WIP: exporters

CHANGELOG.md

@@ -3,6 +3,19 @@ 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.
+
+### Changed
+* `dir_path` is now the directory for resources (modules, files), and the output dir has been renamed to `outdir`
+
+## 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
+
 ## [0.13.8]
 ### Changed
 * Moved TerroristNetworkModel to examples

examples/complete.yml

@@ -1,5 +1,6 @@
 ---
 name: simple
+group: tests
 dir_path: "/tmp/"
 num_trials: 3
 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
+pandas>=0.23
+scipy>=1.2
+SALib>=1.3
+Jinja2

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()
 
@@ -64,8 +66,9 @@ def main():
         simulation.run_from_config(args.file,
                                    dry_run=args.dry_run,
                                    dump=dump,
+                                   exporters=args.exporter,
                                    parallel=(not args.synchronous),
-                                   results_dir=args.output)
+                                   outdir=args.output)
     except Exception:
         if args.pdb:
             pdb.post_mortem()

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
 
 

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):
@@ -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

@@ -14,7 +14,7 @@ from networkx.readwrite import json_graph
 import networkx as nx
 import nxsim
 
-from . import utils, agents, analysis, history
+from . import serialization, agents, analysis, history
 
 # These properties will be copied when pickling/unpickling the environment
 _CONFIG_PROPS = [ 'name',
@@ -22,7 +22,7 @@ _CONFIG_PROPS = [ 'name',
                  'default_state',
                  'interval',
                  'dry_run',
-                 'dir_path',
+                 'outdir',
                  ]
 
 class Environment(nxsim.NetworkEnvironment):
@@ -44,7 +44,7 @@ class Environment(nxsim.NetworkEnvironment):
                  interval=1,
                  seed=None,
                  dry_run=False,
-                 dir_path=None,
+                 outdir=None,
                  topology=None,
                  *args, **kwargs):
         self.name = name or 'UnnamedEnvironment'
@@ -58,11 +58,11 @@ class Environment(nxsim.NetworkEnvironment):
         self._env_agents = {}
         self.dry_run = dry_run
         self.interval = interval
-        self.dir_path = dir_path or tempfile.mkdtemp('soil-env')
+        self.outdir = outdir 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,
+                                        outdir=self.outdir,
                                         backup=True)
         # Add environment agents first, so their events get
         # executed before network agents
@@ -124,7 +124,7 @@ 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)
 
@@ -169,7 +169,7 @@ class Environment(nxsim.NetworkEnvironment):
     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 +180,7 @@ 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
@@ -222,14 +222,14 @@ 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):
+    def get_path(self, outdir=None):
+        outdir = outdir or self.outdir
+        if not os.path.exists(outdir):
             try:
-                os.makedirs(dir_path)
+                os.makedirs(outdir)
             except FileExistsError:
                 pass
-        return dir_path
+        return outdir
 
     def get_agent(self, agent_id):
         return self.G.node[agent_id]['agent']
@@ -239,8 +239,8 @@ 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),
+    def dump_csv(self, outdir=None):
+        csv_name = os.path.join(self.get_path(outdir),
                                 '{}.environment.csv'.format(self.name))
 
         with open(csv_name, 'w') as f:
@@ -249,9 +249,9 @@ class Environment(nxsim.NetworkEnvironment):
             for i in self.history_to_tuples():
                 cr.writerow(i)
 
-    def dump_gexf(self, dir_path=None):
+    def dump_gexf(self, outdir=None):
         G = self.history_to_graph()
-        graph_path = os.path.join(self.get_path(dir_path),
+        graph_path = os.path.join(self.get_path(outdir),
                                   self.name+".gexf")
         # Workaround for geometric models
         # See soil/soil#4
@@ -262,7 +262,7 @@ class Environment(nxsim.NetworkEnvironment):
 
         nx.write_gexf(G, graph_path, version="1.2draft")
 
-    def dump(self, dir_path=None, formats=None):
+    def dump(self, outdir=None, formats=None):
         if not formats:
             return
         functions = {
@@ -271,7 +271,7 @@ class Environment(nxsim.NetworkEnvironment):
         }
         for f in formats:
             if f in functions:
-                functions[f](dir_path)
+                functions[f](outdir)
             else:
                 raise ValueError('Unknown format: {}'.format(f))
 
