diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ARCSReductionTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ARCSReductionTest.py
index e92eb2ce790a19cc4f6cae7c962761a3c5bb86d2..176facd12fd724dfd39ada35300a742bcbd621f9 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ARCSReductionTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ARCSReductionTest.py
@@ -10,6 +10,10 @@ from numpy import *
 
 class ARCSReductionTest(stresstesting.MantidStressTest):
 
+    vanFile1=''
+    vanFile0=''
+    nxspeFile=''
+
     def requiredFiles(self):
         return ["ARCS_23961_event.nxs","WBARCS.nxs"]
 
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/BASISAutoReduction.py b/Code/Mantid/Testing/SystemTests/tests/analysis/BASISAutoReduction.py
index 7c999280f9683ea343b430c81b9b058d51245205..96d7cde15414977eff8d5c313750eb2255758f73 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/BASISAutoReduction.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/BASISAutoReduction.py
@@ -21,7 +21,29 @@ class BASISAutoReductionTest(stresstesting.MantidStressTest):
         autows_monitor = 'monitor_ws'
         Load(Filename='BSS_13387_event.nxs', OutputWorkspace=autows)
         LoadMask(Instrument='BASIS', OutputWorkspace='BASIS_MASK', InputFile='BASIS_AutoReduction_Mask.xml')
-        MaskDetectors(Workspace=autows, DetectorList="5,49,69,113,133,177,197,241,261,305,325,369,389,433,453,497,517,561,581,625,645,689,709,753,773,817,837,881,901,945,965,1009,1029,1073,1093,1137,1157,1201,1221,1265,1285,1329,1349,1393,1413,1457,1477,1521,1541,1585,1605,1649,1669,1713,1733,1777,1797,1841,1861,1905,1925,1969,1989,2033,2053,2097,2117,2161,2181,2225,2245,2289,2309,2353,2373,2417,2437,2481,2501,2545,2565,2609,2629,2673,2693,2737,2757,2801,2821,2865,2885,2929,2949,2993,3013,3057,3077,3121,3141,3185,3205,3249,3269,3313,3333,3377,3397,3441,3461,3505,3525,3569,3589-3633,3653-3697,3717-3761,3781-3825,3845-3889,3909-3953,3973-4017,4037-4081,4110,4154,4174,4218,4238,4282,4302,4346,4366,4410,4430,4474,4494,4538,4558,4602,4622,4666,4686,4730,4750,4794,4814,4858,4878,4922,4942,4986,5006,5050,5070,5114,5134,5178,5198,5242,5262,5306,5326,5370,5390,5434,5454,5498,5518,5562,5582,5626,5646,5690,5710,5754,5774,5818,5838,5882,5902,5946,5966,6010,6030,6074,6094,6138,6158,6202,6222,6266,6286,6330,6350,6394,6414,6458,6478,6522,6542,6586,6606,6650,6670,6714,6734,6778,6798,6842,6862,6906,6926,6970,6990,7034,7054,7098,7118,7162,7182,7226,7246,7290,7310,7354,7374,7418,7438,7482,7502,7546,7566,7610,7630,7674,7694-7738,7758-7802,7822-7866,7886-7930,7950-7994,8014-8058,8078-8122,8142-8186,8192-15871") #MaskedWorkspace='BASIS_MASK')
+        MaskDetectors(Workspace=autows, DetectorList="5,49,69,113,133,177,197,241,261,305,325,369,389,433,453,497,517,"
+                                                     "561,581,625,645,689,709,753,773,817,837,881,901,945,965,1009,"
+                                                     "1029,1073,1093,1137,1157,1201,1221,1265,1285,1329,1349,"
+                                                     "1393,1413,1457,1477,1521,1541,1585,1605,1649,1669,1713,"
+                                                     "1733,1777,1797,1841,1861,1905,1925,1969,1989,2033,2053,"
+                                                     "2097,2117,2161,2181,2225,2245,2289,2309,2353,2373,2417,"
+                                                     "2437,2481,2501,2545,2565,2609,2629,2673,2693,2737,2757,"
+                                                     "2801,2821,2865,2885,2929,2949,2993,3013,3057,3077,"
+                                                     "3121,3141,3185,3205,3249,3269,3313,3333,3377,3397,3441,"
+                                                     "3461,3505,3525,3569,3589-3633,3653-3697,3717-3761,"
+                                                     "3781-3825,3845-3889,3909-3953,3973-4017,4037-4081,4110,"
+                                                     "4154,4174,4218,4238,4282,4302,4346,4366,4410,4430,4474,4494,"
+                                                     "4538,4558,4602,4622,4666,4686,4730,4750,4794,4814,4858,"
+                                                     "4878,4922,4942,4986,5006,5050,5070,5114,5134,5178,5198,"
+                                                     "5242,5262,5306,5326,5370,5390,5434,5454,5498,5518,5562,5582,5626,5646,"
+                                                     "5690,5710,5754,5774,5818,5838,5882,5902,5946,5966,6010,"
+                                                     "6030,6074,6094,6138,6158,6202,6222,6266,6286,6330,6350,"
+                                                     "6394,6414,6458,6478,6522,6542,6586,6606,6650,6670,"
+                                                     "6714,6734,6778,6798,6842,6862,6906,6926,6970,6990,"
+                                                     "7034,7054,7098,7118,7162,7182,7226,7246,7290,7310,7354,"
+                                                     "7374,7418,7438,7482,7502,7546,7566,7610,7630,7674,"
+                                                     "7694-7738,7758-7802,7822-7866,7886-7930,7950-7994,"
+                                                     "8014-8058,8078-8122,8142-8186,8192-15871") #MaskedWorkspace='BASIS_MASK')
         ModeratorTzeroLinear(InputWorkspace=autows,OutputWorkspace=autows)
         LoadParameterFile(Workspace=autows, Filename=os.path.join(idfdir,'BASIS_silicon_111_Parameters.xml'))
         LoadNexusMonitors(Filename='BSS_13387_event.nxs', OutputWorkspace=autows_monitor)
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/BuildSQWTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/BuildSQWTest.py
index 99e7da5989780b097de968f70f4799123c0a91ff..2797e473841e47c199d92ca86e994f0a0f721068 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/BuildSQWTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/BuildSQWTest.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+#pylint: disable=invalid-name,super-on-old-class
 """
     Defines a system test for converting a set of reduced direct inelastic data
     to a single SQW file.
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/CNCSReductionTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/CNCSReductionTest.py
index b81c988db7b2329e15c647c28e6d505ee4da450c..56f96796b7078e2054f11a00c97f0763ffaf2c9d 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/CNCSReductionTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/CNCSReductionTest.py
@@ -8,6 +8,10 @@ import os
 import stresstesting
 
