Merge remote-tracking branch 'origin/master' into 11706_color_map_vsi…

…_link_color_map_editor_to_color_selection_widget_lineedits

Conflicts:
	Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/src/ViewBase.cpp

spurious conflict in principle, re #11706

Code/Mantid/Build/CMake/FindQwt.cmake

@@ -18,7 +18,7 @@ find_package_handle_standard_args( Qwt DEFAULT_MSG QWT_LIBRARY QWT_INCLUDE_DIR )
 
 # Parse version string from qwt_global.h
 file ( STRINGS ${QWT_INCLUDE_DIR}/qwt_global.h QWT_VERSION 
-       REGEX "^#define[ \t]+QWT_VERSION_STR[ \t]+\"[0-9]+.[0-9]+.[0-9]+\"$" )
+       REGEX "^#define[ \t]+QWT_VERSION_STR[ \t]+\"[0-9]+.[0-9]+.[0-9]+(.*)?\"$" )
 if ( NOT QWT_VERSION )
     message ( FATAL_ERROR "Unrecognized Qwt version (cannot find QWT_VERSION_STR in qwt_global.h)" )
 endif()

Code/Mantid/Build/CMake/GNUSetup.cmake

@@ -14,6 +14,11 @@ elseif ( "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" )
   message( STATUS "clang version ${CMAKE_CXX_COMPILER_VERSION}" )
 endif()
 
+#Use the old ABI until the dust has settled and all dependencies are built with the new ABI.
+if ( CMAKE_COMPILER_IS_GNUCXX AND NOT (GCC_COMPILER_VERSION VERSION_LESS "5.1.0"))
+  add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0)
+endif()
+
 # Global warning flags.
 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
@@ -46,6 +51,20 @@ if(WITH_ASAN)
   set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -fsanitize=address -lasan" )
 endif()
 
+option(WITH_UBSAN "Enable undefined behavior sanitizer" OFF)
+if(WITH_UBSAN)
+  message(STATUS "enabling undefined behavior sanitizers")
+  set( UBSAN_NO_RECOVER "-fno-sanitize-recover")
+  if ( CMAKE_COMPILER_IS_GNUCXX AND GCC_COMPILER_VERSION VERSION_LESS "5.1.0")
+    set( UBSAN_NO_RECOVER "")
+  endif()
+  set(SAN_FLAGS "-fno-omit-frame-pointer -fno-common -fsanitize=undefined ${UBSAN_NO_RECOVER}")
+  add_compile_options(-fno-omit-frame-pointer -fno-common -fsanitize=undefined ${UBSAN_NO_RECOVER})
+  set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${SAN_FLAGS}" )
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${SAN_FLAGS}" )
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${SAN_FLAGS}" )
+endif()
+
 # Set the options for gcc and g++
 set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GNUFLAGS}" )
 # -Wno-overloaded-virtual is down here because it's not applicable to the C_FLAGS

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -164,6 +164,6 @@ if not "%JOB_NAME%"=="%JOB_NAME:pull_requests=%" (
 
   :: Remove Mantid
   cd %BUILD_DIR%
-  python !SYSTEMTESTS_DIR!\scripts\mantidinstaller.py uninstall %BUILD_DIR%
+  start "Uninstall Mantid" /B /WAIT python !SYSTEMTESTS_DIR!\scripts\mantidinstaller.py uninstall %BUILD_DIR%
   if !RETCODE! NEQ 0 exit /B 1
 )

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.4/DEBIAN/control

@@ -3,7 +3,7 @@ Version: 1.2.4
 Section: main
 Priority: optional
 Architecture: all
-Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme, graphviz
+Depends: g++, git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme, graphviz
 Installed-Size: 0
 Maintainer: Mantid Project <mantid-help@mantidproject.org>
 Description: Installs all packages required for a Mantid developer

