Merge branch 'master' into 11188_paalman_pings_flat_plate

Refs #11188

Code/Mantid/Build/CMake/PylintSetup.cmake

@@ -32,10 +32,12 @@ if ( PYLINT_FOUND )
   set ( PYLINT_INCLUDES
         Framework/PythonInterface/plugins
         scripts
+        Testing/SystemTests/tests/analysis
   )
   set ( PYLINT_EXCLUDES
         scripts/lib1to2
         scripts/test
+        Testing/SystemTests/tests/analysis/reference
   )
   add_custom_target ( pylintcheck
                       COMMAND ${PYTHON_EXECUTABLE} ${PYLINT_RUNNER_SCRIPT} --format=${PYLINT_OUTPUT_FORMAT}

Code/Mantid/Build/Jenkins/buildscript

@@ -10,6 +10,8 @@
 # slave.
 ###############################################################################
 SCRIPT_DIR=$(dirname "$0")
+# Package by default
+BUILDPKG=true
 
 ###############################################################################
 # Print out the versions of things we are using
@@ -88,7 +90,6 @@ fi
 ###############################################################################
 if [[ ${JOB_NAME} == *clean* ]]; then
   CLEANBUILD=true
-  BUILDPKG=true
 fi
 
 if [[ -e $WORKSPACE/build/CMakeCache.txt ]]; then
@@ -99,10 +100,6 @@ if [[ -e $WORKSPACE/build/CMakeCache.txt ]]; then
   fi
 fi
 
-if [[ ${JOB_NAME} == *pull_requests* ]]; then
-  BUILDPKG=true
-fi
-
 ###############################################################################
 # Packaging options
 ###############################################################################

Code/Mantid/Build/Jenkins/systemtests

@@ -17,11 +17,11 @@ echo "SHA1=${sha1}"
 ###############################################################################
 # Set up the location for the local object store outside of the build and
 # source tree, which can be shared by multiple builds.
-# It defaults to the parent directory of the workspace but can be overridden
-# by setting the MANTID_DATA_STORE environment variable.
+# It defaults to a MantidExternalData directory within the HOME directory.
+# It can be overridden by setting the MANTID_DATA_STORE environment variable.
 ###############################################################################
 if [ -z "$MANTID_DATA_STORE" ]; then
-  export MANTID_DATA_STORE=$(dirname $WORKSPACE)
+  export MANTID_DATA_STORE=$HOME/MantidExternalData
 fi
 
 ###############################################################################

Code/Mantid/Build/Jenkins/systemtests.bat

@@ -1,4 +1,4 @@
-setlocal enbaleextensions enabledelayedexpansion
+setlocal enableextensions enabledelayedexpansion
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: WINDOWS SCRIPT TO DRIVE THE SYSTEM TESTS OF MANTID
 ::
@@ -46,8 +46,8 @@ if not EXIST %WORKSPACE%\build\CMakeCache.txt (
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Build step
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-"%CMAKE_BIN_DIR%\cmake" --build . -- StandardTestData
-"%CMAKE_BIN_DIR%\cmake" --build . -- SystemTestData
+msbuild /nologo /nr:false /p:Configuration=Release StandardTestData.vcxproj
+msbuild /nologo /nr:false /p:Configuration=Release SystemTestData.vcxproj
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Run the tests

Code/Mantid/Build/coverity_model.c

@@ -0,0 +1,18 @@
+/* Coverity Scan model
+ *
+ * This is a modeling file for Coverity Scan. Modeling helps to avoid false
+ * positives.
+ *
+ * - A model file can't import any header files.
+ * - Therefore only some built-in primitives like int, char and void are
+ *   available but not wchar_t, NULL etc.
+ * - Modeling doesn't need full structs and typedefs. Rudimentary structs
+ *   and similar types are sufficient.
+ * - An uninitialized local pointer is not an error. It signifies that the
+ *   variable could be either NULL or have some data.
+ *
+ * Coverity Scan doesn't pick up modifications automatically. The model file
+ * must be uploaded by an admin in the analysis settings of
+ * http://scan.coverity.com/projects/2832
+ */
+

