Merge branch 'master' into feature/9782_add_autodiff_function

.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/CommonSetup.cmake

@@ -242,6 +242,11 @@ endif ()
 ###########################################################################
 include ( CppCheckSetup )
 
+###########################################################################
+# Setup pylint
+###########################################################################
+include ( PylintSetup )
+
 ###########################################################################
 # Set up the unit tests target
 ###########################################################################

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -81,6 +81,13 @@ 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} -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" )

Code/Mantid/Build/CMake/FindPylint.cmake

@@ -0,0 +1,40 @@
+# - Find Pylint
+# Find the Pylint executable and extract the version number
+#
+# OUTPUT Variables
+#
+#   PYLINT_FOUND
+#       True if the pylint package was found
+#   PYLINT_EXECUTABLE
+#       The pylint executable location
+#   PYLINT_VERSION
+#       A string denoting the version of pylint that has been found
+#   PYLINT_RUNNER_SCRIPT
+#       Location of python script that will actually run pylint
+#   PYLINT_CFG_FILE
+#       Location of configuration file
+#
+
+#=============================================================
+# main()
+#=============================================================
+
+find_program ( PYLINT_EXECUTABLE pylint PATHS /usr/bin )
+
+if ( PYLINT_EXECUTABLE )
+  execute_process ( COMMAND ${PYLINT_EXECUTABLE} --version OUTPUT_VARIABLE PYLINT_VERSION_RAW ERROR_QUIET )
+  if (PYLINT_VERSION_RAW)
+    string ( REGEX REPLACE "^pylint ([0-9]+.[0-9]+.[0-9]+),.*" "\\1" PYLINT_VERSION ${PYLINT_VERSION_RAW})
+  else ()
+    set ( PYLINT_VERSION "unknown" )
+  endif()
+  # Script to find all .py files and execute pylint
+  set ( PYLINT_RUNNER_SCRIPT ${CMAKE_SOURCE_DIR}/../Tools/Pylint/run_pylint.py )
+  # Configuration file
+  set ( PYLINT_CFG_FILE ${CMAKE_SOURCE_DIR}/../Tools/Pylint/pylint.cfg )
+endif ()
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS ( Pylint DEFAULT_MSG PYLINT_EXECUTABLE )
+
+mark_as_advanced ( PYLINT_EXECUTABLE PYLINT_VERSION )

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

@@ -6,13 +6,39 @@
 # set:
 #  SPHINX_FOUND
 #  SPHINX_EXECUTABLE
+#
+#=============================================================
+# main()
+#=============================================================
 
 find_program( SPHINX_EXECUTABLE NAME sphinx-build
   PATHS ${CMAKE_LIBRARY_PATH}/Python27/Scripts
   PATH_SUFFIXES bin
   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/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/CMake/PylintSetup.cmake

@@ -0,0 +1,50 @@
+########################################################
+# Setup target to run pylint checking if it is available
+########################################################
+find_package ( Pylint )
+
+if ( PYLINT_FOUND AND PYLINT_VERSION VERSION_LESS "1.0.0" )
+  message ( STATUS "pylint found but version is < 1.0.0 (${PYLINT_VERSION}): no target generated." )
+  set ( PYLINT_FOUND FALSE )
+endif()
+
+if ( PYLINT_FOUND )
+  message ( STATUS "pylint version: ${PYLINT_VERSION}" )
+
+  # Output format options
+  if ( NOT  PYLINT_OUTPUT_FORMAT )
+    # Use msvs for MSVC generator, colorized for everything else. The buildservers can
+    # set it to parseable for Jenkins
+    if ( MSVC )
+      set ( DEFAULT_FORMAT "msvs" )
+    else ()
+      set ( DEFAULT_FORMAT "colorized" )
+    endif ()
+    set ( PYLINT_OUTPUT_FORMAT ${DEFAULT_FORMAT} CACHE STRING "Desired pylint output format" )
+
+    # There are a limited set of allowed options
+    set_property( CACHE PYLINT_OUTPUT_FORMAT PROPERTY STRINGS "text" "html" "msvs" "parseable" "colorized" )
+  endif()
+
+  # add a pylint-check target to run pylint on the required files and directories
+  # relative to the root source directory
+  set ( BASE_DIR ${CMAKE_SOURCE_DIR} )
+  set ( PYLINT_INCLUDES
+        Framework/PythonInterface/plugins
+        scripts
+  )
+  set ( PYLINT_EXCLUDES
+        scripts/lib1to2
+        scripts/test
+  )
+  add_custom_target ( pylintcheck
+                      COMMAND ${PYTHON_EXECUTABLE} ${PYLINT_RUNNER_SCRIPT} --format=${PYLINT_OUTPUT_FORMAT}
+                              --rcfile=${PYLINT_CFG_FILE}
+                              --mantidpath=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}
+                              --basedir=${BASE_DIR} --nofail
+                              --exclude="${PYLINT_EXCLUDES}"
+                              ${PYLINT_INCLUDES}
+                      COMMENT "Running pylint on selected python files"
+                    )
+  set_target_properties ( pylintcheck PROPERTIES EXCLUDE_FROM_ALL TRUE )
+endif ()

