Merge branch 'master' into feature/7860_indirect_symmetrise

Conflicts:
	Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/Symmetrise.py
	Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt
	Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.ui
	Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReductionTab.cpp
	Code/Mantid/scripts/Inelastic/IndirectSymm.py

Refs #7860

.gitignore

@@ -162,4 +162,8 @@ Desktop.ini
 # Mac OS X Finder
 .DS_Store
 
+# Ctags index files
+.tags
+.tags_sorted_by_file
+
 Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -81,6 +81,14 @@ endif ()
 ###########################################################################
 set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64" )
 set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -std=c++0x" )
+set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LANGUAGE_STANDARD "c++0x" )
+
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+  set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++" )
+  set ( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-register" )
+  set ( CMAKE_XCODE_ATTRIBUTE_OTHER_CPLUSPLUSFLAGS "-Wno-deprecated-register")
+  set ( CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libc++" )
+endif()
 
 if( ${CMAKE_C_COMPILER} MATCHES "icc.*$" )
   set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -no-intel-extensions" )
@@ -113,8 +121,16 @@ if (OSX_VERSION VERSION_LESS 10.9)
  set ( SITEPACKAGES /Library/Python/${PY_VER}/site-packages )
 else()
  # Assume we are using homebrew for now
+ # set Deployment target to 10.8
+ set ( CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk )
+ set ( CMAKE_OSX_ARCHITECTURES x86_64 )
+ set ( CMAKE_OSX_DEPLOYMENT_TARGET 10.8 )
  set ( PYQT4_PYTHONPATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
  set ( SITEPACKAGES /usr/local/lib/python${PY_VER}/site-packages )
+ # use homebrew OpenSSL package
+ EXEC_PROGRAM( brew ARGS info openssl | grep openssl: | cut -c 17-22 OUTPUT_VARIABLE _openssl_version )
+ MESSAGE(STATUS "OpenSSL version: ${_openssl_version}")
+ set ( OPENSSL_ROOT_DIR /usr/local/Cellar/openssl/${_openssl_version}/ )
 endif()
 
 # Python packages

Code/Mantid/Build/CMake/FindQwt.cmake

@@ -1,47 +1,36 @@
 ###############################################################################
-# - Attempt to find Qwt libraries and include files. 
-# QWT_INCLUDE_DIR where to find qwt_plot.h, etc.
-# QWT_LIBRARIES libraries to link against
-# QWT_FOUND If false, do not try to use Qwt
-# QWT_VERSION Sets a string containing the version number parsed from 
-#             qwt_global.h
+# Attempt to find Qwt libraries and include files.
+# Set
+#   QWT_INCLUDE_DIR: where to find qwt_plot.h, etc.
+#   QWT_LIBRARIES:   libraries to link against
+#   QWT_VERSION:     a string containing the version number
 ###############################################################################
 
-find_path ( QWT_INCLUDE_DIR qwt.h PATHS
-            /usr/local/include 
-            /usr/include/qwt-qt4 
-            /usr/include/qwt 
-            /usr/include/qwt5 
-            /usr/include/qwt5-qt4
-	    ${CMAKE_INCLUDE_PATH}/qwt 
-)
-find_library ( QWT_LIBRARY NAMES qwt-qt4 qwt qwt5-qt4 )
+find_path ( QWT_INCLUDE_DIR qwt.h 
+            PATHS /opt/include /usr/local/include /usr/include ${CMAKE_INCLUDE_PATH}
+            PATH_SUFFIXES qwt5 qwt5-qt4 qwt-qt4 qwt )
+find_library ( QWT_LIBRARY NAMES qwt5-qt4 qwt-qt4 qwt )
 find_library ( QWT_LIBRARY_DEBUG qwtd )
 
-# handle the QUIETLY and REQUIRED arguments and set QWT_FOUND to TRUE if 
-# all listed variables are TRUE
+# in REQUIRED mode: terminate if one of the above find commands failed
 include ( FindPackageHandleStandardArgs )
 find_package_handle_standard_args( Qwt DEFAULT_MSG QWT_LIBRARY QWT_INCLUDE_DIR )
 
-if ( QWT_INCLUDE_DIR )
-  # Look for line in qwt_global.h containing version string
-  file ( STRINGS ${QWT_INCLUDE_DIR}/qwt_global.h QWT_VERSION 
-         REGEX "^#define[ \t]+QWT_VERSION_STR[ \t]+\"[0-9]+.[0-9]+.[0-9]+\"$" )
-  if ( NOT QWT_VERSION )
-    message ( WARNING "Unrecognized Qwt version, cannot find QWT_VERSION_STR in qwt_global.h" )
-    set ( QWT_VERSION "0.0.0" )
-  else()
-    # Hack off the portion up to and including the first double quote 
-    string( REGEX REPLACE "^#define[ \t]+QWT_VERSION_STR[ \t]+\"" "" QWT_VERSION ${QWT_VERSION} )
-    # Hack off the portion from the second double quote to the end of the line
-    string( REGEX REPLACE "\"$" "" QWT_VERSION ${QWT_VERSION} )
-  endif()
-
-  if ( QWT_LIBRARY_DEBUG )
-    set( QWT_LIBRARIES optimized ${QWT_LIBRARY} debug ${QWT_LIBRARY_DEBUG} )
-  else ()
-    set( QWT_LIBRARIES ${QWT_LIBRARY} )
-  endif ()
+# Parse version string from qwt_global.h
+file ( STRINGS ${QWT_INCLUDE_DIR}/qwt_global.h QWT_VERSION 
+       REGEX "^#define[ \t]+QWT_VERSION_STR[ \t]+\"[0-9]+.[0-9]+.[0-9]+\"$" )
+if ( NOT QWT_VERSION )
+    message ( FATAL_ERROR "Unrecognized Qwt version (cannot find QWT_VERSION_STR in qwt_global.h)" )
 endif()
+#   hack off the portion up to and including the first double quote 
+string( REGEX REPLACE "^#define[ \t]+QWT_VERSION_STR[ \t]+\"" "" QWT_VERSION ${QWT_VERSION} )
+#   hack off the portion from the second double quote to the end of the line
+string( REGEX REPLACE "\"$" "" QWT_VERSION ${QWT_VERSION} )
+
+if ( QWT_LIBRARY_DEBUG )
+  set( QWT_LIBRARIES optimized ${QWT_LIBRARY} debug ${QWT_LIBRARY_DEBUG} )
+else ()
+  set( QWT_LIBRARIES ${QWT_LIBRARY} )
+endif ()
 
