sci-libs/linbox: new C++ template library for linear algebra.

This is a straightforward import of the sci-libs/linbox package from
the sage-on-gentoo overlay where François Bissey has been maintaining
it. Linbox is a dependency of SageMath, and users will soon be able to
use the system copy of linbox; see ticket 29631 on the SageMath Trac
instance. Having this in Gentoo will therefore avoid pointless
rebuilds of linbox for our SageMath users.

Closes: https://bugs.gentoo.org/227813
Package-Manager: Portage-2.3.89, Repoman-2.3.20
Signed-off-by: Michael Orlitzky <mjo@gentoo.org>

4 files changed, 158 insertions, 0 deletions

diff --git a/sci-libs/linbox/Manifest b/sci-libs/linbox/Manifest
new file mode 100644
index 000000000000..11458f317018
--- /dev/null
+++ b/sci-libs/linbox/Manifest
@@ -0,0 +1 @@
+DIST linbox-1.6.3.tar.gz 1968034 BLAKE2B 55fb83db7da375d8d97f2567c6a120ac48fefc41eb02db68152cc32f1f16009b8c8108a07bbc68087ad2ef3279108db61b48b805c9ce39f4c5f0072ab6e96304 SHA512 ccef3b4c7b9d8f999e5e4ce4e544f22cd869154513827501ecb7e1abf132ff585dfb3315cced963abe842feecda9331dda9081efb3948987365d338223a8305c
diff --git a/sci-libs/linbox/files/linbox-1.6.3-pc.patch b/sci-libs/linbox/files/linbox-1.6.3-pc.patch
new file mode 100644
index 000000000000..de0025108b89
--- /dev/null
+++ b/sci-libs/linbox/files/linbox-1.6.3-pc.patch
@@ -0,0 +1,25 @@
+From 8fb95a5dba51fbfcd37db10da4db69d518f7b0f4 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= <frp.bissey@gmail.com>
+Date: Fri, 24 Apr 2020 14:10:05 +1200
+Subject: [PATCH] Remove @LINBOX_SAGE@ from linbox.pc.in. linbox_sage is gone
+ and the string stays as garbage in the final .pc file.
+
+---
+ linbox.pc.in | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/linbox.pc.in b/linbox.pc.in
+index f54285e..1f83834 100644
+--- a/linbox.pc.in
++++ b/linbox.pc.in
+@@ -9,6 +9,6 @@ Description: Exact Linear Algebra library
+ URL: http://github.com/linbox-team/linbox
+ Version: @VERSION@
+ Requires: fflas-ffpack >= 2.4.0, givaro >= 4.1.0
+-Libs: -L${libdir} -llinbox @LINBOXSAGE_LIBS@ @NTL_LIBS@ @MPFR_LIBS@ @FPLLL_LIBS@ @IML_LIBS@ @FLINT_LIBS@ @OCL_LIBS@
++Libs: -L${libdir} -llinbox @NTL_LIBS@ @MPFR_LIBS@ @FPLLL_LIBS@ @IML_LIBS@ @FLINT_LIBS@ @OCL_LIBS@
+ Cflags: @DEFAULT_CFLAGS@ -DDISABLE_COMMENTATOR -I${includedir} @NTL_CFLAGS@ @MPFR_CFLAGS@ @FPLLL_CFLAGS@  @IML_CFLAGS@ @FLINT_CFLAGS@ 
+ \-------------------------------------------------------
+-- 
+2.26.2
+
diff --git a/sci-libs/linbox/linbox-1.6.3.ebuild b/sci-libs/linbox/linbox-1.6.3.ebuild
new file mode 100644
index 000000000000..db82ccb781cd
--- /dev/null
+++ b/sci-libs/linbox/linbox-1.6.3.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="C++ template library for integer and finite-field linear algebra"
+HOMEPAGE="https://linalg.org/"
+SRC_URI="https://github.com/linbox-team/${PN}/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos"
+IUSE="doc opencl openmp static-libs cpu_flags_x86_fma3 cpu_flags_x86_fma4 cpu_flags_x86_sse cpu_flags_x86_sse2 cpu_flags_x86_sse3 cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+BDEPEND="doc? ( app-doc/doxygen )"
+
+# The project README says that gmp, givaro, and blas/lapack are required
+# transitively via fflas-ffpack, but that's not true. The build system
+# checks for them, and `git grep` shows that they're used directly.
+DEPEND="dev-libs/gmp[cxx]
+	=sci-libs/givaro-4.1*
+	=sci-libs/fflas-ffpack-2.4*
+	virtual/cblas
+	virtual/lapack
+	opencl? ( virtual/opencl )
+	dev-libs/ntl:=
+	sci-libs/iml
+	dev-libs/mpfr:=
+	sci-mathematics/flint"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}/${PN}-1.6.3-pc.patch" )
+
+pkg_pretend() {
+	[[ "${MERGE_TYPE}" != "binary" ]] && use openmp && tc-check-openmp
+}
+
+src_configure() {
+	#
+	# The --with-all flag includes,
+	#
+	#   --with-givaro: used for finite fields, integer, etc. (required)
+	#   --with-fflas-ffpack:  small field dense linear algebra (required)
+	#   --with-ntl: used for finite field, polynomial arithmetic (optional)
+	#   --with-iml: used for fast integer/rational linear algebra (optional)
+	#   --with-mpfr: not sure, doesn't seem to be used? (optional)
+	#   --with-flint: used in algorithms/matrix-blas3 once (optional)
+	#   --with-fplll: an fplll interface not directly used (optional)
+	#   --with-doxygen: needed with --enable-doc to build them (optional)
+	#
+	# Some of these could be behind USE flags, but the ./configure output
+	# says that they're "not yet mandatory," which makes me think we might
+	# be overcomplicating things to make them optional right now.
+	#
+	# Note: after v1.6.3, we'll need to append --without-archnative to
+	# these flags to avoid -march=native being appended by default.
+	#
+	econf \
+		--with-docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		--with-all="${EPREFIX}"/usr \
+		--without-fplll \
+		$(use_enable doc) \
+		$(use_enable openmp) \
+		$(use_with opencl ocl) \
+		$(use_enable cpu_flags_x86_fma3 fma) \
+		$(use_enable cpu_flags_x86_fma4 fma4) \
+		$(use_enable cpu_flags_x86_sse3 sse) \
+		$(use_enable cpu_flags_x86_sse3 sse2) \
+		$(use_enable cpu_flags_x86_sse3 sse3) \
+		$(use_enable cpu_flags_x86_ssse3 ssse3) \
+		$(use_enable cpu_flags_x86_sse4_1 sse41) \
+		$(use_enable cpu_flags_x86_sse4_2 sse42) \
+		$(use_enable cpu_flags_x86_avx avx) \
+		$(use_enable cpu_flags_x86_avx2 avx2) \
+		$(use_enable static-libs static)
+}
+
+src_install(){
+	default
+	find "${ED}" -name '*.la' -delete || die
+	if use doc; then
+		# These files are used for incremental doxygen builds but aren't
+		# part of the final output. Check on
+		#
+		#   https://github.com/linbox-team/linbox/issues/252
+		#
+		# periodically to see if this is pointless.
+		find "${ED}/usr/share/doc/${PF}" -type f -name '*.md5' -delete || die
+		find "${ED}/usr/share/doc/${PF}" -type f -name '*.map' -delete || die
+	fi
+}
diff --git a/sci-libs/linbox/metadata.xml b/sci-libs/linbox/metadata.xml
new file mode 100644
index 000000000000..b8fdd1af15d4
--- /dev/null
+++ b/sci-libs/linbox/metadata.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <maintainer type="person">
+    <email>mjo@gentoo.org</email>
+  </maintainer>
+  <!--
+      mjo: François maintained this package in the sage-on-gentoo overlay
+      long before I moved it into ::gentoo. You don't need an ACK from me
+      to merge his changes.
+  -->
+  <maintainer type="person">
+    <email>frp.bissey@gmail.com</email>
+    <name>François Bissey</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>proxy-maint@gentoo.org</email>
+    <name>Proxy Maintainers</name>
+  </maintainer>
+
+  <use>
+    <flag name="opencl">
+      Enable the use of OpenCL in LinBox
+    </flag>
+  </use>
+
+  <longdescription lang="en">
+    LinBox is a C++ template library for exact, high-performance
+    linear algebra computation with dense, sparse, and structured
+    matrices over the integers and over finite fields. LinBox relies
+    on closely aligned libraries fflas-ffpack (exact dense matrix
+    linear algebra kernels), and Givaro (finite fields, integers, and
+    polynomials).
+  </longdescription>
+
+  <upstream>
+    <remote-id type="github">linbox-team/linbox</remote-id>
+  </upstream>
+</pkgmetadata>