Refs #6473. Merge remote-tracking branch 'origin/master' into 6473

Conflicts:
	Code/Mantid/MantidQt/MantidWidgets/CMakeLists.txt

Code/Mantid/Build/CMake/CppCheckSetup.cmake

@@ -57,6 +57,8 @@ if ( CPPCHECK_EXECUTABLE )
         Framework/Kernel/src/Math/Optimization/SLSQPMinimizer.cpp
         MantidPlot/src/nrutil.cpp
         MantidPlot/src/origin/OPJFile.cpp
+        MantidPlot/src/zlib123/minigzip.c
+        Framework/SINQ/src/PoldiPeakFit.cpp
       )
 
   # Header files to be ignored require different handling
@@ -114,7 +116,7 @@ if ( CPPCHECK_EXECUTABLE )
   # put the finishing bits on the final command call
   set (_cppcheck_xml_args)
   if (CPPCHECK_GENERATE_XML)
-    list( APPEND _cppcheck_xml_args --xml --xml-version=2 ${_cppcheck_source_dirs} 2> ${CMAKE_BINARY_DIR}/cppcheck.xml )
+    list( APPEND _cppcheck_xml_args  --xml --xml-version=2 ${_cppcheck_source_dirs} 2> ${CMAKE_BINARY_DIR}/cppcheck.xml )
   else (CPPCHECK_GENERATE_XML)
     list( APPEND _cppcheck_xml_args  ${_cppcheck_source_dirs} )
   endif (CPPCHECK_GENERATE_XML)

Code/Mantid/Build/CMake/CppCheck_Suppressions.txt

@@ -0,0 +1,11 @@
+// suppress memleak and exceptNew errors in the file src/file1.cpp
+//memleak:src/file1.cpp
+//exceptNew:src/file1.cpp
+
+// suppress in all files - BE CAREFULL not to leave trailing spaces after the rule id. or empty lines
+// This finds false positives where private member variable names reused by inheriting classes
+duplInheritedMember
+// For a library this is not a problem per se
+unusedFunction
+// cppcheck has problems handling the number of pre-processor definitions used in the DLL_EXPORTs
+class_X_Y

Code/Mantid/Build/CMake/FindCppcheck.cmake

@@ -29,7 +29,7 @@ endif()
 find_program(CPPCHECK_EXECUTABLE NAMES cppcheck)
 
 if(MSVC)
-  set(CPPCHECK_TEMPLATE_ARG --template vs)
+  set(CPPCHECK_TEMPLATE_ARG --template "{file}({line}): warning : ({severity}-{id}) {message}")
   set(CPPCHECK_FAIL_REGULAR_EXPRESSION "[(]error[)]")
   set(CPPCHECK_WARN_REGULAR_EXPRESSION "[(]style[)]")
 elseif(CMAKE_COMPILER_IS_GNUCXX)
@@ -61,7 +61,7 @@ if(CPPCHECK_EXECUTABLE)
 endif()
 
 mark_as_advanced(CPPCHECK_EXECUTABLE)
-set ( CPPCHECK_ARGS --enable=all --inline-suppr CACHE STRING "Arguments for running cppcheck" )
+set ( CPPCHECK_ARGS --enable=all --inline-suppr CACHE STRING "Arguments for running cppcheck" --suppressions ${CMAKE_CURRENT_SOURCE_DIR}/Build/CMake/CppCheck_Suppressions.txt )
 set ( CPPCHECK_NUM_THREADS 0 CACHE STRING "Number of threads to use when running cppcheck" )
 set ( CPPCHECK_GENERATE_XML OFF CACHE BOOL "Generate xml output files from cppcheck" )
 

Code/Mantid/Build/CMake/WindowsNSIS.cmake

@@ -83,11 +83,6 @@
         install ( FILES ${VC_REDIST}/${REDIST_SUBDIR}/${DLL} DESTINATION bin )
     endforeach() 
 
-    # Copy Intel fortran libraries from numpy to general bin directory. Both numpy & scipy are compiled with intel compiler as it is the only way to get 64-bit libs at the moment.
-    # This means scipy requires the intel libraries that are stuck in numpy/core.
-    file ( GLOB INTEL_DLLS "${CMAKE_LIBRARY_PATH}/Python27/Lib/site-packages/numpy/core/*.dll" )
-    install ( FILES ${INTEL_DLLS} DESTINATION ${INBUNDLE}bin )
-
     # Copy third party dlls excluding selected Qt ones and debug ones
     install ( DIRECTORY ${CMAKE_LIBRARY_PATH}/ DESTINATION bin FILES_MATCHING PATTERN "*.dll"
     REGEX "${CMAKE_LIBRARY_PATH}/CRT/*" EXCLUDE

Code/Mantid/Framework/API/CMakeLists.txt

@@ -95,6 +95,7 @@ set ( SRC_FILES
 	src/Run.cpp
 	src/Sample.cpp
 	src/SampleEnvironment.cpp
+	src/ScopedWorkspace.cpp
 	src/ScriptRepository.cpp
 	src/ScriptRepositoryFactory.cpp
 	src/SpectraAxis.cpp
@@ -241,6 +242,7 @@ set ( INC_FILES
 	inc/MantidAPI/Run.h
 	inc/MantidAPI/Sample.h
 	inc/MantidAPI/SampleEnvironment.h
+	inc/MantidAPI/ScopedWorkspace.h
 	inc/MantidAPI/ScriptRepository.h
 	inc/MantidAPI/ScriptRepositoryFactory.h
 	inc/MantidAPI/SingleValueParameter.h
@@ -288,25 +290,25 @@ set ( TEST_FILES
 	FilePropertyTest.h
 	FrameworkManagerTest.h
 	FuncMinimizerFactoryTest.h
-  FunctionAttributeTest.h
-  FunctionDomainTest.h
-  FunctionFactoryTest.h
+	FunctionAttributeTest.h
+	FunctionDomainTest.h
+	FunctionFactoryTest.h
 	FunctionPropertyTest.h
 	FunctionTest.h
 	FunctionValuesTest.h
 	IEventListTest.h
 	IFunction1DTest.h
 	IFunctionMDTest.h
-	IkedaCarpenterModeratorTest.h
 	ILiveListenerTest.h
 	IMDWorkspaceTest.h
 	ISpectrumTest.h
+	IkedaCarpenterModeratorTest.h
 	ImmutableCompositeFunctionTest.h
 	ImplicitFunctionParserFactoryTest.h
 	IncreasingAxisValidatorTest.h
 	InstrumentDataServiceTest.h
 	LiveListenerFactoryTest.h
-        LogManagerTest.h
+	LogManagerTest.h
 	MDGeometryTest.h
 	MatrixWorkspaceMDIteratorTest.h
 	MemoryManagerTest.h
@@ -324,6 +326,7 @@ set ( TEST_FILES
 	RunTest.h
 	SampleEnvironmentTest.h
 	SampleTest.h
+	ScopedWorkspaceTest.h
 	SpectraAxisTest.h
 	SpectrumDetectorMappingTest.h
 	TextAxisTest.h

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

@@ -50,7 +50,9 @@ class DLLExport ICatalog
   /// logout from catalog
   virtual void logout()=0;
   ///Search investigations
-  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr &)=0;
+  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr&, const int &offset,const int &limit)=0;
+  /// Obtain the number of results returned by the search method.
+  virtual int64_t getNumberOfSearchResults(const ICat::CatalogSearchParam&)=0;
   /// search logged in users data
   virtual void myData(ITableWorkspace_sptr &)=0;
   /// get datasets.

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

@@ -422,7 +422,8 @@ class MANTID_API_DLL IFunction
   /// Set an attribute value
   template<typename T>
   void setAttributeValue(const std::string& attName,const T& value){setAttribute(attName,Attribute(value));}
-  void setAttributeValue(const std::string& attName,const char* value){setAttribute(attName,Attribute(std::string(value)));}
+  void setAttributeValue(const std::string& attName,const char* value);
+  void setAttributeValue(const std::string& attName,const std::string& value);
   //@}
 
   /// Set up the function for a fit.

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

@@ -68,6 +68,8 @@ namespace API
 
     /// Return the type of event contained, as a string. MDEvent or MDLeanEvent
     virtual std::string getEventTypeName() const = 0;
+    /// Return the size(in bytes) for the event, which this workspace contains
+    virtual size_t  sizeofEvent()const = 0;
 
     /// Split all boxes that exceed the split threshold.
     virtual void splitAllIfNeeded(Kernel::ThreadScheduler * ts) = 0;

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

@@ -209,6 +209,8 @@ class IMDNode
     virtual coord_t * getVertexesArray(size_t & numVertices, const size_t outDimensions, const bool * maskDim) const=0;
     virtual void transformDimensions(std::vector<double> & scaling, std::vector<double> & offset)=0;
 
+    // to avoid casting (which need also the number of dimensions) method say if Node is a box. if not, it is gridbox
+    virtual bool isBox()const=0;
   // ----------------------------- Helper Methods --------------------------------------------------------
   //-----------------------------------------------------------------------------------------------
   /** Helper method for sorting MDBoxBasees by file position.

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

@@ -120,6 +120,7 @@ namespace Mantid
       virtual ITableWorkspace_sptr makeBoxTable(size_t /*start*/, size_t /* num*/)
       {throw Kernel::Exception::NotImplementedError("This method is not generally implemented ");}
 
+
     protected:
       virtual const std::string toString() const;
     };

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

@@ -0,0 +1,92 @@
+#ifndef MANTID_API_SCOPEDWORKSPACE_H_
+#define MANTID_API_SCOPEDWORKSPACE_H_
+
+#include <string>
+
+#include "MantidKernel/ClassMacros.h"
+#include "MantidKernel/System.h"
+#include "MantidAPI/Workspace.h"
+
+namespace Mantid
+{
+namespace API
+{
+  /** ScopedWorkspace : scoped workspace ADS entry.
+
+    This class is provided for situations when you need a workspace to be in the ADS to run an 
+    algorithm, but you don't really need to keep it there after the algorithm has finished. In
+    these circumstances you can create ScopedWorkspace, set it's name as a workspace property
+    for the algorithm and retrieve it when algorithm has finished. The workspace will be
+    removed from the ADS when the object goes out of scope, or exception is thrown.
+
+    Primarily, it was created to overcome some limitations of WorkspaceProperties, but it can be
+    useful in other places, e.g. tests.
+    
+    Copyright &copy; 2013 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+
+    This file is part of Mantid.
+
+    Mantid is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or
+    (at your option) any later version.
+
+    Mantid is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+    File change history is stored at: <https://github.com/mantidproject/mantid>
+    Code Documentation is available at: <http://doxygen.mantidproject.org>
+  */
+  class DLLExport ScopedWorkspace 
+  {
+  public:
+    /// Empty constructor
+    ScopedWorkspace();
+
+    /// Workspace constructor
+    ScopedWorkspace(Workspace_sptr ws);
+
+    /// Destructor
+    virtual ~ScopedWorkspace();
+
+    /// Returns ADS name of the workspace
+    std::string name() const { return m_name; }
+
+    /// Retrieve workspace from the ADS
+    Workspace_sptr retrieve() const;
+
+    /// Removes the workspace entry from the ADS
+    void remove();
+
+    /// Operator for conversion to boolean
+    operator bool() const;
+
+    /// Make ADS entry to point to the given workspace
+    void set(Workspace_sptr newWS);
+
+  private:
+    DISABLE_COPY_AND_ASSIGN(ScopedWorkspace);
+
+    /// ADS name of the workspace
+    const std::string m_name;
+
+    /// Generates a tricky name which is unique within ADS 
+    static std::string generateUniqueName();
+
+    /// Generates a random alpha-numeric string
+    static std::string randomString(size_t len);
+
+    /// Length of workspace names generated
+    static const size_t NAME_LENGTH;
+  };
+
+
+} // namespace API
+} // namespace Mantid
+
+#endif  /* MANTID_API_SCOPEDWORKSPACE_H_ */

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

@@ -147,6 +147,11 @@ namespace Mantid
        */
       virtual boost::shared_ptr<TYPE>& operator=( const boost::shared_ptr<TYPE>& value )
       {
+        std::string wsName = value->name();
+        if ( this->direction() == Kernel::Direction::Input && !wsName.empty() )
+        {
+          m_workspaceName = wsName;
+        }
         return Kernel::PropertyWithValue< boost::shared_ptr<TYPE> >::operator=( value );
       }
 
@@ -215,6 +220,11 @@ namespace Mantid
         boost::shared_ptr<TYPE> typed = boost::dynamic_pointer_cast<TYPE>(value);
         if(typed)
         {
+          std::string wsName = typed->name();
+          if ( this->direction() == Kernel::Direction::Input && !wsName.empty() )
+          {
+            m_workspaceName = wsName;
+          }
           Kernel::PropertyWithValue< boost::shared_ptr<TYPE> >::m_value = typed;
         }
         else

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

@@ -715,22 +715,53 @@ namespace Mantid
     void Algorithm::store()
     {
       const std::vector< Property*> &props = getProperties();
+			std::vector<int> groupWsIndicies;
+
+      //add any regular/child workspaces first, then add the groups
       for (unsigned int i = 0; i < props.size(); ++i)
       {
         IWorkspaceProperty *wsProp = dynamic_cast<IWorkspaceProperty*>(props[i]);
         if (wsProp)
-        {
-          try
-          {
-            wsProp->store();
-          }
-          catch (std::runtime_error&)
-          {
-            g_log.error("Error storing output workspace in AnalysisDataService");
-            throw;
-          }
+        { 
+					//check if the workspace is a group, if so remember where it is and add it later
+					auto group = boost::dynamic_pointer_cast<WorkspaceGroup>( wsProp->getWorkspace() );
+					if ( !group )
+					{
+						try
+						{
+							wsProp->store();
+						}
+						catch (std::runtime_error&)
+						{
+							g_log.error("Error storing output workspace in AnalysisDataService");
+							throw;
+						}
+					}
+					else
+					{
+						groupWsIndicies.push_back(i);
+					}
         }
       }
+
+			//now store workspace groups once their members have been added
+			std::vector<int>::const_iterator wsIndex;
+			for (wsIndex = groupWsIndicies.begin(); wsIndex != groupWsIndicies.end(); ++wsIndex)
+			{
+				IWorkspaceProperty *wsProp = dynamic_cast<IWorkspaceProperty*>(props[*wsIndex]);
+				if(wsProp)
+				{
+					try
+					{
+						wsProp->store();
+					}
+					catch (std::runtime_error&)
+					{
+						g_log.error("Error storing output workspace in AnalysisDataService");
+						throw;
+					}
+				}
+			}
     }
 
     //---------------------------------------------------------------------------------------------

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

@@ -42,7 +42,7 @@ FileProperty::FileProperty(const std::string & name, const std::string& default_
                                    /* Create either a FileValidator or a DirectoryValidator, depending on Action */
                                    (action == FileProperty::Directory || action == FileProperty::OptionalDirectory) ?
                                    boost::make_shared<DirectoryValidator>(action == FileProperty::Directory) :
-                                   boost::make_shared<FileValidator>(exts, (action == FileProperty::Load) )
+                                   boost::make_shared<FileValidator>(exts, (action == FileProperty::Load), (action == FileProperty::Save) )
                                    , direction),
     m_action(action),
     m_defaultExt(""),
@@ -69,7 +69,7 @@ FileProperty::FileProperty(const std::string & name, const std::string& default_
       /* Create either a FileValidator or a DirectoryValidator, depending on Action */
       (action == FileProperty::Directory || action == FileProperty::OptionalDirectory) ?
           boost::make_shared<DirectoryValidator>(action == FileProperty::Directory) :
-          boost::make_shared<FileValidator>(std::vector<std::string>(1,ext), (action == FileProperty::Load) )
+          boost::make_shared<FileValidator>(std::vector<std::string>(1,ext), (action == FileProperty::Load), (action == FileProperty::Save) )
       , direction),
     m_action(action),
     m_defaultExt(ext),
@@ -370,27 +370,30 @@ std::string FileProperty::createDirectory(const std::string & path) const
   {
     stempath.makeParent();
   }
-  std::string error("");
+
   if( !stempath.toString().empty() )
   {
     Poco::File stem(stempath);
     if( !stem.exists() )
     {
       try
       {
-	stem.createDirectories();
+        stem.createDirectories();
       }
       catch(Poco::Exception &e)
       {
-	error = e.what();
+        std::stringstream msg;
+        msg << "Failed to create directory \"" << stempath.toString()
+            << "\": " << e.what() ;
+        return msg.str();
       }
     }
   }
   else
   {
-    error = "Invalid directory.";
+    return "Invalid directory.";
   }
-  return error;
+  return ""; // everything went fine
 }
 
 /**