Refs #8020. Merge remote-tracking branch 'origin/master' into 8020

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/src/MuonAnalysis.cpp

Code/Mantid/Build/CMake/CppCheck_Suppressions.txt

@@ -3,8 +3,6 @@
 //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

Code/Mantid/Build/CMake/FindCppcheck.cmake

@@ -61,7 +61,8 @@ if(CPPCHECK_EXECUTABLE)
 endif()
 
 mark_as_advanced(CPPCHECK_EXECUTABLE)
-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_ARGS --enable=all --inline-suppr 
+                    --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/VersionNumber.cmake

@@ -1,7 +1,7 @@
 # Set the version number here for MantidVersion and the package filenames
 
 set ( VERSION_MAJOR 3 )
-set ( VERSION_MINOR 0 )
+set ( VERSION_MINOR 1 )
 
 # UNCOMMENT the next 'set' line to 'force' the patch version number to
 # a value (instead of using the count coming out of 'git describe')

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.0/DEBIAN/control

@@ -1,9 +1,9 @@
 Package: mantid-developer
-Version: 1.0
+Version: 1.1
 Section: main
 Priority: optional
 Architecture: all
-Depends: cmake-qt-gui (>= 2.8.5), build-essential, subversion, libhdf4-dev, libhdf5-serial-dev, libmxml-dev, libgsl0-dev, libopencascade-modeling-dev, libopencascade-foundation-dev, libssl-dev, openssl, libpoco-dev, libpococrypto9-dbg, libpocodata9-dbg, libpocofoundation9-dbg, libpocomysql9-dbg, libpoconet9-dbg, libpoconetssl9-dbg, libpocoodbc9-dbg, libpocosqlite9-dbg, libpocoutil9-dbg, libpocoxml9-dbg, libpocozip9-dbg, python-dev, python-dbg, python-numpy, libmuparser-dev, libnexus0-dev, libqt4-assistant, libqt4-dbus, libqt4-designer, libqt4-dev, libqt4-help, libqt4-network, libqt4-opengl, libqt4-opengl-dev, libqt4-qt3support, libqt4-script, libqt4-scripttools, libqt4-sql, libqt4-sql-mysql, libqt4-svg, libqt4-test, libqt4-webkit, libqt4-xml, libqt4-xmlpatterns, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dbg, python-qt4-dev, qt4-designer, qt4-qmake, python-sip-dbg, python-sip-dev, libqscintilla2-dev, qt4-dev-tools, libboost-signals-dev, libboost-date-time-dev, libboost-regex-dev, libboost-python-dev, git, libgoogle-perftools-dev,texlive-latex-recommended,texlive-latex-extra,texlive-fonts-recommended,dvipng
+Depends: cmake-qt-gui (>= 2.8.5), build-essential, subversion, libhdf4-dev, libhdf5-serial-dev, libmxml-dev, ipython (>= 1.1), libgsl0-dev, libopencascade-modeling-dev, libopencascade-foundation-dev, libssl-dev, openssl, libpoco-dev, libpococrypto9-dbg, libpocodata9-dbg, libpocofoundation9-dbg, libpocomysql9-dbg, libpoconet9-dbg, libpoconetssl9-dbg, libpocoodbc9-dbg, libpocosqlite9-dbg, libpocoutil9-dbg, libpocoxml9-dbg, libpocozip9-dbg, python-dev, python-dbg, python-numpy, python-scipy, libmuparser-dev, libnexus0-dev, libqt4-assistant, libqt4-dbus, libqt4-designer, libqt4-dev, libqt4-help, libqt4-network, libqt4-opengl, libqt4-opengl-dev, libqt4-qt3support, libqt4-script, libqt4-scripttools, libqt4-sql, libqt4-sql-mysql, libqt4-svg, libqt4-test, libqt4-webkit, libqt4-xml, libqt4-xmlpatterns, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dbg, python-qt4-dev, qt4-designer, qt4-qmake, python-sip-dbg, python-sip-dev, libqscintilla2-dev, qt4-dev-tools, libboost-signals-dev, libboost-date-time-dev, libboost-regex-dev, libboost-python-dev, git, libgoogle-perftools-dev,texlive-latex-recommended,texlive-latex-extra,texlive-fonts-recommended,dvipng
 Installed-Size: 0
 Maintainer: Mantid Project
 Description: Installs all packages required for a Mantid developer

