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