Merge branch 'master' into feature/10513_calibration_show_pre_post_sm…

…ooth

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectCalibration.cpp

Refs #10513

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -301,6 +301,35 @@ else()
   message ( STATUS "Could not find Squish - GUI testing not available. Try specifying your SQUISH_INSTALL_DIR cmake variable." )
 endif()
 
+###########################################################################
+# External Data for testing
+###########################################################################
+if ( CXXTEST_FOUND OR PYUNITTEST_FOUND )
+ include ( MantidExternalData )
+
+# None of our tests reference files directly as arguments so we have to manually
+# call ExternalData_Expand_Arguments to register the files with the ExternalData
+# mechanism
+get_filename_component ( EXTERNALDATATEST_SOURCE_DIR ${PROJECT_SOURCE_DIR} ABSOLUTE )
+file( GLOB_RECURSE doctest_content_links
+  RELATIVE "${EXTERNALDATATEST_SOURCE_DIR}" "Testing/Data/DocTest/*.md5" )
+file( GLOB_RECURSE unittest_content_links
+  RELATIVE "${EXTERNALDATATEST_SOURCE_DIR}" "Testing/Data/UnitTest/*.md5" )
+set ( content_links "${doctest_content_links};${unittest_content_links}" )
+foreach(link ${content_links})
+  string( REGEX REPLACE "\\.md5$" "" link ${link} )
+  ExternalData_Expand_Arguments( StandardTestData
+    link_location
+    DATA{${link}}
+    )
+endforeach()
+
+# Create target to download data from the StandardTestData group.  This must come after
+# all tests have been added that reference the group, so we put it last.
+ExternalData_Add_Target(StandardTestData)
+set_target_properties(StandardTestData PROPERTIES EXCLUDE_FROM_ALL TRUE)
+endif()
+
 ###########################################################################
 # Set a flag to indicate that this script has been called
 ###########################################################################

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -102,6 +102,7 @@ endif()
 ###########################################################################
 # Mac-specific installation setup
 ###########################################################################
+
 set ( CMAKE_INSTALL_PREFIX "" )
 set ( CPACK_PACKAGE_EXECUTABLES MantidPlot )
 set ( INBUNDLE MantidPlot.app/ )
@@ -119,27 +120,50 @@ set ( PVPLUGINS_DIR MantidPlot.app/pvplugins )
 set ( PVPLUGINS_SUBDIR pvplugins ) # Need to tidy these things up!
 
 if (OSX_VERSION VERSION_LESS 10.9)
+ set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PREFIX}/${PLUGINS_DIR};${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR} )
  set ( PYQT4_PYTHONPATH /Library/Python/${PY_VER}/site-packages/PyQt4 )
  set ( SITEPACKAGES /Library/Python/${PY_VER}/site-packages )
 else()
+ set(CMAKE_MACOSX_RPATH 1)
  # Assume we are using homebrew for now
  # set Deployment target to 10.8
  set ( CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk )
  set ( CMAKE_OSX_ARCHITECTURES x86_64 )
  set ( CMAKE_OSX_DEPLOYMENT_TARGET 10.8 )
- set ( PYQT4_PYTHONPATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
- set ( SITEPACKAGES /usr/local/lib/python${PY_VER}/site-packages )
+ # Follow symlinks so cmake copies the file
+ # 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)
+ set  ( PYQT4_PYTHONPATH ${PYQT4_PATH}/${PYQT4_SYMLINK} )
+ string(REGEX REPLACE "/$" "" PYQT4_PYTHONPATH "${PYQT4_PYTHONPATH}")
+
+ 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)
+ 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
 
 install ( PROGRAMS ${SITEPACKAGES}/sip.so DESTINATION ${BIN_DIR} )
 
 # Explicitly specify which PyQt libraries we want because just taking the whole
-# directory will swell the install kit unnecessarily.
-install ( FILES ${PYQT4_PYTHONPATH}/Qt.so
+#directory will swell the install kit unnecessarily.
+ install ( FILES ${PYQT4_PYTHONPATH}/Qt.so
                 ${PYQT4_PYTHONPATH}/QtCore.so
                 ${PYQT4_PYTHONPATH}/QtGui.so
                 ${PYQT4_PYTHONPATH}/QtOpenGL.so
@@ -156,16 +180,19 @@ endif ()
 
 install ( DIRECTORY ${PYQT4_PYTHONPATH}/uic DESTINATION ${BIN_DIR}/PyQt4 )
 
