Re #11063 Where these conflicts on master have came from?

Merge branch 'master' into 11063_ParValidation

Conflicts:
	Code/Mantid/scripts/Inelastic/Direct/DirectEnergyConversion.py
	Code/Mantid/scripts/Inelastic/Direct/PropertiesDescriptors.py
	Code/Mantid/scripts/Inelastic/Direct/PropertyManager.py
	Code/Mantid/scripts/Inelastic/Direct/ReductionWrapper.py
	Code/Mantid/scripts/Inelastic/Direct/RunDescriptor.py

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -131,20 +131,30 @@ else()
  set ( CMAKE_OSX_ARCHITECTURES x86_64 )
  set ( CMAKE_OSX_DEPLOYMENT_TARGET 10.8 )
  # Follow symlinks so cmake copies the file
- set ( PYQT4_PATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
+ # PYQT4_PATH, SITEPACKAGES_PATH, OPENSSL_ROOT_DIR may be defined externally (cmake -D)
+ # it would be good do not overwrite them (important for the compilation with macports)
+ if (NOT PYQT4_PATH)
+  set ( PYQT4_PATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
+ endif(NOT PYQT4_PATH)
  execute_process(COMMAND readlink ${PYQT4_PATH}/Qt.so OUTPUT_VARIABLE PYQT4_SYMLINK_Qtso)
- string(FIND ${PYQT4_SYMLINK_Qtso} "Qt.so" STOPPOS)
- string(SUBSTRING ${PYQT4_SYMLINK_Qtso} 0 ${STOPPOS} PYQT4_SYMLINK)
+ string(FIND "${PYQT4_SYMLINK_Qtso}" "Qt.so" STOPPOS)
+ string(SUBSTRING "${PYQT4_SYMLINK_Qtso}" 0 ${STOPPOS} PYQT4_SYMLINK)
  set  ( PYQT4_PYTHONPATH ${PYQT4_PATH}/${PYQT4_SYMLINK} )
+ string(REGEX REPLACE "/$" "" PYQT4_PYTHONPATH "${PYQT4_PYTHONPATH}")
 
- set ( SITEPACKAGES_PATH /usr/local/lib/python${PY_VER}/site-packages )
+ if (NOT SITEPACKAGES_PATH)
+   set ( SITEPACKAGES_PATH /usr/local/lib/python${PY_VER}/site-packages )
+ endif(NOT SITEPACKAGES_PATH)
  execute_process(COMMAND readlink ${SITEPACKAGES_PATH}/sip.so OUTPUT_VARIABLE SITEPACKAGES_SYMLINK_sipso)
- string(FIND ${SITEPACKAGES_SYMLINK_sipso} "sip.so" STOPPOS)
- string(SUBSTRING ${SITEPACKAGES_SYMLINK_sipso} 0 ${STOPPOS} SITEPACKAGES_SYMLINK)
+ string(FIND "${SITEPACKAGES_SYMLINK_sipso}" "sip.so" STOPPOS)
+ string(SUBSTRING "${SITEPACKAGES_SYMLINK_sipso}" 0 ${STOPPOS} SITEPACKAGES_SYMLINK)
  set  ( SITEPACKAGES ${SITEPACKAGES_PATH}/${SITEPACKAGES_SYMLINK} )
+ string(REGEX REPLACE "/$" "" SITEPACKAGES "${SITEPACKAGES}")
 
  # use homebrew OpenSSL package
- set ( OPENSSL_ROOT_DIR /usr/local/opt/openssl )
+ if (NOT OPENSSL_ROOT_DIR)
+   set ( OPENSSL_ROOT_DIR /usr/local/opt/openssl )
+ endif(NOT OPENSSL_ROOT_DIR)
 endif()
 
 # Python packages

Code/Mantid/Build/CMake/FindOpenCascade.cmake

@@ -60,7 +60,7 @@ find_library ( OPENCASCADE_LIB_TKGEOMBASE
                  NAMES TKGeomBase
 )
 
-find_library ( OPENCASCADE_LIB_TKGEOMAlgo
+find_library ( OPENCASCADE_LIB_TKGEOMALGO
                  NAMES TKGeomAlgo
 )
 

Code/Mantid/Build/CMake/LinuxPackageScripts.cmake

@@ -22,6 +22,10 @@ endif()
 
 set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PREFIX}/${PLUGINS_DIR};${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR} )
 
+# Tell rpm that this package does not own /opt /usr/share/{applications,pixmaps}
+# Required for Fedora >= 18 and RHEL >= 7
+set ( CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION /opt /usr/share/applications /usr/share/pixmaps )
+
 ###########################################################################
 # LD_PRELOAD TCMalloc
 ###########################################################################

Code/Mantid/Build/Jenkins/buildscript

@@ -15,7 +15,17 @@
 cmake --version
 echo "SHA1=${sha1}"
 
+
+#determine if should use the clang compiler.
 if [[ ${JOB_NAME} == *clang* ]]; then
+  USE_CLANG=true
+elif [[ $(uname) == 'Darwin' ]] ; then
+  if [[ ! $(command -v icpc) ]] ; then
+    USE_CLANG=true
+  fi
+fi  
+
+if [[ $USE_CLANG ]]; then
   # Assuming we are using the clang compiler
   echo "Using clang/llvm compiler."
   clang --version
@@ -35,7 +45,7 @@ fi
 ###############################################################################
 # OS X 10.8 setup steps
 ###############################################################################
-if [[ $(uname) == 'Darwin' ]] && [[ ${JOB_NAME} != *clang* ]]; then
+if [[ $(uname) == 'Darwin' ]] && [[ ! $USE_CLANG ]]; then
   # Assuming we are using the Intel compiler
   cd $WORKSPACE/Code
   ./fetch_Third_Party.sh

Code/Mantid/Build/Jenkins/jenkins-slave.sh

@@ -0,0 +1,84 @@
+#!/bin/sh
+#####################################################################
+# Starts the Jenkins slave process if it is not already running.
+# It also downloads the slave.jar to /tmp if it does not already
+# exist.
+#
+# The settings at the top must be filled in for each slave.
+#####################################################################
+# Crontab setting should be something like
+# 0,30 * * * * /home/builder/jenkins-linode/jenkins-slave.sh nodename secret
+# or (on mac)
+# 0,30 * * * * /Users/builder/jenkins-linode/jenkins-slave.sh nodename secret
+#####################################################################
+# User configuration
+#####################################################################
+# Main url for Jenkins
+JENKINS_URL=http://builds.mantidproject.org
+# URL for proxy (if required)
+PROXY_HOST=${3}
+# Port for proxy (if required)
+PROXY_PORT=${4}
+# Name of the node as it appears on jenkins
+NODE_NAME=${1}
+# Copy the secret from the command line given at the above URL
+SECRET=${2}
+
+#####################################################################
+# Constants
+#####################################################################
+# URL of jnlp file for slave
+SLAVE_AGENT_URL="${JENKINS_URL}/computer/${NODE_NAME}/slave-agent.jnlp"
+# name of the slave jar - full path is determined later
+JAR_FILE=slave.jar
+
+#####################################################################
+# Script
+#####################################################################
+# exit if it is already running
+RUNNING=$(ps aux | grep java | grep ${JAR_FILE})
+if [ ! -z "${RUNNING}" ]; then
+  echo "Slave process is already running"
+  exit 0
+else
+  echo "Slave process is not running"
+fi
+
+# error out if there isn't a node name and secret
+if [ "$#" -lt 2 ]; then
+  echo "Usage: `basename ${0}` <NODE_NAME> <SECRET> [PROXY_HOST] [PROXY_PORT]"
+  exit -1
+fi
+
+# setup the proxy
+if [ ! -z "${PROXY_HOST}" ]; then
+  PROXY_ARGS="-Dhttp.proxyHost=${PROXY_HOST} -Dhttp.proxyPort=${PROXY_PORT}"
+  echo "using proxy ${PROXY_HOST} ${PROXY_PORT}"
+  # For curl
+  export http_proxy=http://$PROXY_HOST:$PROXY_PORT
+fi
+
+# find the jar file if it exists
+if [ -f ${HOME}/jenkins-linode/${JAR_FILE} ]; then
+  JAR_FILE=${HOME}/jenkins-linode/${JAR_FILE}
+elif [ -f ${HOME}/Jenkins/${JAR_FILE} ]; then
+  JAR_FILE=${HOME}/Jenkins/${JAR_FILE}
+else
+  JAR_FILE=/tmp/${JAR_FILE}
+  if [ ! -f ${JAR_FILE} ]; then
+    echo "Downloading slave jar file to ${JAR_FILE}"
+    if [ $(command -v curl) ]; then
+      echo "curl -o ${JAR_FILE} ${JENKINS_URL}/jnlpJars/slave.jar"
+      curl -o ${JAR_FILE} ${JENKINS_URL}/jnlpJars/slave.jar
+    else
+      echo "Need curl to download ${JENKINS_URL}/jnlpJars/slave.jar"
+      exit -1
+    fi
+  fi
+fi
+
+echo "starting ..."
+JAVA=`which java`
+JAVA_ARGS="${PROXY_ARGS} -jar ${JAR_FILE} -jnlpUrl ${SLAVE_AGENT_URL} -secret ${SECRET}"
+echo "${JAVA} ${JAVA_ARGS}"
+${JAVA} ${JAVA_ARGS}

Code/Mantid/Build/dev-packages/deb/mantid-developer/README

@@ -2,5 +2,5 @@ This directory contains the structure required to build the simple mantid-develo
 
 To build the package:
    * Switch to the directory containing this file
-   * Run "dpkg --build mantid-developer-1.2.3"
-   * A file called mantid-developer-1.2.3.deb will appear in the current directory.
+   * Run "dpkg --build mantid-developer-1.2.4"
+   * A file called mantid-developer-1.2.4.deb will appear in the current directory.

