refs #9184. Merge branch 'master'

Merge branch 'master' into feature/9184_correct_positions_rro

Conflicts:
	Code/Mantid/Framework/Algorithms/src/ReflectometryReductionOne.cpp

Code/Mantid/Build/CMake/FindSphinx.cmake

@@ -8,6 +8,7 @@
 #  SPHINX_EXECUTABLE
 
 find_program( SPHINX_EXECUTABLE NAME sphinx-build
+  PATHS ${CMAKE_LIBRARY_PATH}/Python27/Scripts
   PATH_SUFFIXES bin
   DOC "Sphinx documentation generator"
 )

Code/Mantid/Build/Jenkins/buildscript

@@ -35,7 +35,7 @@ if [[ ${JOB_NAME} == *clean* ]]; then
   # Set some variables relating to the linux packages created from clean builds
   if [[ $(uname) != 'Darwin' ]]; then
     if [[ ${JOB_NAME} == *master* ]]; then
-      PACKAGINGVARS="-DENVVARS_ON_INSTALL=False -DCMAKE_INSTALL_PREFIX=/opt/mantidnightly -DCPACK_PACKAGE_SUFFIX=nightly -DCPACK_SET_DESTDIR=OFF -DQT_ASSISTANT_FETCH_IMAGES=ON"
+      PACKAGINGVARS="-DENVVARS_ON_INSTALL=False -DCMAKE_INSTALL_PREFIX=/opt/mantidnightly -DCPACK_PACKAGE_SUFFIX=nightly -DCPACK_SET_DESTDIR=OFF"
     elif [[ ${JOB_NAME} == *develop* ]]; then
       PACKAGINGVARS="-DENVVARS_ON_INSTALL=False -DCMAKE_INSTALL_PREFIX=/opt/mantidunstable -DCPACK_PACKAGE_SUFFIX=unstable -DCPACK_SET_DESTDIR=OFF"
     fi
@@ -84,7 +84,6 @@ $SCL_ON_RHEL6 "ctest --output-on-failure -R MantidPlot"
 rm -f *.dmg *.rpm *.deb *.tar.gz
 # Always build a package on linux
 if [[ $(uname) != 'Darwin' ]]; then
-  $SCL_ON_RHEL6 "make -j$BUILD_THREADS qtassistant"
   $SCL_ON_RHEL6 "cpack"
 fi
 

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -25,9 +25,6 @@ if "%JOB_NAME%"=="%JOB_NAME:clean=%" (
 ) else  (
     set CLEANBUILD=yes
     rmdir /S /Q build
-    if NOT "%JOB_NAME%"=="%JOB_NAME:master=%" (
-        set DOC_IMAGES=-DQT_ASSISTANT_FETCH_IMAGES=ON
-    )
 )
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -39,7 +36,7 @@ cd %WORKSPACE%\build
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: CMake configuration
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-"C:\Program Files (x86)\CMake 2.8\bin\cmake.exe" -G "Visual Studio 11 Win64" -DCONSOLE=OFF -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=%PARAVIEW_DIR% -DUSE_PRECOMPILED_HEADERS=ON %DOC_IMAGES% ..\Code\Mantid
+"C:\Program Files (x86)\CMake 2.8\bin\cmake.exe" -G "Visual Studio 11 Win64" -DCONSOLE=OFF -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=%PARAVIEW_DIR% -DUSE_PRECOMPILED_HEADERS=ON ..\Code\Mantid
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -61,7 +58,6 @@ if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 :: Create the install kit if this is a clean build
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 if "%CLEANBUILD%" EQU "yes" (
-    msbuild /nologo /m:%BUILD_THREADS% /nr:false /p:Configuration=Release docs/qtassistant/qtassistant.vcxproj
     if ERRORLEVEL 1 exit /B %ERRORLEVEL%
     cpack -C Release --config CPackConfig.cmake
 )

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

@@ -125,6 +125,9 @@ class MANTID_API_DLL AlgorithmFactoryImpl : public Kernel::DynamicFactory<Algori
   /// Get the algorithm names and version - mangled use decodeName to separate
   const std::vector<std::string> getKeys() const;
   const std::vector<std::string> getKeys(bool includeHidden) const;
+
+  /// Returns the highest version of the algorithm currently registered
+  int highestVersion(const std::string & algorithmName) const;
 
