Merge branch 'master' into feature/10855_rewrite_indirect_diffraction…

…_reduction

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

Refs #10855

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -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
 
@@ -71,7 +72,7 @@ set ( CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH}/zlib123 )
 find_package ( ZLIB REQUIRED )
 set ( CMAKE_INCLUDE_PATH ${MAIN_CMAKE_INCLUDE_PATH} )
 
-if (${CMAKE_SYSTEM_NAME} MATCHES "Windows" OR OSX_VERSION VERSION_LESS 10.9)
+if (${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 )

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 -Wextra -Winit-self -Wpointer-arith -Wcast-qual -fno-common  -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/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/Packaging/launch_mantidplot.sh.in

@@ -20,7 +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 \
+    PV_PLUGIN_PATH=${PV_PLUGIN_PATH} \
     @WRAPPER_PREFIX@$INSTALLDIR/@MANTIDPLOT_EXEC@ $*@WRAPPER_POSTFIX@

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

@@ -21,6 +21,9 @@ 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 "${PYTHONPATH}" ]; then
@@ -30,5 +33,6 @@ fi
 # Launch
 LD_PRELOAD=${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/Jenkins/buildscript

@@ -19,6 +19,46 @@ BUILDPKG=true
 cmake --version
 echo "SHA1=${sha1}"
 
+###############################################################################
+# Check job requirements from the name
+###############################################################################
+if [[ ${JOB_NAME} == *clean* ]]; then
+  CLEANBUILD=true
+fi
+
+if [[ ${JOB_NAME} == *debug* ]]; then
+  BUILD_CONFIG="Debug"
+elif [[ ${JOB_NAME} == *relwithdbg* ]]; then
+  BUILD_CONFIG="RelWithDbg"
+else
+  BUILD_CONFIG="Release"
+fi
+
+###############################################################################
+# Setup the build directory
+# For a clean build the entire thing is removed to guarantee it is clean. All
+# other build types are assumed to be incremental and the following items
+# are removed to ensure stale build objects don't interfere with each other:
+#   - build/bin/**: if libraries are removed from cmake they are not deleted
+#                   from bin and can cause random failures
+#   - build/ExternalData/**: data files will change over time and removing
+#                            the links helps keep it fresh
+###############################################################################
+BUILD_DIR=$WORKSPACE/build
+if [ -z "$BUILD_DIR" ]; then
+  echo "Build directory not set. Cannot continue"
+  exit 1
+fi
+
+if [[ "$CLEANBUILD" == true ]]; then
+  rm -rf $BUILD_DIR
+fi
+if [ -d $BUILD_DIR ]; then
+  rm -rf $BUILD_DIR/bin $BUILD_DIR/ExternalData
+else
+  mkdir $BUILD_DIR
+fi
+
 ###############################################################################
 # Setup clang
 ###############################################################################
@@ -38,11 +78,11 @@ if [[ $USE_CLANG ]]; then
   export CXX=clang++
   #check if CMakeCache.txt exists and if so that the cxx compiler is clang++
   #only needed with incremental builds. Clean builds delete this directory in a later step. 
-  if [[ -e $WORKSPACE/build/CMakeCache.txt ]] && [[ ${JOB_NAME} != *clean* ]]; then
-    COMPILERFILEPATH=`grep 'CMAKE_CXX_COMPILER:FILEPATH' $WORKSPACE/build/CMakeCache.txt` 
+  if [[ -e $BUILD_DIR/CMakeCache.txt ]] && [[ ${JOB_NAME} != *clean* ]]; then
+    COMPILERFILEPATH=`grep 'CMAKE_CXX_COMPILER:FILEPATH' $BUILD_DIR/CMakeCache.txt` 
     if [[ $COMPILERFILEPATH != *clang++* ]]; then 
       # Removing the build directory entirely guarantees clang is used.
-      rm -rf $WORKSPACE/build
+      rm -rf $BUILD_DIR
     fi
   fi 
 fi
@@ -85,19 +125,8 @@ else
   SCL_ON_RHEL6="eval"
 fi
 
