sci-mathematics/petsc: version bump to 3.6.5, major overhaul

 - bump to EAPI 6

 - respect upstream decision to install in a monolithic way. Now, the full
   petsc distribution is installed into

     /usr/lib/petsc

 - add metis support

Package-Manager: Portage-2.3.5, Repoman-2.3.2

8 files changed, 48 insertions, 449 deletions

diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 3fca09f39..812a209c3 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,4 +1,3 @@
-DIST petsc-3.4.2.tar.gz 18658689 SHA256 f13b0dc978fe0dcc1df032f8142a2fd345217f02b9967936d9aac26ce4b2b52e SHA512 f839e4cfadbee720e53993eb8de74a2d82bfe2a46a418f528b4cdb2e9245b8ecafbc02d6d1718034cfe80d291095187b0946ebe237c8f985e4213c4c35bc345b WHIRLPOOL a00f4340e5dc151c57d9f5e2b764a609a508490756d8337d52bec4712fb26b8c06edf46293ed838f08ff34e1c068549ea9680657b7282cb884df4c1314c58cdb
 DIST petsc-3.5.4.tar.gz 20750322 SHA256 a85febf92c9ed2dd9a8f4305f31cd51f9514c01d3c31fb9fb69fb6f22bd3a960 SHA512 248b0c7d6c0076f65d66a325265baa20b8846d4f6902044c4fcd16ecfc586618075c4b0f470d2a674eaa954b8b7e08afadcea783bb84ae276091728607323204 WHIRLPOOL 42e3cb00778cebb7de08b7410ff5ea3fa48964679413959f56aff10b46d436cb9d9e2317d7314bd4501fdd4fb9f964f4e572f07b58a197f3d435b6f625d91c41
 DIST petsc-3.6.4.tar.gz 21792990 SHA256 eb09925a139b52b4dd5a071b3da4fe2165f1d6e8f71d410479603c9976c940f0 SHA512 3e0a69b35424c519c9af43e2323b14f5ba650bf8fc653985769fe65d618223418ebd03c166bca0b7d3affaffa51b907a50b5d9cf714f2f94d044e9c592a84965 WHIRLPOOL b94faf0140e948cb01962fd9e240e5470858e76e7d26f007056001750cc6579724fcc01cab88bfa6cbb66ced8b177ec7d7fecd171c047df0b7c03454b2ecb250
-DIST petsc-3.7.5.tar.gz 23194357 SHA256 493ab0b6c1b3fe68e71d990eff87c84f499f680e6d2c0c394e78646a82ed4be3 SHA512 6583bb5fbb0703d96024e1a665c626d81c7a9d7dae56bae15b0396f8a01b9fac05230ba378587cf79bed8bfa08056595a43be89d3b6180243c0a3f1497335625 WHIRLPOOL b8a7cbf828edec25c51c82c75b34250483db80dcf20171bf91ce2cd611dd152784f80d1670d7c05b02d1d98631b95362451f6cd92662af7a548b7cae355e0c79
+DIST petsc-3.7.6.tar.gz 23197699 SHA256 3c8ee051349587d45baa7910c54ce8e0a571592e3b40f3054a7b7f986919d449 SHA512 a5a18bbd24034b22e7d4847bbf382502f92117b072b5a9bb0e2067a60c16eaa2edcae9c9b0c57f54047ecd36d307d668af5e3029759582cec77dd59070b4ebb0 WHIRLPOOL 238d7ff27fb2e750d937068e3c0991a814c5833a470cbc734da1fa2c9ac2bef371e536b63ccb8b67d52de79fe2f708850dcc01911631f6c088c06a73e734a8ae
diff --git a/sci-mathematics/petsc/files/petsc-3.3-configure-pic.patch b/sci-mathematics/petsc/files/petsc-3.3-configure-pic.patch
deleted file mode 100644
index bbfdae1c8..000000000
--- a/sci-mathematics/petsc/files/petsc-3.3-configure-pic.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- config/BuildSystem/config/setCompilers.py.old	2010-09-07 21:41:32.693103846 +0200
-+++ config/BuildSystem/config/setCompilers.py	2010-09-07 21:41:45.322093881 +0200
-@@ -875,7 +875,7 @@
-       languages.append('FC')
-     for language in languages:
-       self.pushLanguage(language)
--      for testFlag in ['-PIC', '-fPIC', '-KPIC','-qpic']:
-+      for testFlag in ['-fPIC', '-PIC', '-KPIC', '-qpic']:
-         try:
-           self.framework.logPrint('Trying '+language+' compiler flag '+testFlag)
-           if not self.checkLinkerFlag(testFlag):
diff --git a/sci-mathematics/petsc/files/petsc-3.3-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.3-disable-rpath.patch
deleted file mode 100644
index 3c443b29f..000000000
--- a/sci-mathematics/petsc/files/petsc-3.3-disable-rpath.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- config/BuildSystem/config/setCompilers.py	2010-11-24 18:01:17.110124425 +0100
-+++ config/BuildSystem/config/setCompilers.py	2010-11-24 18:02:28.710104226 +0100
-@@ -1186,12 +1186,7 @@
-     for language in languages:
-       flag = '-L'
-       self.pushLanguage(language)
--      # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
--      if not Configure.isDarwin():      
--        testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,']
--      else:
--        testFlags = []
--      # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but  f90 & CC do not.
