sci-chemistry/autodock: update EAPI 7 -> 8, update HOMEPAGE, SRC_URI

Fix C++17 does not allow register storage class

Closes: https://bugs.gentoo.org/898130
Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com>
Closes: https://github.com/gentoo/gentoo/pull/31489
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

2 files changed, 112 insertions, 0 deletions

diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest
index 338b56af17cb..8b5de32f0db1 100644
--- a/sci-chemistry/autodock/Manifest
+++ b/sci-chemistry/autodock/Manifest
@@ -1 +1,2 @@
+DIST autodock-4.2.6-drop-register-keyword.patch 36676 BLAKE2B d91969d9d84b8940ddabf34dc017174deb1dafe0867f9ff5d2e528c4f3b4086b285f299220caa9406139146d460c2fba529e8b85c4aee927cabbdf34e91d3541 SHA512 39358c1d70f80c0a54066eb9ef600980c993dffaf1f7b7d558d29a4404c00a4d02ba0e871ae538474e452425f79795aad38eb0fca38a2663ccf6a64f57a40933
 DIST autodocksuite-4.2.6-src.tar.gz 35438010 BLAKE2B 88e036ecc0492fb83f31b90fd0983ec57d889a61d17249f672a3e30e942f6c329dc2494088a8fc7c5bc39a5bdbb38fb1514f1750c7145374f202a928d477faa9 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb
diff --git a/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild b/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild
new file mode 100644
index 000000000000..463c23ee2e01
--- /dev/null
+++ b/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools readme.gentoo-r1
+
+MY_PN="autodocksuite"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="A suite of automated docking tools"
+HOMEPAGE="https://autodock.scripps.edu/"
+SRC_URI="
+	https://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(ver_rs 1- '')/${MY_P}-src.tar.gz
+	https://dev.gentoo.org/~andrewammerlaan/${PN}-4.2.6-drop-register-keyword.patch
+"
+S="${WORKDIR}/src"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples openmp"
+# Tests require python2
+RESTRICT="test"
+
+# False positives caused by nested configure scripts
+QA_CONFIGURE_OPTIONS=".*"
+
+DISABLE_AUTOFORMATTING="yes"
+DOC_CONTENTS="
+The AutoDock development team requests all users to fill out the
+registration form at:
+
+http://autodock.scripps.edu/downloads/autodock-registration
+
+The number of unique users of AutoDock is used by Prof. Arthur J.
+Olson and the Scripps Research Institude to support grant
+applications.
+"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-buildsystem.patch
+	"${DISTDIR}"/${PN}-4.2.6-drop-register-keyword.patch
+)
+
+src_prepare() {
+	default
+
+	local i
+
+	sed \
+		-e "s/\tcsh/\tsh/" \
+		-i auto{dock,grid}/Makefile.am || die
+	for i in autodock autogrid; do
+		pushd $i &>/dev/null
+		eautoreconf
+		popd &>/dev/null
+	done
+}
+
+src_configure() {
+	local i
+	for i in autodock autogrid; do
+		pushd $i &>/dev/null
+		econf $(use_enable openmp)
+		popd &>/dev/null
+	done
+}
+
+src_compile() {
+	emake -C autodock
+	emake -C autogrid
+}
+
+# Refer: https://github.com/gentoo/gentoo/pull/31489/files#r1321120609
+#src_test() {
+#	elog "Testing autodock"
+#	cd "${S}/autodock/Tests" || die
+#	cp ../*.dat . || die
+#	${EPYTHON} test_autodock4.py || die "AutoDock tests failed."
+#	einfo "Testing autogrid"
+#	cd "${S}/autogrid/Tests" || die
+#	${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed."
+#}
+
+src_install() {
+	if use openmp; then
+		newbin autodock/autodock4.omp ${PN}4
+		dobin autogrid/autogrid4
+	else
+		dobin autodock/autodock4 autogrid/autogrid4
+	fi
+
+	insinto /usr/share/${PN}
+	doins -r \
+		autodock/{AD4_parameters.dat,AD4_PARM99.dat} \
+		$(usex examples "autodock/EXAMPLES" "")
+
+	DOCS=(
+		RELEASENOTES
+		autodock/{AUTHORS,README}
+		autodock/USERGUIDES/AutoDock4.{0,1,2}_UserGuide.doc
+		autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf
+	)
+	einstalldocs
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	readme.gentoo_print_elog
+}