Code/Mantid/Framework/API/CMakeLists.txt

@@ -31,6 +31,7 @@ set ( SRC_FILES
 	src/ExperimentInfo.cpp
 	src/Expression.cpp
 	src/FermiChopperModel.cpp
+	src/FileBackedExperimentInfo.cpp
 	src/FileFinder.cpp
 	src/FileLoaderRegistry.cpp
 	src/FileProperty.cpp
@@ -39,6 +40,7 @@ set ( SRC_FILES
 	src/FunctionDomain1D.cpp
 	src/FunctionDomainMD.cpp
 	src/FunctionFactory.cpp
+        src/FunctionParameterDecorator.cpp
 	src/FunctionProperty.cpp
 	src/FunctionValues.cpp
 	src/GridDomain.cpp
@@ -93,7 +95,7 @@ set ( SRC_FILES
 	src/ParamFunction.cpp
 	src/ParameterReference.cpp
 	src/ParameterTie.cpp
-        src/PeakFunctionIntegrator.cpp
+	src/PeakFunctionIntegrator.cpp
 	src/PeakTransform.cpp
 	src/PeakTransformHKL.cpp
 	src/PeakTransformQLab.cpp
@@ -171,6 +173,7 @@ set ( INC_FILES
 	inc/MantidAPI/ExperimentInfo.h
 	inc/MantidAPI/Expression.h
 	inc/MantidAPI/FermiChopperModel.h
+	inc/MantidAPI/FileBackedExperimentInfo.h
 	inc/MantidAPI/FileFinder.h
 	inc/MantidAPI/FileLoaderRegistry.h
 	inc/MantidAPI/FileProperty.h
@@ -180,6 +183,7 @@ set ( INC_FILES
 	inc/MantidAPI/FunctionDomain1D.h
 	inc/MantidAPI/FunctionDomainMD.h
 	inc/MantidAPI/FunctionFactory.h
+        inc/MantidAPI/FunctionParameterDecorator.h
 	inc/MantidAPI/FunctionProperty.h
 	inc/MantidAPI/FunctionValues.h
 	inc/MantidAPI/GridDomain.h
@@ -253,7 +257,7 @@ set ( INC_FILES
 	inc/MantidAPI/ParamFunction.h
 	inc/MantidAPI/ParameterReference.h
 	inc/MantidAPI/ParameterTie.h
-        inc/MantidAPI/PeakFunctionIntegrator.h
+	inc/MantidAPI/PeakFunctionIntegrator.h
 	inc/MantidAPI/PeakTransform.h
 	inc/MantidAPI/PeakTransformFactory.h
 	inc/MantidAPI/PeakTransformHKL.h
@@ -311,12 +315,14 @@ set ( TEST_FILES
 	ExperimentInfoTest.h
 	ExpressionTest.h
 	FermiChopperModelTest.h
+	FileBackedExperimentInfoTest.h
 	FileFinderTest.h
 	FilePropertyTest.h
 	FrameworkManagerTest.h
 	FuncMinimizerFactoryTest.h
 	FunctionAttributeTest.h
 	FunctionDomainTest.h
+        FunctionParameterDecoratorTest.h
 	FunctionFactoryTest.h
 	FunctionPropertyTest.h
 	FunctionTest.h
@@ -350,7 +356,7 @@ set ( TEST_FILES
 	ParamFunctionAttributeHolderTest.h
 	ParameterReferenceTest.h
 	ParameterTieTest.h
-        PeakFunctionIntegratorTest.h
+	PeakFunctionIntegratorTest.h
 	PeakTransformHKLTest.h
 	PeakTransformQLabTest.h
 	PeakTransformQSampleTest.h

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

@@ -34,8 +34,6 @@ class ModeratorModel;
  * - Run object (sample logs)
  * - Sample object (sample info)
  *
- * @author Janik Zikovsky
- * @date 2011-06-20
  */
 class MANTID_API_DLL ExperimentInfo {
 public:
@@ -48,94 +46,94 @@ class MANTID_API_DLL ExperimentInfo {
   /// Copy everything from the given experiment object
   void copyExperimentInfoFrom(const ExperimentInfo *other);
   /// Clone us
-  ExperimentInfo *cloneExperimentInfo() const;
+  virtual ExperimentInfo *cloneExperimentInfo() const;
 
   /// Returns a string description of the object
-  const std::string toString() const;
+  virtual const std::string toString() const;
 
   /// Instrument accessors
   void setInstrument(const Geometry::Instrument_const_sptr &instr);
   /// Returns the parameterized instrument
-  Geometry::Instrument_const_sptr getInstrument() const;
+  virtual Geometry::Instrument_const_sptr getInstrument() const;
 
   /// Returns the set of parameters modifying the base instrument
   /// (const-version)
-  const Geometry::ParameterMap &instrumentParameters() const;
+  virtual const Geometry::ParameterMap &instrumentParameters() const;
   /// Returns a modifiable set of instrument parameters
-  Geometry::ParameterMap &instrumentParameters();
+  virtual Geometry::ParameterMap &instrumentParameters();
   /// Const version
-  const Geometry::ParameterMap &constInstrumentParameters() const;
+  virtual const Geometry::ParameterMap &constInstrumentParameters() const;
   // Add parameters to the instrument parameter map
   virtual void populateInstrumentParameters();
 
   /// Replaces current parameter map with copy of given map
-  void replaceInstrumentParameters(const Geometry::ParameterMap &pmap);
+  virtual void replaceInstrumentParameters(const Geometry::ParameterMap &pmap);
   /// exchange contents of current parameter map with contents of other map)
-  void swapInstrumentParameters(Geometry::ParameterMap &pmap);
+  virtual void swapInstrumentParameters(Geometry::ParameterMap &pmap);
 
   /// Cache a lookup of grouped detIDs to member IDs
-  void cacheDetectorGroupings(const det2group_map &mapping);
+  virtual void cacheDetectorGroupings(const det2group_map &mapping);
   /// Returns the detector IDs that make up the group that this ID is part of
-  const std::vector<detid_t> &getGroupMembers(const detid_t detID) const;
+  virtual const std::vector<detid_t> &getGroupMembers(const detid_t detID) const;
   /// Get a detector or detector group from an ID
-  Geometry::IDetector_const_sptr getDetectorByID(const detid_t detID) const;
+  virtual  Geometry::IDetector_const_sptr getDetectorByID(const detid_t detID) const;
 
   /// Set an object describing the source properties and take ownership
-  void setModeratorModel(ModeratorModel *source);
+  virtual void setModeratorModel(ModeratorModel *source);
   /// Returns a reference to the source properties object
-  ModeratorModel &moderatorModel() const;
+  virtual ModeratorModel &moderatorModel() const;
 
   /// Set a chopper description specified by index where 0 is closest to the
   /// source
-  void setChopperModel(ChopperModel *chopper, const size_t index = 0);
+  virtual void setChopperModel(ChopperModel *chopper, const size_t index = 0);
   /// Returns a reference to a chopper description
-  ChopperModel &chopperModel(const size_t index = 0) const;
+  virtual ChopperModel &chopperModel(const size_t index = 0) const;
 
   /// Sample accessors
-  const Sample &sample() const;
+  virtual const Sample &sample() const;
   /// Writable version of the sample object
-  Sample &mutableSample();
+  virtual Sample &mutableSample();
 
   /// Run details object access
-  const Run &run() const;
+  virtual const Run &run() const;
   /// Writable version of the run object
-  Run &mutableRun();
+  virtual Run &mutableRun();
   /// Access a log for this experiment.
-  Kernel::Property *getLog(const std::string &log) const;
+  virtual Kernel::Property *getLog(const std::string &log) const;
   /// Access a single value from a log for this experiment.
-  double getLogAsSingleValue(const std::string &log) const;
+  virtual double getLogAsSingleValue(const std::string &log) const;
 
   /// Utility method to get the run number
-  int getRunNumber() const;
+  virtual int getRunNumber() const;
   /// Returns the emode for this run
-  Kernel::DeltaEMode::Type getEMode() const;
+  virtual Kernel::DeltaEMode::Type getEMode() const;
   /// Easy access to the efixed value for this run & detector ID
-  double getEFixed(const detid_t detID) const;
+  virtual double getEFixed(const detid_t detID) const;
   /// Easy access to the efixed value for this run & optional detector
-  double getEFixed(const Geometry::IDetector_const_sptr detector =
+  virtual double getEFixed(const Geometry::IDetector_const_sptr detector =
                        Geometry::IDetector_const_sptr()) const;
   /// Set the efixed value for a given detector ID
-  void setEFixed(const detid_t detID, const double value);
+  virtual void setEFixed(const detid_t detID, const double value);
 
   /// Saves this experiment description to the open NeXus file
-  void saveExperimentInfoNexus(::NeXus::File *file) const;
+  virtual void saveExperimentInfoNexus(::NeXus::File *file) const;
   /// Loads an experiment description from the open NeXus file
-  void loadExperimentInfoNexus(::NeXus::File *file, std::string &parameterStr);
+  virtual void loadExperimentInfoNexus(::NeXus::File *file, std::string &parameterStr);
   /// Load the instrument from an open NeXus file.
-  void loadInstrumentInfoNexus(::NeXus::File *file, std::string &parameterStr);
+  virtual void loadInstrumentInfoNexus(::NeXus::File *file, std::string &parameterStr);
   /// Load the sample and log info from an open NeXus file.
-  void loadSampleAndLogInfoNexus(::NeXus::File *file);
+  virtual void loadSampleAndLogInfoNexus(::NeXus::File *file);
   /// Populate the parameter map given a string
-  void readParameterMap(const std::string &parameterStr);
+  virtual void readParameterMap(const std::string &parameterStr);
 
   /// Returns the start date for this experiment (or current time if no info
   /// available)
-  std::string getWorkspaceStartDate() const;
+  virtual std::string getWorkspaceStartDate() const;
 
   // run/experiment stat time if available, empty otherwise
-  std::string getAvailableWorkspaceStartDate() const;
+  virtual std::string getAvailableWorkspaceStartDate() const;
   // run end time if available, empty otherwise
-  std::string getAvailableWorkspaceEndDate() const;
+  virtual std::string getAvailableWorkspaceEndDate() const;
 
   /// Utility to retrieve the validity dates for the given IDF
   static void getValidFromTo(const std::string &IDFfilename,