-+      testFlags = []
-       if self.isSun(self.framework.getCompiler()):
-         testFlags.insert(0,'-R')
-       for testFlag in testFlags:
diff --git a/sci-mathematics/petsc/files/petsc-3.3-fix-complex-threads.patch b/sci-mathematics/petsc/files/petsc-3.3-fix-complex-threads.patch
deleted file mode 100644
index ae41bab66..000000000
--- a/sci-mathematics/petsc/files/petsc-3.3-fix-complex-threads.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-As reported by disperato
-at https://github.com/gentoo-science/sci/issues/47
-compilation fails if complex scalars are used together with
-threads support.
-This fix to VecNorm_SeqPThread(...) was inspired by the
-implementation of VecNorm_Seq(...) in src/vec/vec/impls/seq/bvec2.c
-
-Index: petsc-3.3-p5/src/vec/vec/impls/seq/seqpthread/vecpthread.c
-===================================================================
---- a/src/vec/vec/impls/seq/seqpthread/vecpthread.c
-+++ b/src/vec/vec/impls/seq/seqpthread/vecpthread.c
-@@ -589,17 +589,33 @@ PetscErrorCode VecNorm_SeqPThread(...)
-     }
-     ierr = PetscThreadsRunKernel(VecNorm_Kernel,(void**)vec_pdata,tmap->nthreads,tmap->affinity);
-     /* collect results */
--    *z = (PetscReal)vec_kerneldatap[0].result;
-+#if defined(PETSC_USE_COMPLEX)
-+    *z = PetscRealPart(vec_kerneldatap[0].result);
-+#else
-+    *z = (PetscReal)vec_kerneldatap[0].result;
-+#endif
-     if(type == NORM_1) {
-       for(i=1; i<tmap->nthreads; i++) {
--        *z += (PetscReal)vec_kerneldatap[i].result;
-+#if defined(PETSC_USE_COMPLEX)
-+        *z += PetscRealPart(vec_kerneldatap[i].result);
-+#else
-+        *z += (PetscReal)vec_kerneldatap[i].result;
-+#endif
-       }
-       ierr = PetscLogFlops(PetscMax(xin->map->n-1.0+tmap->nthreads-1,0.0));CHKERRQ(ierr);
-     }
-     else if(type == NORM_2 || type == NORM_FROBENIUS) {
--      *z = (PetscReal)vec_kerneldatap[0].result;
-+#if defined(PETSC_USE_COMPLEX)
-+      *z = PetscRealPart(vec_kerneldatap[0].result);
-+#else
-+      *z = (PetscReal)vec_kerneldatap[0].result;
-+#endif
-       for(i=1; i<tmap->nthreads; i++) {
--        *z += (PetscReal)vec_kerneldatap[i].result;
-+#if defined(PETSC_USE_COMPLEX)
-+        *z += PetscRealPart(vec_kerneldatap[i].result);
-+#else
-+        *z += (PetscReal)vec_kerneldatap[i].result;
-+#endif
-       }
-       *z = PetscSqrtReal(*z);
-       ierr = PetscLogFlops(PetscMax(2.0*xin->map->n-1+tmap->nthreads-1,0.0));CHKERRQ(ierr);
-@@ -607,7 +623,11 @@
-     else {
-       PetscReal    maxv = 0.0,tmp;
-       for(i=0; i<tmap->nthreads; i++) {
--        tmp = (PetscReal)vec_kerneldatap[i].result;
-+#if defined(PETSC_USE_COMPLEX)
-+        tmp = PetscRealPart(vec_kerneldatap[i].result);
-+#else
-+        tmp = (PetscReal)vec_kerneldatap[i].result;
-+#endif
-         if(tmp>maxv) {
-           maxv = tmp;
-         }
diff --git a/sci-mathematics/petsc/files/petsc-3.4.2-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.4.2-disable-rpath.patch
deleted file mode 100644
index 0ccf45ded..000000000
--- a/sci-mathematics/petsc/files/petsc-3.4.2-disable-rpath.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- config/BuildSystem/config/setCompilers.py	2013-10-08 19:45:00.581513389 +0200
-+++ config/BuildSystem/config/setCompilers.py	2013-05-13 23:35:20.000000000 +0200
-@@ -1303,12 +1303,7 @@
-     for language in languages:
-       flag = '-L'
-       self.pushLanguage(language)
--      # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
--      if not Configure.isDarwin():
--        testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,']
--      else:
--        testFlags = []
--      # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but  f90 & CC do not.
-+      testFlags = []
-       if self.isSun(self.framework.getCompiler()):
-         testFlags.insert(0,'-R')
-       for testFlag in testFlags:
diff --git a/sci-mathematics/petsc/metadata.xml b/sci-mathematics/petsc/metadata.xml
index 4a93a4e06..e2722b4e3 100644
--- a/sci-mathematics/petsc/metadata.xml
+++ b/sci-mathematics/petsc/metadata.xml
@@ -10,6 +10,7 @@
     <flag name="boost">Use boost (dev-libs/boost)</flag>
