Merge branch 'master' into 11163_ill_calibration_tab

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt

Refs #11163

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 )
@@ -60,6 +60,7 @@ include_directories ( SYSTEM ${NEXUS_INCLUDE_DIR} )
 find_package ( MuParser REQUIRED )
 
 find_package ( JsonCPP REQUIRED )
+include_directories ( SYSTEM ${JSONCPP_INCLUDE_DIR} )
 
 find_package ( Doxygen ) # optional
 
@@ -71,6 +72,14 @@ set ( CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH}/zlib123 )
 find_package ( ZLIB REQUIRED )
 set ( CMAKE_INCLUDE_PATH ${MAIN_CMAKE_INCLUDE_PATH} )
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows" OR (APPLE AND OSX_VERSION VERSION_LESS 10.9))
+  set (HDF5_DIR "${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 )

Code/Mantid/Build/CMake/CommonVatesSetup.cmake

@@ -7,7 +7,6 @@ Framework/API
 Framework/Geometry
 Framework/Kernel
 Framework/DataObjects
-Framework/MDEvents
 )
 
 set ( COMMONVATES_SETUP_DONE TRUE )

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 -pedantic -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/FindJsonCPP.cmake

@@ -10,7 +10,8 @@
 #  JSONCPP_LIBRARIES      - All required libraries, including the configuration type
 
 # Headers
-find_path ( JSONCPP_INCLUDE_DIR jsoncpp/json/json.h )
+find_path ( JSONCPP_INCLUDE_DIR json/reader.h
+            PATH_SUFFIXES jsoncpp )
 
 # Libraries
 find_library ( JSONCPP_LIBRARY NAMES jsoncpp ) # optimized

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
                  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/FindQwt.cmake

@@ -9,7 +9,7 @@
 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 NAMES qwt5-qt4 qwt-qt4 qwt5 qwt )
 find_library ( QWT_LIBRARY_DEBUG qwtd )
 
 # in REQUIRED mode: terminate if one of the above find commands failed

Code/Mantid/Build/CMake/GNUSetup.cmake

@@ -24,9 +24,10 @@ set( GNUFLAGS "-Wall -Wextra -Wconversion -Winit-self -Wpointer-arith -Wcast-qua
 set( GNUFLAGS "${GNUFLAGS} -Wno-deprecated -Wno-write-strings")
 
 # Check if we have a new enough version for this flag
+# some -pedantic warnings remain with gcc 4.4.7
 if ( CMAKE_COMPILER_IS_GNUCXX )
-  if (GCC_COMPILER_VERSION VERSION_GREATER "4.3")
-    set(GNUFLAGS "${GNUFLAGS} -Wno-unused-result")
+  if (NOT (GCC_COMPILER_VERSION VERSION_LESS "4.5"))
+    set(GNUFLAGS "${GNUFLAGS} -Wno-unused-result -pedantic")
   endif ()
 elseif ( "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" )
     set(GNUFLAGS "${GNUFLAGS} -Wno-sign-conversion")

Code/Mantid/Build/CMake/LinuxPackageScripts.cmake

@@ -26,21 +26,6 @@ set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PRE
 # Required for Fedora >= 18 and RHEL >= 7
 set ( CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION /opt /usr/share/applications /usr/share/pixmaps )
 
-###########################################################################
-# LD_PRELOAD TCMalloc
-###########################################################################
-# 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)
 ###########################################################################
@@ -151,6 +136,12 @@ configure_file ( ${CMAKE_MODULE_PATH}/Packaging/launch_mantidplot.sh.in
 # Needs to be executable
 execute_process ( COMMAND "chmod" "+x" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/launch_mantidplot.sh"
                   OUTPUT_QUIET ERROR_QUIET )
+configure_file ( ${CMAKE_MODULE_PATH}/Packaging/mantidpython.in 
+                 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/mantidpython @ONLY )
+# Needs to be executable
+execute_process ( COMMAND "chmod" "+x" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/mantidpython"
+                  OUTPUT_QUIET ERROR_QUIET )
+
 # Package version
 set ( MANTIDPLOT_EXEC MantidPlot_exe )
 configure_file ( ${CMAKE_MODULE_PATH}/Packaging/launch_mantidplot.sh.in 
@@ -161,3 +152,11 @@ install ( FILES ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh.install
           GROUP_EXECUTE GROUP_READ
           WORLD_EXECUTE WORLD_READ
 )
+configure_file ( ${CMAKE_MODULE_PATH}/Packaging/mantidpython.in 
+                 ${CMAKE_CURRENT_BINARY_DIR}/mantidpython.install @ONLY )
+install ( FILES ${CMAKE_CURRENT_BINARY_DIR}/mantidpython.install
+          DESTINATION ${BIN_DIR} RENAME mantidpython
+          PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
+          GROUP_EXECUTE GROUP_READ
+          WORLD_EXECUTE WORLD_READ
+)