Code/Mantid/Framework/API/CMakeLists.txt

@@ -63,7 +63,6 @@ set ( SRC_FILES
 	src/IMDIterator.cpp
 	src/IMDWorkspace.cpp
 	src/IPawleyFunction.cpp
-	src/IPeak.cpp
 	src/IPeakFunction.cpp
 	src/IPeaksWorkspace.cpp
 	src/IPowderDiffPeakFunction.cpp
@@ -99,11 +98,6 @@ set ( SRC_FILES
 	src/ParameterReference.cpp
 	src/ParameterTie.cpp
 	src/PeakFunctionIntegrator.cpp
-	src/PeakTransform.cpp
-	src/PeakTransformHKL.cpp
-	src/PeakTransformQLab.cpp
-	src/PeakTransformQSample.cpp
-	src/PeakTransformSelector.cpp
 	src/Progress.cpp
 	src/Projection.cpp
 	src/PropertyManagerDataService.cpp
@@ -165,7 +159,6 @@ set ( INC_FILES
 	inc/MantidAPI/CompositeDomain.h
 	inc/MantidAPI/CompositeDomainMD.h
 	inc/MantidAPI/CompositeFunction.h
-	inc/MantidAPI/ConcretePeakTransformFactory.h
 	inc/MantidAPI/ConstraintFactory.h
 	inc/MantidAPI/CoordTransform.h
 	inc/MantidAPI/CostFunctionFactory.h
@@ -223,7 +216,6 @@ set ( INC_FILES
 	inc/MantidAPI/IMDWorkspace.h
 	inc/MantidAPI/IMaskWorkspace.h
 	inc/MantidAPI/IPawleyFunction.h
-	inc/MantidAPI/IPeak.h
 	inc/MantidAPI/IPeakFunction.h
 	inc/MantidAPI/IPeaksWorkspace.h
 	inc/MantidAPI/IPowderDiffPeakFunction.h
@@ -267,12 +259,6 @@ set ( INC_FILES
 	inc/MantidAPI/ParameterReference.h
 	inc/MantidAPI/ParameterTie.h
 	inc/MantidAPI/PeakFunctionIntegrator.h
-	inc/MantidAPI/PeakTransform.h
-	inc/MantidAPI/PeakTransformFactory.h
-	inc/MantidAPI/PeakTransformHKL.h
-	inc/MantidAPI/PeakTransformQLab.h
-	inc/MantidAPI/PeakTransformQSample.h
-	inc/MantidAPI/PeakTransformSelector.h
 	inc/MantidAPI/Progress.h
 	inc/MantidAPI/Projection.h
 	inc/MantidAPI/PropertyManagerDataService.h
@@ -370,10 +356,6 @@ set ( TEST_FILES
 	ParameterReferenceTest.h
 	ParameterTieTest.h
 	PeakFunctionIntegratorTest.h
-	PeakTransformHKLTest.h
-	PeakTransformQLabTest.h
-	PeakTransformQSampleTest.h
-	PeakTransformSelectorTest.h
 	ProjectionTest.h
 	PropertyManagerDataServiceTest.h
 	PropertyNexusTest.h

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

@@ -1,5 +1,5 @@
 #ifndef MANTID_API_IPEAKSPACE_H_
-#define MANTID_API_IPEAKSPACE_H_ 1
+#define MANTID_API_IPEAKSPACE_H_
 
 //----------------------------------------------------------------------
 // Includes
@@ -10,9 +10,11 @@
 #include <boost/optional.hpp>
 
 namespace Mantid {
-
-namespace API {
+namespace Geometry {
 class IPeak;
+}
+namespace API {
+
 
 //==========================================================================================
 /** Interface to the class Mantid::DataObjects::PeaksWorkspace
@@ -70,28 +72,28 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
   /** Add a peak to the list
    * @param ipeak :: Peak object to add (copy) into this.
    */
-  virtual void addPeak(const IPeak &ipeak) = 0;
+  virtual void addPeak(const Mantid::Geometry::IPeak &ipeak) = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Return a reference to the Peak
    * @param peakNum :: index of the peak to get.
    * @return a reference to a Peak object.
    */
-  virtual IPeak &getPeak(int peakNum) = 0;
+  virtual Mantid::Geometry::IPeak &getPeak(int peakNum) = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Return a reference to the Peak (const version)
    * @param peakNum :: index of the peak to get.
    * @return a reference to a Peak object.
    */
-  virtual const IPeak &getPeak(int peakNum) const = 0;
+  virtual const Mantid::Geometry::IPeak &getPeak(int peakNum) const = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Return a pointer to the Peak
    * @param peakNum :: index of the peak to get.
    * @return a pointer to a Peak object.
    */
-  IPeak *getPeakPtr(const int peakNum) { return &this->getPeak(peakNum); }
+  Mantid::Geometry::IPeak *getPeakPtr(const int peakNum) { return &this->getPeak(peakNum); }
 
   //---------------------------------------------------------------------------------------------
   /** Create an instance of a Peak
@@ -101,15 +103,15 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
    * detector. Calculated if not provided.
    * @return a pointer to a new Peak object.
    */
-  virtual IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
+  virtual Mantid::Geometry::IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
                             boost::optional<double> detectorDistance) const = 0;
 
   /**
    * Create an instance of a peak using a V3D
    * @param HKL V3D
    * @return a pointer to a new Peak object.
    */
-  virtual IPeak *createPeakHKL(Mantid::Kernel::V3D HKL) const = 0;
+  virtual Mantid::Geometry::IPeak *createPeakHKL(Mantid::Kernel::V3D HKL) const = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Determine if the workspace has been integrated using a peaks integration

