Merge branch 'master' into ILL_loaders_cleanup

.style.yapf

 [style]
 based_on_style = pep8
-column_limit = 100
+column_limit = 140
 allow_split_before_dict_value = false
 each_dict_entry_on_separate_line = true

CMakeLists.txt

@@ -30,8 +30,11 @@ set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/buildconfig/CMake")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
 
-option(ENABLE_MANTIDPLOT "Enable Qt4-based gui & components" ON)
+option(ENABLE_MANTIDPLOT "Enable Qt4-based gui & components" OFF)
 option(ENABLE_WORKBENCH "Enable Qt5-based gui & components" ON)
+if(ENABLE_MANTIDPLOT)
+  message( FATAL_ERROR "MantidPlot has been removed from the source code")
+endif()
 
 set(CPACK_INSTALL_CMAKE_PROJECTS "${CMAKE_BINARY_DIR}" "Mantid" "ALL" "/")
 
@@ -56,6 +59,13 @@ set_property(CACHE CPACK_PACKAGE_SUFFIX
                       unstable
                       "")
 # empty string and release are treated as the same thing
+if(CPACK_PACKAGE_SUFFIX)
+  # Camelcase version of suffix for Windows/Mac
+  string(TOUPPER ${CPACK_PACKAGE_SUFFIX} CPACK_PACKAGE_SUFFIX_CAMELCASE)
+  string(SUBSTRING ${CPACK_PACKAGE_SUFFIX_CAMELCASE} 0 1 CPACK_PACKAGE_SUFFIX_CAMELCASE)
+  string(SUBSTRING ${CPACK_PACKAGE_SUFFIX} 1 -1 _tmp_suffix_remainder)
+  string(CONCAT CPACK_PACKAGE_SUFFIX_CAMELCASE ${CPACK_PACKAGE_SUFFIX_CAMELCASE} ${_tmp_suffix_remainder})
+endif()
 
 # Set package name here
 set(CPACK_PACKAGE_NAME "mantid${CPACK_PACKAGE_SUFFIX}")
@@ -69,23 +79,8 @@ include(Eigen)
 include(Span)
 
 # Set ParaView information since later items depend on it
-
 # VATES flag. Requires ParaView
-option(MAKE_VATES "Switch for compiling the Vates project")
-if(ENABLE_MANTIDPLOT AND MAKE_VATES)
-  find_package(ParaView)
-  if(ParaView_FOUND)
-    add_definitions(-DMAKE_VATES)
-    # Poco::File throws an exception when a backslash is used.
-    string(REPLACE "\\"
-                   "/"
-                   ParaView_DIR
-                   ${ParaView_DIR})
-  endif()
-endif()
-if(ENABLE_MANTIDPLOT)
-  include(ParaViewSetup)
-endif()
+option(MAKE_VATES "Switch for compiling the Vates project" Off)
 
 if( MSVC )
   include ( MSVCSetup )
@@ -115,42 +110,13 @@ if(COVERALLS)
   coveralls_turn_on_coverage()
 endif()
 
-# Qt/Qwt/PyQt/sip
-if(ENABLE_MANTIDPLOT)
-  set(QT_USE_IMPORTED_TARGETS ON)
-  find_package(Qt4
-               COMPONENTS QtCore
-                          QtDesigner
-                          QtGui
-                          QtOpenGL
-                          QtScript
-                          QtSvg
-                          QtXml
-               REQUIRED)
-  find_package(QScintillaQt4 REQUIRED)
-  find_package(Qwt5 REQUIRED)
-  if(QWT5_VERSION VERSION_LESS 5.0
-     OR QWT5_VERSION VERSION_EQUAL 6.0
-     OR QWT5_VERSION VERSION_GREATER 6.0)
-    message(FATAL_ERROR "Qwt version 5 is required, found: ${QWT5_VERSION}")
-  endif()
-
-  if(UNIX_DIST MATCHES "RedHatEnterprise" AND UNIX_RELEASE MATCHES "7\..*")
-    set(USE_PRIVATE_SIPPYQT4 ON)
-    include(ExternalSipPyQt4)
-  else()
-    find_package(PyQt4 REQUIRED)
-    find_package(SIP REQUIRED)
-  endif()
-  separate_arguments(PYQT4_SIP_FLAGS)
-endif()
-
 if(ENABLE_WORKBENCH)
   find_package(Qt5
                COMPONENTS Core
                           Gui
                           Widgets
                           OpenGL
+                          Test
                REQUIRED)
   if(Qt5_FOUND)
     message(STATUS "Found Qt ${Qt5_VERSION}: ${Qt5_DIR}")
@@ -187,33 +153,6 @@ include_directories(Framework/NexusGeometry/inc)
 
 set(CORE_MANTIDLIBS Kernel HistogramData Indexing Beamline Geometry API Types)
 
