Updates to PKGBUILD and install script, patch for src

PKGBUILD: sources petsc and slepc profiles
install file: corrected path
CMakeLists.txt: allow use of system's cmake Find modules
FindSCOTCH.cmake:  also find libbz2 because SCOTCH on Arch Linux
  is built against it and is needed to run the test program during
  dolfin configuring
FindPaStiX.cmake: list all the libs needed before trying to
  compile the test program during config

4 files changed, 69 insertions, 17 deletions

diff --git a/.SRCINFO b/.SRCINFO
index ea2c53685ade..3234589395b0 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = dolfin-git
 	pkgdesc = the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.
-	pkgver = 20140909
+	pkgver = 20151005
 	pkgrel = 1
 	url = https://bitbucket.org/fenics-project/dolfin
 	install = dolfin.install
@@ -31,9 +31,11 @@ pkgbase = dolfin-git
 	conflicts = dolfin
 	options = !emptydirs
 	source = dolfin::git+https://bitbucket.org/fenics-project/dolfin.git#branch=master
+	source = src.patch
 	source = dolfin.install
 	md5sums = SKIP
-	md5sums = 0659b73a58b92be0ca70fc0135668809
+	md5sums = 3d0750480196e26dced7435a00e70206
+	md5sums = 284f97c4471a044dd296572fe7024686
 
 pkgname = dolfin-git
 
diff --git a/PKGBUILD b/PKGBUILD
index 91bca3031491..4655bcbe4222 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,7 +1,7 @@
 # Maintainer: Myles English <myles at rockhead dot biz>
 pkgname=dolfin-git
 pkgdesc="the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations."
-pkgver=20140909
+pkgver=20151005
 pkgrel=1
 _branch=master
 arch=('i686' 'x86_64')
@@ -17,9 +17,11 @@ conflicts=('dolfin')
 options=(!emptydirs)
 install="dolfin.install"
 source=("dolfin::git+https://bitbucket.org/fenics-project/dolfin.git#branch=${_branch}"
+        "src.patch"
         "${install}")
 md5sums=('SKIP'
-         '0659b73a58b92be0ca70fc0135668809')
+         '3d0750480196e26dced7435a00e70206'
+         '284f97c4471a044dd296572fe7024686')
 
 # to stop /common/timing.cpp.o coming before /common/defines.cpp.o
 export MAKEFLAGS="-j1"
@@ -27,14 +29,14 @@ export MAKEFLAGS="-j1"
 # export CXXFLAGS="$CXXFLAGS -Wall -Wshadow -Wextra -Werror"
 
 pkgver() {
-  cd dolfin
-  git log --format="%cd" --date=short -1 | sed 's/-//g'
+    cd dolfin
+    git log --format="%cd" --date=short -1 | sed 's/-//g'
 }
 
 prepare() {
-  cd dolfin
+    patch -p2 < src.patch
 
-    #patch -Np1 -i "${srcdir}/debug_cxxflags.diff"
+    cd dolfin
 
     find ./ -name "*" -type f -exec \
         sed -i 's|^#!.*python$|#!/usr/bin/python2|' {} \;
@@ -59,20 +61,23 @@ build() {
     local py2_inc="${py2_interp/\/bin\///include/}"
     local py2_lib=`ldd ${py2_interp} | grep python | cut -d " " -f 3 | sed 's/\(.*.so\).*/\1/'`
 
-    cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/g++ \
-	-DCMAKE_INSTALL_PREFIX="${pkg}"/usr \
+    [ -z "$PETSC_DIR" ] && source /etc/profile.d/petsc.sh
+    [ -z "$SLEPC_DIR" ] && source /etc/profile.d/slepc.sh
+
+    cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/g++   \
+	-DCMAKE_INSTALL_PREFIX="${pkg}"/usr      \
         -DPYTHON_EXECUTABLE:PATH="${py2_interp}" \
-        -DPYTHON_INCLUDE_DIR:PATH="${py2_inc}" \
-        -DPYTHON_LIBRARY:FILEPATH="${py2_lib}" \
-	-DDOLFIN_ENABLE_VTK=ON \
-        -DCMAKE_SKIP_BUILD_RPATH=TRUE \
-	-DCMAKE_SKIP_RPATH=TRUE \
+        -DPYTHON_INCLUDE_DIR:PATH="${py2_inc}"   \
+        -DPYTHON_LIBRARY:FILEPATH="${py2_lib}"   \
+	-DDOLFIN_ENABLE_VTK=ON                   \
+        -DCMAKE_SKIP_BUILD_RPATH=TRUE            \
+	-DCMAKE_SKIP_RPATH=TRUE                  \
 	-DCMAKE_BUILD_TYPE="Debug"
 	# -DDOLFIN_ENABLE_TESTING=ON
 
