Merge remote-tracking branch 'origin/master' into feature/7840_c2e_ad…

…d_scale_to_res

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ConvertToEnergy.ui

Refs #7840

Code/Mantid/Build/CMake/CPackCommon.cmake

@@ -7,7 +7,6 @@ set ( CPACK_PACKAGE_DESCRIPTION_SUMMARY "Neutron Scattering Data Analysis" )
 set ( CPACK_PACKAGE_VENDOR "ISIS Rutherford Appleton Laboratory and NScD Oak Ridge National Laboratory" )
 set ( CPACK_PACKAGE_URL http://www.mantidproject.org/ )
 set ( CPACK_PACKAGE_CONTACT mantid-help@mantidproject.org )
-include ( PatchVersionNumber )
 set ( CPACK_PACKAGE_VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH} )
 set ( CPACK_PACKAGE_VERSION_MAJOR ${VERSION_MAJOR} )
 set ( CPACK_PACKAGE_VERSION_MINOR ${VERSION_MINOR} )

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -80,7 +80,6 @@ endif()
 # Also makes sure our commit hooks are linked in the right place.
 ###########################################################################
 
-set ( MtdVersion_WC_LAST_CHANGED_REV 0 )
 set ( MtdVersion_WC_LAST_CHANGED_DATE Unknown )
 set ( MtdVersion_WC_LAST_CHANGED_DATETIME 0 )
 set ( NOT_GIT_REPO "Not" )
@@ -94,14 +93,12 @@ if ( GIT_FOUND )
                     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
   )
   if ( NOT NOT_GIT_REPO ) # i.e This is a git repository!
-
     # Remove the tag name part
     string ( REGEX MATCH "[-](.*)" MtdVersion_WC_LAST_CHANGED_REV ${GIT_DESCRIBE} )
     # Extract the SHA1 part (with a 'g' prefix which stands for 'git')
     # N.B. The variable comes back from 'git describe' with a line feed on the end, so we need to lose that
     string ( REGEX MATCH "(g.*)[^\n]" MtdVersion_WC_LAST_CHANGED_SHA ${MtdVersion_WC_LAST_CHANGED_REV} )
-    # Get the number part (number of commits since tag)
-    string ( REGEX MATCH "[0-9]+" MtdVersion_WC_LAST_CHANGED_REV ${MtdVersion_WC_LAST_CHANGED_REV} )
+
     # Get the date of the last commit
     execute_process ( COMMAND ${GIT_EXECUTABLE} log -1 --format=format:%cD OUTPUT_VARIABLE MtdVersion_WC_LAST_CHANGED_DATE 
                       WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
@@ -190,27 +187,28 @@ else()
   message ( STATUS "Git not found - using dummy revision number and date" )
 endif()
 
-mark_as_advanced( MtdVersion_WC_LAST_CHANGED_REV MtdVersion_WC_LAST_CHANGED_DATE
-                  MtdVersion_WC_LAST_CHANGED_DATETIME )
+mark_as_advanced( MtdVersion_WC_LAST_CHANGED_DATE MtdVersion_WC_LAST_CHANGED_DATETIME )
 
-###########################################################################
-# Include the file that contains the version number
-# This must come after the git describe business above because it can be
-# used to override the patch version number (MtdVersion_WC_LAST_CHANGED_REV)
-###########################################################################
-
-include ( VersionNumber )
 
 if ( NOT NOT_GIT_REPO ) # i.e This is a git repository!
   ###########################################################################
   # Create the file containing the patch version number for use by cpack
-  # The patch number make have been overridden by VerisonNumber so create
+  # The patch number make have been overridden by VersionNumber so create
   # the file used by cpack here
   ###########################################################################
   configure_file ( ${GIT_TOP_LEVEL}/Code/Mantid/Build/CMake/PatchVersionNumber.cmake.in
                    ${GIT_TOP_LEVEL}/Code/Mantid/Build/CMake/PatchVersionNumber.cmake )
+  include ( PatchVersionNumber )
 endif()
 
+###########################################################################
+# Include the file that contains the version number
+# This must come after the git describe business above because it can be
+# used to override the patch version number (MtdVersion_WC_LAST_CHANGED_REV)
+###########################################################################
+include ( VersionNumber )
+
+
 ###########################################################################
 # Look for OpenMP and set compiler flags if found
 ###########################################################################

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -60,7 +60,6 @@ set ( PVPLUGINS_DIR MantidPlot.app/pvplugins )
 set ( PVPLUGINS_SUBDIR pvplugins ) # Need to tidy these things up!
 
