Re #11374 Fix minor merge issue

mantidproject · Mar 20, 2015 · 6bc614b · 6bc614b
2 parents 25ed51f + ac8dd14
commit 6bc614b
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Showing 254 changed files with 10,162 additions and 1,337 deletions.
diff --git a/Code/Mantid/Build/CMake/CommonSetup.cmake b/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 )

diff --git a/Code/Mantid/Build/CMake/FindJsonCPP.cmake b/Code/Mantid/Build/CMake/FindJsonCPP.cmake
@@ -9,8 +9,14 @@
 #  JSONCPP_LIBRARY_DEBUG  - library files for linking (debug version)
 #  JSONCPP_LIBRARIES      - All required libraries, including the configuration type
 
+# Using unset here is a temporary hack to force FindJson to find the correct
+# path in an incremental build. It should be removed a day or two after the
+# branch introducing this is merged.
+unset ( JSONCPP_INCLUDE_DIR CACHE )
+
 # 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

diff --git a/Code/Mantid/Build/CMake/FindOpenCascade.cmake b/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 

diff --git a/Code/Mantid/Build/CMake/FindQwt.cmake b/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

diff --git a/Code/Mantid/Build/CMake/LinuxPackageScripts.cmake b/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 ${BIN_DIR} RENAME mantidpython
+          PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
+          GROUP_EXECUTE GROUP_READ
+          WORLD_EXECUTE WORLD_READ
+)
diff --git a/Code/Mantid/Build/CMake/Packaging/launch_mantidplot.sh.in b/Code/Mantid/Build/CMake/Packaging/launch_mantidplot.sh.in
@@ -9,7 +9,7 @@ SCRIPTFILE=$(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
@@ -21,4 +21,6 @@ else
 fi
 
 # 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 \
+    @WRAPPER_PREFIX@$INSTALLDIR/@MANTIDPLOT_EXEC@ $*@WRAPPER_POSTFIX@
diff --git a/Code/Mantid/Build/CMake/Packaging/mantidpython.in b/Code/Mantid/Build/CMake/Packaging/mantidpython.in
@@ -0,0 +1,34 @@
+#!/bin/sh
+#
+# Launch Mantidplot using any necessary LD_PRELOAD or software collection behaviour
+#
+# Script is configured by CMake
+
+# Find out where we are
+SCRIPTFILE=$(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=${TCMALLOC_RELEASE_RATE}
+fi
+
+# Define extra libraries for python
+LOCAL_PYTHONPATH=@WRAPPER_PREFIX@$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 \
+    PYTHONPATH=${LOCAL_PYTHONPATH} \
+    ${IPYTHON} $*@WRAPPER_POSTFIX@
diff --git a/Code/Mantid/Build/Jenkins/buildscript b/Code/Mantid/Build/Jenkins/buildscript
@@ -85,6 +85,10 @@ else
   SCL_ON_RHEL6="eval"
 fi
 
+if [[ ${NODE_LABELS} == *rhel7* ]]; then
+  ON_RHEL7=true
+fi
+
 ###############################################################################
 # Check job requirements from the name
 ###############################################################################
@@ -212,6 +216,6 @@ fi
 # Run the system tests on RHEL6 when doing a pull request build. Run
 # from a package to have at least one Linux checks it install okay
 ###############################################################################
-if [[ "${ON_RHEL6}" == true ]] && [[ ${JOB_NAME} == *pull_requests* ]]; then
+if [[ "${ON_RHEL7}" == true ]] && [[ ${JOB_NAME} == *pull_requests* ]]; then
   $SCRIPT_DIR/systemtests
 fi
diff --git a/Code/Mantid/Build/Jenkins/buildscript.bat b/Code/Mantid/Build/Jenkins/buildscript.bat
@@ -87,7 +87,7 @@ 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

diff --git a/Code/Mantid/CMakeLists.txt b/Code/Mantid/CMakeLists.txt
@@ -121,6 +121,7 @@ set( DOCS_BUILDDIR ${CMAKE_BINARY_DIR}/docs )
 # Framework Build options
 set ( CXXTEST_SINGLE_LOGFILE CACHE BOOL "Switch to have the tests for each package run together")
 set ( CXXTEST_ADD_PERFORMANCE OFF CACHE BOOL "Switch to add Performance tests to the list of tests run by ctest?")
+set ( ENABLE_OPENCASCADE ON CACHE BOOL "Enable OpenCascade-based 3D visualisation")
 
 add_subdirectory ( Framework )
 

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/FunctionDomain1D.h b/Code/Mantid/Framework/API/inc/MantidAPI/FunctionDomain1D.h
@@ -52,6 +52,8 @@ class MANTID_API_DLL FunctionDomain1D : public FunctionDomain {
   double operator[](size_t i) const { return m_data[i]; }
   /// Get a pointer to i-th value
   const double *getPointerAt(size_t i) const { return m_data + i; }
+  /// Convert to a vector
+  std::vector<double> toVector() const;
 
 protected:
   /// Protected constructor, shouldn't be created directly. Use

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/FunctionValues.h b/Code/Mantid/Framework/API/inc/MantidAPI/FunctionValues.h
@@ -103,6 +103,9 @@ class MANTID_API_DLL FunctionValues {
   /// instance.
   void setFitDataFromCalculated(const FunctionValues &values);
 