-###############################################################################
-# Check job requirements from the name
-###############################################################################
-if [[ ${JOB_NAME} == *clean* ]]; then
-  CLEANBUILD=true
-fi
-
-if [[ -e $WORKSPACE/build/CMakeCache.txt ]]; then
-  # Temporary while the builds flick between old & new TestingTools locations
-  TESTINGTOOLS_DIR=$(grep 'Code/Mantid/TestingTools/cxxtest' $WORKSPACE/build/CMakeCache.txt || true)
-  if [ ! -z "$TESTINGTOOLS_DIR"  ]; then
-    rm -fr $WORKSPACE/build
-  fi
+if [[ ${NODE_LABELS} == *rhel7* ]]; then
+  ON_RHEL7=true
 fi
 
 ###############################################################################
@@ -121,31 +150,16 @@ if [[ "$BUILDPKG" == true ]]; then
 fi
 
 ###############################################################################
-# Setup the build directory
+# Work in the build directory
 ###############################################################################
-if [[ "$CLEANBUILD" == true ]]; then
-  rm -rf $WORKSPACE/build
-fi
-[ -d $WORKSPACE/build ] || mkdir $WORKSPACE/build
-cd $WORKSPACE/build
+cd $BUILD_DIR
 
 ###############################################################################
 # Clean up any artifacts from last build so that if it fails
 # they don't get archived again
 ###############################################################################
 rm -f *.dmg *.rpm *.deb *.tar.gz
 
-###############################################################################
-## Check the required build configuration
-###############################################################################
-if [[ ${JOB_NAME} == *debug* ]]; then
-  BUILD_CONFIG="Debug"
-elif [[ ${JOB_NAME} == *relwithdbg* ]]; then
-  BUILD_CONFIG="RelWithDbg"
-else
-  BUILD_CONFIG="Release"
-fi
-
 ###############################################################################
 # CMake configuration
 ###############################################################################
@@ -212,6 +226,6 @@ fi
 # Run the system tests on RHEL6 when doing a pull request build. Run
 # from a package to have at least one Linux checks it install okay
 ###############################################################################
-if [[ "${ON_RHEL6}" == true ]] && [[ ${JOB_NAME} == *pull_requests* ]]; then
+if [[ "${ON_RHEL7}" == true ]] && [[ ${JOB_NAME} == *pull_requests* ]]; then
   $SCRIPT_DIR/systemtests
 fi

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -39,16 +39,31 @@ if not "%JOB_NAME%" == "%JOB_NAME:clean=%" (
   set BUILDPKG=yes
 )
 
-if EXIST %WORKSPACE%\build\CMakeCache.txt (
-  FINDSTR "Code/Mantid/TestingTools/cxxtest" %WORKSPACE%\build\CMakeCache.txt && (
-    rmdir /S /Q %WORKSPACE%\build
-  )
-)
-
 if not "%JOB_NAME%" == "%JOB_NAME:pull_requests=%" (
   set BUILDPKG=yes
 )
 
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: Setup the build directory
+:: For a clean build the entire thing is removed to guarantee it is clean. All
+:: other build types are assumed to be incremental and the following items
+:: are removed to ensure stale build objects don't interfere with each other:
+::   - build/bin: if libraries are removed from cmake they are not deleted
+::                   from bin and can cause random failures
+::   - build/ExternalData/**: data files will change over time and removing
+::                            the links helps keep it fresh
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+set BUILD_DIR=%WORKSPACE%\build
+if "%CLEANBUILD%" == "yes" (
+  rmdir /S /Q %BUILD_DIR%
+)
+
+if EXIST %BUILD_DIR% (
+  rmdir /S /Q %BUILD_DIR%\bin %BUILD_DIR%\ExternalData
+) else (
+  md %BUILD_DIR%
+)
+
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Packaging options
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -57,14 +72,7 @@ if "%BUILDPKG%" == "yes" (
   set PACKAGE_DOCS=-DPACKAGE_DOCS=ON
 )
 
-:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-:: Setup the build directory
-:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-if "%CLEANBUILD%" == "yes" (
-  rmdir /S /Q %WORKSPACE%\build
-)
-md %WORKSPACE%\build
-cd %WORKSPACE%\build
+cd %BUILD_DIR%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Clean up any artifacts from last build so that if it fails
@@ -87,7 +95,7 @@ if not "%JOB_NAME%"=="%JOB_NAME:relwithdbg=%" (
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Update the PATH so that we can find everything
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-set PATH=%WORKSPACE%\Code\Third_Party\lib\win64;%WORKSPACE%\Code\Third_Party\lib\win64\Python27;%PARAVIEW_DIR%\bin\%BUILD_CONFIG%;%PATH%
+set PATH=%WORKSPACE%\Code\Third_Party\lib\win64;%WORKSPACE%\Code\Third_Party\lib\win64\Python27;%WORKSPACE%\Code\Third_Party\lib\win64\mingw;%PARAVIEW_DIR%\bin\%BUILD_CONFIG%;%PATH%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: CMake configuration
@@ -132,7 +140,7 @@ if "%BUILDPKG%" == "yes" (
 if not "%JOB_NAME%"=="%JOB_NAME:pull_requests=%" (
   :: Install package
   set SYSTEMTESTS_DIR=%WORKSPACE%\Code\Mantid\Testing\SystemTests
-  python !SYSTEMTESTS_DIR!\scripts\mantidinstaller.py install %WORKSPACE%\build
+  python !SYSTEMTESTS_DIR!\scripts\mantidinstaller.py install %BUILD_DIR%
 
   ::Remove user properties, disable instrument updating & usage reports and add data paths
   del /Q C:\MantidInstall\bin\Mantid.user.properties
@@ -144,13 +152,13 @@ if not "%JOB_NAME%"=="%JOB_NAME:pull_requests=%" (
   echo datasearch.directories = !DATA_ROOT!/UnitTest;!DATA_ROOT!/DocTest;!WORKSPACE_UNIX_STYLE!/Code/Mantid/instrument >> C:\MantidInstall\bin\Mantid.user.properties
 
   :: Run tests
-  cd %WORKSPACE%\build\docs
+  cd %BUILD_DIR%\docs
   C:\MantidInstall\bin\MantidPlot.exe -xq runsphinx_doctest.py
   set RETCODE=!ERRORLEVEL!
 
   :: Remove Mantid
-  cd %WORKSPACE%\build
-  python !SYSTEMTESTS_DIR!\scripts\mantidinstaller.py uninstall %WORKSPACE%\build
+  cd %BUILD_DIR%
+  python !SYSTEMTESTS_DIR!\scripts\mantidinstaller.py uninstall %BUILD_DIR%
   if !RETCODE! NEQ 0 exit /B 1
 )
 

Code/Mantid/Build/Jenkins/jenkins-slave.sh

@@ -31,12 +31,15 @@ SECRET=${2}
 SLAVE_AGENT_URL="${JENKINS_URL}/computer/${NODE_NAME}/slave-agent.jnlp"
 # name of the slave jar - full path is determined later
 JAR_FILE=slave.jar
+# Some versions of cron don't set the USER environment variable
+# required by vnc
+[ -z "$USER" ] && export USER=$(whoami)
 
 #####################################################################
 # Script
 #####################################################################
 # exit if it is already running
-RUNNING=$(ps aux | grep java | grep ${JAR_FILE})
+RUNNING=$(ps u -u $(whoami) | grep java | grep ${JAR_FILE})
 if [ ! -z "${RUNNING}" ]; then
   echo "Slave process is already running"
   exit 0

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer.spec

@@ -1,5 +1,5 @@
 Name:           mantid-developer
-Version:        1.9
+Version:        1.10
 Release:        1%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
@@ -30,7 +30,7 @@ Requires: poco-devel
 Requires: PyQt4-devel
 Requires: python-devel
 Requires: python-ipython >= 1.1
-Conflicts: python-ipython >= 2.0
+%{?el6:Conflicts: python-ipython >= 2.0}
 Requires: python-pip
 Requires: python-sphinx
 Requires: qscintilla-devel