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 TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id C81E01581C1 for ; Sun, 14 Jul 2024 15:27:20 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id D90E8E2B54; Sun, 14 Jul 2024 15:27:19 +0000 (UTC) Received: from smtp.gentoo.org (dev.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id BC833E2B54 for ; Sun, 14 Jul 2024 15:27:19 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id BA7AC342F9B for ; Sun, 14 Jul 2024 15:27:18 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id BD22C1E2A for ; Sun, 14 Jul 2024 15:27:15 +0000 (UTC) From: "Haelwenn Monnier" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Haelwenn Monnier" Message-ID: <1720942039.1a76004eaaa74e01bdbe8f2afacac8306fbe6d6f.lanodan@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/cmdock-0.2.0-r1.ebuild sci-biology/cmdock/cmdock-0.2.0-r2.ebuild sci-biology/cmdock/files/app_info_0.2.0-r1.xml sci-biology/cmdock/files/app_info_0.2.0.xml sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml X-VCS-Directories: sci-biology/cmdock/files/ sci-biology/cmdock/ X-VCS-Committer: lanodan X-VCS-Committer-Name: Haelwenn Monnier X-VCS-Revision: 1a76004eaaa74e01bdbe8f2afacac8306fbe6d6f X-VCS-Branch: master Date: Sun, 14 Jul 2024 15:27:15 +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: f832b41e-2493-414c-9fc3-00db13e4da10 X-Archives-Hash: 7f69cf3ca7c067709ff74455b7dbb391 commit: 1a76004eaaa74e01bdbe8f2afacac8306fbe6d6f Author: Anna (cybertailor) Vyalkova sysrq in> AuthorDate: Tue Jul 9 15:56:46 2024 +0000 Commit: Haelwenn Monnier hacktivis me> CommitDate: Sun Jul 14 07:27:19 2024 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=1a76004e sci-biology/cmdock: boinc fixes * Update cmdline to the upstream current. Particularly, the option that causes CmDock to get stuck in an infinite loop in 1-5% of runs is removed. * Sync with boinc-app.eclass updates. Closes: https://bugs.gentoo.org/935231 Signed-off-by: Anna (cybertailor) Vyalkova sysrq.in> ...dock-0.2.0-r1.ebuild => cmdock-0.2.0-r2.ebuild} | 25 +++++++++++----------- .../{app_info_0.2.0.xml => app_info_0.2.0-r1.xml} | 14 ++++++------ ...k-l_job_0.2.0.xml => cmdock-l_job_0.2.0-r1.xml} | 2 +- 3 files changed, 20 insertions(+), 21 deletions(-) diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild similarity index 83% rename from sci-biology/cmdock/cmdock-0.2.0-r1.ebuild rename to sci-biology/cmdock/cmdock-0.2.0-r2.ebuild index f46747447..55e83bffb 100644 --- a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild +++ b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild @@ -4,7 +4,7 @@ EAPI=8 PYTHON_COMPAT=( python3_{10..12} ) -BOINC_APP_OPTIONAL="true" +BOINC_APP_OPTIONAL=1 inherit boinc-app flag-o-matic meson optfeature python-any-r1 DESCRIPTION="Program for docking ligands to proteins and nucleic acids" @@ -15,14 +15,11 @@ S="${WORKDIR}/${PN}-v${PV}" LICENSE="LGPL-3 ZLIB" SLOT="0/${PV}" KEYWORDS="~amd64" -IUSE="apidoc boinc cpu_flags_x86_sse2 doc test" +IUSE="apidoc cpu_flags_x86_sse2 doc test" # Flaky tests RESTRICT="test" -RDEPEND=" - boinc? ( sci-misc/boinc-wrapper ) -" DEPEND=" dev-cpp/eigen:3 >=dev-cpp/indicators-2.3-r1 @@ -58,6 +55,8 @@ is to attach it to SiDock@home BOINC project." INSTALL_PREFIX="${EPREFIX}/opt/${P}" +boinc-app_add_deps + python_check_deps() { use doc || return 0 @@ -77,7 +76,7 @@ src_prepare() { src_configure() { # very weird directory layout local emesonargs=( - --prefix="${INSTALL_PREFIX}" + --prefix="${INSTALL_PREFIX:?}" $(meson_use apidoc) $(meson_use doc) $(meson_use test tests) @@ -90,22 +89,22 @@ src_configure() { src_install() { meson_src_install - python_optimize "${D}${INSTALL_PREFIX}"/bin + python_optimize "${D}${INSTALL_PREFIX:?}"/bin if use boinc; then - doappinfo "${FILESDIR}"/app_info_${PV}.xml - dowrapper cmdock-l + boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml + boinc_install_wrapper cmdock-l_wrapper \ + "${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml # install cmdock executable exeinto "$(get_project_root)" exeopts --owner root --group boinc - newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV} + doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock # install a blank file - touch "${T}"/docking_out || die insinto "$(get_project_root)" - insopts --owner root --group boinc - doins "${T}"/docking_out + insopts -m 0644 --owner root --group boinc + newins - docking_out fi } diff --git a/sci-biology/cmdock/files/app_info_0.2.0.xml b/sci-biology/cmdock/files/app_info_0.2.0-r1.xml similarity index 68% rename from sci-biology/cmdock/files/app_info_0.2.0.xml rename to sci-biology/cmdock/files/app_info_0.2.0-r1.xml index ad23f7890..b9eb040fb 100644 --- a/sci-biology/cmdock/files/app_info_0.2.0.xml +++ b/sci-biology/cmdock/files/app_info_0.2.0-r1.xml @@ -1,22 +1,22 @@ cmdock-l - CurieMarieDock 0.2.0 long tasks + CurieMarieDock @PV@ long tasks - cmdock-l_wrapper_@PV@ + cmdock-l_wrapper - cmdock-@PV@ + cmdock - cmdock-l_job_@PV@.xml + cmdock-l_job.xml @@ -28,16 +28,16 @@ cmdock-l 100 - cmdock-l_wrapper_@PV@ + cmdock-l_wrapper - cmdock-@PV@ + cmdock cmdock - cmdock-l_job_@PV@.xml + cmdock-l_job.xml job.xml diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml b/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml similarity index 77% rename from sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml rename to sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml index a163eb29c..6d626fb82 100644 --- a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml +++ b/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml @@ -2,7 +2,7 @@ cmdock docking_log - -c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out + -c -j 1 -b 1 -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out docking_out.chk docking_out.progress CMDOCK_ROOT=@PREFIX@