   ///Get the algorithm categories
   const std::set<std::string> getCategories(bool includeHidden=false) const;

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

@@ -73,6 +73,8 @@ namespace API
 
     /// Replaces current parameter map with copy of given map
     void replaceInstrumentParameters(const Geometry::ParameterMap & pmap);
+    /// exchange contents of current parameter map with contents of other map)
+    void swapInstrumentParameters(Geometry::ParameterMap & pmap);
 
     /// Cache a lookup of grouped detIDs to member IDs
     void cacheDetectorGroupings(const det2group_map & mapping);

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

@@ -227,6 +227,21 @@ namespace Mantid
     }
   }
 
+  /**
+   * @param algorithmName The name of an algorithm registered with the factory
+   * @return An integer corresponding to the highest version registered
+   * @throw std::invalid_argument if the algorithm cannot be found
+   */
+  int AlgorithmFactoryImpl::highestVersion(const std::string &algorithmName) const
+  {
+    VersionMap::const_iterator viter = m_vmap.find(algorithmName);
+    if(viter != m_vmap.end()) return viter->second;
+    else
+    {
+      throw std::invalid_argument("AlgorithmFactory::highestVersion() - Unknown algorithm '" + algorithmName + "'");
+    }
+  }
+
 /**
   * Return the categories of the algorithms. This includes those within the Factory itself and 
   * any cleanly constructed algorithms stored here.

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

@@ -1,34 +1,3 @@
-/*WIKI*
-A composite function is a function containing other functions. It combines the values calculated by the member functions by adding them. The members are indexed from 0 to the number of functions minus 1. The indices are defined by the order in which the functions were added. Composite functions do not have their own parameters, instead they use parameters of the member functions. Parameter names are formed from the member function's index and its parameter name: f[index].[name]. For example, name "f0.Sigma" would be given to the "Sigma" parameter of a Gaussian added first to the composite function. If a member function is a composite function itself the same principle applies: 'f[index].' is prepended to a name, e.g. "f0.f1.Sigma".
-
-The input string to the Fit algorithm for a CompositeFunction is constructed by joining the inputs of the member functions using the semicolon ';' as a separator. For example, the string for two [[Gaussian]]s with tied sigma parameters may look like the following:
-
- name=Gaussian,PeakCentre=0,Height=1,Sigma=0.1,constraints=(0<Sigma<1);name=Gaussian,PeakCentre=1,Height=1,Sigma=0.1;ties=(f1.Sigma=f0.Sigma)
-
-Note that the ties clause is also separated by a semicolon. It is done because the parameters are from different functions. Ties between parameters of the same function can be placed inside the member definition in which the local parameter names must be used, for example:
-
- name = FunctionType, P1=0, ties=( P2 = 2*P1 ); name = FunctionType, P1=0, ties=( P2 = 3 )
-
-which is equivalent to
-
- name = FunctionType, P1=0; name = FunctionType, P1=0; ties=( f0.P2 = 2*f0.P1, f1.P2 = 3 )
-
-Boundary constraints usually make sense to put in a local function definition but they can also be moved to the composite function level, i.e. can be separated by ';'. In this case the full parameter name must be used, for example:
-
- name=Gaussian,PeakCentre=0,Height=1,Sigma=0.1;name=Gaussian,PeakCentre=1,Height=1,Sigma=0.1;ties=(f1.Sigma=f0.Sigma);constraints=(0<f0.Sigma<1)
-
-
-Mantid defines a number of fitting functions which extend CompositeFunction. These are functions which also include other functions but use different operations to combine them. Examples are [[ProductFunction]] and [[Convolution]]. Everything said about parameters of the CompositeFunction applies to these functions.
-
-Input strings of an extended composite function must start with "composite=FunctionName;" and followed by the definitions of its members as described for CompositeFunction. For example,
-
- composite=ProductFunction;name=LinearBackground;name=ExpDecay
-
-To define a composite function inside a composite function enclose the inner one in brackets:
-
- name=LinearBackground;(composite=Convolution;name=Resolution;name=Lorentzian)
-
- *WIKI*/
 //----------------------------------------------------------------------
 // Includes
 //----------------------------------------------------------------------

