* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2021-05-19 20:32 Andrew Ammerlaan
0 siblings, 0 replies; 12+ messages in thread
From: Andrew Ammerlaan @ 2021-05-19 20:32 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: Andrew Ammerlaan <andrewammerlaan <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] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2021-07-22 8:29 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2021-07-22 8:29 UTC (permalink / raw
To: gentoo-commits
commit: ff56baf97e8c8a3551b3a1875d3d480c56782331
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Thu Jul 22 08:12:11 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu Jul 22 08:27:39 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=ff56baf9
sci-biology/cmdock: revbump (new eclass)
Also includes a hack to install both sphinx and doxygen docs.
pkgcheck isn't very happy about it, but who cares.
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.1.3-r1.ebuild | 98 +++++++++++++++++++++++++++++++
sci-biology/cmdock/metadata.xml | 5 +-
2 files changed, 102 insertions(+), 1 deletion(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild b/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
new file mode 100644
index 000000000..099977f0a
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
@@ -0,0 +1,98 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+BOINC_APP_OPTIONAL="true"
+
+DOCS_BUILDER="sphinx"
+DOCS_AUTODOC=0
+DOCS_DIR="docs"
+
+inherit python-any-r1 boinc-app docs meson
+
+DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
+HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"
+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="apidoc boinc"
+REQUIRED_USE="apidoc? ( doc )"
+
+RDEPEND="
+ dev-lang/perl
+ boinc? ( sci-misc/boinc-wrapper )
+"
+BDEPEND="
+ dev-cpp/eigen:3
+ dev-cpp/indicators
+ >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
+ dev-libs/cxxopts
+ apidoc? ( app-doc/doxygen )
+"
+
+DOCS=( INSTALL.md README.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."
+
+foreach_wrapper_job() {
+ sed -i "$1" \
+ -e "s:@PREFIX@:${EPREFIX}/opt/${P}:g" || die
+}
+
+src_prepare() {
+ default
+ rm -r include/indicators || die
+}
+
+src_configure() {
+ # very weird directory layout
+ local emesonargs=(
+ --prefix="${EPREFIX}/opt/${P}"
+ )
+ meson_src_configure
+}
+
+src_compile() {
+ meson_src_compile
+
+ # subshell prevents from overriding global
+ # DOCS_BUILDER and DOCS_OUTDIR
+ use apidoc && (
+ DOCS_BUILDER="doxygen"
+ DOCS_OUTDIR="${S}/_build/html/api"
+ docs_compile
+ )
+ docs_compile
+}
+
+src_install() {
+ meson_src_install
+
+ if use boinc; then
+ doappinfo "${FILESDIR}"/app_info_${PV}.xml
+ dowrapper ${PN}-boinc-zcp
+
+ # install a blank file
+ insinto $(get_project_root)
+ insopts --owner boinc --group boinc
+ : newins - docking_out.sd
+ fi
+}
+
+pkg_postinst() {
+ use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+ use boinc && boinc-app_pkg_postrm
+}
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
index f0cb44b3d..beddf8090 100644
--- a/sci-biology/cmdock/metadata.xml
+++ b/sci-biology/cmdock/metadata.xml
@@ -4,13 +4,16 @@
<upstream>
<remote-id type="gitlab">Jukic/cmdock</remote-id>
<bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
- <doc>https://www.rxdock.org/api-documentation/devel/html</doc>
+ <doc>https://www.rxdock.org/documentation/devel/html</doc>
</upstream>
<maintainer type="person">
<email>cyber+gentoo@sysrq.in</email>
<name>Anna</name>
</maintainer>
<use>
+ <flag name="apidoc">
+ Build API documentation using <pkg>app-doc/doxygen</pkg>
+ </flag>
<flag name="boinc">
Use CmDock with SiDock@home BOINC project
</flag>
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2022-06-25 17:43 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2022-06-25 17:43 UTC (permalink / raw
To: gentoo-commits
commit: bec2b834dd663f30d9bc508ee6043959b50fccfb
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Wed Jun 22 19:31:16 2022 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sat Jun 25 17:42:15 2022 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=bec2b834
sci-biology/cmdock: boinc fix
See https://www.sidock.si/sidock/forum_thread.php?id=125&postid=1427