 class CNCSReductionTest(stresstesting.MantidStressTest):
+    parFile=''
+    groupingFile=''
+    nxspeFile=''
+    vanFile=''
 
     def requiredFiles(self):
         return ["CNCS_51936_event.nxs","CNCS_23936_event.nxs","CNCS_23937_event.nxs"]
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/CalibrateRectangularDetector_Test.py b/Code/Mantid/Testing/SystemTests/tests/analysis/CalibrateRectangularDetector_Test.py
index f4bcac786a4bb6bbcce9842157170474a7546c8b..3ca4556213d7212b22369095aba5b4e8c6f31813 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/CalibrateRectangularDetector_Test.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/CalibrateRectangularDetector_Test.py
@@ -11,7 +11,7 @@ def _skip_test():
     if "redhat-6" in platform.platform():
         return True
     # run on any other linux
-    return ("Linux" not in platform.platform())
+    return "Linux" not in platform.platform()
 
 class PG3Calibration(stresstesting.MantidStressTest):
     def cleanup(self):
@@ -34,9 +34,11 @@ class PG3Calibration(stresstesting.MantidStressTest):
 
         # run the actual code
         output = CalibrateRectangularDetectors(OutputDirectory = savedir, SaveAs = 'calibration', FilterBadPulses = True,
-                          GroupDetectorsBy = 'All', DiffractionFocusWorkspace = False, Binning = '0.5, -0.0004, 2.5',
-                          MaxOffset=0.01, PeakPositions = '.6866,.7283,.8185,.8920,1.0758,1.2615,2.0599',
-                          CrossCorrelation = False, Instrument = 'PG3', RunNumber = '2538', Extension = '_event.nxs')
+                                               GroupDetectorsBy = 'All', DiffractionFocusWorkspace = False,
+                                               Binning = '0.5, -0.0004, 2.5',
+                                               MaxOffset=0.01, PeakPositions = '.6866,.7283,.8185,.8920,1.0758,1.2615,2.0599',
+                                               CrossCorrelation = False, Instrument = 'PG3', RunNumber = '2538',
+                                               Extension = '_event.nxs')
 
         if isinstance(output, basestring):
             self.saved_cal_file = output
@@ -45,11 +47,11 @@ class PG3Calibration(stresstesting.MantidStressTest):
 
         # load saved cal file
         LoadCalFile(InputWorkspace="PG3_2538_calibrated", CalFileName=self.saved_cal_file, WorkspaceName="PG3_2538",
-            MakeGroupingWorkspace=False)
+                    MakeGroupingWorkspace=False)
         MaskDetectors(Workspace="PG3_2538_offsets",MaskedWorkspace="PG3_2538_mask")
         # load golden cal file
         LoadCalFile(InputWorkspace="PG3_2538_calibrated", CalFileName="PG3_golden.cal", WorkspaceName="PG3_2538_golden",
-            MakeGroupingWorkspace=False)
+                    MakeGroupingWorkspace=False)
         MaskDetectors(Workspace="PG3_2538_golden_offsets",MaskedWorkspace="PG3_2538_golden_mask")
 
     def validateMethod(self):
@@ -80,9 +82,11 @@ class PG3CCCalibration(stresstesting.MantidStressTest):
 
         # run the actual code
         output = CalibrateRectangularDetectors(OutputDirectory = savedir, SaveAs = 'calibration', FilterBadPulses = True,
-                          GroupDetectorsBy = 'All', DiffractionFocusWorkspace = False, Binning = '0.5, -0.0004, 2.5',
-                          MaxOffset=0.01, PeakPositions = '0.7282933,1.261441',DetectorsPeaks = '17,6',
-                          CrossCorrelation = True, Instrument = 'PG3', RunNumber = '2538', Extension = '_event.nxs')
+                                               GroupDetectorsBy = 'All', DiffractionFocusWorkspace = False,
+                                               Binning = '0.5, -0.0004, 2.5',
+                                               MaxOffset=0.01, PeakPositions = '0.7282933,1.261441',DetectorsPeaks = '17,6',
+                                               CrossCorrelation = True, Instrument = 'PG3', RunNumber = '2538',
+                                               Extension = '_event.nxs')
 
         if isinstance(output, basestring):
             self.saved_cal_file = output
@@ -91,11 +95,11 @@ class PG3CCCalibration(stresstesting.MantidStressTest):
 
         # load saved cal file
         LoadCalFile(InputWorkspace="PG3_2538_calibrated", CalFileName=self.saved_cal_file, WorkspaceName="PG3_2538",
-            MakeGroupingWorkspace=False)
+                    MakeGroupingWorkspace=False)
         MaskDetectors(Workspace="PG3_2538_offsets",MaskedWorkspace="PG3_2538_mask")
         # load golden cal file
         LoadCalFile(InputWorkspace="PG3_2538_calibrated", CalFileName="PG3_goldenCC.cal", WorkspaceName="PG3_2538_golden",
-            MakeGroupingWorkspace=False)
+                    MakeGroupingWorkspace=False)
         MaskDetectors(Workspace="PG3_2538_golden_offsets",MaskedWorkspace="PG3_2538_golden_mask")
 
     def validateMethod(self):
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ConvertToMDworkflow.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ConvertToMDworkflow.py
index a2e17aef9868585b07505fdfae1364d2ec6877e7..1dcb95c1ee83a1a4d40402ac0fad5d48e78bb6f2 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ConvertToMDworkflow.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ConvertToMDworkflow.py
@@ -1,7 +1,6 @@
 #pylint: disable=no-init
 import stresstesting
 from mantid.simpleapi import *
-from mantid.api import Workspace
 
 
 #----------------------------------------------------------------------
@@ -9,7 +8,7 @@ class ConvertToMDworkflow(stresstesting.MantidStressTest):
     """
     """
 
-
+    tolerance = 1e-5
 
     def runTest(self):
 
@@ -55,13 +54,12 @@ class ConvertToMDworkflow(stresstesting.MantidStressTest):
     def validate(self):
         """Returns the name of the workspace & file to compare"""
         self.tolerance = 1e-5
-      #elf.disableChecking.append('SpectraMap')
-      #elf.disableChecking.append('Instrument')
+        #self.disableChecking.append('SpectraMap')
+        #self.disableChecking.append('Instrument')
         result = 'WS_4D'
         reference = "ConvertToMDSample.nxs"
 
         valNames = [result,reference]
-        from mantid.simpleapi import Load,CompareMDWorkspaces,FrameworkManager,SaveNexus
 
         Load(Filename=reference,OutputWorkspace=valNames[1])
 
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py b/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py
index 42fff86f1f76f145c7b1d590f2ac38f35d21ceb9..68013568761616b530f8466ddf4c5e8bff863938 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py
@@ -14,6 +14,8 @@ def getNamedParameter(ws, name):
 
 class DirectInelasticDiagnostic2(MantidStressTest):
 
+    saved_diag_file=''
+
     def requiredMemoryMB(self):
         """Requires 4Gb"""
         return 4000
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/HRPDPowderDiffraction.py b/Code/Mantid/Testing/SystemTests/tests/analysis/HRPDPowderDiffraction.py
index 1deba78de7197b4fa07693a3549aacfef157b27b..2616ed9e5a9c4d6d7f5dd35dcabb15051065d1d0 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/HRPDPowderDiffraction.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/HRPDPowderDiffraction.py
@@ -65,8 +65,8 @@ class HRPDPowderDiffraction(stresstesting.MantidStressTest):
         ConvertUnits(InputWorkspace="Vanadium",OutputWorkspace="Vanadium",Target="Wavelength")
         #Correct for cylinderAbsorption
         CylinderAbsorption(InputWorkspace="Vanadium",OutputWorkspace="Transmission",CylinderSampleHeight="2",
-                            CylinderSampleRadius="0.4",AttenuationXSection="5.1",ScatteringXSection="5.08",
-                            SampleNumberDensity="0.072",NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="100")
+                           CylinderSampleRadius="0.4",AttenuationXSection="5.1",ScatteringXSection="5.08",
+                           SampleNumberDensity="0.072",NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="100")
         Divide(LHSWorkspace="Vanadium",RHSWorkspace="Transmission",OutputWorkspace="Vanadium")
         #convert to dspacing and focuss
         ConvertUnits(InputWorkspace="Vanadium",OutputWorkspace="Vanadium",Target="dSpacing")
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/HYSPECReductionTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/HYSPECReductionTest.py
index 0642cf4249e5bd30db968c8573d1cf0f1c9a53ef..fac02c33a0aa0e014e26d465d10c958320780ce8 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/HYSPECReductionTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/HYSPECReductionTest.py
@@ -8,6 +8,8 @@ import os
 import stresstesting
 
 class HYSPECReductionTest(stresstesting.MantidStressTest):
+    groupingFile = ''
+    tolerance=1e-8
 
     def requiredMemoryMB(self):
         return 5000
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD2BTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD2BTest.py
index 59490f63f0c20bdb7298342812d877ab2e406554..165cf6971dbdc2feaee14fc475bb518abdb29eec 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD2BTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD2BTest.py
@@ -2,7 +2,7 @@
 import stresstesting
 
 from mantid.api import mtd, IMDEventWorkspace
-from mantid.simpleapi import LoadILLAscii
+import mantid.simpleapi
 
 import unittest
 
@@ -31,7 +31,7 @@ class ILLD2BLoadTest(unittest.TestCase):
         """
         ILL Loader
         """
-        LoadILLAscii(Filename=dataFile,OutputWorkspace=self.ws_name)
+        mantid.simpleapi.LoadILLAscii(Filename=dataFile,OutputWorkspace=self.ws_name)
         self._do_ads_check(self.ws_name)
 
     def _do_ads_check(self, name):
@@ -42,6 +42,8 @@ class ILLD2BLoadTest(unittest.TestCase):
 
 class ILLD2BTest(stresstesting.MantidStressTest):
 
+    _success=False
+
     def requiredMemoryMB(self):
         """Set a limit of 2.5Gb to avoid 32-bit environment"""
         return 2500
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD33Test.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD33Test.py
index a429727bb91db045ba034e33f17134a96ff27805..38be10fae2729df40012e422c0a4ae30f17896e2 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD33Test.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ILLD33Test.py
@@ -2,7 +2,7 @@
 import stresstesting
 
 from mantid.api import mtd
-from mantid.simpleapi import SetupILLD33Reduction, SANSReduction,Rebin,SANSAzimuthalAverage1D
+import mantid.simpleapi as ms
 
 import unittest
 
@@ -17,7 +17,7 @@ class ILLD33SANSTest(unittest.TestCase):
 
     def test_all(self):
 
-        SetupILLD33Reduction(
+        ms.SetupILLD33Reduction(
             # Beam center shouldn't work
             #BeamCenterMethod="None",
             MaskedDetectorList=[14709,14710,14711,14712,14713,14714,14715,14716,14717,14718,14719,
@@ -67,12 +67,12 @@ class ILLD33SANSTest(unittest.TestCase):
             ComputeResolution=True,
             ReductionProperties=self.prefix + "props")
 
-        output=SANSReduction(Filename='ILL/001425.nxs', ReductionProperties=self.prefix + "props",
-                             OutputWorkspace=self.prefix + "out")
-        Rebin(InputWorkspace=self.prefix + 'out',OutputWorkspace=self.prefix + 'out_rebin',
-              Params='4,0.1,15')
-        SANSAzimuthalAverage1D(InputWorkspace=self.prefix + 'out_rebin',Binning='0.001,0.0002,0.03',
-                               OutputWorkspace=self.prefix + 'final')
+        ms.SANSReduction(Filename='ILL/001425.nxs', ReductionProperties=self.prefix + "props",
+                         OutputWorkspace=self.prefix + "out")
+        ms.Rebin(InputWorkspace=self.prefix + 'out',OutputWorkspace=self.prefix + 'out_rebin',
+                 Params='4,0.1,15')
+        ms.SANSAzimuthalAverage1D(InputWorkspace=self.prefix + 'out_rebin',Binning='0.001,0.0002,0.03',
+                                  OutputWorkspace=self.prefix + 'final')
 
