Merge branch 'master' into 11056_loadsqw_v2

Conflicts:
	Framework/DataObjects/inc/MantidDataObjects/MDBox.h
	Framework/DataObjects/inc/MantidDataObjects/MDBox.tcc
	Framework/DataObjects/inc/MantidDataObjects/MDGridBox.h
Refs #11056

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,33 @@
+Description of work.
+
+**To test:**
+
+<!-- Instructions for testing. -->
+
+Fixes #xxxx.
+
+[Release notes](/docs/source/release/)
+<!-- Replace with a link above to the updated file or state "Does not need to be in the release notes." -->
+
+---
+
+#### Reviewer ####
+
+Please comment on the following ([full description](http://www.mantidproject.org/Individual_Ticket_Testing)):
+
+##### Code Review #####
+
+- [ ] Is the code of an acceptable quality?
+- [ ] Does the code conform to the coding standards? Is it well structured with small focussed classes/methods/functions?
+- [ ] Are there unit/system tests in place? Are the unit tests small and test the a class in isolation?
+- [ ] If there are changes in the release notes then do they describe the changes appropriately?
+
+##### Functional Tests #####
+
+- [ ] Do changes function as described? Add comments below that describe the tests performed?
+- [ ] How do the changes handle unexpected situations, e.g. bad input?
+- [ ] Has the relevant documentation been added/updated?
+- [ ] Is user-facing documentation written in a user-friendly manner?
+- [ ] Has developer documentation been updated if required?
+
+- Does everything look good? Comment with the ship it emoji but don't merge. A member of `@mantidproject/gatekeepers` will take care of it.

.gitignore

@@ -77,8 +77,9 @@ local.properties
 *.log
 
 # Build results
-[Dd]ebug/
-[Rr]elease/
+build/
+/[Rr]elease/
+/[Dd]ebug/
 *_i.c
 *_p.c
 *.ilk

CMakeLists.txt

@@ -10,6 +10,13 @@ else()
   cmake_minimum_required ( VERSION 2.8.12 )
 endif()
 
+if(POLICY CMP0053)
+  #Simplify variable reference and escape sequence evaluation.
+  #Claims to dramatically improve CMake configure and generate time
+  #requires CMake 3.1 or later
+  cmake_policy(SET CMP0053 NEW)
+endif()
+
 # Define the project name.
 project ( Mantid )
 
@@ -244,7 +251,7 @@ if ( ENABLE_CPACK )
       message ( STATUS " CPACK_PACKAGE_FILE_NAME = ${CPACK_PACKAGE_FILE_NAME}" )
 
       # rhel requirements
-      set ( CPACK_RPM_PACKAGE_REQUIRES "boost >= 1.34.1,qt4 >= 4.2,nexus >= 4.3.1,nexus-python >= 4.3.1,gsl,glibc,qwtplot3d-qt4,muParser,numpy" )
+      set ( CPACK_RPM_PACKAGE_REQUIRES "qt4 >= 4.2,nexus >= 4.3.1,nexus-python >= 4.3.1,gsl,glibc,qwtplot3d-qt4,muParser,numpy" )
       # OCE
       set( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},OCE-draw,OCE-foundation,OCE-modeling,OCE-ocaf,OCE-visualization")
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},poco-crypto,poco-data,poco-mysql,poco-sqlite,poco-odbc,poco-util,poco-xml,poco-zip,poco-net,poco-netssl,poco-foundation,PyQt4,sip" )
@@ -255,11 +262,11 @@ if ( ENABLE_CPACK )
 
       if( "${UNIX_CODENAME}" MATCHES "Santiago" )
         # On RHEL6 we have to use an updated qscintilla to fix an auto complete bug
-        set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} qscintilla >= 2.4.6" )
+        set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} qscintilla >= 2.4.6, boost157" )
         # On RHEL6 we are using SCL packages for Qt
         set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},scl-utils,mantidlibs34,mantidlibs34-runtime,mantidlibs34-qt,mantidlibs34-qt-x11,mantidlibs34-qt-webkit,mantidlibs34-qwt5-qt4" )
       else()
-        set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} qscintilla,qwt5-qt4,python-matplotlib-qt4" )
+        set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES} qscintilla,qwt5-qt4,python-matplotlib-qt4,boost >= 1.53.0" )
       endif()
 
