Remove Invalid Escape Sequences

framework/CodeInterfaces/AccelerateCFD/AccelerateCFD.py

@@ -109,7 +109,7 @@ def initialize(self, runInfo, oriInputFiles):
         self.romName = xmlFind('./rom/romName')
         self.romType = xmlFind('./rom/romType')
         # read data from FOM
-        datai = pd.read_csv(self.fomDataFolder,skiprows=3,header=None,sep='\s+').iloc[:,[0,1,2]].replace('[()]','',regex=True).astype(float)
+        datai = pd.read_csv(self.fomDataFolder,skiprows=3,header=None,sep=r'\s+').iloc[:,[0,1,2]].replace('[()]','',regex=True).astype(float)
         datai = datai.rename(columns={0:'t',1:'ux',2:'uy'})
         dataList = [datai]
         self.dataFom = pd.concat(dataList,keys=['fom'])
@@ -322,7 +322,7 @@ def finalizeCodeOutput(self, command, output, workingDir):
       # process post-processing file for rom
       ppRomFile = os.path.join(workingDir,"rom",self.romType +"_"+ self.romName,"postProcessing","probe","0","Urom")
       if os.path.exists(ppRomFile):
-        datai = pd.read_csv(ppRomFile,skiprows=3,header=None,sep='\s+').iloc[:,[0,1,2]].replace('[()]','',regex=True).astype(float)
+        datai = pd.read_csv(ppRomFile,skiprows=3,header=None,sep=r'\s+').iloc[:,[0,1,2]].replace('[()]','',regex=True).astype(float)
         datai = datai.rename(columns={0:'t',1:'ux',2:'uy'})
         dataList = [datai]
         romData = pd.concat(dataList,keys=['rom'])

framework/CodeInterfaces/Dymola/DymolaInterface.py

@@ -262,8 +262,8 @@ def createNewInput(self, currentInputFiles, oriInputFiles, samplerType, **Kwargs
     patterns = [# Dymola 1- or 2-line parameter specification
                 (r'(^\s*%s\s+)%s(\s+%s\s+%s\s+%s\s+%s\s*#\s*%s\s*$)'
                  % (i, f, f, f, u, u, '%s')),
-                (r'(^\s*)' + i + '(\s*#\s*%s)'),
-                (r'(^\s*)' + f + '(\s*#\s*%s)'),
+                (r'(^\s*)' + i + r'(\s*#\s*%s)'),
+                (r'(^\s*)' + f + r'(\s*#\s*%s)'),
                 # From Dymola:
                 # column 1: Type of initial value
                 #           = -2: special case: for continuing simulation

framework/CodeInterfaces/MELCOR/MELCORdata.py

@@ -68,10 +68,10 @@ def returnControlFunctions(self, timeBlock):
       @ Out, functionValuesForEachTime, dict, {"time":{"functionName":"functionValue"}}
     """
     functionValuesForEachTime = {'time': []}
-    timeOneRegex_name = re.compile("^\s*CONTROL\s+FUNCTION\s+(?P<name>[^\(]*)\s+(\(.*\))?\s*IS\s+.+\s+TYPE.*$")
-    timeOneRegex_value = re.compile("^\s*VALUE\s+=\s+(?P<value>[^\s]*)")
-    startRegex = re.compile("\s*CONTROL\s*FUNCTION\s*NUMBER\s*CURRENT\s*VALUE")
-    regex = re.compile("^\s*(?P<name>( ?([0-9a-zA-Z-]+))*)\s+([0-9]+)\s*(?P<value>((([0-9.-]+)E(\+|-)[0-9][0-9])|((T|F))))\s*.*$")
+    timeOneRegex_name = re.compile(r"^\s*CONTROL\s+FUNCTION\s+(?P<name>[^\(]*)\s+(\(.*\))?\s*IS\s+.+\s+TYPE.*$")
+    timeOneRegex_value = re.compile(r"^\s*VALUE\s+=\s+(?P<value>[^\s]*)")
+    startRegex = re.compile(r"\s*CONTROL\s*FUNCTION\s*NUMBER\s*CURRENT\s*VALUE")
+    regex = re.compile(r"^\s*(?P<name>( ?([0-9a-zA-Z-]+))*)\s+([0-9]+)\s*(?P<value>((([0-9.-]+)E(\+|-)[0-9][0-9])|((T|F))))\s*.*$")
     for time,listOfLines in timeBlock.items():
       functionValuesForEachTime['time'].append(float(time))
       start = -1

framework/CodeInterfaces/MooseBasedApp/BISONMESHSCRIPTparser.py

@@ -84,7 +84,7 @@ def __init__(self,inputFile):
           # Append string of non-varying parts of input file to file storage and reset the collection string
           if len(between_str) > 0:
             self.fileOrderStorage.append(between_str); between_str = ''
-          dictname, varname, varvalue = re.split("\['|'] = |'] =|']= ", line)
+          dictname, varname, varvalue = re.split(r"\['|'] = |'] =|']= ", line)
           if dictname in self.AllVarDict.keys():
             self.AllVarDict[dictname][varname] = varvalue.strip()
           else:
@@ -119,7 +119,7 @@ def __init__(self,inputFile):
             # Append string of non-varying parts of input file to file storage and reset the collection string
             if len(between_str) > 0:
               self.fileOrderStorage.append(between_str); between_str = ''
-            dictname, varname, varvalue = re.split("\['|'] = |'] =|']= ", line)
+            dictname, varname, varvalue = re.split(r"\['|'] = |'] =|']= ", line)
             if dictname in self.AllVarDict.keys():
               self.AllVarDict[dictname][varname] = varvalue.strip()
             else:

framework/CodeInterfaces/OpenModelica/OpenModelicaInterface.py

@@ -11,7 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""
+r"""
 Created on May 22, 2015
 
