From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id A3A8D139345 for ; Thu, 1 Jul 2021 05:20:32 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A99BCE083E; Thu, 1 Jul 2021 05:20:31 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 7A9A3E083E for ; Thu, 1 Jul 2021 05:20:31 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id E2A0933D3CD for ; Thu, 1 Jul 2021 05:20:29 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 15FDC4C3 for ; Thu, 1 Jul 2021 05:20:28 +0000 (UTC) From: "Jian Lin" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Jian Lin" Message-ID: <1625115505.eb972dae4900efd571efe420cf683200a997d924.jian@gentoo> Subject: [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/files/, sci-biology/cmdock/ X-VCS-Repository: repo/proj/guru X-VCS-Files: sci-biology/cmdock/Manifest sci-biology/cmdock/cmdock-0.1.2.ebuild sci-biology/cmdock/cmdock-0.1.3.ebuild sci-biology/cmdock/files/app_info_0.1.2.xml sci-biology/cmdock/files/app_info_0.1.3.xml sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml X-VCS-Directories: sci-biology/cmdock/ sci-biology/cmdock/files/ X-VCS-Committer: jian X-VCS-Committer-Name: Jian Lin X-VCS-Revision: eb972dae4900efd571efe420cf683200a997d924 X-VCS-Branch: master Date: Thu, 1 Jul 2021 05:20:28 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: f46ddc95-65b9-41ca-b9d8-b2dd551912f0 X-Archives-Hash: af43413585316da576c6685211f20f4c commit: eb972dae4900efd571efe420cf683200a997d924 Author: Anna (cybertailor) Vyalkova sysrq in> AuthorDate: Sun Jun 27 08:51:43 2021 +0000 Commit: Jian Lin outlook com> CommitDate: Thu Jul 1 04:58:25 2021 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=eb972dae sci-biology/cmdock: drop obsolete Signed-off-by: Anna (cybertailor) Vyalkova sysrq.in> sci-biology/cmdock/Manifest | 1 - sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 ---------------------- sci-biology/cmdock/cmdock-0.1.3.ebuild | 13 ++-- sci-biology/cmdock/files/app_info_0.1.2.xml | 66 ------------------- sci-biology/cmdock/files/app_info_0.1.3.xml | 58 ----------------- .../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 14 ---- .../cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 --- .../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 --- 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 @@ - - - cmdock-boinc - CurieMarieDock on BOINC - - - cmdock-boinc-zip - CurieMarieDock on BOINC + zipped input - - - - cmdock-wrapper_0.1.2 - - - - cmdock-boinc-zip_wrapper_0.1.2 - - - - - cmdock-boinc_job_0.1.2.xml - - - cmdock-boinc-zip_job_0.1.2.xml - - - docking_out.sd - - - - cmdock-boinc - 102 - - cmdock-wrapper_0.1.2 - - - - cmdock-boinc_job_0.1.2.xml - job.xml - - - - docking_out.sd - docking_out.sd - - - - - cmdock-boinc-zip - 204 - - cmdock-boinc-zip_wrapper_0.1.2 - - - - cmdock-boinc-zip_job_0.1.2.xml - job.xml - - - - docking_out.sd - docking_out.sd - - - - 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 @@ -1,61 +1,21 @@ - - cmdock-boinc - CurieMarieDock on BOINC - - - cmdock-boinc-zip - CurieMarieDock on BOINC + zipped input - cmdock-boinc-zcp CurieMarieDock on BOINC + zipped input, checkpoints and progress bar - - cmdock-wrapper_0.1.3 - - cmdock-boinc-zcp_wrapper_0.1.3 - - cmdock-boinc-zip_wrapper_0.1.3 - - - - cmdock-boinc_job_0.1.3.xml - cmdock-boinc-zcp_job_0.1.3.xml - - cmdock-boinc-zip_job_0.1.3.xml - docking_out.sd - - cmdock-boinc - 103 - - cmdock-wrapper_0.1.3 - - - - cmdock-boinc_job_0.1.3.xml - job.xml - - - - docking_out.sd - docking_out.sd - - - cmdock-boinc-zcp 100 @@ -74,22 +34,4 @@ - - cmdock-boinc-zip - 300 - - cmdock-boinc-zip_wrapper_0.1.3 - - - - cmdock-boinc-zip_job_0.1.3.xml - job.xml - - - - docking_out.sd - docking_out.sd - - - 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 @@ - - - /opt/cmdock-0.1.2/build/cmdock - docking_log - -c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out - docking_out.chk - CMDOCK_ROOT=/opt/cmdock-0.1.2 - LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH - PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB - - - ligands.zip - - diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml deleted file mode 100644 index c670b677e..000000000 --- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - /opt/cmdock-0.1.2/build/cmdock - docking_log - -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out - CMDOCK_ROOT=/opt/cmdock-0.1.2 - LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH - PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB - - diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml deleted file mode 100644 index 6082dc8fe..000000000 --- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - /opt/cmdock-0.1.3/build/cmdock - docking_log - -r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out - CMDOCK_ROOT=/opt/cmdock-0.1.3 - LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH - PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB - -