From bbc280302422f9a4e29bc5867894f415d8a3ec0d Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sat, 8 Feb 2020 11:55:49 +0100
Subject: sci-chemistry/autodock_vina: Port to EAPI 7

Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: David Seifert <soap@gentoo.org>
---
 .../autodock_vina/autodock_vina-1.1.2.ebuild       | 29 ++++++++++++----------
 .../autodock_vina-1.1.2-missing-debug-decl.patch   | 11 ++++++++
 2 files changed, 27 insertions(+), 13 deletions(-)
 create mode 100644 sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch

diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
index bbff27f85e2f..59f14e8086c9 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -1,40 +1,43 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils flag-o-matic versionator
+inherit flag-o-matic
 
-MY_P="${PN}_$(replace_all_version_separators _)"
+MY_P="${PN}_$(ver_rs 1- _)"
 
 DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
 HOMEPAGE="http://vina.scripps.edu/"
 SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz"
 
+LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="amd64 x86"
-LICENSE="Apache-2.0"
 IUSE="debug"
 
-RDEPEND="dev-libs/boost[threads]"
+RDEPEND="dev-libs/boost:=[threads]"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/${MY_P}/build/linux/release
 
+PATCHES=(
+	"${FILESDIR}"/${PV}-gentoo.patch
+	"${FILESDIR}"/${P}-boost-filesystem.patch
+	"${FILESDIR}"/${P}-missing-debug-decl.patch
+)
+
 src_prepare() {
 	cd "${WORKDIR}"/${MY_P} || die
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${P}-boost-filesystem.patch
+	default
 }
 
-src_compile() {
-	local c_options
-
+src_configure() {
 	use debug || c_options="-DNDEBUG"
-
 	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3
+}
 
+src_compile() {
 	emake \
 		BASE="${EPREFIX}"/usr/ \
 		GPP="$(tc-getCXX)" \
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch
new file mode 100644
index 000000000000..c68adb1bff21
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch
@@ -0,0 +1,11 @@
+--- a/src/lib/quaternion.h
++++ b/src/lib/quaternion.h
+@@ -70,6 +70,8 @@
+ 	return sqr(q.R_component_1()) + sqr(q.R_component_2()) + sqr(q.R_component_3()) + sqr(q.R_component_4());
+ }
+ 
++bool quaternion_is_normalized(const qt& q);
++
+ inline void quaternion_normalize(qt& q) {
+ 	const fl s = quaternion_norm_sqr(q);
+ 	assert(eq(s, sqr(boost::math::abs(q))));
-- 
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