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

@@ -90,8 +90,7 @@ class MANTID_API_DLL MatrixWorkspace : public IMDWorkspace,
   Geometry::IDetector_const_sptr getDetector(const size_t workspaceIndex) const;
   double detectorTwoTheta(Geometry::IDetector_const_sptr det) const;
   double detectorSignedTwoTheta(Geometry::IDetector_const_sptr det) const;
-  double gravitationalDrop(Geometry::IDetector_const_sptr det,
-                           const double waveLength) const;
+
   //@}
 
   virtual void populateInstrumentParameters();

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

@@ -145,6 +145,7 @@ void ExperimentInfo::setInstrument(const Instrument_const_sptr &instr) {
     m_parmap = instr->getParameterMap();
   } else {
     sptr_instrument = instr;
+    m_parmap = boost::make_shared<ParameterMap>();
   }
 }
 
@@ -290,7 +291,7 @@ void ExperimentInfo::populateInstrumentParameters() {
         }
         if (rtpValues.haveRadius) // Just overwrite x,y,z
         {
-          // convert spherical coordinates to cartesian coordinate values
+          // convert spherical coordinates to Cartesian coordinate values
           double x = rtpValues.radius * std::sin(rtpValues.theta) *
                      std::cos(rtpValues.phi);
           paramMap.addPositionCoordinate(paramInfo->m_component, "x", x);
@@ -1122,13 +1123,17 @@ void ExperimentInfo::populateWithParameter(
   ParameterValue paramValue(paramInfo,
                             runData); // Defines implicit conversion operator
 
+  const std::string * pDescription=NULL;
+  if(!paramInfo.m_description.empty())
+      pDescription = &paramInfo.m_description;
+
   // Some names are special. Values should be convertible to double
   if (name.compare("x") == 0 || name.compare("y") == 0 ||
       name.compare("z") == 0) {
     paramMap.addPositionCoordinate(paramInfo.m_component, name, paramValue);
   } else if (name.compare("rot") == 0 || name.compare("rotx") == 0 ||
              name.compare("roty") == 0 || name.compare("rotz") == 0) {
-    paramMap.addRotationParam(paramInfo.m_component, name, paramValue);
+    paramMap.addRotationParam(paramInfo.m_component, name, paramValue,pDescription);
   } else if (category.compare("fitting") == 0) {
     std::ostringstream str;
     str << paramInfo.m_value << " , " << paramInfo.m_fittingFunction << " , "
@@ -1137,16 +1142,15 @@ void ExperimentInfo::populateWithParameter(
         << " , " << paramInfo.m_tie << " , " << paramInfo.m_formula << " , "
         << paramInfo.m_formulaUnit << " , " << paramInfo.m_resultUnit << " , "
         << (*(paramInfo.m_interpolation));
-    paramMap.add("fitting", paramInfo.m_component, name, str.str());
+    paramMap.add("fitting", paramInfo.m_component, name, str.str(),pDescription);
   } else if (category.compare("string") == 0) {
-    paramMap.addString(paramInfo.m_component, name, paramInfo.m_value);
+    paramMap.addString(paramInfo.m_component, name, paramInfo.m_value,pDescription);
   } else if (category.compare("bool") == 0) {
-    paramMap.addBool(paramInfo.m_component, name, paramValue);
+    paramMap.addBool(paramInfo.m_component, name, paramValue,pDescription);
   } else if (category.compare("int") == 0) {
-    paramMap.addInt(paramInfo.m_component, name, paramValue);
-  } else // assume double
-  {
-    paramMap.addDouble(paramInfo.m_component, name, paramValue);
+    paramMap.addInt(paramInfo.m_component, name, paramValue,pDescription);
+  } else{ // assume double
+    paramMap.addDouble(paramInfo.m_component, name, paramValue,pDescription);
   }
 }
 

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

@@ -219,7 +219,9 @@ CompositeFunction_sptr FunctionFactoryImpl::createComposite(
     }
   }
 
-  cfun->applyTies();
+  if (cfun) {
+    cfun->applyTies();
+  }
   return cfun;
 }
 

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

@@ -813,33 +813,7 @@ MatrixWorkspace::detectorTwoTheta(Geometry::IDetector_const_sptr det) const {
   return det->getTwoTheta(samplePos, beamLine);
 }
 
