger('soil')
+logger.setLevel(logging.INFO)
+
+
+def load_network(network_params, dir_path=None):
+    if network_params is None:
+        return nx.Graph()
+    path = network_params.get('path', None)
+    if path:
+        if dir_path and not os.path.isabs(path):
+            path = os.path.join(dir_path, path)
+        extension = os.path.splitext(path)[1][1:]
+        kwargs = {}
+        if extension == 'gexf':
+            kwargs['version'] = '1.2draft'
+            kwargs['node_type'] = int
+        try:
+            method = getattr(nx.readwrite, 'read_' + extension)
+        except AttributeError:
+            raise AttributeError('Unknown format')
+        return method(path, **kwargs)
+
+    net_args = network_params.copy()
+    if 'generator' not in net_args:
+        return nx.Graph()
+
+    net_gen = net_args.pop('generator')
+
+    if dir_path not in sys.path:
+        sys.path.append(dir_path)
+
+    method = deserializer(net_gen,
+                          known_modules=['networkx.generators',])
+
+    return method(**net_args)
+
+
+def load_file(infile):
+    with open(infile, 'r') as f:
+        return list(chain.from_iterable(map(expand_template, load_string(f))))
+
+
+def load_string(string):
+    yield from yaml.load_all(string, Loader=yaml.FullLoader)
+
+
+def expand_template(config):
+    if 'template' not in config:
+        yield config
+        return
+    if 'vars' not in config:
+        raise ValueError(('You must provide a definition of variables'
+                          ' for the template.'))
+
+    template = Template(config['template'])
+
+    sampler_name = config.get('sampler', 'SALib.sample.morris.sample')
+    n_samples = int(config.get('samples', 100))
+    sampler = deserializer(sampler_name)
+    bounds = config['vars']['bounds']
+
+    problem = {
+        'num_vars': len(bounds),
+        'names': list(bounds.keys()),
+        'bounds': list(v for v in bounds.values())
+    }
+    samples = sampler(problem, n_samples)
+
+    lists = config['vars'].get('lists', {})
+    names = list(lists.keys())
+    values = list(lists.values())
+    combs = list(product(*values))
+
+    allnames = names + problem['names']
+    allvalues = [(list(i[0])+list(i[1])) for i in product(combs, samples)]
+    params = list(map(lambda x: dict(zip(allnames, x)), allvalues))
+
+
+    blank_str = template.render({k: 0 for k in allnames})
+    blank = list(load_string(blank_str))
+    if len(blank) > 1:
+        raise ValueError('Templates must not return more than one configuration')
+    if 'name' in blank[0]:
+        raise ValueError('Templates cannot be named, use group instead')
+
+    confs = []
+    for ps in params:
+        string = template.render(ps)
+        for c in load_string(string):
+            yield c
+
+
+def load_files(*patterns, **kwargs):
+    for pattern in patterns:
+        for i in glob(pattern, **kwargs):
+            for config in load_file(i):
+                path = os.path.abspath(i)
+                if 'dir_path' not in config:
+                    config['dir_path'] = os.path.dirname(path)
+                yield config, path
+
+
+def load_config(config):
+    if isinstance(config, dict):
+        yield config, None
+    else:
+        yield from load_files(config)
+
+
+builtins = importlib.import_module('builtins')
+
+def name(value, known_modules=[]):
+    '''Return a name that can be imported, to serialize/deserialize an object'''
+    if value is None:
+        return 'None'
+    if not isinstance(value, type):  # Get the class name first
+        value = type(value)
+    tname = value.__name__
+    if hasattr(builtins, tname):
+        return tname
+    modname = value.__module__
+    if modname == '__main__':
+        return tname
+    if known_modules and modname in known_modules:
+        return tname
+    for kmod in known_modules:
+        if not kmod:
+            continue
+        module = importlib.import_module(kmod)
+        if hasattr(module, tname):
+            return tname
+    return '{}.{}'.format(modname, tname)
+
+
+def serializer(type_):
+    if type_ != 'str' and hasattr(builtins, type_):
+        return repr
+    return lambda x: x
+
+
+def serialize(v, known_modules=[]):
+    '''Get a text representation of an object.'''
+    tname = name(v, known_modules=known_modules)
+    func = serializer(tname)
+    return func(v), tname
+
+def deserializer(type_, known_modules=[]):
+    if type(type_) != str:  # Already deserialized
+        return type_
+    if type_ == 'str':
+        return lambda x='': x
+    if type_ == 'None':
+        return lambda x=None: None
+    if hasattr(builtins, type_):  # Check if it's a builtin type
+        cls = getattr(builtins, type_)
+        return lambda x=None: ast.literal_eval(x) if x is not None else cls()
+    # Otherwise, see if we can find the module and the class
+    modules = known_modules or []
+    options = []
+
+    for mod in modules:
+        if mod:
+            options.append((mod, type_))
+
+    if '.' in type_:  # Fully qualified module
+        module, type_ = type_.rsplit(".", 1)
+        options.append ((module, type_))
+
+    errors = []
+    for modname, tname in options:
+        try:
+            module = importlib.import_module(modname)
+            cls = getattr(module, tname)
+            return getattr(cls, 'deserialize', cls)
+        except (ModuleNotFoundError, AttributeError) as ex:
+            errors.append((modname, tname, ex))
+    raise Exception('Could not find type {}. Tried: {}'.format(type_, errors))
+
+
+def deserialize(type_, value=None, **kwargs):
+    '''Get an object from a text representation'''
+    if not isinstance(type_, str):
+        return type_
+    des = deserializer(type_, **kwargs)
+    if value is None:
+        return des
+    return des(value)

