Merge commit '9d7b56399ac235e1d53725c22f09c9556de0a788'

doc/workshop/ExternalModels/projectile.py

@@ -25,8 +25,10 @@
 #       (x,y) - vector positions of projectile in time
 #       t - corresponding time steps
 #
+from __future__ import division, print_function, unicode_literals, absolute_import
 import numpy as np
 
+
 def prange(v,th,y0=0,g=9.8):
   """
     Calculates the analytic range.
@@ -106,9 +108,9 @@ def run(self,Input):
 #can be used as a code as well
 if __name__=="__main__":
   import sys
-  print 'Welcome to RAVEN\'s Simple Projectile Motion Simulator!'
+  print('Welcome to RAVEN\'s Simple Projectile Motion Simulator!')
   inFile = sys.argv[sys.argv.index('-i')+1]
-  print 'Reading input from',inFile,'...'
+  print('Reading input from',inFile,'...')
   outFile = sys.argv[sys.argv.index('-o')+1]
   #construct the input
   Input = {}
@@ -125,10 +127,10 @@ class IO:
     pass
   io = IO()
   #run the code
-  print 'Simulating ...'
+  print('Simulating ...')
   run(io,Input)
   #write output
-  print 'Writing output to',outFile+'.txt','...'
+  print('Writing output to',outFile+'.txt','...')
   outFile = open(outFile+'.txt','w')
   header = ' '.join("{:8s}".format(i) for i in ('x0','y0','v0','ang','r','x','y','t'))+ '\n'
   outFile.writelines(header.strip()+'\n')
@@ -138,5 +140,5 @@ class IO:
   outFile.writelines('-'*(8*8+4)+'\n')
   outFile.writelines('SUCCESS'+'\n')
   outFile.close()
-  print 'Done!'
-  print ''
+  print('Done!')
+  print('')

framework/CodeInterfaces/MooseBasedApp/MOOSEparser.py

@@ -64,7 +64,7 @@ def __init__(self, inputFile):
         if not line.startswith(b'#'):
           ind = line.find(b'=')
           if ind != -1:
-            listLine = line.split(b'=')
+            listLine = line.split(b'=', 1)
             attribName = listLine[0].strip()
             if b'#' not in listLine[1]:
               attribValue = listLine[1].strip()

framework/CodeInterfaces/PHISICS/DecayParser.py

@@ -52,10 +52,10 @@ def matrixPrinter(self, line, outfile, atomicNumber):
     """
     line = line.upper().split()
     line[0] = re.sub(r'(.*?)(\w+)(-)(\d+M?)', r'\1\2\4', line[0])  # remove isotope dashes
-    for isotopeID in self.listedDict.iterkeys():
+    for isotopeID in self.listedDict.keys():
       if line[0] == isotopeID:
         typeOfDecayPerturbed = []
-        typeOfDecayPerturbed = self.listedDict.get(isotopeID, {}).keys()
+        typeOfDecayPerturbed = list(self.listedDict.get(isotopeID, {}).keys())
         for i in range(len(typeOfDecayPerturbed)):
           try:
             if self.isotopeClassifier.get(isotopeID) == self.isotopeParsed[0]:  # it means the isotope is an actinide
@@ -189,7 +189,7 @@ def fileReconstruction(self):
       @ Out, None
     """
     perturbedIsotopes = []
-    for key in self.pertDict.iterkeys():
+    for key in self.pertDict.keys():
       splittedDecayKeywords = key.split('|')
       perturbedIsotopes.append(splittedDecayKeywords[2])
     for i in range(len(perturbedIsotopes)):

framework/CodeInterfaces/PHISICS/MassParser.py

@@ -48,7 +48,7 @@ def matrixPrinter(self, line, outfile):
       """
       line = line.upper().split()
       line[0] = re.sub(r'(.*?)(\w+)(-)(\d+M?)', r'\1\2\4', line[0])
-      for isotopeID in self.listedDict['MASS'].iterkeys():
+      for isotopeID in self.listedDict['MASS'].keys():
         if line[0] == isotopeID:
           try:
             line[2] = str(
@@ -89,7 +89,7 @@ def fileReconstruction(self, deconstructedDict):
         perturbedIsotopes = []
         perturbedMaterials = []
         perturbedPhysicalParameters = []
-        for key in deconstructedDict.iterkeys():
+        for key in deconstructedDict.keys():
             perturbedIsotopes.append(key.split('|')[1])
             perturbedPhysicalParameters.append(key.split('|')[0])
         for i in range(len(perturbedPhysicalParameters)):