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
...dock-0.1.4-r1.ebuild => cmdock-0.1.4-r2.ebuild} | 28 +++++++++++++++-------
1 file changed, 20 insertions(+), 8 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.4-r1.ebuild b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
similarity index 74%
rename from sci-biology/cmdock/cmdock-0.1.4-r1.ebuild
rename to sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
index cf79531ec..422d56da2 100644
--- a/sci-biology/cmdock/cmdock-0.1.4-r1.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..11} pypy3 )
+PYTHON_COMPAT=( python3_{8..11} )
BOINC_APP_OPTIONAL="true"
@@ -11,27 +11,32 @@ DOCS_BUILDER="sphinx"
DOCS_AUTODOC=0
DOCS_DIR="docs"
-inherit python-any-r1 boinc-app docs flag-o-matic meson
+inherit python-single-r1 boinc-app docs flag-o-matic meson optfeature
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}"
+INSTALL_PREFIX="${EPREFIX}/opt/${P}"
LICENSE="LGPL-3 ZLIB"
SLOT="0/${PV}"
KEYWORDS="~amd64"
IUSE="apidoc boinc cpu_flags_x86_sse2"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="
- dev-lang/perl
+ ${PYTHON_DEPS}
+ dev-lang/perl:*
boinc? ( sci-misc/boinc-wrapper )
"
-BDEPEND="
+DEPEND="
dev-cpp/eigen:3
dev-cpp/indicators
>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
dev-libs/cxxopts
+"
+BDEPEND="
doc? ( app-doc/doxygen )
"
@@ -46,8 +51,12 @@ BOINC_APP_HELPTEXT=\
is to attach it to SiDock@home BOINC project."
foreach_wrapper_job() {
- sed -i "$1" \
- -e "s:@PREFIX@:${EPREFIX}/opt/${P}:g" || die
+ sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
+}
+
+src_prepare() {
+ default
+ python_fix_shebang "${S}"/bin
}
src_configure() {
@@ -75,19 +84,22 @@ src_compile() {
src_install() {
meson_src_install
+ python_optimize "${ED}"/opt/${P}/
if use boinc; then
doappinfo "${FILESDIR}"/app_info_${PV}.xml
dowrapper ${PN}-boinc-zcp
# install a blank file
+ touch "${T}"/docking_out || die
insinto $(get_project_root)
- insopts --owner boinc --group boinc
- : newins - docking_out.sd
+ insopts -m 0644 --owner boinc --group boinc
+ doins "${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
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2022-06-25 19:42 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2022-06-25 19:42 UTC (permalink / raw
To: gentoo-commits
commit: e41cb6fdcdeee98756bad4f3e77113f2a59db1e1
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sat Jun 25 19:17:06 2022 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sat Jun 25 19:40:36 2022 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=e41cb6fd
sci-biology/cmdock: set file owner to root
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.1.4-r2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
index 422d56da2..46968da14 100644
--- a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
@@ -93,7 +93,7 @@ src_install() {
# install a blank file
touch "${T}"/docking_out || die
insinto $(get_project_root)
- insopts -m 0644 --owner boinc --group boinc
+ insopts -m 0644 --owner root --group boinc
doins "${T}"/docking_out
fi
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2022-12-12 11:44 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2022-12-12 11:44 UTC (permalink / raw
To: gentoo-commits
commit: b1a2cd7094d51b66191a84fe23be6d8fde91db1c
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Fri Dec 9 09:32:45 2022 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Mon Dec 12 11:22:53 2022 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=b1a2cd70
sci-biology/cmdock: fix docs build
Closes: https://bugs.gentoo.org/884905
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.1.4-r2.ebuild | 27 ++++++++++++++-------------
1 file changed, 14 insertions(+), 13 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
index 46968da14..05961204a 100644
--- a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
@@ -4,13 +4,8 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..11} )
-
BOINC_APP_OPTIONAL="true"
-
DOCS_BUILDER="sphinx"
-DOCS_AUTODOC=0
-DOCS_DIR="docs"
-
inherit python-single-r1 boinc-app docs flag-o-matic meson optfeature
DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
@@ -37,7 +32,10 @@ DEPEND="
dev-libs/cxxopts
"
