Merge branch 'master' into feature/10271_tcmalloc_ldpreload

Conflicts:
	Code/Mantid/Build/CMake/FindTcmalloc.cmake
	Code/Mantid/Framework/API/src/MemoryManager.cpp
	Code/Mantid/Framework/Kernel/CMakeLists.txt
	Code/Mantid/Framework/Kernel/src/Memory.cpp
	Code/Mantid/Framework/PythonInterface/mantid/api/CMakeLists.txt
	Code/Mantid/Framework/PythonInterface/mantid/geometry/CMakeLists.txt
	Code/Mantid/Framework/PythonInterface/mantid/kernel/CMakeLists.txt
Refs #10271

.clang-format

@@ -0,0 +1,2 @@
+BasedOnStyle: LLVM
+

.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

@@ -47,7 +47,7 @@ add_definitions ( -DBOOST_ALL_DYN_LINK )
 # Need this defined globally for our log time values
 add_definitions ( -DBOOST_DATE_TIME_POSIX_TIME_STD_CONFIG )
 
-find_package ( Poco REQUIRED )
+find_package ( Poco 1.4.2 REQUIRED )
 include_directories( SYSTEM ${POCO_INCLUDE_DIRS} )
 
 find_package ( Nexus 4.3.0 REQUIRED )

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 "${CMAKE_C_FLAGS} -no-intel-extensions" )
@@ -113,8 +121,14 @@ if (OSX_VERSION VERSION_LESS 10.9)
  set ( SITEPACKAGES /Library/Python/${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
+ set ( OPENSSL_ROOT_DIR /usr/local/opt/openssl )
 endif()
 
 # Python packages
@@ -145,6 +159,8 @@ file ( GLOB THIRDPARTY_PYTHON_PACKAGES ${CMAKE_LIBRARY_PATH}/Python/* )
 foreach ( PYPACKAGE ${THIRDPARTY_PYTHON_PACKAGES} )
   if ( IS_DIRECTORY ${PYPACKAGE} )
     install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+  else()
+    install ( FILES ${PYPACKAGE} DESTINATION ${BIN_DIR} )
   endif()
   file ( COPY ${PYPACKAGE} DESTINATION ${PROJECT_BINARY_DIR}/bin )
 endforeach( PYPACKAGE )

Code/Mantid/Build/CMake/FindPoco.cmake

@@ -47,10 +47,42 @@ set ( POCO_LIBRARIES ${POCO_LIB_FOUNDATION}
 
 endif()
 
+# Set a version string by examining either the Poco/Version.h header or 
+# the Poco/Foundation.h header if Version.h does not exist
+if( POCO_INCLUDE_DIR ) 
+  if ( EXISTS ${POCO_INCLUDE_DIR}/Poco/Version.h )
+    set ( VERSION_FILE ${POCO_INCLUDE_DIR}/Poco/Version.h )
+  else ()
+    set ( VERSION_FILE ${POCO_INCLUDE_DIR}/Poco/Foundation.h )
+  endif ()
+  # regex quantifiers like {8} don't seem to work so we'll stick with + even though
+  # it's not strictly true
+  set ( VERS_REGEX "^#define[ \t]+POCO_VERSION[ \t]+0x([0-9]+)$" )
+  file ( STRINGS ${VERSION_FILE} POCO_VERSION REGEX ${VERS_REGEX} )
+  # pull out just the part after the 0x
+  string( REGEX REPLACE ${VERS_REGEX} "\\1" POCO_VERSION ${POCO_VERSION} )
+  # Pretty format
+  string( SUBSTRING ${POCO_VERSION} 0 2 POCO_VERSION_MAJOR )
+  string( REGEX REPLACE "^0" "" POCO_VERSION_MAJOR ${POCO_VERSION_MAJOR} )
+  string( SUBSTRING ${POCO_VERSION} 2 2 POCO_VERSION_MINOR )
+  string( REGEX REPLACE "^0" "" POCO_VERSION_MINOR ${POCO_VERSION_MINOR} )
+  string( SUBSTRING ${POCO_VERSION} 4 2 POCO_VERSION_PATCH )
+  string( REGEX REPLACE "^0" "" POCO_VERSION_PATCH ${POCO_VERSION_PATCH} )
+
+  set ( POCO_VERSION "${POCO_VERSION_MAJOR}.${POCO_VERSION_MINOR}.${POCO_VERSION_PATCH}" )
+endif()
+
+
 # handle the QUIETLY and REQUIRED arguments and set POCO_FOUND to TRUE if 
 # all listed variables are TRUE
 include ( FindPackageHandleStandardArgs )
-find_package_handle_standard_args( Poco DEFAULT_MSG POCO_LIBRARIES POCO_INCLUDE_DIR )
+if (POCO_VERSION)
+  find_package_handle_standard_args( Poco REQUIRED_VARS POCO_LIBRARIES POCO_INCLUDE_DIR 
+                                     VERSION_VAR POCO_VERSION )
+else ()
+  message (status "Failed to determine Poco version: Ignoring requirement")
+  find_package_handle_standard_args( Poco DEFAULT_MSG POCO_LIBRARIES POCO_INCLUDE_DIR )
+endif ()
 