soil/simulation.py

@@ -13,9 +13,10 @@ import pickle
 
 from nxsim import NetworkSimulation
 
-from . import utils, basestring, agents
+from . import serialization, utils, basestring, agents
 from .environment import Environment
 from .utils import logger
+from .exporters import for_sim as exporters_for_sim
 
 
 class Simulation(NetworkSimulation):
@@ -50,6 +51,8 @@ class Simulation(NetworkSimulation):
     ---------
     name : str, optional
         name of the Simulation
+    group : str, optional
+        a group name can be used to link simulations
     topology : networkx.Graph instance, optional
     network_params : dict
         parameters used to create a topology with networkx, if no topology is given
@@ -60,8 +63,8 @@ class Simulation(NetworkSimulation):
     states : list, optional
         List of initial states corresponding to the nodes in the topology. Basic form is a list of integers
         whose value indicates the state
-    dir_path : str, optional
-        Directory path where to save pickled objects
+    dir_path: str, optional
+        Directory path to load simulation assets (files, modules...)
     seed : str, optional
         Seed to use for the random generator
     num_trials : int, optional
@@ -80,38 +83,37 @@ class Simulation(NetworkSimulation):
 
     """
 
-    def __init__(self, name=None, topology=None, network_params=None,
+    def __init__(self, name=None, group=None, topology=None, network_params=None,
                  network_agents=None, agent_type=None, states=None,
-                 default_state=None, interval=1, dump=None, dry_run=False,
-                 dir_path=None, num_trials=1, max_time=100,
-                 load_module=None, seed=None,
-                 environment_agents=None, environment_params=None,
-                 environment_class=None, **kwargs):
+                 default_state=None, interval=1, num_trials=1,
+                 max_time=100, load_module=None, seed=None,
+                 dir_path=None, environment_agents=None,
+                 environment_params=None, environment_class=None,
+                 **kwargs):
 
         self.seed = str(seed) or str(time.time())
         self.load_module = load_module
         self.network_params = network_params
-        self.name = name or 'UnnamedSimulation'
+        self.name = name or 'Unnamed_' + time.strftime("%Y-%m-%d_%H:%M:%S")
+        self.group = group or None
         self.num_trials = num_trials
         self.max_time = max_time
         self.default_state = default_state or {}
         self.dir_path = dir_path or os.getcwd()
         self.interval = interval
-        self.dump = dump
-        self.dry_run = dry_run
 
-        sys.path += [self.dir_path, os.getcwd()]
+        sys.path += list(x for x in [os.getcwd(), self.dir_path] if x not in sys.path)
 
         if topology is None:
-            topology = utils.load_network(network_params,
-                                          dir_path=self.dir_path)
+            topology = serialization.load_network(network_params,
+                                                  dir_path=self.dir_path)
         elif isinstance(topology, basestring) or isinstance(topology, dict):
             topology = json_graph.node_link_graph(topology)
         self.topology = nx.Graph(topology)
 
 
         self.environment_params = environment_params or {}
-        self.environment_class = utils.deserialize(environment_class,
+        self.environment_class = serialization.deserialize(environment_class,
                                                    known_modules=['soil.environment', ]) or Environment
 