 # Python packages
-set ( PYTHON_PACKAGES_DIR ${CMAKE_LIBRARY_PATH}/Python )
 
 install ( PROGRAMS /Library/Python/${PY_VER}/site-packages/sip.so DESTINATION ${BIN_DIR} )
 # Explicitly specify which PyQt libraries we want because just taking the whole
@@ -75,8 +74,13 @@ install ( FILES /Library/Python/${PY_VER}/site-packages/PyQt4/Qt.so
                 /Library/Python/${PY_VER}/site-packages/PyQt4/__init__.py
           DESTINATION ${BIN_DIR}/PyQt4 )
 install ( DIRECTORY /Library/Python/${PY_VER}/site-packages/PyQt4/uic DESTINATION ${BIN_DIR}/PyQt4 )
-# nxs package
-install ( DIRECTORY ${PYTHON_PACKAGES_DIR}/nxs DESTINATION ${BIN_DIR} )
+
+# 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} )
+  file ( COPY ${PYPACKAGE} DESTINATION ${PROJECT_BINARY_DIR}/bin )
+endforeach( PYPACKAGE )
 
 install ( DIRECTORY ${QT_PLUGINS_DIR}/imageformats DESTINATION MantidPlot.app/Contents/Frameworks/plugins )
 

Code/Mantid/Build/CMake/VersionNumber.cmake

@@ -6,5 +6,5 @@ set ( VERSION_MINOR 6 )
 # UNCOMMENT the next 'set' line to 'force' the patch version number to
 # a value (instead of using the count coming out of 'git describe')
 # DO NOT COMMIT THIS TO MASTER UNCOMMENTED, ONLY TO A RELEASE BRANCH
-#set ( MtdVersion_WC_LAST_CHANGED_REV 1 )
+#set ( VERSION_PATCH 0 )
 

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

@@ -48,13 +48,15 @@ namespace Mantid
     {
     public:
       std::string getFullPath(const std::string& filename)const;
-      std::string getPath(const std::vector<IArchiveSearch_sptr>& archs, const std::set<std::string>& filename, const std::vector<std::string>& extensions)const;
+      std::string getPath(const std::vector<IArchiveSearch_sptr>& archs, const std::set<std::string>& filename,
+                          const std::vector<std::string>& extensions)const;
       /// DO NOT USE! MADE PUBLIC FOR TESTING ONLY.
       std::string makeFileName(const std::string& hint, const Kernel::InstrumentInfo& instrument)const;
       void setCaseSensitive(const bool cs);
       bool getCaseSensitive() const;
-      std::string findRun(const std::string& hintstr,const std::set<std::string> *exts)const;
-      std::string findRun(const std::string& hintstr,const std::vector<std::string> &exts  = std::vector<std::string>())const;
+      std::string findRun(const std::string& hintstr,const std::set<std::string> & exts)const;
+      std::string findRun(const std::string& hintstr,
+                          const std::vector<std::string> &exts  = std::vector<std::string>())const;
       std::vector<std::string> findRuns(const std::string& hintstr)const;
       /// DO NOT USE! MADE PUBLIC FOR TESTING ONLY.
       const Kernel::InstrumentInfo getInstrument(const std::string& hint) const;

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

@@ -143,6 +143,8 @@ namespace Mantid
 
       /// Empty the values out of all TimeSeriesProperty logs
       void clearTimeSeriesLogs();
+      /// Empty all but the last value out of all TimeSeriesProperty logs
+      void clearOutdatedTimeSeriesLogValues();
 
       /// Save the run to a NeXus file with a given group name
       virtual void saveNexus(::NeXus::File * file, const std::string & group,bool keepOpen=false) const;

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

@@ -550,10 +550,12 @@ They will work as was expected for folders @ref folders-sec.
         
         @param option: flag to set for auto-update, or not. If true, new versions of the path will replace the local file as soon as they are available at the central repository.
         
+        @return int: number of files changed (because of the cascading of folders)
+
         @exception ScriptRepoException : Invalid entry.
                 
     */
-    virtual void setAutoUpdate(const std::string & path, bool option = true) = 0;
+    virtual int setAutoUpdate(const std::string & path, bool option = true) = 0;
 
 
   };

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

@@ -780,6 +780,8 @@ namespace API
   *  date is selected. If no such files are found the file with the latest from date is 
   *  selected.
   *
+  *  If no file is found for the given instrument, an empty string is returned.
+  *
   *  @param instrumentName :: Instrument name e.g. GEM, TOPAS or BIOSANS
   *  @param date :: ISO 8601 date
   *  @return full path of IDF

