[Refactoring] making the code more Pythonic (#1930)

* Utilize NumPy APIs more

* Remove loop and use join instead

* use multi_dot

* define axis for np.sum

* use with stmt

developer_tools/createRegressionTestDocumentation.py

@@ -105,19 +105,18 @@ def noDescriptionTestsAndInformationOnTheOther(self):
     for testInfoFile in __testInfoList:
       if 'moose' in testInfoFile.split(os.sep) or not os.path.isfile(testInfoFile):
         continue
-      fileObject = open(testInfoFile,"r+")
-      fileLines = fileObject.readlines()
-      dirName = os.path.dirname(testInfoFile)
-      # I do not want to use getpot!
-      for line in fileLines:
-        if line.strip().startswith("input"):
-          fileName = line.split("=")[-1].replace("'", "").replace('"', '').rstrip().strip()
-          fileName = os.path.join(dirName,fileName)
-          if os.path.split(fileName)[-1].lower().endswith('xml'):
-            __testList.append(os.path.abspath(fileName))
-          if os.path.split(fileName)[-1].lower().endswith('py'):
-            __testList.append(os.path.abspath(fileName))
-      fileObject.close()
+      with open(testInfoFile,"r+") as fileObject:
+        fileLines = fileObject.readlines()
+        dirName = os.path.dirname(testInfoFile)
+        # I do not want to use getpot!
+        for line in fileLines:
+          if line.strip().startswith("input"):
+            fileName = line.split("=")[-1].replace("'", "").replace('"', '').rstrip().strip()
+            fileName = os.path.join(dirName,fileName)
+            if os.path.split(fileName)[-1].lower().endswith('xml'):
+              __testList.append(os.path.abspath(fileName))
+            if os.path.split(fileName)[-1].lower().endswith('py'):
+              __testList.append(os.path.abspath(fileName))
     for testFile in __testList:
       if testFile.endswith('xml'):
         try: root = ET.parse(testFile).getroot()

developer_tools/readRequirementsAndCreateLatex.py

@@ -30,18 +30,17 @@ def writeLatexFromDictionaryOfRequirements(applicationName,requirementGroups,out
   """
   sections = ["section","subsection","subsubsection","paragraph"]
   indexSec = 0
-  fileObject = open(outputFileName,"w+")
-  fileObject.write("\\"+sections[0].strip()+"{System Requirements: " +applicationName.strip()+"}\n")
-  for group, value in requirementGroups.items():
-    fileObject.write("\\"+sections[1].strip()+"{" +group.strip()+"}\n")
-    for reqSet, requirements in value.items():
-      # construct table
-      fileObject.write("\\"+sections[2].strip()+"{" +reqSet.strip()+"}\n")
-      # start write the requirements for this set
-      for req, content in requirements.items():
-        fileObject.write("\\"+sections[3].strip()+"{" +req.strip()+"} \n")
-        fileObject.write(content['description'].strip() + "\n")
-  fileObject.close()
+  with open(outputFileName,"w+") as fileObject:
+    fileObject.write("\\"+sections[0].strip()+"{System Requirements: " +applicationName.strip()+"}\n")
+    for group, value in requirementGroups.items():
+      fileObject.write("\\"+sections[1].strip()+"{" +group.strip()+"}\n")
+      for reqSet, requirements in value.items():
+        # construct table
+        fileObject.write("\\"+sections[2].strip()+"{" +reqSet.strip()+"}\n")
+        # start write the requirements for this set
+        for req, content in requirements.items():
+          fileObject.write("\\"+sections[3].strip()+"{" +req.strip()+"} \n")
+          fileObject.write(content['description'].strip() + "\n")
 
 
 def readRequirementsXml(fileName):

ravenframework/CodeInterfaceClasses/MooseBasedApp/BISONMESHSCRIPTparser.py

@@ -147,13 +147,12 @@ def writeNewInput(self,outfile=None):
     """
     if outfile==None:
       outfile = self.inputfile
-    IOfile = open(outfile,'w')
-    for e, entry in enumerate(self.fileOrderStorage):
-      if type(entry) == unicode:
-        IOfile.writelines(entry)
-      elif type(entry) == list:
-        DictBlockName = self.fileOrderStorage[e][0]
-        DictBlock = self.AllVarDict[DictBlockName]
-        for key, value in DictBlock.items():
-          IOfile.writelines(DictBlockName + "['" + key + "'] = " + str(value) + '\n')
-    IOfile.close()
+    with open(outfile,'w') as IOfile:
+      for e, entry in enumerate(self.fileOrderStorage):
+        if type(entry) == unicode:
+          IOfile.writelines(entry)
+        elif type(entry) == list:
+          DictBlockName = self.fileOrderStorage[e][0]
+          DictBlock = self.AllVarDict[DictBlockName]
+          for key, value in DictBlock.items():
+            IOfile.writelines(DictBlockName + "['" + key + "'] = " + str(value) + '\n')