 @author: bobk

framework/CodeInterfaces/PHISICS/PhisicsInterface.py

@@ -267,7 +267,7 @@ def generateCommand(self, inputFiles, executable, clargs=None, fargs=None, preEx
       )]].getFilename() + ' -dep ' + inputFiles[mapDict['Depletion_input'.lower(
       )]].getFilename() + ' -o ' + self.instantOutput
       commandToRun = commandToRun.replace("\n", " ")
-      commandToRun = re.sub("\s\s+", " ", commandToRun)
+      commandToRun = re.sub(r"\s\s+", " ", commandToRun)
       outputfile = 'out~' + inputFiles[mapDict['inp'.lower()]].getBase()
     returnCommand = [('parallel', commandToRun)], outputfile
     return returnCommand

framework/CodeInterfaces/PHISICS/PhisicsRelapInterface.py

@@ -134,7 +134,7 @@ def generateCommand(self, inputFiles, executable, clargs=None, fargs=None, preEx
     self.outputExt = '.o'
     commandToRun = executable + ' -i ' +inputFiles[mapDict['relapInp'.lower()]].getFilename() + ' -o  ' + self.outFileName + self.outputExt
     commandToRun = commandToRun.replace("\n"," ")
-    commandToRun  = re.sub("\s\s+", " ",commandToRun)
+    commandToRun  = re.sub(r"\s\s+", " ",commandToRun)
     returnCommand = [('parallel',commandToRun)], outputfile
     return returnCommand
 

framework/CodeInterfaces/RELAP5/RELAPparser.py

@@ -367,7 +367,7 @@ def retrieveCardValues(self, listOfCards):
       for lineNum, line in enumerate(self.deckLines[deck]):
         if all(foundAllCards[deck].values()):
           break
-        if not re.match('^\s*\n',line):
+        if not re.match(r'^\s*\n',line):
           readCard = line.split()[0].strip()
           if readCard in deckCards[deck].keys():
             foundWord = False

framework/CodeInterfaces/RELAP5/Relap5Interface.py

@@ -142,7 +142,7 @@ def generateCommand(self,inputFiles,executable,clargs=None,fargs=None, preExec=N
       addflags = ''
     commandToRun = executable + ' -i ' + inputFiles[index].getFilename() + ' -o ' + outputfile  + '.o ' +  addflags
     commandToRun = commandToRun.replace("\n"," ")
-    commandToRun  = re.sub("\s\s+" , " ", commandToRun )
+    commandToRun  = re.sub(r"\s\s+" , " ", commandToRun )
     returnCommand = [('parallel',commandToRun)], outputfile
     return returnCommand
 

framework/CodeInterfaces/SCALE/tritonAndOrigenData.py

@@ -207,7 +207,7 @@ def retrieveConcentrationTables(self):
       if uom not in totals:
         totals[uom] = []
       indexConcTable+=4
-      timeUom = re.split('(\d+)', self.lines[indexConcTable].split()[0])[-1].strip()
+      timeUom = re.split(r'(\d+)', self.lines[indexConcTable].split()[0])[-1].strip()
       timeGrid = [float(elm.replace(timeUom.strip(),"")) for elm in  self.lines[indexConcTable].split()]
 
       if outputDict is None:

framework/InputTemplates/TemplateBaseClass.py

@@ -185,7 +185,7 @@ def _updateCommaSeperatedList(self, node, new, position=None, before=None, after
   # OTHER UTILITIES              #
   ################################
   def _getRavenLocation(self, which='framework'):
-    """
+    r"""
       Returns the (string) path to RAVEN
       NOTE this is problematic in mingw windows, since using abspath includes e.g. C:\msys64\home\etc.
       @ In, framework, bool, optional, if True then give location of "raven/framework" else "raven/"

framework/Optimizers/GeneticAlgorithm.py

@@ -725,7 +725,7 @@ def _ahdp(self,a,b,p):
     return max(self._GDp(a,b,p),self._GDp(b,a,p))
 
   def _GDp(self,a,b,p):
-    """
+    r"""
       Modified Generational Distance Indicator
       @ In, a, np.array, old population A
       @ In, b, np.array, new population B
@@ -739,7 +739,7 @@ def _GDp(self,a,b,p):
     return (1/n * s)**(1/p)
 
   def _popDist(self,ai,b,q=2):
-    """
+    r"""
       Minimum Minkowski distance from a_i to B (nearest point in B)
       @ In, ai, 1d array, the ith chromosome in the generation A
       @ In, b, np.array, population B
@@ -761,7 +761,7 @@ def _ahd(self,a,b):
     return max(self._GD(a,b),self._GD(b,a))
 
   def _GD(self,a,b):
-    """
+    r"""
       Generational Distance Indicator
       @ In, a, np.array, old population A
       @ In, b, np.array, new population B

framework/Optimizers/SimulatedAnnealing.py

@@ -626,7 +626,7 @@ def _coolingSchedule(self, iter, T0):
       self.raiseAnError(NotImplementedError,'cooling schedule type not implemented.')
 