 mark_as_advanced ( POCO_INCLUDE_DIR
                    POCO_LIB_FOUNDATION POCO_LIB_FOUNDATION_DEBUG
@@ -59,4 +91,4 @@ mark_as_advanced ( POCO_INCLUDE_DIR
                    POCO_LIB_NET POCO_LIB_NET_DEBUG
                    POCO_LIB_CRYPTO POCO_LIB_CRYPTO_DEBUG
                    POCO_LIB_NETSSL POCO_LIB_NETSSL_DEBUG
-)
+)

Code/Mantid/Build/CMake/FindPyQt.py

@@ -1,25 +1,48 @@
 # Copyright (c) 2007, Simon Edwards <simon@simonzone.com>
+# Copyright (c) 2014, Raphael Kubo da Costa <rakuco@FreeBSD.org>
 # Redistribution and use is allowed according to the terms of the BSD license.
 # For details see the accompanying COPYING-CMAKE-SCRIPTS file.
 
-import PyQt4.pyqtconfig
+import PyQt4.QtCore
+import os
+import sys
 
-pyqtcfg = PyQt4.pyqtconfig.Configuration()
-print("pyqt_version:%06.0x" % pyqtcfg.pyqt_version)
-print("pyqt_version_str:%s" % pyqtcfg.pyqt_version_str)
-
-pyqt_version_tag = ""
-in_t = False
-for item in pyqtcfg.pyqt_sip_flags.split(' '):
-    if item=="-t":
-        in_t = True
-    elif in_t:
-        if item.startswith("Qt_4"):
-            pyqt_version_tag = item
+def get_default_sip_dir():
+    # This is based on QScintilla's configure.py, and only works for the
+    # default case where installation paths have not been changed in PyQt's
+    # configuration process.
+    if sys.platform == 'win32':
+        pyqt_sip_dir = os.path.join(sys.platform, 'sip', 'PyQt4')
     else:
-        in_t = False
-print("pyqt_version_tag:%s" % pyqt_version_tag)
+        pyqt_sip_dir = os.path.join(sys.platform, 'share', 'sip', 'PyQt4')
+    return pyqt_sip_dir
+
+def get_qt4_tag(sip_flags):
+    in_t = False
+    for item in sip_flags.split(' '):
+        if item == '-t':
+            in_t = True
+        elif in_t:
+            if item.startswith('Qt_4'):
+                return item
+        else:
+            in_t = False
+    raise ValueError('Cannot find Qt\'s tag in PyQt4\'s SIP flags.')
 
-print("pyqt_sip_dir:%s" % pyqtcfg.pyqt_sip_dir)
-print("pyqt_sip_flags:%s" % pyqtcfg.pyqt_sip_flags)
+if __name__ == '__main__':
+    try:
+        import PyQt4.pyqtconfig
+        pyqtcfg = PyQt4.pyqtconfig.Configuration()
+        sip_dir = pyqtcfg.pyqt_sip_dir
+        sip_flags = pyqtcfg.pyqt_sip_flags
+    except ImportError:
+        # PyQt4 >= 4.10.0 was built with configure-ng.py instead of
+        # configure.py, so pyqtconfig.py is not installed.
+        sip_dir = get_default_sip_dir()
+        sip_flags = PyQt4.QtCore.PYQT_CONFIGURATION['sip_flags']
 
+    print('pyqt_version:%06.x' % PyQt4.QtCore.PYQT_VERSION)
+    print('pyqt_version_str:%s' % PyQt4.QtCore.PYQT_VERSION_STR)
+    print('pyqt_version_tag:%s' % get_qt4_tag(sip_flags))
+    print('pyqt_sip_dir:%s' % sip_dir)
+    print('pyqt_sip_flags:%s' % sip_flags)