     make
 
-    # Uncomment this line for documentation
+    # Uncomment the line below to build the documentation
     #make SPHINXBUILD=sphinx-build2 doc
 }
 
diff --git a/dolfin.install b/dolfin.install
index 9dba4cc68a88..35d53f36a860 100644
--- a/dolfin.install
+++ b/dolfin.install
@@ -5,7 +5,7 @@ cat << EOF
 If you just ran makepkg in this directory then
 to build the documentation you can try:
 
-$ cd src/dolfin-build/build/doc
+$ cd src/dolfin/build/doc
 $ make doc SPHINXBUILD=sphinx-build2
 
 EOF
diff --git a/src.patch b/src.patch
new file mode 100644
index 000000000000..036fe68d6fc1
--- /dev/null
+++ b/src.patch
@@ -0,0 +1,45 @@
+diff --git a/src/dolfin/CMakeLists.txt b/src/dolfin/CMakeLists.txt
+index afb33ce..96a5460 100644
+--- a/src/dolfin/CMakeLists.txt
++++ b/src/dolfin/CMakeLists.txt
+@@ -61,7 +61,7 @@ endif()
+ 
+ # Set location of our FindFoo.cmake modules
+ set(DOLFIN_CMAKE_DIR "${DOLFIN_SOURCE_DIR}/cmake" CACHE INTERNAL "")
+-set(CMAKE_MODULE_PATH "${DOLFIN_CMAKE_DIR}/modules")
++set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${DOLFIN_CMAKE_DIR}/modules")
+ 
+ # Make sure CMake uses the correct DOLFINConfig.cmake for tests and demos
+ set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} ${CMAKE_CURRENT_BINARY_DIR}/dolfin)
+diff --git a/src/dolfin/cmake/modules/FindPaStiX.cmake b/src/dolfin/cmake/modules/FindPaStiX.cmake
+index be2f60a..6b2566a 100644
+--- a/src/dolfin/cmake/modules/FindPaStiX.cmake
++++ b/src/dolfin/cmake/modules/FindPaStiX.cmake
+@@ -123,6 +123,8 @@ elseif (PASTIX_INCLUDE_DIRS AND PASTIX_LIBRARIES)
+     set(CMAKE_REQUIRED_FLAGS     "${CMAKE_REQUIRED_FLAGS} ${MPI_C_COMPILE_FLAGS}")
+   endif()
+ 
++ set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} "-lpastix -llapack  -lbz2 -lptscotch -lscotcherr")
++
+   # Build and run test program
+   include(CheckCSourceRuns)
+   check_c_source_runs("
+diff --git a/src/dolfin/cmake/modules/FindSCOTCH.cmake b/src/dolfin/cmake/modules/FindSCOTCH.cmake
+index 58b96b4..97d7264 100644
+--- a/src/dolfin/cmake/modules/FindSCOTCH.cmake
++++ b/src/dolfin/cmake/modules/FindSCOTCH.cmake
+@@ -159,6 +159,14 @@ elseif (SCOTCH_INCLUDE_DIRS AND SCOTCH_LIBRARIES)
+   set(CMAKE_REQUIRED_INCLUDES ${SCOTCH_INCLUDE_DIRS})
+   set(CMAKE_REQUIRED_LIBRARIES ${SCOTCH_LIBRARIES})
+   #set(CMAKE_REQUIRED_LIBRARIES ${SCOTCH_LIBRARY} ${SCOTCHERR_LIBRARY})
++  # TODO: see if scotch was built against bzip2 before finding
++  # nm --dynamic /usr/lib/libscotch.so | grep -w BZ2_bzRead
++  if (NOT BZIP2_FOUND)
++    find_package(BZip2)
++  endif()
++  if (BZIP2_FOUND)
++    set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${BZIP2_LIBRARIES})
++  endif()
+ 
+   # Add MPI variables if MPI has been found
+   if (MPI_CXX_FOUND)