   def _nextNeighbour(self, rlz,fraction=1):
-    """
+    r"""
       Perturbs the state to find the next random neighbour based on the cooling schedule
       @ In, rlz, dict, current realization
       @ In, fraction, float, optional, the current iteration divided by the iteration limit i.e., $\frac{iter}{Limit}$

framework/Optimizers/fitness/fitness.py

@@ -28,7 +28,7 @@
 
 # @profile
 def invLinear(rlz,**kwargs):
-  """
+  r"""
     Inverse linear fitness method requires that the fitness value is inversely proportional to the objective function
     This method is designed such that:
     For minimization Problems:
@@ -76,7 +76,7 @@ def invLinear(rlz,**kwargs):
   return fitness
 
 def feasibleFirst(rlz,**kwargs):
-  """
+  r"""
     Efficient Parameter-less Feasible First Penalty Fitness method
     This method is designed such that:
     For minimization Problems:

framework/SupervisedLearning/ARMA.py

@@ -230,7 +230,7 @@ class cls.
     specs.addSub(InputData.parameterInputFactory("nyquistScalar", contentType=InputTypes.IntegerType, default=1))
     ### ARMA zero filter
     zeroFilt = InputData.parameterInputFactory('ZeroFilter', contentType=InputTypes.StringType,
-                                               descr="""turns on \emph{zero filtering}
+                                               descr=r"""turns on \emph{zero filtering}
                                                  for the listed targets. Zero filtering is a very specific algorithm, and should not be used without
                                                  understanding its application.  When zero filtering is enabled, the ARMA will remove all the values from
                                                  the training data equal to zero for the target, then train on the remaining data (including Fourier detrending

framework/contrib/pyDOE/doe_factorial.py

@@ -190,7 +190,7 @@ def fracfact(gen):
     """
     # Recognize letters and combinations
     #### fixed for python 3.7 by alfoa
-    A = [item for item in re.split('\-|\s|\+', gen) if item] # remove empty strings
+    A = [item for item in re.split(r'\-|\s|\+', gen) if item] # remove empty strings
 
     C = [len(item) for item in A]
 

scripts/TestHarness/testers/RavenFramework.py

@@ -18,7 +18,6 @@
 import os
 import subprocess
 import sys
-import distutils.version
 import platform
 from Tester import Tester
 import OrderedCSVDiffer
@@ -209,8 +208,8 @@ def check_runnable(self):
       if not found:
         self.set_skip('skipped (Unable to import library: "'+libraryName+'")')
         return False
-      if distutils.version.LooseVersion(actualVersion) < \
-         distutils.version.LooseVersion(libraryVersion):
+      if library_handler.parseVersion(actualVersion) < \
+         library_handler.parseVersion(libraryVersion):
         self.set_skip('skipped (Outdated library: "'+libraryName+'")')
         return False
       i += 2

scripts/TestHarness/testers/RavenPython.py

@@ -19,7 +19,6 @@
 import os
 import sys
 import subprocess
-import distutils.version
 from Tester import Tester
 
 scriptsDir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))
@@ -130,8 +129,8 @@ def check_runnable(self):
       if not found:
         self.set_skip('skipped (Unable to import library: "'+libraryName+'")')
         return False
-      if distutils.version.LooseVersion(actualVersion) < \
-         distutils.version.LooseVersion(libraryVersion):
+      if library_handler.parseVersion(actualVersion) < \
+         library_handler.parseVersion(libraryVersion):
         self.set_skip('skipped (Outdated library: "'+libraryName+'")')
         return False
       i += 2

scripts/library_handler.py

@@ -17,6 +17,7 @@
 """
 import os
 import sys
+import re
 import platform
 import argparse
 import subprocess
@@ -112,6 +113,22 @@ def checkLibraries(buildReport=False):
     return messages
   return missing, notQA
 
+def parseVersion(versionString):
+  """
+    Parses a version string into its components
+    @ In, versionStirng, str, the version string to parse
+    @ Out, version, list, list of components as integers and strings
+  """
+  version = []
+  for part in re.split(r'([0-9]+|[a-z]+|\.)',versionString):
+    if len(part) == 0 or part == ".":
+      continue
+    try:
+      version.append(int(part))
+    except ValueError:
+      version.append(part)
+  return version
+
 def checkSameVersion(expected, received):
   """
     Compares "expected" to "received" for a version match.