Code/Mantid/Build/CMake/FindPyQt4.cmake

@@ -9,16 +9,20 @@
 # Find the installed version of PyQt4. FindPyQt4 should only be called after
 # Python has been found.
 #
-# This file defines the following variables:
+# This file defines the following variables, which can also be overriden by
+# users:
 #
 # PYQT4_VERSION - The version of PyQt4 found expressed as a 6 digit hex number
-#     suitable for comparision as a string
+#     suitable for comparison as a string
 #
 # PYQT4_VERSION_STR - The version of PyQt4 as a human readable string.
 #
-# PYQT4_VERSION_TAG - The PyQt version tag using by PyQt's sip files.
+# PYQT4_VERSION_TAG - The Qt4 version tag used by PyQt's sip files.
 #
-# PYQT4_SIP_DIR - The directory holding the PyQt4 .sip files.
+# PYQT4_SIP_DIR - The directory holding the PyQt4 .sip files. This can be unset
+# if PyQt4 was built using its new build system and pyqtconfig.py is not
+# present on the system, as in this case its value cannot be determined
+# automatically.
 #
 # PYQT4_SIP_FLAGS - The SIP flags used to build PyQt.
 
@@ -30,19 +34,38 @@ ELSE(EXISTS PYQT4_VERSION)
   FIND_FILE(_find_pyqt_py FindPyQt.py PATHS ${CMAKE_MODULE_PATH})
 
   EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} ${_find_pyqt_py} OUTPUT_VARIABLE pyqt_config)
-  IF( NOT ${pyqt_config} MATCHES "Traceback" )
-    STRING(REGEX REPLACE "^pyqt_version:([^\n]+).*$" "\\1" PYQT4_VERSION ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_version_str:([^\n]+).*$" "\\1" PYQT4_VERSION_STR ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_version_tag:([^\n]+).*$" "\\1" PYQT4_VERSION_TAG ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_sip_dir:([^\n]+).*$" "\\1" PYQT4_SIP_DIR ${pyqt_config})
-    STRING(REGEX REPLACE ".*\npyqt_sip_flags:([^\n]+).*$" "\\1" PYQT4_SIP_FLAGS ${pyqt_config})
+  IF(pyqt_config)
+    STRING(REGEX MATCH "^pyqt_version:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_VERSION "${CMAKE_MATCH_1}" CACHE STRING "PyQt4's version as a 6-digit hexadecimal number")
 
-    SET(PYQT4_FOUND TRUE)
-  ENDIF()
+    STRING(REGEX MATCH ".*\npyqt_version_str:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_VERSION_STR "${CMAKE_MATCH_1}" CACHE STRING "PyQt4's version as a human-readable string")
 
-  include ( FindPackageHandleStandardArgs )
-  find_package_handle_standard_args ( PyQt4 DEFAULT_MSG PYQT4_VERSION )
+    STRING(REGEX MATCH ".*\npyqt_version_tag:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_VERSION_TAG "${CMAKE_MATCH_1}" CACHE STRING "The Qt4 version tag used by PyQt4's .sip files")
 
-  mark_as_advanced ( _find_pyqt_py )
+    STRING(REGEX MATCH ".*\npyqt_sip_dir:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_SIP_DIR "${CMAKE_MATCH_1}" CACHE FILEPATH "The base directory where PyQt4's .sip files are installed")
+
+    STRING(REGEX MATCH ".*\npyqt_sip_flags:([^\n]+).*$" _dummy ${pyqt_config})
+    SET(PYQT4_SIP_FLAGS "${CMAKE_MATCH_1}" CACHE STRING "The SIP flags used to build PyQt4")
+
+    IF(NOT IS_DIRECTORY "${PYQT4_SIP_DIR}")
+      MESSAGE(WARNING "The base directory where PyQt4's SIP files are installed could not be determined. This usually means PyQt4 was built with its new build system and pyqtconfig.py is not present.\n"
+                      "Please set the PYQT4_SIP_DIR variable manually.")
+    ELSE(NOT IS_DIRECTORY "${PYQT4_SIP_DIR}")
+      SET(PYQT4_FOUND TRUE)
+    ENDIF(NOT IS_DIRECTORY "${PYQT4_SIP_DIR}")
+  ENDIF(pyqt_config)
+
+  IF(PYQT4_FOUND)
+    IF(NOT PYQT4_FIND_QUIETLY)
+      MESSAGE(STATUS "Found PyQt4 version: ${PYQT4_VERSION_STR}")
+    ENDIF(NOT PYQT4_FIND_QUIETLY)
+  ELSE(PYQT4_FOUND)
+    IF(PYQT4_FIND_REQUIRED)
+      MESSAGE(FATAL_ERROR "Could not find Python")
+    ENDIF(PYQT4_FIND_REQUIRED)
+  ENDIF(PYQT4_FOUND)
 
 ENDIF(EXISTS PYQT4_VERSION)

Code/Mantid/Build/CMake/FindTcmalloc.cmake

@@ -7,7 +7,7 @@
 # TCMALLOC_FOUND If false, do not try to use TCMALLOC
 
 find_path ( TCMALLOC_INCLUDE_DIR tcmalloc.h
-            PATHS /usr/include/google
+            PATHS /usr/include/gperftools
 )
 
 find_library ( TCMALLOC_LIB NAMES tcmalloc_minimal tcmalloc )

