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# Copyright 1999-2022 Gentoo Authors
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# Copyright 1999-2021 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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inherit toolchain-funcs
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DESCRIPTION="Bayesian Inference of Phylogeny"
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HOMEPAGE="http://mrbayes.csit.fsu.edu/"
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SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
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HOMEPAGE="https://nbisweden.github.io/MrBayes/"
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SRC_URI="https://github.com/NBISweden/MrBayes/releases/download/v${PV}/${P}.tar.gz"
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LICENSE="GPL-2"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
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IUSE="debug mpi readline"
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# --with-readline was given, but MPI support requires readline to be disabled.
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REQUIRED_USE="mpi? ( !readline )"
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DEPEND="
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sys-libs/ncurses:=
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"
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RDEPEND="${DEPEND}"
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src_prepare() {
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default
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if use mpi; then
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sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support."
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fi
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if ! use readline; then
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sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \
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-i Makefile || die "Patching readline support."
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else
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# Only needed for OSX with an old (4.x) version of
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# libreadline, but it doesn't hurt for other distributions.
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eapply "${FILESDIR}"/mb_readline_312.patch
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fi
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sed -e 's:-ggdb::g' -i Makefile || die
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src_configure() {
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econf \
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"$(use_with mpi)" \
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"$(use_with readline)" \
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"$(use_enable debug )" \
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# configure checks cpuid and enables fma{3,4}, sse{1..4} if detected.
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# Configure options only allow disabling the auto-detection, but do not
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# actually allow toggling the individual cpu instruction sets. The only
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# way to guarantee that cross-compiling and binpkgs will work on machines
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# other than the host is to unconditionally disable sse/fma/avx.
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#"$(use_enable cpu_flags_x86_sse sse )" \
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#"$(use_enable cpu_flags_x86_avx avx )" \
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#"$(use_enable cpu_flags_x86_fma3 fma )" \
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# Has optional support for sci-biology/beagle::science
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# "$(use_with beagle)"
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}
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src_compile() {
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local myconf mycc
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if use mpi; then
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mycc=mpicc
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else
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mycc="$(tc-getCC)"
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fi
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use mpi && myconf="MPI=yes"
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use readline || myconf="${myconf} USEREADLINE=no"
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use debug && myconf="${myconf} DEBUG=yes"
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emake \
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OPTFLAGS="${CFLAGS}" \
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LDFLAGS="${LDFLAGS}" \
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CC=${mycc} \
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${myconf}
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}
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src_install() {
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dobin mb
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insinto /usr/share/${PN}
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doins *.nex
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# The --disable options for the cpu instruction sets don't actually work so
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# we override it here and also set the user specified CFLAGS.
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emake SIMD_FLAGS= CPUEXT_FLAGS= CFLAGS="${CFLAGS}"
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}
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