Refs #7363. Fixing conflicts.

Merge branch 'master' into feature/7363_vates_paraview_git

Conflicts:
	Code/Mantid/Build/Jenkins/buildscript
	Code/Mantid/Build/Jenkins/buildscript.bat

CONTRIBUTING.md

@@ -4,3 +4,11 @@ The [developer documentation](http://www.mantidproject.org/Category:Development)
  2. Make changes as you see fit. Please still follow the guidelines for [running the unit tests](http://www.mantidproject.org/Running_the_unit_tests) and the [build servers](http://www.mantidproject.org/The_automated_build_process).
  3. Before submitting pull requests email mantid-help@mantidproject.org, and a developer will set up a branch that you can submit pull requests to.
  4. Submit a [pull request](https://help.github.com/articles/using-pull-requests) to this branch.
+
+
+Hints to make the integration of your changes easy:
+- Keep your pull requests small
+- Don't forget your unit tests
+- All algorithms need documentation, don't forget the .rst file
+- Contact us before creating the pull request
+- Don't take changes requests to change your code personally

Code/Mantid/Build/CMake/CPackLinuxSetup.cmake

@@ -11,7 +11,7 @@ set ( CPACK_SOURCE_GENERATOR TGZ )
 include (DetermineLinuxDistro)
 
 # define which binary generators to use
-if ( ${UNIX_DIST} MATCHES "Ubuntu" )
+if ( "${UNIX_DIST}" MATCHES "Ubuntu" )
   find_program (DPKG_CMD dpkg)
   if ( DPKG_CMD )
     set ( CPACK_GENERATOR "DEB" )
@@ -22,23 +22,23 @@ if ( ${UNIX_DIST} MATCHES "Ubuntu" )
     set( CPACK_PACKAGE_FILE_NAME
       "${CPACK_PACKAGE_NAME}_${CPACK_PACKAGE_VERSION}-${CPACK_DEBIAN_PACKAGE_RELEASE}_${CPACK_DEBIAN_PACKAGE_ARCHITECTURE}")   
   endif ( DPKG_CMD ) 
-endif ( ${UNIX_DIST} MATCHES "Ubuntu" )
+endif ( "${UNIX_DIST}" MATCHES "Ubuntu" )
 
 #RedHatEnterpriseClient RedHatEnterpriseWorkstation
-if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR ${UNIX_DIST} MATCHES "SUSE LINUX" )
+if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" OR "${UNIX_DIST}" MATCHES "Fedora" OR "${UNIX_DIST}" MATCHES "SUSE LINUX" )
   find_program ( RPMBUILD_CMD rpmbuild )
   if ( RPMBUILD_CMD )
     set ( CPACK_GENERATOR "RPM" )
     set ( CPACK_RPM_PACKAGE_ARCHITECTURE "${CMAKE_SYSTEM_PROCESSOR}" )
     set ( CPACK_RPM_PACKAGE_URL "http://www.mantidproject.org" )
 
     # reset the release name to include the RHEL version if known
-    if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" )
+    if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
       string ( REGEX REPLACE "^([0-9])\\.[0-9]+$" "\\1" TEMP ${UNIX_RELEASE} )
       set ( CPACK_RPM_PACKAGE_RELEASE "1.el${TEMP}" )
-    elseif ( ${UNIX_DIST} MATCHES "Fedora" )
+    elseif ( "${UNIX_DIST}" MATCHES "Fedora" )
       set ( CPACK_RPM_PACKAGE_RELEASE "1.fc${UNIX_RELEASE}" )
-    endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" )
+    endif ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
 
     # If CPACK_SET_DESTDIR is ON then the Prefix doesn't get put in the spec file
     if( CPACK_SET_DESTDIR )
@@ -50,5 +50,5 @@ if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR
     set ( CPACK_PACKAGE_FILE_NAME
       "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_RPM_PACKAGE_RELEASE}.${CPACK_RPM_PACKAGE_ARCHITECTURE}" )
   endif ( RPMBUILD_CMD)
-endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR ${UNIX_DIST} MATCHES "SUSE LINUX" )
+endif ()
 

Code/Mantid/Build/CMake/CommonSetup.cmake

@@ -242,6 +242,11 @@ endif ()
 ###########################################################################
 include ( CppCheckSetup )
 
+###########################################################################
+# Setup pylint
+###########################################################################
+include ( PylintSetup )
+
 ###########################################################################
 # Set up the unit tests target
 ###########################################################################

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -95,6 +95,7 @@ endif()
 set ( CMAKE_INSTALL_PREFIX "" )
 set ( CPACK_PACKAGE_EXECUTABLES MantidPlot )
 set ( INBUNDLE MantidPlot.app/ )
+
 # We know exactly where this has to be on Darwin
 set ( PARAVIEW_APP_DIR "/Applications/${OSX_PARAVIEW_APP}" )
 set ( PARAVIEW_APP_BIN_DIR "${PARAVIEW_APP_DIR}/Contents/MacOS" )
@@ -107,45 +108,59 @@ set ( PLUGINS_DIR MantidPlot.app/plugins )
 set ( PVPLUGINS_DIR MantidPlot.app/pvplugins )
 set ( PVPLUGINS_SUBDIR pvplugins ) # Need to tidy these things up!
 
+if (OSX_VERSION VERSION_LESS 10.9)
+ set ( PYQT4_PYTHONPATH /Library/Python/${PY_VER}/site-packages/PyQt4 )
+ set ( SITEPACKAGES /Library/Python/${PY_VER}/site-packages )
+else()
+ # Assume we are using homebrew for now
+ set ( PYQT4_PYTHONPATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
+ set ( SITEPACKAGES /usr/local/lib/python${PY_VER}/site-packages )
+endif()
+
 # Python packages
 
-install ( PROGRAMS /Library/Python/${PY_VER}/site-packages/sip.so DESTINATION ${BIN_DIR} )
+install ( PROGRAMS ${SITEPACKAGES}/sip.so DESTINATION ${BIN_DIR} )
+
 # Explicitly specify which PyQt libraries we want because just taking the whole
 # directory will swell the install kit unnecessarily.
-install ( FILES /Library/Python/${PY_VER}/site-packages/PyQt4/Qt.so
-                /Library/Python/${PY_VER}/site-packages/PyQt4/QtCore.so
-                /Library/Python/${PY_VER}/site-packages/PyQt4/QtGui.so
-                /Library/Python/${PY_VER}/site-packages/PyQt4/QtOpenGL.so
-                /Library/Python/${PY_VER}/site-packages/PyQt4/QtSql.so
-                /Library/Python/${PY_VER}/site-packages/PyQt4/QtSvg.so
-                /Library/Python/${PY_VER}/site-packages/PyQt4/QtXml.so
-                /Library/Python/${PY_VER}/site-packages/PyQt4/__init__.py
+install ( FILES ${PYQT4_PYTHONPATH}/Qt.so
+                ${PYQT4_PYTHONPATH}/QtCore.so
+                ${PYQT4_PYTHONPATH}/QtGui.so
+                ${PYQT4_PYTHONPATH}/QtOpenGL.so
+                ${PYQT4_PYTHONPATH}/QtSql.so
+                ${PYQT4_PYTHONPATH}/QtSvg.so
+                ${PYQT4_PYTHONPATH}/QtXml.so
+                ${PYQT4_PYTHONPATH}/__init__.py
           DESTINATION ${BIN_DIR}/PyQt4 )
 # Newer PyQt versions have a new internal library that we need to take
-if ( EXISTS /Library/Python/${PY_VER}/site-packages/PyQt4/_qt.so )
-  install ( FILES /Library/Python/${PY_VER}/site-packages/PyQt4/_qt.so
+if ( EXISTS ${PYQT4_PYTHONPATH}/_qt.so )
+  install ( FILES ${PYQT4_PYTHONPATH}/_qt.so
             DESTINATION ${BIN_DIR}/PyQt4 )
 endif ()
 
-install ( DIRECTORY /Library/Python/${PY_VER}/site-packages/PyQt4/uic DESTINATION ${BIN_DIR}/PyQt4 )
+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} )
-  install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+  if ( IS_DIRECTORY ${PYPACKAGE} )
+    install ( DIRECTORY ${PYPACKAGE} DESTINATION ${BIN_DIR} )
+  endif()
   file ( COPY ${PYPACKAGE} DESTINATION ${PROJECT_BINARY_DIR}/bin )
 endforeach( PYPACKAGE )
 
 install ( DIRECTORY ${QT_PLUGINS_DIR}/imageformats DESTINATION MantidPlot.app/Contents/Frameworks/plugins )
+install ( DIRECTORY ${QT_PLUGINS_DIR}/sqldrivers DESTINATION MantidPlot.app/Contents/Frameworks/plugins )
 
 install ( FILES ${CMAKE_SOURCE_DIR}/Images/MantidPlot.icns
                 ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/qt.conf
           DESTINATION MantidPlot.app/Contents/Resources/
 )
 
+set ( CPACK_DMG_BACKGROUND_IMAGE ${CMAKE_SOURCE_DIR}/Images/osx-bundle-background.png )
+set ( CPACK_DMG_DS_STORE ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/osx_DS_Store)
 set ( MACOSX_BUNDLE_ICON_FILE MantidPlot.icns )
-  
+
 string (REPLACE " " "" CPACK_SYSTEM_NAME ${OSX_CODENAME})
 
 set ( CPACK_GENERATOR DragNDrop )
-

Code/Mantid/Build/CMake/FindOpenCascade.cmake

@@ -60,6 +60,10 @@ find_library ( OPENCASCADE_LIB_TKGEOMBASE
                  NAMES TKGeomBase
 )
 
+find_library ( OPENCASCADE_LIB_TKGEOMAlgo
+                 NAMES TKGeomAlgo
+)
+
 set ( OPENCASCADE_LIBRARIES
         ${OPENCASCADE_LIB_TKERNEL}
         ${OPENCASCADE_LIB_TKBO}
@@ -71,6 +75,7 @@ set ( OPENCASCADE_LIBRARIES
         ${OPENCASCADE_LIB_TKG2D}
         ${OPENCASCADE_LIB_TKG3D}
         ${OPENCASCADE_LIB_TKGEOMBASE}
+        ${OPENCASCADE_LIB_TKGEOMALGO}
 )
 
 # handle the QUIETLY and REQUIRED arguments and set OPENCASCADE_FOUND to TRUE if 
@@ -83,4 +88,6 @@ mark_as_advanced ( OPENCASCADE_INCLUDE_DIR
                    OPENCASCADE_LIB_TKPRIM OPENCASCADE_LIB_TKMESH
                    OPENCASCADE_LIB_TKBREP OPENCASCADE_LIB_TKTOPALGO 
                    OPENCASCADE_LIB_TKMATH OPENCASCADE_LIB_TKG2D
+                   OPENCASCADE_LIB_TKG3D OPENCASCADE_LIB_TKGEOMBASE
+                   OPENCASCADE_LIB_TKGEOMALGO
 )