BDEPEND="
- doc? ( app-doc/doxygen )
+ apidoc? (
+ app-doc/doxygen
+ dev-texlive/texlive-fontutils
+ )
"
PATCHES=( "${FILESDIR}"/cmdock-0.1.4-fix-detection.patch )
@@ -72,14 +70,17 @@ src_configure() {
src_compile() {
meson_src_compile
- # subshell prevents overriding global
- # DOCS_BUILDER and DOCS_OUTDIR
- (
+ if use doc; then
+ DOCS_AUTODOC=0
+ DOCS_DIR="docs"
+ sphinx_compile
+ fi
+
+ if use apidoc; then
DOCS_BUILDER="doxygen"
- DOCS_OUTDIR="${S}/_build/html/api"
- docs_compile
- )
- docs_compile
+ DOCS_DIR="docs"
+ doxygen_compile
+ fi
}
src_install() {
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2022-12-12 11:44 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2022-12-12 11:44 UTC (permalink / raw
To: gentoo-commits
commit: 2c7621909ee00689a9aaf0be8f8c0539d6bcc70a
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Mon Dec 12 11:42:12 2022 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Mon Dec 12 11:43:44 2022 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=2c762190
sci-biology/cmdock: update SRC_URI
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 2 +-
sci-biology/cmdock/cmdock-0.1.4-r2.ebuild | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 92078ebaa..5f5d12c7f 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1 @@
-DIST cmdock-v0.1.4.tar.gz 14487352 BLAKE2B 3f212d596a12046f9a3b04376ca3e6d67f4391edba6f9c6e1fd372e7c7dbb23727ebd77787f125e57afca16e0cffc9b734dcdc7a83a825c52737218df371cbfd SHA512 6e1a366d82b311da0fdcd99ecf3e10962073453c7fdec9142854d472336f7f918bb76368b52e5904bf30e0aea6b8476a3ab522469daeaef52293ac481741b4bb
+DIST cmdock-v0.1.4.tar.bz2 14095825 BLAKE2B 80d5d86dc11e842689255d2b673545436404fb92815bb33b5ff15eba0cd3e8970a750dfeb657d018ef31024a2ecf591bcb5c6c1f427be1d0c86a0cfc017c8aa0 SHA512 d0d9a96ef0fad8cd4b320a2339a1889e481a825c5712259e04c9e91b34de597def3100c3c9f71fa63f3eef43892a17c0114d4cc93e99424bcdcc1fc97c25f51e
diff --git a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
index 05961204a..3338c03ac 100644
--- a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
@@ -6,11 +6,12 @@ EAPI=8
PYTHON_COMPAT=( python3_{8..11} )
BOINC_APP_OPTIONAL="true"
DOCS_BUILDER="sphinx"
+DOCS_AUTODOC=0
inherit python-single-r1 boinc-app docs flag-o-matic meson optfeature
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"
+SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
S="${WORKDIR}/${PN}-v${PV}"
INSTALL_PREFIX="${EPREFIX}/opt/${P}"
@@ -71,7 +72,6 @@ src_compile() {
meson_src_compile
if use doc; then
- DOCS_AUTODOC=0
DOCS_DIR="docs"
sphinx_compile
fi
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2023-02-19 5:26 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2023-02-19 5:26 UTC (permalink / raw
To: gentoo-commits
commit: 5921ae942a5c831957c1d975278befd4d8cb5e28
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sun Feb 19 05:26:31 2023 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sun Feb 19 05:26:31 2023 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=5921ae94
sci-biology/cmdock: drop 0.1.4-r2
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 -
sci-biology/cmdock/cmdock-0.1.4-r2.ebuild | 109 ------------------------------
2 files changed, 110 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 8757cee0d..708adb269 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1,2 +1 @@
-DIST cmdock-v0.1.4.tar.bz2 14095825 BLAKE2B 80d5d86dc11e842689255d2b673545436404fb92815bb33b5ff15eba0cd3e8970a750dfeb657d018ef31024a2ecf591bcb5c6c1f427be1d0c86a0cfc017c8aa0 SHA512 d0d9a96ef0fad8cd4b320a2339a1889e481a825c5712259e04c9e91b34de597def3100c3c9f71fa63f3eef43892a17c0114d4cc93e99424bcdcc1fc97c25f51e
DIST cmdock-v0.2.0.tar.bz2 14155812 BLAKE2B daf2f1ac137761bf24b2295dd025e81b29eefae23b5b33c7319f87cf6ea938bcb2ce619229d84dd2af9f31785b63bab4dda95bba3e7cd4de122f94f953913694 SHA512 67eda7e712650641219d7d4d4f9c455923bc6241aa687c5b3f489e251b9e838c3bcdcc7184540ab28f96ab8f573320599669e4b52989ce33a015bceec89717c5
diff --git a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild b/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
deleted file mode 100644
index 3338c03ac..000000000
--- a/sci-biology/cmdock/cmdock-0.1.4-r2.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 2021-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..11} )
-BOINC_APP_OPTIONAL="true"
-DOCS_BUILDER="sphinx"
-DOCS_AUTODOC=0
-inherit python-single-r1 boinc-app docs flag-o-matic meson optfeature
-
-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}"
-INSTALL_PREFIX="${EPREFIX}/opt/${P}"
-
-LICENSE="LGPL-3 ZLIB"
-SLOT="0/${PV}"
-KEYWORDS="~amd64"
-IUSE="apidoc boinc cpu_flags_x86_sse2"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
- ${PYTHON_DEPS}
- dev-lang/perl:*
- boinc? ( sci-misc/boinc-wrapper )
-"
-DEPEND="
- dev-cpp/eigen:3
- dev-cpp/indicators
- >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
- dev-libs/cxxopts
-"
-BDEPEND="
- apidoc? (
- app-doc/doxygen
- dev-texlive/texlive-fontutils
- )
-"
-
-PATCHES=( "${FILESDIR}"/cmdock-0.1.4-fix-detection.patch )
-
-DOCS=( INSTALL.md README.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."
-
-foreach_wrapper_job() {
- sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
-}
-
-src_prepare() {
- default
- python_fix_shebang "${S}"/bin
-}
-
-src_configure() {
- # very weird directory layout
- local emesonargs=(
- --prefix="${EPREFIX}/opt/${P}"
- )
- meson_src_configure
-
- use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
-}
-
-src_compile() {
- meson_src_compile
-
- if use doc; then
- DOCS_DIR="docs"
- sphinx_compile
- fi
-
- if use apidoc; then
- DOCS_BUILDER="doxygen"
- DOCS_DIR="docs"
- doxygen_compile
- fi
-}
-
-src_install() {
- meson_src_install
- python_optimize "${ED}"/opt/${P}/
-
- if use boinc; then
- doappinfo "${FILESDIR}"/app_info_${PV}.xml
- dowrapper ${PN}-boinc-zcp
-
- # install a blank file
- touch "${T}"/docking_out || die
- insinto $(get_project_root)
- insopts -m 0644 --owner root --group boinc
- doins "${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] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2024-01-16 11:46 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2024-01-16 11:46 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: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
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 "${1}" || die
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2024-01-20 8:45 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2024-01-20 8:45 UTC (permalink / raw
To: gentoo-commits
commit: a395a6f2ccebd4bcea65ef71c86abf6c5ee9e8bf
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sat Jan 20 08:39:36 2024 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sat Jan 20 08:39:36 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=a395a6f2
Revert "sci-biology/cmdock: make python optional"
This reverts commit d1a766a47405d4cfeced96a49b3bd70f81bd9a94.
Closes: https://bugs.gentoo.org/922486
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0-r1.ebuild | 7 -------
1 file changed, 7 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
index 09ab9cc5cc..f46747447a 100644
--- a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
+++ b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
@@ -65,13 +65,6 @@ python_check_deps() {
python_has_version "dev-python/insipid-sphinx-theme[${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] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2024-07-14 7:27 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2024-07-14 7:27 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: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
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] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2024-08-22 0:27 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2024-08-22 0:27 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: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
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] 12+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/
@ 2024-10-07 0:31 Anna Vyalkova
0 siblings, 0 replies; 12+ messages in thread
From: Anna Vyalkova @ 2024-10-07 0:31 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: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
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] 12+ messages in thread
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