       # Add software collections for RHEL

Framework/API/CMakeLists.txt

@@ -12,7 +12,6 @@ set ( SRC_FILES
 	src/Axis.cpp
 	src/BinEdgeAxis.cpp
 	src/BoxController.cpp
-	src/CatalogFactory.cpp
 	src/CatalogManager.cpp
 	src/CatalogSession.cpp
 	src/ChopperModel.cpp
@@ -44,8 +43,11 @@ set ( SRC_FILES
 	src/FunctionParameterDecorator.cpp
 	src/FunctionProperty.cpp
 	src/FunctionValues.cpp
+	src/GeometryInfoFactory.cpp
+	src/GeometryInfo.cpp
 	src/GridDomain.cpp
 	src/GridDomain1D.cpp
+	src/GroupingLoader.cpp
 	src/HistogramValidator.cpp
 	src/HistoryItem.cpp
 	src/HistoryView.cpp
@@ -69,7 +71,6 @@ set ( SRC_FILES
 	src/IPeaksWorkspace.cpp
 	src/IPowderDiffPeakFunction.cpp
 	src/ISpectrum.cpp
-	src/ISplittersWorkspace.cpp
 	src/ITableWorkspace.cpp
 	src/IkedaCarpenterModerator.cpp
 	src/ImmutableCompositeFunction.cpp
@@ -196,8 +197,11 @@ set ( INC_FILES
 	inc/MantidAPI/FunctionParameterDecorator.h
 	inc/MantidAPI/FunctionProperty.h
 	inc/MantidAPI/FunctionValues.h
+	inc/MantidAPI/GeometryInfoFactory.h
+	inc/MantidAPI/GeometryInfo.h
 	inc/MantidAPI/GridDomain.h
 	inc/MantidAPI/GridDomain1D.h
+	inc/MantidAPI/GroupingLoader.h
 	inc/MantidAPI/HistogramValidator.h
 	inc/MantidAPI/HistoryItem.h
 	inc/MantidAPI/HistoryView.h
@@ -356,6 +360,9 @@ set ( TEST_FILES
 	FunctionPropertyTest.h
 	FunctionTest.h
 	FunctionValuesTest.h
+	GeometryInfoFactoryTest.h
+	GeometryInfoTest.h
+	GroupingLoaderTest.h
 	HistogramValidatorTest.h
 	HistoryItemTest.h
 	HistoryViewTest.h

Framework/API/inc/MantidAPI/Algorithm.h

@@ -1,9 +1,8 @@
 #ifndef MANTID_API_ALGORITHM_H_
 #define MANTID_API_ALGORITHM_H_
 
-//----------------------------------------------------------------------
-// Includes
-//----------------------------------------------------------------------
+#include <atomic>
+
 #include "MantidAPI/DllConfig.h"
 #include "MantidAPI/IAlgorithm.h"
 #include "MantidKernel/PropertyManagerOwner.h"
@@ -12,7 +11,6 @@
 #include "MantidAPI/AlgorithmFactory.h" //for the factory macro
 #include "MantidAPI/Progress.h"
 #include "MantidAPI/WorkspaceProperty.h"
-#include "MantidAPI/WorkspaceFactory.h"
 #include "MantidAPI/WorkspaceOpOverloads.h"
 #include "MantidKernel/MultiThreaded.h"
 #include "MantidKernel/EmptyValues.h"
@@ -107,7 +105,7 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
   public:
     StartedNotification(const Algorithm *const alg)
         : AlgorithmNotification(alg) {} ///< Constructor
-    virtual std::string name() const {
+    std::string name() const override {
       return "StartedNotification";
     } ///< class name
   };
@@ -117,7 +115,7 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
   public:
     FinishedNotification(const Algorithm *const alg, bool res)
         : AlgorithmNotification(alg), success(res) {} ///< Constructor
-    virtual std::string name() const {
+    std::string name() const override {
       return "FinishedNotification";
     }             ///< class name
     bool success; ///< true if the finished algorithm was successful or false if
@@ -134,7 +132,7 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
                          int progressPrecision)
         : AlgorithmNotification(alg), progress(p), message(msg),
           estimatedTime(estimatedTime), progressPrecision(progressPrecision) {}
-    virtual std::string name() const {
+    std::string name() const override {
       return "ProgressNotification";
     }                      ///< class name
     double progress;       ///< Current progress. Value must be between 0 and 1.
@@ -151,7 +149,7 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
     /// Constructor
     ErrorNotification(const Algorithm *const alg, const std::string &str)
         : AlgorithmNotification(alg), what(str) {}
-    virtual std::string name() const {
+    std::string name() const override {
       return "ErrorNotification";
     }                 ///< class name
     std::string what; ///< message string
@@ -166,117 +164,113 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
   /// and throws CancelException if needed.
   class CancelException : public std::exception {
   public:
-    CancelException() : outMessage("Algorithm terminated") {}
-    CancelException(const CancelException &A)
-        : outMessage(A.outMessage) {} ///< Copy constructor
-    /// Assignment operator
-    CancelException &operator=(const CancelException &A);
-    /// Destructor
-    ~CancelException() throw() {}
-
     /// Returns the message string.
-    const char *what() const throw() { return outMessage.c_str(); }
+    const char *what() const throw() override { return outMessage.c_str(); }
 
   private:
     /// The message returned by what()
-    std::string outMessage;
+    std::string outMessage{"Algorithm terminated"};
   };
 
   //============================================================================
   Algorithm();
-  virtual ~Algorithm();
+  Algorithm(const Algorithm &) = delete;
+  Algorithm &operator=(const Algorithm &) = delete;
+  ~Algorithm() override;
 
   /** @name Algorithm Information */
   /// function to return a name of the algorithm, must be overridden in all
   /// algorithms
-  virtual const std::string name() const = 0;
+  const std::string name() const override = 0;
   /// function to return a version of the algorithm, must be overridden in all
   /// algorithms
-  virtual int version() const = 0;
+  int version() const override = 0;
   /// function returns a summary message that will be displayed in the default
   /// GUI, and in the help.
-  virtual const std::string summary() const = 0;
+  const std::string summary() const override = 0;
   /// function to return a category of the algorithm. A default implementation
   /// is provided
-  virtual const std::string category() const { return "Misc"; }
+  const std::string category() const override { return "Misc"; }
   /// Function to return all of the categories that contain this algorithm
-  virtual const std::vector<std::string> categories() const;
+  const std::vector<std::string> categories() const override;
   /// Function to return the separator token for the category string. A default
   /// implementation ';' is provided
-  virtual const std::string categorySeparator() const { return ";"; }
+  const std::string categorySeparator() const override { return ";"; }
   /// function to return any aliases to the algorithm;  A default implementation
   /// is provided
-  virtual const std::string alias() const { return ""; }
+  const std::string alias() const override { return ""; }
 
-  const std::string workspaceMethodName() const;
-  const std::vector<std::string> workspaceMethodOn() const;
-  const std::string workspaceMethodInputProperty() const;
+  const std::string workspaceMethodName() const override;
+  const std::vector<std::string> workspaceMethodOn() const override;
+  const std::string workspaceMethodInputProperty() const override;
 
   /// Algorithm ID. Unmanaged algorithms return 0 (or NULL?) values. Managed
   /// ones have non-zero.
-  AlgorithmID getAlgorithmID() const { return m_algorithmID; }
+  AlgorithmID getAlgorithmID() const override { return m_algorithmID; }
 
   /** @name IAlgorithm methods */
-  void initialize();
-  bool execute();
-  void executeAsChildAlg();
-  virtual std::map<std::string, std::string> validateInputs();
-  virtual bool isInitialized() const;
-  virtual bool isExecuted() const;
-  bool isRunning() const;
+  void initialize() override;
+  bool execute() override;
+  void executeAsChildAlg() override;
+  std::map<std::string, std::string> validateInputs() override;
+  bool isInitialized() const override;
+  bool isExecuted() const override;
+  bool isRunning() const override;
 
   using Kernel::PropertyManagerOwner::getProperty;
 
-  bool isChild() const;
-  void setChild(const bool isChild);
-  void enableHistoryRecordingForChild(const bool on);
+  bool isChild() const override;
+  void setChild(const bool isChild) override;
+  void enableHistoryRecordingForChild(const bool on) override;
   bool isRecordingHistoryForChild() { return m_recordHistoryForChild; }
-  void setAlwaysStoreInADS(const bool doStore);
-  void setRethrows(const bool rethrow);
+  void setAlwaysStoreInADS(const bool doStore) override;
+  void setRethrows(const bool rethrow) override;
 