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

@@ -316,6 +316,16 @@ namespace API
   {
     this->m_parmap.reset(new ParameterMap(pmap));
   }
+  //---------------------------------------------------------------------------------------
+  /**
+   * exchanges contents of current parameter map with contents of other map)
+   * @ pmap reference to parameter map which would exchange its contents with current map
+   */
+  void ExperimentInfo::swapInstrumentParameters(Geometry::ParameterMap & pmap)
+  {
+    this->m_parmap->swap(pmap);
+  }
+
 
   //---------------------------------------------------------------------------------------
   /**

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

@@ -106,6 +106,23 @@ class AlgorithmFactoryTest : public CxxTest::TestSuite
     TS_ASSERT_THROWS_NOTHING(keys = AlgorithmFactory::Instance().getKeys());
     TS_ASSERT_EQUALS(noOfAlgs - 1, keys.size());
   }
+
+  void test_HighestVersion()
+  {
+    auto & factory = AlgorithmFactory::Instance();
+
+    TS_ASSERT_THROWS(factory.highestVersion("ToyAlgorithm"), std::invalid_argument);
+
+    AlgorithmFactory::Instance().subscribe<ToyAlgorithm>();
+    TS_ASSERT_EQUALS(1, factory.highestVersion("ToyAlgorithm"));
+
+    Mantid::Kernel::Instantiator<ToyAlgorithmTwo, Algorithm>* newTwo = new Mantid::Kernel::Instantiator<ToyAlgorithmTwo, Algorithm>;
+    AlgorithmFactory::Instance().subscribe(newTwo);
+    TS_ASSERT_EQUALS(2, factory.highestVersion("ToyAlgorithm"));
+
+    AlgorithmFactory::Instance().unsubscribe("ToyAlgorithm",1);
+    AlgorithmFactory::Instance().unsubscribe("ToyAlgorithm",2);
+  }
 
   void testCreate()
   {
@@ -201,4 +218,4 @@ class AlgorithmFactoryTest : public CxxTest::TestSuite
 
 };
 
-#endif
+#endif

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

@@ -234,13 +234,13 @@ class FileFinderTest: public CxxTest::TestSuite
   {
     ConfigService::Instance().setString("default.facility","ISIS");
     std::vector<std::string> files;
-    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189-n15199"), std::invalid_argument);
-    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189n-15199"), std::invalid_argument);
-    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189-15199n"), std::invalid_argument);
-    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189-151n99"), std::invalid_argument);
-    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15n189-151n99"), Exception::NotFoundError);
-    TS_ASSERT_THROWS_NOTHING(files = FileFinder::Instance().findRuns("MUSR15189-15199"));
-    TS_ASSERT_EQUALS(files.size(), 11);
+    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189-n15193"), std::invalid_argument);
+    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189n-15193"), std::invalid_argument);
+    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189-15193n"), std::invalid_argument);
+    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15189-151n93"), std::invalid_argument);
+    TS_ASSERT_THROWS(files = FileFinder::Instance().findRuns("MUSR15n189-151n93"), Exception::NotFoundError);
+    TS_ASSERT_THROWS_NOTHING(files = FileFinder::Instance().findRuns("MUSR15189-15193"));
+    TS_ASSERT_EQUALS(files.size(), 5);
     std::vector<std::string>::iterator it = files.begin();
 
     for (; it != files.end(); ++it)

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

@@ -91,8 +91,8 @@ namespace Algorithms
     void processSingleValueFilter(double minvalue, double maxvalue,
         bool filterincrease, bool filterdecrease);
 
-    void processMultipleValueFilters(double minvalue, double maxvalue,
-        bool filterincrease, bool filterdecrease);
+    void processMultipleValueFilters(double minvalue, double valueinterval, double maxvalue,
+                                     bool filterincrease, bool filterdecrease);
 
     void makeFilterByValue(Kernel::TimeSplitterType& split, double min, double max, double TimeTolerance, bool centre,
         bool filterIncrease, bool filterDecrease, Kernel::DateAndTime startTime, Kernel::DateAndTime stopTime,