Code/Mantid/Build/Jenkins/buildscript

@@ -13,20 +13,30 @@
 # Print out the versions of things we are using
 ###############################################################################
 cmake --version
+echo "SHA1=${sha1}"
 
 ###############################################################################
 # OS X setup steps
 ###############################################################################
 if [[ $(uname) == 'Darwin' ]]; then
-  cd $WORKSPACE/Code
-  ./fetch_Third_Party.sh
-  cd $WORKSPACE
-  # Setup environment variables
-  source /opt/intel/bin/iccvars.sh intel64
-  export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$WORKSPACE/Code/Third_Party/lib/mac64:/Library/Frameworks
-  # Make sure we pick up the Intel compiler
-  export CC=icc
-  export CXX=icpc
+  if [[ ${JOB_NAME} == *clang* ]]; then
+    # Assuming we are using the clang compiler
+    echo "Using clang/llvm compiler."
+    clang --version
+  else
+    # Assuming we are using the Intel compiler
+    cd $WORKSPACE/Code
+    ./fetch_Third_Party.sh
+    cd $WORKSPACE
+    # Setup environment variables
+    source /opt/intel/bin/iccvars.sh intel64
+    export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$WORKSPACE/Code/Third_Party/lib/mac64:/Library/Frameworks
+    # Make sure we pick up the Intel compiler
+    export CC=icc
+    export CXX=icpc
+    echo "Using Intel compiler."
+    icpc --version
+  fi
 fi
 
 ###############################################################################
@@ -102,14 +112,10 @@ $SCL_ON_RHEL6 "ctest --output-on-failure -R MantidPlot"
 
 ###############################################################################
 # Documentation
-# Only run tests on RHEL6 incremental but have to build html on all platforms
-# for a clean build so that it can be packaged
+# Build Qt help on all platforms for a clean build so that it can be packaged
 ###############################################################################
-if [[ "$ON_RHEL6" == true ]]; then
-  $SCL_ON_RHEL6 "make docs-test"
-fi
 if [[ "$CLEANBUILD" == true ]]; then
-  # Workaround so that the html target can find the properties file
+  # Workaround so that the target can find the properties file
   # CMake doesn't easily allow environment variables on custom targets
   if [[ $(uname) == 'Darwin' ]]; then
     export MANTIDPATH=$PWD/bin

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -8,6 +8,20 @@
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 
 "C:\Program Files (x86)\CMake 2.8\bin\cmake.exe" --version 
+echo %sha1%
+
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: Check the required build configuration
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+set BUILD_CONFIG=
+if not "%JOB_NAME%"=="%JOB_NAME:debug=%" (
+    set BUILD_CONFIG=Debug
+) else (
+if not "%JOB_NAME%"=="%JOB_NAME:relwithdbg=%" (
+    set BUILD_CONFIG=RelWithDbg
+) else (
+    set BUILD_CONFIG=Release
+    ))
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Get or update the third party dependencies
@@ -16,7 +30,7 @@ cd %WORKSPACE%\Code
 call fetch_Third_Party win64
 cd %WORKSPACE%
 
-set PATH=%WORKSPACE%\Code\Third_Party\lib\win64;%WORKSPACE%\Code\Third_Party\lib\win64\Python27;%PARAVIEW_DIR%\bin\Release;%PATH%
+set PATH=%WORKSPACE%\Code\Third_Party\lib\win64;%WORKSPACE%\Code\Third_Party\lib\win64\Python27;%PARAVIEW_DIR%\bin\%BUILD_CONFIG%;%PATH%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Check whether this is a clean build (must have 'clean' in the job name)
@@ -42,19 +56,6 @@ cd %WORKSPACE%\build
 "C:\Program Files (x86)\CMake 2.8\bin\cmake.exe" -G "Visual Studio 11 Win64" -DCONSOLE=OFF -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=%PARAVIEW_DIR% -DUSE_PRECOMPILED_HEADERS=ON %PACKAGE_DOCS% ..\Code\Mantid
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 
-:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-:: Check the required build configuration
-:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-set BUILD_CONFIG=
-if not "%JOB_NAME%"=="%JOB_NAME:debug=%" (
-    set BUILD_CONFIG=Debug
-) else (
-if not "%JOB_NAME%"=="%JOB_NAME:relwithdbg=%" (
-    set BUILD_CONFIG=RelWithDbg
-) else (
-    set BUILD_CONFIG=Release
-    ))
-
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Build step
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -68,7 +69,7 @@ if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 "C:\Program Files (x86)\CMake 2.8\bin\ctest.exe" -C %BUILD_CONFIG% -j%BUILD_THREADS% --schedule-random --output-on-failure -E MantidPlot
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 :: Run GUI tests serially
-ctest -C Release --output-on-failure -R MantidPlot
+ctest -C %BUILD_CONFIG% --output-on-failure -R MantidPlot
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::