+  /// Return the calculated values as a vector
+  std::vector<double> toVector() const {return m_calculated;}
+
 protected:
   /// Copy calculated values to a buffer
   /// @param to :: Pointer to the buffer

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IMDEventWorkspace.h b/Code/Mantid/Framework/API/inc/MantidAPI/IMDEventWorkspace.h
@@ -51,11 +51,6 @@ class MANTID_API_DLL IMDEventWorkspace : public API::IMDWorkspace,
   virtual void getBoxes(std::vector<API::IMDNode *> &boxes, size_t maxDepth,
                         bool leafOnly) = 0;
 
-  /// TODO: The meaning of this method have changed! Helper method that makes a
-  /// table workspace with some box data
-  // virtual Mantid::API::ITableWorkspace_sptr makeBoxTable(size_t start, size_t
-  // num) = 0;
-
   /// @return true if the workspace is file-backed
   virtual bool isFileBacked() const = 0;
 

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IMDHistoWorkspace.h b/Code/Mantid/Framework/API/inc/MantidAPI/IMDHistoWorkspace.h
@@ -89,7 +89,7 @@ class DLLExport IMDHistoWorkspace : public IMDWorkspace,
   virtual double &operator[](const size_t &index) = 0;
 
   virtual void setCoordinateSystem(
-      const Mantid::Kernel::SpecialCoordinateSystem coordinateSystem) = 0;
+      const Kernel::SpecialCoordinateSystem coordinateSystem) = 0;
 
   virtual boost::shared_ptr<IMDHistoWorkspace> clone() const = 0;
 

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IMDWorkspace.h b/Code/Mantid/Framework/API/inc/MantidAPI/IMDWorkspace.h
@@ -67,8 +67,7 @@ enum MDNormalization {
  Code Documentation is available at: <http://doxygen.mantidproject.org>
 */
 
-class MANTID_API_DLL IMDWorkspace : public Workspace,
-                                    public Mantid::API::MDGeometry {
+class MANTID_API_DLL IMDWorkspace : public Workspace, public API::MDGeometry {
 public:
   IMDWorkspace();
   IMDWorkspace(const IMDWorkspace &other);
@@ -119,11 +118,11 @@ class MANTID_API_DLL IMDWorkspace : public Workspace,
   /// Clear existing masks
   virtual void clearMDMasking() = 0;
   ///
-  virtual Mantid::Kernel::SpecialCoordinateSystem
+  virtual Kernel::SpecialCoordinateSystem
   getSpecialCoordinateSystem() const = 0;
   /// if a workspace was filebacked, this should clear file-based status, delete
   /// file-based information and close related files.
-  virtual void clearFileBacked(bool /* loadFileContentsToMemory*/){};
+  virtual void clearFileBacked(bool /* loadFileContentsToMemory*/) {}
   /// this is the method to build table workspace from any workspace. It does
   /// not have much sence and may be placed here erroneously
   virtual ITableWorkspace_sptr makeBoxTable(size_t /*start*/, size_t /* num*/) {

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IPeaksWorkspace.h b/Code/Mantid/Framework/API/inc/MantidAPI/IPeaksWorkspace.h
@@ -55,10 +55,6 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
   /// Destructor
   virtual ~IPeaksWorkspace();
 
-  // boost::shared_ptr<IPeaksWorkspace> clone() = 0;
-  // void appendFile( std::string filename, Mantid::Geometry::Instrument_sptr
-  // inst) = 0;
-
   //---------------------------------------------------------------------------------------------
   /** @return the number of peaks
    */
@@ -99,14 +95,15 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
 
   //---------------------------------------------------------------------------------------------
   /** Create an instance of a Peak
-   * @param QLabFrame :: Q of the center of the peak in the lab frame, in reciprocal space
-   * @param detectorDistance :: Optional distance between the sample and the detector. Calculated if not provided.
+   * @param QLabFrame :: Q of the center of the peak in the lab frame, in
+   * reciprocal space
+   * @param detectorDistance :: Optional distance between the sample and the
+   * detector. Calculated if not provided.
    * @return a pointer to a new Peak object.
    */
   virtual IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
                             boost::optional<double> detectorDistance) const = 0;
 
-
   /**
    * Create an instance of a peak using a V3D
    * @param HKL V3D
@@ -136,16 +133,16 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
    * @param coordinateSystem : Special Q3D coordinate system to use.
    */
   virtual void setCoordinateSystem(
-      const Mantid::Kernel::SpecialCoordinateSystem coordinateSystem) = 0;
-
+      const Kernel::SpecialCoordinateSystem coordinateSystem) = 0;
   //---------------------------------------------------------------------------------------------
   /**
    * Get the special coordinate system.
    * @returns special Q3D coordinate system to use being used by this
    * PeaksWorkspace object. Probably the one the workspace was generated with.
    */
-  virtual Mantid::Kernel::SpecialCoordinateSystem
+  virtual Kernel::SpecialCoordinateSystem
   getSpecialCoordinateSystem() const = 0;
+
   virtual std::vector<std::pair<std::string, std::string>>
   peakInfo(Kernel::V3D QFrame, bool labCoords) const = 0;
   virtual int peakInfoNumber(Kernel::V3D qLabFrame, bool labCoords) const = 0;