ravenframework/CodeInterfaceClasses/MooseBasedApp/CUBITparser.py

@@ -86,11 +86,10 @@ def writeNewInput(self,outFile=None):
     """
     if outFile == None:
       outFile = self.inputfile
-    IOfile = open(outFile,'w')
-    for entry in self.fileOrderStorage:
-      if type(entry) == unicode:
-        IOfile.writelines(entry)
-      elif type(entry) == list:
-        for key, value in self.keywordDictionary.items():
-          IOfile.writelines('#{ '+key+' = '+str(value)+'}'+'\n')
-    IOfile.close()
+    with open(outFile,'w') as IOfile:
+      for entry in self.fileOrderStorage:
+        if type(entry) == unicode:
+          IOfile.writelines(entry)
+        elif type(entry) == list:
+          for key, value in self.keywordDictionary.items():
+            IOfile.writelines('#{ '+key+' = '+str(value)+'}'+'\n')

ravenframework/CodeInterfaceClasses/Neutrino/neutrinoInterface.py

@@ -203,23 +203,20 @@ def finalizeCodeOutput(self, command, output, workingDir):
       return newOutputPath'''
 
     # open original output file (the working directory is provided)
-    outputFile = open(outputPath,"r+")
+    with open(outputPath,"r+") as outputFile:
+      #Open the new output file so the results can be written to it and put in the form for RAVEN to read
+      with open(newOutputPath + ".csv", 'w') as resultsFile:
 
-    #Open the new output file so the results can be written to it and put in the form for RAVEN to read
-    resultsFile = open(newOutputPath + ".csv", 'w')
+        lines = outputFile.readlines()
 
-    lines = outputFile.readlines()
+        #Needed for RAVEN to read output
+        #These need to match RAVEN input file output names
+        resultsFile.write('time,result\n')
 
-    #Needed for RAVEN to read output
-    #These need to match RAVEN input file output names
-    resultsFile.write('time,result\n')
+        #Write Neutrino results to a new file for RAVEN
+        for line in lines:
+          resultsFile.write(line)
 
-    #Write Neutrino results to a new file for RAVEN
-    for line in lines:
-      resultsFile.write(line)
 
-    resultsFile.close()
-
-    outputFile.close()
 
     return newOutputPath

ravenframework/CodeInterfaceClasses/OpenModelica/OpenModelicaInterface.py

@@ -270,12 +270,11 @@ def finalizeCodeOutput(self, command, output, workingDir):
     print('sourcefilename:',sourceFileName)
     destFileName = sourceFileName.replace('rawout~', 'out~')  # When fix the CSV, change rawout~ to out~
     sourceFileName += '.csv'
-    inputFile = open(sourceFileName)
-    for line in inputFile:
-      # Line ends with a comma followed by a newline
-      #XXX toBytes seems to be needed here in python3, despite the text = True
-      os.write(tempOutputFD, utils.toBytes(line.replace('"','').strip().strip(',') + '\n'))
-    inputFile.close()
+    with open(sourceFileName) as inputFile:
+      for line in inputFile:
+        # Line ends with a comma followed by a newline
+        #XXX toBytes seems to be needed here in python3, despite the text = True
+        os.write(tempOutputFD, utils.toBytes(line.replace('"','').strip().strip(',') + '\n'))
     os.close(tempOutputFD)
     shutil.move(tempOutputFileName, destFileName + '.csv')
     return destFileName   # Return the name without the .csv on it...RAVEN will add it

ravenframework/CodeInterfaceClasses/PHISICS/DecayParser.py

@@ -30,9 +30,8 @@ def __init__(self, inputFiles, workingDir, **pertDict):
     self.inputFiles = inputFiles
     self.pertDict = self.scientificNotation(pertDict)
     # open the unperturbed file
-    openInputFile = open(self.inputFiles, "r")
-    lines = openInputFile.readlines()
-    openInputFile.close()
+    with open(self.inputFiles, "r") as openInputFile:
+      lines = openInputFile.readlines()
 
     self.characterizeLibrary(lines)
     self.fileReconstruction()

ravenframework/CodeInterfaceClasses/PHISICS/FissionYieldParser.py

@@ -34,9 +34,8 @@ def __init__(self, inputFiles, workingDir, **pertDict):
         pertDict)  # Perturbed variables
 
     # open the unperturbed file
-    openInputFile = open(self.inputFiles, "r")
-    lines = openInputFile.readlines()
-    openInputFile.close()
+    with open(self.inputFiles, "r") as openInputFile:
+      lines = openInputFile.readlines()
 
     self.characterizeLibrary(lines)
     self.isotopeList = list(set(

ravenframework/CodeInterfaceClasses/PHISICS/MassParser.py

@@ -109,9 +109,8 @@ def printInput(self, workingDir):
         @ Out, None
       """
       # open the unperturbed file
-      openInputFile = open(self.inputFiles, "r")
-      lines = openInputFile.readlines()
-      openInputFile.close()
+      with open(self.inputFiles, "r") as openInputFile:
+        lines = openInputFile.readlines()
 
