Merge branch 'master' into feature/10855_rewrite_indirect_diffraction…

…_reduction

Conflicts:
	Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSGDiffractionReduction.py
	Code/Mantid/scripts/Inelastic/IndirectDiffractionReduction.py

Refs #10855

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -41,7 +41,7 @@ set ( TESTING_TIMEOUT 300 CACHE INTEGER
       "Timeout in seconds for each test (default 300=5minutes)")
 
 ###########################################################################
-# Look for dependencies - bail out if any not found
+# Look for dependencies
 ###########################################################################
 
 set ( Boost_NO_BOOST_CMAKE TRUE )
@@ -71,6 +71,14 @@ set ( CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH}/zlib123 )
 find_package ( ZLIB REQUIRED )
 set ( CMAKE_INCLUDE_PATH ${MAIN_CMAKE_INCLUDE_PATH} )
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows" OR OSX_VERSION VERSION_LESS 10.9)
+  set (HDF5_DIR "${CMAKE_MODULE_PATH}")
+  find_package ( HDF5 COMPONENTS HL REQUIRED
+    CONFIGS hdf5-config.cmake )
+else()
+  find_package ( HDF5 COMPONENTS HL REQUIRED )
+endif()
+
 find_package ( PythonInterp )
 
 if ( MSVC )
@@ -305,29 +313,7 @@ endif()
 # External Data for testing
 ###########################################################################
 if ( CXXTEST_FOUND OR PYUNITTEST_FOUND )
- include ( MantidExternalData )
-
-# None of our tests reference files directly as arguments so we have to manually
-# call ExternalData_Expand_Arguments to register the files with the ExternalData
-# mechanism
-get_filename_component ( EXTERNALDATATEST_SOURCE_DIR ${PROJECT_SOURCE_DIR} ABSOLUTE )
-file( GLOB_RECURSE doctest_content_links
-  RELATIVE "${EXTERNALDATATEST_SOURCE_DIR}" "Testing/Data/DocTest/*.md5" )
-file( GLOB_RECURSE unittest_content_links
-  RELATIVE "${EXTERNALDATATEST_SOURCE_DIR}" "Testing/Data/UnitTest/*.md5" )
-set ( content_links "${doctest_content_links};${unittest_content_links}" )
-foreach(link ${content_links})
-  string( REGEX REPLACE "\\.md5$" "" link ${link} )
-  ExternalData_Expand_Arguments( StandardTestData
-    link_location
-    DATA{${link}}
-    )
-endforeach()
-
-# Create target to download data from the StandardTestData group.  This must come after
-# all tests have been added that reference the group, so we put it last.
-ExternalData_Add_Target(StandardTestData)
-set_target_properties(StandardTestData PROPERTIES EXCLUDE_FROM_ALL TRUE)
+  include( SetupDataTargets )
 endif()
 
 ###########################################################################

Code/Mantid/Build/CMake/CppCheck_Suppressions.txt

@@ -4,6 +4,6 @@
 
 // suppress in all files - BE CAREFULL not to leave trailing spaces after the rule id. or empty lines
 // For a library this is not a problem per se
-unusedFunction
+// unusedFunction
 // cppcheck has problems handling the number of pre-processor definitions used in the DLL_EXPORTs
-class_X_Y
+class_X_Y

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -80,7 +80,7 @@ endif ()
 # Force 64-bit compiler as that's all we support
 ###########################################################################
 
-set ( CLANG_WARNINGS "-Wall -Wno-deprecated-register")
+set ( CLANG_WARNINGS "-Wall -Wextra -Winit-self -Wpointer-arith -Wcast-qual -fno-common  -Wno-deprecated-register")
 
 set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64 ${CLANG_WARNINGS}" )
 set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -std=c++0x" )