-# Python packages in Third_Party need copying to build directory and the final package
-file ( GLOB THIRDPARTY_PYTHON_PACKAGES ${CMAKE_LIBRARY_PATH}/Python/* )
-foreach ( PYPACKAGE ${THIRDPARTY_PYTHON_PACKAGES} )
-  if ( IS_DIRECTORY ${PYPACKAGE} )
-    install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} USE_SOURCE_PERMISSIONS )
-  else()
-    install ( FILES ${PYPACKAGE} DESTINATION ${BIN_DIR} )
-  endif()
-  file ( COPY ${PYPACKAGE} DESTINATION ${PROJECT_BINARY_DIR}/bin )
-endforeach( PYPACKAGE )
+# done as part of packaging step in 10.9+ builds.
+if (OSX_VERSION VERSION_LESS 10.9)
+  # Python packages in Third_Party need copying to build directory and the final package
+  file ( GLOB THIRDPARTY_PYTHON_PACKAGES ${CMAKE_LIBRARY_PATH}/Python/* )
+  foreach ( PYPACKAGE ${THIRDPARTY_PYTHON_PACKAGES} )
+    if ( IS_DIRECTORY ${PYPACKAGE} )
+      install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} USE_SOURCE_PERMISSIONS )
+    else()
+      install ( FILES ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+    endif()
+    file ( COPY ${PYPACKAGE} DESTINATION ${PROJECT_BINARY_DIR}/bin )
+  endforeach( PYPACKAGE )
+endif ()
 
 install ( DIRECTORY ${QT_PLUGINS_DIR}/imageformats DESTINATION MantidPlot.app/Contents/Frameworks/plugins )
 install ( DIRECTORY ${QT_PLUGINS_DIR}/sqldrivers DESTINATION MantidPlot.app/Contents/Frameworks/plugins )

Code/Mantid/Build/CMake/MantidExternalData.cmake

@@ -0,0 +1,38 @@
+################################################################################
+# Setup the ExternalData variables for the project
+################################################################################
+include(ExternalData)
+
+if(NOT MANTID_DATA_STORE)
+  # Select a default in the home directory
+  set(MANTID_DATA_STORE_DEFAULT "$ENV{HOME}/MantidExternalData")
+endif()
+
+# Provide users with an option to select a local object store,
+# starting with the above-selected default.
+set(MANTID_DATA_STORE "${MANTID_DATA_STORE_DEFAULT}" CACHE PATH
+  "Local directory holding ExternalData objects in the layout %(algo)/%(hash).")
+mark_as_advanced(MANTID_DATA_STORE)
+
+if(NOT MANTID_DATA_STORE)
+  message(FATAL_ERROR "MANTID_DATA_STORE not set. It is required for external data")
+endif()
+
+# Tell ExternalData module about selected object stores.
+list(APPEND ExternalData_OBJECT_STORES
+  # Store selected by Mantid-specific configuration above.
+  ${MANTID_DATA_STORE}
+)
+
+# Default binary root to build directory
+set(ExternalData_BINARY_ROOT ${CMAKE_BINARY_DIR}/ExternalData CACHE STRING
+  "A directory holding the links (copies on windows) to the real content files.")
+
+set(ExternalData_URL_TEMPLATES "" CACHE STRING
+  "Additional URL templates for the ExternalData CMake script to look for testing data. E.g.
+file:///var/bigharddrive/%(algo)/%(hash)")
+mark_as_advanced(ExternalData_URL_TEMPLATES)
+list(APPEND ExternalData_URL_TEMPLATES
+  "http://198.74.56.37/ftp/external-data/%(algo)/%(hash)"
+)
+

Code/Mantid/Build/Jenkins/buildscript

@@ -50,6 +50,16 @@ if [[ $(uname) == 'Darwin' ]] && [[ ${JOB_NAME} != *clang* ]]; then
   icpc --version
 fi
 
