sci-mathematics/polymake: new upstream version 4.5.

Lots of ebuild improvements (EAPI=8,...) in this one. Several bugs
have been fixed, and some new ones likely introduced; best not to
dwell. Now that we have something passable in the tree, it will be a
lot easier to make incremental improvements.

Closes: https://bugs.gentoo.org/618332
Closes: https://bugs.gentoo.org/625512
Closes: https://bugs.gentoo.org/648804
Closes: https://github.com/gentoo/gentoo/pull/17925
Package-Manager: Portage-3.0.20, Repoman-3.0.3
Signed-off-by: Michael Orlitzky <mjo@gentoo.org>

4 files changed, 158 insertions, 103 deletions

diff --git a/sci-mathematics/polymake/Manifest b/sci-mathematics/polymake/Manifest
index 46fae3d858fd..913e6a1540b0 100644
--- a/sci-mathematics/polymake/Manifest
+++ b/sci-mathematics/polymake/Manifest
@@ -1 +1 @@
-DIST polymake-3.0r2.tar.bz2 37695790 BLAKE2B 101dda48128b51737b81d3dc09a8ef32d07c5f67605370c5ef0d5638ee6de427c6e8ff66094f96593ad21fa937ca5890af772f6e877fab0e31f4c98ec7c6730b SHA512 b4c22b2c6da8ef597dc05a44a30c7a55fd924a96854cde3f725095465972eabe1e24508f8e5d544f3131c82c973117b15983c38a0242fc7f1d4a4a8ecddb1d46
+DIST polymake-4.5-minimal.tar.bz2 5634046 BLAKE2B dc8a10885b23f8c690e9b8e36d6b55193bbc6d77d56c3b2facea70221860c33d2df58a8a693b9d43c0f613962ce2bd1b3258f1a558af8335297092a60876054a SHA512 07fcc9c20c4e48fc6d83845c50c12b2cadeaf55f74619985d21e252970ad76d6ee8cc528cd419e71ed5927d83758e5d6862e41c1610f93ea95127ad9115a333b
diff --git a/sci-mathematics/polymake/metadata.xml b/sci-mathematics/polymake/metadata.xml
index 8eb7d9d63199..5834e17347b0 100644
--- a/sci-mathematics/polymake/metadata.xml
+++ b/sci-mathematics/polymake/metadata.xml
@@ -6,19 +6,47 @@
   <name>Gentoo Mathematics Project</name>
 </maintainer>
 <use>
-  <flag name="cdd">Enable sci-libs/cddlib interface for convex hull
-  computations (Should be kept enabled).</flag>
-  <flag name="lrs">Enable sci-libs/lrslib interface for convex hull computations.</flag>
-  <flag name="ppl">Enable dev-libs/ppl interface for convex hull computations.</flag>
-  <flag name="bliss">Enable sci-libs/bliss interface for graph and face lattice isomorphism computations.</flag>
-  <flag name="group">Build extension for dealing with permutation groups and symmetric objects.</flag>
-  <flag name="libnormaliz">Build the bundled extension for lattice related computations.</flag>
-  <flag name="singular">Enable the interface to sci-mathematics/singular for ideal related computations.</flag>
-  <flag name="libpolymake">Build the polymake library to build applications using the C++ interface.</flag>
+  <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 started out as a tool for the algorithmic treatment of convex
-polyhedra. By now it also deals with finite simplicial complexes,
-tight spans of finite metric spaces, and other objects. 
+  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. Supported platforms include various flavors of Linux,
+  FreeBSD, and Mac OS.
 </longdescription>
 </pkgmetadata>
diff --git a/sci-mathematics/polymake/polymake-3.0_p2.ebuild b/sci-mathematics/polymake/polymake-3.0_p2.ebuild
deleted file mode 100644
index bff44f4d9bb6..000000000000
--- a/sci-mathematics/polymake/polymake-3.0_p2.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic
-
-DESCRIPTION="research tool for polyhedral geometry and combinatorics"
-SRC_URI="https://polymake.org/lib/exe/fetch.php/download/polymake-3.0r2.tar.bz2"
-HOMEPAGE="https://polymake.org"
-
-IUSE="+cdd lrs ppl bliss group +libnormaliz singular libpolymake"
-
-REQUIRED_USE="group? ( cdd lrs )"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND="dev-lang/perl
-	dev-libs/gmp:0=
-	dev-libs/mpfr:0
-	dev-libs/libxml2:2
-	dev-libs/libxslt
-	ppl? ( dev-libs/ppl )
-	cdd? ( sci-libs/cddlib )
-	lrs? ( >=sci-libs/lrslib-051[gmp] )
-	bliss? ( sci-libs/bliss[gmp] )
-	group? ( dev-libs/boost:= )
-	libnormaliz? ( dev-libs/boost:= )
-	singular? ( >=sci-mathematics/singular-4.0.1 )"
-RDEPEND="${DEPEND}
-	dev-perl/XML-LibXML
-	dev-perl/XML-LibXSLT
-	dev-perl/XML-Writer
-	dev-perl/Term-ReadLine-Gnu"
-
-S="${WORKDIR}/${PN}-3.0"
-
-pkg_pretend() {
-	einfo "During compile this package uses up to"
-	einfo "750MB of RAM per process. Use MAKEOPTS=\"-j1\" if"
-	einfo "you run into trouble."
-}
-
-src_configure() {
-	export CXXOPT=$(get-flag -O)
-
-	# 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.
-	if use bliss ; then
-		append-cxxflags -DBLISS_USE_GMP
-	fi
-
-	# Configure does not accept --host, therefore econf cannot be used
-
-	# Some of the options do not support using just '--with-option'
-	local myconf=""
-	use !group && myconf="$myconf --without-group"
-	use !libnormaliz && myconf="$myconf --without-libnormaliz"
-	use !libpolymake && myconf="$myconf --without-callable"
-
-	# And many other --with-arguments expect a path: --with-option=/path
-	./configure --prefix="${EPREFIX}/usr" \
-		--libdir="${EPREFIX}/usr/$(get_libdir)" \
-		--libexecdir="${EPREFIX}/usr/$(get_libdir)/polymake" \
-		--without-prereq \
-		--without-java \
-		$(use_with cdd cdd "${EPREFIX}/usr") \
-		$(use_with lrs lrs "${EPREFIX}/usr") \
-		$(use_with ppl ppl "${EPREFIX}/usr") \
-		$(use_with bliss bliss "${EPREFIX}/usr") \
-		$(use_with singular singular "${EPREFIX}/usr") \
-		${myconf} || die
-}
-
-src_install() {
-	emake -j1 DESTDIR="${D}" install
-}
-
-pkg_postinst() {
-	elog "Docs can be found on https://www.polymake.org/doku.php/documentation"
-	elog " "
-	elog "Support for jreality is missing, sorry (see bug #346073)."
-	elog " "
-	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'."
-}
diff --git a/sci-mathematics/polymake/polymake-4.5.ebuild b/sci-mathematics/polymake/polymake-4.5.ebuild
new file mode 100644
index 000000000000..0ee01c641a11
--- /dev/null
+++ b/sci-mathematics/polymake/polymake-4.5.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2021 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/${P}-minimal.tar.bz2"
+HOMEPAGE="https://polymake.org/"
+
+# polymake itself is GPL-2, but even the minimal tarball bundles a lot
+# of other code. I've included everything that turns up with a
+#
+#   find ./ -name 'LICENSE' -o -name 'COPYING'
+#
+# in the list below. If any of these bother you, you may want to take a
+# closer look at how (or even if) the corresponding code is being used.
+LICENSE="BSD GPL-2 GPL-2+ MIT WTFPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="bliss +cdd +flint +normaliz libpolymake lrs nauty ppl singular"
+
+REQUIRED_USE="^^ ( bliss nauty )"
+
+# The "configure" script isn't autotools; it basically exists just to
+# exec some other perl script but using the familiar name.
+BDEPEND="dev-util/ninja
+	dev-lang/perl"
+
+DEPEND="
+	libpolymake? ( dev-lang/perl )
+	dev-libs/boost:=
+	dev-libs/gmp:=
+	dev-libs/libxml2:2=
+	dev-libs/libxslt:=
+	dev-libs/mpfr:=
+	sys-libs/readline:=
+	bliss? ( sci-libs/bliss:=[gmp] )
+	cdd? ( sci-libs/cddlib:= )
+	lrs? ( >=sci-libs/lrslib-051:=[gmp] )
+	nauty? ( sci-mathematics/nauty:= )
+	normaliz? ( sci-mathematics/normaliz:= )
+	ppl? ( dev-libs/ppl:= )
+	singular? ( sci-mathematics/singular:= )"
+
+RDEPEND="${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
+
+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=$(get-flag -O)
+
+	tc-export CC CXX
+
+	# We need to define BLISS_USE_GMP if bliss was built with gmp support.
+	# Therefore we require gmp support on bliss, so that the package
+	# manager can prevent rebuilds with changed gmp flag. Yes, this should
+	# be append-cppflags; but the build system doesn't respect CPPFLAGS.
+	use bliss && append-cxxflags -DBLISS_USE_GMP
+
+	# This isn't an autotools ./configure script, so a lot of things
+	# don't work the way you'd expect.
+	./configure --prefix="${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 \
+		$(use_with bliss bliss "${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'."
+}