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer-el6.spec

@@ -1,6 +1,6 @@
 Name:           mantid-developer
 Version:        1.1
-Release:        2%{?dist}
+Release:        4%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
 Group:          Development/Tools
@@ -18,6 +18,7 @@ Requires: gcc-c++
 Requires: gsl-devel
 Requires: hdf-devel
 Requires: hdf5-devel
+Requires: python-ipython >= 1.1
 Requires: muParser-devel
 Requires: mxml-devel
 Requires: nexus >= 4.2
@@ -33,6 +34,7 @@ Requires: qwt-devel
 Requires: qwtplot3d-qt4-devel
 Requires: redhat-lsb
 Requires: rpmdevtools
+Requires: scipy
 Requires: sip-devel
 Requires: git
 Requires: openssl-devel
@@ -63,6 +65,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Tue Feb 04 2014 Stuart Campbell <campbellsi@ornl.gov>
+- Added scipy and ipython >= 1.1 dependency
+
 * Tue May 07 2013 Stuart Campbell <campbellsi@ornl.gov>
 - Added dvipng and latex for qt-assistant stuff
 - Added software collection dependencies

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer-f19.spec

@@ -1,6 +1,6 @@
 Name:           mantid-developer
 Version:        1.2
-Release:        2%{?dist}
+Release:        4%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
 Group:          Development/Tools
@@ -27,12 +27,14 @@ Requires: OpenCASCADE-devel
 Requires: poco-devel
 Requires: PyQt4-devel
 Requires: python-devel
+Requires: python-ipython
 Requires: qscintilla-devel
 Requires: qt-devel >= 4.6
 Requires: qwt5-qt4-devel
 Requires: qwtplot3d-qt4-devel
 Requires: redhat-lsb
 Requires: rpmdevtools
+Requires: scipy 
 Requires: sip-devel
 Requires: git
 Requires: openssl-devel
@@ -62,6 +64,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Tue Feb 04 2014 Stuart Campbell <campbellsi@ornl.gov>
+- Added scipy and ipython >= 1.1 dependency
+
 * Tue Aug 20 2013 Peter Peterson <petersonpf@ornl.gov>
 - Removed things not necessary for fedora 19.
 

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer-f20.spec

@@ -1,6 +1,6 @@
 Name:           mantid-developer
 Version:        1.3
-Release:        3%{?dist}
+Release:        5%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
 Group:          Development/Tools
@@ -27,13 +27,15 @@ Requires: OCE-devel
 Requires: poco-devel
 Requires: PyQt4-devel
 Requires: python-devel
+Requires: python-ipython
 Requires: python-sphinx
 Requires: qscintilla-devel
 Requires: qt-devel >= 4.6
 Requires: qwt5-qt4-devel
 Requires: qwtplot3d-qt4-devel
 Requires: redhat-lsb
 Requires: rpmdevtools
+Requires: scipy
 Requires: sip-devel
 Requires: git
 Requires: openssl-devel
@@ -63,6 +65,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Tue Feb 04 2014 Stuart Campbell <campbellsi@ornl.gov>
+- Added scipy and ipython >= 1.1 dependency
+
 * Fri Dec 20 2013 Stuart Campbell <campbellsi@ornl.gov>
 - Added python-sphinx
 

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

@@ -9,25 +9,30 @@
 #include "MantidKernel/PropertyManagerOwner.h"
 
 // -- These headers will (most-likely) be used by every inheriting algorithm
+#include "MantidAPI/AlgorithmFactory.h" //for the factory macro
 #include "MantidAPI/Progress.h"
-#include "MantidAPI/AlgorithmFactory.h"
 #include "MantidAPI/WorkspaceProperty.h"
 #include "MantidAPI/WorkspaceFactory.h"
 #include "MantidAPI/WorkspaceOpOverloads.h"
 #include "MantidKernel/MultiThreaded.h"
 #include "MantidKernel/EmptyValues.h"
 
-#include <boost/shared_ptr.hpp>
-#include <Poco/ActiveMethod.h>
-#include <Poco/NotificationCenter.h>
-#include <Poco/Notification.h>
-#include <Poco/NObserver.h>
-#include <Poco/Void.h>
+//----------------------------------------------------------------------
+// Forward Declaration
+//----------------------------------------------------------------------
+namespace boost
+{
+  template <class T> class weak_ptr;
+}
 