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.3/DEBIAN/control

@@ -3,7 +3,7 @@ Version: 1.2.3
 Section: main
 Priority: optional
 Architecture: all
-Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil
+Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive, texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme
 Installed-Size: 0
 Maintainer: Mantid Project <mantid-help@mantidproject.org>
 Description: Installs all packages required for a Mantid developer

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.4/DEBIAN/control

@@ -0,0 +1,13 @@
+Package: mantid-developer
+Version: 1.2.4
+Section: main
+Priority: optional
+Architecture: all
+Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme, graphviz
+Installed-Size: 0
+Maintainer: Mantid Project <mantid-help@mantidproject.org>
+Description: Installs all packages required for a Mantid developer
+ A metapackage which requires all the dependencies and tools that are 
+ required for Mantid development. It works for Ubuntu version 14.04, 14.10
+ Some packages (poco) must be newer than those in the Ubuntu repository. Please 
+ follow instructions at http://www.mantidproject.org/Mantid_Prerequisites#Repositories

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

@@ -1,5 +1,5 @@
 Name:           mantid-developer
-Version:        1.7
+Version:        1.9
 Release:        1%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
@@ -64,6 +64,7 @@ Requires: scl-utils
 Requires: qt-devel
 Requires: qtwebkit-devel
 %endif
+Requires: graphviz
 
 BuildArch: noarch
 
@@ -86,6 +87,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Thu Feb 12 2015 Harry Jeffery <henry.jeffery@stfc.ac.uk>
+- Added graphviz dependency
+
 * Wed Aug 13 2014 Peter Peterson <petersonpf@ornl.gov>
 - Merged all three distribution spec files into one
 

Code/Mantid/Framework/API/CMakeLists.txt

@@ -93,6 +93,7 @@ set ( SRC_FILES
 	src/ParamFunction.cpp
 	src/ParameterReference.cpp
 	src/ParameterTie.cpp
+        src/PeakFunctionIntegrator.cpp
 	src/PeakTransform.cpp
 	src/PeakTransformHKL.cpp
 	src/PeakTransformQLab.cpp
@@ -252,6 +253,7 @@ set ( INC_FILES
 	inc/MantidAPI/ParamFunction.h
 	inc/MantidAPI/ParameterReference.h
 	inc/MantidAPI/ParameterTie.h
+        inc/MantidAPI/PeakFunctionIntegrator.h
 	inc/MantidAPI/PeakTransform.h
 	inc/MantidAPI/PeakTransformFactory.h
 	inc/MantidAPI/PeakTransformHKL.h
@@ -348,6 +350,7 @@ set ( TEST_FILES
 	ParamFunctionAttributeHolderTest.h
 	ParameterReferenceTest.h
 	ParameterTieTest.h
+        PeakFunctionIntegratorTest.h
 	PeakTransformHKLTest.h
 	PeakTransformQLabTest.h
 	PeakTransformQSampleTest.h

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

@@ -7,6 +7,7 @@
 #include "MantidKernel/Matrix.h"
 #include "MantidKernel/V3D.h"
 #include "MantidKernel/PhysicalConstants.h"
+#include <boost/optional.hpp>
 
 namespace Mantid {
 namespace API {
@@ -50,9 +51,9 @@ class MANTID_API_DLL IPeak {
   virtual bool findDetector() = 0;
 
   virtual void setQSampleFrame(Mantid::Kernel::V3D QSampleFrame,
-                               double detectorDistance = 1.0) = 0;
+                               boost::optional<double> detectorDistance) = 0;
   virtual void setQLabFrame(Mantid::Kernel::V3D QLabFrame,
-                            double detectorDistance = 1.0) = 0;
+                            boost::optional<double> detectorDistance) = 0;
 
   virtual void setWavelength(double wavelength) = 0;
   virtual double getWavelength() const = 0;

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

@@ -49,6 +49,12 @@ class MANTID_API_DLL IPeakFunction : public IFunctionWithLocation {
   /// Sets the parameters such that FWHM = w
   virtual void setFwhm(const double w) = 0;
 
+  /// Returns the integral intensity of the peak
+  virtual double intensity() const;
+
+  /// Sets the integral intensity of the peak
+  virtual void setIntensity(const double newIntensity);
+
   /// General implementation of the method for all peaks.
   void function1D(double *out, const double *xValues, const size_t nData) const;
   /// General implementation of the method for all peaks.