Code/Mantid/Build/CMake/MantidExternalData.cmake

@@ -36,3 +36,10 @@ list(APPEND ExternalData_URL_TEMPLATES
   "http://198.74.56.37/ftp/external-data/%(algo)/%(hash)"
 )
 
+# Increase network timeout defaults to avoid our slow server connection but don't override what a user provides
+if(NOT ExternalData_TIMEOUT_INACTIVITY)
+  set(ExternalData_TIMEOUT_INACTIVITY 120)
+endif()
+if(NOT ExternalData_TIMEOUT_ABSOLUTE)
+  set(ExternalData_TIMEOUT_ABSOLUTE 600)
+endif()

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=@TCMALLOC_PRELOAD@
+LOCAL_PRELOAD=`readlink --no-newline --canonicalize-existing @TCMALLOC_LIBRARIES@`
 if [ -n "${LD_PRELOAD}" ]; then
     LOCAL_PRELOAD=${LOCAL_PRELOAD}:${LD_PRELOAD}
 fi
@@ -20,5 +20,11 @@ else
     TCM_RELEASE=${TCMALLOC_RELEASE_RATE}
 fi
 
+# Define paraview information
+PV_PLUGIN_PATH="${INSTALLDIR}/pvplugins/pvplugins"
+
 # Launch
-LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} LD_LIBRARY_PATH=${LOCAL_LDPATH} QT_API=pyqt @WRAPPER_PREFIX@$INSTALLDIR/@MANTIDPLOT_EXEC@ $*@WRAPPER_POSTFIX@
+LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} \
+    LD_LIBRARY_PATH=${LOCAL_LDPATH} QT_API=pyqt \
+    PV_PLUGIN_PATH=${PV_PLUGIN_PATH} \
+    @WRAPPER_PREFIX@$INSTALLDIR/@MANTIDPLOT_EXEC@ $*@WRAPPER_POSTFIX@

Code/Mantid/Build/CMake/Packaging/mantidpython.in

@@ -0,0 +1,38 @@
+#!/bin/sh
+#
+# Launch Mantidplot using any necessary LD_PRELOAD or software collection behaviour
+#
+# Script is configured by CMake
+
+# Find out where we are
+SCRIPTFILE=$(readlink -f "$0")
+INSTALLDIR=$(echo $SCRIPTFILE | sed -r -e 's|^(.*)/(.*)$|\1|g') #.* is greedy and eats up until the final slash
+IPYTHON=$(command -v ipython)
+
+# Define extra libraries and load paths
+LOCAL_PRELOAD=`readlink --no-newline --canonicalize-existing @TCMALLOC_LIBRARIES@`
+if [ -n "${LD_PRELOAD}" ]; then
+    LOCAL_PRELOAD=${LOCAL_PRELOAD}:${LD_PRELOAD}
+fi
+LOCAL_LDPATH=@EXTRA_LDPATH@:${LD_LIBRARY_PATH}
+if [ -z "${TCMALLOC_RELEASE_RATE}" ]; then
+    TCM_RELEASE=10000
+else
+    TCM_RELEASE=${TCMALLOC_RELEASE_RATE}
+fi
+
+# Define paraview information
+PV_PLUGIN_PATH="${INSTALLDIR}/pvplugins/pvplugins"
+
+# Define extra libraries for python
+LOCAL_PYTHONPATH=@WRAPPER_PREFIX@$INSTALLDIR
+if [ -n "${PYTHONPATH}" ]; then
+    LOCAL_PYTHONPATH=${LOCAL_PYTHONPATH}:${PYTHONPATH}
+fi
+
+# Launch
+LD_PRELOAD=${LOCAL_PRELOAD} TCMALLOC_RELEASE_RATE=${TCM_RELEASE} \
+    LD_LIBRARY_PATH=${LOCAL_LDPATH} QT_API=pyqt \
+    PV_PLUGIN_PATH=${PV_PLUGIN_PATH} \
+    PYTHONPATH=${LOCAL_PYTHONPATH} \
+    ${IPYTHON} $*@WRAPPER_POSTFIX@

Code/Mantid/Build/CMake/PylintSetup.cmake

@@ -32,10 +32,12 @@ if ( PYLINT_FOUND )
   set ( PYLINT_INCLUDES
         Framework/PythonInterface/plugins
         scripts
+        Testing/SystemTests/tests/analysis
   )
   set ( PYLINT_EXCLUDES
         scripts/lib1to2
         scripts/test
+        Testing/SystemTests/tests/analysis/reference
   )
   add_custom_target ( pylintcheck
                       COMMAND ${PYTHON_EXECUTABLE} ${PYLINT_RUNNER_SCRIPT} --format=${PYLINT_OUTPUT_FORMAT}