gentoo auto-resync : 14:11:2023 - 04:26:45

6 files changed, 257 insertions, 0 deletions

diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index f1806f8d5a9d..fa200b660496 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/polymake/Manifest b/sci-mathematics/polymake/Manifest
new file mode 100644
index 000000000000..987a3369b0ec
--- /dev/null
+++ b/sci-mathematics/polymake/Manifest
@@ -0,0 +1,5 @@
+AUX polymake-4.11-barycentric-subdiv.patch 807 BLAKE2B e2e632146e6d96e5966444283a0226caf26dfd7dab482a35289e2b6f9acaa791db015787b4b91f5c2f3abc47323227377dd296dfc21b777315979e58d2e36af8 SHA512 f5332d3a558a0b3dc1b0cc0846131210857d2a6ad11647fd64cd5366c04c349752d06e30da3f93568ff5d2f04f8419b8c9ef6e71460e997c295cb6959a8964e1
+AUX polymake-4.11-singular-sat.patch 2212 BLAKE2B 659d07040141617f7ac6cb8572c44bf4d9ba332f1f4ddb5434987ea900009ef2b3ebefa27ead63a60c6048b58c3a853c797d82af1f3c8793f2c506f09dfd43f0 SHA512 fc46ec6753ddf14d389b9e03421a909bf572e4e7d6acf3dec7319d3bf704ba7710ba1c4719bf6b9153599f523e36cf83ac8b8218141f72a43343c94373fc5b57
+DIST polymake-4.11-minimal.tar.bz2 7325783 BLAKE2B 87e62741e4e44c5fea7454d5cc8cb205cf13f8ee743c1d72100f937d0677505ce0c5c8f5b37c118f89079ca88f313991eaefb2ea02c49b6c7b45c438c6f9e13b SHA512 94adf3fcec21de50451091a04ca17010f5e71b44e3dcd4e2d52b9f952b94ee0cf3f6df15657b761b0bda20eb47cbdc0cb2481bb440c7243442be34f913292246
+EBUILD polymake-4.11.ebuild 3938 BLAKE2B 3be7f4538453e5d588176a5976e4bc8c3f7e8d5771096445bb82840846fee0dbb70cb04cf461663747b0c56066a8eb91eeb04f080d6c3d1a3ae83b3b052f0f59 SHA512 759382797478ae27197b0f760d5780e6643879ae0589dc21f9224d3a4e49ef381a6587f01080d78c6d48d8b68ce9e59916b59194584324c8c733de77be4ca45d
+MISC metadata.xml 1765 BLAKE2B 4e13dfb267c8100df81d8be89e7915ba850f55fea4256882264b13a0307c60cd8346ff46bf972018b334bf2d0dc387761244c1e0c3b8c7a1f4613a2a87458538 SHA512 7fd8af42bccc7710bd7c4159759b42ace43f638365a83defee96568e6ab4d6c186f49e71cbf68291fcd3b8b30fd7f883e8096c001c6bbf233d6f7336fa266f7c
diff --git a/sci-mathematics/polymake/files/polymake-4.11-barycentric-subdiv.patch b/sci-mathematics/polymake/files/polymake-4.11-barycentric-subdiv.patch
new file mode 100644
index 000000000000..2f58b0f76299
--- /dev/null
+++ b/sci-mathematics/polymake/files/polymake-4.11-barycentric-subdiv.patch
@@ -0,0 +1,23 @@
+commit d55dc6bd7f2da9245884f86706cb96e2d11fa83a
+Author: Benjamin Lorenz <lorenz@math.tu-berlin.de>
+Date:   Tue Nov 7 16:49:33 2023 +0100
+
+    barycentric_subdivision: dont call back on empty strings
+    
+    thanks jamesjer
+    
+    @Jenkins: merge
+
+diff --git a/apps/topaz/src/barycentric_subdivision.cc b/apps/topaz/src/barycentric_subdivision.cc
+index 753afb4040..e2d4130bc3 100644
+--- a/apps/topaz/src/barycentric_subdivision.cc
++++ b/apps/topaz/src/barycentric_subdivision.cc
+@@ -139,7 +139,7 @@ bs_data2Object(const bool realize,
+    else
+       desc << k << "th ";
+    desc << "barycentric subdivision of " << description;
+-   if (description.back() != '\n')
++   if (description.empty() || description.back() != '\n')
+       desc << endl;
+    p_out.set_description() << desc.str();
+    return p_out;
diff --git a/sci-mathematics/polymake/files/polymake-4.11-singular-sat.patch b/sci-mathematics/polymake/files/polymake-4.11-singular-sat.patch
new file mode 100644
index 000000000000..739e503ac246
--- /dev/null
+++ b/sci-mathematics/polymake/files/polymake-4.11-singular-sat.patch
@@ -0,0 +1,53 @@
+commit 4ce0549f510d246c8f69c85c509fc2d13d882442
+Author: Benjamin Lorenz <lorenz@math.tu-berlin.de>
+Date:   Thu Nov 9 11:15:06 2023 +0100
+
+    singular: support new return types for saturation command
+    
+    This was changed from (ideal, exponent) to just the ideal in singular 4-3-2p5.
