sci-libs/suitesparse: bump to version 5.3.0

With update to 5.3.0 the package no longer comes in several shared
packages, but in a single package containing the complete suite of
sparse matrix packages.

Package-Manager: Portage-2.3.51, Repoman-2.3.12
Manifest-Sign-Key: 0x2E246A4E715AA683
Signed-off-by: Bernd Waibel <[email protected]>

sci-libs/suitesparse/Manifest

@@ -0,0 +1,5 @@
+AUX suitesparse-5.3.0-Makefile.patch 1468 BLAKE2B 355a5855bc3bf621c4304f66abb0b487a07ab4ee87558251e375ea883aca54c0bec1fc1ef4045271d0655240e66ef2bc04c6fdec3975e342addc4ab2a1e4b21b SHA512 73011af1eeb35a7f9f4bcbc147e83216cdd0a3a37bbe27ec3ce1172578d9a2a02c94c0de491eba1e51bdf8a9546e8a4ecf1cfb58710d3eb79f0bc6a5d54a0366
+AUX suitesparse-5.3.0-config.patch 531 BLAKE2B d8f627b4f4278f0d934fb1800ced683139bf47354e8f1c221f9bd6ea380223c8065df0a802bc2f757d3a24bf04c67b523a1601757a6da5d899b8d2f64446ac5a SHA512 ba45ad732f301d9da6783dc6519ac63cb4693b4a1dfed8f35496097f5e7dd10579cc29e5a4ef0b4f2cbbdfe7ce0a6943ff733fa6873d5268869a8a8013d21628
+DIST suitesparse-5.3.0.tar.gz 50500894 BLAKE2B 6af9fd39052a55a6f07dbac2e9199455747e61ab08be3e65ec5bb9cf2d0b42dd240edd9abfba560217232482b59ee74be3911de1b4bdf5e16dce77b719282e9e SHA512 a7ac655c5454c8270a52ece802946893f02d12c1bfb10546e24cd8355e59b733961526e9d702cd649b90b47bb325ace5110f70054db3754c732bc3ec1fa42cf9
+EBUILD suitesparse-5.3.0.ebuild 4622 BLAKE2B 734ce26700aeeaafdec7b94b1ffabe6806bac9c6c71db276412747b836215e2964df836679214c85361465280e8de4d41c3c16698e682739c74a143b6d5e3e8a SHA512 70d9e29f47e514784bc895e3c5aa9627ddb4b29cb610e10877194e4fdfd25ee6e93e245327422716ae17ff608ebdba2bd2ee3e3a5a2e87eac7c1f95be5a95386
+MISC metadata.xml 1699 BLAKE2B fd298ed713a1bb29de7a9e874e8b73ce6bc1a4cb45889e3a1d786d746e35c243fd8ce6dc1d74b03a18b70c29475f499fe21682d1dd1e63dead15bedbb54fa199 SHA512 19952506e14cd08ccb0182b468b9459bc05330fbd302ed92349b55b45ffda956a180f2b88c54a3702ee5fe515e791431cc179263ba85f32632c9b8652e0c61d8

sci-libs/suitesparse/files/suitesparse-5.3.0-Makefile.patch

@@ -0,0 +1,42 @@
+diff --git a/AMD/Lib/Makefile b/AMD/Lib/Makefile
+index 3b92f6a..3c40cc2 100644
+--- a/AMD/Lib/Makefile
++++ b/AMD/Lib/Makefile
+@@ -62,7 +62,7 @@ $(AR_TARGET): $(OBJ)
+ # compile the Fortran versions and the libamdf77.a library (static only)
+ #-------------------------------------------------------------------------------
+
+-fortran: libamdf77.a
++fortran: libamdf77.a libamdf77.so.$(VERSION)
+
+ AMDF77 = amd.o amdbar.o
+
+@@ -76,6 +76,12 @@ libamdf77.a: $(AMDF77)
+ 	$(ARCHIVE) libamdf77.a $^
+ 	- $(RANLIB) libamdf77.a
+
++libamdf77.so.$(VERSION): $(AMDF77)
++	$(CC) $(SO_OPTS) $^ -o $@ $(LDLIBS)
++	ln -sf $@ libamdf77.so.$(SO_VERSION)
++	ln -sf $@ libamdf77.so
++	chmod 755 $@
++
+ #-------------------------------------------------------------------------------
+ # install (shared C version only)
+ #-------------------------------------------------------------------------------
+@@ -98,6 +104,15 @@ $(INSTALL_LIB)/$(SO_TARGET): $(OBJ)
+ 	chmod 644 $(INSTALL_DOC)/AMD_UserGuide.pdf
+ 	chmod 644 $(INSTALL_DOC)/AMD_README.txt
+
++install-fortran: $(INSTALL_LIB)/libamdf77.so.$(VERSION)
++
++$(INSTALL_LIB)/libamdf77.so.$(VERSION): fortran
++	@mkdir -p $(INSTALL_LIB)
++	$(CC) $(SO_OPTS) $(AMDF77) -o $@ $(LDLIBS)
++	( cd $(INSTALL_LIB) ; ln -sf libamdf77.so.$(VERSION) libamdf77.so.$(SO_VERSION) )
++	( cd $(INSTALL_LIB) ; ln -sf libamdf77.so.$(VERSION) libamdf77.so )
++	chmod 755 $(INSTALL_LIB)/libamdf77.so.$(VERSION)
++
+ # uninstall AMD
+ uninstall:
+ 	$(RM) $(INSTALL_LIB)/$(SO_TARGET)