@@ -356,7 +356,7 @@ 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 +1,43 @@
+from .serialization import deserialize
+import os
+import time
+
+
+def for_sim(simulation, names, dir_path=None):
+    exporters = []
+    for name in names:
+        mod = deserialize(name, known_modules=['soil.exporters'])
+        exporters.append(mod(simulation))
+    return exporters
+
+
+class Base:
+
+    def __init__(self, simulation):
+        self.sim = simulation
+
+    def start(self):
+        pass
+
+    def end(self):
+        pass
+
+    def env(self):
+        pass
+
+
+class Dummy(Base):
+
+    def start(self):
+        with open(os.path.join(self.sim.outdir, 'dummy')) as f:
+            f.write('simulation started @ {}'.format(time.time()))
+
+    def env(self, env):
+        with open(os.path.join(self.sim.outdir, 'dummy-trial-{}'.format(env.name))) as f:
+            for i in env.history_to_tuples():
+                f.write(','.join(i))
+
+
+    def end(self):
+        with open(os.path.join(self.sim.outdir, 'dummy')) as f:
+            f.write('simulation ended @ {}'.format(time.time()))

soil/history.py

@@ -9,7 +9,7 @@ logger = logging.getLogger(__name__)
 
 from collections import UserDict, namedtuple
 
-from . import utils
+from . import serialization
 
 
 class History:
@@ -17,9 +17,9 @@ class History:
     Store and retrieve values from a sqlite database.
     """
 
-    def __init__(self, db_path=None, name=None, dir_path=None, backup=False):
+    def __init__(self, db_path=None, name=None, outdir=None, backup=False):
         if db_path is None and name:
-            db_path = os.path.join(dir_path or os.getcwd(),
+            db_path = os.path.join(outdir or os.getcwd(),
                                    '{}.db.sqlite'.format(name))
         if db_path:
             if backup and os.path.exists(db_path):
@@ -94,9 +94,9 @@ 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))
@@ -135,8 +135,8 @@ 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):

soil/serialization.py

@@ -0,0 +1,199 @@
+import os
+import logging
+import ast
+import sys
+import yaml
+import importlib
+from glob import glob
+from random import random
+from copy import deepcopy
+from itertools import product, chain
+
+from jinja2 import Template
+
+import networkx as nx
+
+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(chain.from_iterable(map(expand_template, load_string(f))))
+
+def load_string(string):
+    yield from yaml.load_all(string)
+
+
+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 .serialization 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 +63,10 @@ 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...)
+    outdir : str, optional
+        Directory path to save simulation results
     seed : str, optional
         Seed to use for the random generator
     num_trials : int, optional
@@ -80,38 +85,45 @@ 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,
+                 outdir=None, 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 {}
+        if not outdir:
+            outdir = os.path.join(os.getcwd(),
+                                       'soil_output')
+        self.outdir = os.path.join(outdir,
+                                   self.group or '',
+                                   self.name)
         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 [self.outdir, 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 []
@@ -130,34 +142,51 @@ class Simulation(NetworkSimulation):
         return self.run(*args, **kwargs)
 
     def run(self, *args, **kwargs):
-        return list(self.run_simulation_gen(*args, **kwargs))
+        return list(self._run_simulation_gen(*args, **kwargs))
 
-    def run_simulation_gen(self, *args, parallel=False, dry_run=False,
-                           **kwargs):
-        p = Pool()
+    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{}'.format(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, **kwargs):
+        exporters = exporters_for_sim(self,
+                                      exporters or [])
         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)
+                logger.info('Dumping results to {}'.format(self.outdir))
+                self.dump_pickle(self.outdir)
+                self.dump_yaml(self.outdir)
             else:
                 logger.info('NOT dumping results')
+            for exporter in exporters:
+                exporter.start()
+
+            for env in self._run_sync_or_async(*args, parallel=parallel,
+                                               dry_run=dry_run, **kwargs):
+                for exporter in exporters:
+                    exporter.env(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)
+        opts = self.environment_params.copy()
+        env_name = '{}_trial_{}'.format(self.name, trial_id)
         opts.update({
             'name': env_name,
             'topology': self.topology.copy(),
@@ -169,13 +198,13 @@ class Simulation(NetworkSimulation):
             'states': self.states,
             'default_state': self.default_state,
             'environment_agents': self.environment_agents,
-            'dir_path': self.dir_path,
+            'outdir': self.outdir,
         })
         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, dry_run=False, **opts):
         """Run a single trial of the simulation
 
