* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/
@ 2024-01-16 13:54 David Roman
0 siblings, 0 replies; 6+ messages in thread
From: David Roman @ 2024-01-16 13:54 UTC (permalink / raw
To: gentoo-commits
commit: d1a766a47405d4cfeced96a49b3bd70f81bd9a94
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Tue Jan 16 11:12:58 2024 +0000
Commit: David Roman <davidroman96 <AT> gmail <DOT> com>
CommitDate: Tue Jan 16 11:14:42 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=d1a766a4
sci-biology/cmdock: make python optional
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0-r1.ebuild | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
index f46747447a..09ab9cc5cc 100644
--- a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
+++ b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
@@ -65,6 +65,13 @@ python_check_deps() {
python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
}
+pkg_setup() {
+ if use doc || use test; then
+ python-any-r1_pkg_setup
+ fi
+ return 0
+}
+
foreach_wrapper_job() {
sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/
@ 2024-10-07 10:03 David Roman
0 siblings, 0 replies; 6+ messages in thread
From: David Roman @ 2024-10-07 10:03 UTC (permalink / raw
To: gentoo-commits
commit: 716c7719158ce9c31340b35f97e8ca72e423f3a1
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Mon Oct 7 00:25:39 2024 +0000
Commit: David Roman <davidroman96 <AT> gmail <DOT> com>
CommitDate: Mon Oct 7 00:25:39 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=716c7719
sci-biology/cmdock: add myself as a maintainer
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/metadata.xml | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
index dfcb664e4..3a8432392 100644
--- a/sci-biology/cmdock/metadata.xml
+++ b/sci-biology/cmdock/metadata.xml
@@ -1,12 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
+ <maintainer type="person">
+ <email>cyber+gentoo@sysrq.in</email>
+ <name>Anna</name>
+ </maintainer>
<upstream>
<remote-id type="gitlab">Jukic/cmdock</remote-id>
<bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
<doc>https://rxdock.gitlab.io/documentation/devel/html/</doc>
</upstream>
- <!-- maintainer-needed -->
<use>
<flag name="apidoc">
Build API documentation using <pkg>app-text/doxygen</pkg>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/
@ 2024-08-23 0:18 David Roman
0 siblings, 0 replies; 6+ messages in thread
From: David Roman @ 2024-08-23 0:18 UTC (permalink / raw
To: gentoo-commits
commit: de2cb421545b839fe097d6c04089989d12ed4b23
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Thu Aug 22 00:25:42 2024 +0000
Commit: David Roman <davidroman96 <AT> gmail <DOT> com>
CommitDate: Thu Aug 22 00:27:10 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=de2cb421
sci-biology/cmdock: fix boinc deps
Add "--wrapper" to "boinc-app_add_deps" call.
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0-r3.ebuild | 118 ++++++++++++++++++++++++++++++
1 file changed, 118 insertions(+)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r3.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r3.ebuild
new file mode 100644
index 000000000..f367dbdc6
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.2.0-r3.ebuild
@@ -0,0 +1,118 @@
+# Copyright 2021-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..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/${P}"
+
+boinc-app_add_deps --wrapper
+
+python_check_deps() {
+ use doc || return 0
+
+ python_has_version "dev-python/sphinx[${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 "$(get_project_root)"
+ insopts -m 0644 --owner root --group boinc
+ newins - docking_out
+ fi
+}
+
+pkg_postinst() {
+ optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
+ use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+ use boinc && boinc-app_pkg_postrm
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/
@ 2024-07-14 15:27 Haelwenn Monnier
0 siblings, 0 replies; 6+ messages in thread
From: Haelwenn Monnier @ 2024-07-14 15:27 UTC (permalink / raw
To: gentoo-commits
commit: e9427f8954a1efb68fa1c95e9e111f226e9500a1
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Tue Jul 9 15:47:57 2024 +0000
Commit: Haelwenn Monnier <contact <AT> hacktivis <DOT> me>
CommitDate: Sun Jul 14 07:27:10 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=e9427f89
sci-biology/cmdock: drop 0.2.0-r0
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0.ebuild | 112 ---------------------------------
1 file changed, 112 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.2.0.ebuild b/sci-biology/cmdock/cmdock-0.2.0.ebuild
deleted file mode 100644
index 3d1c2f035..000000000
--- a/sci-biology/cmdock/cmdock-0.2.0.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 2021-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..12} )
-BOINC_APP_OPTIONAL="true"
-inherit boinc-app flag-o-matic meson optfeature python-any-r1
-
-DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
-HOMEPAGE="https://gitlab.com/Jukic/cmdock"
-SRC_URI="https://gitlab.com/Jukic/${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 boinc cpu_flags_x86_sse2 doc test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- boinc? ( sci-misc/boinc-wrapper )
-"
-DEPEND="
- dev-cpp/eigen:3
- dev-cpp/indicators
- >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
- dev-libs/cxxopts
-"
-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? ( ${PYTHON_DEPS} )
-"
-
-DOCS=( README.md changelog.md )
-
-BOINC_MASTER_URL="https://www.sidock.si/sidock/"
-BOINC_INVITATION_CODE="Crunch_4Science"
-BOINC_APP_HELPTEXT=\
-"The easiest way to do something useful with this application
-is to attach it to SiDock@home BOINC project."
