ENH: add a patch mechanism for ParaView build

- this adds some flexiblity/robustness to the build

README.org

@@ -2,7 +2,7 @@
 #
 #+TITLE:                 OpenFOAM Third-Party packages
 #+AUTHOR:                  The OpenFOAM Foundation
-#+DATE:                       31th May 2016
+#+DATE:                           2016-06-14
 #+LINK:                     http://www.openfoam.org
 #+OPTIONS: author:nil ^:{}
 # Copyright (c) 2014-2016 OpenFOAM Foundation.
@@ -15,6 +15,8 @@
   + makeCmake (if the system cmake version is < 2.8.8)
   + makeParaView
 *** Optional Build Components:
+    + makeLLVM  (Replaces makeGcc in the above description
+    - to use clang as compiler)
     + makeCCMIO (Only required for conversion of STAR-CCM+ meshes)
     + Allclean  (Only required to save disk space)
 * Versions and locations to download the third party packages
@@ -65,13 +67,21 @@
     directory:
     + wget https://raw.githubusercontent.com/Kitware/VTK/40937e934308e5009e80769dc0c451ee4f157749/IO/Geometry/vtkSTLReader.cxx -O ParaView-4.4.0/VTK/IO/Geometry/vtkSTLReader.cxx
     See also http://www.openfoam.org/mantisbt/view.php?id=1887
+
+    For ParaView-5.0.1, the necessary patches are supplied with the
+    ThirdParty repository (see the etc/patches directory) and are applied
+    when building paraview.
+
 *** Building ParaView-5.0.1 with gcc-6.1.0
 ***** Add support for gcc-6.?.?
       The following cmake files
       + ParaView-5.0.1/VTK/CMake/vtkCompilerExtras.cmake
       + ParaView-5.0.1/VTK/CMake/GenerateExportHeader.cmake
-      specifically limit the gcc versions supported.  To add support gcc-6.?.?
-      replace '[345]' with '[3456]'
+      specifically limit the gcc versions supported.
+      To add support gcc-6.?.? replace the '[345]' with '[3456]'.
+      This patch is also supplied with the ThirdParty repository and
+      applied when building paraview.
+
 ***** SciberQuestToolKit
       The SciberQuestToolKit plugin fails to compile with gcc-6.1.0 and causes
       the compilation of ParaView to halt.  The easiest solution is to delete

etc/patches/mkdiff-paraview-5.0.1

+#!/bin/sh
+
+# simple script to generate patches
+paraview=ParaView-5.0.1
+
+for i in \
+    $paraview/VTK/CMake/vtkCompilerExtras.cmake \
+    $paraview/VTK/CMake/GenerateExportHeader.cmake \
+    $paraview/Qt/Components/CMakeLists.txt \
+    ;
+do
+    diff -uw $i.orig $i
+done

etc/patches/paraview-5.0.1

+--- ParaView-5.0.1/VTK/CMake/vtkCompilerExtras.cmake.orig	2016-03-28 17:07:10.000000000 +0200
++++ ParaView-5.0.1/VTK/CMake/vtkCompilerExtras.cmake	2016-06-11 15:10:14.820958942 +0200
+@@ -32,7 +32,7 @@
+     OUTPUT_VARIABLE _gcc_version_info
+     ERROR_VARIABLE _gcc_version_info)
+ 
+-  string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]*"
++  string (REGEX MATCH "[3-6]\\.[0-9]\\.[0-9]*"
+     _gcc_version "${_gcc_version_info}")
+   if(NOT _gcc_version)
+     string (REGEX REPLACE ".*\\(GCC\\).*([34]\\.[0-9]).*" "\\1.0"
+--- ParaView-5.0.1/VTK/CMake/GenerateExportHeader.cmake.orig	2016-03-28 17:07:10.000000000 +0200
++++ ParaView-5.0.1/VTK/CMake/GenerateExportHeader.cmake	2016-06-11 15:12:16.344357746 +0200
+@@ -166,7 +166,7 @@
+     execute_process(COMMAND ${CMAKE_C_COMPILER} ARGS --version
+       OUTPUT_VARIABLE _gcc_version_info
+       ERROR_VARIABLE _gcc_version_info)
+-    string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]*"
++    string(REGEX MATCH "[3-6]\\.[0-9]\\.[0-9]*"
+       _gcc_version "${_gcc_version_info}")
+     # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+     # patch level, handle this here:
+--- ParaView-5.0.1/Qt/Components/CMakeLists.txt.orig	2016-06-13 09:27:27.827849525 +0200
++++ ParaView-5.0.1/Qt/Components/CMakeLists.txt	2016-06-13 09:29:28.599318445 +0200
+@@ -656,10 +656,10 @@
+ #the pqSGExportStateWizard has subclasses that directly access
+ #the UI file, and currently we don't have a clean way to break this hard
+ #dependency, so for no we install this ui file.
+-if(PARAVIEW_INSTALL_DEVELOPMENT_FILES)
+-  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/ui_pqExportStateWizard.h"
+-          DESTINATION "${VTK_INSTALL_INCLUDE_DIR}")
+-endif()
++#OPENFOAM patch#if(PARAVIEW_INSTALL_DEVELOPMENT_FILES)
++#OPENFOAM patch#  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/ui_pqExportStateWizard.h"
++#OPENFOAM patch#          DESTINATION "${VTK_INSTALL_INCLUDE_DIR}")
++#OPENFOAM patch#endif()
+ 
+ #IF (NOT PV_INSTALL_NO_DEVELOPMENT)
+ #  # Headers

