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From: "Anna Vyalkova" <cyber+gentoo@sysrq.in>
To: gentoo-commits@lists.gentoo.org
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Reply-To: gentoo-dev@lists.gentoo.org, "Anna Vyalkova" <cyber+gentoo@sysrq.in>
Message-ID: <1670845389.c7742604b7a71c99ce1d96cd72380c5021bb4613.cybertailor@gentoo>
Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
X-VCS-Repository: repo/proj/guru
X-VCS-Files: sci-biology/cmdock/Manifest sci-biology/cmdock/cmdock-0.1.3-r1.ebuild sci-biology/cmdock/files/app_info_0.1.3.xml sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
X-VCS-Directories: sci-biology/cmdock/files/ sci-biology/cmdock/
X-VCS-Committer: cybertailor
X-VCS-Committer-Name: Anna Vyalkova
X-VCS-Revision: c7742604b7a71c99ce1d96cd72380c5021bb4613
X-VCS-Branch: dev
Date: Mon, 12 Dec 2022 11:44:19 +0000 (UTC)
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commit: c7742604b7a71c99ce1d96cd72380c5021bb4613
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Mon Dec 12 11:41:07 2022 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Mon Dec 12 11:43:09 2022 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=c7742604
sci-biology/cmdock: drop 0.1.3-r1
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 -
sci-biology/cmdock/cmdock-0.1.3-r1.ebuild | 98 ----------------------
sci-biology/cmdock/files/app_info_0.1.3.xml | 37 --------
.../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 15 ----
4 files changed, 151 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index cac8acdf0..92078ebaa 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1,2 +1 @@
-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-r1.ebuild b/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
deleted file mode 100644
index 099977f0a..000000000
--- a/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
+++ /dev/null
@@ -1,98 +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 )
-
-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/files/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml
deleted file mode 100644
index 162ad0c05..000000000
--- a/sci-biology/cmdock/files/app_info_0.1.3.xml
+++ /dev/null
@@ -1,37 +0,0 @@
-<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_0.1.3</name>
- <executable/>
-</file_info>
-
-<file_info>
- <name>cmdock-boinc-zcp_job_0.1.3.xml</name>
-</file_info>
-<file_info>
- <name>docking_out.sd</name>
-</file_info>
-
-<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_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
deleted file mode 100644
index 074bb29d4..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<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>