Code/Mantid/Build/CMake/EmbeddedGTest.cmake

@@ -3,8 +3,8 @@
 # GTEST_FOUND If false, do not try to use Google Test
 
 find_path ( GTEST_INCLUDE_DIR gtest/gtest.h
-            PATHS ${PROJECT_SOURCE_DIR}/TestingTools/gmock-${GMOCK_VERSION}/gtest/include
-                  ${PROJECT_SOURCE_DIR}/../TestingTools/gmock-${GMOCK_VERSION}/gtest/include 
+            PATHS ${PROJECT_SOURCE_DIR}/Testing/Tools/gmock-${GMOCK_VERSION}/gtest/include
+                  ${PROJECT_SOURCE_DIR}/../Testing/Tools/gmock-${GMOCK_VERSION}/gtest/include 
             NO_DEFAULT_PATH )
 
 # handle the QUIETLY and REQUIRED arguments and set GTEST_FOUND to TRUE if 

Code/Mantid/Build/CMake/FindCxxTest.cmake

@@ -194,8 +194,8 @@ endmacro(CXXTEST_ADD_TEST)
 #=============================================================
 
 find_path(CXXTEST_INCLUDE_DIR cxxtest/TestSuite.h
-          PATHS ${PROJECT_SOURCE_DIR}/TestingTools/cxxtest
-	        ${PROJECT_SOURCE_DIR}/../TestingTools/cxxtest )
+          PATHS ${PROJECT_SOURCE_DIR}/Testing/Tools/cxxtest
+	        ${PROJECT_SOURCE_DIR}/../Testing/Tools/cxxtest )
 
 find_program(CXXTEST_TESTGEN_EXECUTABLE python/scripts/cxxtestgen
              PATHS ${CXXTEST_INCLUDE_DIR})

Code/Mantid/Build/CMake/FindGMock.cmake

@@ -17,8 +17,8 @@ ENDIF()
 set (GMOCK_VERSION ${GMOCK_VERSION} CACHE INTERNAL "")
 
 find_path ( GMOCK_INCLUDE_DIR gmock/gmock.h
-            PATHS ${PROJECT_SOURCE_DIR}/TestingTools/gmock-${GMOCK_VERSION}/include
-                  ${PROJECT_SOURCE_DIR}/../TestingTools/gmock-${GMOCK_VERSION}/include
+            PATHS ${PROJECT_SOURCE_DIR}/Testing/Tools/gmock-${GMOCK_VERSION}/include
+                  ${PROJECT_SOURCE_DIR}/../Testing/Tools/gmock-${GMOCK_VERSION}/include
             NO_DEFAULT_PATH )
 
 SET(GMOCK_LIB gmock)

Code/Mantid/Build/CMake/FindOpenCascade.cmake

@@ -18,50 +18,61 @@ if ( WIN32 )
   add_definitions ( -DWNT )
 endif ( WIN32 )
 
-set ( OC_REDHAT_RPM /opt/OpenCASCADE/lib64 )
+find_path ( OPENCASCADE_LIBRARY_DIR libTKernel.so PATHS
+                /opt/OpenCASCADE/lib64
+                $ENV{CASROOT}/lib64
+                /opt/OpenCASCADE/lib
+                $ENV{CASROOT}/lib
+                /opt/OpenCASCADE/lib32
+                $ENV{CASROOT}/lib32
+)
+
 find_library ( OPENCASCADE_LIB_TKERNEL
                  NAMES TKernel
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKBO
                  NAMES TKBO
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKPRIM
                  NAMES TKPrim
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKMESH
                  NAMES TKMesh
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKBREP
                  NAMES TKBRep
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKTOPALGO
                  NAMES TKTopAlgo
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKMATH
                  NAMES TKMath
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 find_library ( OPENCASCADE_LIB_TKG2D
                  NAMES TKG2d
-                 PATHS ${OC_REDHAT_RPM}         
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
 find_library ( OPENCASCADE_LIB_TKG3D
                  NAMES TKG3d
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
 find_library ( OPENCASCADE_LIB_TKGEOMBASE
                  NAMES TKGeomBase
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
-find_library ( OPENCASCADE_LIB_TKGEOMAlgo
+find_library ( OPENCASCADE_LIB_TKGEOMALGO
                  NAMES TKGeomAlgo
+                 PATHS ${OPENCASCADE_LIBRARY_DIR}
 )
 
 set ( OPENCASCADE_LIBRARIES
@@ -83,7 +94,7 @@ set ( OPENCASCADE_LIBRARIES
 include ( FindPackageHandleStandardArgs )
 find_package_handle_standard_args( OpenCascade DEFAULT_MSG OPENCASCADE_LIBRARIES OPENCASCADE_INCLUDE_DIR )
 
