gentoo resync : 02.02.2022

3 files changed, 58 insertions, 10 deletions

diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
index 507d61d3e4db..3569573fdd5a 100644
--- a/sci-biology/mrbayes/Manifest
+++ b/sci-biology/mrbayes/Manifest
@@ -1,4 +1,6 @@
 AUX mb_readline_312.patch 586 BLAKE2B 6505a8d9fc40c0470264b6e293f2f4e51a5d6b4a73dfeaff747e2f4acd122369d810cdc86ae0d7cead3a3741cfffc02080c07618c2847985553322a1c9bf79b5 SHA512 8427c83ccb98c0b57274914d8f0d0f539ace7dbc475eb10bd586762efa3465b595b91907b55d6809b94e6b9c4f65aa139bc16a7d81b1c76f7623eae46d495aa8
 DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14
+DIST mrbayes-3.2.7.tar.gz 9787214 BLAKE2B 2d0ebbc376712e15fc1ed146053d977ad1af96f44c31b8fd0fdbd47ef9bafc41cbb8904db94bc8d30c753c0267a1dcce0d08c73d8b35c20e0f15206bc8fef6ff SHA512 4dc869cd07cf384b3a3945ac8d91a7cc2982e8c5cd8d1f097b46a479a071cb71e71c60e152aa4fc01b0bb296295c5fa9f5a48aa8e913b920c33e30cbb3a6ed37
 EBUILD mrbayes-3.1.2-r2.ebuild 1346 BLAKE2B 282f7f2bf6abb8370b5a007a8e680009f3f5e8e839d7817a1cb3b83e515b2909d5a9c7aa3eae6355ab59c4e1e2e4b9a7f8694076d50b019232fa367cd93df231 SHA512 60541b7af0243c4263d302d69ea38c6f1fcee96739eba121a48bf42e2b46f210efa971d65d0d517ed6b383fb6ce337008b13655c4f52e2783d456a04b43b9eb7
-MISC metadata.xml 917 BLAKE2B b4eb74008ced11d00c41b3262ace2a00439e6b8b91abeeb9539d4237d4cfab92bc07bcf8b979e2407e58714e38004acdc3714ee9c01b849f855a7ad023286521 SHA512 03fec6e855e5d22c653b2f04fb128f0286cafbad83ca3793bf4e7c79df769c7a3234ed964be25e884c5f1a1c278174ce041343c97dd818a650020cc350ee8012
+EBUILD mrbayes-3.2.7.ebuild 1533 BLAKE2B 6c5039d1cd8622700e1ccfcc94123bbf02561e4845394b4548eb137f74313b03c76c728089d65561c547197b5cfa3661f1e265d6b1a9acc4ff86db9196dfd2b7 SHA512 11c760fcc89c0585b3bc1f2cd8a71fba42c76180da7373c819b30d7d0cf46baad167bb065f096c1d7ad3df1f4b2dd87f6c75116a2cbf7d4eb1474ba395bb49ab
+MISC metadata.xml 964 BLAKE2B 6530733a29250579b0981a2712a8878094f1b347951d8c565449d46e1dcfd28459b9cfbc82d4cd6e79ee2e06d275673227c068a1b57bea3edec024dbbf3895bd SHA512 e5f7e98b69c437e3ffe18ca05d2dbefa1aaeee6b630e481b346576d46edd35784f174953b4616f7463d561bb8dae962288c9f9180967fc845c43bf29525aa47a
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
index 348542381e73..2fbcd4fa4f98 100644
--- a/sci-biology/mrbayes/metadata.xml
+++ b/sci-biology/mrbayes/metadata.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <longdescription>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<longdescription>
 MrBayes is a program for the Bayesian estimation of phylogeny.
 Bayesian inference of phylogeny is based upon a quantity called the
 posterior probability distribution of trees, which is the probability of a
@@ -14,8 +14,9 @@ Bayes's theorem. The posterior probability distribution of trees is
 impossible to calculate analytically; instead, MrBayes uses a simulation
 technique called Markov chain Monte Carlo (or MCMC) to approximate the
 posterior probabilities of trees.
-</longdescription>
-  <upstream>
-    <remote-id type="sourceforge">mrbayes</remote-id>
-  </upstream>
+	</longdescription>
+	<upstream>
+		<remote-id type="sourceforge">mrbayes</remote-id>
+		<remote-id type="github">NBISweden/MrBayes</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild
new file mode 100644
index 000000000000..ad87554eb31e
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="https://nbisweden.github.io/MrBayes/"
+SRC_URI="https://github.com/NBISweden/MrBayes/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE="debug mpi readline"
+# --with-readline was given, but MPI support requires readline to be disabled.
+REQUIRED_USE="mpi? ( !readline )"
+
+DEPEND="
+	sys-libs/ncurses:=
+	mpi? ( virtual/mpi )
+	readline? ( sys-libs/readline:= )
+"
+RDEPEND="${DEPEND}"
+
+src_configure() {
+	econf \
+		"$(use_with mpi)" \
+		"$(use_with readline)" \
+		"$(use_enable debug )" \
+		# configure checks cpuid and enables fma{3,4}, sse{1..4} if detected.
+		# Configure options only allow disabling the auto-detection, but do not
+		# actually allow toggling the individual cpu instruction sets. The only
+		# way to guarantee that cross-compiling and binpkgs will work on machines
+		# other than the host is to unconditionally disable sse/fma/avx.
+		#"$(use_enable cpu_flags_x86_sse sse )" \
+		#"$(use_enable cpu_flags_x86_avx avx )" \
+		#"$(use_enable cpu_flags_x86_fma3 fma )" \
+		# Has optional support for sci-biology/beagle::science
+		# "$(use_with beagle)"
+}
+
+src_compile() {
+	# The --disable options for the cpu instruction sets don't actually work so
+	# we override it here and also set the user specified CFLAGS.
+	emake SIMD_FLAGS= CPUEXT_FLAGS= CFLAGS="${CFLAGS}"
+}