-/**Calculates the distance a neutron coming from the sample will have deviated
-* from a
-*  straight tragetory before hitting a detector. If calling this function many
-* times
-*  for the same detector you can call this function once, with waveLength=1, and
-* use
-*  the fact drop is proportional to wave length squared .This function has no
-* knowledge
-*  of which axis is vertical for a given instrument
-*  @param det :: the detector that the neutron entered
-*  @param waveLength :: the neutrons wave length in meters
-*  @return the deviation in meters
-*/
-double MatrixWorkspace::gravitationalDrop(Geometry::IDetector_const_sptr det,
-                                          const double waveLength) const {
-  using namespace PhysicalConstants;
-  /// Pre-factor in gravity calculation: gm^2/2h^2
-  static const double gm2_OVER_2h2 =
-      g * NeutronMass * NeutronMass / (2.0 * h * h);
-
-  const V3D samplePos = getInstrument()->getSample()->getPos();
-  const double pathLength = det->getPos().distance(samplePos);
-  // Want L2 (sample-pixel distance) squared, times the prefactor g^2/h^2
-  const double L2 = gm2_OVER_2h2 * std::pow(pathLength, 2);
 
-  return waveLength * waveLength * L2;
-}
 
 //---------------------------------------------------------------------------------------
 /** Add parameters to the instrument parameter map that are defined in

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -32,6 +32,7 @@ set ( SRC_FILES
 	src/ChangeBinOffset.cpp
 	src/ChangeLogTime.cpp
 	src/ChangePulsetime.cpp
+	src/ChangeTimeZero.cpp
 	src/CheckWorkspacesMatch.cpp
 	src/ChopData.cpp
 	src/ClearInstrumentParameters.cpp
@@ -41,6 +42,7 @@ set ( SRC_FILES
 	src/ConjoinWorkspaces.cpp
 	src/ConvertAxesToRealSpace.cpp
 	src/ConvertAxisByFormula.cpp
+	src/ConvertDiffCal.cpp
 	src/ConvertEmptyToTof.cpp
 	src/ConvertFromDistribution.cpp
 	src/ConvertSpectrumAxis.cpp
@@ -250,6 +252,7 @@ set ( SRC_FILES
 	src/UnwrapMonitor.cpp
 	src/UnwrapSNS.cpp
 	src/UpdateScriptRepository.cpp
+	src/VesuvioL1ThetaResolution.cpp
 	src/WeightedMean.cpp
 	src/WeightedMeanOfWorkspace.cpp
 	src/WeightingStrategy.cpp
@@ -292,6 +295,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/ChangeBinOffset.h
 	inc/MantidAlgorithms/ChangeLogTime.h
 	inc/MantidAlgorithms/ChangePulsetime.h
+	inc/MantidAlgorithms/ChangeTimeZero.h
 	inc/MantidAlgorithms/CheckWorkspacesMatch.h
 	inc/MantidAlgorithms/ChopData.h
 	inc/MantidAlgorithms/ClearInstrumentParameters.h
@@ -301,6 +305,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/ConjoinWorkspaces.h
 	inc/MantidAlgorithms/ConvertAxesToRealSpace.h
 	inc/MantidAlgorithms/ConvertAxisByFormula.h
+	inc/MantidAlgorithms/ConvertDiffCal.h
 	inc/MantidAlgorithms/ConvertEmptyToTof.h
 	inc/MantidAlgorithms/ConvertFromDistribution.h
 	inc/MantidAlgorithms/ConvertSpectrumAxis.h
@@ -511,6 +516,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/UnwrapMonitor.h
 	inc/MantidAlgorithms/UnwrapSNS.h
 	inc/MantidAlgorithms/UpdateScriptRepository.h
+	inc/MantidAlgorithms/VesuvioL1ThetaResolution.h
 	inc/MantidAlgorithms/WeightedMean.h
 	inc/MantidAlgorithms/WeightedMeanOfWorkspace.h
 	inc/MantidAlgorithms/WeightingStrategy.h
@@ -563,6 +569,7 @@ set ( TEST_FILES
 	ChangeBinOffsetTest.h
 	ChangeLogTimeTest.h
 	ChangePulsetimeTest.h
+	ChangeTimeZeroTest.h
 	CheckWorkspacesMatchTest.h
 	ChopDataTest.h
 	ClearInstrumentParametersTest.h
@@ -572,6 +579,7 @@ set ( TEST_FILES
 	ConjoinWorkspacesTest.h
 	ConvertAxesToRealSpaceTest.h
 	ConvertAxisByFormulaTest.h
+	ConvertDiffCalTest.h
 	ConvertEmptyToTofTest.h
 	ConvertFromDistributionTest.h
 	ConvertSpectrumAxis2Test.h
@@ -757,6 +765,7 @@ set ( TEST_FILES
 	UnGroupWorkspaceTest.h
 	UnaryOperationTest.h
 	UnwrapSNSTest.h
+	VesuvioL1ThetaResolutionTest.h
 	WeightedMeanOfWorkspaceTest.h
 	WeightedMeanTest.h
 	WeightingStrategyTest.h