sci-biology/cmdock: drop obsolete

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

8 files changed, 4 insertions, 242 deletions

diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index c20f5e305..84968a8f8 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1,2 +1 @@
-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
deleted file mode 100644
index 00934f81c..000000000
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# 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/pcg-cpp
-	dev-libs/cxxopts
-"
-
-src_prepare() {
-	default
-	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 "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
-
-		dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
-		dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${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/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
index c4a2da7b4..e42b1f253 100644
--- a/sci-biology/cmdock/cmdock-0.1.3.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild
@@ -1,9 +1,9 @@
 # Copyright 2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-PYTHON_COMPAT=( python3_{7..10} pypy3 )
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
 DOCS_BUILDER="sphinx"
 DOCS_AUTODOC=0
 DOCS_DIR="docs"
@@ -26,14 +26,13 @@ RDEPEND="
 BDEPEND="
 	dev-cpp/eigen:3
 	dev-cpp/indicators
-	dev-cpp/pcg-cpp
+	>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
 	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() {
@@ -55,13 +54,9 @@ 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_${PV}
+		dosym -r /usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
 	fi
 }
 
diff --git a/sci-biology/cmdock/files/app_info_0.1.2.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml
deleted file mode 100644
index f7575656b..000000000
--- a/sci-biology/cmdock/files/app_info_0.1.2.xml
+++ /dev/null
@@ -1,66 +0,0 @@
-<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>
-
-<file_info>
-	<name>cmdock-wrapper_0.1.2</name>
-	<executable/>
-</file_info>
-<file_info>
-	<name>cmdock-boinc-zip_wrapper_0.1.2</name>
-	<executable/>
-</file_info>
-
-<file_info>
-	<name>cmdock-boinc_job_0.1.2.xml</name>
-</file_info>
-<file_info>
-	<name>cmdock-boinc-zip_job_0.1.2.xml</name>
-</file_info>
-<file_info>
-	<name>docking_out.sd</name>
-</file_info>
-
-<app_version>
-	<app_name>cmdock-boinc</app_name>
-	<version_num>102</version_num>
-	<file_ref>
-		<file_name>cmdock-wrapper_0.1.2</file_name>
-		<main_program/>
-	</file_ref>
-	<file_ref>
-		<file_name>cmdock-boinc_job_0.1.2.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>204</version_num>
-	<file_ref>
-		<file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
-		<main_program/>
-	</file_ref>
-	<file_ref>
-		<file_name>cmdock-boinc-zip_job_0.1.2.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/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml
index 5c901eba8..162ad0c05 100644
--- a/sci-biology/cmdock/files/app_info_0.1.3.xml
+++ b/sci-biology/cmdock/files/app_info_0.1.3.xml
@@ -1,62 +1,22 @@
 <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>
@@ -74,22 +34,4 @@
 		<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-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
deleted file mode 100644
index a11f1fe9b..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<job_desc>
-	<task>
-		<application>/opt/cmdock-0.1.2/build/cmdock</application>
-		<stdout_filename>docking_log</stdout_filename>
-		<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>
-	</task>
-	<unzip_input>
-		<zipfilename>ligands.zip</zipfilename>
-	</unzip_input>
-</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
deleted file mode 100644
index c670b677e..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<job_desc>
-	<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>
-		<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>
-	</task>
-</job_desc>
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
deleted file mode 100644
index 6082dc8fe..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<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>