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

@@ -7,6 +7,7 @@
 #include "MantidAPI/ITableWorkspace.h"
 #include "MantidAPI/ExperimentInfo.h"
 #include "MantidKernel/SpecialCoordinateSystem.h"
+#include <boost/optional.hpp>
 
 namespace Mantid {
 
@@ -98,12 +99,20 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
 
   //---------------------------------------------------------------------------------------------
   /** Create an instance of a Peak
-   * @param QLabFrame :: Q of the center of the peak, in reciprocal space
-   * @param detectorDistance :: distance between the sample and the detector.
+   * @param QLabFrame :: Q of the center of the peak in the lab frame, in reciprocal space
+   * @param detectorDistance :: Optional distance between the sample and the detector. Calculated if not provided.
    * @return a pointer to a new Peak object.
    */
   virtual IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
-                            double detectorDistance = 1.0) const = 0;
+                            boost::optional<double> detectorDistance) const = 0;
+
+
+  /**
+   * Create an instance of a peak using a V3D
+   * @param HKL V3D
+   * @return a pointer to a new Peak object.
+   */
+  virtual IPeak *createPeakHKL(Mantid::Kernel::V3D HKL) const = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Determine if the workspace has been integrated using a peaks integration

Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PeakFunctionIntegrator.h → Code/Mantid/Framework/API/inc/MantidAPI/PeakFunctionIntegrator.h

@@ -1,22 +1,25 @@
 #ifndef PEAKFUNCTIONINTEGRATOR_H
 #define PEAKFUNCTIONINTEGRATOR_H
 
-#include "MantidSINQ/DllConfig.h"
+#include "MantidAPI/DllConfig.h"
 #include "MantidAPI/IPeakFunction.h"
 #include "gsl/gsl_integration.h"
 
 namespace Mantid {
-namespace Poldi {
+namespace API {
 
 /** PeakFunctionIntegrator :
  *
   General integration of peaks (in the form of IPeakFunction) by wrapping the
   corresponding GSL-functions. Integration with infinity limits is supported.
 
+  PeakFunctionIntegrator allocates a GSL integration workspace on construction
+  and frees the memory when it's destroyed.
+
     @author Michael Wedel, Paul Scherrer Institut - SINQ
     @date 24/04/2014
 
-    Copyright © 2014 PSI-MSS
+    Copyright © 2014,2015 PSI-MSS
 
   This file is part of Mantid.
 
@@ -37,7 +40,7 @@ namespace Poldi {
   Code Documentation is available at: <http://doxygen.mantidproject.org>
 */
 
-struct MANTID_SINQ_DLL IntegrationResult {
+struct MANTID_API_DLL IntegrationResult {
   double result;
   double error;
   size_t intervals;
@@ -46,7 +49,7 @@ struct MANTID_SINQ_DLL IntegrationResult {
   bool success;
 };
 
-class MANTID_SINQ_DLL PeakFunctionIntegrator {
+class MANTID_API_DLL PeakFunctionIntegrator {
 public:
   PeakFunctionIntegrator(double requiredRelativePrecision = 1e-8);
   virtual ~PeakFunctionIntegrator();
@@ -55,27 +58,26 @@ class MANTID_SINQ_DLL PeakFunctionIntegrator {
   double requiredRelativePrecision() const;
 
   IntegrationResult
-  integrateInfinity(API::IPeakFunction_const_sptr peakFunction) const;
+  integrateInfinity(const IPeakFunction &peakFunction) const;
   IntegrationResult
-  integratePositiveInfinity(API::IPeakFunction_const_sptr peakFunction,
+  integratePositiveInfinity(const IPeakFunction &peakFunction,
                             double lowerLimit) const;
   IntegrationResult
-  integrateNegativeInfinity(API::IPeakFunction_const_sptr peakFunction,
+  integrateNegativeInfinity(const IPeakFunction &peakFunction,
                             double upperLimit) const;
 
-  IntegrationResult integrate(API::IPeakFunction_const_sptr peakFunction,
+  IntegrationResult integrate(const IPeakFunction &peakFunction,
                               double lowerLimit, double upperLimit) const;
 
 protected:
-  gsl_function getGSLFunction(API::IPeakFunction_const_sptr peakFunction) const;
-  void throwIfInvalid(API::IPeakFunction_const_sptr peakFunction) const;
+  gsl_function getGSLFunction(const IPeakFunction &peakFunction) const;
 
   gsl_integration_workspace *m_integrationWorkspace;
 
   double m_relativePrecision;
 };
 
-double MANTID_SINQ_DLL gsl_peak_wrapper(double x, void *parameters);
+double MANTID_API_DLL gsl_peak_wrapper(double x, void *parameters);
 }
 }