-mark_as_advanced ( OPENCASCADE_INCLUDE_DIR
+mark_as_advanced ( OPENCASCADE_INCLUDE_DIR OPENCASCADE_LIBRARY_DIR
                    OPENCASCADE_LIB_TKERNEL OPENCASCADE_LIB_TKBO 
                    OPENCASCADE_LIB_TKPRIM OPENCASCADE_LIB_TKMESH
                    OPENCASCADE_LIB_TKBREP OPENCASCADE_LIB_TKTOPALGO 

Code/Mantid/Build/CMake/FindPoco.cmake

@@ -61,14 +61,14 @@ if( POCO_INCLUDE_DIR )
   file ( STRINGS ${VERSION_FILE} POCO_VERSION REGEX ${VERS_REGEX} )
   # pull out just the part after the 0x
   string( REGEX REPLACE ${VERS_REGEX} "\\1" POCO_VERSION ${POCO_VERSION} )
+
   # Pretty format
   string( SUBSTRING ${POCO_VERSION} 0 2 POCO_VERSION_MAJOR )
-  string( REGEX REPLACE "^0" "" POCO_VERSION_MAJOR ${POCO_VERSION_MAJOR} )
+  string( REGEX REPLACE "^0\(.\)" "\\1" POCO_VERSION_MAJOR ${POCO_VERSION_MAJOR} )
   string( SUBSTRING ${POCO_VERSION} 2 2 POCO_VERSION_MINOR )
-  string( REGEX REPLACE "^0" "" POCO_VERSION_MINOR ${POCO_VERSION_MINOR} )
+  string( REGEX REPLACE "^0\(.\)" "\\1" POCO_VERSION_MINOR ${POCO_VERSION_MINOR} )
   string( SUBSTRING ${POCO_VERSION} 4 2 POCO_VERSION_PATCH )
-  string( REGEX REPLACE "^0" "" POCO_VERSION_PATCH ${POCO_VERSION_PATCH} )
-
+  string( REGEX REPLACE "^0\(.\)" "\\1" POCO_VERSION_PATCH ${POCO_VERSION_PATCH} )
   set ( POCO_VERSION "${POCO_VERSION_MAJOR}.${POCO_VERSION_MINOR}.${POCO_VERSION_PATCH}" )
 endif()
 

Code/Mantid/Build/CMake/FindPyUnitTest.cmake

@@ -59,13 +59,13 @@ endmacro ( PYUNITTEST_ADD_TEST )
 
 # find the driver script
 find_program ( PYUNITTEST_GEN_EXEC pyunit_gen.py
-               PATHS ${PROJECT_SOURCE_DIR}/TestingTools/pyunit_gen
-                     ${PROJECT_SOURCE_DIR}/../TestingTools/pyunit_gen )
+               PATHS ${PROJECT_SOURCE_DIR}/Testing/Tools/pyunit_gen
+                     ${PROJECT_SOURCE_DIR}/../Testing/Tools/pyunit_gen )
 
 # determine where the xmlrunner lives
 find_path ( PYUNITTEST_XMLRUNNER xmlrunner/__init__.py
-            PATHS ${PROJECT_SOURCE_DIR}/TestingTools/unittest-xml-reporting/src/
-                  ${PROJECT_SOURCE_DIR}/../TestingTools/unittest-xml-reporting/src/ )
+            PATHS ${PROJECT_SOURCE_DIR}/Testing/Tools/unittest-xml-reporting/src/
+                  ${PROJECT_SOURCE_DIR}/../Testing/Tools/unittest-xml-reporting/src/ )
 
 # let people know whether or not it was found
 if (PYUNITTEST_GEN_EXEC)