Merge branch 'master' into feature/9445_poldi_spectrum_domain_function

Conflicts:
	Code/Mantid/Framework/SINQ/CMakeLists.txt

Code/Mantid/Build/CMake/CPackLinuxSetup.cmake

@@ -11,7 +11,7 @@ set ( CPACK_SOURCE_GENERATOR TGZ )
 include (DetermineLinuxDistro)
 
 # define which binary generators to use
-if ( ${UNIX_DIST} MATCHES "Ubuntu" )
+if ( "${UNIX_DIST}" MATCHES "Ubuntu" )
   find_program (DPKG_CMD dpkg)
   if ( DPKG_CMD )
     set ( CPACK_GENERATOR "DEB" )
@@ -22,23 +22,23 @@ if ( ${UNIX_DIST} MATCHES "Ubuntu" )
     set( CPACK_PACKAGE_FILE_NAME
       "${CPACK_PACKAGE_NAME}_${CPACK_PACKAGE_VERSION}-${CPACK_DEBIAN_PACKAGE_RELEASE}_${CPACK_DEBIAN_PACKAGE_ARCHITECTURE}")   
   endif ( DPKG_CMD ) 
-endif ( ${UNIX_DIST} MATCHES "Ubuntu" )
+endif ( "${UNIX_DIST}" MATCHES "Ubuntu" )
 
 #RedHatEnterpriseClient RedHatEnterpriseWorkstation
-if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR ${UNIX_DIST} MATCHES "SUSE LINUX" )
+if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" OR "${UNIX_DIST}" MATCHES "Fedora" OR "${UNIX_DIST}" MATCHES "SUSE LINUX" )
   find_program ( RPMBUILD_CMD rpmbuild )
   if ( RPMBUILD_CMD )
     set ( CPACK_GENERATOR "RPM" )
     set ( CPACK_RPM_PACKAGE_ARCHITECTURE "${CMAKE_SYSTEM_PROCESSOR}" )
     set ( CPACK_RPM_PACKAGE_URL "http://www.mantidproject.org" )
 
     # reset the release name to include the RHEL version if known
-    if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" )
+    if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
       string ( REGEX REPLACE "^([0-9])\\.[0-9]+$" "\\1" TEMP ${UNIX_RELEASE} )
       set ( CPACK_RPM_PACKAGE_RELEASE "1.el${TEMP}" )
-    elseif ( ${UNIX_DIST} MATCHES "Fedora" )
+    elseif ( "${UNIX_DIST}" MATCHES "Fedora" )
       set ( CPACK_RPM_PACKAGE_RELEASE "1.fc${UNIX_RELEASE}" )
-    endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" )
+    endif ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
 
     # If CPACK_SET_DESTDIR is ON then the Prefix doesn't get put in the spec file
     if( CPACK_SET_DESTDIR )
@@ -50,5 +50,5 @@ if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR
     set ( CPACK_PACKAGE_FILE_NAME
       "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_RPM_PACKAGE_RELEASE}.${CPACK_RPM_PACKAGE_ARCHITECTURE}" )
   endif ( RPMBUILD_CMD)
-endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR ${UNIX_DIST} MATCHES "SUSE LINUX" )
+endif ()
 

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -132,7 +132,9 @@ install ( DIRECTORY /Library/Python/${PY_VER}/site-packages/PyQt4/uic DESTINATIO
 # Python packages in Third_Party need copying to build directory and the final package
 file ( GLOB THIRDPARTY_PYTHON_PACKAGES ${CMAKE_LIBRARY_PATH}/Python/* )
 foreach ( PYPACKAGE ${THIRDPARTY_PYTHON_PACKAGES} )
-  install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+  if ( IS_DIRECTORY ${PYPACKAGE} )
+    install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+  endif()
   file ( COPY ${PYPACKAGE} DESTINATION ${PROJECT_BINARY_DIR}/bin )
 endforeach( PYPACKAGE )
 

Code/Mantid/Build/CMake/LinuxSetup.cmake

@@ -90,7 +90,7 @@ endif()
 