         # Check some data
         wsOut = mtd[self.prefix + 'out']
@@ -92,6 +92,7 @@ class ILLD33SANSTest(unittest.TestCase):
 #====================================================================================
 
 class ILLD33Test(stresstesting.MantidStressTest):
+    _success = False
 
     def requiredMemoryMB(self):
         """Set a limit of 2.5Gb to avoid 32-bit environment"""
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ILLIN4Test.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ILLIN4Test.py
index aabdcdfbf69a52a5f54d316d752f8d53cce07e99..370120cf82cf5fb1c1d7e910f517fb9d8a589c2f 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ILLIN4Test.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ILLIN4Test.py
@@ -2,7 +2,7 @@
 import stresstesting
 
 from mantid.api import MatrixWorkspace, mtd
-from mantid.simpleapi import LoadILL
+import mantid.simpleapi as ms
 from mantid.kernel import V3D
 
 import unittest
@@ -48,7 +48,7 @@ class ILLIN4Tests(unittest.TestCase):
         """
         ILL Loader
         """
-        LoadILL(Filename=dataFile,OutputWorkspace=self.ws_name)
+        ms.LoadILL(Filename=dataFile,OutputWorkspace=self.ws_name)
         self._do_ads_check(self.ws_name)
 
     def _do_ads_check(self, name):
@@ -59,6 +59,8 @@ class ILLIN4Tests(unittest.TestCase):
 
 class LoadILLIN4Test(stresstesting.MantidStressTest):
 
+    _success = False
+
     def runTest(self):
         self._success = False
         # Custom code to create and run this single test suite
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/INTERLoadingTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/INTERLoadingTest.py
index 74921f7c23019b198b676be39135eb7f97ec8c72..f4ed2c8462d210aefd33e04eed7425ce64b2ecc9 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/INTERLoadingTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/INTERLoadingTest.py
@@ -1,9 +1,9 @@
 #pylint: disable=no-init
 from LoadAndCheckBase import *
 
-'''
-Test File loading and basic data integrity checks of INTER data in Mantid.
-'''
+#
+#Test File loading and basic data integrity checks of INTER data in Mantid.
+#
 class INTERLoadingTest(LoadAndCheckBase):
     def get_raw_workspace_filename(self):
         return "INTER00007709.raw"
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectBayesTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectBayesTest.py
index 1e3c1a496bf52e1e7831d5c668ccc31c6645fb24..b0aa455ee7c303f8e47d118657147e500616d293 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectBayesTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectBayesTest.py
@@ -1,4 +1,4 @@
-#pylint: disable=no-init,attribute-defined-outside-init
+#pylint: disable=no-init,attribute-defined-outside-init, too-few-public-methods
 import stresstesting
 import os
 from abc import ABCMeta, abstractmethod
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
index 2b7702622f0995a6eff52b9bd160b25a37e50091..bcf63cb6f4a141a6352a7c561b9b2d1b203d5c92 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
@@ -1,4 +1,5 @@
-#pylint: disable=no-init,invalid-name,attribute-defined-outside-init,too-many-lines,too-many-instance-attributes,non-parent-init-called,abstract-method
+#pylint: disable=no-init,invalid-name,attribute-defined-outside-init,too-many-lines
+#pylint: disable=too-many-instance-attributes,non-parent-init-called,abstract-method,too-few-public-methods
 # non-parent-init-called is disabled to remove false positives from a bug in pyLint < 1.4
 # abstract-mehod checking seems to ignore the fact some classes are declared abstract using abc
 
@@ -106,8 +107,7 @@ class ISISIndirectInelasticBase(stresstesting.MantidStressTest):
             raise RuntimeError("The result workspace(s) should be in a list")
         if num_ref_files != num_results:
             raise RuntimeError("The number of result workspaces (%d) does not match"
-                               " the number of reference files (%d)." % (
-                               num_ref_files, num_results))
+                               " the number of reference files (%d)." % (num_ref_files, num_results))
         if num_ref_files < 1 or num_results < 1:
             raise RuntimeError("There needs to be a least one result and "
                                "reference.")
@@ -1143,8 +1143,8 @@ class IRISConvFit(ISISIndirectInelasticConvFit):
         self.resolution = FileFinder.getFullPath('irs53664_graphite002_res.nxs')
         #ConvFit fit function
         self.func = 'name=LinearBackground,A0=0.060623,A1=0.001343;(composite=Convolution,FixResolution=true,NumDeriv=true;'\
-                    'name=Resolution,Workspace=\"%s\";name=Lorentzian,Amplitude=1.033150,PeakCentre=-0.000841,FWHM=0.001576)' % (
-                    self.resolution)
+                    'name=Resolution,Workspace=\"%s\";name=Lorentzian,Amplitude=1.033150,PeakCentre=-0.000841,FWHM=0.001576)'\
+                    % (self.resolution)
         self.ftype = '1L'
         self.startx = -0.2
         self.endx = 0.2
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ISISReflInstrumentIDFTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ISISReflInstrumentIDFTest.py
index 9a3737b1c7026c61cfd048ffb5f71180a0c74cc1..cbd1f4739e9d35cf77f0332db0596f0c07f1f2b3 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ISISReflInstrumentIDFTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ISISReflInstrumentIDFTest.py
@@ -1,4 +1,4 @@
-#pylint: disable=no-init,invalid-name
+#pylint: disable=no-init,invalid-name,too-few-public-methods
 """
 These system tests are to verify that the IDF and parameter files for POLREF, CRISP, INTER and SURF are read properly
 """
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/IndirectDiffractionTests.py b/Code/Mantid/Testing/SystemTests/tests/analysis/IndirectDiffractionTests.py
index b847316984025ec3dc07581d4871215e23d04538..45ba4c68a47a93c3d65a0c3ae659f796447c07d9 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/IndirectDiffractionTests.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/IndirectDiffractionTests.py
@@ -1,4 +1,4 @@
-#pylint: disable=no-init,non-parent-init-called
+#pylint: disable=no-init,non-parent-init-called,too-few-public-methods
 # non-parent-init-called is disabled to remove false positives from a bug in pyLint < 1.4
 
 from abc import ABCMeta, abstractmethod
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/LRScalingFactorsTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/LRScalingFactorsTest.py
index afdf17e061eddf25049f34bb30598695e5b9f161..e5d97c36024d4e02ed9c18d3a584e8d31f33ba65 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/LRScalingFactorsTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/LRScalingFactorsTest.py
@@ -10,8 +10,10 @@ class LRPrimaryFractionTest(stresstesting.MantidStressTest):
     #
     #lambdaRequested[Angstroms] S1H[mm] (S2/Si)H[mm] S1W[mm] (S2/Si)W[mm] a b error_a error_b
     #
-    IncidentMedium=Air LambdaRequested=5.0 S1H=0.202 S2iH=0.196767 S1W=9.002 S2iW=9.004654 a=7.79202718645 b=3.39894488089e-05 error_a=0.0936282133631 error_b=5.79945870854e-06
-    IncidentMedium=Air LambdaRequested=5.0 S1H=0.202 S2iH=0.196767 S1W=20.0 S2iW=20.007348 a=24.4210636894 b=0.00010609255313 error_a=0.390001391338 error_b=2.51447482677e-05
+    #IncidentMedium=Air LambdaRequested=5.0 S1H=0.202 S2iH=0.196767 S1W=9.002 S2iW=9.004654
+    #a=7.79202718645 b=3.39894488089e-05 error_a=0.0936282133631 error_b=5.79945870854e-06
+    #IncidentMedium=Air LambdaRequested=5.0 S1H=0.202 S2iH=0.196767 S1W=20.0 S2iW=20.007348
+    #a=24.4210636894 b=0.00010609255313 error_a=0.390001391338 error_b=2.51447482677e-05
 
     """
     def runTest(self):
@@ -19,7 +21,7 @@ class LRPrimaryFractionTest(stresstesting.MantidStressTest):
         LRScalingFactors(DirectBeamRuns=[124168, 124169, 124170, 124171, 124172],
                          Attenuators = [0, 1, 1, 2, 2, 2],
                          TOFRange=[10008, 35000], TOFSteps=200,
-                         SignalPeakPixelRange=[150, 160], 
+                         SignalPeakPixelRange=[150, 160],
                          SignalBackgroundPixelRange=[147, 163],
                          ScalingFactorFile=self.cfg_file)
 
@@ -30,31 +32,31 @@ class LRPrimaryFractionTest(stresstesting.MantidStressTest):
         reference = [[7.82, 3.20e-05, 0.054, 3.3e-06],
                      [24.42, 0.000105, 0.225, 1.45e-05]]
         tolerances = [[0.1, 5e-6, 0.1, 3e-6], [0.1, 1e-5, 0.2, 2e-5]]
-        fd = open(self.cfg_file, 'r')
+        filed = open(self.cfg_file, 'r')
         item_number = 0
-        for line in fd.readlines():
+        for line in filed.readlines():
             if line.startswith("#"):
                 continue
             toks = line.split()
             for token in toks:
                 pair = token.split('=')
                 if pair[0].strip() == 'a':
-                    a = float(pair[1])
+                    data_a = float(pair[1])
                 elif pair[0].strip() == 'b':
-                    b = float(pair[1])
+                    data_b = float(pair[1])
                 elif pair[0].strip() == 'error_a':
                     error_a = float(pair[1])
                 elif pair[0].strip() == 'error_b':
                     error_b = float(pair[1])
-            if not (abs(reference[item_number][0]- a ) < tolerances[item_number][0] \
-                and abs(reference[item_number][1] - b) < tolerances[item_number][1] \
+            if not (abs(reference[item_number][0]- data_a ) < tolerances[item_number][0] \
+                and abs(reference[item_number][1] - data_b) < tolerances[item_number][1] \
                 and abs(reference[item_number][2]-error_a) < tolerances[item_number][2] \
                 and abs(reference[item_number][3] - error_b) < tolerances[item_number][3]):
-                logger.error("Found    %5.3g %5.3g %5.3g %5.3g" % (a, b, error_a, error_b))
+                logger.error("Found    %5.3g %5.3g %5.3g %5.3g" % (data_a, data_b, error_a, error_b))
                 logger.error("Expected %5.3g %5.3g %5.3g %5.3g" % (reference[item_number][0], reference[item_number][1],
                                                                    reference[item_number][2], reference[item_number][3]))
                 return False
             item_number += 1
-        fd.close()
+        filed.close()
         os.remove(self.cfg_file)
         return True
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadAndCheckBase.py b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadAndCheckBase.py
index 324527385f7881411d841469415cc0c210cef8d4..e66d1ab75053d8ce431cfe43ff9f6bed995fe97e 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadAndCheckBase.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadAndCheckBase.py
@@ -5,7 +5,7 @@ These system tests are to verify the behaviour of the ISIS reflectometry reducti
 
 import stresstesting
 from mantid.simpleapi import *
-import mantid.api._api
+import mantid.api
 
 from abc import ABCMeta, abstractmethod
 
@@ -67,14 +67,14 @@ class LoadAndCheckBase(stresstesting.MantidStressTest):
         self.assertTrue(type(a) == type(b))
 
         #raise NotImplementedError()
-        if isinstance(a,mantid.api._api.WorkspaceGroup):
+        if isinstance(a,mantid.api.WorkspaceGroup):
             self.assertEqual(a.size(), b.size())
             self.assertEqual(a.size(), n_periods)
             # Loop through each workspace in the group and apply some simple comaprison checks.
             for i in range(0, a.size()):
                 self.do_check_workspace_shape(a[i], b[i])
             if self.enable_instrument_checking():
-                self.do_check_instrument_applied(a[i], b[i])
+                self.do_check_instrument_applied(a[-1], b[-1])
             if self.enable_reference_result_checking():
                 Integration(InputWorkspace=a[0], OutputWorkspace=self.__comparison_out_workspace_name)
         else:
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadEmbeddedInstrumentInfo.py b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadEmbeddedInstrumentInfo.py
index 7ab8f0630bc47aac3c127af14760fbd7381f0cc7..944933366c93b86086652b675816ff4fa4f49b92 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadEmbeddedInstrumentInfo.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadEmbeddedInstrumentInfo.py
@@ -2,13 +2,12 @@
 import stresstesting
 from mantid.simpleapi import *
 
-"""
-Here testing against embedded instrument info in different raw file formats
-
-This include to test that embedded information in raw ISIS Nexus file formats
-get loaded correctly.
-
-"""
+#
+#Here testing against embedded instrument info in different raw file formats
+#
+#This include to test that embedded information in raw ISIS Nexus file formats
+#get loaded correctly.
+#
 
 # here test against a custom made ISIS raw hist nexus file created by Freddie
 # where the A1_window has be, for the purpose of testing, been put at a
@@ -16,12 +15,11 @@ get loaded correctly.
 class ISISRawHistNexus(stresstesting.MantidStressTest):
 
     def runTest(self):
-
-    # ISIS raw hist nexus file with A1_window at location (0,3,0)
+        # ISIS raw hist nexus file with A1_window at location (0,3,0)
+        #pylint: disable=(unused-variable
         MAPS00018314_raw_ISIS_hist = Load('MAPS00018314.nxs')
 
     def validate(self):
-
         MAPS00018314_raw_ISIS_hist = mtd['MAPS00018314_raw_ISIS_hist']
         inst = MAPS00018314_raw_ISIS_hist.getInstrument()
         A1window = inst.getComponentByName('MAPS/A1_window')
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py
index 39998642b3115a590c5d30cd2f8526c4c167b0d3..58d6da4fc707f3bdd6676960de74d5d616d338db 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py
@@ -9,7 +9,7 @@ class LoadMuonNexusTest(stresstesting.MantidStressTest):
       # Checked specifically because stores resulution (used to calculate FirstGoodData)
       # as NX_FLOAT32 opposed to NX_INT32 in other Muon files.
         loadResult = LoadMuonNexus(Filename = "EMU03087.nxs",
-                                 OutputWorkspace = "EMU03087")
+                                   OutputWorkspace = "EMU03087")
 
         firstGoodData = loadResult[3]
         self.assertDelta(firstGoodData, 0.416, 0.0001)
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/MuonLoadTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/MuonLoadTest.py
index 7ea0ee850a68ff3215c56b191a1a66b862e2389c..721b8828f7bf3c6788e62223dda9dd77539b46e1 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/MuonLoadTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/MuonLoadTest.py
@@ -21,22 +21,21 @@ class MuonLoadTest(stresstesting.MantidStressTest):
         mtd.addOrReplace("MuonLoad_DeadTimes", deadTimes)
 
         MuonLoad(Filename = "MUSR00015192",
-               DetectorGroupingTable = "MuonLoad_Grouping",
-               ApplyDeadTimeCorrection = True,
-               CustomDeadTimeTable = "MuonLoad_DeadTimes",
-               FirstPeriod = 1,
-               SecondPeriod = 0,
-               PeriodOperation = "-",
-               TimeZero = 0.6,
-               Xmin = 0.11,
-               Xmax = 10.0,
-               RebinParams = "0.032",
-               OutputType = "PairAsymmetry",
-               PairFirstIndex = 0,
-               PairSecondIndex = 1,
-               Alpha = 0.8,
-               OutputWorkspace = "MuonLoad_MUSR00015192"
-              )
+                 DetectorGroupingTable = "MuonLoad_Grouping",
+                 ApplyDeadTimeCorrection = True,
+                 CustomDeadTimeTable = "MuonLoad_DeadTimes",
+                 FirstPeriod = 1,
+                 SecondPeriod = 0,
+                 PeriodOperation = "-",
+                 TimeZero = 0.6,
+                 Xmin = 0.11,
+                 Xmax = 10.0,
+                 RebinParams = "0.032",
+                 OutputType = "PairAsymmetry",
+                 PairFirstIndex = 0,
+                 PairSecondIndex = 1,
+                 Alpha = 0.8,
+                 OutputWorkspace = "MuonLoad_MUSR00015192")
 
     def validate(self):
         return "MuonLoad_MUSR00015192", "MuonLoad_MUSR00015192.nxs"
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/OFFSPECReflRedOneAuto.py b/Code/Mantid/Testing/SystemTests/tests/analysis/OFFSPECReflRedOneAuto.py
index e86dabf6354e37d567d82f96a3f9a82de75815be..091f0275ffd49a514e4f5788f2f253f612375ac6 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/OFFSPECReflRedOneAuto.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/OFFSPECReflRedOneAuto.py
@@ -15,22 +15,20 @@ class OFFSPECReflRedOneAuto(stresstesting.MantidStressTest):
         offspec85 = Load("OFFSPEC00027585.raw") #transmission run
 
         #Process using ReflectometryReductionOneAuto
-        ivq_75, __, __ = ReflectometryReductionOneAuto(
-                offspec75,
-                ThetaIn=0.35,
-                FirstTransmissionRun=offspec85)
+        ivq_75, __, __ = ReflectometryReductionOneAuto(offspec75,
+                                                       ThetaIn=0.35,
+                                                       FirstTransmissionRun=offspec85)
 
-        ivq_76, __, __ = ReflectometryReductionOneAuto(
-                offspec76,
-                ThetaIn=1.00,
-                FirstTransmissionRun=offspec85)
+        ivq_76, __, __ = ReflectometryReductionOneAuto(offspec76,
+                                                       ThetaIn=1.00,
+                                                       FirstTransmissionRun=offspec85)
 
-        ivq_78, __, __ = ReflectometryReductionOneAuto(
-                offspec78,
-                ThetaIn=1.70,
-                FirstTransmissionRun=offspec85)
+        ivq_78, __, __ = ReflectometryReductionOneAuto(offspec78,
+                                                       ThetaIn=1.70,
+                                                       FirstTransmissionRun=offspec85)
 
         ivq_75_76, __ = Stitch1D(ivq_75, ivq_76, Params="1e-3")
+        #pylint: disable=unused-variable
         ivq_75_76_78, __ = Stitch1D(ivq_75_76, ivq_78, Params="0,1e-3,0.08")
         return True
 
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/PEARLPowderDiffraction.py b/Code/Mantid/Testing/SystemTests/tests/analysis/PEARLPowderDiffraction.py
index a4537f331cd3e7f357570d9fa4614bac7a8d85b1..abc2e1693accd11d623037ce33d0e4ce20121eff 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/PEARLPowderDiffraction.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/PEARLPowderDiffraction.py
@@ -19,7 +19,7 @@ class PEARLPowderDiffraction(stresstesting.MantidStressTest):
         LoadRaw(Filename=self.sample, OutputWorkspace='monitor73987',LoadLogFiles='0',SpectrumMax='1')
         ConvertUnits(InputWorkspace='monitor73987',OutputWorkspace='monitor73987',Target='Wavelength')
         CropWorkspace(InputWorkspace='monitor73987',OutputWorkspace='monitor73987',
-                  XMin=0.03,XMax=6.0)
+                      XMin=0.03,XMax=6.0)
 
         MaskBins(InputWorkspace='monitor73987',OutputWorkspace='monitor73987',XMin=3.45,XMax=3.7)
         MaskBins(InputWorkspace='monitor73987',OutputWorkspace='monitor73987',XMin=2.96,XMax=3.2)
@@ -28,14 +28,14 @@ class PEARLPowderDiffraction(stresstesting.MantidStressTest):
 
         SplineBackground(InputWorkspace='monitor73987',OutputWorkspace='monitor73987',NCoeff=20)
         NormaliseToMonitor(InputWorkspace='work',OutputWorkspace='work',MonitorWorkspace='monitor73987',
-                       IntegrationRangeMin=0.6,IntegrationRangeMax=5.0)
+                           IntegrationRangeMin=0.6,IntegrationRangeMax=5.0)
         ConvertUnits(InputWorkspace='work',OutputWorkspace='work',Target='TOF')
 
         rb_params = [1500,-0.0006,19900]
         Rebin(InputWorkspace='work',OutputWorkspace='work',Params=rb_params)
         AlignDetectors(InputWorkspace='work',OutputWorkspace='work', CalibrationFile=self.calfile)
         DiffractionFocussing(InputWorkspace='work',OutputWorkspace='focus',
-                         GroupingFileName=self.groupfile)
+                             GroupingFileName=self.groupfile)
 