-
-INSTALL_PREFIX="${EPREFIX}/opt/${P}"
-
-python_check_deps() {
- use doc || return 0
-
- python_has_version "dev-python/sphinx[${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}${INSTALL_PREFIX}"/bin
-
- if use boinc; then
- doappinfo "${FILESDIR}"/app_info_${PV}.xml
- dowrapper cmdock-l
-
- # install cmdock executable
- exeinto "$(get_project_root)"
- exeopts --owner root --group boinc
- newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV}
-
- # install a blank file
- touch "${T}"/docking_out || die
- insinto "$(get_project_root)"
- insopts --owner root --group boinc
- doins "${T}"/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
-}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/
@ 2024-01-20 22:13 David Roman
0 siblings, 0 replies; 6+ messages in thread
From: David Roman @ 2024-01-20 22:13 UTC (permalink / raw
To: gentoo-commits
commit: a395a6f2ccebd4bcea65ef71c86abf6c5ee9e8bf
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sat Jan 20 08:39:36 2024 +0000
Commit: David Roman <davidroman96 <AT> gmail <DOT> com>
CommitDate: Sat Jan 20 08:39:36 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=a395a6f2
Revert "sci-biology/cmdock: make python optional"
This reverts commit d1a766a47405d4cfeced96a49b3bd70f81bd9a94.
Closes: https://bugs.gentoo.org/922486
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0-r1.ebuild | 7 -------
1 file changed, 7 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
index 09ab9cc5cc..f46747447a 100644
--- a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
+++ b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
@@ -65,13 +65,6 @@ python_check_deps() {
python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
}
-pkg_setup() {
- if use doc || use test; then
- python-any-r1_pkg_setup
- fi
- return 0
-}
-
foreach_wrapper_job() {
sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/
@ 2021-05-21 14:10 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2021-05-21 14:10 UTC (permalink / raw
To: gentoo-commits
commit: 745983646dd24ced02f842ce010c431c1b499a45
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed May 19 12:56:19 2021 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed May 19 20:22:47 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=74598364
sci-biology/cmdock: add missing PYTHON_DEPS
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/cmdock/cmdock-0.1.2.ebuild | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild
index 34c37a5ee..03f3d769e 100644
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild
@@ -17,9 +17,11 @@ DOCS_DIR="${S}/docs"
LICENSE="LGPL-3"
SLOT="${PV}"
KEYWORDS="~amd64"
+
IUSE="boinc"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-DEPEND="
+DEPEND="${PYTHON_DEPS}
dev-cpp/eigen
dev-libs/cxxopts
boinc? ( sci-misc/boinc-wrapper )
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2024-10-07 10:03 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2024-01-16 13:54 [gentoo-commits] repo/proj/guru:master commit in: sci-biology/cmdock/ David Roman
-- strict thread matches above, loose matches on Subject: below --
2024-10-07 10:03 David Roman
2024-08-23 0:18 David Roman
2024-07-14 15:27 Haelwenn Monnier
2024-01-20 22:13 David Roman
2021-05-21 14:10 Michał Górny
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox