sci-biology/clustalw-mpi: Port to EAPI 7

* Rename USE flags to avoid underscore
* Fix building against GCC 10 / -fno-common

Closes: https://bugs.gentoo.org/695122
Closes: https://bugs.gentoo.org/706960
Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: David Seifert <soap@gentoo.org>

4 files changed, 32 insertions, 18 deletions

diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
index 76d3b80cde32..334c34e78ce6 100644
--- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -12,28 +12,31 @@ SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="mpi_njtree static_pairalign"
+IUSE="mpi-njtree static-pairalign"
 
 DEPEND="virtual/mpi"
 RDEPEND="${DEPEND}"
 
-PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch )
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
 
 src_prepare() {
 	default
 
-	if use mpi_njtree; then
+	if use mpi-njtree; then
 		sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \
 			die "Failed to configure MPI code for NJ trees"
 	fi
 
-	if use static_pairalign; then
+	if use static-pairalign; then
 		sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \
 			die "Failed to configure static scheduling for pair alignments"
 	fi
 }
 
 src_install() {
-	dobin ${PN}
-	newdoc README.${PN} README
+	dobin clustalw-mpi
+	newdoc README.clustalw-mpi README
 }
diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch
new file mode 100644
index 000000000000..da74f0ba172d
--- /dev/null
+++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch
@@ -0,0 +1,13 @@
+--- a/parallel_compare.c
++++ b/parallel_compare.c
+@@ -74,8 +74,8 @@
+ static sint 	**accum;
+ static sint 	*diag_index;
+ static char 	*slopes;
+-sint ktup,window,wind_gap,signif; 
+-sint *zza, *zzb, *zzc, *zzd;
++extern sint ktup,window,wind_gap,signif;
++extern sint *zza, *zzb, *zzc, *zzd;
+ extern Boolean percent;
+ static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l);
+ static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len);
diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
index 6e36061cbb39..6e36061cbb39 100644
--- a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
+++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
index 8ab4494152c8..ffe2c4efec87 100644
--- a/sci-biology/clustalw-mpi/metadata.xml
+++ b/sci-biology/clustalw-mpi/metadata.xml
@@ -1,14 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<maintainer type="project">
-  <email>sci-biology@gentoo.org</email>
-  <name>Gentoo Biology Project</name>
-</maintainer>
-<use>
-  <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing
-    neighbor-joining trees</flag>
-  <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling
-    for pair alignments</flag>
-</use>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<use>
+		<flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag>
+		<flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag>
+	</use>
 </pkgmetadata>