[gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/

["Anna Vyalkova" <cyber+gentoo@sysrq.in>]

commit:     50bb2e29704a88fb6d53a79ed4eda6a064d23c1a
Author:     Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Thu Nov 25 07:15:21 2021 +0000
Commit:     Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu Nov 25 07:15:21 2021 +0000
URL:        https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=50bb2e29

sci-biology/cmdock: add 0.1.4

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>

 sci-biology/cmdock/Manifest                        |  1 +
 sci-biology/cmdock/cmdock-0.1.3.ebuild             | 90 ---------------------
 sci-biology/cmdock/cmdock-0.1.4.ebuild             | 94 ++++++++++++++++++++++
 sci-biology/cmdock/files/app_info_0.1.4.xml        | 37 +++++++++
 .../cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml    | 15 ++++
 5 files changed, 147 insertions(+), 90 deletions(-)

diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 84968a8f8..cac8acdf0 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1,2 @@
 DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
+DIST cmdock-v0.1.4.tar.gz 14487352 BLAKE2B 3f212d596a12046f9a3b04376ca3e6d67f4391edba6f9c6e1fd372e7c7dbb23727ebd77787f125e57afca16e0cffc9b734dcdc7a83a825c52737218df371cbfd SHA512 6e1a366d82b311da0fdcd99ecf3e10962073453c7fdec9142854d472336f7f918bb76368b52e5904bf30e0aea6b8476a3ab522469daeaef52293ac481741b4bb

diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
deleted file mode 100644
index 13e4bc2cc..000000000
--- a/sci-biology/cmdock/cmdock-0.1.3.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
-DOCS_BUILDER="sphinx"
-DOCS_AUTODOC=0
-DOCS_DIR="docs"
-inherit python-any-r1 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="boinc"
-
-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
-"
-
-MY_PREFIX="${EPREFIX}/opt/${P}"
-
-src_prepare() {
-	default
-	rm -r include/indicators || die
-}
-
-src_configure() {
-	# very weird directory layout
-	local emesonargs=(
-		--prefix="${MY_PREFIX}"
-	)
-	meson_src_configure
-}
-
-src_compile() {
-	meson_src_compile
-	docs_compile
-}
-
-src_install() {
-	meson_src_install
-
-	if use boinc ; then
-		local project_root="/var/lib/boinc/projects/www.sidock.si_sidock"
-
-		local wrappers=( ${PN}-boinc-zcp )
-
-		insinto ${project_root}
-		insopts --owner boinc --group boinc
-
-		newins "${FILESDIR}"/app_info_${PV}.xml app_info.xml
-		touch "${ED}${project_root}"/docking_out.sd || die
-		fowners boinc:boinc ${project_root}/docking_out.sd
-
-		for app in "${wrappers[@]}" ; do
-			wrapperjob="${app}_job_${PV}.xml"
-			wrapperexe="${app}_wrapper_${PV}"
-
-			dosym -r /usr/bin/boinc-wrapper "${project_root}/${wrapperexe}"
-
-			cp "${FILESDIR}"/${wrapperjob} "${S}" || die
-			sed "s:@PREFIX@:${MY_PREFIX}:g" -i ${wrapperjob} || die
-			doins ${wrapperjob}
-		done
-	fi
-}
-
-pkg_postinst() {
-	if use boinc ; then
-		elog
-		elog "The easiest way to do something useful with this application"
-		elog "is to attach it to SiDock@home BOINC project."
-		elog
-		elog "- Master URL: https://sidock.si/sidock/"
-		elog "- Invitation code: Crunch_4Science"
-	fi
-}

diff --git a/sci-biology/cmdock/cmdock-0.1.4.ebuild b/sci-biology/cmdock/cmdock-0.1.4.ebuild
new file mode 100644
index 000000000..70befcfcc
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.1.4.ebuild
@@ -0,0 +1,94 @@
+# 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 flag-o-matic 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${PV}"
+
+LICENSE="LGPL-3 ZLIB"
+SLOT="0/${PV}"
+KEYWORDS="~amd64"
+IUSE="apidoc boinc cpu_flags_x86_sse2"
+
+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
+	doc? ( 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/${P}:g" || die
+}
+
+src_configure() {
+	# very weird directory layout
+	local emesonargs=(
+		--prefix="${EPREFIX}/opt/${P}"
+	)
+	meson_src_configure
+
+	use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
+}
+
+src_compile() {
+	meson_src_compile
+
+	# subshell prevents overriding global
+	# DOCS_BUILDER and DOCS_OUTDIR
+	(
+		DOCS_BUILDER="doxygen"
+		DOCS_OUTDIR="${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/files/app_info_0.1.4.xml b/sci-biology/cmdock/files/app_info_0.1.4.xml
new file mode 100644
index 000000000..85dcdb16a
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.1.4.xml
@@ -0,0 +1,37 @@
+<app_info>
+<app>
+	<name>cmdock-boinc-zcp</name>
+	<user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name>
+</app>
+
+<file_info>
+	<name>cmdock-boinc-zcp_wrapper_0.1.4</name>
+	<executable/>
+</file_info>
+
+<file_info>
+	<name>cmdock-boinc-zcp_job_0.1.4.xml</name>
+</file_info>
+<file_info>
+	<name>docking_out.sd</name>
+</file_info>
+
+<app_version>
+	<app_name>cmdock-boinc-zcp</app_name>
+	<version_num>200</version_num>
+	<file_ref>
+		<file_name>cmdock-boinc-zcp_wrapper_0.1.4</file_name>
+		<main_program/>
+	</file_ref>
+	<file_ref>
+		<file_name>cmdock-boinc-zcp_job_0.1.4.xml</file_name>
+		<open_name>job.xml</open_name>
+		<copy_file/>
+	</file_ref>
+	<file_ref>
+		<file_name>docking_out.sd</file_name>
+		<open_name>docking_out.sd</open_name>
+		<copy_file/>
+	</file_ref>
+</app_version>
+</app_info>

diff --git a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
new file mode 100644
index 000000000..074bb29d4
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
@@ -0,0 +1,15 @@
+<job_desc>
+	<task>
+		<application>@PREFIX@/build/cmdock</application>
+		<stdout_filename>docking_log</stdout_filename>
+		<command_line>-c -j 1 -r target.prm -p @PREFIX@/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+		<checkpoint_filename>docking_out.chk</checkpoint_filename>
+		<fraction_done_filename>docking_out.progress</fraction_done_filename>
+		<setenv>CMDOCK_ROOT=@PREFIX@</setenv>
+		<setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv>
+		<setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
+	</task>
+	<unzip_input>
+		<zipfilename>ligands.zip</zipfilename>
+	</unzip_input>
+</job_desc>