         ConvertUnits(InputWorkspace='focus',OutputWorkspace='focus',Target='TOF')
         Rebin(InputWorkspace='focus',OutputWorkspace='focus',Params=rb_params)
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/POLDIAutoCorrelationTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/POLDIAutoCorrelationTest.py
index c586c6714315f3e5d5e4f221219cac18273714a4..70b4c876caf9ce02689d064558cc55dec98b2b9e 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/POLDIAutoCorrelationTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/POLDIAutoCorrelationTest.py
@@ -32,8 +32,8 @@ class POLDIAutoCorrelationTest(stresstesting.MantidStressTest):
             calculatedData = mtd["%sCorr" % (dataFile)].dataY(0)
 
             self.assertEqual(calculatedData.shape[0], referenceData.shape[0],
-                             "Number of d-values does not match for %s (is: %i, should: %i)" % (
-                             dataFile, calculatedData.shape[0], referenceData.shape[0]))
+                             "Number of d-values does not match for %s (is: %i, should: %i)" % (dataFile,\
+                             calculatedData.shape[0], referenceData.shape[0]))
 
             CreateWorkspace(referenceData, calculatedData, OutputWorkspace=workspaceNameTemplate)
 
@@ -47,18 +47,18 @@ class POLDIAutoCorrelationTest(stresstesting.MantidStressTest):
             self.assertDelta(slope, 1.0, 1e-4, "Slope is larger than 1.0 for %s (is: %d)" % (dataFile, slope))
 
             relativeSlopeError = fitResult.cell(1, 2) / slope
-            self.assertLessThan(relativeSlopeError, 5e-4, "Relative error of slope is too large for %s (is: %d)" % (
-                                                          dataFile, relativeSlopeError))
+            self.assertLessThan(relativeSlopeError, 5e-4, "Relative error of slope is too large "
+                                "for %s (is: %d)" % (dataFile, relativeSlopeError))
 
             intercept = fitResult.cell(0, 1)
             self.assertDelta(intercept, 0.0, 1.0, "Intercept deviates too far from 0 %s (is: %d)" % (dataFile, intercept))
 
             relativeInterceptError = fitResult.cell(0, 2) / intercept
-            self.assertLessThan(relativeInterceptError, 1, "Relative error of intercept is too large for %s (is: %d)" % (
-                                                           dataFile, relativeInterceptError))
+            self.assertLessThan(relativeInterceptError, 1, "Relative error of intercept is too large "
+                                "for %s (is: %d)" % (dataFile, relativeInterceptError))
 
             residuals = mtd[fitNameTemplate + "_Workspace"].dataY(2)
             maxAbsoluteResidual = np.max(np.abs(residuals))
-            self.assertLessThan(maxAbsoluteResidual, 1.0, "Maximum absolute residual is too large for %s (is: %d)" % (
-                                                          dataFile, maxAbsoluteResidual))
+            self.assertLessThan(maxAbsoluteResidual, 1.0, "Maximum absolute residual is too large "
+                                "for %s (is: %d)" % (dataFile, maxAbsoluteResidual))
 
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/POLDICreatePeaksFromCellTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/POLDICreatePeaksFromCellTest.py
index b74ba222a4a944f8bd9b158ed297a777ee456a8e..9bbea035571187aca4c2ff90d5da97b075083ad9 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/POLDICreatePeaksFromCellTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/POLDICreatePeaksFromCellTest.py
@@ -1,4 +1,4 @@
-# pylint: disable=no-init,invalid-name,too-many-locals
+# pylint: disable=no-init,invalid-name,too-many-locals,too-few-public-methods
 import stresstesting
 from mantid.simpleapi import *
 
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/PowderDiffProfileCalibrateTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/PowderDiffProfileCalibrateTest.py
index bd6148ee6421b4cd24dd4a1255794aa4479ec2aa..73ef84ab1d06cb57a9ead72d642eb701a9cda82d 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/PowderDiffProfileCalibrateTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/PowderDiffProfileCalibrateTest.py
@@ -17,6 +17,7 @@ class VulcanExamineProfile(stresstesting.MantidStressTest):
     irf_file = 'arg_powder.irf'
     dat_file = 'arg_si.dat'
     bkgd_file = 'arg_si_bkgd_polynomial.nxs'
+    tolerance=1.0e-6
 
     def requiredFiles(self):
         files = [self.irf_file, self.dat_file, self.bkgd_file]
@@ -60,6 +61,7 @@ class VulcanSeqRefineProfileFromScratch(stresstesting.MantidStressTest):
     """
     irf_file = 'VULCAN_SNS_1.irf'
     dat_file = 'VULCAN_22946_NOM.dat'
+    tolerance=1.0e-6
 
     def requiredFiles(self):
         files = [self.irf_file, self.dat_file]
@@ -184,6 +186,7 @@ class VulcanSeqRefineProfileLoadPlus(stresstesting.MantidStressTest):
     """ System test for sequential refinement
     """
     seqfile = "VULCAN_Calibrate_Seq.nxs"
+    tolerance=1.0e-6
 
     def requiredFiles(self):
         files = [self.seqfile]
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/RawVNexus.py b/Code/Mantid/Testing/SystemTests/tests/analysis/RawVNexus.py
index 12081a8b6be0809f5ec2a31ca2ebda3ae2b1790f..41790da97816f8ac78af1031e5b2fc333a994197 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/RawVNexus.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/RawVNexus.py
@@ -1,4 +1,4 @@
-#pylint: disable=no-init
+#pylint: disable=no-init,unused-variable
 import stresstesting
 from mantid.simpleapi import *
 