-#include <string>
-#include <vector>
-#include <map>
-#include <cmath>
+namespace Poco
+{
+  template <class R, class A, class O, class S> class ActiveMethod;
+  template <class O> class ActiveStarter;
+  class NotificationCenter;
+  template <class C, class N> class NObserver;
+  class Void;
+}
 
 namespace Mantid
 {
@@ -209,10 +214,10 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   Poco::ActiveResult<bool> executeAsync();
 
   /// Add an observer for a notification
-  void addObserver(const Poco::AbstractObserver& observer)const;
+  void addObserver(const Poco::AbstractObserver& observer) const;
 
   /// Remove an observer
-  void removeObserver(const Poco::AbstractObserver& observer)const;
+  void removeObserver(const Poco::AbstractObserver& observer) const;
 
   /// Raises the cancel flag.
   virtual void cancel();
@@ -289,19 +294,19 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   void setInitialized();
   void setExecuted(bool state);
 
-  /// Sends notifications to observers. Observers can subscribe to notificationCenter
-  /// using Poco::NotificationCenter::addObserver(...);
-  mutable Poco::NotificationCenter m_notificationCenter;
-
   /** @name Progress Reporting functions */
   friend class Progress;
   void progress(double p, const std::string& msg = "", double estimatedTime = 0.0, int progressPrecision = 0);
   void interruption_point();
 
+  /// Return a reference to the algorithm's notification dispatcher
+  Poco::NotificationCenter & notificationCenter() const;
+
   ///Observation slot for child algorithm progress notification messages, these are scaled and then signalled for this algorithm.
   void handleChildProgressNotification(const Poco::AutoPtr<ProgressNotification>& pNf);
-  ///Child algorithm progress observer
-  Poco::NObserver<Algorithm, ProgressNotification> m_progressObserver;
+  /// Return a reference to the algorithm's object that is reporting progress
+  const Poco::AbstractObserver & progressObserver() const;
+
   ///checks that the value was not set by users, uses the value in empty double/int.
   template <typename NumT>
   static bool isEmpty(const NumT toCheck);
@@ -347,12 +352,19 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
 
   void logAlgorithmInfo() const;
 
-
-  /// Poco::ActiveMethod used to implement asynchronous execution.
-  Poco::ActiveMethod<bool, Poco::Void, Algorithm> m_executeAsync;
   bool executeAsyncImpl(const Poco::Void & i);
 
   // --------------------- Private Members -----------------------------------
+
+  /// Poco::ActiveMethod used to implement asynchronous execution.
+  Poco::ActiveMethod<bool, Poco::Void, Algorithm, Poco::ActiveStarter<Algorithm>> *m_executeAsync;
+
+  /// Sends notifications to observers. Observers can subscribe to notificationCenter
+  /// using Poco::NotificationCenter::addObserver(...);
+  mutable Poco::NotificationCenter *m_notificationCenter;
+  ///Child algorithm progress observer
+  mutable Poco::NObserver<Algorithm, ProgressNotification> *m_progressObserver;
+
   bool m_isInitialized; ///< Algorithm has been initialized flag
   bool m_isExecuted; ///< Algorithm is executed flag
   bool m_isChildAlgorithm; ///< Algorithm is a child algorithm
@@ -367,7 +379,7 @@ class MANTID_API_DLL Algorithm : public IAlgorithm, public Kernel::PropertyManag
   std::string m_OptionalMessage; ///< An optional message string to be displayed in the GUI.
   std::string m_WikiSummary; ///< A summary line for the wiki page.
   std::string m_WikiDescription; ///< Description in the wiki page.
-  std::vector<IAlgorithm_wptr> m_ChildAlgorithms; ///< A list of weak pointers to any child algorithms created
+  std::vector<boost::weak_ptr<IAlgorithm>> m_ChildAlgorithms; ///< A list of weak pointers to any child algorithms created
 
 
   /// Vector of all the workspaces that have been read-locked

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

@@ -8,14 +8,20 @@
 #include "MantidAPI/IAlgorithm.h"
 #include "MantidKernel/PropertyManagerOwner.h"
 #include <boost/shared_ptr.hpp>
-#include <Poco/ActiveMethod.h>
+
 
 #ifdef _MSC_VER
   #pragma warning( disable: 4250 ) // Disable warning regarding inheritance via dominance, we have no way around it with the design
 #endif
 
+
+//----------------------------------------------------------------------
+// Forward Declaration
+//----------------------------------------------------------------------
 namespace Poco
 {
+  template <class R, class A, class O, class S> class ActiveMethod;
+  template <class O> class ActiveStarter;
   class Void;
 }
 