Code/Mantid/Framework/Algorithms/src/AbsorptionCorrection.cpp

@@ -1,24 +1,3 @@
-/*WIKI* 
-This algorithm uses a numerical integration method to calculate attenuation factors resulting from absorption and single scattering in a sample with the material properties given. Factors are calculated for each spectrum (i.e. detector position) and wavelength point, as defined by the input workspace. 
-The sample is first bounded by a cuboid, which is divided up into small cubes. The cubes whose centres lie within the sample make up the set of integration elements (so you have a kind of 'Lego' model of the sample) and path lengths through the sample are calculated for the centre-point of each element, and a numerical integration is carried out using these path lengths over the volume elements.
-
-Note that the duration of this algorithm is strongly dependent on the element size chosen, and that too small an element size can cause the algorithm to fail because of insufficient memory.
-
-Note that The number density of the sample is in <math> \mathrm{\AA}^{-3} </math>
-
-== Choosing an absorption correction algorithm ==
-
-This flow chart is given as a way of selecting the most appropriate of the absorption correction algorithms. It also shows the algorithms that must be run first in each case. Note that this does not cover the following absorption correction algorithms: [[MonteCarloAbsorption]] (correction factors for a generic sample using a Monte Carlo instead of a numerical integration method), [[MultipleScatteringCylinderAbsorption]] & [[AnvredCorrection]] (corrections in a spherical sample, using a method imported from ISAW). Also, HRPD users can use the [[HRPDSlabCanAbsorption]] to add rudimentary calculations of the effects of the sample holder.
-[[File:AbsorptionFlow.png]]
-
-
-==== Assumptions ====
-This algorithm assumes that the (parallel) beam illuminates the entire sample '''unless''' a 'gauge volume' has been defined using the [[DefineGaugeVolume]] algorithm (or by otherwise adding a valid XML string [[HowToDefineGeometricShape | defining a shape]] to a [[Run]] property called "GaugeVolume"). In this latter case only scattering within this volume (and the sample) is integrated, because this is all the detector can 'see'. The full sample is still used for the neutron paths. ('''N.B.''' If your gauge volume is of axis-aligned cuboid shape and fully enclosed by the sample then you will get a more accurate result from the [[CuboidGaugeVolumeAbsorption]] algorithm.)
-
-==== Restrictions on the input workspace ====
-The input workspace must have units of wavelength. The [[instrument]] associated with the workspace must be fully defined because detector, source & sample position are needed.
-
-*WIKI*/
 //----------------------------------------------------------------------
 // Includes
 //----------------------------------------------------------------------

Code/Mantid/Framework/Algorithms/src/AddLogDerivative.cpp

@@ -1,17 +1,3 @@
-/*WIKI* 
-
-This algorithm performs a simple numerical derivative of the values in a sample log.
-
-The 1st order derivative is simply: dy = (y1-y0) / (t1-t0), which is placed in the log at t=(t0+t1)/2
-
-Higher order derivatives are obtained by performing the equation above N times.
-Since this is a simple numerical derivative, you can expect the result to quickly
-get noisy at higher derivatives.
-
-If any of the times in the logs are repeated, then those repeated time values will be skipped,
-and the output derivative log will have fewer points than the input.
-
-*WIKI*/
 #include "MantidAlgorithms/AddLogDerivative.h"
 #include "MantidKernel/System.h"
 #include "MantidKernel/TimeSeriesProperty.h"
@@ -163,4 +149,3 @@ namespace Algorithms
 
 } // namespace Mantid
 } // namespace Algorithms
-

Code/Mantid/Framework/Algorithms/src/AddPeak.cpp

@@ -1,9 +1,3 @@
-/*WIKI* 
-
-Adds a [[IPeak]] to a [[PeaksWorkspace]].
-
-*WIKI*/
-
 #include "MantidAlgorithms/AddPeak.h"
 #include "MantidKernel/System.h"
 #include "MantidAPI/IPeaksWorkspace.h"
@@ -148,4 +142,3 @@ namespace Algorithms
 
 } // namespace Mantid
 } // namespace Algorithms
-

Code/Mantid/Framework/Algorithms/src/AddSampleLog.cpp

@@ -1,10 +1,3 @@
-/*WIKI* 
-Workspaces contain information in logs. Often these detail what happened to the sample during the experiment. This algorithm allows one named log to be entered. 
-
-The log can be either a String, a Number, or a Number Series. If you select Number Series, the workspace start time will be used as the time of the log entry, and the number in the text used as the (only) value.
-
-If the LogText contains a numeric value, the created log will be of integer type if an integer is passed and floating point (double) otherwise. This applies to both the Number & Number Series options.
-*WIKI*/
 //----------------------------------------------------------------------
 // Includes
 //----------------------------------------------------------------------

Code/Mantid/Framework/Algorithms/src/AddTimeSeriesLog.cpp

@@ -1,23 +1,3 @@
-/*WIKI*
-Creates/updates a time-series log entry on a chosen workspace. The given timestamp & value are appended to the
-named log entry. If the named entry does not exist then a new log is created. A time stamp must be given in
-ISO8601 format, e.g. 2010-09-14T04:20:12.
-
-By default, the given value is interpreted as a double and a double series is either created or expected. However,
-if the "Type" is set to "int" then the value is interpreted as an integer and an integer is either created
-or expected.
-*WIKI*/
-/*WIKI_USAGE*
-'''Python'''
- import datetime as dt
-
- # Add an entry for the current time
- log_name = "temperature"
- log_value = 21.5
- AddTimeSeriesLog(inOutWS, Name=log_name, Time=dt.datetime.utcnow().isoformat(), Value=log_value)
-
-*WIKI_USAGE*/
-
 #include "MantidAlgorithms/AddTimeSeriesLog.h"
 #include "MantidKernel/DateTimeValidator.h"
 #include "MantidKernel/MandatoryValidator.h"

Code/Mantid/Framework/Algorithms/src/AlignDetectors.cpp

@@ -1,19 +1,3 @@
-/*WIKI* 
-
-
-The offsets are a correction to the dSpacing values and are applied during the conversion from time-of-flight to dSpacing as follows:
-
-:<math> d = \frac{h}{2m_N} \frac{t.o.f.}{L_{tot} sin \theta} (1+ \rm{offset})</math>
-
-The detector offsets can be obtained from either: an [[OffsetsWorkspace]] where each pixel has one value, the offset; or a .cal file (in the form created by the ARIEL software). 
-
-'''Note:''' the workspace that this algorithms outputs is a [[Ragged Workspace]].
-
-==== Restrictions on the input workspace ====
-The input workspace must contain histogram or event data where the X unit is time-of-flight and the Y data is raw counts. The [[instrument]] associated with the workspace must be fully defined because detector, source & sample position are needed.
-
-
-*WIKI*/
 //----------------------------------------------------------------------
 // Includes
 //----------------------------------------------------------------------

Code/Mantid/Framework/Algorithms/src/AlphaCalc.cpp

@@ -1,12 +1,3 @@
-/*WIKI* 
-
-
-Returns the relative efficiency of the forward detector group compared to the backward detector group. If Alpha is larger than 1 more counts has been collected in the forward group.
-
-This algorithm leave the input workspace unchanged. To group detectors in a workspace use [[GroupDetectors]].
-
-
-*WIKI*/
 //----------------------------------------------------------------------
 // Includes
 //----------------------------------------------------------------------
@@ -156,5 +147,3 @@ void AlphaCalc::exec()
 
 } // namespace Algorithm
 } // namespace Mantid
-
-

Code/Mantid/Framework/Algorithms/src/AppendSpectra.cpp

@@ -1,38 +1,3 @@
-/*WIKI*
-
-This algorithm appends the spectra of two workspaces together.
-
-The output workspace from this algorithm will be a copy of the first
-input workspace, to which the data from the second input workspace
-will be appended.
-
-Workspace data members other than the data (e.g. instrument etc.) will be copied
-from the first input workspace (but if they're not identical anyway,
-then you probably shouldn't be using this algorithm!).
-
-==== Restrictions on the input workspace ====
-
-For [[EventWorkspace]]s, there are no restrictions on the input workspaces if ValidateInputs=false.
-
-For [[Workspace2D]]s, the number of bins must be the same in both inputs.
-
-If ValidateInputs is selected, then the input workspaces must also:
-* Come from the same instrument
-* Have common units
-* Have common bin boundaries
-
-==== Spectrum Numbers ====
-
-If there is an overlap in the spectrum numbers of both inputs, then the output
-workspace will have its spectrum numbers reset starting at 0 and increasing by
-1 for each spectrum.
-
-==== See Also ====
-
-* [[ConjoinWorkspaces]] for joining parts of the same workspace.
-
-*WIKI*/
-
 #include "MantidAlgorithms/AppendSpectra.h"
 #include "MantidKernel/System.h"
 #include "MantidAPI/WorkspaceValidators.h"