repo/proj/guru:master commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
"David Roman" <[email protected]> Tue, 04 Aug 2026 08:49:39 +0000 (UTC)
| Newsgroups | gmane.linux.gentoo.cvs |
|---|---|
| Message-ID | <1785705971.c8ae13091fed1c9bc02b372e71af8d8b8e3c3816.davidroman@gentoo> |
commit: c8ae13091fed1c9bc02b372e71af8d8b8e3c3816
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sun Aug 2 21:16:20 2026 +0000
Commit: David Roman <stkw0 <AT> disroot <DOT> org>
CommitDate: Sun Aug 2 21:26:11 2026 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=c8ae1309
sci-biology/cmdock: fixes
Bug: https://bugs.gentoo.org/979500
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0-r2.ebuild | 118 ---------------------
...dock-0.2.0-r3.ebuild => cmdock-0.2.0-r4.ebuild} | 36 +++++--
...app_info_0.2.0-r1.xml => app_info_0.2.0-r2.xml} | 17 +--
...ock-l_job_0.2.0-r1.xml => sidock_job_0.2.0.xml} | 2 +-
sci-biology/cmdock/metadata.xml | 2 +-
5 files changed, 37 insertions(+), 138 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild
deleted file mode 100644
index 1b0157ac30..0000000000
--- a/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright 2021-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_12 )
-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"
-HOMEPAGE="https://gitlab.com/Jukic/cmdock"
-SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
-S="${WORKDIR}/${PN}-v${PV}"
-
-LICENSE="LGPL-3 ZLIB"
-SLOT="0/${PV}"
-KEYWORDS="~amd64"
-IUSE="apidoc cpu_flags_x86_sse2 doc test"
-
-# Flaky tests
-RESTRICT="test"
-
-DEPEND="
- dev-cpp/eigen:3
- >=dev-cpp/indicators-2.3-r1
- >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
- >=dev-libs/cxxopts-3
-"
-BDEPEND="
- apidoc? (
- app-text/doxygen
- dev-texlive/texlive-fontutils
- )
- doc? (
- $(python_gen_any_dep '
- dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]
- dev-python/sphinx[${PYTHON_USEDEP}]
- ')
- )
- test? ( ${PYTHON_DEPS} )
-"
-
-PATCHES=(
- "${FILESDIR}"/${P}-include.patch
- "${FILESDIR}"/${P}-cxxopts.patch
-)
-
-DOCS=( README.md changelog.md )
-
-BOINC_MASTER_URL="https://www.sidock.si/sidock/"
-BOINC_INVITATION_CODE="Crunch_4Science"
-BOINC_APP_HELPTEXT=\
-"The easiest way to do something useful with this application
-is to attach it to SiDock@home BOINC project."
-
-INSTALL_PREFIX="${EPREFIX}/opt/${P}"
-
-boinc-app_add_deps
-
-python_check_deps() {
- use doc || return 0
-
- python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" &&
- python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
-}
-
-foreach_wrapper_job() {
- sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
-}
-
-src_prepare() {
- default
- python_fix_shebang "${S}"/bin
-}
-
-src_configure() {
- # very weird directory layout
- local emesonargs=(
- --prefix="${INSTALL_PREFIX:?}"
- $(meson_use apidoc)
- $(meson_use doc)
- $(meson_use test tests)
- -Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
- )
- meson_src_configure
-
- use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
-}
-
-src_install() {
- meson_src_install
- python_optimize "${D}${INSTALL_PREFIX:?}"/bin
-
- if use boinc; then
- boinc_install_appinfo "${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
- doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock
-
- # install a blank file
- insinto "$(get_project_root)"
- insopts -m 0644 --owner root --group boinc
- newins - docking_out
- fi
-}
-
-pkg_postinst() {
- optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
- use boinc && boinc-app_pkg_postinst
-}
-
-pkg_postrm() {
- use boinc && boinc-app_pkg_postrm
-}
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r3.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r4.ebuild
similarity index 76%
rename from sci-biology/cmdock/cmdock-0.2.0-r3.ebuild
rename to sci-biology/cmdock/cmdock-0.2.0-r4.ebuild
index 394b454452..7df9beea5e 100644
--- a/sci-biology/cmdock/cmdock-0.2.0-r3.ebuild
+++ b/sci-biology/cmdock/cmdock-0.2.0-r4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{12..13} )
+PYTHON_COMPAT=( python3_{12..14} )
BOINC_APP_OPTIONAL=1
inherit boinc-app flag-o-matic meson optfeature python-any-r1
@@ -13,18 +13,20 @@ SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
S="${WORKDIR}/${PN}-v${PV}"
LICENSE="LGPL-3 ZLIB"
-SLOT="0/${PV}"
+SLOT="0"
KEYWORDS="~amd64"
IUSE="apidoc cpu_flags_x86_sse2 doc test"
# Flaky tests
RESTRICT="test"
+RDEPEND="dev-libs/icu:="
DEPEND="
+ ${RDEPEND}
dev-cpp/eigen:3
>=dev-cpp/indicators-2.3-r1
>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
- >=dev-libs/cxxopts-3
+ >=dev-libs/cxxopts-3.1[icu]
"
BDEPEND="
apidoc? (
@@ -48,7 +50,6 @@ PATCHES=(
DOCS=( README.md changelog.md )
BOINC_MASTER_URL="https://www.sidock.si/sidock/"
-BOINC_INVITATION_CODE="Crunch_4Science"
BOINC_APP_HELPTEXT=\
"The easiest way to do something useful with this application
is to attach it to SiDock@home BOINC project."