Code/Mantid/Build/CMake/FindPylint.cmake

@@ -0,0 +1,40 @@
+# - Find Pylint
+# Find the Pylint executable and extract the version number
+#
+# OUTPUT Variables
+#
+#   PYLINT_FOUND
+#       True if the pylint package was found
+#   PYLINT_EXECUTABLE
+#       The pylint executable location
+#   PYLINT_VERSION
+#       A string denoting the version of pylint that has been found
+#   PYLINT_RUNNER_SCRIPT
+#       Location of python script that will actually run pylint
+#   PYLINT_CFG_FILE
+#       Location of configuration file
+#
+
+#=============================================================
+# main()
+#=============================================================
+
+find_program ( PYLINT_EXECUTABLE pylint PATHS /usr/bin )
+
+if ( PYLINT_EXECUTABLE )
+  execute_process ( COMMAND ${PYLINT_EXECUTABLE} --version OUTPUT_VARIABLE PYLINT_VERSION_RAW ERROR_QUIET )
+  if (PYLINT_VERSION_RAW)
+    string ( REGEX REPLACE "^pylint ([0-9]+.[0-9]+.[0-9]+),.*" "\\1" PYLINT_VERSION ${PYLINT_VERSION_RAW})
+  else ()
+    set ( PYLINT_VERSION "unknown" )
+  endif()
+  # Script to find all .py files and execute pylint
+  set ( PYLINT_RUNNER_SCRIPT ${CMAKE_SOURCE_DIR}/../Tools/Pylint/run_pylint.py )
+  # Configuration file
+  set ( PYLINT_CFG_FILE ${CMAKE_SOURCE_DIR}/../Tools/Pylint/pylint.cfg )
+endif ()
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS ( Pylint DEFAULT_MSG PYLINT_EXECUTABLE )
+
+mark_as_advanced ( PYLINT_EXECUTABLE PYLINT_VERSION )

Code/Mantid/Build/CMake/FindSphinx.cmake

@@ -6,12 +6,39 @@
 # set:
 #  SPHINX_FOUND
 #  SPHINX_EXECUTABLE
+#
+#=============================================================
+# main()
+#=============================================================
 
 find_program( SPHINX_EXECUTABLE NAME sphinx-build
+  PATHS ${CMAKE_LIBRARY_PATH}/Python27/Scripts
   PATH_SUFFIXES bin
   DOC "Sphinx documentation generator"
 )
 
+if (SPHINX_EXECUTABLE)
+    # run sphinx-build to attempt to get the version
+    execute_process (COMMAND ${SPHINX_EXECUTABLE} --version
+                     OUTPUT_STRIP_TRAILING_WHITESPACE
+                     OUTPUT_VARIABLE version_string
+                     ERROR_VARIABLE version_error_string
+                     ERROR_STRIP_TRAILING_WHITESPACE)
+
+    # if it wasn't successful it is hiding in stderr
+    if (NOT version_string)
+        if ( version_error_string )
+            string (REGEX REPLACE "\n" ";" version_string ${version_error_string})
+            list (GET version_string 0 version_string)
+        else ( version_error_string )
+            set ( version_string "1.1.0" )
+        endif ( version_error_string )
+    endif (NOT version_string)
+
+    # chop out the version number
+    string (REGEX REPLACE ".*([0-9]+\\.[0-9]+\\.[0-9]+).*" "\\1" SPHINX_VERSION ${version_string})
+endif (SPHINX_EXECUTABLE)
+
 include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(Sphinx DEFAULT_MSG SPHINX_EXECUTABLE )

Code/Mantid/Build/CMake/LinuxSetup.cmake

@@ -90,7 +90,7 @@ endif()
 
 
 # RHEL6 specific stuff (as we need to use software collections)
-if ( ${UNIX_DIST} STREQUAL "RedHatEnterprise" )
+if ( "${UNIX_DIST}" MATCHES "RedHatEnterprise" )
 	file ( APPEND ${CMAKE_CURRENT_BINARY_DIR}/rpm_post_install.sh "\n"
 								     "if [ -f $RPM_INSTALL_PREFIX0/${BIN_DIR}/MantidPlot ]; then\n"
                                                                      "  mv $RPM_INSTALL_PREFIX0/${BIN_DIR}/MantidPlot $RPM_INSTALL_PREFIX0/${BIN_DIR}/MantidPlot_exe\n"
@@ -101,12 +101,12 @@ if ( ${UNIX_DIST} STREQUAL "RedHatEnterprise" )
 								      "scl enable mantidlibs \"${CMAKE_INSTALL_PREFIX}/${BIN_DIR}/MantidPlot_exe $*\" \n"
 	)
 
-install ( FILES  ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh 
+    install ( FILES  ${CMAKE_CURRENT_BINARY_DIR}/launch_mantidplot.sh
           DESTINATION ${BIN_DIR}
 	      PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
 	                  GROUP_EXECUTE GROUP_READ
 	                  WORLD_EXECUTE WORLD_READ
-)
+    )
 
 endif()
 