framework/CodeInterfaces/PHISICS/PhisicsInterface.py

@@ -186,7 +186,7 @@ def distributeVariablesToParsers(self, perturbedVars):
     """
     distributedPerturbedVars = {}
     pertType = []
-    for i in perturbedVars.iterkeys(
+    for i in perturbedVars.keys(
     ):  # teach what are the type of perturbation (decay FY etc...)
       splittedKeywords = i.split('|')
       pertType.append(splittedKeywords[0])
@@ -485,7 +485,7 @@ def createNewInput(self, currentInputFiles, oriInputFiles, samplerType,
       self.numberOfMPI = 1
     else:
       self.numberOfMPI = self.getNumberOfMpi(Kwargs['precommand'])
-    for perturbedParam in self.distributedPerturbedVars.iterkeys():
+    for perturbedParam in self.distributedPerturbedVars.keys():
       if perturbedParam == 'DECAY':
         DecayParser.DecayParser(
             currentInputFiles[self.typeDict['decay']].getAbsFile(),

framework/CodeInterfaces/PHISICS/phisicsdata.py

@@ -362,7 +362,7 @@ def getMrtauIsotopeList(self, atomsInp):
           line = re.sub(r'TIME\s+\(days\)', r'', line)
           line = re.sub(r' ', r'', line)
           line = re.sub(r'\n', r'', line)
-          self.isotopeListMrtau = filter(None, line.split(','))
+          self.isotopeListMrtau = list(filter(None, line.split(',')))
           break
 
   def getInstantTimeSteps(self, input):
@@ -826,7 +826,7 @@ def locateMaterialInFile(self, numberOfMPI):
           for line in outfile:
             if re.search(r'Density spatial moment', line):
               count = count + 1
-              matLine = filter(None, line.split(' '))
+              matLine = list(filter(None, line.split(' ')))
               materialsDict['MPI-' + str(mpi)][count] = matLine[
                   matLine.index('Material') + 1]
               if count == mediaUsed:
@@ -870,7 +870,7 @@ def getDecayHeat(self, timeStepIndex, matchedTimeSteps, decayHeatFlag):
               breakFlag = 1
             if decayFlag == 1 and breakFlag == 0:
               line = line.rstrip()
-              decayLine = filter(None, line.split(' '))
+              decayLine = list(filter(None, line.split(' ')))
               if decayLine != []:
                 stringIsFloatNumber = self.isFloatNumber(decayLine)
               if stringIsFloatNumber and decayLine != []:
@@ -910,7 +910,7 @@ def getDecayHeatMrtau(self, timeStepIndex, matchedTimeSteps,
           breakFlag = 1
         if decayFlag == 1 and breakFlag == 0:
           line = line.rstrip()
-          decayLine = filter(None, line.split(' '))
+          decayLine = list(filter(None, line.split(' ')))
           if decayLine != []:
             stringIsFloatNumber = self.isFloatNumber(decayLine)
           if stringIsFloatNumber and decayLine != []:
@@ -952,7 +952,7 @@ def getBurnUp(self, timeStepIndex, matchedTimeSteps):
             breakFlag = 1
           if buFlag == 1 and breakFlag == 0:
             line = line.rstrip()
-            buLine = filter(None, line.split(' '))
+            buLine = list(filter(None, line.split(' ')))
             if buLine != []:
               stringIsFloatNumber = self.isFloatNumber(buLine)
             if stringIsFloatNumber and buLine != []:
@@ -1062,8 +1062,8 @@ def writeMrtauCSV(self, mrtauDict):
     with open(csvOutput, 'a+') as f:
       mrtauWriter = csv.writer(
           f,
-          delimiter=str(u',').encode('utf-8'),
-          quotechar=str(u',').encode('utf-8'),
+          delimiter=str(','),
+          quotechar=str(','),
           quoting=csv.QUOTE_MINIMAL)
       if mrtauDict.get('timeStepIndex') == 0:
         mrtauWriter.writerow(['timeMrTau'] + self.numDensityLabelListMrtau +

framework/CodeInterfaces/RELAP5/relapdata.py

@@ -244,13 +244,13 @@ def writeCSV(self,filen):
     if len(self.ravenData) > 0:
       IOcsvfile.write(',')
     for j in range(len(self.ravenData.keys())):
-      IOcsvfile.write('%s' %(self.ravenData.keys()[j]))
+      IOcsvfile.write('%s' %(list(self.ravenData.keys())[j]))
       if j+1<len(self.ravenData.keys()): IOcsvfile.write(',')
     IOcsvfile.write('\n')
     for i in range(len(self.minordata.get(list(self.minordata.keys())[0]))):
-      IOcsvfile.write(','.join(self.minordata.get(self.minordata.keys()[j])[i] for j in range(len(self.minordata.keys()))))
+      IOcsvfile.write(','.join(self.minordata.get(list(self.minordata.keys())[j])[i] for j in range(len(self.minordata.keys()))))
       if len(self.ravenData)>0:
         IOcsvfile.write(',')
-      IOcsvfile.write(','.join(self.ravenData[self.ravenData.keys()[k]] for k in range(len(self.ravenData.keys()))))
+      IOcsvfile.write(','.join(self.ravenData[list(self.ravenData.keys())[k]] for k in range(len(self.ravenData.keys()))))
       IOcsvfile.write('\n')
     IOcsvfile.close()

framework/CrossValidations/SklCrossValidation.py

@@ -76,7 +76,10 @@ def __init__(self, messageHandler, **kwargs):
 
     self.__class__.returnType = self.__class__.availImpl[self.SKLType][1]
 
-    for key, value in self.initOptionDict.items():
+    #Need to keep a copy of the keys since the dict is changing
+    keys = list(self.initOptionDict.keys())
+    for key in keys:
+      value = self.initOptionDict[key]
       try:
         newValue = ast.literal_eval(value)
         if type(newValue) == list:

framework/GridEntities.py

@@ -420,6 +420,8 @@ def initialize(self,initDictionary=None):
       self.gridContainer['transformationMethods'] = initDict["transformationMethods"]
     self.nVar                            = len(self.gridInitDict["dimensionNames"]) if "dimensionNames" in self.gridInitDict.keys() else len(initDict["dimensionNames"])
     self.gridContainer['dimensionNames'] = self.gridInitDict["dimensionNames"] if "dimensionNames" in self.gridInitDict.keys() else initDict["dimensionNames"]
+    #expand iterator with list()
+    self.gridContainer['dimensionNames'] = list(self.gridContainer['dimensionNames'])
     upperkeys                            = list(self.gridInitDict["upperBounds"].keys() if "upperBounds" in self.gridInitDict.keys() else initDict["upperBounds"  ].keys())
     lowerkeys                            = list(self.gridInitDict["lowerBounds"].keys() if "lowerBounds" in self.gridInitDict.keys() else initDict["lowerBounds"  ].keys())
     self.gridContainer['dimensionNames'].sort()

framework/Metrics/MetricUtilities.py

@@ -70,7 +70,7 @@ def _getPDFandCDFfromWeightedData(data, weights, numBins, uniformBins, interpola
     @ Out, (dataStats, cdfFunc, pdfFunc), tuple, dataStats is dictionary with things like "mean" and "stdev", cdfFunction is a function that returns the CDF value and pdfFunc is a function that returns the PDF value.
   """
   # Sort the data
-  sortedData = zip(data, weights)
+  sortedData = list(zip(data, weights))
   sortedData.sort() #Sort the data.
   weightSum = sum(weights)
   value = 0 #Read only

framework/Models/HybridModel.py

@@ -27,6 +27,7 @@
 import numpy as np
 from numpy import linalg
 import time
+import itertools
 from collections import OrderedDict
 #External Modules End--------------------------------------------------------------------------------
 
@@ -609,7 +610,7 @@ def evaluateSample(self, myInput, samplerType, kwargs):
       @ Out, rlz, dict, This holds the output information of the evaluated sample.
     """
     self.raiseADebug("Evaluate Sample")
-    kwargsKeys = kwargs.keys()
+    kwargsKeys = list(kwargs.keys())
     kwargsKeys.pop(kwargsKeys.index("jobHandler"))
     kwargsToKeep = {keepKey: kwargs[keepKey] for keepKey in kwargsKeys}
     jobHandler = kwargs['jobHandler']
@@ -619,7 +620,7 @@ def evaluateSample(self, myInput, samplerType, kwargs):
     # assure rlz has all metadata
     rlz = dict((var,np.atleast_1d(kwargsToKeep[var])) for var in kwargsToKeep.keys())
     # update rlz with input space from inRun and output space from result
-    rlz.update(dict((var,np.atleast_1d(kwargsToKeep['SampledVars'][var] if var in kwargs['SampledVars'] else result[var])) for var in set(result.keys()+kwargsToKeep['SampledVars'].keys())))
+    rlz.update(dict((var,np.atleast_1d(kwargsToKeep['SampledVars'][var] if var in kwargs['SampledVars'] else result[var])) for var in set(itertools.chain(result.keys(),kwargsToKeep['SampledVars'].keys()))))
 