etc/tools/ParaViewFunctions

@@ -3,7 +3,7 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-#    \\/     M anipulation  |
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 #------------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
@@ -364,6 +364,34 @@ addQtSupport()
 }
 
 
+#
+# Apply source-code patch if possible
+#
+applyPatch()
+{
+    local patch="$WM_THIRD_PARTY_DIR/etc/patches/paraview-$ParaView_VERSION"
+    local sentinel="PATCHED_DURING_OPENFOAM_BUILD"
+
+    if [ -r "$patch" ]
+    then
+    (
+        cd $ParaView_SOURCE_DIR || exit 1
+        if [ -f "$sentinel" ]
+        then
+            echo "patch for paraview-$ParaView_VERSION was already applied"
+        else
+            echo "apply patch for paraview-$ParaView_VERSION"
+            touch "$sentinel"
+            patch -p1 < $patch
+
+        fi
+    )
+    else
+        echo "no patch found for paraview-$ParaView_VERSION"
+    fi
+}
+
+
 #
 # Configure via cmake, but don't actually build anything
 #

makeParaView

@@ -4,7 +4,7 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-#    \\/     M anipulation  |
+#    \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 #------------------------------------------------------------------------------
 # License
 #     This file is part of OpenFOAM.
@@ -111,6 +111,7 @@ For example,
 to add tests
 
 For finer control, the build stages can be selected or deselected individually:
+  -patch     -no-patch
   -config    -no-config
   -make      -no-make
   -install   -no-install
@@ -144,7 +145,7 @@ setVersion
 #
 # various building stages
 #
-unset runCONFIG runMAKE runINSTALL
+unset runPATCH runCONFIG runMAKE runINSTALL
 runDEFAULT=true
 buildType=Release
 
@@ -163,6 +164,15 @@ do
         export CXX=g++   # use g++
         shift
         ;;
+    -patch)              # stage 0: patch sources
+        runPATCH=true
+        unset runDEFAULT
+        shift
+        ;;
+    -no-patch)
+        runPATCH=false
+        shift
+        ;;
     -config)             # stage 1: config only
         runCONFIG=true
         unset runDEFAULT
@@ -285,6 +295,7 @@ done
 
 if [ "$runDEFAULT" = true ]
 then
+    : ${runPATCH:=true}
     : ${runCONFIG:=true}
     : ${runMAKE:=true}
     : ${runINSTALL:=true}
@@ -309,6 +320,7 @@ cat<<SUMMARY
 
 Build stages selected
 ---------------------
+    -patch    ${runPATCH:-false}
     -config   ${runCONFIG:-false}
     -make     ${runMAKE:-false}
     -install  ${runINSTALL:-false}
@@ -328,6 +340,7 @@ $(checkVersion)
 ---------------------
 SUMMARY
 
+[ "$runPATCH"   = true ] && applyPatch
 [ "$runCONFIG"  = true ] && configParaView
 [ "$runMAKE"    = true ] && makeParaView
 [ "$runINSTALL" = true ] && installParaView