sci-biology/cmdock: add 0.1.3

* revise deps
* fix symlinks
* replace slotting with subslotting

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

8 files changed, 215 insertions, 18 deletions

diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 25663d438..c20f5e305 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1,2 @@
 DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226
+DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild
index aa5a4546b..00934f81c 100644
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild
@@ -3,34 +3,31 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{7..10} pypy3 )
 DOCS_BUILDER="sphinx"
 DOCS_AUTODOC=0
-inherit python-r1 docs meson
+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"
 SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
 S="${WORKDIR}/${PN}-v${PV}"
-DOCS_DIR="${S}/docs"
 
 LICENSE="LGPL-3"
-SLOT="${PV}"
+SLOT="0/${PV}"
 KEYWORDS="~amd64"
-
 IUSE="boinc"
-REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )"
 
-DEPEND="
-	dev-cpp/eigen
-	dev-libs/cxxopts
+RDEPEND="
+	dev-lang/perl
 	boinc? ( sci-misc/boinc-wrapper )
-	doc? ( ${PYTHON_DEPS} )
 "
-RDEPEND="${DEPEND}
-	dev-lang/perl
+BDEPEND="
+	dev-cpp/eigen:3
+	dev-cpp/pcg-cpp
+	dev-libs/cxxopts
 "
-BDEPEND="dev-cpp/pcg-cpp"
 
 src_prepare() {
 	default
@@ -55,12 +52,12 @@ src_install() {
 
 	if use boinc ; then
 		insinto /var/lib/boinc/projects/www.sidock.si_sidock
-		doins "${FILESDIR}/app_info.xml"
+		newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
 		doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
 		doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
 
-		dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}"
-		dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}"
+		dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
+		dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
 	fi
 }
 
diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
new file mode 100644
index 000000000..c4a2da7b4
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild
@@ -0,0 +1,78 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..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"
+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
+	dev-libs/cxxopts
+"
+
+src_prepare() {
+	default
+	rm -r include/indicators || die
+	sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
+}
+
+src_configure() {
+	# very weird directory layout
+	local emesonargs=(
+		--prefix="${EPREFIX}/opt/cmdock-${PV}"
+	)
+	meson_src_configure
+}
+
+src_compile() {
+	meson_src_compile
+	docs_compile
+}
+
+src_install() {
+	meson_src_install
+
+	if use boinc ; then
+		insinto /var/lib/boinc/projects/www.sidock.si_sidock
+		newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
+		doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
+		doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml"
+		newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" cmdock-boinc-zip_job_${PV}.xml
+
+		dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
+		dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
+		dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
+	fi
+}
+
+pkg_postinst() {
+	if use boinc ; then
+		touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die
+		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/files/app_info.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml
index eb222052b..f7575656b 100644
--- a/sci-biology/cmdock/files/app_info.xml
+++ b/sci-biology/cmdock/files/app_info_0.1.2.xml
@@ -47,7 +47,7 @@
 </app_version>
 <app_version>
 	<app_name>cmdock-boinc-zip</app_name>
-	<version_num>200</version_num>
+	<version_num>204</version_num>
 	<file_ref>
 		<file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
 		<main_program/>
diff --git a/sci-biology/cmdock/files/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml
new file mode 100644
index 000000000..5c901eba8
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.1.3.xml
@@ -0,0 +1,95 @@
+<app_info>
+<app>
+	<name>cmdock-boinc</name>
+	<user_friendly_name>CurieMarieDock on BOINC</user_friendly_name>
+</app>
+<app>
+	<name>cmdock-boinc-zip</name>
+	<user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name>
+</app>
+<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-wrapper_0.1.3</name>
+	<executable/>
+</file_info>
+<file_info>
+	<name>cmdock-boinc-zcp_wrapper_0.1.3</name>
+	<executable/>
+</file_info>
+<file_info>
+	<name>cmdock-boinc-zip_wrapper_0.1.3</name>
+	<executable/>
+</file_info>
+
+<file_info>
+	<name>cmdock-boinc_job_0.1.3.xml</name>
+</file_info>
+<file_info>
+	<name>cmdock-boinc-zcp_job_0.1.3.xml</name>
+</file_info>
+<file_info>
+	<name>cmdock-boinc-zip_job_0.1.3.xml</name>
+</file_info>
+<file_info>
+	<name>docking_out.sd</name>
+</file_info>
+
+<app_version>
+	<app_name>cmdock-boinc</app_name>
+	<version_num>103</version_num>
+	<file_ref>
+		<file_name>cmdock-wrapper_0.1.3</file_name>
+		<main_program/>
+	</file_ref>
+	<file_ref>
+		<file_name>cmdock-boinc_job_0.1.3.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_version>
+	<app_name>cmdock-boinc-zcp</app_name>
+	<version_num>100</version_num>
+	<file_ref>
+		<file_name>cmdock-boinc-zcp_wrapper_0.1.3</file_name>
+		<main_program/>
+	</file_ref>
+	<file_ref>
+		<file_name>cmdock-boinc-zcp_job_0.1.3.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_version>
+	<app_name>cmdock-boinc-zip</app_name>
+	<version_num>300</version_num>
+	<file_ref>
+		<file_name>cmdock-boinc-zip_wrapper_0.1.3</file_name>
+		<main_program/>
+	</file_ref>
+	<file_ref>
+		<file_name>cmdock-boinc-zip_job_0.1.3.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_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
new file mode 100644
index 000000000..3c7818151
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
@@ -0,0 +1,15 @@
+<job_desc>
+	<task>
+		<application>/opt/cmdock-0.1.3/build/cmdock</application>
+		<stdout_filename>docking_log</stdout_filename>
+		<command_line>-c -j 1 -r target.prm -p /opt/cmdock-0.1.3/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=/opt/cmdock-0.1.3</setenv>
+		<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
+		<setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
+	</task>
+	<unzip_input>
+		<zipfilename>ligands.zip</zipfilename>
+	</unzip_input>
+</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
index 2691d09ea..a11f1fe9b 100644
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
+++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
@@ -2,7 +2,8 @@
 	<task>
 		<application>/opt/cmdock-0.1.2/build/cmdock</application>
 		<stdout_filename>docking_log</stdout_filename>
-		<command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+		<command_line>-c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+		<checkpoint_filename>docking_out.chk</checkpoint_filename>
 		<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
 		<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
 		<setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
new file mode 100644
index 000000000..6082dc8fe
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
@@ -0,0 +1,10 @@
+<job_desc>
+	<task>
+		<application>/opt/cmdock-0.1.3/build/cmdock</application>
+		<stdout_filename>docking_log</stdout_filename>
+		<command_line>-r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+		<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
+		<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
+		<setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
+	</task>
+</job_desc>