         Parameters
@@ -183,16 +212,16 @@ 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)
+        dry_run = self.dry_run or dry_run
         # 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:
+        if self.dump and not 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.
@@ -211,22 +240,22 @@ 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)
+    def dump_yaml(self, outdir = None, file_name = None):
+        outdir = outdir or self.outdir
+        if not os.path.exists(outdir):
+            os.makedirs(outdir)
         if not file_name:
-            file_name=os.path.join(dir_path,
+            file_name=os.path.join(outdir,
                                      '{}.dumped.yml'.format(self.name))
         with open(file_name, '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)
+    def dump_pickle(self, outdir = None, pickle_name = None):
+        outdir = outdir or self.outdir
+        if not os.path.exists(outdir):
+            os.makedirs(outdir)
         if not pickle_name:
-            pickle_name=os.path.join(dir_path,
+            pickle_name=os.path.join(outdir,
                                        '{}.simulation.pickle'.format(self.name))
         with open(pickle_name, 'wb') as f:
             pickle.dump(self, f)
@@ -235,14 +264,14 @@ class Simulation(NetworkSimulation):
         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
@@ -250,19 +279,28 @@ class Simulation(NetworkSimulation):
     def __setstate__(self, state):
         self.__dict__ = state
         self.load_module = getattr(self, 'load_module', None)
+        if self.outdir not in sys.path:
+            sys.path += [self.outdir, os.getcwd()]
         if self.dir_path not in sys.path:
             sys.path += [self.dir_path, os.getcwd()]
         self.topology = json_graph.node_link_graph(state['topology'])
         self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
         self.environment_agents = agents._convert_agent_types(self.environment_agents,
                                                               known_modules=[self.load_module])
-        self.environment_class = 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]
@@ -270,10 +308,10 @@ 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, outdir=None, dump=None, timestamp=False,  **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))
 
@@ -282,9 +320,12 @@ def run_from_config(*configs, results_dir='soil_output', dump=None, timestamp=Fa
                                             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))
+            outdir = config.pop('outdir', outdir)
+            sim = Simulation(dir_path=dir_path,
+                             outdir=outdir,
+                             **config)
+            logger.info('Dumping results to {} : {}'.format(sim.outdir, sim.dump))
             sim.run_simulation(**kwargs)

soil/utils.py

@@ -1,72 +1,12 @@
-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
 
 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()
@@ -80,83 +20,3 @@ def timer(name='task', pre="", function=logger.info, to_object=None):
     if to_object:
         to_object.start = start
         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 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/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_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_main.py

@@ -7,7 +7,8 @@ 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__))
@@ -32,7 +33,7 @@ class TestMain(TestCase):
                 '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):
@@ -42,7 +43,7 @@ class TestMain(TestCase):
                     '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):
@@ -57,10 +58,10 @@ class TestMain(TestCase):
             }
         }
         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):
@@ -153,7 +154,7 @@ 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)
@@ -180,7 +181,7 @@ 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'):
@@ -189,6 +190,7 @@ class TestMain(TestCase):
             recovered = yaml.load(serial)
         with utils.timer('deleting'):
             del recovered['topology']
+            del recovered['outdir']
         assert config == recovered
 
     def test_configuration_changes(self):
@@ -196,13 +198,14 @@ 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()
             del nconfig['topology']
+            del nconfig['outdir']
             assert config == nconfig
 
     def test_row_conversion(self):
@@ -245,11 +248,11 @@ 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 +260,9 @@ 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):
@@ -336,3 +339,10 @@ 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
+
+