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

@@ -360,15 +360,15 @@ namespace Mantid
      *  this argument is ignored.
      * @return The full path to the file or empty string if not found
      */
-    std::string FileFinderImpl::findRun(const std::string& hintstr, const std::set<std::string> *exts) const
+    std::string FileFinderImpl::findRun(const std::string& hintstr, const std::set<std::string> &exts) const
     {
       std::string hint = Kernel::Strings::strip(hintstr);
-      g_log.debug() << "set findRun(\'" << hintstr << "\', exts[" << exts->size() << "])\n";
+      g_log.debug() << "set findRun(\'" << hintstr << "\', exts[" << exts.size() << "])\n";
       if (hint.empty())
         return "";
       std::vector<std::string> exts_v;
-      if (exts != NULL && exts->size() > 0)
-        exts_v.assign(exts->begin(), exts->end());
+      if (!exts.empty())
+        exts_v.assign(exts.begin(), exts.end());
 
       return this->findRun(hint, exts_v);
     }

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

@@ -378,7 +378,22 @@ Kernel::Logger& LogManager::g_log = Kernel::Logger::get("LogManager");
     }
   }
 
-
+  /** Clears out all but the last entry of all logs of type TimeSeriesProperty
+   *  Check the documentation/definition of TimeSeriesProperty::clearOutdated for
+   *  the definition of 'last entry'.
+   */
+  void LogManager::clearOutdatedTimeSeriesLogValues()
+  {
+    auto & props = getProperties();
+    for ( auto it = props.begin(); it != props.end(); ++it)
+    {
+      if ( auto tsp = dynamic_cast<ITimeSeriesProperty*>(*it) )
+      {
+        tsp->clearOutdated();
+      }
+    }
+  }
+
   //--------------------------------------------------------------------------------------------
   /** Save the object to an open NeXus file.
    * @param file :: open NeXus file

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

@@ -538,11 +538,13 @@ class ExperimentInfoTest : public CxxTest::TestSuite
         {
           if (it1 != it2)
           {
-            if ( it2->second.from == it1->second.from )
-            {
-              // some more intelligent stuff here later
-              TS_ASSERT_EQUALS("Two IDFs for one instrument have equal valid-from dates", "0");
-            }
+            // some more intelligent stuff here later
+            std::stringstream messageBuffer;
+            messageBuffer << "Two IDFs for one instrument have equal valid-from dates" << 
+              "IDFs are: " << it1->first << " and " << it2->first <<
+              " Date One: "<< it1->second.from.toFormattedString() <<
+              " Date Two: "<< it2->second.from.toFormattedString();
+            TSM_ASSERT_DIFFERS(messageBuffer.str(), it2->second.from, it1->second.from);
           }
         }
 

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

@@ -259,7 +259,37 @@ class LogManagerTest : public CxxTest::TestSuite
     TS_ASSERT_EQUALS( runInfo.getPropertyValueAsType<int>(intProp), 99 );
   }
 
+  void clearOutdatedTimeSeriesLogValues()
+  {
+    // Set up a Run object with 3 properties in it (1 time series, 2 single value)
+    LogManager runInfo;
+    const std::string stringProp("aStringProp");
+    const std::string stringVal("testing");
+    runInfo.addProperty(stringProp,stringVal);
+    const std::string intProp("anIntProp");
+    runInfo.addProperty(intProp,99);
+    const std::string tspProp("tsp");
+    addTestTimeSeries(runInfo,"tsp");
 
+    // Check it's set up right
+    TS_ASSERT_EQUALS( runInfo.getProperties().size(), 3 );
+    auto tsp = runInfo.getTimeSeriesProperty<double>(tspProp);
+    TS_ASSERT_EQUALS( tsp->realSize(), 10 );
+
+    auto lastTime = tsp->lastTime();
+    auto lastValue = tsp->lastValue();
+
+    // Do the clearing work
+    TS_ASSERT_THROWS_NOTHING( runInfo.clearOutdatedTimeSeriesLogValues() );
+
+    // Check the time-series property has 1 entry, & the others are unchanged
+    TS_ASSERT_EQUALS( runInfo.getProperties().size(), 3 );
+    TS_ASSERT_EQUALS( tsp->realSize(), 1 );
+    TS_ASSERT_EQUALS( tsp->firstTime(), lastTime );
+    TS_ASSERT_EQUALS( tsp->firstValue(), lastValue );
+    TS_ASSERT_EQUALS( runInfo.getPropertyValueAsType<std::string>(stringProp), stringVal );
+    TS_ASSERT_EQUALS( runInfo.getPropertyValueAsType<int>(intProp), 99 );
+  }
 
   /** Save and load to NXS file */
   void test_nexus()

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -104,7 +104,6 @@ set ( SRC_FILES
 	src/FindDetectorsOutsideLimits.cpp
 	src/FindPeaks.cpp
 	src/FindPeakBackground.cpp
-	src/FlatBackground.cpp
 	src/FlatPlateAbsorption.cpp
 	src/GeneralisedSecondDifference.cpp
 	src/GenerateEventsFilter.cpp
@@ -328,7 +327,6 @@ set ( INC_FILES
 	inc/MantidAlgorithms/FindDetectorsOutsideLimits.h
 	inc/MantidAlgorithms/FindPeaks.h
 	inc/MantidAlgorithms/FindPeakBackground.h
-	inc/MantidAlgorithms/FlatBackground.h
 	inc/MantidAlgorithms/FlatPlateAbsorption.h
 	inc/MantidAlgorithms/GSLFunctions.h
 	inc/MantidAlgorithms/GeneralisedSecondDifference.h
@@ -556,7 +554,6 @@ set ( TEST_FILES
 	FindDetectorsOutsideLimitsTest.h
 	FindPeaksTest.h
 	FindPeakBackgroundTest.h
-	FlatBackgroundTest.h
 	FlatPlateAbsorptionTest.h
 	GenerateEventsFilterTest.h
 	GeneratePeaksTest.h

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/BinaryOperation.h

@@ -73,12 +73,13 @@ namespace Mantid
        * Index into vector: workspace index in the lhs;
        * Value at that index: workspace index of the rhs to apply to the WI in the lhs. -1 if not found.
        */
-      typedef std::vector< int64_t >  BinaryOperationTable;
+      typedef std::vector< int64_t>  BinaryOperationTable;
+      typedef boost::shared_ptr<BinaryOperationTable>  BinaryOperationTable_sptr;
 
-      static BinaryOperationTable * buildBinaryOperationTable(API::MatrixWorkspace_const_sptr lhs, API::MatrixWorkspace_const_sptr rhs);
+      static BinaryOperationTable_sptr
+        buildBinaryOperationTable(const API::MatrixWorkspace_const_sptr & lhs, const API::MatrixWorkspace_const_sptr & rhs);
 
 
-    //protected:
     private:
       // Overridden Algorithm methods
       void init();

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/CheckWorkspacesMatch.h

@@ -5,6 +5,8 @@
 // Includes
 //----------------------------------------------------------------------
 #include "MantidAPI/Algorithm.h"
+#include "MantidAPI/IPeaksWorkspace.h"
+#include "MantidDataObjects/EventWorkspace.h"
 
 namespace Mantid
 {
@@ -38,10 +40,7 @@ namespace Algorithms
     <LI> Result - Contains 'success' if the workspaces match, the reason for the failure otherwise </LI>
     </UL>
 
-    @author Russell Taylor, Tessella Support Services plc
-    @date 01/12/2009
-
-    Copyright &copy; 2009 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+    Copyright &copy; 2009-2013 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
 
     This file is part of Mantid.
 
@@ -92,11 +91,11 @@ class DLLExport CheckWorkspacesMatch : public API::Algorithm
   /// Execution code
   void exec();
 
-  // property indicate that relative error tolerance in data is set up rather then absolute error. 
-  bool m_ErrorIsRelative;
   void doComparison();
-  // Compare two MD workspaces
+  void doPeaksComparison(API::IPeaksWorkspace_sptr tws1, API::IPeaksWorkspace_sptr tws2);
+  void doTableComparison(API::ITableWorkspace_const_sptr tws1, API::ITableWorkspace_const_sptr tws2);
   void doMDComparison(API::Workspace_sptr w1, API::Workspace_sptr w2);
+  bool checkEventLists(DataObjects::EventWorkspace_const_sptr ews1, DataObjects::EventWorkspace_const_sptr ews2);
   bool checkData(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
   bool checkAxes(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
   bool checkSpectraMap(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/CopySample.h

@@ -55,7 +55,8 @@ namespace Algorithms
     virtual int version() const { return 1;};
     /// Algorithm's category for identification
     virtual const std::string category() const { return "Sample;Utility\\Workspaces;DataHandling";}
-
+    /// @inheritdocs
+    virtual std::map<std::string, std::string> validateInputs();
   private:
     /// Sets documentation strings for this algorithm
     virtual void initDocs();
@@ -64,9 +65,7 @@ namespace Algorithms
     /// Run the algorithm
     void exec();
     /// Function to copy information from one sample to another
-    void copyParameters(API::Sample& from,API::Sample& to,bool nameFlag,bool materialFlag, bool environmentFlag, bool shapeFlag,bool latticeFlag);
-
-
+    void copyParameters(API::Sample& from, API::Sample& to, bool nameFlag, bool materialFlag, bool environmentFlag, bool shapeFlag, bool latticeFlag, bool orientationOnlyFlag);
 
   };