+    To allow older versions we keep using sat but support both return types
+    instead of switching to the new sat_with_exp.
+
+diff --git a/bundled/singular/apps/ideal/src/singularIdeal.cc b/bundled/singular/apps/ideal/src/singularIdeal.cc
+index 4cbc00a6f4..bdade5c29d 100644
+--- a/bundled/singular/apps/ideal/src/singularIdeal.cc
++++ b/bundled/singular/apps/ideal/src/singularIdeal.cc
+@@ -236,22 +236,24 @@ public:
+       arg.next->data=(void *)idCopy(J);
+       // call primdecSY
+       BOOLEAN res=iiMake_proc(sathdl, nullptr ,&arg);
+-      if(!res && (iiRETURNEXPR.Typ() == LIST_CMD)){
+-         lists L = (lists)iiRETURNEXPR.Data();
+-         SingularIdeal_wrap* result;
+-         if(L->m[0].Typ() == IDEAL_CMD){
+-            result = new SingularIdeal_impl((::ideal) (L->m[0].Data()),singRing);
+-         } else {
+-            throw std::runtime_error("Something went wrong for the primary decomposition");
++      if(!res) {
++         ::ideal iddata = nullptr;
++         if (iiRETURNEXPR.Typ() == LIST_CMD) {
++            lists L = (lists)iiRETURNEXPR.Data();
++            if(L->m[0].Typ() == IDEAL_CMD)
++               iddata = (::ideal) L->m[0].Data();
++         } else if (iiRETURNEXPR.Typ() == IDEAL_CMD) {
++            iddata = (::ideal) iiRETURNEXPR.Data();
++         }
++         if (iddata != nullptr) {
++            SingularIdeal_wrap* result = new SingularIdeal_impl(iddata, singRing);
++            iiRETURNEXPR.CleanUp();
++            iiRETURNEXPR.Init();
++            return result;
+          }
+-         iiRETURNEXPR.CleanUp();
+-         iiRETURNEXPR.Init();
+-         return result;
+-      } else {
+-         iiRETURNEXPR.Init();
+-         throw std::runtime_error("Something went wrong for the saturation");
+       }
+-
++      iiRETURNEXPR.Init();
++      throw std::runtime_error("saturation: unable to parse ideal from return value");
+    }
+ 
+    Array<SingularIdeal_wrap*> primary_decomposition() const
diff --git a/sci-mathematics/polymake/metadata.xml b/sci-mathematics/polymake/metadata.xml
new file mode 100644
index 000000000000..e8e79ebd3fc8
--- /dev/null
+++ b/sci-mathematics/polymake/metadata.xml
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+  <email>sci-mathematics@gentoo.org</email>
+  <name>Gentoo Mathematics Project</name>
+</maintainer>
+<use>
+  <flag name="bliss">
+    Enable <pkg>sci-libs/bliss</pkg> interface for graph and face lattice
+    isomorphism computations.
+  </flag>
+  <flag name="cdd">
+    Enable <pkg>sci-libs/cddlib</pkg> interface for convex hull
+    computations (Should be kept enabled).
+  </flag>
+  <flag name="flint">
+    Build with "strongly recommended" support for
+    <pkg>sci-mathematics/flint</pkg>.
+  </flag>
+  <flag name="libpolymake">
+    Build the polymake library to build applications using the C++
+    interface.
+  </flag>
+  <flag name="lrs">
+    Enable <pkg>sci-libs/lrslib</pkg> interface for convex hull
+    computations.
+  </flag>
+  <flag name="nauty">
+    Build the extension for graph automorphism computations using
+    <pkg>sci-mathematics/nauty</pkg>.
+  </flag>
+  <flag name="normaliz">
+    Build the bundled extension for lattice computations using
+    <pkg>sci-mathematics/normaliz</pkg>.
+  </flag>
+  <flag name="ppl">
+    Enable <pkg>dev-libs/ppl</pkg> interface for convex hull computations.
+  </flag>
+  <flag name="singular">
+    Enable the interface to <pkg>sci-mathematics/singular</pkg> for
+    ideal related computations.
+  </flag>
+</use>
+<longdescription lang="en">
+  Polymake is open source software for research in polyhedral
+  geometry. It deals with polytopes, polyhedra, and fans as well as
+  simplicial complexes, matroids, graphs, tropical hypersurfaces, and
+  other objects.