@@ -156,7 +162,8 @@ namespace Mantid
       void dropWorkspaceReferences();
 
       /// Poco::ActiveMethod used to implement asynchronous execution.
-      Poco::ActiveMethod<bool, Poco::Void, AlgorithmProxy> _executeAsync;
+      Poco::ActiveMethod<bool, Poco::Void, AlgorithmProxy,
+                         Poco::ActiveStarter<AlgorithmProxy>> *m_executeAsync;
       /// Execute asynchronous implementation
       bool executeAsyncImpl(const Poco::Void & dummy);
 

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

@@ -135,21 +135,7 @@ class MANTID_API_DLL Column
     }
 
     /// Set plot type where 
-    /// None = 0 (means it has specifically been set to 'no plot type')
-    /// NotSet = -1000 (this is the default and means plot style has not been set)
-    /// X = 1, Y = 2, Z = 3, xErr = 4, yErr = 5, Label = 6
-    /// @param t plot type as defined above
-    void setPlotType(int t)
-    {
-      if ( t == -1000 || t == 0 || t == 1 || t == 2 || t == 3 || t == 4 ||
-           t == 5 || t == 6 )
-        m_plotType = t;
-      else 
-      {
-        g_log.error() << "Cannot set plot of column to " << t 
-          << " . Ignore this attempt." << std::endl;
-      }
-    }
+    void setPlotType(int t);
 
     /**
      * Fills a std vector with values from the column if the types are compatible.

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

@@ -120,6 +120,8 @@ namespace API
     void saveExperimentInfoNexus(::NeXus::File * file) const;
     /// Loads an experiment description from the open NeXus file
     void loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr);
+    /// Load the instrument from an open NeXus file.
+    void loadInstrumentInfoNexus(::NeXus::File * file, std::string & parameterStr);
     /// Load the sample and log info from an open NeXus file.
     void loadSampleAndLogInfoNexus(::NeXus::File * file);
     /// Populate the parameter map given a string

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

@@ -6,13 +6,11 @@
 //----------------------------------------------------------------------
 #include "MantidAPI/DllConfig.h"
 #include "MantidKernel/IPropertyManager.h"
-#include <Poco/ActiveResult.h>
-#include <boost/weak_ptr.hpp>
-#include <string>
 
 namespace Poco
 {
   class AbstractObserver;
+  template<class T> class ActiveResult;
 }
 
 namespace Mantid
@@ -176,7 +174,6 @@ class MANTID_API_DLL IAlgorithm : virtual public Kernel::IPropertyManager
 
 typedef boost::shared_ptr<IAlgorithm> IAlgorithm_sptr;
 typedef boost::shared_ptr<const IAlgorithm> IAlgorithm_const_sptr;
-typedef boost::weak_ptr<IAlgorithm> IAlgorithm_wptr;
 
 } // namespace API
 } // namespace Mantid

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

@@ -50,25 +50,25 @@ class DLLExport ICatalog
   /// logout from catalog
   virtual void logout()=0;
   ///Search investigations
-  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr&, const int &offset,const int &limit)=0;
+  virtual void search(const ICat::CatalogSearchParam&,ITableWorkspace_sptr&, const int &,const int &)=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.
-  virtual void getDataSets(const long long& ,ITableWorkspace_sptr&)=0;
+  virtual void getDataSets(const std::string& ,ITableWorkspace_sptr&)=0;
   /// get datafiles
-  virtual void getDataFiles(const long long&,ITableWorkspace_sptr &)=0;
+  virtual void getDataFiles(const std::string&,ITableWorkspace_sptr &)=0;
   ///  instrument list
-  virtual void listInstruments(std::vector<std::string>& )=0;
+  virtual void listInstruments(std::vector<std::string>&)=0;
   /// get investigationtype lists
   virtual void listInvestigationTypes(std::vector<std::string>&)=0;
   /// get file locations
-  virtual void getFileLocation(const long long&,std::string& )=0;
+  virtual void getFileLocation(const long long&,std::string&)=0;
   /// get URLs of the files
-  virtual void getDownloadURL(const long long& fileid,std::string&)=0;
+  virtual void getDownloadURL(const long long&,std::string&)=0;
   /// get URL of where to PUT (publish) files.
-  virtual const std::string getUploadURL(const std::string &, const std::string &)=0;
+  virtual const std::string getUploadURL(const std::string&,const std::string&,const std::string&)=0;
   /// keep alive
   virtual void keepAlive()=0;
   ///keep alive in minutes