* [gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: ChangeLog pdb2pqr-1.9.0-r1.ebuild
@ 2014-10-28 9:00 Justin Lecher (jlec)
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher (jlec) @ 2014-10-28 9:00 UTC (permalink / raw
To: gentoo-commits
jlec 14/10/28 09:00:32
Modified: ChangeLog
Added: pdb2pqr-1.9.0-r1.ebuild
Log:
sci-chemistry/pdb2pqr: Allow multi py ABI installations, clean installation
(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path
1.43 sci-chemistry/pdb2pqr/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.43&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.43&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?r1=1.42&r2=1.43
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- ChangeLog 27 Oct 2014 17:17:03 -0000 1.42
+++ ChangeLog 28 Oct 2014 09:00:32 -0000 1.43
@@ -1,6 +1,12 @@
# ChangeLog for sci-chemistry/pdb2pqr
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.42 2014/10/27 17:17:03 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.43 2014/10/28 09:00:32 jlec Exp $
+
+*pdb2pqr-1.9.0-r1 (28 Oct 2014)
+
+ 28 Oct 2014; Justin Lecher <jlec@gentoo.org> +pdb2pqr-1.9.0-r1.ebuild,
+ +files/pdb2pka, +files/pdb2pqr-1.9.0-install-py.patch, +files/pdb2pqr:
+ Allow multi py ABI installations, clean installation
27 Oct 2014; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.9.0.ebuild:
Add missing PYTHON_USEDEP
1.1 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.1&content-type=text/plain
Index: pdb2pqr-1.9.0-r1.ebuild
===================================================================
# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.1 2014/10/28 09:00:32 jlec Exp $
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit autotools scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs
DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
HOMEPAGE="http://www.poissonboltzmann.org/"
SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
SLOT="0"
LICENSE="BSD"
IUSE="doc examples opal +pdb2pka"
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="${PYTHON_DEPS}
dev-python/numpy[${PYTHON_USEDEP}]
sci-chemistry/openbabel[python]
sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
DEPEND="${RDEPEND}
dev-lang/swig:0"
PATCHES=(
"${FILESDIR}"/${P}-flags.patch
"${FILESDIR}"/${P}-install-py.patch
)
pkg_setup() {
if [[ -z ${MAXATOMS} ]]; then
einfo "If you like to have support for more then 10000 atoms,"
einfo "export MAXATOMS=\"your value\""
export MAXATOMS=10000
else
einfo "Allow usage of ${MAXATOMS} during calculations"
fi
fortran-2_pkg_setup
}
src_prepare() {
find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
export CXXFLAGS="${CXXFLAGS}"
export LDFLAGS="${LDFLAGS}"
epatch ${PATCHES[@]}
tc-export CXX
rm -rf scons || die
python_copy_sources
}
src_configure() {
python_configure() {
cd "${BUILD_DIR}" || die
cat > build_config.py <<- EOF
PREFIX="${ED}/$(python_get_sitedir)/${PN}"
#URL="http://<COMPUTER NAME>/pdb2pqr/"
APBS="${EPREFIX}/usr/bin/apbs"
#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"
MAX_ATOMS=${MAXATOMS}
BUILD_PDB2PKA=$(usex pdb2pka True False)
REBUILD_SWIG=True
EOF
}
python_foreach_impl python_configure
}
src_compile() {
python_compile() {
cd "${BUILD_DIR}" || die
escons
}
python_foreach_impl python_compile
}
src_test() {
python_test() {
local myesconsargs=( -j1 )
cd "${BUILD_DIR}" || die
escons test
escons advtest
escons complete-test
}
python_foreach_impl python_test
}
src_install() {
dodir /usr/share/doc/${PF}/html
python_install() {
local lib
cd "${BUILD_DIR}" || die
escons install
find "${ED}"$(python_get_sitedir)/${PN}/{jmol,examples,doc,contrib} -delete || die
python_doscript "${FILESDIR}"/{${PN},pdb2pka}
for lib in apbslib.py{,c,o}; do
dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
done
dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
python_optimize
}
python_foreach_impl python_install
if use doc; then
pushd doc > /dev/null
docinto html
dodoc -r *.html images pydoc
popd > /dev/null
fi
use examples && \
insinto /usr/share/${PN}/ && \
doins -r examples
dodoc *md NEWS
}
^ permalink raw reply [flat|nested] 4+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: ChangeLog pdb2pqr-1.9.0-r1.ebuild
@ 2014-11-21 8:56 Justin Lecher (jlec)
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher (jlec) @ 2014-11-21 8:56 UTC (permalink / raw
To: gentoo-commits
jlec 14/11/21 08:56:20
Modified: ChangeLog pdb2pqr-1.9.0-r1.ebuild
Log:
sci-chemistry/pdb2pqr: Avoid double prefix
(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path
1.45 sci-chemistry/pdb2pqr/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.45&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.45&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?r1=1.44&r2=1.45
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v
retrieving revision 1.44
retrieving revision 1.45
diff -u -r1.44 -r1.45
--- ChangeLog 29 Oct 2014 02:42:21 -0000 1.44
+++ ChangeLog 21 Nov 2014 08:56:20 -0000 1.45
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/pdb2pqr
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.44 2014/10/29 02:42:21 patrick Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.45 2014/11/21 08:56:20 jlec Exp $
+
