re #10549 merge master and resolve conflict

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -47,14 +47,16 @@ 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 )
 include_directories ( SYSTEM ${NEXUS_INCLUDE_DIR} )
 
 find_package ( MuParser REQUIRED )
 
+find_package ( JsonCPP REQUIRED )
+
 find_package ( Doxygen ) # optional
 
 # Need to change search path to find zlib include on Windows.

Code/Mantid/Build/CMake/FindJsonCPP.cmake

@@ -0,0 +1,33 @@
+# - Find jsoncpp include dirs and libraries
+# Use this module by invoking find_package with the form:
+#  find_package(JsonCPP [required] [quiet] )
+#
+# The module sets the following variables 
+#  JSONCPP_FOUND          - True if headers and libraries were found
+#  JSONCPP_INCLUDE_DIR    - jsoncpp include directories
+#  JSONCPP_LIBRARY        - library files for linking (optimised version)
+#  JSONCPP_LIBRARY_DEBUG  - library files for linking (debug version)
+#  JSONCPP_LIBRARIES      - All required libraries, including the configuration type
+
+# Headers
+find_path ( JSONCPP_INCLUDE_DIR jsoncpp/json/json.h )
+
+# Libraries
+find_library ( JSONCPP_LIBRARY NAMES jsoncpp ) # optimized
+find_library ( JSONCPP_LIBRARY_DEBUG NAMES jsoncpp_d ) # debug
+
+if ( JSONCPP_LIBRARY AND JSONCPP_LIBRARY_DEBUG )
+  set ( JSONCPP_LIBRARIES optimized ${JSONCPP_LIBRARY} debug ${JSONCPP_LIBRARY_DEBUG} )
+else()
+  set ( JSONCPP_LIBRARIES ${JSONCPP_LIBRARY} )
+endif()
+
+# Handle the QUIETLY and REQUIRED arguments and set JSONCPP_FOUND to TRUE if 
+# all listed variables are TRUE
+include ( FindPackageHandleStandardArgs )
+find_package_handle_standard_args( JsonCPP DEFAULT_MSG JSONCPP_INCLUDE_DIR JSONCPP_LIBRARIES )
+
+# Advanced variables
+mark_as_advanced ( JSONCPP_INCLUDE_DIR JSONCPP_LIBRARIES )
+
+

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/WindowsSetup.cmake

@@ -82,7 +82,7 @@ set ( PYTHONW_EXECUTABLE "${CMAKE_LIBRARY_PATH}/Python27/pythonw.exe" CACHE FILE
 ###########################################################################
 add_definitions ( -DWIN32 -D_WINDOWS -DMS_VISUAL_STUDIO )
 add_definitions ( -D_USE_MATH_DEFINES -DNOMINMAX )
-add_definitions ( -DGSL_DLL )
+add_definitions ( -DGSL_DLL -DJSON_DLL )
 add_definitions ( -DPOCO_NO_UNWINDOWS )
 add_definitions ( -D_SCL_SECURE_NO_WARNINGS )
 add_definitions ( -D_CRT_SECURE_NO_WARNINGS )

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

Code/Mantid/Build/paraview-deb-packaging/README

@@ -1,14 +1,19 @@
 --Author: Owen Arnold
---Date: 06/March/2012
+--Date: 06/March/2012, updated 14/Nov/2014
 
 Info:
 The bash script in this directory is used to build and package ParaView to Debian packages for Ubuntu platforms.
-At the time of writing custom deployment is necessary for these reasons:
+At the time of writing custom deployment is necessary for two reasons:
 
-1) Current versions of Ubuntu distribute much older versions of ParaView from their repositories
-2) The distributed source version of ParaView 3.10.1 contains bugs which we have fixed in our modified source code. This script can be used with our patched source. Currently available at http://download.mantidproject.org/VatesDownload.psp
-3) The default ParaView packaging puts libraries in subdirectories of lib and they therefore cannot be found by Mantid without manually modifying the LD_LIBRARY_PATH. This packaging script will fix that issue.
+1) We distribute a slightly modified source version of ParaView 3.98.1. This script can be used with our patched source.
+   Currently available at http://download.mantidproject.org
+2) The default ParaView packaging puts libraries in subdirectories of lib and they therefore cannot be found by Mantid
+   without manually modifying the LD_LIBRARY_PATH. This packaging script will fix that issue.
 
 Usage:
-In order to build the binary packages. Place the *.tar.gz  paraview source compressed file from http://download.mantidproject.org/VatesDownload.psp into an empty directory. Copy the accompanying *.sh script associated with this README into the same directory. Run the bash script. The packaged .*Deb binaries will appear in the /paraview/install directory at the end of the process.
 
+- In order to build the binary packages. Place the *.tar.gz  paraview source compressed file from
+   http://download.mantidproject.org into an empty directory.
+
+- Copy the accompanying *.sh script associated with this README into the same directory. Run the bash script.
+  The packaged .*Deb binaries will appear in the /paraview/install directory at the end of the process.