+</longdescription>
+<upstream>
+  <remote-id type="github">polymake/polymake</remote-id>
+</upstream>
+</pkgmetadata>
diff --git a/sci-mathematics/polymake/polymake-4.11.ebuild b/sci-mathematics/polymake/polymake-4.11.ebuild
new file mode 100644
index 000000000000..5feccaae668e
--- /dev/null
+++ b/sci-mathematics/polymake/polymake-4.11.ebuild
@@ -0,0 +1,122 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic ninja-utils toolchain-funcs
+
+DESCRIPTION="Tool for polyhedral geometry and combinatorics"
+SRC_URI="https://polymake.org/lib/exe/fetch.php/download/${P}-minimal.tar.bz2"
+HOMEPAGE="https://polymake.org/"
+
+# polymake itself is GPL-2, but even the minimal tarball bundles a lot
+# of other code. I've included everything that turns up with a
+#
+#   find ./ -name 'LICENSE' -o -name 'COPYING'
+#
+# in the list below. If any of these bother you, you may want to take a
+# closer look at how (or even if) the corresponding code is being used.
+LICENSE="BSD GPL-2 GPL-2+ MIT WTFPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~riscv ~x86 ~amd64-linux ~x86-linux"
+IUSE="bliss +cdd +flint +normaliz libpolymake lrs nauty ppl singular"
+
+REQUIRED_USE="^^ ( bliss nauty )"
+
+# The "configure" script isn't autotools; it basically exists just to
+# exec some other perl script but using the familiar name.
+BDEPEND="dev-lang/perl
+	${NINJA_DEPEND}"
+
+DEPEND="
+	libpolymake? ( dev-lang/perl )
+	dev-libs/boost:=
+	dev-libs/gmp:=
+	dev-libs/libxml2:2=
+	dev-libs/libxslt:=
+	dev-libs/mpfr:=
+	sys-libs/readline:=
+	bliss? ( sci-libs/bliss:=[gmp] )
+	cdd? ( sci-libs/cddlib:= )
+	flint? ( sci-mathematics/flint:= )
+	lrs? ( >=sci-libs/lrslib-051:=[gmp] )
+	nauty? ( sci-mathematics/nauty:= )
+	normaliz? ( >=sci-mathematics/normaliz-3.8:= )
+	ppl? ( dev-libs/ppl:= )
+	singular? ( sci-mathematics/singular:= )"
+
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	dev-perl/JSON
+	dev-perl/Term-ReadLine-Gnu
+	dev-perl/TermReadKey
+	dev-perl/XML-SAX
+	dev-perl/XML-Writer"
+
+PATCHES=(
+	"${FILESDIR}/${P}-singular-sat.patch"
+	"${FILESDIR}/${P}-barycentric-subdiv.patch"
+)
+
+src_configure() {
+	# Without this, the build system tries to use "the highest possible"
+	# optimization level and will override what's in your CXXFLAGS.
+	export CXXOPT=""
+
+	tc-export CC CXX
+
+	# We need to define BLISS_USE_GMP if bliss was built with gmp support.
+	# Therefore we require gmp support on bliss, so that the package
+	# manager can prevent rebuilds with changed gmp flag. Yes, this should
+	# be append-cppflags; but the build system doesn't respect CPPFLAGS.
+	use bliss && append-cxxflags -DBLISS_USE_GMP
+
+	# This isn't an autotools ./configure script, so a lot of things
+	# don't work the way you'd expect. We disable openmp unconditionally
+	# because it's only supposedly only used for building the bundled
+	# libnormaliz (we unbundle it) and for something called to_simplex
+	# that I can't find anywhere in the polymake source.
+	./configure --prefix="${EPREFIX}/usr" \
+		--libdir="${EPREFIX}/usr/$(get_libdir)" \
+		--libexecdir="${EPREFIX}/usr/$(get_libdir)/polymake" \
+		$(usev !libpolymake "--without-callable") \
+		--without-java \
+		--without-javaview \
+		--without-native \
+		--without-scip \
+		--without-soplex \
+		--without-openmp \
+		$(use_with bliss bliss "${EPREFIX}/usr") \
+		$(use_with cdd cdd "${EPREFIX}/usr") \
+		$(use_with flint flint "${EPREFIX}/usr") \
+		$(use_with lrs lrs "${EPREFIX}/usr") \
+		$(use_with nauty nauty "${EPREFIX}/usr") \
+		$(use_with normaliz libnormaliz "${EPREFIX}/usr") \
+		$(use_with ppl ppl "${EPREFIX}/usr") \
+		$(use_with singular singular "${EPREFIX}/usr") \
+		|| die
+}
+
+# There is a backwards-compatible Makefile that would call ninja for us
+# in src_compile/src_install, but it doesn't handle MAKEOPTS correctly.
+src_compile() {
+	eninja -C build/Opt
+}
+
+src_install() {
+	# DESTDIR needs to find its way into the real install script,
+	# support/install.pl.
+	export DESTDIR="${D}"
+	eninja -C build/Opt install
+}
+
+src_test() {
+	perl/polymake --script run_testcases --emacs-style \
+		|| die "test suite failed"
+}
+
+pkg_postinst() {
+	elog "Additional features for polymake are available through external"
+	elog "software such as sci-mathematics/4ti2 and sci-mathematics/topcom."
+	elog "After installing new external software run 'polymake --reconfigure'."
+}