Merge branch 'feature/8116_fltabs_code_tidy' of

github.com:mantidproject/mantid into feature/8116_fltabs_code_tidy

Conflicts:
	Code/Mantid/scripts/Inelastic/IndirectAbsCor.py

Refs #8116

.gitattributes

@@ -8,6 +8,6 @@
 *.xml              hooks.MaxObjectKiB130902=2048
 
 # Allowing gSoap generated files to be committed.
-/Code/Mantid/Framework/ICat/inc/MantidICat/ICat3/GSoapGenerated/ICat3H.h              hooks.MaxObjectKiB130819=2048 
-/Code/Mantid/Framework/ICat/src/ICat3/GSoapGenerated/ICat3C.cpp                       hooks.MaxObjectKiB130819=5120
-/Code/Mantid/Framework/ICat/src/ICat4/GSoapGenerated/ICat4C.cpp                       hooks.MaxObjectKiB130819=2048
+/Code/Mantid/Framework/ICat/inc/MantidICat/ICat3/GSoapGenerated/ICat3H.h              hooks.MaxObjectKiB131025=2048 
+/Code/Mantid/Framework/ICat/src/ICat3/GSoapGenerated/ICat3C.cpp                       hooks.MaxObjectKiB131025=5120
+/Code/Mantid/Framework/ICat/src/ICat4/GSoapGenerated/ICat4C.cpp                       hooks.MaxObjectKiB131025=2048

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/CMakeLists.txt

@@ -173,7 +173,11 @@ if ( ENABLE_CPACK )
     include ( CPackCommon )
 
     # Mac Packagemaker settings
-    set ( CPACK_RESOURCE_FILE_README ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/MacOSX-README.rtf )
+    if (OSX_VERSION VERSION_LESS 10.8)
+      set ( CPACK_RESOURCE_FILE_README ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/MacOSX-README.rtf )
+    else()
+      set ( CPACK_RESOURCE_FILE_README ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/MacOSX10-8-README.rtf )
+    endif ()
     set ( CPACK_RESOURCE_FILE_LICENSE ${CMAKE_SOURCE_DIR}/Installers/WinInstaller/License.rtf )
 
     IF ( ${CMAKE_SYSTEM_NAME} STREQUAL "Linux" )
@@ -184,7 +188,8 @@ if ( ENABLE_CPACK )
       # rhel requirements
       set ( CPACK_RPM_PACKAGE_REQUIRES "boost >= 1.34.1,qt4 >= 4.2,nexus,nexus-python,qwt,gsl,glibc,qwtplot3d-qt4,OpenCASCADE-libs-modelling >= 6.3.0,OpenCASCADE-libs-foundation >= 6.3.0,OpenCASCADE-libs-visualization >= 6.3.0,OpenCASCADE-libs-ocaf >= 6.3.0,OpenCASCADE-libs-ocaf-lite >= 6.3.0,muParser,numpy" )
       set ( CPACK_RPM_PACKAGE_REQUIRES "${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" )
-      # scipy & matplotlib (ipython is too low a version to be used)
+      set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},python-ipython >= 1.1.0" )
+      # scipy & matplotlib
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},scipy,python-matplotlib" )
       set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},mxml,hdf,hdf5" )
 

Code/Mantid/Framework/API/CMakeLists.txt

@@ -297,6 +297,7 @@ set ( TEST_FILES
 	IEventListTest.h
 	IFunction1DTest.h
 	IFunctionMDTest.h
+	IkedaCarpenterModeratorTest.h
 	ILiveListenerTest.h
 	IMDWorkspaceTest.h
 	ISpectrumTest.h

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

@@ -180,6 +180,11 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   virtual const std::string categorySeparator() const {return ";";}
   /// function to return any aliases to the algorithm;  A default implementation is provided
   virtual const std::string alias() const {return "";}
+
+  const std::string workspaceMethodName() const;
+  const std::vector<std::string> workspaceMethodOn() const;
+  const std::string workspaceMethodInputProperty() const;
+
   /// Algorithm ID. Unmanaged algorithms return 0 (or NULL?) values. Managed ones have non-zero.
   AlgorithmID getAlgorithmID()const{return m_algorithmID;}
 
@@ -218,6 +223,12 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   void setLogging(const bool value){g_log.setEnabled(value);}
   ///returns the status of logging, True = enabled
   bool isLogging() const {return g_log.getEnabled();}
+
+  ///sets the logging priority offset
+  void setLoggingOffset(const int value) {g_log.setLevelOffset(value);}
+  ///returns the logging priority offset
+  int getLoggingOffset() const {return g_log.getLevelOffset();}
+
   /// Returns a reference to the logger.
   Kernel::Logger& getLogger() const { return g_log; }
 
@@ -267,6 +278,9 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   /// Method defining summary, optional
   virtual void initDocs() {};
 
+  /// Returns a semi-colon separated list of workspace types to attach this algorithm
+  virtual const std::string workspaceMethodOnTypes() const { return ""; }
+
   void cacheWorkspaceProperties();
 
   friend class AlgorithmProxy;

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

@@ -101,6 +101,10 @@ namespace Mantid
       void enableHistoryRecordingForChild(const bool) {};
       void setRethrows(const bool rethrow);
 
+      const std::string workspaceMethodName() const;
+      const std::vector<std::string> workspaceMethodOn() const;
+      const std::string workspaceMethodInputProperty() const;
+
       /** @name PropertyManager methods */
       //@{
       /// Set the property value
@@ -120,6 +124,11 @@ namespace Mantid
       void setLogging(const bool value) { m_isLoggingEnabled=value; }
       /// Is the algorithm have logging enabled
       bool isLogging() const { return m_isLoggingEnabled; }
+
+      ///returns the logging priority offset
+      void setLoggingOffset(const int value)  { m_loggingOffset=value; }
+      ///returns the logging priority offset
+      int getLoggingOffset() const { return m_loggingOffset; }
 
       ///setting the child start progress
       void setChildStartProgress(const double startProgress)const;
@@ -162,6 +171,7 @@ namespace Mantid
       mutable boost::shared_ptr<Algorithm> m_alg;  ///< Shared pointer to a real algorithm. Created on demand
       bool m_isExecuted;     ///< Executed flag
       bool m_isLoggingEnabled;///< is the logging of the underlying algorithm enabled
+      int m_loggingOffset; ///< the logging priority offset
       bool m_rethrow; ///< Whether or not to rethrow exceptions.
       bool m_isChild; ///< Is this a child algo
 

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

@@ -80,6 +80,9 @@ namespace Mantid
         m_log.debug() << "Registered '" << nameVersion.first << "' version '" << nameVersion.second << "' as file loader\n";
       }
 
+      /// Unsubscribe a named algorithm and version from the loader registration
+      void unsubscribe(const std::string &name, const int version = -1);
+
       /// Returns the name of an Algorithm that can load the given filename
       const boost::shared_ptr<IAlgorithm> chooseLoader(const std::string &filename) const;
       /// Checks whether the given algorithm can load the file
@@ -121,6 +124,10 @@ namespace Mantid
         }
       };
 
+      /// Remove a named algorithm & version from the given map
+      void removeAlgorithm(const std::string & name, const int version, 
+                           std::multimap<std::string,int> & typedLoaders);
+
       /// The list of names. The index pointed to by LoaderFormat defines a set for that format
       std::vector<std::multimap<std::string,int> > m_names;
       /// Total number of names registered

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

@@ -79,6 +79,16 @@ class MANTID_API_DLL IAlgorithm : virtual public Kernel::IPropertyManager
   /// function to return any aliases of the algorithm.
   virtual const std::string alias() const = 0;
 
+  /** @name Algorithms As Methods */
+  ///@{
+  /// Returns a name that will be used when attached as a workspace method. Empty string indicates do not attach
+  virtual const std::string workspaceMethodName() const = 0;
+  /// Returns a set of class names that will have the method attached. Empty list indicates all types
+  virtual const std::vector<std::string> workspaceMethodOn() const = 0;
+  /// Returns the name of the input workspace property used by the calling object
+  virtual const std::string workspaceMethodInputProperty() const = 0;
+  ///@}
+
   /// Algorithm ID. Unmanaged algorithms return 0 (or NULL?) values. Managed ones have non-zero.
   virtual AlgorithmID getAlgorithmID()const = 0;
 
@@ -149,7 +159,11 @@ class MANTID_API_DLL IAlgorithm : virtual public Kernel::IPropertyManager
   ///Logging can be disabled by passing a value of false
   virtual void setLogging(const bool value) = 0;
   ///returns the status of logging, True = enabled
-  virtual bool isLogging() const = 0;
+  virtual bool isLogging() const = 0;  
+  ///gets the logging priority offset
+  virtual void setLoggingOffset(const int value) = 0;
+  ///returns the logging priority offset
+  virtual int getLoggingOffset() const = 0;
   ///setting the child start progress
   virtual void setChildStartProgress(const double startProgress)const = 0;
   /// setting the child end progress

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

@@ -45,6 +45,8 @@ class DLLExport IBackgroundFunction : public IFunctionWithLocation
   virtual void fit(const std::vector<double>& X,const std::vector<double>& Y) = 0;
 };
 
+typedef boost::shared_ptr<IBackgroundFunction> IBackgroundFunction_sptr;
+
 } // namespace API
 } // namespace Mantid
 

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

@@ -64,7 +64,7 @@ namespace Mantid
       virtual void initialize(Kernel::IPropertyManager* , const std::string&, DomainType) {}
 
       /// Toggle output of either just composite or composite + members
-      void separateCompositeMembersInOutput(const bool value);
+      void separateCompositeMembersInOutput(const bool value, const bool conv = false);
 
       /// Declare properties that specify the dataset within the workspace to fit to.
       /// @param suffix :: A suffix to give to all new properties.
@@ -117,6 +117,8 @@ namespace Mantid
       DomainType m_domainType;
       /// Output separate composite function values
       bool m_outputCompositeMembers;
+      /// Perform convolution of output composite components
+      bool m_convolutionCompositeMembers;
       /// Flag to ignore nans, infinities and zero errors.
       bool m_ignoreInvalidData;
     };

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/Algorithm.cpp

@@ -36,6 +36,12 @@ namespace Mantid
 {
   namespace API
   {
+    namespace
+    {
+      /// Separator for workspace types in workspaceMethodOnTypes member
+      const std::string WORKSPACE_TYPES_SEPARATOR = ";";
+    }
+
     // Doxygen can't handle member specialization at the moment: https://bugzilla.gnome.org/show_bug.cgi?id=406027
     // so we have to ignore them
     ///@cond
@@ -213,7 +219,7 @@ namespace Mantid
       Poco::StringTokenizer tokenizer(category(), categorySeparator(),
           Poco::StringTokenizer::TOK_TRIM | Poco::StringTokenizer::TOK_IGNORE_EMPTY);
       Poco::StringTokenizer::Iterator h = tokenizer.begin();
-
+      
       for (; h != tokenizer.end(); ++h)
       {
         res.push_back(*h);
@@ -227,6 +233,40 @@ namespace Mantid
       return res;
     }
 
+    /**
+     * @return A string giving the method name that should be attached to a workspace
+     */
+    const std::string Algorithm::workspaceMethodName() const
+    {
+      return "";
+    }
+
+    /**
+     *
+     * @return A list of workspace class names that should have the workspaceMethodName attached
+     */
+    const std::vector<std::string> Algorithm::workspaceMethodOn() const
+    {
+      Poco::StringTokenizer tokenizer(this->workspaceMethodOnTypes(), WORKSPACE_TYPES_SEPARATOR,
+                                      Poco::StringTokenizer::TOK_TRIM | Poco::StringTokenizer::TOK_IGNORE_EMPTY);
+      std::vector<std::string> res;
+      res.reserve(tokenizer.count());
+      for( auto iter = tokenizer.begin(); iter != tokenizer.end(); ++iter )
+      {
+        res.push_back(*iter);
+      }      
+
+      return res;
+    }
+
+    /**
+     * @return The name of the property that the calling object will be passed to.
+     */
+    const std::string Algorithm::workspaceMethodInputProperty() const
+    {
+      return "";
+    }
+
 
     //=============================================================================================
     //================================== Initialization ===========================================
@@ -911,6 +951,7 @@ namespace Mantid
       copyPropertiesFrom(proxy);
       m_algorithmID = proxy.getAlgorithmID();
       setLogging(proxy.isLogging());
+      setLoggingOffset(proxy.getLoggingOffset());
       setChild(proxy.isChild());
     }
 

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

@@ -25,7 +25,7 @@ namespace Mantid
     PropertyManagerOwner(),_executeAsync(this,&AlgorithmProxy::executeAsyncImpl),
       m_name(alg->name()),m_category(alg->category()), m_categorySeparator(alg->categorySeparator()),
       m_alias(alg->alias()), m_version(alg->version()), m_alg(alg),
-      m_isExecuted(),m_isLoggingEnabled(true), m_rethrow(false),
+      m_isExecuted(),m_isLoggingEnabled(true), m_loggingOffset(0), m_rethrow(false),
       m_isChild(false)
     {
       if (!alg)
@@ -183,6 +183,33 @@ namespace Mantid
       if(m_alg) m_alg->setRethrows(rethrow);
     }
 
+    /**
+     * @return A string giving the method name that should be attached to a workspace
+     */
+    const std::string AlgorithmProxy::workspaceMethodName() const
+    {
+      if(m_alg) return m_alg->workspaceMethodName();
+      else return "";
+    }
+
+    /**
+     * @return A set of workspace class names that should have the workspaceMethodName attached
+     */
+    const std::vector<std::string> AlgorithmProxy::workspaceMethodOn() const
+    {
+      if(m_alg) return m_alg->workspaceMethodOn();
+      else return std::vector<std::string>();
+    }
+
+    /**
+     * @return The name of the property that the calling object will be passed to
+     */
+    const std::string AlgorithmProxy::workspaceMethodInputProperty() const
+    {
+      if(m_alg) return m_alg->workspaceMethodInputProperty();
+      else return "";
+    }
+
     /**
     * Override setPropertyValue
     * @param name The name of the property