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ReflectometryQuickPointDetectorMakeTransmission.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ReflectometryQuickPointDetectorMakeTransmission.py
index d32736ea18b346433ca9312a4be21767be380d2b..c6910ec9e46e575eefe3a1c07b25c675950c3529 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ReflectometryQuickPointDetectorMakeTransmission.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ReflectometryQuickPointDetectorMakeTransmission.py
@@ -23,7 +23,7 @@ class ReflectometryQuickPointDetectorMakeTransmission(stresstesting.MantidStress
             runNo = '13460'
             incidentAngle = 0.7
             transmissionWs=quick.make_trans_corr(transmissionRuns, stitch_start_overlap=10,
-                                  stitch_end_overlap=12, stitch_params=[1.5,0.02,17])
+                                                 stitch_end_overlap=12, stitch_params=[1.5,0.02,17])
             quick.quick(runNo, trans=transmissionWs, theta=incidentAngle)
         finally:
             config[defaultInstKey] = defaultInstrument
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SANS2DMultiPeriod.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SANS2DMultiPeriod.py
index 9be38098fc830d44baad26e0e9a078f9044d3e9d..82205ed962add9119ecc29d4505c3e8fce09b115 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SANS2DMultiPeriod.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SANS2DMultiPeriod.py
@@ -1,4 +1,4 @@
-#pylint: disable=no-init
+#pylint: disable=no-init,too-few-public-methods
 import stresstesting
 
 from mantid.simpleapi import *
@@ -9,6 +9,8 @@ from SANSBatchMode import *
 # test batch mode with sans2d and selecting a period in batch mode
 class SANS2DMultiPeriodSingle(stresstesting.MantidStressTest):
 
+    reduced=''
+
     def runTest(self):
 
         SANS2D()
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py
index 34ffa09f049369bea5aea8f378fa48b389872824..4843ba44cc37039c0f32d8e5b6125c3cefbc65af 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py
@@ -81,7 +81,6 @@ def validateMD(result,reference,tol=1.e-5,class_name='dummy',mismatchName=None):
       #elf.disableChecking.append('Instrument')
 
     valNames = [result,reference]
-    from mantid.simpleapi import Load
 
     if not reference in mtd:
         Load(Filename=reference,OutputWorkspace=valNames[1])
@@ -112,6 +111,9 @@ def validateMD(result,reference,tol=1.e-5,class_name='dummy',mismatchName=None):
 
 class SNSConvertToMDNoHistNoProjTest(stresstesting.MantidStressTest):
     truth_file = "SEQ_11499_md_enp.nxs"
+    output_ws=None
+    tolerance=0.0
+    gold_ws_name =''
 
     def requiredMemoryMB(self):
         """ Require about 2.5GB free """
@@ -134,6 +136,9 @@ class SNSConvertToMDNoHistNoProjTest(stresstesting.MantidStressTest):
 
 class SNSConvertToMDHistNoProjTest(stresstesting.MantidStressTest):
     truth_file = "SEQ_11499_md_hnp.nxs"
+    output_ws=None
+    tolerance=0.0
+    gold_ws_name =''
 
     def requiredMemoryMB(self):
         """ Require about 2.5GB free """
@@ -156,6 +161,9 @@ class SNSConvertToMDHistNoProjTest(stresstesting.MantidStressTest):
 
 class SNSConvertToMDNoHistProjTest(stresstesting.MantidStressTest):
     truth_file = "SEQ_11499_md_ewp.nxs"
+    output_ws=None
+    tolerance=0.0
+    gold_ws_name =''
 
     def requiredMemoryMB(self):
         """ Require about 2.5GB free """
@@ -179,6 +187,9 @@ class SNSConvertToMDNoHistProjTest(stresstesting.MantidStressTest):
 
 class SNSConvertToMDHistProjTest(stresstesting.MantidStressTest):
     truth_file = "SEQ_11499_md_hwp.nxs"
+    output_ws=None
+    tolerance=0.0
+    gold_ws_name =''
 
     def requiredMemoryMB(self):
         """ Require about 2.5GB free """
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SXDAnalysis.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SXDAnalysis.py
index c859e0b3748a8dfce1eeac60c72470cedd343e6e..affb6c1416bf60fa64fa40a49166b7153cf85b21 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SXDAnalysis.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SXDAnalysis.py
@@ -22,7 +22,7 @@ class SXDAnalysis(stresstesting.MantidStressTest):
 
         #  NaCl has a relatively small unit cell, so the distance between peaks is relatively large.  Setting the PeakDistanceThreshold
         #  higher avoids finding high count regions on the sides of strong peaks as separate peaks.
-        peaks_qLab = FindPeaksMD(InputWorkspace='QLab', MaxPeaks=300, DensityThresholdFactor=10, PeakDistanceThreshold=1.0)
+        peaks_qLab = FindPeaksMD(InputWorkspace=QLab, MaxPeaks=300, DensityThresholdFactor=10, PeakDistanceThreshold=1.0)
 
         FindUBUsingFFT(PeaksWorkspace=peaks_qLab, MinD='3', MaxD='5',Tolerance=0.08)
 
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py
index 6aac43d5a79a5981661fc0539cf7ca88a0fa626b..997de79533fa67b76e7be09a13094132e02e6331 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py
@@ -25,7 +25,7 @@ class SpaceGroupFactoryTest(stresstesting.MantidStressTest):
 
         self.assertTrue(group.isGroup(),
                         ("Space group " + str(group.getNumber()) + " (" + symbol + ") does not "
-                        "fulfill group axioms"))
+                         "fulfill group axioms"))
 
         groupOperations = set(group.getSymmetryOperationStrings())
         referenceOperations = self.spaceGroupData[group.getNumber()]
@@ -51,10 +51,9 @@ class SpaceGroupFactoryTest(stresstesting.MantidStressTest):
         self.assertFalse(
             set(onlyMatrices.getSymmetryOperationStrings()).isdisjoint(pointGroup.getSymmetryOperationStrings()),
             ("Point group of space group " + spaceGroup.getHMSymbol() + " does not match group obtained from"
-            " matrices of symmetry operations."))
+             " matrices of symmetry operations."))
 
     def loadReferenceData(self):
-        from mantid.api import FileFinder
         # Reference data, generated using sginfo (http://cci.lbl.gov/sginfo/)
         # Dictionary has a string set for each space group number.
         separatorMatcher = re.compile(r"(\d+)")
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SurfLoadingTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SurfLoadingTest.py
index f39d1f222932cbbefbeb2ea8d080e2a949a1ebc6..aa7b36d1c6b155b90bc760c77e06f995a9850cd7 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SurfLoadingTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SurfLoadingTest.py
@@ -1,10 +1,11 @@
 #pylint: disable=no-init
 from LoadAndCheckBase import *
 
-'''
-Test File loading and basic data integrity checks of SURF data in Mantid.
-'''
 class SurfLoadingTest(LoadAndCheckBase):
+    '''
+    Test File loading and basic data integrity checks of SURF data in Mantid.
+    '''
+
     def get_raw_workspace_filename(self):
         return "SRF92132.raw"