         environment_agents = environment_agents or []
@@ -130,52 +132,69 @@ class Simulation(NetworkSimulation):
         return self.run(*args, **kwargs)
 
     def run(self, *args, **kwargs):
-        return list(self.run_simulation_gen(*args, **kwargs))
+        '''Run the simulation and return the list of resulting environments'''
+        return list(self._run_simulation_gen(*args, **kwargs))
+
+    def _run_sync_or_async(self, parallel=False, *args, **kwargs):
+        if parallel:
+            p = Pool()
+            func = partial(self.run_trial_exceptions,
+                           *args,
+                           **kwargs)
+            for i in p.imap_unordered(func, range(self.num_trials)):
+                if isinstance(i, Exception):
+                    logger.error('Trial failed:\n\t%s', i.message)
+                    continue
+                yield i
+        else:
+            for i in range(self.num_trials):
+                yield self.run_trial(i,
+                                     *args,
+                                     **kwargs)
+
+    def _run_simulation_gen(self, *args, parallel=False, dry_run=False,
+                            exporters=None, outdir=None, exporter_params={}, **kwargs):
+        logger.info('Using exporters: %s', exporters or [])
+        logger.info('Output directory: %s', outdir)
+        exporters = exporters_for_sim(self,
+                                      exporters or [],
+                                      dry_run=dry_run,
+                                      outdir=outdir,
+                                      **exporter_params)
 
-    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_exceptions, dry_run=dry_run or self.dry_run,
-                                                         return_env=True,
-                                                         **kwargs)
-                for i in p.imap_unordered(func, range(self.num_trials)):
-                    if isinstance(i, Exception):
-                        logger.error('Trial failed:\n\t{}'.format(i.message))
-                        continue
-                    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')
+            for exporter in exporters:
+                exporter.start()
+
+            for env in self._run_sync_or_async(*args, parallel=parallel,
+                                               **kwargs):
+                for exporter in exporters:
+                    exporter.trial_end(env)
+                yield env
+
+            for exporter in exporters:
+                exporter.end()
 
     def get_env(self, trial_id = 0, **kwargs):
-        opts=self.environment_params.copy()
-        env_name='{}_trial_{}'.format(self.name, trial_id)
+        '''Create an environment for a trial of the simulation'''
+        opts = self.environment_params.copy()
+        env_name = '{}_trial_{}'.format(self.name, trial_id)
         opts.update({
             'name': env_name,
             '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=self.environment_class(**opts)
+        env = self.environment_class(**opts)
         return env
 
-    def run_trial(self, trial_id = 0, until = None, return_env = True, **opts):
+    def run_trial(self, trial_id=0, until=None, **opts):
         """Run a single trial of the simulation
 
         Parameters
@@ -183,16 +202,12 @@ class Simulation(NetworkSimulation):
         trial_id : int
         """
         # Set-up trial environment and graph
-        until=until or self.max_time
-        env=self.get_env(trial_id = trial_id, **opts)
+        until = until or self.max_time
+        env = self.get_env(trial_id = trial_id, **opts)
         # Set up agents on nodes
         with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
             env.run(until)
-        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
+        return env
     def run_trial_exceptions(self, *args, **kwargs):
         '''
         A wrapper for run_trial that catches exceptions and returns them.
@@ -211,38 +226,39 @@ class Simulation(NetworkSimulation):
     def to_yaml(self):
         return yaml.dump(self.to_dict())
 
-    def dump_yaml(self, dir_path = None, file_name = None):
-        dir_path=dir_path or self.dir_path
-        if not os.path.exists(dir_path):
-            os.makedirs(dir_path)
-        if not file_name:
-            file_name=os.path.join(dir_path,
-                                     '{}.dumped.yml'.format(self.name))
-        with open(file_name, 'w') as f:
+
+    def dump_yaml(self, f=None, outdir=None):
+        if not f and not outdir:
+            raise ValueError('specify a file or an output directory')
+
+        if not f:
+            f = os.path.join(outdir, '{}.dumped.yml'.format(self.name))
+
+        with utils.open_or_reuse(f, 'w') as f:
             f.write(self.to_yaml())
 
