Merge branch 'master' into feature/10143_display_non_detector_parameters

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -54,7 +54,7 @@ add_definitions ( -DBOOST_DATE_TIME_POSIX_TIME_STD_CONFIG )
 find_package ( Poco 1.4.2 REQUIRED )
 include_directories( SYSTEM ${POCO_INCLUDE_DIRS} )
 
-find_package ( Nexus 4.3.0 REQUIRED )
+find_package ( Nexus 4.3.1 REQUIRED )
 include_directories ( SYSTEM ${NEXUS_INCLUDE_DIR} )
 
 find_package ( MuParser REQUIRED )
@@ -242,7 +242,10 @@ endif ()
 if ( CMAKE_COMPILER_IS_GNUCXX )
   include ( GNUSetup )
 elseif ( "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" )
-  include ( GNUSetup )
+  # Remove once clang warnings have been fixed. 
+  if ( NOT APPLE)
+    include ( GNUSetup )
+  endif ()
 endif ()
 
 ###########################################################################

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -160,7 +160,7 @@ install ( DIRECTORY ${PYQT4_PYTHONPATH}/uic DESTINATION ${BIN_DIR}/PyQt4 )
 file ( GLOB THIRDPARTY_PYTHON_PACKAGES ${CMAKE_LIBRARY_PATH}/Python/* )
 foreach ( PYPACKAGE ${THIRDPARTY_PYTHON_PACKAGES} )
   if ( IS_DIRECTORY ${PYPACKAGE} )
-    install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+    install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} USE_SOURCE_PERMISSIONS )
   else()
     install ( FILES ${PYPACKAGE} DESTINATION ${BIN_DIR} )
   endif()

Code/Mantid/Build/CMake/FindPyUnitTest.cmake

@@ -30,8 +30,8 @@ macro ( PYUNITTEST_ADD_TEST _test_src_dir _testname_prefix )
                  COMMAND ${PYTHON_EXECUTABLE_DEBUG} -B ${_test_src_dir}/${_filename} )
       # Set the PYTHONPATH so that the built modules can be found
       set_tests_properties ( ${_pyunit_separate_name}_Debug PROPERTIES
-                             ENVIRONMENT "PYTHONPATH=${_module_dir}"
-                             WORKING_DIRECTORY ${_working_dir}
+                             ENVIRONMENT "PYTHONPATH=${_module_dir_debug}"
+                             WORKING_DIRECTORY ${_working_dir_debug}
                              TIMEOUT ${TESTING_TIMEOUT} )
       # Release
       add_test ( NAME ${_pyunit_separate_name} CONFIGURATIONS Release

Code/Mantid/Build/CMake/LinuxPackageScripts.cmake

@@ -23,9 +23,19 @@ endif()
 set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PREFIX}/${PLUGINS_DIR};${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR} )
 
 ###########################################################################
-# LD_PRELOAD libraries
+# LD_PRELOAD TCMalloc
 ###########################################################################
-set ( EXTRA_LDPRELOAD_LIBS "${TCMALLOC_LIBRARIES}" )
+# User systems will only have the libraries and not the symbolic link
+# so we must set the preload to the versioned library. We will assume it is
+# in the same location as the system that the package was built on
+if ( TCMALLOC_LIBRARIES )
+  execute_process ( COMMAND readlink --no-newline --canonicalize-existing ${TCMALLOC_LIBRARIES}
+                    OUTPUT_VARIABLE TCMALLOC_PRELOAD
+                    RESULT_VARIABLE READLINK_RESULT )
+  if ( READLINK_RESULT EQUAL 1 )
+    message ( FATAL_ERROR "Unable to find real file that tcmalloc symlink, ${TCMALLOC_LIBRARIES}, points to." )
+  endif()
+endif()
 
 ###########################################################################
 # Environment scripts (profile.d)
@@ -84,10 +94,12 @@ set ( POST_UNINSTALL_FILE ${CMAKE_CURRENT_BINARY_DIR}/postrm )
 
 if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" OR "${UNIX_DIST}" MATCHES "^Fedora" ) # RHEL/Fedora
   if ( "${UNIX_CODENAME}" MATCHES "Santiago" ) # el6
-    set ( WRAPPER_COMMAND "scl enable mantidlibs" )
+    set ( WRAPPER_PREFIX "scl enable mantidlibs \"" )
+    set ( WRAPPER_POSTFIX "\"" )
     set ( EXTRA_LDPATH "/usr/lib64/paraview" )
   else()
-    set ( WRAPPER_COMMAND "eval" )
+    set ( WRAPPER_PREFIX "" )
+    set ( WRAPPER_POSTFIX "" )
   endif()
 
   if ( NOT MPI_BUILD )
@@ -106,7 +118,8 @@ if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" OR "${UNIX_DIST}" MATCHES "^Fedor
     set ( CPACK_RPM_POST_UNINSTALL_SCRIPT_FILE ${POST_UNINSTALL_FILE} )
   endif()
 elseif ( "${UNIX_DIST}" MATCHES "Ubuntu" )
-  set ( WRAPPER_COMMAND "eval" )
+  set ( WRAPPER_PREFIX "" )
+  set ( WRAPPER_POSTFIX "" )
 
   if ( NOT MPI_BUILD )
     configure_file ( ${CMAKE_MODULE_PATH}/Packaging/deb/scripts/deb_pre_inst.in