Code/Mantid/Build/CMake/PylintSetup.cmake

@@ -0,0 +1,50 @@
+########################################################
+# Setup target to run pylint checking if it is available
+########################################################
+find_package ( Pylint )
+
+if ( PYLINT_FOUND AND PYLINT_VERSION VERSION_LESS "1.0.0" )
+  message ( STATUS "pylint found but version is < 1.0.0 (${PYLINT_VERSION}): no target generated." )
+  set ( PYLINT_FOUND FALSE )
+endif()
+
+if ( PYLINT_FOUND )
+  message ( STATUS "pylint version: ${PYLINT_VERSION}" )
+
+  # Output format options
+  if ( NOT  PYLINT_OUTPUT_FORMAT )
+    # Use msvs for MSVC generator, colorized for everything else. The buildservers can
+    # set it to parseable for Jenkins
+    if ( MSVC )
+      set ( DEFAULT_FORMAT "msvs" )
+    else ()
+      set ( DEFAULT_FORMAT "colorized" )
+    endif ()
+    set ( PYLINT_OUTPUT_FORMAT ${DEFAULT_FORMAT} CACHE STRING "Desired pylint output format" )
+
+    # There are a limited set of allowed options
+    set_property( CACHE PYLINT_OUTPUT_FORMAT PROPERTY STRINGS "text" "html" "msvs" "parseable" "colorized" )
+  endif()
+
+  # add a pylint-check target to run pylint on the required files and directories
+  # relative to the root source directory
+  set ( BASE_DIR ${CMAKE_SOURCE_DIR} )
+  set ( PYLINT_INCLUDES
+        Framework/PythonInterface/plugins
+        scripts
+  )
+  set ( PYLINT_EXCLUDES
+        scripts/lib1to2
+        scripts/test
+  )
+  add_custom_target ( pylintcheck
+                      COMMAND ${PYTHON_EXECUTABLE} ${PYLINT_RUNNER_SCRIPT} --format=${PYLINT_OUTPUT_FORMAT}
+                              --rcfile=${PYLINT_CFG_FILE}
+                              --mantidpath=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}
+                              --basedir=${BASE_DIR} --nofail
+                              --exclude="${PYLINT_EXCLUDES}"
+                              ${PYLINT_INCLUDES}
+                      COMMENT "Running pylint on selected python files"
+                    )
+  set_target_properties ( pylintcheck PROPERTIES EXCLUDE_FROM_ALL TRUE )
+endif ()

Code/Mantid/Build/CMake/UseSystemQt4.cmake

@@ -74,7 +74,7 @@ SET(QT_QAXSERVER_MODULE_DEPENDS QTGUI QTCORE)
 SET(QT_QTSCRIPTTOOLS_MODULE_DEPENDS QTGUI QTCORE)
 
 # Qt modules  (in order of dependence)
-FOREACH(module QT3SUPPORT QTOPENGL QTASSISTANT QTDESIGNER QTMOTIF QTNSPLUGIN
+FOREACH(module QT3SUPPORT QTOPENGL QTDESIGNER QTMOTIF QTNSPLUGIN
                QAXSERVER QAXCONTAINER QTSCRIPT QTSVG QTUITOOLS QTHELP 
                QTWEBKIT PHONON QTSCRIPTTOOLS QTGUI QTTEST QTDBUS QTXML QTSQL 
                QTXMLPATTERNS QTNETWORK QTCORE)

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 1 )
+set ( VERSION_MINOR 2 )
 
 # 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/CMake/WindowsNSIS.cmake

@@ -97,9 +97,6 @@
               REGEX "^.*d4.dll$" EXCLUDE  )
     install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/Installers/WinInstaller/qt.conf DESTINATION bin )
 
-    # Copy assistant.exe
-    install ( FILES ${CMAKE_LIBRARY_PATH}/assistant.exe DESTINATION bin )
-
     # Release deployments do modify enviromental variables, other deployments do not.
     if(CPACK_PACKAGE_SUFFIX STREQUAL "") 
         # On install