-    def dump_pickle(self, dir_path = None, pickle_name = None):
-        dir_path=dir_path or self.dir_path
-        if not os.path.exists(dir_path):
-            os.makedirs(dir_path)
-        if not pickle_name:
-            pickle_name=os.path.join(dir_path,
-                                       '{}.simulation.pickle'.format(self.name))
-        with open(pickle_name, 'wb') as f:
+    def dump_pickle(self, f=None, outdir=None):
+        if not outdir and not f:
+            raise ValueError('specify a file or an output directory')
+
+        if not f:
+            f = os.path.join(outdir,
+                             '{}.simulation.pickle'.format(self.name))
+        with utils.open_or_reuse(f, 'wb') as f:
             pickle.dump(self, f)
 
     def __getstate__(self):
         state={}
         for k, v in self.__dict__.items():
             if k[0] != '_':
-                state[k]=v
-        state['topology']=json_graph.node_link_data(self.topology)
-        state['network_agents']=agents.serialize_distribution(self.network_agents,
-                                                                known_modules = [])
-        state['environment_agents']=agents.serialize_distribution(self.environment_agents,
-                                                                    known_modules = [])
-        state['environment_class']=utils.serialize(self.environment_class,
-                                                     known_modules=['soil.environment'])[1]  # func, name
+                state[k] = v
+                state['topology'] = json_graph.node_link_data(self.topology)
+                state['network_agents'] = agents.serialize_distribution(self.network_agents,
+                                                                        known_modules = [])
+                state['environment_agents'] = agents.serialize_distribution(self.environment_agents,
+                                                                            known_modules = [])
+                state['environment_class'] = serialization.serialize(self.environment_class,
+                                                                     known_modules=['soil.environment'])[1]  # func, name
         if state['load_module'] is None:
             del state['load_module']
         return state
@@ -256,13 +272,20 @@ class Simulation(NetworkSimulation):
         self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
         self.environment_agents = agents._convert_agent_types(self.environment_agents,
                                                               known_modules=[self.load_module])
-        self.environment_class = utils.deserialize(self.environment_class,
+        self.environment_class = serialization.deserialize(self.environment_class,
                                                    known_modules=[self.load_module, 'soil.environment', ])  # func, name
         return state
 
 
-def from_config(config):
-    config = list(utils.load_config(config))
+def all_from_config(config):
+    configs = list(serialization.load_config(config))
+    for config, _ in configs:
+        sim = Simulation(**config)
+        yield sim
+
+
+def from_config(conf_or_path):
+    config = list(serialization.load_config(conf_or_path))
     if len(config) > 1:
         raise AttributeError('Provide only one configuration')
     config = config[0][0]
@@ -270,21 +293,14 @@ def from_config(config):
     return sim
 
 
-def run_from_config(*configs, results_dir='soil_output', dump=None, timestamp=False,  **kwargs):
+def run_from_config(*configs, **kwargs):
     for config_def in configs:
         # logger.info("Found {} config(s)".format(len(ls)))
-        for config, _ in utils.load_config(config_def):
+        for config, path in serialization.load_config(config_def):
             name = config.get('name', 'unnamed')
             logger.info("Using config(s): {name}".format(name=name))
 
-            if timestamp:
-                sim_folder = '{}_{}'.format(name,
-                                            time.strftime("%Y-%m-%d_%H:%M:%S"))
-            else:
-                sim_folder = name
-            dir_path = os.path.join(results_dir, sim_folder)
-            if dump is not None:
-                config['dump'] = dump
-            sim = Simulation(dir_path=dir_path, **config)
-            logger.info('Dumping results to {} : {}'.format(sim.dir_path, sim.dump))
+            dir_path = config.pop('dir_path', os.path.dirname(path))
+            sim = Simulation(dir_path=dir_path,
+                             **config)
             sim.run_simulation(**kwargs)

soil/utils.py

@@ -1,72 +1,13 @@
-import os
-import ast
-import sys
-import yaml
 import logging
-import importlib
 import time
-from glob import glob
-from random import random
-from copy import deepcopy
-
-import networkx as nx
+import os
 