sci-libs/suitesparse/files/suitesparse-5.3.0-config.patch

@@ -0,0 +1,13 @@
+diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
+index f991b7a..1fbb7e9 100644
+--- a/SuiteSparse_config/SuiteSparse_config.mk
++++ b/SuiteSparse_config/SuiteSparse_config.mk
+@@ -348,7 +348,7 @@ SUITESPARSE_VERSION = 5.3.0
+
+     ifeq ($(UNAME),Linux)
+         # add the realtime library, librt, and SuiteSparse/lib
+-        LDLIBS += -lrt -Wl,-rpath=$(INSTALL_LIB)
++        LDLIBS += -lrt
+     endif
+
+     #---------------------------------------------------------------------------

sci-libs/suitesparse/metadata.xml

@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+	<email>[email protected]</email>
+	<name>Gentoo Science Project</name>
+</maintainer>
+<longdescription lang="en">
+<!-- FIXME: rework this -->
+SuiteSparse is a suite of sparse matrix libraries from University of
+Florida Computer Science Department. Currently, this includes:
+	* AMD: symmetric approximate minimum degree
+	* BTF: permutation to block triangular form
+	* CAMD: symmetric approximate minimum degree
+	* CCOLAMD: constrained column approximate minimum degree
+	* COLAMD: column approximate minimum degree
+	* CHOLMOD: sparse supernodal Cholesky factorization and update/downdate
+	* CSparse: a concise sparse matrix package
+	* CXSparse: an extended version of CSparse
+	* GraphBLAS: graph algorithms implemented with BLAS
+	* KLU: sparse LU factorization, for circuit simulation
+	* LDL: a simple LDL^T factorization
+	* Mongoose: graph partioning package
+	* RBio: read/write sparse matrices in Rutherford / Boeing format
+	* SPQR: multifrontal sparse QT factorization
+	* SuiteSparse_config: common configuration for all but CSparse
+	* UMFPACK: sparse multifrontal LU factorization
+The Gentoo package does not include the suitesparse MATLAB tools from
+upstream, from the packages above and the following MATLAB-only packages:
+	* LINFACTOR: solve Ax=b using LU or CHOL
+	* MESHND: 2D and 3D mesh generation and nested dissection
+	* SSMULT: sparse matrix times sparse matrix 
+</longdescription>
+<use>
+	<flag name="cuda">Use CUDA for cholmod and spqr</flag>
+	<flag name="tbb">Use Intel's <pkg>dev-cpp/tbb</pkg> for threading</flag>
+</use>
+</pkgmetadata>