+ 21 Nov 2014; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
+ Avoid double prefix
29 Oct 2014; Patrick Lauer <patrick@gentoo.org> pdb2pqr-1.9.0-r1.ebuild,
pdb2pqr-1.9.0.ebuild:
1.3 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?r1=1.2&r2=1.3
Index: pdb2pqr-1.9.0-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- pdb2pqr-1.9.0-r1.ebuild 29 Oct 2014 02:42:21 -0000 1.2
+++ pdb2pqr-1.9.0-r1.ebuild 21 Nov 2014 08:56:20 -0000 1.3
@@ -1,6 +1,6 @@
# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.2 2014/10/29 02:42:21 patrick Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.3 2014/11/21 08:56:20 jlec Exp $
EAPI=5
@@ -62,7 +62,7 @@
cd "${BUILD_DIR}" || die
cat > build_config.py <<- EOF
- PREFIX="${ED}/$(python_get_sitedir)/${PN}"
+ PREFIX="${D}/$(python_get_sitedir)/${PN}"
#URL="http://<COMPUTER NAME>/pdb2pqr/"
APBS="${EPREFIX}/usr/bin/apbs"
#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
@@ -104,7 +104,7 @@
escons install
- find "${ED}"$(python_get_sitedir)/${PN}/{jmol,examples,doc,contrib} -delete || die
+ find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
python_doscript "${FILESDIR}"/{${PN},pdb2pka}
^ permalink raw reply [flat|nested] 4+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: ChangeLog pdb2pqr-1.9.0-r1.ebuild
@ 2015-01-04 19:15 Justin Lecher (jlec)
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher (jlec) @ 2015-01-04 19:15 UTC (permalink / raw
To: gentoo-commits
jlec 15/01/04 19:15:11
Modified: ChangeLog pdb2pqr-1.9.0-r1.ebuild
Log:
sci-chemistry/pdb2pqr: Drop obsolete dep
(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path
1.46 sci-chemistry/pdb2pqr/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.46&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.46&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?r1=1.45&r2=1.46
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -r1.45 -r1.46
--- ChangeLog 21 Nov 2014 08:56:20 -0000 1.45
+++ ChangeLog 4 Jan 2015 19:15:11 -0000 1.46
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/pdb2pqr
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.45 2014/11/21 08:56:20 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.46 2015/01/04 19:15:11 jlec Exp $
+
+ 04 Jan 2015; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
+ Drop obsolete dep
21 Nov 2014; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
Avoid double prefix
1.4 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?r1=1.3&r2=1.4
Index: pdb2pqr-1.9.0-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- pdb2pqr-1.9.0-r1.ebuild 21 Nov 2014 08:56:20 -0000 1.3
+++ pdb2pqr-1.9.0-r1.ebuild 4 Jan 2015 19:15:11 -0000 1.4
@@ -1,6 +1,6 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.3 2014/11/21 08:56:20 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.4 2015/01/04 19:15:11 jlec Exp $
EAPI=5
@@ -21,7 +21,6 @@
RDEPEND="${PYTHON_DEPS}
dev-python/numpy[${PYTHON_USEDEP}]
- sci-chemistry/openbabel[python]
sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
^ permalink raw reply [flat|nested] 4+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: ChangeLog pdb2pqr-1.9.0-r1.ebuild
@ 2015-05-13 6:47 Jack Morgan (jmorgan)
0 siblings, 0 replies; 4+ messages in thread
From: Jack Morgan (jmorgan) @ 2015-05-13 6:47 UTC (permalink / raw
To: gentoo-commits
jmorgan 15/05/13 06:47:49
Modified: ChangeLog pdb2pqr-1.9.0-r1.ebuild
Log:
ppc stable wrt bug #534696
(Portage version: 2.2.18/cvs/Linux x86_64, RepoMan options: --include-arches="ppc", signed Manifest commit with key )
Revision Changes Path
1.48 sci-chemistry/pdb2pqr/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.48&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.48&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?r1=1.47&r2=1.48
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- ChangeLog 4 Jan 2015 19:17:35 -0000 1.47
+++ ChangeLog 13 May 2015 06:47:49 -0000 1.48
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/pdb2pqr
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.47 2015/01/04 19:17:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.48 2015/05/13 06:47:49 jmorgan Exp $
+
+ 13 May 2015; Jack Morgan <jmorgan@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
+ ppc stable wrt bug #534696
04 Jan 2015; Justin Lecher <jlec@gentoo.org> -pdb2pqr-1.7.0.ebuild,
-pdb2pqr-1.7.0-r2.ebuild, -pdb2pqr-1.8.0-r1.ebuild, -pdb2pqr-1.9.0.ebuild:
1.5 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild?r1=1.4&r2=1.5
Index: pdb2pqr-1.9.0-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- pdb2pqr-1.9.0-r1.ebuild 4 Jan 2015 19:15:11 -0000 1.4
+++ pdb2pqr-1.9.0-r1.ebuild 13 May 2015 06:47:49 -0000 1.5
@@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.4 2015/01/04 19:15:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.5 2015/05/13 06:47:49 jmorgan Exp $
EAPI=5
@@ -15,7 +15,7 @@
SLOT="0"
LICENSE="BSD"
IUSE="doc examples opal +pdb2pka"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
^ permalink raw reply [flat|nested] 4+ messages in thread
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2015-01-04 19:15 [gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: ChangeLog pdb2pqr-1.9.0-r1.ebuild Justin Lecher (jlec)
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