Re #9249 Fix merge with master.

Code/Mantid/Build/Jenkins/buildscript

@@ -78,6 +78,15 @@ $SCL_ON_RHEL6 "ctest -j$BUILD_THREADS --schedule-random --output-on-failure -E M
 # Run GUI tests serially
 $SCL_ON_RHEL6 "ctest --output-on-failure -R MantidPlot"
 
+###############################################################################
+# Build the documentation - tests first then html
+# Only rhel6 nodes to avoid redundant work
+###############################################################################
+if [[ "$ON_RHEL6" == true ]]; then
+  $SCL_ON_RHEL6 "make docs-test"
+  $SCL_ON_RHEL6 "make docs-html"
+fi
+
 ###############################################################################
 # Create the install kit if this is a clean or non-Mac build
 ###############################################################################
@@ -94,7 +103,11 @@ if [[ "$CLEANBUILD" == true ]]; then
   fi
 
   # We could build the source tarball anywhere, but we choose to do it on RHEL6
+  # We also parcel up the documentation into a tar file that is easier to move around
+  # and labelled by the commit id it was built with. This assumes the Jenkins git plugin
+  # has set the GIT_COMMIT environment variable
   if [[ "$ON_RHEL6" == true ]]; then
+    tar -cjf mantiddocs-g${GIT_COMMIT:0:7}.tar.bz2 --exclude='*.buildinfo' docs/html
     # The ..._PREFIX argument avoids opt/Mantid directories at the top of the tree
     $SCL_ON_RHEL6 "cpack --config CPackSourceConfig.cmake -D CPACK_PACKAGING_INSTALL_PREFIX="
   fi

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

@@ -256,9 +256,13 @@ namespace Mantid
       typedef std::map<size_t,double> MaskList;
       const MaskList& maskedBins(const size_t& spectrumIndex) const;
 
+      // Methods handling the internal monitor workspace
+      void setMonitorWorkspace(const boost::shared_ptr<MatrixWorkspace>& monitorWS);
+      boost::shared_ptr<MatrixWorkspace> monitorWorkspace() const;
+
       void saveInstrumentNexus(::NeXus::File * file) const;
       void loadInstrumentNexus(::NeXus::File * file);
-       void saveSpectraMapNexus(::NeXus::File * file, const std::vector<int>& spec,
+      void saveSpectraMapNexus(::NeXus::File * file, const std::vector<int>& spec,
           const ::NeXus::NXcompression compression = ::NeXus::LZW) const;
 
       //=====================================================================================
@@ -292,14 +296,13 @@ namespace Mantid
       virtual std::vector<IMDIterator*> createIterators(size_t suggestedNumCores = 1,
           Mantid::Geometry::MDImplicitFunction * function = NULL) const;
 
-       /// Apply masking.
-       void setMDMasking(Mantid::Geometry::MDImplicitFunction* maskingRegion);
-
-       /// Clear exsting masking.
-       void clearMDMasking();
+      /// Apply masking.
+      void setMDMasking(Mantid::Geometry::MDImplicitFunction* maskingRegion);
+      /// Clear exsting masking.
+      void clearMDMasking();
 
-       /// @return the special coordinate system used if any.
-       virtual Mantid::API::SpecialCoordinateSystem getSpecialCoordinateSystem() const;
+      /// @return the special coordinate system used if any.
+      virtual Mantid::API::SpecialCoordinateSystem getSpecialCoordinateSystem() const;
 
       //=====================================================================================
       // End IMDWorkspace methods
@@ -332,6 +335,9 @@ namespace Mantid
       /// The set of masked bins in a map keyed on spectrum index
       std::map< int64_t, MaskList > m_masks;
 
+      /// A workspace holding monitor data relating to the main data in the containing workspace (null if none).
+      boost::shared_ptr<MatrixWorkspace> m_monitorWorkspace;
+
     protected:
       /// Assists conversions to and from 2D histogram indexing to 1D indexing.
       MatrixWSIndexCalculator m_indexCalculator;