       # remove the file if was already existing
       if os.path.exists(self.inputFiles):

ravenframework/CodeInterfaceClasses/PHISICS/PathParser.py

@@ -95,9 +95,8 @@ def printInput(self, workingDir):
       @ Out, None
     """
     # open the unperturbed file
-    openInputFile = open(self.inputFiles, "r")
-    lines = openInputFile.readlines()
-    openInputFile.close()
+    with open(self.inputFiles, "r") as openInputFile:
+      lines = openInputFile.readlines()
 
     # remove the file if was already existing
     if os.path.exists(self.inputFiles):

ravenframework/CodeInterfaceClasses/PHISICS/QValuesParser.py

@@ -105,9 +105,8 @@ def printInput(self, workingDir):
       @ Out, None
     """
     # open the unperturbed file
-    openInputFile = open(self.inputFiles, "r")
-    lines = openInputFile.readlines()
-    openInputFile.close()
+    with open(self.inputFiles, "r") as openInputFile:
+      lines = openInputFile.readlines()
 
     # remove the file if was already existing
     if os.path.exists(self.inputFiles):

ravenframework/CodeInterfaceClasses/PHISICS/XSCreator.py

@@ -95,9 +95,8 @@ def generateXML(self,workingDir,bool,inputFiles,tabMapFileName):
                 for count,(group,value) in enumerate(self.listedDict.get('XS').get(tabulation).get(material).get(isotope).get(typeOfXs).get(reaction).items()):
                   reactionChild = SubElement(libraryChild, self.formatXS(reaction), {'g':group})
                   reactionChild.text = value
-    fileObj = open(inputFiles, 'w')
-    fileObj.write(self.prettify(top))
-    fileObj.close()
+    with open(inputFiles, 'w') as fileObj:
+      fileObj.write(self.prettify(top))
 
   def formatXS(self,reaction):
     """

ravenframework/CodeInterfaceClasses/Prescient/PrescientCodeInterface.py

@@ -93,10 +93,9 @@ def createNewInput(self, inputs, oinputs, samplerType, **Kwargs):
           elif line.lstrip().startswith("--output-directory="):
             self._outputDirectory = line.split("=",1)[1].rstrip()
           newLines.append(line)
-        newFile = open(singleInput.getAbsFile(),"w")
-        for line in newLines:
-          newFile.write(line)
-        newFile.close()
+        with open(singleInput.getAbsFile(),"w") as newFile:
+          for line in newLines:
+            newFile.write(line)
       elif singleInput.getType() == 'PrescientInput':
         #print("SampledVars", Kwargs["SampledVars"])
         #print("Modifying", singleInput)

ravenframework/CodeInterfaceClasses/Rattlesnake/YakInstantLibraryParser.py

@@ -456,16 +456,15 @@ def writeNewInput(self,inFiles=None,**Kwargs):
       @ Out, None.
     """
     for outFile in inFiles:
-      newFile = open(outFile.getAbsFile(),'w')
-      tree = self.xmlsDict[outFile.getFilename()]
-      root = tree.getroot()
-      for child in root:
-        for mat in child:
-          matID = mat.attrib['ID'].strip()
-          if matID not in self.aliases.keys():
-            continue
-          self._replaceXMLNodeText(mat,self.pertLib[matID])
+      with open(outFile.getAbsFile(),'w') as newFile:
+        tree = self.xmlsDict[outFile.getFilename()]
+        root = tree.getroot()
+        for child in root:
+          for mat in child:
+            matID = mat.attrib['ID'].strip()
+            if matID not in self.aliases.keys():
+              continue
+            self._replaceXMLNodeText(mat,self.pertLib[matID])
 
-      toWrite = self._prettify(tree)
-      newFile.writelines(toWrite)
-      newFile.close()
+        toWrite = self._prettify(tree)
+        newFile.writelines(toWrite)

ravenframework/CodeInterfaceClasses/Utilities/dynamicEventTreeUtilities.py

@@ -52,6 +52,5 @@ def writeXmlForDET(filename,trigger,listDict,stopInfo):
     var.set('actual_value',str(varInfo['new_value']))
     if 'associated_pb' in varInfo.keys():
       var.set('probability',str(varInfo['associated_pb']))
-  fileObject = open(filename,'w')
-  fileObject.write(minidom.parseString(ET.tostring(root, 'utf-8')).toprettyxml(indent="\t"))
-  fileObject.close()
+  with open(filename,'w') as fileObject:
+    fileObject.write(minidom.parseString(ET.tostring(root, 'utf-8')).toprettyxml(indent="\t"))