 mark_as_advanced ( QWT_INCLUDE_DIR QWT_LIBRARY QWT_LIBRARY_DEBUG )

Code/Mantid/Build/CMake/FindSphinx.cmake

@@ -17,6 +17,28 @@ find_program( SPHINX_EXECUTABLE NAME sphinx-build
   DOC "Sphinx documentation generator"
 )
 
+if (SPHINX_EXECUTABLE)
+    # run sphinx-build to attempt to get the version
+    execute_process (COMMAND ${SPHINX_EXECUTABLE} --version
+                     OUTPUT_STRIP_TRAILING_WHITESPACE
+                     OUTPUT_VARIABLE version_string
+                     ERROR_VARIABLE version_error_string
+                     ERROR_STRIP_TRAILING_WHITESPACE)
+
+    # if it wasn't successful it is hiding in stderr
+    if (NOT version_string)
+        if ( version_error_string )
+            string (REGEX REPLACE "\n" ";" version_string ${version_error_string})
+            list (GET version_string 0 version_string)
+        else ( version_error_string )
+            set ( version_string "1.1.0" )
+        endif ( version_error_string )
+    endif (NOT version_string)
+
+    # chop out the version number
+    string (REGEX REPLACE ".*([0-9]+\\.[0-9]+\\.[0-9]+).*" "\\1" SPHINX_VERSION ${version_string})
+endif (SPHINX_EXECUTABLE)
+
 include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(Sphinx DEFAULT_MSG SPHINX_EXECUTABLE )

Code/Mantid/Build/CMake/GNUSetup.cmake

@@ -6,16 +6,12 @@
 # project settings should be included in the relevant CMakeLists.txt file
 # for that project.
 
-# Get the GCC version
-EXEC_PROGRAM(${CMAKE_CXX_COMPILER} ARGS --version | cut -d \" \" -f 3 OUTPUT_VARIABLE _compiler_output)
-STRING(REGEX REPLACE ".*([0-9]\\.[0-9]\\.[0-9]).*" "\\1" GCC_COMPILER_VERSION ${_compiler_output})
-MESSAGE(STATUS "gcc version: ${GCC_COMPILER_VERSION}")
-
-# Export the GCC compiler version globally
-set(GCC_COMPILER_VERSION ${GCC_COMPILER_VERSION} CACHE INTERNAL "")
+# Set our own compiler version flag from the cmake one and export it globally
+set( GCC_COMPILER_VERSION ${CMAKE_CXX_COMPILER_VERSION} CACHE INTERNAL "")
+message( STATUS "gcc version: ${GCC_COMPILER_VERSION}" )
 
 # Global warning flags.
-set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" ) 
+set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qual -Wcast-align -fno-common" )
 # Disable some warnings about deprecated headers and type conversions that
 # we can't do anything about
 # -Wno-deprecated: Do not warn about use of deprecated headers.
@@ -38,4 +34,3 @@ set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GNUFLAGS}" )
 set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GNUFLAGS} -Woverloaded-virtual -fno-operator-names -std=c++0x" )
 # Cleanup
 set ( GNUFLAGS )
-

Code/Mantid/Build/CMake/LinuxSetup.cmake

@@ -97,9 +97,15 @@ if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
 							             "  ln -s $RPM_INSTALL_PREFIX0/${BIN_DIR}/launch_mantidplot.sh $RPM_INSTALL_PREFIX0/${BIN_DIR}/MantidPlot\n"
                                                                      "fi\n"
 	)
-	file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh "#!/bin/sh\n"
-								      "scl enable mantidlibs \"${CMAKE_INSTALL_PREFIX}/${BIN_DIR}/MantidPlot_exe $*\" \n"
+        if ( "${UNIX_CODENAME}" MATCHES "Santiago" ) # el6
+            file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh "#!/bin/sh\n"
+	           "scl enable mantidlibs \"${CMAKE_INSTALL_PREFIX}/${BIN_DIR}/MantidPlot_exe $*\" \n"
 	)
+        else ()
+            file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh "#!/bin/sh\n"
+	           "LD_LIBRARY_PATH=/usr/lib64/paraview:${LD_LIBRARY_PATH} ${CMAKE_INSTALL_PREFIX}/${BIN_DIR}/MantidPlot_exe $* \n"
+	)
+	endif()
 
     install ( FILES  ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh
           DESTINATION ${BIN_DIR}

Code/Mantid/Build/Jenkins/buildscript

@@ -13,6 +13,7 @@
 # Print out the versions of things we are using
 ###############################################################################
 cmake --version
+echo "SHA1=${sha1}"
 
 ###############################################################################
 # OS X setup steps

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -8,6 +8,7 @@
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 
 "C:\Program Files (x86)\CMake 2.8\bin\cmake.exe" --version 
+echo %sha1%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Check the required build configuration