commit: 1a76004eaaa74e01bdbe8f2afacac8306fbe6d6f Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> AuthorDate: Tue Jul 9 15:56:46 2024 +0000 Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> 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 <cyber+gentoo <AT> 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 @@ <app_info> <app> <name>cmdock-l</name> - <user_friendly_name>CurieMarieDock 0.2.0 long tasks</user_friendly_name> + <user_friendly_name>CurieMarieDock @PV@ long tasks</user_friendly_name> </app> <file_info> - <name>cmdock-l_wrapper_@PV@</name> + <name>cmdock-l_wrapper</name> <sticky/> <executable/> </file_info> <file_info> - <name>cmdock-@PV@</name> + <name>cmdock</name> <sticky/> <executable/> </file_info> <file_info> - <name>cmdock-l_job_@[email protected]</name> + <name>cmdock-l_job.xml</name> <sticky/> </file_info> <file_info> @@ -28,16 +28,16 @@ <app_name>cmdock-l</app_name> <version_num>100</version_num> <file_ref> - <file_name>cmdock-l_wrapper_@PV@</file_name> + <file_name>cmdock-l_wrapper</file_name> <main_program/> </file_ref> <file_ref> - <file_name>cmdock-@PV@</file_name> + <file_name>cmdock</file_name> <open_name>cmdock</open_name> <copy_file/> </file_ref> <file_ref> - <file_name>cmdock-l_job_@[email protected]</file_name> + <file_name>cmdock-l_job.xml</file_name> <open_name>job.xml</open_name> <copy_file/> </file_ref> 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 @@ <task> <application>cmdock</application> <stdout_filename>docking_log</stdout_filename> - <command_line>-c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line> + <command_line>-c -j 1 -b 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>
