commit: c5e5ffa9e5052ad286c2ed2e5fee818bd9630686 Author: Michael Orlitzky <mjo <AT> gentoo <DOT> org> AuthorDate: Mon Nov 13 19:36:06 2023 +0000 Commit: Michael Orlitzky <mjo <AT> gentoo <DOT> org> CommitDate: Mon Nov 13 22:17:04 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c5e5ffa9
sci-mathematics/polymake: new old package, add 4.11 This is back from the dead after being removed for lack of perl-5.38 support. Only a month ago, upstream's opinion was that "any hacks we would try here will be in vain," but it looks like they've decided to adopt a short-term fix for perl-5.38. We bring it back, and make use of $NINJA_DEPEND while we're at it (samurai works fine). The new patch (and a short explanation from upstream) can be found on Debian bug 1042521. Bug: https://bugs.gentoo.org/909570 Closes: https://bugs.gentoo.org/917155 Signed-off-by: Michael Orlitzky <mjo <AT> gentoo.org> sci-mathematics/polymake/Manifest | 1 + .../files/polymake-4.11-singular-sat.patch | 53 +++++++++ sci-mathematics/polymake/metadata.xml | 54 +++++++++ sci-mathematics/polymake/polymake-4.11.ebuild | 124 +++++++++++++++++++++ 4 files changed, 232 insertions(+) diff --git a/sci-mathematics/polymake/Manifest b/sci-mathematics/polymake/Manifest new file mode 100644 index 000000000000..64de0ecea8e1 --- /dev/null +++ b/sci-mathematics/polymake/Manifest @@ -0,0 +1 @@ +DIST polymake-4.11-minimal.tar.bz2 7325783 BLAKE2B 87e62741e4e44c5fea7454d5cc8cb205cf13f8ee743c1d72100f937d0677505ce0c5c8f5b37c118f89079ca88f313991eaefb2ea02c49b6c7b45c438c6f9e13b SHA512 94adf3fcec21de50451091a04ca17010f5e71b44e3dcd4e2d52b9f952b94ee0cf3f6df15657b761b0bda20eb47cbdc0cb2481bb440c7243442be34f913292246 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 <[email protected]> +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>[email protected]</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..56790dcb5cc9 --- /dev/null +++ b/sci-mathematics/polymake/polymake-4.11.ebuild @@ -0,0 +1,124 @@ +# 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" + +# Tests observed failing after upgrade to polymake-4.5. No idea if they +# worked prior to that. Someone who actually understands polymake will +# have to get these working (at least briefly) before we re-enable them. +RESTRICT=test + +PATCHES=( "${FILESDIR}/${P}-singular-sat.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'." +}