     <flag name="hypre">Use HYPRE (sci-mathematics/hypre) and for preconditioning</flag>
     <flag name="complex-scalars">Make scalars complex</flag>
+    <flag name="metis">Add support for metis (<pkg>sci-libs/parmetis</pkg>)</flag>
     <flag name="sparse">Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization</flag>
     <flag name="superlu">Use superlu (sci-libs/superlu) for preconditioning</flag>
     <flag name="mumps">PLEASE FIX MY DESCRIPTION</flag>
diff --git a/sci-mathematics/petsc/petsc-3.4.2.ebuild b/sci-mathematics/petsc/petsc-3.4.2.ebuild
deleted file mode 100644
index 6e5c434c7..000000000
--- a/sci-mathematics/petsc/petsc-3.4.2.ebuild
+++ /dev/null
@@ -1,240 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator
-
-MY_P="${PN}-$(replace_version_separator _ -)"
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="http://www.mcs.anl.gov/petsc/"
-SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz"
-
-LICENSE="petsc"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="afterimage complex-scalars cxx debug doc
-	fortran hdf5 hypre mpi mumps scotch sparse superlu threads X"
-# Failed: boost imagemagick metis
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
-	afterimage? ( X )
-	hdf5? ( mpi )
-	hypre? ( cxx mpi )
-	mumps? ( mpi scotch )
-	scotch? ( mpi )
-	^^ ( hypre superlu )
-"
-#	imagemagick? ( X )
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	afterimage? ( media-libs/libafterimage )
-	hdf5? ( sci-libs/hdf5[mpi?] )
-	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
-	mpi? ( virtual/mpi[cxx?,fortran?] )
-	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
-	scotch? ( sci-libs/scotch[mpi?] )
-	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
-	superlu? ( sci-libs/superlu )
-	X? ( x11-libs/libX11 )
-"
-#	boost? ( dev-libs/boost )
-#	metis? ( sci-libs/parmetis )
-#	imagemagick? ( media-gfx/imagemagick )
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-# cmake is used for parallel building
-# in some configuration setups, legacy build is used (slow)
-
-#
-# PETSc does not want its Makefiles to be invoked with anything higher than
-# -j1. The underlying build system does automatically invoke a parallel
-# build. This might not be what you want, but *hey* not your choice.
-#
-MAKEOPTS="${MAKEOPTS} -j1"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P%_*}-disable-rpath.patch
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-src_configure() {
-	# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
-	petsc_enable() {
-		use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
-	}
-	# add external library:
-	# petsc_with use_flag libname libdir
-	# petsc_with use_flag libname include linking_libs
-	petsc_with() {
-		local myuse p=${2:-${1}}
-		if use ${1}; then
-			myuse="--with-${p}=1"
-			if [[ $# -ge 4 ]]; then
-				myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
-				shift 3
-				myuse="${myuse} --with-${p}-lib=$@"
-			else
-				myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
-			fi
-		else
-			myuse="--with-${p}=0"
-		fi
-		echo ${myuse}
-	}
-
-	# select between configure options depending on use flag
-	petsc_select() {
-		use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
-	}
-
-	local mylang
-	local myopt
-
-	use cxx && mylang="cxx" || mylang="c"
-	use debug && myopt="debug" || myopt="opt"
-
-	# environmental variables expected by petsc during build
-	export PETSC_DIR="${S}"
-	export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
-
-	if use debug; then
-		strip-flags
-		filter-flags -O*
-	fi
-
-	# C Support on Cxx builds is enabled if possible
-	# i.e. when not using complex scalars
-	# (no complex type for both available at the same time)
-
-	if use threads; then
-		ewarn "Threads support may be incomplete on $PN-3.3 release and is not officially supported."
-		ewarn "Upstream recommends not to enable threads support for production runs."
-	fi
-
-	# run petsc configure script
-	econf \
-		scrollOutput=1 \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		--with-shared-libraries \
-		--with-single-library \
-		--with-clanguage=${mylang} \