   /** @name Asynchronous Execution */
-  Poco::ActiveResult<bool> executeAsync();
+  Poco::ActiveResult<bool> executeAsync() override;
 
   /// Add an observer for a notification
-  void addObserver(const Poco::AbstractObserver &observer) const;
+  void addObserver(const Poco::AbstractObserver &observer) const override;
 
   /// Remove an observer
-  void removeObserver(const Poco::AbstractObserver &observer) const;
+  void removeObserver(const Poco::AbstractObserver &observer) const override;
 
   /// Raises the cancel flag.
-  virtual void cancel();
+  void cancel() override;
   /// Returns the cancellation state
   bool getCancel() const { return m_cancel; }
 
   /// Returns a reference to the logger.
   Kernel::Logger &getLogger() const { return g_log; }
   /// Logging can be disabled by passing a value of false
-  void setLogging(const bool value) { g_log.setEnabled(value); }
+  void setLogging(const bool value) override { g_log.setEnabled(value); }
   /// returns the status of logging, True = enabled
-  bool isLogging() const { return g_log.getEnabled(); }
+  bool isLogging() const override { return g_log.getEnabled(); }
 
   /// sets the logging priority offset
-  void setLoggingOffset(const int value) { g_log.setLevelOffset(value); }
+  void setLoggingOffset(const int value) override {
+    g_log.setLevelOffset(value);
+  }
   /// returns the logging priority offset
-  int getLoggingOffset() const { return g_log.getLevelOffset(); }
+  int getLoggingOffset() const override { return g_log.getLevelOffset(); }
   /// disable Logging of start and end messages
-  void setAlgStartupLogging(const bool enabled);
+  void setAlgStartupLogging(const bool enabled) override;
   /// get the state of Logging of start and end messages
-  bool getAlgStartupLogging() const;
+  bool getAlgStartupLogging() const override;
 
   /// setting the child start progress
-  void setChildStartProgress(const double startProgress) const {
+  void setChildStartProgress(const double startProgress) const override {
     m_startChildProgress = startProgress;
   }
   /// setting the child end progress
-  void setChildEndProgress(const double endProgress) const {
+  void setChildEndProgress(const double endProgress) const override {
     m_endChildProgress = endProgress;
   }
 
   /** @name Serialization functions */
   //@{
   /// Serialize an object to a string
-  virtual std::string toString() const;
+  std::string toString() const override;
   /// Serialize an object to a json object
   ::Json::Value toJson() const;
   /// De-serialize an object from a string
@@ -356,9 +350,9 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
   virtual void fillHistory();
 
   /// Set to true to stop execution
-  bool m_cancel;
+  std::atomic<bool> m_cancel;
   /// Set if an exception is thrown, and not caught, within a parallel region
-  bool m_parallelException;
+  std::atomic<bool> m_parallelException;
 
   friend class WorkspaceHistory; // Allow workspace history loading to adjust
                                  // g_execCount
@@ -388,11 +382,6 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
   size_t m_groupSize;
 
 private:
-  /// Private Copy constructor: NO COPY ALLOWED
-  Algorithm(const Algorithm &);
-  /// Private assignment operator: NO ASSIGNMENT ALLOWED
-  Algorithm &operator=(const Algorithm &);
-
   void lockWorkspaces();
   void unlockWorkspaces();
 
@@ -427,7 +416,7 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
   /// recorded. Applicable to child algs only
   bool m_alwaysStoreInADS; ///< Always store in the ADS, even for child algos
   bool m_runningAsync;     ///< Algorithm is running asynchronously
-  bool m_running;          ///< Algorithm is running
+  std::atomic<bool> m_running; ///< Algorithm is running
   bool m_rethrow; ///< Algorithm should rethrow exceptions while executing
   bool m_isAlgStartupLoggingEnabled; /// Whether to log alg startup and
                                      /// closedown messages from the base class
@@ -459,8 +448,6 @@ class MANTID_API_DLL Algorithm : public IAlgorithm,
   int m_singleGroup;
   /// All the groups have similar names (group_1, group_2 etc.)
   bool m_groupsHaveSimilarNames;
-  /// A non-recursive mutex for thread-safety
-  mutable Kernel::Mutex m_mutex;
 };
 
 /// Typedef for a shared pointer to an Algorithm