     return rlz
 

framework/PostProcessorFunctions/TypicalHistoryFromHistorySet.py

@@ -57,7 +57,7 @@ def readMoreXML(self,xmlNode):
     self.name = xmlNode.attrib['name']
     for child in xmlNode:
       if child.tag == 'subseqLen':
-        self.subseqLen = map(int, child.text.split(','))
+        self.subseqLen = list(map(int, child.text.split(',')))
       elif child.tag == 'pivotParameter':
         self.pivotParameter = child.text
       elif child.tag == 'outputLen':

framework/PostProcessors/CrossValidation.py

@@ -122,7 +122,7 @@ def initialize(self, runInfo, inputs, initDict=None) :
       if metricIn[2] in self.metricsDict.keys():
         self.metricsDict[metricIn[2]] = metricIn[3]
 
-    if self.metricsDict.values().count(None) != 0:
+    if list(self.metricsDict.values()).count(None) != 0:
       metricName = self.metricsDict.keys()[list(self.metricsDict.values()).index(None)]
       self.raiseAnError(IOError, "Missing definition for Metric: ", metricName)
 

framework/PostProcessors/DataClassifier.py

@@ -28,7 +28,7 @@
 
 #Internal Modules---------------------------------------------------------------
 from BaseClasses import BaseType
-from utils import InputData
+from utils import InputData, utils
 from .PostProcessor import PostProcessor
 import MessageHandler
 import Files
@@ -232,7 +232,7 @@ def run(self, inputIn):
     if outputType == 'HistorySet':
       outputDict['historySizes'] = copy.copy(targetDict['historySizes'])
 
-    numRlz = targetDict['input'].values()[0].size
+    numRlz = utils.first(targetDict['input'].values()).size
     outputDict[self.label] = np.empty(numRlz)
     for i in range(numRlz):
       tempTargDict = {}

framework/PostProcessors/DataMining.py

@@ -659,7 +659,7 @@ def __runSciKitLearn(self, Input):
           ##FIXME: You may also want to output the covariances of each pair of
           ## dimensions as well, this is currently only accessible from the solution export metadata
           ## We should list the variables name the solution export in order to access this data
-          for joffset,col in enumerate(self.unSupervisedEngine.features.keys()[i:]):
+          for joffset,col in enumerate(list(self.unSupervisedEngine.features.keys())[i:]):
             j = i+joffset
             covValues = mixtureCovars[:,i,j]
             covName = 'cov_'+str(key)+'_'+str(col)
@@ -820,7 +820,7 @@ def __runTemporalSciKitLearn(self, Input):
         rlzDims = {}
         rlzs = {}
         ## First store the label as the input for this cluster
-        mixLabels = range(int(np.max(componentMeanIndices.values()))+1)
+        mixLabels = range(int(np.max(list(componentMeanIndices.values())))+1)
         rlzs[self.labelFeature] = np.atleast_1d(mixLabels)
         rlzs[self.pivotParameter] = self.pivotVariable
         for rlzIndex in mixLabels:
@@ -851,7 +851,7 @@ def __runTemporalSciKitLearn(self, Input):
           ## dimensions as well
           if mixtureCovars is not None:
             for i,row in enumerate(self.unSupervisedEngine.features.keys()):
-              for joffset,col in enumerate(self.unSupervisedEngine.features.keys()[i:]):
+              for joffset,col in enumerate(list(self.unSupervisedEngine.features.keys())[i:]):
                 j = i+joffset
                 timeSeries = np.zeros(numberOfHistoryStep)
                 for timeIdx in range(numberOfHistoryStep):