@@ -74,13 +75,28 @@ src_prepare() {
}
src_configure() {
- # very weird directory layout
+ mkdir "${T}/pkg-config" || die
+ export PKG_CONFIG_PATH="${T}/pkg-config${PKG_CONFIG_PATH+:${PKG_CONFIG_PATH}}"
+ cat >> "${T}/pkg-config/pcg-cpp.pc" <<-EOF || die
+ Name: pcg-cpp
+ Version: 9999
+ Description:
+ EOF
+ cat >> "${T}/pkg-config/icu-cu.pc" <<-EOF || die
+ Name: icu-cu
+ Version: 9999
+ Description:
+ Requires: icu-uc
+ EOF
+
+ # extremely weird directory layout
local emesonargs=(
--prefix="${INSTALL_PREFIX:?}"
$(meson_use apidoc)
$(meson_use doc)
$(meson_use test tests)
-Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
+ -Dcpp_std=c++17
)
meson_src_configure
@@ -92,16 +108,16 @@ src_install() {
python_optimize "${D}${INSTALL_PREFIX:?}"/bin
if use boinc; then
- boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml
- boinc_install_wrapper cmdock-l_wrapper \
- "${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml
+ boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r2.xml
+ boinc_install_wrapper cmdock_wrapper \
+ "${FILESDIR}"/sidock_job_0.2.0.xml sidock_job.xml
- # install cmdock executable
+ # install the main executable
exeinto "$(get_project_root)"
exeopts --owner root --group boinc
doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock
- # install a blank file
+ # install an empty file
insinto "$(get_project_root)"
insopts -m 0644 --owner root --group boinc
newins - docking_out
diff --git a/sci-biology/cmdock/files/app_info_0.2.0-r1.xml b/sci-biology/cmdock/files/app_info_0.2.0-r2.xml
similarity index 67%
rename from sci-biology/cmdock/files/app_info_0.2.0-r1.xml
rename to sci-biology/cmdock/files/app_info_0.2.0-r2.xml
index b9eb040fbd..fed302a07a 100644
--- a/sci-biology/cmdock/files/app_info_0.2.0-r1.xml
+++ b/sci-biology/cmdock/files/app_info_0.2.0-r2.xml
@@ -1,11 +1,11 @@
<app_info>
<app>
- <name>cmdock-l</name>
- <user_friendly_name>CurieMarieDock @PV@ long tasks</user_friendly_name>
+ <name>sidock</name>
+ <user_friendly_name>SiDock@home CurieMarieDock</user_friendly_name>
</app>
<file_info>
- <name>cmdock-l_wrapper</name>
+ <name>cmdock_wrapper</name>
<sticky/>
<executable/>
</file_info>
@@ -16,7 +16,7 @@
</file_info>
<file_info>
- <name>cmdock-l_job.xml</name>
+ <name>sidock_job.xml</name>
<sticky/>
</file_info>
<file_info>
@@ -25,19 +25,19 @@
</file_info>
<app_version>
- <app_name>cmdock-l</app_name>
+ <app_name>sidock</app_name>
<version_num>100</version_num>
<file_ref>
- <file_name>cmdock-l_wrapper</file_name>
+ <file_name>cmdock_wrapper</file_name>
<main_program/>
</file_ref>
<file_ref>
<file_name>cmdock</file_name>
- <open_name>cmdock</open_name>
+ <open_name>sidock</open_name>
<copy_file/>
</file_ref>
<file_ref>
- <file_name>cmdock-l_job.xml</file_name>
+ <file_name>sidock_job.xml</file_name>
<open_name>job.xml</open_name>
<copy_file/>
</file_ref>
@@ -46,5 +46,6 @@
<open_name>docking_out</open_name>
<copy_file/>
</file_ref>
+ <is_wrapper/>
</app_version>
</app_info>
diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml b/sci-biology/cmdock/files/sidock_job_0.2.0.xml
similarity index 94%
rename from sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml
rename to sci-biology/cmdock/files/sidock_job_0.2.0.xml
index 6d626fb826..99d3627add 100644
--- a/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml
+++ b/sci-biology/cmdock/files/sidock_job_0.2.0.xml
@@ -1,6 +1,6 @@
<job_desc>
<task>
- <application>cmdock</application>
+ <application>sidock</application>
<stdout_filename>docking_log</stdout_filename>
<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>
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
index 3a84323920..234b93fc4c 100644
--- a/sci-biology/cmdock/metadata.xml
+++ b/sci-biology/cmdock/metadata.xml
@@ -7,7 +7,7 @@
</maintainer>
<upstream>
<remote-id type="gitlab">Jukic/cmdock</remote-id>
- <bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
+ <bugs-to>https://gitlab.com/Jukic/cmdock/-/work_items</bugs-to>
<doc>https://rxdock.gitlab.io/documentation/devel/html/</doc>
</upstream>
<use>