 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):
-            path = os.path.join(dir_path, path)
-        extension = os.path.splitext(path)[1][1:]
-        kwargs = {}
-        if extension == 'gexf':
-            kwargs['version'] = '1.2draft'
-            kwargs['node_type'] = int
-        try:
-            method = getattr(nx.readwrite, 'read_' + extension)
-        except AttributeError:
-            raise AttributeError('Unknown format')
-        return method(path, **kwargs)
-
-    net_args = network_params.copy()
-    net_gen = net_args.pop('generator')
-
-    if dir_path not in sys.path:
-        sys.path.append(dir_path)
-
-    method = deserializer(net_gen,
-                          known_modules=['networkx.generators',])
-
-    return method(**net_args)
-
-
-def load_file(infile):
-    with open(infile, 'r') as f:
-        return list(yaml.load_all(f))
-
-
-def load_files(*patterns):
-    for pattern in patterns:
-        for i in glob(pattern):
-            for config in load_file(i):
-                yield config, os.path.abspath(i)
-
-
-def load_config(config):
-    if isinstance(config, dict):
-        yield config, None
-    else:
-        yield from load_files(config)
-
-
 @contextmanager
 def timer(name='task', pre="", function=logger.info, to_object=None):
     start = time.time()
@@ -82,81 +23,15 @@ def timer(name='task', pre="", function=logger.info, to_object=None):
         to_object.end = end
 
 
-builtins = importlib.import_module('builtins')
-
-def name(value, known_modules=[]):
-    '''Return a name that can be imported, to serialize/deserialize an object'''
-    if value is None:
-        return 'None'
-    if not isinstance(value, type):  # Get the class name first
-        value = type(value)
-    tname = value.__name__
-    if hasattr(builtins, tname):
-        return tname
-    modname = value.__module__
-    if modname == '__main__':
-        return tname
-    if known_modules and modname in known_modules:
-        return tname
-    for kmod in known_modules:
-        if not kmod:
-            continue
-        module = importlib.import_module(kmod)
-        if hasattr(module, tname):
-            return tname
-    return '{}.{}'.format(modname, tname)
+def safe_open(path, *args, **kwargs):
+    outdir = os.path.dirname(path)
+    if outdir and not os.path.exists(outdir):
+        os.makedirs(outdir)
+    return open(path, *args, **kwargs)
 
 
-def serializer(type_):
-    if type_ != 'str' and hasattr(builtins, type_):
-        return repr
-    return lambda x: x
-
-
-def serialize(v, known_modules=[]):
-    '''Get a text representation of an object.'''
-    tname = name(v, known_modules=known_modules)
-    func = serializer(tname)
-    return func(v), tname
-
-def deserializer(type_, known_modules=[]):
-    if type(type_) != str:  # Already deserialized
-        return type_
-    if type_ == 'str':
-        return lambda x='': x
-    if type_ == 'None':
-        return lambda x=None: None
-    if hasattr(builtins, type_):  # Check if it's a builtin type
-        cls = getattr(builtins, type_)
-        return lambda x=None: ast.literal_eval(x) if x is not None else cls()
-    # Otherwise, see if we can find the module and the class
-    modules = known_modules or []
-    options = []
-
-    for mod in modules:
-        if mod:
-            options.append((mod, type_))
-
-    if '.' in type_:  # Fully qualified module
-        module, type_ = type_.rsplit(".", 1)
-        options.append ((module, type_))
-
-    errors = []
-    for modname, tname in options:
-        try:
-            module = importlib.import_module(modname)
-            cls = getattr(module, tname)
-            return getattr(cls, 'deserialize', cls)
-        except (ModuleNotFoundError, AttributeError) as ex:
-            errors.append((modname, tname, ex))
-    raise Exception('Could not find type {}. Tried: {}'.format(type_, errors))
-
-
-def deserialize(type_, value=None, **kwargs):
-    '''Get an object from a text representation'''
-    if not isinstance(type_, str):
-        return type_
-    des = deserializer(type_, **kwargs)
-    if value is None:
-        return des
-    return des(value)
+def open_or_reuse(f, *args, **kwargs):
+    try:
+        return safe_open(f, *args, **kwargs)
+    except TypeError:
+        return f

soil/web/__init__.py

@@ -180,7 +180,7 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
         with self.logging(self.simulation_name):
             try:
                 config = dict(**self.config)
-                config['dir_path'] = os.path.join(self.application.dir_path, config['name'])
+                config['outdir'] = os.path.join(self.application.outdir, config['name'])
                 config['dump'] = self.application.dump
                 self.trials = yield self.nonblocking(config)
 
@@ -232,12 +232,12 @@ class ModularServer(tornado.web.Application):
     settings = {'debug': True,
                 'template_path': ROOT + '/templates'}
 
-    def __init__(self, dump=False, dir_path='output', name='SOIL', verbose=True, *args, **kwargs):
+    def __init__(self, dump=False, outdir='output', name='SOIL', verbose=True, *args, **kwargs):
         
         self.verbose = verbose
         self.name = name
         self.dump = dump
-        self.dir_path = dir_path
+        self.outdir = outdir
 
         # Initializing the application itself:
         super().__init__(self.handlers, **self.settings)

tests/test_analysis.py

@@ -39,7 +39,6 @@ class TestAnalysis(TestCase):
         agent should be able to update its state."""
         config = {
             'name': 'analysis',
-            'dry_run': True,
             'seed': 'seed',
             'network_params': {
                 'generator': 'complete_graph',
@@ -53,7 +52,7 @@ class TestAnalysis(TestCase):
             }
         }
         s = simulation.from_config(config)
-        self.env = s.run_simulation()[0]
+        self.env = s.run_simulation(dry_run=True)[0]
 
     def test_saved(self):
         env = self.env
@@ -65,7 +64,7 @@ class TestAnalysis(TestCase):
 
     def test_count(self):
         env = self.env
-        df = analysis.read_sql(env._history._db)
+        df = analysis.read_sql(env._history.db_path)
         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

tests/test_examples.py

@@ -2,7 +2,7 @@ from unittest import TestCase
 import os
 from os.path import join
 
-from soil import utils, simulation
+from soil import serialization, simulation
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
 EXAMPLES = join(ROOT, '..', 'examples')
@@ -17,31 +17,32 @@ class TestExamples(TestCase):
 def make_example_test(path, config):
     def wrapped(self):
         root = os.getcwd()
-        os.chdir(os.path.dirname(path))
-        s = simulation.from_config(config)
-        iterations = s.max_time * s.num_trials
-        if iterations > 1000:
-            s.max_time = 100
-            s.num_trials = 1
-        if config.get('skip_test', False) and not FORCE_TESTS:
-            self.skipTest('Example ignored.')
-        envs = s.run_simulation(dry_run=True)
-        assert envs
-        for env in envs:
-            assert env
-            try:
-                n = config['network_params']['n']
-                assert len(list(env.network_agents)) == n
-                assert env.now > 2  # It has run
-                assert env.now <= config['max_time']  # But not further than allowed
-            except KeyError:
-                pass
-        os.chdir(root)
+        for s in simulation.all_from_config(path):
+            iterations = s.max_time * s.num_trials
+            if iterations > 1000:
+                s.max_time = 100
+                s.num_trials = 1
+            if config.get('skip_test', False) and not FORCE_TESTS:
+                self.skipTest('Example ignored.')
+            envs = s.run_simulation(dry_run=True)
+            assert envs
+            for env in envs:
+                assert env
+                try:
+                    n = config['network_params']['n']
+                    assert len(list(env.network_agents)) == n
+                    assert env.now > 2  # It has run
+                    assert env.now <= config['max_time']  # But not further than allowed
+                except KeyError:
+                    pass
     return wrapped
 
 
 def add_example_tests():
-    for config, path in utils.load_config(join(EXAMPLES, '**', '*.yml')):
+    for config, path in serialization.load_files(
+            join(EXAMPLES, '*', '*.yml'),
+            join(EXAMPLES, '*.yml'),
+    ):
         p = make_example_test(path=path, config=config)
         fname = os.path.basename(path)
         p.__name__ = 'test_example_file_%s' % fname