Code/Mantid/Build/CMake/Packaging/launch_mantidplot.sh.in

@@ -9,7 +9,7 @@ SCRIPTFILE=$(readlink -f "$0")
 INSTALLDIR=$(echo $SCRIPTFILE | sed -r -e 's|^(.*)/(.*)$|\1|g') #.* is greedy and eats up until the final slash
 
 # Define extra libraries and load paths
-LOCAL_PRELOAD=$(readlink -f @EXTRA_LDPRELOAD_LIBS@)
+LOCAL_PRELOAD=@TCMALLOC_PRELOAD@
 if [ -n "${LD_PRELOAD}" ]; then
     LOCAL_PRELOAD=${LOCAL_PRELOAD}:${LD_PRELOAD}
 fi
@@ -21,4 +21,4 @@ else
 fi
 
 # Launch
-LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} LD_LIBRARY_PATH=${LOCAL_LDPATH} @WRAPPER_COMMAND@ "$INSTALLDIR/@MANTIDPLOT_EXEC@ $*" 
+LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} LD_LIBRARY_PATH=${LOCAL_LDPATH} @WRAPPER_PREFIX@$INSTALLDIR/@MANTIDPLOT_EXEC@ $*@WRAPPER_POSTFIX@

Code/Mantid/Build/CMake/VersionNumber.cmake

@@ -1,7 +1,7 @@
 # Set the version number here for MantidVersion and the package filenames
 
 set ( VERSION_MAJOR 3 )
-set ( VERSION_MINOR 2 )
+set ( VERSION_MINOR 3 )
 
 # UNCOMMENT the next 'set' line to 'force' the patch version number to
 # a value (instead of using the count coming out of 'git describe')

Code/Mantid/CMakeLists.txt

@@ -185,7 +185,7 @@ if ( ENABLE_CPACK )
       message ( STATUS " CPACK_PACKAGE_FILE_NAME = ${CPACK_PACKAGE_FILE_NAME}" )
 
       # rhel requirements
-      set ( CPACK_RPM_PACKAGE_REQUIRES "boost >= 1.34.1,qt4 >= 4.2,nexus,nexus-python,gsl,glibc,qwtplot3d-qt4,muParser,numpy" )
+      set ( CPACK_RPM_PACKAGE_REQUIRES "boost >= 1.34.1,qt4 >= 4.2,nexus >= 4.3.1,nexus-python >= 4.3.1,gsl,glibc,qwtplot3d-qt4,muParser,numpy" )
       # OCE
       set( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},OCE-draw,OCE-foundation,OCE-modeling,OCE-ocaf,OCE-visualization")
       # Qwt is qwt5-qt4 in RHEL7
@@ -199,7 +199,7 @@ if ( ENABLE_CPACK )
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},python-ipython >= 1.1.0" )
       # scipy & matplotlib
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},scipy,python-matplotlib" )
-      set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},mxml,hdf,hdf5" )
+      set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},mxml,hdf,hdf5,jsoncpp" )
 
       if( "${UNIX_CODENAME}" MATCHES "Santiago" )
         # On RHEL6 we have to use an updated qscintilla to fix an auto complete bug
@@ -222,7 +222,7 @@ if ( ENABLE_CPACK )
                            "libboost-python${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
                            "libnexus0 (>= 4.3),libgsl0ldbl,libqtcore4 (>= 4.2),libqtgui4 (>= 4.2),libqt4-opengl (>= 4.2),"
                            "libqt4-xml (>= 4.2),libqt4-svg (>= 4.2),libqt4-qt3support (>= 4.2),qt4-dev-tools,"
-                           "libqwt5-qt4,libqwtplot3d-qt4-0,python-numpy,python-sip,python-qt4" )
+                           "libqwt5-qt4,libqwtplot3d-qt4-0,python-numpy,python-sip,python-qt4,libjsoncpp0" )
         set ( PERFTOOLS_DEB_PACKAGE "libgoogle-perftools0 (>= 1.7)" )
         if( "${UNIX_CODENAME}" MATCHES "lucid" )
           list ( APPEND DEPENDS_LIST ",libqscintilla2-5,"