framework/PostProcessors/FTGate.py

@@ -122,25 +122,25 @@ def evaluateGate(self,argumentValues):
       @ Out, outcome, float, calculated outcome of the gate
     """
     if self.gate == 'and':
-      outcome = andGate(argumentValues.values())
+      outcome = andGate(list(argumentValues.values()))
     elif self.gate == 'or':
-      outcome = orGate(argumentValues.values())
+      outcome = orGate(list(argumentValues.values()))
     elif self.gate == 'nor':
-      outcome = norGate(argumentValues.values())
+      outcome = norGate(list(argumentValues.values()))
     elif self.gate == 'nand':
-      outcome = nandGate(argumentValues.values())
+      outcome = nandGate(list(argumentValues.values()))
     elif self.gate == 'xor':
-      outcome = xorGate(argumentValues.values())
+      outcome = xorGate(list(argumentValues.values()))
     elif self.gate == 'iff':
-      outcome = iffGate(argumentValues.values())
+      outcome = iffGate(list(argumentValues.values()))
     elif self.gate == 'atleast':
-      outcome = atLeastGate(argumentValues.values(),float(self.params['min']))
+      outcome = atLeastGate(list(argumentValues.values()),float(self.params['min']))
     elif self.gate == 'cardinality':
-      outcome = cardinalityGate(argumentValues.values(),float(self.params['min']),float(self.params['max']))
+      outcome = cardinalityGate(list(argumentValues.values()),float(self.params['min']),float(self.params['max']))
     elif self.gate == 'imply':
       outcome = implyGate(argumentValues)
     elif self.gate == 'not':
-      outcome = notGate(argumentValues.values())
+      outcome = notGate(list(argumentValues.values()))
     return outcome
 
 def notGate(value):
@@ -242,7 +242,7 @@ def implyGate(argumentValues):
     @ In, argumentValues, list, list of values
     @ Out, outcome, float, calculated outcome of the gate
   """
-  keys = argumentValues.keys()
+  keys = list(argumentValues.keys())
   if argumentValues[keys[0]]==1 and argumentValues[keys[1]]==0:
     outcome = 0
   else:

framework/PostProcessors/FTStructure.py

@@ -96,15 +96,15 @@ def FTsolver(self):
     """
     self.gateSequence = []
     availBasicEvents = copy.deepcopy(self.basicEvents)
-    availBasicEvents = availBasicEvents + self.houseEvents.keys()
+    availBasicEvents = availBasicEvents + list(self.houseEvents.keys())
     counter = 0
     while True:
       complete=False
       for gate in self.gateList.keys():
         if set(self.gateList[gate].returnArguments()) <= set(availBasicEvents):
           self.gateSequence.append(gate)
           availBasicEvents.append(gate)
-        if set(availBasicEvents) == set(self.basicEvents+self.gateID+self.houseEvents.keys()):
+        if set(availBasicEvents) == set(itertools.chain(self.basicEvents,self.gateID,self.houseEvents.keys())):
           complete=True
           break
         if counter > len(self.gateList.keys()):

framework/PostProcessors/RavenOutput.py

@@ -193,7 +193,7 @@ class RavenOutput(PostProcessor):
 #    outputDict={'realizations':[]}
 #    if self.dynamic:
 #      #outputs are basically a point set with pivot as input and requested XML path entries as output
-#      fileName = self.files.values()[0]['fileObject'].getAbsFile()
+#      fileName = utils.first(self.files.values())['fileObject'].getAbsFile()
 #      root,_ = xmlUtils.loadToTree(fileName)
 #      #determine the pivot parameter
 #      pivot = root[0].tag
@@ -202,7 +202,7 @@ class RavenOutput(PostProcessor):
 #      for p,pivotStep in enumerate(root):
 #        realization = {'inputs':{},'outputs':{},'metadata':{'loadedFromRavenFile':fileName}}
 #        realization['inputs'][pivot] = float(pivotStep.attrib['value'])
-#        for name,path in self.files.values()[0]['paths'].items():
+#        for name,path in utils.first(self.files.values())['paths'].items():
 #          desiredNode = self._readPath(pivotStep,path,fileName)
 #          realization['outputs'][name] = float(desiredNode.text)
 #        outputDict['realizations'].append(realization)

framework/Runners/Runner.py

@@ -74,7 +74,7 @@ def __del__(self):
     """
     if self.__printTimings:
       # print timing history
-      pairs = self.timings.items()
+      pairs = list(self.timings.items())
       pairs.sort(key=lambda x:x[1])
       prof = ""
       prof += 'TIMINGS for job "{}":'.format(self.identifier)