tests/test_exporters.py

@@ -0,0 +1,110 @@
+import os
+import io
+import tempfile
+import shutil
+from time import time
+
+from unittest import TestCase
+from soil import exporters
+from soil.utils import safe_open
+from soil import simulation
+
+
+class Dummy(exporters.Exporter):
+    started = False
+    trials = 0
+    ended = False
+    total_time = 0
+
+    def start(self):
+        self.__class__.started = True
+
+    def trial_end(self, env):
+        assert env
+        self.__class__.trials += 1
+        self.__class__.total_time += env.now
+
+    def end(self):
+        self.__class__.ended = True
+
+
+class Exporters(TestCase):
+    def test_basic(self):
+        config = {
+            'name': 'exporter_sim',
+            'network_params': {},
+            'agent_type': 'CounterModel',
+            'max_time': 2,
+            'num_trials': 5,
+            'environment_params': {}
+        }
+        s = simulation.from_config(config)
+        s.run_simulation(exporters=[Dummy], dry_run=True)
+        assert Dummy.started
+        assert Dummy.ended
+        assert Dummy.trials == 5
+        assert Dummy.total_time == 2*5
+
+    def test_distribution(self):
+        '''The distribution exporter should write the number of agents in each state'''
+        config = {
+            'name': 'exporter_sim',
+            'network_params': {
+                'generator': 'complete_graph',
+                'n': 4
+            },
+            'agent_type': 'CounterModel',
+            'max_time': 2,
+            'num_trials': 5,
+            'environment_params': {}
+        }
+        output = io.StringIO()
+        s = simulation.from_config(config)
+        s.run_simulation(exporters=[exporters.Distribution], dry_run=True, exporter_params={'copy_to': output})
+        result = output.getvalue()
+        assert 'count' in result
+        assert 'SEED,Noneexporter_sim_trial_3,1,,1,1,1,1' in result
+
+    def test_writing(self):
+        '''Try to write CSV, GEXF, sqlite and YAML (without dry_run)'''
+        n_trials = 5
+        config = {
+            'name': 'exporter_sim',
+            'network_params': {
+                'generator': 'complete_graph',
+                'n': 4
+            },
+            'agent_type': 'CounterModel',
+            'max_time': 2,
+            'num_trials': n_trials,
+            'environment_params': {}
+        }
+        output = io.StringIO()
+        s = simulation.from_config(config)
+        tmpdir = tempfile.mkdtemp()
+        envs = s.run_simulation(exporters=[
+            exporters.Default,
+            exporters.CSV,
+            exporters.Gexf,
+            exporters.Distribution,
+        ],
+                                outdir=tmpdir,
+                                exporter_params={'copy_to': output})
+        result = output.getvalue()
+
+        simdir = os.path.join(tmpdir, s.group or '', s.name)
+        with open(os.path.join(simdir, '{}.dumped.yml'.format(s.name))) as f:
+            result = f.read()
+            assert result
+
+        try:
+            for e in envs:
+                with open(os.path.join(simdir, '{}.gexf'.format(e.name))) as f:
+                    result = f.read()
+                    assert result
+
+                with open(os.path.join(simdir, '{}.csv'.format(e.name))) as f:
+                    result = f.read()
+                    assert result
+        finally:
+            shutil.rmtree(tmpdir)

tests/test_main.py

@@ -1,13 +1,15 @@
 from unittest import TestCase
 
 import os
+import io
 import yaml
 import pickle
 import networkx as nx
 from functools import partial
 
 from os.path import join
-from soil import simulation, Environment, agents, utils, history
+from soil import (simulation, Environment, agents, serialization,
+                  history, utils)
 
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -27,22 +29,20 @@ class TestMain(TestCase):
         Raise an exception otherwise.
         """
         config = {
-            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             }
         }
-        G = utils.load_network(config['network_params'])
+        G = serialization.load_network(config['network_params'])
         assert G
         assert len(G) == 2
         with self.assertRaises(AttributeError):
             config = {
-            'dry_run': True,
                 'network_params': {
                     'path': join(ROOT, 'unknown.extension')
                 }
             }
-            G = utils.load_network(config['network_params'])
+            G = serialization.load_network(config['network_params'])
             print(G)
 
     def test_generate_barabasi(self):
@@ -51,22 +51,20 @@ class TestMain(TestCase):
         should be used to generate a network
         """
         config = {
-            'dry_run': True,
             'network_params': {
                 'generator': 'barabasi_albert_graph'
             }
         }
         with self.assertRaises(TypeError):
-            G = utils.load_network(config['network_params'])
+            G = serialization.load_network(config['network_params'])
         config['network_params']['n'] = 100
         config['network_params']['m'] = 10
-        G = utils.load_network(config['network_params'])
+        G = serialization.load_network(config['network_params'])
         assert len(G) == 100
 
     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')
             },
@@ -83,7 +81,6 @@ class TestMain(TestCase):
         agent should be able to update its state."""
         config = {
             'name': 'CounterAgent',
-            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -107,7 +104,6 @@ class TestMain(TestCase):
         """
         config = {
             'name': 'CounterAgent',
-            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -133,7 +129,6 @@ class TestMain(TestCase):
     def test_custom_agent(self):
         """Allow for search of neighbors with a certain state_id"""
         config = {
-            'dry_run': True,
             'network_params': {
                 'path': join(ROOT, 'test.gexf')
             },
@@ -153,12 +148,11 @@ class TestMain(TestCase):
 