sci-libs/suitesparse/suitesparse-5.3.0.ebuild

@@ -0,0 +1,161 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+# FIXME: currently this is a safety measure. Is it really needed by the
+#	fortran modules?
+FORTRAN_NEED_OPENMP=1
+
+# FIXME: how to handle cmake without having a root CMakeLists.txt?
+inherit fortran-2 toolchain-funcs
+
+MY_PN="SuiteSparse"
+
+DESCRIPTION="Package for a suite of sparse matrix tools"
+HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html"
+SRC_URI="http://faculty.cse.tamu.edu/davis/${MY_PN}/${MY_PN}-${PV}.tar.gz -> ${P}.tar.gz"
+
+# BSD: amd, camd, ccolamd, colamd, ssget
+# LGPL-2.1+: btf, cholmod/Check, choldmod/Cholesky, cholmod/Core,
+#	cholmod/Partition, cxsparse, klu, ldl
+# GPL-2+: choldmod/Demo, cholmod/Matlab, cholmod/MatrixOps,
+#	cholmod/Modify, cholmod/Supernodal, cholmod/Tcov, cholmod/Valgrind,
+#	GPUQREngine, RBio, spqr, SuiteSparse_GPURuntime, umfpack
+# Apache-2.0: GraphBLAS
+# GPL-3: Mongoose
+LICENSE="Apache-2.0 BSD GPL-2+ GPL-3 LGPL-2.1+"
+SLOT="0"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+FORTRAN_NEEDED="amd"
+
+# FIXME: currently not included:
+#	Piro_Band, Skyline_SVD
+# GraphBLAS and Mongoose are cmake based builds
+# SuiteSparse_GPURuntime and GPUQREngine are part of spqr[cuda]
+# FIXME: cuda is not compiling due to C/C++ mixing
+# FIXME: testing
+IUSE="cuda fortran tbb test"
+
+RESTRICT="!test? ( test )"
+
+# FIXME: Exclude the old packages. These could be removed once the package
+# and revdeps are fully updated.
+RDEPEND="
+	!<sci-libs/suitesparse-5
+	!sci-libs/amd
+	!sci-libs/btf
+	!sci-libs/camd
+	!sci-libs/ccolamd
+	!sci-libs/cholmod
+	!sci-libs/colamd
+	!sci-libs/cxsparse
+	!sci-libs/klu
+	!sci-libs/ldl
+	!sci-libs/spqr
+	!sci-libs/suitesparseconfig
+	!sci-libs/umfpack
+	|| ( >=sci-libs/metis-5.1.0-r3[openmp(+)] >=sci-libs/parmetis-4.0.3[openmp(+)] )
+	virtual/blas:=
+	virtual/lapack:=
+	cuda? (
+		>=dev-util/nvidia-cuda-toolkit-9.2.88:=
+		>=sci-libs/magma-2.4.0:=
+	)
+	tbb? ( >=dev-cpp/tbb-2017.20161128:= )
+"
+
+DEPEND="
+	${RDEPEND}
+	>=dev-util/indent-2.2.11-r1
+	>=sys-apps/grep-3.1
+	test? ( >=app-shells/tcsh-6.20.00 )
+"
+
+S=${WORKDIR}/${MY_PN}
+
+PATCHES=(
+	"${FILESDIR}/${P}-config.patch"
+	"${FILESDIR}/${P}-Makefile.patch"
+)
+
+DOCS=( README.txt )
+
+pkg_setup() {
+	# several of the packages need openmp support, so check for it early
+	tc-check-openmp || die "Need OpenMP to build ${P}"
+}
+
+src_compile() {
+	local myblas=$($(tc-getPKG_CONFIG) --libs blas)
+	local mylapack=$($(tc-getPKG_CONFIG) --libs lapack)
+	# FIXME: AUTOCC auto-enables intel compilers
+	local mymakeopts="OPTIMIZATION= AUTOCC=no"
+	mymakeopts="${mymakeopts} LAPACK=\"${mylapack}\" BLAS=\"${myblas}\""
+	mymakeopts="${mymakeopts} MY_METIS_LIB=-lmetis"
+	if use cuda; then
+		mymakeopts="${mymakeopts} CUDA=yes magma_inc=/usr magma_lib=/usr/$(get_libdir)"
+	else
+		mymakeopts="${mymakeopts} CUDA=no"
+	fi
+	if use fortran; then
+		local myf77=$(tc-getF77)
+		mymakeopts="${mymakeopts} F77=${myf77}"
+	fi
+	if use tbb; then
+		mymakeopts="${mymakeopts} TBB=-ltbb SPQR_CONFIG+=-DHAVE_TBB"
+	fi
+	use test && mymakeopts="${mymakeopts} TCOV=yes"
+	export LD_LIBRARY_PATH="${S}/lib"
+	emake ${mymakeopts} config # FIXME: remove on final ebuild
+	emake ${mymakeopts}
+	if use fortran; then
+		emake -C "${S}/AMD" fortran ${mymakeopts}
+	fi
+}
+
+src_test() {
+	local myblas=$($(tc-getPKG_CONFIG) --libs blas)
+	local mylapack=$($(tc-getPKG_CONFIG) --libs lapack)
+	local mytestargs="OPTIMIZATION= AUTOCC=no BLAS=${myblas} LAPACK=${mylapack}"
+	mytestargs="${mytestargs} MY_METIS_LIB=-lmetis"
+	if use cuda; then
+		mytestargs="${mytestargs} CUDA=yes magma_inc=/usr magma_lib=/usr/$(get_libdir)"
+	else
+		mytestargs="${mytestargs} CUDA=no"
+	fi
+	if use fortran; then
+		local myf77=$(tc-getF77)
+		mytestargs="${mytestargs} F77=${myf77}"
+	fi
+	if use tbb; then
+		mytestargs="${mytestargs} TBB=-ltbb SPQR_CONFIG+=-DHAVE_TBB"
+	fi
+	export LD_LIBRARY_PATH="${S}/lib"
+	emake ${mytestargs} cov
+}
+
+src_install() {
+	local myblas=$($(tc-getPKG_CONFIG) --libs blas)
+	local mylapack=$($(tc-getPKG_CONFIG) --libs lapack)
+	local myinstallargs="INSTALL=${ED%/}/usr INSTALL_LIB=${ED%/}/usr/$(get_libdir)"
+	myinstallargs="${myinstallargs} BLAS=${myblas} LAPACK=${mylapack} MY_METIS_LIB=-lmetis"
+	if use cuda; then
+		myinstallargs="${myinstallargs} CUDA=yes magma_inc=/usr magma_lib=/usr/$(get_libdir)"
+	else
+		myinstallargs="${myinstallargs} CUDA=no"
+	fi
+	if use fortran; then
+		local myf77=$(tc-getF77)
+		myinstallargs="${myinstallargs} F77=${myf77}"
+	fi
+	if use tbb; then
+		myinstallargs="${myinstallargs} TBB=-ltbb SPQR_CONFIG+=-DHAVE_TBB"
+	fi
+	emake ${myinstallargs} install
+	if use fortran; then
+		emake -C "${S}/AMD/Lib" ${myinstallargs} install-fortran
+	fi
+}