def check_dependencies():
try:
import nose
logger.debug("\tNose: %s\n" % str(nose.__version__))
except ImportError:
raise ImportError("Nose cannot be imported. Are you sure it's "
"installed?")
try:
import networkx
logger.debug("\tnetworkx: %s\n" % str(networkx.__version__))
except ImportError:
raise ImportError("Networkx cannot be imported. Are you sure it's "
"installed?")
try:
import pymongo
logger.debug("\tpymongo: %s\n" % str(pymongo.version))
from bson.objectid import ObjectId
except ImportError:
raise ImportError("Pymongo cannot be imported. Are you sure it's"
" installed?")
try:
import numpy
logger.debug("\tnumpy: %s" % str(numpy.__version__))
except ImportError:
raise ImportError("Numpy cannot be imported. Are you sure that it's"
" installed?")
try:
import scipy
logger.debug("\tscipy: %s" % str(scipy.__version__))
except ImportError:
raise ImportError("Scipy cannot be imported. Are you sure that it's"
" installed?")
python类__version__()的实例源码
def check_dependencies():
try:
import nose
logger.debug("\tNose: %s\n" % str(nose.__version__))
except ImportError:
raise ImportError("Nose cannot be imported. Are you sure it's "
"installed?")
try:
import networkx
logger.debug("\tnetworkx: %s\n" % str(networkx.__version__))
except ImportError:
raise ImportError("Networkx cannot be imported. Are you sure it's "
"installed?")
try:
import pymongo
logger.debug("\tpymongo: %s\n" % str(pymongo.version))
from bson.objectid import ObjectId
except ImportError:
raise ImportError("Pymongo cannot be imported. Are you sure it's"
" installed?")
try:
import numpy
logger.debug("\tnumpy: %s" % str(numpy.__version__))
except ImportError:
raise ImportError("Numpy cannot be imported. Are you sure that it's"
" installed?")
try:
import scipy
logger.debug("\tscipy: %s" % str(scipy.__version__))
except ImportError:
raise ImportError("Scipy cannot be imported. Are you sure that it's"
" installed?")
def check_dependencies():
try:
import nose
logger.debug("\tNose: %s\n" % str(nose.__version__))
except ImportError:
raise ImportError("Nose cannot be imported. Are you sure it's "
"installed?")
try:
import networkx
logger.debug("\tnetworkx: %s\n" % str(networkx.__version__))
except ImportError:
raise ImportError("Networkx cannot be imported. Are you sure it's "
"installed?")
try:
import pymongo
logger.debug("\tpymongo: %s\n" % str(pymongo.version))
from bson.objectid import ObjectId
except ImportError:
raise ImportError("Pymongo cannot be imported. Are you sure it's"
" installed?")
try:
import numpy
logger.debug("\tnumpy: %s" % str(numpy.__version__))
except ImportError:
raise ImportError("Numpy cannot be imported. Are you sure that it's"
" installed?")
try:
import scipy
logger.debug("\tscipy: %s" % str(scipy.__version__))
except ImportError:
raise ImportError("Scipy cannot be imported. Are you sure that it's"
" installed?")
def __loadGMLFiles__(self):
"""
Iterates through all of the files inside of support directory
merges these graphs with the whole gapGraph
creates a dictionary of {"readName":[gapName or nodeName,...] }
"""
self.readSupport = defaultdict(list)
for i in glob.glob(os.path.join(self.protocol.outDir,"support","*.gml")):
truncNxVer = float('.'.join(networkx.__version__.split('.')[:2]))
if truncNxVer >= 1.7:
try:
inputGml = networkx.read_gml(i, relabel=True)
except ValueError:
logging.warning("GML file %s is empty" % i)
continue
elif truncNxVer == 1.1:
inputGml = networkx.read_gml(i)
else:
logging.warning("It is unknown if networkx version %s will work." % networkx.__version__)
logging.warning("If you get an error here, please report it!!!")
inputGml = networkx.read_gml(i)
for node in inputGml.nodes_iter():
for readName in inputGml.node[node]['extenders'].split(':'):
if readName == '':
continue
trimInfo = self.__cleanReadName__(readName)
self.gapGraph.add_extend(node, trimInfo.name)
self.readSupport[trimInfo.name].append((node, trimInfo))
for source, target, evidence in inputGml.edges_iter(data=True):
for readName in evidence['evidence'].split(':'):
if readName == '':
continue
trimInfo = self.__cleanReadName__(readName)
self.gapGraph.add_evidence(source, target, trimInfo.name)
self.readSupport[trimInfo.name].append((source, target, trimInfo))
self.readSupport = dict(self.readSupport)
def __loadGMLFiles__(self):
"""
Iterates through all of the files inside of support directory
merges these graphs with the whole gapGraph
creates a dictionary of {"readName":[gapName or nodeName,...] }
"""
self.readSupport = defaultdict(list)
for i in glob.glob(os.path.join(self.protocol.outDir,"support","*.gml")):
truncNxVer = float('.'.join(networkx.__version__.split('.')[:2]))
if truncNxVer >= 1.7:
try:
inputGml = networkx.read_gml(i, relabel=True)
except ValueError:
logging.warning("GML file %s is empty" % i)
continue
elif truncNxVer == 1.1:
inputGml = networkx.read_gml(i)
else:
logging.warning("It is unknown if networkx version %s will work." % networkx.__version__)
logging.warning("If you get an error here, please report it!!!")
inputGml = networkx.read_gml(i)
for node in inputGml.nodes_iter():
for readName in inputGml.node[node]['extenders'].split(':'):
if readName == '':
continue
trimInfo = self.__cleanReadName__(readName)
self.gapGraph.add_extend(node, trimInfo.name)
self.readSupport[trimInfo.name].append((node, trimInfo))
for source, target, evidence in inputGml.edges_iter(data=True):
for readName in evidence['evidence'].split(':'):
if readName == '':
continue
trimInfo = self.__cleanReadName__(readName)
self.gapGraph.add_evidence(source, target, trimInfo.name)
self.readSupport[trimInfo.name].append((source, target, trimInfo))
self.readSupport = dict(self.readSupport)
def loadParameters(self):
print("NetworkX version %s running" % nx.__version__)
print("Matplotlib version %s running\n" % mplt.__version__)
nxv = nx.__version__
vOK = checkVersion(nxv, 'NetworkX', 1, 9, 1)
if not vOK:
print("NetworkX 1.9.1 or greater required")
os.sys.exit(1)
mpltv = mplt.__version__
vOK = checkVersion(mpltv, 'Matplotlib', 1, 5, 1)
if not vOK:
print("Matplotlib 1.5.1 or greater required")
os.sys.exit(1)
mySeed = eval(input("random number seed (1 to get it from the clock) "))
if mySeed == 1:
random.seed()
else:
random.seed(mySeed)
self.nAgents = 0
print("No 'bland' agents")
#self.worldXSize= input("X size of the world? ")
self.worldXSize = 1
print("X size of the world not relevant")
#self.worldYSize= input("Y size of the world? ")
self.worldYSize = 50
print("y size of the world not relevant")
# recipes
common.maxLenght = 10
common.maxSector = 6
print(
"recipes: max lenght",
common.maxLenght,
"and max sector number",
common.maxSector)
self.nCycles = eval(input("How many cycles? (0 = exit) "))
v = input("verbose? (y/[n]) ")
if v == "y" or v == "Y":
common.verbose = True # predefined False