+###############################################################################
+# 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.
+###############################################################################
+if [ -z "$MANTID_DATA_STORE" ]; then
+  export MANTID_DATA_STORE=$(dirname $WORKSPACE)
+fi
+
 ###############################################################################
 # Check whether this is a clean build (must have 'clean' in the job name)
 ###############################################################################
@@ -104,7 +114,7 @@ fi
 ###############################################################################
 # CMake configuration
 ###############################################################################
-$SCL_ON_RHEL6 "cmake -DCMAKE_BUILD_TYPE=${BUILD_CONFIG} -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=${PARAVIEW_DIR} -DDOCS_HTML=ON ${PACKAGINGVARS} ../Code/Mantid"
+$SCL_ON_RHEL6 "cmake -DCMAKE_BUILD_TYPE=${BUILD_CONFIG} -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=${PARAVIEW_DIR} -DMANTID_DATA_STORE=${MANTID_DATA_STORE} -DDOCS_HTML=ON ${PACKAGINGVARS} ../Code/Mantid"
 
 ###############################################################################
 # Coverity build should exit early

Code/Mantid/Build/Jenkins/buildscript.bat

@@ -32,6 +32,16 @@ cd %WORKSPACE%
 
 set PATH=%WORKSPACE%\Code\Third_Party\lib\win64;%WORKSPACE%\Code\Third_Party\lib\win64\Python27;%PARAVIEW_DIR%\bin\%BUILD_CONFIG%;%PATH%
 
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: Set up the location for 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.
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+if NOT DEFINED MANTID_DATA_STORE (
+  for %%F in ("%WORKSPACE%") do set MANTID_DATA_STORE=%%~dpF
+)
+
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Check whether this is a clean build (must have 'clean' in the job name)
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -53,7 +63,7 @@ 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 %PACKAGE_DOCS% ..\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% -DMANTID_DATA_STORE=%MANTID_DATA_STORE% -DUSE_PRECOMPILED_HEADERS=ON %PACKAGE_DOCS% ..\Code\Mantid
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

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

@@ -0,0 +1,82 @@
+#!/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 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-1.2.4/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, 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

@@ -272,7 +272,6 @@ set ( INC_FILES
 	inc/MantidAPI/ScriptRepositoryFactory.h
 	inc/MantidAPI/SingleValueParameter.h
 	inc/MantidAPI/SingleValueParameterParser.h
-	inc/MantidAPI/SpecialCoordinateSystem.h
 	inc/MantidAPI/SpectraAxis.h
 	inc/MantidAPI/SpectrumDetectorMapping.h
 	inc/MantidAPI/TableRow.h
@@ -398,6 +397,11 @@ add_library ( API ${SRC_FILES} ${INC_FILES})
 # Set the name of the generated library
 set_target_properties ( API PROPERTIES OUTPUT_NAME MantidAPI 
                                        COMPILE_DEFINITIONS IN_MANTID_API )
+
+if (OSX_VERSION VERSION_GREATER 10.8)
+  set_target_properties ( API PROPERTIES INSTALL_RPATH "@loader_path/../MacOS")
+endif ()
+
 # Add to the 'Framework' group in VS
 set_property ( TARGET API PROPERTY FOLDER "MantidFramework" )
 

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

@@ -83,7 +83,7 @@ class MANTID_API_DLL IMDEventWorkspace : public API::IMDWorkspace,
   virtual bool threadSafe() const;
 
   virtual void setCoordinateSystem(
-      const Mantid::API::SpecialCoordinateSystem coordinateSystem) = 0;
+      const Mantid::Kernel::SpecialCoordinateSystem coordinateSystem) = 0;
 
 protected:
   virtual const std::string toString() const;

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

@@ -89,7 +89,7 @@ class DLLExport IMDHistoWorkspace : public IMDWorkspace,
   virtual double &operator[](const size_t &index) = 0;
 
   virtual void setCoordinateSystem(
-      const Mantid::API::SpecialCoordinateSystem coordinateSystem) = 0;
+      const Mantid::Kernel::SpecialCoordinateSystem coordinateSystem) = 0;
 
   virtual boost::shared_ptr<IMDHistoWorkspace> clone() const = 0;