-		$(use cxx && ! use complex-scalars && echo "with-c-support=1") \
-		--with-petsc-arch=${PETSC_ARCH} \
-		--with-precision=double \
-		--with-gnu-compilers \
-		--with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		$(petsc_enable debug debugging) \
-		$(petsc_enable mpi) \
-		$(petsc_select mpi cc mpicc $(tc-getCC)) \
-		$(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
-		$(petsc_enable fortran) \
-		$(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
-		$(petsc_enable mpi mpi-compilers) \
-		$(petsc_enable threads pthread) \
-		$(petsc_enable threads pthreadclasses) \
-		$(petsc_select complex-scalars scalar-type complex real) \
-		--with-windows-graphics=0 \
-		--with-matlab=0 \
-		--with-cmake=cmake \
-		$(petsc_with afterimage afterimage \
-			/usr/include/libAfterImage -lAfterImage) \
-		$(petsc_with hdf5) \
-		$(petsc_with hypre hypre \
-			/usr/include/hypre -lHYPRE) \
-		$(petsc_with sparse cholmod) \
-		$(petsc_with superlu superlu \
-			/usr/include/superlu -lsuperlu) \
-		$(petsc_with X x) \
-		$(petsc_with X x11) \
-		$(petsc_with scotch ptscotch \
-			/usr/include/scotch \
-		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
-		$(petsc_with mumps scalapack \
-			/usr/include/scalapack -lscalapack) \
-		$(petsc_with mumps mumps \
-			/usr/include \
-			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
-		--with-imagemagick=0 \
-		--with-python=0
-
-# not yet tested:
-#		python bindings, netcdf
-# non-working:
-#		fftw: no mpi-implementaion available in gentoo
-
-# failed dependencies, perhaps fixed in upstream soon:
-#		$(petsc_with metis parmetis) \ # needs metis too (>=5.0.2)
-#		$(petsc_with boost) \
-#		$(petsc_with imagemagick imagemagick \
-#			/usr/include/ImageMagick $($(tc-getPKG_CONFIG) --libs MagickCore)) \
-}
-
-src_install() {
-	# petsc install structure is very different from
-	# installing headers to /usr/include/petsc and lib to /usr/lib
-	# it also installs many unneeded executables and scripts
-	# so manual install is easier than cleanup after "emake install"
-	insinto /usr/include/${PN}
-	doins include/*.h*
-	insinto /usr/include/${PN}/${PETSC_ARCH}/include
-	doins ${PETSC_ARCH}/include/*
-	if use fortran; then
-		insinto /usr/include/${PN}/finclude
-		doins include/finclude/*.h
-	fi
-	if ! use mpi ; then
-		insinto /usr/include/${PN}/mpiuni
-		doins include/mpiuni/*.h
-	fi
-	insinto /usr/include/${PN}/conf
-	doins conf/{variables,rules,test}
-	insinto /usr/include/${PN}/${PETSC_ARCH}/conf
-	doins ${PETSC_ARCH}/conf/{petscrules,petscvariables,RDict.db}
-	insinto /usr/include/${PN}/petsc-private
-	doins include/petsc-private/*.h
-
-	# fix configuration files: replace "${S}" by installed location
-	sed -i \
-		-e "s:"${S}"::g" \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die
-	sed -i \
-		-e "s:-I/include:-I${EPREFIX}/usr/include/${PN}:g" \
-		-e "s:-I/linux-gnu-cxx-opt/include:-I${EPREFIX}/usr/include/${PN}/${PETSC_ARCH}/include/:g" \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die
-	sed -i \
-		-e "s:usr/lib:usr/$(get_libdir):g" \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h || die
-
-	# add information about installation directory and
-	# PETSC_ARCH to environmental variables
-	cat >> 99petsc <<- EOF
-		PETSC_ARCH=${PETSC_ARCH}
-		PETSC_DIR=${EPREFIX}/usr/include/${PN}
-	EOF
-	doenvd 99petsc
-
-	dolib.so ${PETSC_ARCH}/lib/*.so
-
-	if use doc ; then
-		einfo "installing documentation (this could take a while)"
-		dodoc docs/manual.pdf
-		dohtml -r docs/*.html docs/changes docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/petsc/petsc-3.7.5.ebuild b/sci-mathematics/petsc/petsc-3.7.6.ebuild
index 1ac1003d5..fb856204a 100644
--- a/sci-mathematics/petsc/petsc-3.7.5.ebuild
+++ b/sci-mathematics/petsc/petsc-3.7.6.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
@@ -17,8 +17,7 @@ LICENSE="petsc"
 SLOT="0"
 KEYWORDS="~x86 ~amd64"
 IUSE="afterimage boost complex-scalars cxx debug doc fftw
-	fortran hdf5 hypre mpi mumps scotch sparse superlu threads X"
-# Failed: imagemagick metis
+	fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
 