 
 # RHEL6 specific stuff (as we need to use software collections)
-if ( ${UNIX_DIST} STREQUAL "RedHatEnterprise" )
+if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
 	file ( APPEND ${CMAKE_CURRENT_BINARY_DIR}/rpm_post_install.sh "\n"
 								     "if [ -f $RPM_INSTALL_PREFIX0/${BIN_DIR}/MantidPlot ]; then\n"
                                                                      "  mv $RPM_INSTALL_PREFIX0/${BIN_DIR}/MantidPlot $RPM_INSTALL_PREFIX0/${BIN_DIR}/MantidPlot_exe\n"
@@ -101,12 +101,12 @@ if ( ${UNIX_DIST} STREQUAL "RedHatEnterprise" )
 								      "scl enable mantidlibs \"${CMAKE_INSTALL_PREFIX}/${BIN_DIR}/MantidPlot_exe $*\" \n"
 	)
 
-install ( FILES  ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh 
+    install ( FILES  ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh
           DESTINATION ${BIN_DIR}
 	      PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
 	                  GROUP_EXECUTE GROUP_READ
 	                  WORLD_EXECUTE WORLD_READ
-)
+    )
 
 endif()
 

Code/Mantid/Build/CMake/WindowsNSIS.cmake

@@ -96,6 +96,9 @@
     install ( DIRECTORY ${CMAKE_LIBRARY_PATH}/qt_plugins/imageformats ${CMAKE_LIBRARY_PATH}/qt_plugins/sqldrivers DESTINATION plugins/qtplugins 
               REGEX "^.*d4.dll$" EXCLUDE  )
     install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/Installers/WinInstaller/qt.conf DESTINATION bin )
+
+    # Copy assistant.exe
+    install ( FILES ${CMAKE_LIBRARY_PATH}/assistant.exe DESTINATION bin )
 
     # Release deployments do modify enviromental variables, other deployments do not.
     if(CPACK_PACKAGE_SUFFIX STREQUAL "") 

Code/Mantid/Build/Jenkins/buildscript

@@ -34,12 +34,15 @@ if [[ ${JOB_NAME} == *clean* ]]; then
 
   # Set some variables relating to the linux packages created from clean builds
   if [[ $(uname) != 'Darwin' ]]; then
+    # Use different suffix for linux builds
     if [[ ${JOB_NAME} == *master* ]]; then
-      SUFFIX=nightly
+      PACKAGINGVARS="-DENVVARS_ON_INSTALL=False -DCMAKE_INSTALL_PREFIX=/opt/mantidnightly -DCPACK_PACKAGE_SUFFIX=nightly -DCPACK_SET_DESTDIR=OFF -DPACKAGE_DOCS=ON"
     elif [[ ${JOB_NAME} == *develop* ]]; then
-      SUFFIX=unstable
+      PACKAGINGVARS="-DENVVARS_ON_INSTALL=False -DCMAKE_INSTALL_PREFIX=/opt/mantidunstable -DCPACK_PACKAGE_SUFFIX=unstable -DCPACK_SET_DESTDIR=OFF -DPACKAGE_DOCS=ON"
     fi
-    PACKAGINGVARS="-DENVVARS_ON_INSTALL=False -DCMAKE_INSTALL_PREFIX=/opt/mantid${SUFFIX} -DCPACK_PACKAGE_SUFFIX=${SUFFIX} -DCPACK_SET_DESTDIR=OFF -DPACKAGE_DOCS=True"
+  else
+    # Mac packaging
+    PACKAGINGVARS="-DPACKAGE_DOCS=ON"
   fi
 fi
 
@@ -62,7 +65,7 @@ cd $WORKSPACE/build
 ###############################################################################
 # CMake configuration
 ###############################################################################
-$SCL_ON_RHEL6 "cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=${PARAVIEW_DIR} ${PACKAGINGVARS} ../Code/Mantid"
+$SCL_ON_RHEL6 "cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=${PARAVIEW_DIR} -DDOCS_HTML=ON ${PACKAGINGVARS} ../Code/Mantid"
 
 ###############################################################################
 # Build step
@@ -93,7 +96,7 @@ if [[ "$CLEANBUILD" == true ]]; then
   if [[ $(uname) == 'Darwin' ]]; then
     export MANTIDPATH=$PWD/bin
   fi
-  $SCL_ON_RHEL6 "make docs-html"
+  $SCL_ON_RHEL6 "make docs-qthelp"
 fi
 
 ###############################################################################
@@ -116,7 +119,8 @@ if [[ "$CLEANBUILD" == true ]]; then
   # and labelled by the commit id it was built with. This assumes the Jenkins git plugin
   # has set the GIT_COMMIT environment variable
   if [[ "$ON_RHEL6" == true ]]; then
-    tar -cjf mantiddocs-g${GIT_COMMIT:0:7}.tar.bz2 --exclude='*.buildinfo' docs/html
+    $SCL_ON_RHEL6 "make docs-html"
+    tar -cjf mantiddocs-g${GIT_COMMIT:0:7}.tar.bz2 --exclude='*.buildinfo' --exclude="MantidProject.q*" docs/html
     # The ..._PREFIX argument avoids opt/Mantid directories at the top of the tree
     $SCL_ON_RHEL6 "cpack --config CPackSourceConfig.cmake -D CPACK_PACKAGING_INSTALL_PREFIX="
   fi

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -60,7 +60,7 @@ if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 if "%CLEANBUILD%" EQU "yes" (
     :: Build offline documentation
-    msbuild /nologo /nr:false /p:Configuration=Release docs/docs-html.vcxproj
+    msbuild /nologo /nr:false /p:Configuration=Release docs/docs-qthelp.vcxproj
 
     :: ignore errors as the exit code of the build isn't correct
     ::if ERRORLEVEL 1 exit /B %ERRORLEVEL%

Code/Mantid/CMakeLists.txt

@@ -186,7 +186,7 @@ if ( ENABLE_CPACK )
       # rhel requirements
       set ( CPACK_RPM_PACKAGE_REQUIRES "boost >= 1.34.1,qt4 >= 4.2,nexus,nexus-python,qwt,gsl,glibc,qwtplot3d-qt4,muParser,numpy" )
       # OpenCASCADE changed names when packaged for Fedora 20
-      if( ${UNIX_CODENAME} STREQUAL "Heisenbug" )
+      if( "${UNIX_CODENAME}" MATCHES "Heisenbug" )
         set( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},OCE-devel" )
       else()
         set( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},OpenCASCADE-libs-modelling >= 6.3.0,OpenCASCADE-libs-foundation >= 6.3.0,OpenCASCADE-libs-visualization >= 6.3.0,OpenCASCADE-libs-ocaf >= 6.3.0,OpenCASCADE-libs-ocaf-lite >= 6.3.0" )
@@ -196,8 +196,8 @@ if ( ENABLE_CPACK )
       # 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" )
-
-      if( ${UNIX_CODENAME} STREQUAL "Santiago" )
+      
+      if( "${UNIX_CODENAME}" MATCHES "Santiago" )
         # On RHEL6 we have to use an updated qscintilla to fix an auto complete bug
         set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} qscintilla >= 2.4.6" )
         # On RHEL6 we are using SCL packages for Qt
@@ -207,20 +207,20 @@ if ( ENABLE_CPACK )
       endif()
 
       # Add software collections for RHEL
-      if (  ${UNIX_CODENAME} STREQUAL "Santiago" )
+      if ( "${UNIX_CODENAME}" MATCHES "Santiago" )
         set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} scl-utils" )
       endif()
 
       # qt assistant is in different places in every distro
-      if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" )
+      if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
         set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} qt4-x11" )
-      elseif ( ${UNIX_DIST} MATCHES "Fedora" )
+      elseif ( "${UNIX_DIST}" MATCHES "Fedora" )
         set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} qt4-assistant" )
-      elseif ( ${UNIX_DIST} MATCHES "SUSE LINUX" )
+      elseif ( "${UNIX_DIST}" MATCHES "SUSE LINUX" )
         set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} libqt4-devel-doc" )
-      endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" )
+      endif ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
 