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

@@ -70,6 +70,8 @@ class MANTID_API_DLL WorkspaceHistory
   size_t size() const;
   /// Is the history empty
   bool empty() const;
+  /// remove all algorithm history objects from the workspace history
+  void clearHistory();
   /// Retrieve an algorithm history by index
   AlgorithmHistory_const_sptr getAlgorithmHistory(const size_t index) const;
   /// Add operator[] access

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

@@ -39,6 +39,9 @@ namespace Mantid
      */
     ICatalog_sptr CatalogManagerImpl::getCatalog(const std::string &sessionID)
     {
+      // Checks if a user is logged into the catalog. Inform the user if they are not.
+      if(m_activeCatalogs.empty()) throw std::runtime_error("You are not currently logged into a catalog.");
+
       if(sessionID.empty())
       {
         auto composite = boost::make_shared<CompositeCatalog>();

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

@@ -1060,6 +1060,25 @@ namespace Mantid
       return it->second;
     }
 
+    /** Sets the internal monitor workspace to the provided workspace.
+     *  This method is intended for use by data-loading algorithms.
+     *  Note that no checking is performed as to whether this workspace actually contains data
+     *  pertaining to monitors, or that the spectra point to Detector objects marked as monitors.
+     *  It simply has to be of the correct type to be accepted.
+     *  @param monitorWS The workspace containing the monitor data.
+     */
+    void MatrixWorkspace::setMonitorWorkspace(const boost::shared_ptr<MatrixWorkspace>& monitorWS)
+    {
+      m_monitorWorkspace = monitorWS;
+    }
+
+    /** Returns a pointer to the internal monitor workspace.
+     */
+    boost::shared_ptr<MatrixWorkspace> MatrixWorkspace::monitorWorkspace() const
+    {
+      return m_monitorWorkspace;
+    }
+
     //---------------------------------------------------------------------------------------------
     /** Return memory used by the workspace, in bytes.
      * @return bytes used.

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

@@ -88,6 +88,14 @@ bool WorkspaceHistory::empty() const
   return m_algorithms.empty();
 }
 
+/**
+ * Empty the list of algorithm history objects.
+ */
+void WorkspaceHistory::clearHistory()
+{
+  m_algorithms.clear();
+}
+
 /**
  * Retrieve an algorithm history by index
  * @param index ::  An index within the workspace history

Code/Mantid/Framework/API/test/MatrixWorkspaceTest.h

@@ -787,6 +787,19 @@ class MatrixWorkspaceTest : public CxxTest::TestSuite
     TS_ASSERT_EQUALS(ws->getXMax(), 1.0);
   }
 
+  void test_monitorWorkspace()
+  {
+    auto ws = boost::make_shared<WorkspaceTester>();
+    TSM_ASSERT( "There should be no monitor workspace by default", ! ws->monitorWorkspace() )
+
+    auto ws2 = boost::make_shared<WorkspaceTester>();
+    ws->setMonitorWorkspace(ws2);
+    TSM_ASSERT_EQUALS( "Monitor workspace not successfully set", ws->monitorWorkspace(), ws2 )
+
+    ws->setMonitorWorkspace(boost::shared_ptr<MatrixWorkspace>());
+    TSM_ASSERT( "Monitor workspace not successfully reset", ! ws->monitorWorkspace() )
+  }
+
 private:
   boost::shared_ptr<MatrixWorkspace> ws;
 

Code/Mantid/Framework/API/test/WorkspaceFactoryTest.h

@@ -75,6 +75,8 @@ class WorkspaceFactoryTest : public CxxTest::TestSuite
     ws_child->mutableRun().addProperty("Ei", 12.0);
     ws_child->mutableSample().setName("MySample");
 
+    ws_child->setMonitorWorkspace(boost::make_shared<Workspace1DTest>());
+
     MatrixWorkspace_sptr child;
     TS_ASSERT_THROWS_NOTHING( child = WorkspaceFactory::Instance().create(ws_child) );
     TS_ASSERT_EQUALS( child->id(), "Workspace1DTest");
@@ -102,7 +104,9 @@ class WorkspaceFactoryTest : public CxxTest::TestSuite
     TS_ASSERT_EQUALS("MySample", ws_child->sample().getName());
     TS_ASSERT_EQUALS("MySampleChild", child->sample().getName());
 
-
+    // Monitor workspace
+    TSM_ASSERT( "The workspace factory should not propagate a monitor workspace", ! child->monitorWorkspace() );
+
     MatrixWorkspace_sptr ws2D(new Workspace2DTest);
     ws2D->initialize(3,1,1);
     MatrixWorkspace_sptr child2;

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -181,6 +181,7 @@ set ( SRC_FILES
 	src/RemoveExpDecay.cpp
 	src/RemoveLowResTOF.cpp
 	src/RemovePromptPulse.cpp
+	src/RemoveWorkspaceHistory.cpp
 	src/RenameWorkspace.cpp
 	src/RenameWorkspaces.cpp
 	src/ReplaceSpecialValues.cpp
@@ -210,6 +211,7 @@ set ( SRC_FILES
 	src/SpecularReflectionCalculateTheta.cpp
 	src/SpecularReflectionPositionCorrect.cpp
 	src/SphericalAbsorption.cpp
+	src/Stitch1D.cpp
 	src/StripPeaks.cpp
 	src/StripVanadiumPeaks.cpp
 	src/StripVanadiumPeaks2.cpp
@@ -415,6 +417,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/RemoveExpDecay.h
 	inc/MantidAlgorithms/RemoveLowResTOF.h
 	inc/MantidAlgorithms/RemovePromptPulse.h
+	inc/MantidAlgorithms/RemoveWorkspaceHistory.h
 	inc/MantidAlgorithms/RenameWorkspace.h
 	inc/MantidAlgorithms/RenameWorkspaces.h
 	inc/MantidAlgorithms/ReplaceSpecialValues.h
@@ -444,6 +447,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/SpecularReflectionCalculateTheta.h
 	inc/MantidAlgorithms/SpecularReflectionPositionCorrect.h
 	inc/MantidAlgorithms/SphericalAbsorption.h
+	inc/MantidAlgorithms/Stitch1D.h
 	inc/MantidAlgorithms/StripPeaks.h
 	inc/MantidAlgorithms/StripVanadiumPeaks.h
 	inc/MantidAlgorithms/StripVanadiumPeaks2.h
@@ -642,6 +646,7 @@ set ( TEST_FILES
 	RemoveExpDecayTest.h
 	RemoveLowResTOFTest.h
 	RemovePromptPulseTest.h
+	RemoveWorkspaceHistoryTest.h
 	RenameWorkspaceTest.h
 	RenameWorkspacesTest.h
 	ReplaceSpecialValuesTest.h
@@ -667,6 +672,7 @@ set ( TEST_FILES
 	SpecularReflectionCalculateThetaTest.h
 	SpecularReflectionPositionCorrectTest.h
 	SphericalAbsorptionTest.h
+	Stitch1DTest.h
 	StripPeaksTest.h
 	StripVanadiumPeaks2Test.h
 	StripVanadiumPeaksTest.h

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/RemoveWorkspaceHistory.h

@@ -0,0 +1,58 @@
+#ifndef MANTID_ALGORITHMS_REMOVEWORKSPACEHISTORY_H_
+#define MANTID_ALGORITHMS_REMOVEWORKSPACEHISTORY_H_
+
+#include "MantidKernel/System.h"
+#include "MantidAPI/Algorithm.h"
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+  /** RemoveWorkspaceHistory
+
+    Removes all algorithm history records from the workspace history attached to a workspace.
+    
+    Copyright © 2014 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 RemoveWorkspaceHistory  : public API::Algorithm
+  {
+  public:
+    RemoveWorkspaceHistory();
+    virtual ~RemoveWorkspaceHistory();
+
+    virtual const std::string name() const;
+    virtual const std::string summary() const;
+    virtual int version() const;
+    virtual const std::string category() const;
+
+  private:
+    void init();
+    void exec();
+
+
+  };
+
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif  /* MANTID_ALGORITHMS_REMOVEWORKSPACEHISTORY_H_ */