 # hypre and superlu curretly exclude each other due to missing linking to hypre
 # if both are enabled
@@ -30,7 +29,6 @@ REQUIRED_USE="
 	scotch? ( mpi )
 	^^ ( hypre superlu )
 "
-#	imagemagick? ( X )
 
 RDEPEND="
 	virtual/blas
@@ -40,6 +38,7 @@ RDEPEND="
 	fftw? ( sci-libs/fftw:3.0[mpi?] )
 	hdf5? ( sci-libs/hdf5[mpi?] )
 	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
+	metis? ( >=sci-libs/parmetis-4 )
 	mpi? ( virtual/mpi[cxx?,fortran?] )
 	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
 	scotch? ( sci-libs/scotch[mpi?] )
@@ -47,16 +46,12 @@ RDEPEND="
 	superlu? ( sci-libs/superlu )
 	X? ( x11-libs/libX11 )
 "
-#	metis? ( sci-libs/parmetis )
-#	imagemagick? ( media-gfx/imagemagick )
 
 DEPEND="${RDEPEND}
 	${PYTHON_DEPS}
 	virtual/pkgconfig
 	dev-util/cmake
 "
-# cmake is used for parallel building
-# in some configuration setups, legacy build is used (slow)
 
 #
 # PETSc does not want its Makefiles to be invoked with anything higher than
@@ -69,14 +64,46 @@ MAKEOPTS="${MAKEOPTS} -j1 V=1"
 
 S="${WORKDIR}/${MY_P}"
 
+PATCHES=(
+	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
+	"${FILESDIR}"/${PN}-3.7.0-fix_sandbox_violation.patch
+)
+
 src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
-		"${FILESDIR}"/${PN}-3.7.0-fix_sandbox_violation.patch
+	default
 
 	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
 }
 
+# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
+petsc_enable() {
+	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
+}
+# add external library:
+# petsc_with use_flag libname libdir
+# petsc_with use_flag libname include linking_libs
+petsc_with() {
+	local myuse p=${2:-${1}}
+	if use ${1}; then
+		myuse="--with-${p}=1"
+		if [[ $# -ge 4 ]]; then
+			myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
+			shift 3
+			myuse="${myuse} --with-${p}-lib=$@"
+		else
+			myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
+		fi
+	else
+		myuse="--with-${p}=0"
+	fi
+	echo ${myuse}
+}
+
+# select between configure options depending on use flag
+petsc_select() {
+	use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
+}
+
 src_configure() {
 	# bug 548498
 	# PETSc runs mpi processes during configure that result in a sandbox
@@ -89,35 +116,6 @@ src_configure() {
 	# governor rw.
 	addpredict /sys/devices/system/cpu/
 
-	# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
-	petsc_enable() {
-		use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
-	}
-	# add external library:
-	# petsc_with use_flag libname libdir
-	# petsc_with use_flag libname include linking_libs
-	petsc_with() {
-		local myuse p=${2:-${1}}
-		if use ${1}; then
-			myuse="--with-${p}=1"
-			if [[ $# -ge 4 ]]; then
-				myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
-				shift 3
-				myuse="${myuse} --with-${p}-lib=$@"
-			else
-				myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
-			fi
-		else
-			myuse="--with-${p}=0"
-		fi
-		echo ${myuse}
-	}
-
-	# select between configure options depending on use flag
-	petsc_select() {
-		use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
-	}
-
 	local mylang
 	local myopt
 