-if(ENABLE_MANTIDPLOT AND MAKE_VATES)
-
-  if(NOT APPLE)
-    list(APPEND CPACK_INSTALL_CMAKE_PROJECTS
-                "${ParaView_DIR}"
-                "ParaView Runtime Libs"
-                "Runtime"
-                "${INBUNDLE}/")
-    list(APPEND CPACK_INSTALL_CMAKE_PROJECTS
-                "${ParaView_DIR}"
-                "VTK Runtime Libs"
-                "RuntimeLibraries"
-                "${INBUNDLE}/")
-    list(APPEND CPACK_INSTALL_CMAKE_PROJECTS
-                "${ParaView_DIR}"
-                "HDF5 Core Library"
-                "libraries"
-                "${INBUNDLE}/")
-    list(APPEND CPACK_INSTALL_CMAKE_PROJECTS
-                "${ParaView_DIR}"
-                "HDF5 HL Library"
-                "hllibraries"
-                "${INBUNDLE}/")
-  endif()
-
-endif(ENABLE_MANTIDPLOT AND MAKE_VATES)
-
 if(UNIX)
   # Experimental feature. Unix only at this point.
   option(UNITY_BUILD
@@ -227,7 +166,7 @@ endif()
 add_custom_target(AllTests)
 add_dependencies(AllTests FrameworkTests)
 
-if(ENABLE_MANTIDPLOT OR ENABLE_WORKBENCH)
+if(ENABLE_WORKBENCH)
   add_custom_target(GUITests)
   add_dependencies(check GUITests)
   # Collect all tests together
@@ -235,10 +174,6 @@ if(ENABLE_MANTIDPLOT OR ENABLE_WORKBENCH)
   add_subdirectory(qt)
 endif()
 
-if(ENABLE_MANTIDPLOT)
-  add_subdirectory(MantidPlot)
-endif()
-
 add_subdirectory(scripts)
 
 # Docs requirements
@@ -287,11 +222,6 @@ endif()
 
 # Installation settings
 
-if(ENABLE_MANTIDPLOT)
-  # N.B. INBUNDLE variable is empty except on Mac (set in DarwinSetup.cmake)
-  install(DIRECTORY installers/colormaps/ DESTINATION ${INBUNDLE}colormaps)
-endif()
-
 # Install the files (.desktop and icon) to create a menu items
 if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
   function(uppercase_first_letter output_var input)
@@ -331,17 +261,6 @@ if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
   if(CPACK_PACKAGE_SUFFIX)
     uppercase_first_letter(_app_name_suffix ${CPACK_PACKAGE_SUFFIX})
   endif()
-  if(ENABLE_MANTIDPLOT)
-    set(_icon_filename ${IMAGES_DIR}/mantidplot)
-    if(_icon_suffix)
-      set(_icon_filename ${_icon_filename}${_icon_suffix})
-    endif()
-    install_desktop_files(mantidplot${CPACK_PACKAGE_SUFFIX}.desktop
-                          "Mantid Plot ${_app_name_suffix}"
-                          ${CMAKE_INSTALL_PREFIX}/bin/MantidPlot
-                          ${_icon_filename}.png
-                          mantidplot${CPACK_PACKAGE_SUFFIX}.png )
-  endif()
 