Code/Mantid/Build/paraview-deb-packaging/build_and_package.sh

@@ -9,9 +9,9 @@ PV_LOC=paraview
 
 PV_PKG=ParaView
 
-PV_VER=3.10.1
+PV_VER=3.98.1
 
-PV_NAME=${PV_PKG}-${PV_VER}-patched
+PV_NAME=${PV_PKG}-${PV_VER}-source
 
 PV_SRC=${PV_NAME}.tar.gz
 

Code/Mantid/CMakeLists.txt

@@ -186,12 +186,8 @@ if ( ENABLE_CPACK )
 
       # rhel requirements
       set ( CPACK_RPM_PACKAGE_REQUIRES "boost >= 1.34.1,qt4 >= 4.2,nexus,nexus-python,gsl,glibc,qwtplot3d-qt4,muParser,numpy" )
-      # OpenCASCADE changed names when packaged for Fedora 20 and RHEL7
-      if( "${UNIX_CODENAME}" MATCHES "Heisenbug" OR "${UNIX_CODENAME}" MATCHES "Maipo" )
-        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" )
-      endif()
+      # OCE
+      set( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},OCE-draw,OCE-foundation,OCE-modeling,OCE-ocaf,OCE-visualization")
       # Qwt is qwt5-qt4 in RHEL7
       if( "${UNIX_CODENAME}" MATCHES "Maipo" )
         set( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},qwt5-qt4" )
@@ -224,25 +220,26 @@ if ( ENABLE_CPACK )
         set ( DEPENDS_LIST "libboost-date-time${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
                            "libboost-regex${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
                            "libboost-python${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION},"
-                           "libpocofoundation9,libpocoutil9,libpoconet9,libpoconetssl9,libpococrypto9,libpocoxml9,"
                            "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" )
         set ( PERFTOOLS_DEB_PACKAGE "libgoogle-perftools0 (>= 1.7)" )
         if( "${UNIX_CODENAME}" MATCHES "lucid" )
           list ( APPEND DEPENDS_LIST ",libqscintilla2-5,"
                                      "libopencascade-foundation-6.3.0 (>= 6.3.0),libopencascade-modeling-6.3.0 (>= 6.3.0),"
-                                     "libmuparser0" )
+                                     "libmuparser0,libpocofoundation9,libpocoutil9,libpoconet9,libpoconetssl9,libpococrypto9,libpocoxml9" )
         elseif( "${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,"
-                                     "ipython-qtconsole (>= 1.1),python-matplotlib,python-scipy" )
+                                     "ipython-qtconsole (>= 1.1),python-matplotlib,python-scipy,"
+                                     "libpocofoundation9,libpocoutil9,libpoconet9,libpoconetssl9,libpococrypto9,libpocoxml9")
         elseif( "${UNIX_CODENAME}" STREQUAL "trusty" )
           list ( APPEND DEPENDS_LIST ",libqscintilla2-11,"
                                      "liboce-foundation8,liboce-modeling8,"
                                      "libmuparser2,"
-                                     "ipython-qtconsole (>= 1.1),python-matplotlib,python-scipy" )
+                                     "ipython-qtconsole (>= 1.1),python-matplotlib,python-scipy,"
+                                     "libpocofoundation11,libpocoutil11,libpoconet11,libpoconetssl11,libpococrypto11,libpocoxml11")
           set ( PERFTOOLS_DEB_PACKAGE "libgoogle-perftools4 (>= 1.7)" )
         else()
           message( WARNING "Mantid does not support packaging of this Ubuntu version: ${UNIX_CODENAME}")

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

@@ -150,6 +150,8 @@ namespace Mantid
       virtual void saveNexus(::NeXus::File * file, const std::string & group,bool keepOpen=false) const;
       /// Load the run from a NeXus file with a given group name
       virtual void loadNexus(::NeXus::File * file, const std::string & group,bool keepOpen=false);
+      /// Clear the logs
+      void clearLogs();
 
     protected:
       /// A pointer to a property manager

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

@@ -369,44 +369,6 @@ class DLLExport IncreasingAxisValidator : public MatrixWorkspaceValidator
   }
 };
 
-//===============================================================================================
-/**
- * A validator which checks whether data in each spectrum of the input workspace are monotonically increasing.
- */
-class DLLExport IncreasingDataValidator : public MatrixWorkspaceValidator
-{
-public:
-  ///Gets the type of the validator
-  std::string getType() const { return "increasingdata"; }
-  /// Clone the current state
-  Kernel::IValidator_sptr clone() const { return boost::make_shared<IncreasingDataValidator>(*this); }
-
-private:
-  /** Validate a workspace.
-  *  @param value :: The workspace to test
-  *  @return A message for users with negative results, otherwise ""
-  */
-  std::string checkValidity( const MatrixWorkspace_sptr& value ) const
-  {
-    if ( value->blocksize() < 2 ) 
-    {
-      return "Spectra must have two or more data points (bins).";
-    }
-    for(size_t spec = 0; spec < value->getNumberHistograms(); ++spec)
-    {
-      auto &Y = value->readY( spec );
-      double y = Y.front();
-      for(auto it = Y.begin() + 1; it != Y.end(); ++it)
-      {
-        if ( y > *it ) return "Data in the workspace must monotonically increase.";
-        y = *it;
-      }
-    }
-    return "";
-  }
-
-};
-
 } // namespace API
 } // namespace Mantid
 

Code/Mantid/Framework/API/src/Algorithm.cpp

@@ -1055,15 +1055,35 @@ namespace Mantid
         // Loop over the output workspaces
         for (outWS = outputWorkspaces.begin(); outWS != outputWorkspaces.end(); ++outWS)
         {
+          WorkspaceGroup_sptr wsGroup = boost::dynamic_pointer_cast<WorkspaceGroup>(*outWS);
+
           // Loop over the input workspaces, making the call that copies their history to the output ones
           // (Protection against copy to self is in WorkspaceHistory::copyAlgorithmHistory)
           for (inWS = inputWorkspaces.begin(); inWS != inputWorkspaces.end(); ++inWS)
           {
             (*outWS)->history().addHistory( (*inWS)->getHistory() );
+
+            // Add history to each child of output workspace group
+            if(wsGroup)
+            {
+              for(size_t i = 0; i < wsGroup->size(); i++)
+              {
+                wsGroup->getItem(i)->history().addHistory( (*inWS)->getHistory() );
+              }
+            }
           }
 
           // Add the history for the current algorithm to all the output workspaces
           (*outWS)->history().addHistory(m_history);
+
+          // Add history to each child of output workspace group
+          if(wsGroup)
+          {
+            for(size_t i = 0; i < wsGroup->size(); i++)
+            {
+              wsGroup->getItem(i)->history().addHistory(m_history);
+            }
+          }
         }
       }
       //this is a child algorithm, but we still want to keep the history.

Code/Mantid/Framework/API/src/LogManager.cpp

@@ -434,13 +434,22 @@ using namespace Kernel;
         if (prop)
         {
           if (m_manager.existsProperty(prop->name() ))
+          {
             m_manager.removeProperty(prop->name() );
+          }
           m_manager.declareProperty(prop);
         }
       }
     }
     if (!(group.empty()||keepOpen))file->closeGroup();
-
+  }
+
+  /**
+   * Clear the logs.
+   */
+  void LogManager::clearLogs()
+  {
+    m_manager.clear();
   }
 
   //-----------------------------------------------------------------------------------------------------------------------

Code/Mantid/Framework/API/src/MatrixWorkspace.cpp

@@ -84,6 +84,10 @@ namespace Mantid
       os << "\n"
         << "Y axis: " << YUnitLabel() << "\n";
 
+      os << "Distribution: "
+        << (isDistribution()? "True" : "False")
+        << "\n";
+
       os << ExperimentInfo::toString();
       return os.str();
     }

Code/Mantid/Framework/API/test/MatrixWorkspaceTest.h

@@ -76,14 +76,15 @@ class MatrixWorkspaceTest : public CxxTest::TestSuite
     testWS->setYUnitLabel("Counts");
 
     std::string expected = \
-        "WorkspaceTester\n"
-        "Title: A test run\n"
-        "Histograms: 1\n"
-        "Bins: 1\n"
-        "Histogram\n"
-        "X axis: Time-of-flight / microsecond\n"
-        "Y axis: Counts\n"
-        "Instrument:  (1990-Jan-01 to 1990-Jan-01)\n";
+      "WorkspaceTester\n"
+      "Title: A test run\n"
+      "Histograms: 1\n"
+      "Bins: 1\n"
+      "Histogram\n"
+      "X axis: Time-of-flight / microsecond\n"
+      "Y axis: Counts\n"
+      "Distribution: False\n"
+      "Instrument:  (1990-Jan-01 to 1990-Jan-01)\n";
 
     TS_ASSERT_EQUALS(expected, testWS->toString());
   }

Code/Mantid/Framework/Algorithms/src/GeneratePythonScript.cpp

@@ -11,6 +11,11 @@
 using namespace Mantid::Kernel;
 using namespace Mantid::API;
 
+namespace
+{
+  Mantid::Kernel::Logger g_log("GeneratePythonScript");
+}
+
 namespace Mantid
 {
 namespace Algorithms
@@ -61,6 +66,7 @@ void GeneratePythonScript::exec()
 
   // Get the algorithm histories of the workspace.
   const WorkspaceHistory wsHistory = ws->getHistory();
+  g_log.information() << "Number of history items: " << wsHistory.size() << std::endl;
 
   auto view = wsHistory.createView();