@@ -125,6 +123,7 @@ src_configure() {
 	use debug && myopt="debug" || myopt="opt"
 
 	# environmental variables expected by petsc during build
+
 	export PETSC_DIR="${S}"
 	export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
 
@@ -133,17 +132,16 @@ src_configure() {
 		filter-flags -O*
 	fi
 
-	# C Support on Cxx builds is enabled if possible
-	# i.e. when not using complex scalars
-	# (no complex type for both available at the same time)
+	# C Support on CXX builds is enabled if possible i.e. when not using
+	# complex scalars (no complex type for both available at the same time)
 
-	# run petsc configure script
 	econf \
 		scrollOutput=1 \
 		FFLAGS="${FFLAGS} -fPIC" \
 		CFLAGS="${CFLAGS} -fPIC" \
 		CXXFLAGS="${CXXFLAGS} -fPIC" \
 		LDFLAGS="${LDFLAGS}" \
+		--prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
 		--with-shared-libraries \
 		--with-single-library \
 		--with-clanguage=${mylang} \
@@ -186,73 +184,19 @@ src_configure() {
 		--with-python=0 \
 		$(petsc_with boost) \
 		$(petsc_with fftw)
-
-# not yet tested:
-#		python bindings, netcdf, fftw
-
-# failed dependencies, perhaps fixed in upstream soon:
-#		$(petsc_with metis parmetis) \ # needs metis too (>=5.0.2)
-#		$(petsc_with imagemagick imagemagick \
-#			/usr/include/ImageMagick $($(tc-getPKG_CONFIG) --libs MagickCore)) \
-#		$(petsc_enable threads pthreadclasses) \
 }
 
 src_install() {
-	# petsc install structure is very different from
-	# installing headers to /usr/include/petsc and lib to /usr/lib
-	# it also installs many unneeded executables and scripts
-	# so manual install is easier than cleanup after "emake install"
-	insinto /usr/include/${PN}
-	doins include/*.h*
-	insinto /usr/include/${PN}/${PETSC_ARCH}/include
-	doins ${PETSC_ARCH}/include/*
-	if use fortran; then
-		insinto /usr/include/${PN}/finclude
-		doins -r include/${PN}/finclude/*
-	fi
-	if ! use mpi ; then
-		insinto /usr/include/${PN}/mpiuni
-		doins include/mpiuni/*.h
-	fi
-	insinto /usr/include/${PN}/conf
-	doins lib/${PN}/conf/{variables,rules,test}
-	insinto /usr/include/${PN}/${PETSC_ARCH}/conf
-	doins ${PETSC_ARCH}/lib/${PN}/conf/{petscrules,petscvariables,RDict.db}
-	insinto /usr/include/${PN}/private
-	doins include/${PN}/private/*.h
-
-	# fix configuration files: replace "${S}" by installed location
-	sed -i \
-		-e "s:"${S}"::g" \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die
-	sed -i \
-		-e "s:-I/include:-I${EPREFIX}/usr/include/${PN}:g" \
-		-e "s:-I/linux-gnu-cxx-opt/include:-I${EPREFIX}/usr/include/${PN}/${PETSC_ARCH}/include/:g" \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die
-	sed -i \
-		-e "s:usr/lib:usr/$(get_libdir):g" \
-		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h || die
+	emake DESTDIR="${D}/usr/$(get_libdir)/petsc" install
 
-	# fix the include path of petscvariables in lib/${PN}/conf/variables
-	# bug #559172
-	sed -i -e 's#lib/petsc/conf/#conf/#g' \
-		"${ED}"/usr/include/${PN}/conf/variables || die
-
-	# add information about installation directory and
-	# PETSC_ARCH to environmental variables
+	# add PETSC_DIR to environmental variables
 	cat >> 99petsc <<- EOF
-		PETSC_ARCH=${PETSC_ARCH}
-		PETSC_DIR=${EPREFIX}/usr/include/${PN}
+		PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc
 	EOF
 	doenvd 99petsc
 
-	dolib.so ${PETSC_ARCH}/lib/*.so
-	dolib.so ${PETSC_ARCH}/lib/*.so.*
-
 	if use doc ; then
-		einfo "installing documentation (this could take a while)"
-		dodoc docs/manual.pdf
+		dodoc docs/developers.pdf docs/manual.pdf
 		dohtml -r docs/*.html docs/changes docs/manualpages
 	fi
 }