-      if( ${UNIX_DIST} STREQUAL "Ubuntu" )
+      if( "${UNIX_DIST}" MATCHES "Ubuntu" )
         # common packages
         set ( DEPENDS_LIST "libboost-date-time${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
                            "libboost-regex${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
@@ -229,11 +229,11 @@ if ( ENABLE_CPACK )
                            "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" )
-        if( ${UNIX_CODENAME} STREQUAL "lucid" )
+        if( "${UNIX_CODENAME}" MATCHES "lucid" )
           list ( APPEND DEPENDS_LIST ",libqscintilla2-5,"
                                      "libopencascade-foundation-6.3.0 (>= 6.3.0),libopencascade-modeling-6.3.0 (>= 6.3.0),"
                                      "libmuparser0" )
-        elseif( ${UNIX_CODENAME} STREQUAL "precise" )
+        elseif( "${UNIX_CODENAME}" MATCHES "precise" )
           list ( APPEND DEPENDS_LIST ",libqscintilla2-8,"
                                      "libopencascade-foundation-6.5.0 (>= 6.5.0),libopencascade-modeling-6.5.0 (>= 6.5.0),"
                                      "libmuparser0debian1,"

Code/Mantid/Framework/API/CMakeLists.txt

@@ -42,7 +42,9 @@ set ( SRC_FILES
 	src/FunctionProperty.cpp
 	src/FunctionValues.cpp
 	src/GridDomain.cpp
-	src/GridDomain1D.cpp
+  src/GridDomain1D.cpp
+  src/HistoryItem.cpp
+  src/HistoryView.cpp
 	src/IDomainCreator.cpp
 	src/IEventList.cpp
 	src/IEventWorkspace.cpp
@@ -103,6 +105,7 @@ set ( SRC_FILES
 	src/Sample.cpp
 	src/SampleEnvironment.cpp
 	src/ScopedWorkspace.cpp
+  src/ScriptBuilder.cpp
 	src/ScriptRepository.cpp
 	src/ScriptRepositoryFactory.cpp
 	src/SpectraAxis.cpp
@@ -177,7 +180,9 @@ set ( INC_FILES
 	inc/MantidAPI/FunctionProperty.h
 	inc/MantidAPI/FunctionValues.h
 	inc/MantidAPI/GridDomain.h
-	inc/MantidAPI/GridDomain1D.h
+  inc/MantidAPI/GridDomain1D.h
+	inc/MantidAPI/HistoryItem.h
+  inc/MantidAPI/HistoryView.h
 	inc/MantidAPI/IAlgorithm.h
 	inc/MantidAPI/IArchiveSearch.h
 	inc/MantidAPI/IBackgroundFunction.h
@@ -258,6 +263,7 @@ set ( INC_FILES
 	inc/MantidAPI/Sample.h
 	inc/MantidAPI/SampleEnvironment.h
 	inc/MantidAPI/ScopedWorkspace.h
+  inc/MantidAPI/ScriptBuilder.h
 	inc/MantidAPI/ScriptRepository.h
 	inc/MantidAPI/ScriptRepositoryFactory.h
 	inc/MantidAPI/SingleValueParameter.h
@@ -310,6 +316,8 @@ set ( TEST_FILES
 	FunctionPropertyTest.h
 	FunctionTest.h
 	FunctionValuesTest.h
+  HistoryItemTest.h
+  HistoryViewTest.h
 	IEventListTest.h
 	IFunction1DSpectrumTest.h
 	IFunction1DTest.h
@@ -345,6 +353,7 @@ set ( TEST_FILES
 	RunTest.h
 	SampleEnvironmentTest.h
 	SampleTest.h
+  ScriptBuilderTest.h
 	ScopedWorkspaceTest.h
 	SpectraAxisTest.h
 	SpectrumDetectorMappingTest.h

Code/Mantid/Framework/API/inc/MantidAPI/Algorithm.h

@@ -301,6 +301,8 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
 
   /// get whether we are tracking the history for this algorithm,
   bool trackingHistory();
+  /// Copy workspace history for input workspaces to output workspaces and record the history for ths algorithm
+  virtual void fillHistory();
 
   /// Set to true to stop execution
   bool m_cancel;
@@ -344,12 +346,11 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   void unlockWorkspaces();
 
   void store();
+  void linkHistoryWithLastChild();
 
   void logAlgorithmInfo() const;
 
   bool executeAsyncImpl(const Poco::Void & i);
-  /// Copy workspace history for input workspaces to output workspaces and record the history for ths algorithm
-  void fillHistory();
 
   // --------------------- Private Members -----------------------------------
   /// Poco::ActiveMethod used to implement asynchronous execution.

Code/Mantid/Framework/API/inc/MantidAPI/AlgorithmHistory.h

@@ -22,9 +22,11 @@ namespace API
   class IAlgorithm;
   class Algorithm;
   class AlgorithmHistory;
-
+
+  //typedefs for algorithm history pointers
   typedef boost::shared_ptr<AlgorithmHistory> AlgorithmHistory_sptr;
   typedef boost::shared_ptr<const AlgorithmHistory> AlgorithmHistory_const_sptr;
+
   typedef std::set<AlgorithmHistory_sptr, 
     boost::function<bool(const AlgorithmHistory_const_sptr, const AlgorithmHistory_const_sptr)> > AlgorithmHistories;
 
@@ -59,6 +61,7 @@ namespace API
 
 class MANTID_API_DLL AlgorithmHistory
 {
+
 public:
   /// History container
 
@@ -89,13 +92,13 @@ class MANTID_API_DLL AlgorithmHistory
   ///get the execution count
   const std::size_t& execCount() const {return m_execCount;}
   /// get parameter list of algorithm in history const
-  const std::vector<Kernel::PropertyHistory>& getProperties() const {return m_properties;}
+  const Mantid::Kernel::PropertyHistories& getProperties() const {return m_properties;}
   /// get the child histories of this history object
   const AlgorithmHistories& getChildHistories() const { return m_childHistories; }
   /// Retrieve a child algorithm history by index
-  AlgorithmHistory_const_sptr getChildAlgorithmHistory(const size_t index) const;
+  AlgorithmHistory_sptr getChildAlgorithmHistory(const size_t index) const;
     /// Add operator[] access
-  AlgorithmHistory_const_sptr operator[](const size_t index) const;
+  AlgorithmHistory_sptr operator[](const size_t index) const;
   /// Retrieve the number of child algorithms
   size_t childHistorySize() const;
   /// print contents of object
@@ -123,12 +126,20 @@ class MANTID_API_DLL AlgorithmHistory
   boost::shared_ptr<IAlgorithm> getChildAlgorithm(const size_t index) const;
   /// Write this history object to a nexus file
   void saveNexus(::NeXus::File* file, int& algCount) const;
+  // Set the execution count 
+  void setExecCount(std::size_t execCount) { m_execCount = execCount; }
+  /// Set data on history after it is created
+  void fillAlgorithmHistory(const Algorithm* const alg, 
+                       const Kernel::DateAndTime& start = Kernel::DateAndTime::defaultTime(),
+                       const double& duration = -1.0,std::size_t uexeccount = 0);
   // Allow Algorithm::execute to change the exec count & duration after the algorithm was executed
   friend class Algorithm;
 
-  // Set the execution count 
-  void setExecCount(std::size_t execCount) { m_execCount = execCount; }
 private:
+  //private constructor
+  AlgorithmHistory();
+  // Set properties of algorithm
+  void setProperties(const Algorithm* const alg);
   /// The name of the Algorithm
   std::string m_name;
   /// The version of the algorithm
@@ -138,7 +149,7 @@ class MANTID_API_DLL AlgorithmHistory
   /// The execution duration of the algorithm
   double m_executionDuration;
   /// The PropertyHistory's defined for the algorithm
-  std::vector<Kernel::PropertyHistory> m_properties;
+  Mantid::Kernel::PropertyHistories m_properties;
   ///count keeps track of execution order of an algorithm
   std::size_t m_execCount;
   /// set of child algorithm histories for this history record

Code/Mantid/Framework/API/inc/MantidAPI/FrameworkManager.h

@@ -73,6 +73,9 @@ namespace Mantid
       /// Clear memory associated with the IDS
       void clearInstruments();
 
+      /// Clear memory associated with the PropertyManagers
+      void clearPropertyManagers();
+
       /// Creates and instance of an algorithm
       IAlgorithm* createAlgorithm(const std::string& algName, const int& version=-1);