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/MantidUtils.cmake

@@ -61,29 +61,29 @@ endfunction( SET_TARGET_OUTPUT_DIRECTORY )
 #######################################################################
 
 #
-# NAME: COPY_PYTHON_FILES_TO_DIR
-# Adds a set of custom commands for each python file to copy
+# NAME: COPY_FILES_TO_DIR
+# Adds a set of custom commands for each file to copy
 # the given file to the destination directory
-#   - PY_FILES :: A list of python files to copy. Note you will have
+#   - FILES :: A list of files to copy. Note you will have
 #                 to quote an expanded list
 #   - SRC_DIR :: The src directory of the files to be copied
 #   - DEST_DIR :: The final directory for the copied files
 #   - INSTALLED_FILES :: An output variable containing the list of copied
 #                        files including their full paths
-function( COPY_PYTHON_FILES_TO_DIR PY_FILES SRC_DIR DEST_DIR INSTALLED_FILES )
+function( COPY_FILES_TO_DIR FILES SRC_DIR DEST_DIR INSTALLED_FILES )
     set ( COPIED_FILES ${${INSTALLED_FILES}} )
-    foreach ( PYFILE ${PY_FILES} )
-        get_filename_component( _basefilename ${PYFILE} NAME_WE )
-        set( _py_src ${SRC_DIR}/${PYFILE} )
-        set( _py_bin ${DEST_DIR}/${PYFILE} )
-        add_custom_command ( OUTPUT ${_py_bin}
-                             DEPENDS ${_py_src}
+    foreach ( _FILE ${FILES} )
+        get_filename_component( _basefilename ${_FILE} NAME_WE )
+        set( _src ${SRC_DIR}/${_FILE} )
+        set( _bin ${DEST_DIR}/${_FILE} )
+        add_custom_command ( OUTPUT ${_bin}
+                             DEPENDS ${_src}
                              COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different
-                               ${_py_src} ${_py_bin} )
-    set ( COPIED_FILES ${COPIED_FILES} ${_py_bin} )
-    endforeach ( PYFILE )
+                               ${_src} ${_bin} )
+    set ( COPIED_FILES ${COPIED_FILES} ${_bin} )
+    endforeach ( _FILE )
     set ( ${INSTALLED_FILES} ${COPIED_FILES} PARENT_SCOPE )
-endfunction( COPY_PYTHON_FILES_TO_DIR )
+endfunction( COPY_FILES_TO_DIR )
 
 #######################################################################
 

Code/Mantid/Build/CMake/UseSystemQt4.cmake

@@ -23,8 +23,13 @@
 #  License text for the above reference.)
 
 ADD_DEFINITIONS(${QT_DEFINITIONS})
-SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS_DEBUG QT_DEBUG)
-SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS_RELEASE QT_NO_DEBUG)
+IF("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" VERSION_GREATER 2.8.9)
+  SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS $<$<CONFIG:Debug>:QT_DEBUG>)
+  SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS $<$<NOT:$<CONFIG:Debug>>:QT_NO_DEBUG>)
+ELSE()
+  SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS_DEBUG QT_DEBUG)
+  SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS_RELEASE QT_NO_DEBUG)
+ENDIF()
 SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS_RELWITHDEBINFO QT_NO_DEBUG)
 SET_PROPERTY(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS_MINSIZEREL QT_NO_DEBUG)
 

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

Code/Mantid/Build/class_maker.py

@@ -129,6 +129,8 @@ def write_source(subproject, classname, filename, args):
     algorithm_source = """
   //----------------------------------------------------------------------------------------------
 
+  /// Algorithms name for identification. @see Algorithm::name
+  const std::string %s::name() const { return "%s"; }
 
   /// Algorithm's version for identification. @see Algorithm::version
   int %s::version() const { return 1;};
@@ -156,7 +158,7 @@ def write_source(subproject, classname, filename, args):
     // TODO Auto-generated execute stub
   }
 
-""" % (classname, classname, classname, classname, classname)
+""" % (classname, classname, classname, classname, classname, classname, classname)
 
     if not args.alg:
         algorithm_top = ""

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

@@ -1,5 +1,5 @@
 Name:           mantid-developer
-Version:        1.4
+Version:        1.5
 Release:        1%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
@@ -19,6 +19,7 @@ Requires: git-all
 Requires: gsl-devel
 Requires: hdf-devel
 Requires: hdf5-devel
+Requires: jsoncpp-devel
 Requires: muParser-devel
 Requires: mxml-devel
 Requires: nexus >= 4.2