     def test_torvalds_example(self):
         """A complete example from a documentation should work."""
-        config = utils.load_file(join(EXAMPLES, 'torvalds.yml'))[0]
+        config = serialization.load_file(join(EXAMPLES, 'torvalds.yml'))[0]
         config['network_params']['path'] = join(EXAMPLES,
                                                 config['network_params']['path'])
         s = simulation.from_config(config)
-        s.dry_run = True
-        env = s.run_simulation()[0]
+        env = s.run_simulation(dry_run=True)[0]
         for a in env.network_agents:
             skill_level = a.state['skill_level']
             if a.id == 'Torvalds':
@@ -180,9 +174,8 @@ class TestMain(TestCase):
         should be equivalent to the configuration file used
         """
         with utils.timer('loading'):
-            config = utils.load_file(join(EXAMPLES, 'complete.yml'))[0]
+            config = serialization.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'):
@@ -196,9 +189,8 @@ class TestMain(TestCase):
         The configuration should not change after running
          the simulation.
         """
-        config = utils.load_file(join(EXAMPLES, 'complete.yml'))[0]
+        config = serialization.load_file(join(EXAMPLES, 'complete.yml'))[0]
         s = simulation.from_config(config)
-        s.dry_run = True
         for i in range(5):
             s.run_simulation(dry_run=True)
             nconfig = s.to_dict()
@@ -206,7 +198,7 @@ class TestMain(TestCase):
             assert config == nconfig
 
     def test_row_conversion(self):
-        env = Environment(dry_run=True)
+        env = Environment()
         env['test'] = 'test_value'
 
         res = list(env.history_to_tuples())
@@ -225,8 +217,9 @@ class TestMain(TestCase):
         from geometric models. We should work around it.
         """
         G = nx.random_geometric_graph(20, 0.1)
-        env = Environment(topology=G, dry_run=True)
-        env.dump_gexf('/tmp/dump-gexf')
+        env = Environment(topology=G)
+        f = io.BytesIO()
+        env.dump_gexf(f)
 
     def test_save_graph(self):
         '''
@@ -236,7 +229,7 @@ class TestMain(TestCase):
         '''
         G = nx.cycle_graph(5)
         distribution = agents.calculate_distribution(None, agents.BaseAgent)
-        env = Environment(topology=G, network_agents=distribution, dry_run=True)
+        env = Environment(topology=G, network_agents=distribution)
         env[0, 0, 'testvalue'] = 'start'
         env[0, 10, 'testvalue'] = 'finish'
         nG = env.history_to_graph()
@@ -245,11 +238,11 @@ class TestMain(TestCase):
         assert ('finish', 10, None) in values
 
     def test_serialize_class(self):
-        ser, name = utils.serialize(agents.BaseAgent)
+        ser, name = serialization.serialize(agents.BaseAgent)
         assert name == 'soil.agents.BaseAgent'
         assert ser == agents.BaseAgent
 
-        ser, name = utils.serialize(CustomAgent)
+        ser, name = serialization.serialize(CustomAgent)
         assert name == 'test_main.CustomAgent'
         assert ser == CustomAgent
         pickle.dumps(ser)
@@ -257,9 +250,9 @@ class TestMain(TestCase):
     def test_serialize_builtin_types(self):
 
         for i in [1, None, True, False, {}, [], list(), dict()]:
-            ser, name = utils.serialize(i)
+            ser, name = serialization.serialize(i)
             assert type(ser) == str
-            des = utils.deserialize(name, ser)
+            des = serialization.deserialize(name, ser)
             assert i == des
 
     def test_serialize_agent_type(self):
@@ -312,8 +305,9 @@ class TestMain(TestCase):
         recovered = pickle.loads(pickled)
 
         assert recovered.env.name == 'Test'
-        assert recovered['key'] == 'test'
+        assert list(recovered.env._history.to_tuples())
         assert recovered['key', 0] == 'test'
+        assert recovered['key'] == 'test'
 
     def test_history(self):
         '''Test storing in and retrieving from history (sqlite)'''
@@ -336,3 +330,10 @@ class TestMain(TestCase):
         assert len(a3.subgraph(limit_neighbors=True)) == 1
         assert len(a3.subgraph(limit_neighbors=True, center=False)) == 0
         assert len(a3.subgraph(agent_type=agents.NetworkAgent)) == 3
+
+    def test_templates(self):
+        '''Loading a template should result in several configs'''
+        configs = serialization.load_file(join(EXAMPLES, 'template.yml'))
+        assert len(configs) > 0
+
+