   if(ENABLE_WORKBENCH)
     set(_icon_filename ${IMAGES_DIR}/mantid_workbench)
@@ -394,10 +313,6 @@ if(ENABLE_CPACK)
       "OCE-draw,OCE-foundation,OCE-modeling,OCE-ocaf,OCE-visualization,"
       "poco-crypto,poco-data,poco-mysql,poco-sqlite,poco-odbc,poco-util,poco-xml,poco-zip,poco-net,poco-netssl,poco-foundation,"
       "hdf,hdf5,jsoncpp >= 0.7.0")
-    if(ENABLE_MANTIDPLOT)
-      set(CPACK_RPM_PACKAGE_REQUIRES
-          "${CPACK_RPM_PACKAGE_REQUIRES},qt4 >= 4.2,qscintilla,qwt5-qt4,qwtplot3d-qt4")
-    endif()
     if(ENABLE_WORKBENCH)
       set(CPACK_RPM_PACKAGE_REQUIRES
           "${CPACK_RPM_PACKAGE_REQUIRES},qt5-qtbase,qscintilla-qt5")
@@ -411,11 +326,6 @@ if(ENABLE_CPACK)
       "python36-six,python36-PyYAML,python36-requests,python36-toml,"
       "python36-ipython,python36-ipython-notebook"
     )
-    if(ENABLE_MANTIDPLOT)
-      set(CPACK_RPM_PACKAGE_REQUIRES
-          "${CPACK_RPM_PACKAGE_REQUIRES},python36-QtPy,"
-          "python36-matplotlib-qt4,python36-ipython-gui")
-    endif()
     if(ENABLE_WORKBENCH)
       set(CPACK_RPM_PACKAGE_REQUIRES
           "${CPACK_RPM_PACKAGE_REQUIRES},python36-qt5,python36-QtPy,"
@@ -447,19 +357,6 @@ if(ENABLE_CPACK)
       "librdkafka1,librdkafka++1,"
       "libpocofoundation${POCO_SOLIB_VERSION},libpocoutil${POCO_SOLIB_VERSION},libpoconet${POCO_SOLIB_VERSION},libpoconetssl${POCO_SOLIB_VERSION},libpococrypto${POCO_SOLIB_VERSION},libpocoxml${POCO_SOLIB_VERSION}"
       )
-    if(ENABLE_MANTIDPLOT)
-      set(CPACK_DEBIAN_PACKAGE_DEPENDS
-          "${CPACK_DEBIAN_PACKAGE_DEPENDS},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-qt4-0v5,"
-          "libqtwebkit4")
-    endif()
 
     if("${UNIX_CODENAME}" STREQUAL "bionic")
       set(CPACK_DEBIAN_PACKAGE_DEPENDS
@@ -472,7 +369,7 @@ if(ENABLE_CPACK)
         set(CPACK_DEBIAN_PACKAGE_DEPENDS
             "${CPACK_DEBIAN_PACKAGE_DEPENDS},libqscintilla2-qt5-13")
       endif()
-    else()
+    elseif ( "${UNIX_DIST}" MATCHES "Ubuntu" )
       message(WARNING "Unsupported Debian-like OS: ${UNIX_CODENAME}. Packaging is unlikely to work correctly.")
     endif()
     # python requirements
@@ -490,10 +387,6 @@ if(ENABLE_CPACK)
         "python3-yaml,"
         "ipython3-qtconsole") # transitional package for bionic
 
-    if(ENABLE_MANTIDPLOT)
-      set(CPACK_DEBIAN_PACKAGE_DEPENDS
-          "${CPACK_DEBIAN_PACKAGE_DEPENDS},python3-pyqt4")
-    endif()
     if(ENABLE_WORKBENCH)
       set(CPACK_DEBIAN_PACKAGE_DEPENDS
           "${CPACK_DEBIAN_PACKAGE_DEPENDS},python3-pyqt5,python3-psutil")

Framework/API/inc/MantidAPI/CompositeFunction.h

@@ -107,8 +107,12 @@ public:
   [[nodiscard]] bool isExplicitlySet(size_t i) const override;
   /// Get the fitting error for a parameter
   [[nodiscard]] double getError(size_t i) const override;
+  /// Get the fitting error for a parameter by name
+  [[nodiscard]] double getError(const std::string &name) const override;
   /// Set the fitting error for a parameter
   void setError(size_t i, double err) override;
+  /// Set the fitting error for a parameter by name
+  void setError(const std::string &name, double err) override;
   /// Value of i-th active parameter. Override this method to make fitted
   /// parameters different from the declared
   [[nodiscard]] double activeParameter(size_t i) const override;

Framework/API/inc/MantidAPI/FunctionGenerator.h

@@ -65,8 +65,12 @@ public:
   bool isExplicitlySet(size_t i) const override;
   /// Get the fitting error for a parameter
   double getError(size_t i) const override;
+  /// Get the fitting error for a parameter by name
+  double getError(const std::string &name) const override;
   /// Set the fitting error for a parameter
   void setError(size_t i, double err) override;
+  /// Set the fitting error for a parameter by name
+  void setError(const std::string &name, double err) override;
 
   /// Return parameter index from a parameter reference.
   size_t getParameterIndex(const ParameterReference &ref) const override;

Framework/API/inc/MantidAPI/FunctionParameterDecorator.h

@@ -75,8 +75,12 @@ public:
   bool isExplicitlySet(size_t i) const override;
   /// Get the fitting error for a parameter of decorated function.
   double getError(size_t i) const override;
+  /// Get the fitting error for a parameter of decorated function by name.
+  double getError(const std::string &name) const override;
   /// Set the fitting error for a parameter of decorated function.
   void setError(size_t i, double err) override;
+  /// Set the fitting error for a parameter of decorated function by name.
+  void setError(const std::string &name, double err) override;
 
   /// Return parameter index of decorated function from a parameter reference.
   /// Usefull for constraints and ties in composite functions.

Framework/API/inc/MantidAPI/IFunction.h

@@ -44,6 +44,19 @@ class Workspace;
 class MatrixWorkspace;
 class FunctionHandler;
 
+/**
+ * Attribute visitor structure supporting lambda expressions
+ * Example usage: AttributeLambdaVisitor{[](const int val) {...}, [] (const
+ * double val) {}} would create a visitor capable of "visiting" an integer and
+ * double attribute*
+ * It functions by inheriting the () operator defined in each lambda
+ */
+template <class... Ts> struct AttributeLambdaVisitor : Ts... {
+  using Ts::operator()...;
+};
+template <class... Ts>
+AttributeLambdaVisitor(Ts...)->AttributeLambdaVisitor<Ts...>;
+
 /** This is an interface to a fitting function - a semi-abstarct class.
     Functions derived from IFunction can be used with the Fit algorithm.
     IFunction defines the structure of a fitting funtion.
@@ -250,6 +263,10 @@ public:
     template <typename T> T apply(ConstAttributeVisitor<T> &v) const {
       return boost::apply_visitor(v, m_data);
     }
+    /// Apply a lambda visitor
+    template <typename... Ts> void apply(AttributeLambdaVisitor<Ts...> &v) {
+      boost::apply_visitor(v, m_data);
+    }
 
     /// Returns type of the attribute
     std::string type() const;
@@ -401,8 +418,12 @@ public:
   virtual bool isExplicitlySet(size_t i) const = 0;
   /// Get the fitting error for a parameter
   virtual double getError(size_t i) const = 0;
+  /// Get the fitting error for a parameter by name
+  virtual double getError(const std::string &name) const = 0;
   /// Set the fitting error for a parameter
   virtual void setError(size_t i, double err) = 0;
+  /// Set the fitting error for a parameter by name
+  virtual void setError(const std::string &name, double err) = 0;
 
   /// Check if a parameter i is fixed
   [[nodiscard]] bool isFixed(size_t i) const;
@@ -539,10 +560,10 @@ public:
   std::shared_ptr<const Kernel::Matrix<double>> getCovarianceMatrix() const {
     return m_covar;
   }
-  /// Set the chi^2
-  void setChiSquared(double chi2) { m_chiSquared = chi2; }
-  /// Get the chi^2
-  [[nodiscard]] double getChiSquared() const { return m_chiSquared; }
+  /// Set the reduced chi^2
+  void setReducedChiSquared(double chi2) { m_chiSquared = chi2; }
+  /// Get the reduced chi^2
+  [[nodiscard]] double getReducedChiSquared() const { return m_chiSquared; }
 
   /// Set the parallel hint
   void setParallel(bool on) {

Framework/API/inc/MantidAPI/IPeakFunction.h

@@ -61,6 +61,15 @@ public:
   /// Get name of parameter that is associated to centre.
   std::string getCentreParameterName() const;
 
+  /// Get the name of the parameter that is changed when the
+  /// fwhm is changed. By default this returns an empty string (unless
+  /// overridden in the individual functions) as some functions change two
+  /// params when the fwhm is set and others don't have a width (delta
+  /// func).This is intended for the BackToBackExponential-based peaks where
+  /// the width parameter (S) can be set in the intsurment parameter file and
+  /// this needs to be checked when a peak is added.
+  virtual std::string getWidthParameterName() const { return ""; }
+
   /// Fix a parameter or set up a tie such that value returned
   /// by intensity() is constant during fitting.
   /// @param isDefault :: If true fix intensity by default:

Framework/API/inc/MantidAPI/IndexProperty.h

@@ -36,7 +36,8 @@ public:
                     Kernel::IValidator_sptr(new Kernel::NullValidator));
 
   IndexProperty(const IndexProperty &) = default;
-  IndexProperty &operator=(const IndexProperty &) = default;
+  // Copy assignment is deleted since there are reference type members.
+  IndexProperty &operator=(const IndexProperty &) = delete;
 
   IndexProperty *clone() const override;
 

Framework/API/inc/MantidAPI/MatrixWorkspace.h

@@ -121,6 +121,9 @@ public:
 
   bool hasGroupedDetectors() const;
 
+  /// Returns true if the workspace is ragged (has differently sized spectra).
+  virtual bool isRaggedWorkspace() const = 0;
+
   /// Get the footprint in memory in bytes.
   size_t getMemorySize() const override;
   virtual size_t getMemorySizeForXAxes() const;
@@ -132,6 +135,10 @@ public:
   /// This throws an exception if the lengths are not identical across the
   /// spectra.
   virtual std::size_t blocksize() const = 0;
+  /// Returns the number of bins for a given histogram index.
+  virtual std::size_t getNumberBins(const std::size_t &index) const = 0;
+  /// Returns the maximum number of bins in a workspace (works on ragged data).
+  virtual std::size_t getMaxNumberBins() const = 0;
   /// Returns the number of histograms in the workspace
   virtual std::size_t getNumberHistograms() const = 0;
 
@@ -144,7 +151,7 @@ public:
   Types::Core::DateAndTime getLastPulseTime() const;
 
   /// Returns the y index which corresponds to the X Value provided
-  std::size_t yIndexOfX(const double xValue, const std::size_t = 0,
+  std::size_t yIndexOfX(const double xValue, const std::size_t &index = 0,
                         const double tolerance = 0.0) const;
 
   //----------------------------------------------------------------------
@@ -579,11 +586,10 @@ protected:
 
 private:
   std::size_t binIndexOfValue(Mantid::HistogramData::HistogramX const &xValues,
-                              double const &xValue, bool const &ascendingOrder,
-                              double const &tolerance) const;
-  std::size_t xIndexOfValue(Mantid::HistogramData::HistogramX const &xValues,
-                            double const &xValue,
-                            double const &tolerance) const;
+                              const double xValue,
+                              const bool ascendingOrder) const;
+  std::size_t xIndexOfValue(const Mantid::HistogramData::HistogramX &xValues,
+                            const double xValue, const double tolerance) const;
 
   MatrixWorkspace *doClone() const override = 0;
   MatrixWorkspace *doCloneEmpty() const override = 0;

Framework/API/inc/MantidAPI/ParamFunction.h

@@ -64,8 +64,12 @@ public:
   bool isExplicitlySet(size_t i) const override;
   /// Get the fitting error for a parameter
   double getError(size_t i) const override;
+  /// Get the fitting error for a parameter by name
+  double getError(const std::string &name) const override;
   /// Set the fitting error for a parameter
   void setError(size_t i, double err) override;
+  /// Set the fitting error for a parameter by name
+  void setError(const std::string &name, double err) override;
 
   /// Return parameter index from a parameter reference. Usefull for constraints
   /// and ties in composite functions

Framework/API/inc/MantidAPI/PrecompiledHeader.h

@@ -7,33 +7,15 @@
 #pragma once
 
 // Mantid
+#include "MantidAPI/DllConfig.h"
 #include "MantidGeometry/IComponent.h"
 #include "MantidGeometry/IDetector.h"
 #include "MantidGeometry/Instrument.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/DateAndTime.h"
-#include "MantidKernel/DynamicFactory.h"
-#include "MantidKernel/Exception.h"
-#include "MantidKernel/IPropertyManager.h"
-#include "MantidKernel/Logger.h"
-#include "MantidKernel/Quat.h"
-#include "MantidKernel/System.h"
-#include "MantidKernel/V3D.h"
 
 // STL
-#include <cfloat>
-#include <cmath>
-#include <cstddef>
-#include <map>
-#include <set>
-#include <string>
-#include <utility>
-#include <vector>
 
 // Boost