From ff56baf97e8c8a3551b3a1875d3d480c56782331 Mon Sep 17 00:00:00 2001
From: "Anna (cybertailor) Vyalkova" <cyber+gentoo@sysrq.in>
Date: Thu, 22 Jul 2021 13:12:11 +0500
Subject: sci-biology/cmdock: revbump (new eclass)

Also includes a hack to install both sphinx and doxygen docs.
pkgcheck isn't very happy about it, but who cares.

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
---
 sci-biology/cmdock/cmdock-0.1.3-r1.ebuild | 98 +++++++++++++++++++++++++++++++
 sci-biology/cmdock/metadata.xml           |  5 +-
 2 files changed, 102 insertions(+), 1 deletion(-)
 create mode 100644 sci-biology/cmdock/cmdock-0.1.3-r1.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild b/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
new file mode 100644
index 000000000..099977f0a
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
@@ -0,0 +1,98 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+BOINC_APP_OPTIONAL="true"
+
+DOCS_BUILDER="sphinx"
+DOCS_AUTODOC=0
+DOCS_DIR="docs"
+
+inherit python-any-r1 boinc-app docs meson
+
+DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
+HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"
+SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="LGPL-3"
+SLOT="0/${PV}"
+KEYWORDS="~amd64"
+IUSE="apidoc boinc"
+REQUIRED_USE="apidoc? ( doc )"
+
+RDEPEND="
+	dev-lang/perl
+	boinc? ( sci-misc/boinc-wrapper )
+"
+BDEPEND="
+	dev-cpp/eigen:3
+	dev-cpp/indicators
+	>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
+	dev-libs/cxxopts
+	apidoc? ( app-doc/doxygen )
+"
+
+DOCS=( INSTALL.md README.md )
+
+BOINC_MASTER_URL="https://www.sidock.si/sidock/"
+BOINC_INVITATION_CODE="Crunch_4Science"
+BOINC_APP_HELPTEXT=\
+"The easiest way to do something useful with this application
+is to attach it to SiDock@home BOINC project."
+
+foreach_wrapper_job() {
+	sed -i "$1" \
+		-e "s:@PREFIX@:${EPREFIX}/opt/${P}:g" || die
+}
+
+src_prepare() {
+	default
+	rm -r include/indicators || die
+}
+
+src_configure() {
+	# very weird directory layout
+	local emesonargs=(
+		--prefix="${EPREFIX}/opt/${P}"
+	)
+	meson_src_configure
+}
+
+src_compile() {
+	meson_src_compile
+
+	# subshell prevents from overriding global
+	# DOCS_BUILDER and DOCS_OUTDIR
+	use apidoc && (
+		DOCS_BUILDER="doxygen"
+		DOCS_OUTDIR="${S}/_build/html/api"
+		docs_compile
+	)
+	docs_compile
+}
+
+src_install() {
+	meson_src_install
+
+	if use boinc; then
+		doappinfo "${FILESDIR}"/app_info_${PV}.xml
+		dowrapper ${PN}-boinc-zcp
+
+		# install a blank file
+		insinto $(get_project_root)
+		insopts --owner boinc --group boinc
+		: newins - docking_out.sd
+	fi
+}
+
+pkg_postinst() {
+	use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+	use boinc && boinc-app_pkg_postrm
+}
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
index f0cb44b3d..beddf8090 100644
--- a/sci-biology/cmdock/metadata.xml
+++ b/sci-biology/cmdock/metadata.xml
@@ -4,13 +4,16 @@
 	<upstream>
 		<remote-id type="gitlab">Jukic/cmdock</remote-id>
 		<bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
-		<doc>https://www.rxdock.org/api-documentation/devel/html</doc>
+		<doc>https://www.rxdock.org/documentation/devel/html</doc>
 	</upstream>
 	<maintainer type="person">
 		<email>cyber+gentoo@sysrq.in</email>
 		<name>Anna</name>
 	</maintainer>
 	<use>
+		<flag name="apidoc">
+			Build API documentation using <pkg>app-doc/doxygen</pkg>
+		</flag>
 		<flag name="boinc">
 			Use CmDock with SiDock@home BOINC project
 		</flag>
-- 
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