* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/
@ 2017-09-12 22:58 Matt Turner
0 siblings, 0 replies; 6+ messages in thread
From: Matt Turner @ 2017-09-12 22:58 UTC (permalink / raw
To: gentoo-commits
commit: bea5d2739b62eea6cfb4df528f8bed8113d8b911
Author: Matt Turner <mattst88 <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 12 22:56:56 2017 +0000
Commit: Matt Turner <mattst88 <AT> gentoo <DOT> org>
CommitDate: Tue Sep 12 22:58:17 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bea5d273
sci-chemistry/pdb2pqr: dropped ppc keywords
sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
index a94bbd3dc91..8b58ae48c5c 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -14,7 +14,7 @@ SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${P
SLOT="0"
LICENSE="BSD"
IUSE="doc examples opal +pdb2pka"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/
@ 2017-12-01 23:01 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2017-12-01 23:01 UTC (permalink / raw
To: gentoo-commits
commit: f614fac2421fe5f99aa062cadb21c4a267ce40cc
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 1 22:42:28 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Dec 1 23:00:35 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f614fac2
sci-chemistry/pdb2pqr: [QA] Fix DESCRIPTION.toolong
sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
index 8b58ae48c5c..46766b7715e 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
@@ -7,7 +7,7 @@ PYTHON_COMPAT=( python2_7 )
inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+DESCRIPTION="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"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/
@ 2020-01-16 6:39 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2020-01-16 6:39 UTC (permalink / raw
To: gentoo-commits
commit: 1c501ce62778e8e8dda63bb285de2ae421551826
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 06:27:06 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 06:38:03 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1c501ce6
sci-chemistry/pdb2pqr: Permit numpy-python2
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
index 46766b7715e..8f367caec92 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -19,7 +19,10 @@ KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="${PYTHON_DEPS}
- dev-python/numpy[${PYTHON_USEDEP}]
+ || (
+ dev-python/numpy-python2[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ )
sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/
@ 2020-01-16 6:39 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2020-01-16 6:39 UTC (permalink / raw
To: gentoo-commits
commit: 86dd55fe750ec8bfed6c980e0ae4abc8c4f08b3c
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 06:35:49 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 06:38:22 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=86dd55fe
sci-chemistry/pdb2pqr: Use HTTPS
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
index 8f367caec92..ad95f8f410f 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs
DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-HOMEPAGE="http://www.poissonboltzmann.org/"
+HOMEPAGE="https://www.poissonboltzmann.org/"
SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
SLOT="0"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/
@ 2020-01-22 21:50 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2020-01-22 21:50 UTC (permalink / raw
To: gentoo-commits
commit: a28df1dc4dc33e567509aee29ae78a923e3c2596
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 22 21:44:12 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Jan 22 21:49:54 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a28df1dc
sci-chemistry/pdb2pqr: Revbump post dep change
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
.../pdb2pqr/{pdb2pqr-1.9.0-r1.ebuild => pdb2pqr-1.9.0-r2.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild
similarity index 100%
rename from sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
rename to sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild
^ permalink raw reply [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/
@ 2020-02-09 15:54 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2020-02-09 15:54 UTC (permalink / raw
To: gentoo-commits
commit: 0c2a5cb0f6a062b7da6f9a90cbb06e3784df29a6
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 8 12:36:34 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Feb 9 15:54:21 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0c2a5cb0
sci-chemistry/pdb2pqr: Switch to python-single-r1
Use python-single-r1 as requiered for the dep on sci-chemistry/apbs.
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
...pqr-1.9.0-r2.ebuild => pdb2pqr-1.9.0-r3.ebuild} | 72 ++++++++--------------
1 file changed, 27 insertions(+), 45 deletions(-)
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
similarity index 60%
rename from sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild
rename to sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
index ad95f8f410f..179e6448d60 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
@@ -5,7 +5,7 @@ EAPI=5
PYTHON_COMPAT=( python2_7 )
-inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs
+inherit scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
HOMEPAGE="https://www.poissonboltzmann.org/"
@@ -19,13 +19,15 @@ KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="${PYTHON_DEPS}
- || (
- dev-python/numpy-python2[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- )
- sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
- opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
- pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
+ $(python_gen_cond_dep '
+ || (
+ dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+ dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+ )
+ sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}]
+ opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] )
+ ')
+ pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )"
DEPEND="${RDEPEND}
dev-lang/swig:0"
@@ -43,6 +45,7 @@ pkg_setup() {
einfo "Allow usage of ${MAXATOMS} during calculations"
fi
fortran-2_pkg_setup
+ python-single-r1_pkg_setup
}
src_prepare() {
@@ -54,15 +57,10 @@ src_prepare() {
epatch "${PATCHES[@]}"
tc-export CXX
rm -rf scons || die
-
- python_copy_sources
}
src_configure() {
- python_configure() {
- cd "${BUILD_DIR}" || die
-
- cat > build_config.py <<- EOF
+ cat > build_config.py <<- EOF
PREFIX="${D}/$(python_get_sitedir)/${PN}"
#URL="http://<COMPUTER NAME>/pdb2pqr/"
APBS="${EPREFIX}/usr/bin/apbs"
@@ -71,51 +69,35 @@ src_configure() {
MAX_ATOMS=${MAXATOMS}
BUILD_PDB2PKA=$(usex pdb2pka True False)
REBUILD_SWIG=True
- EOF
- }
-
- python_foreach_impl python_configure
+ EOF
}
src_compile() {
- python_compile() {
- cd "${BUILD_DIR}" || die
- escons
- }
- python_foreach_impl python_compile
+ escons
}
src_test() {
- python_test() {
- local myesconsargs=( -j1 )
- cd "${BUILD_DIR}" || die
- escons test
- escons advtest
- escons complete-test
- }
- python_foreach_impl python_test
+ local myesconsargs=( -j1 )
+ escons test
+ escons advtest
+ escons complete-test
}
src_install() {
dodir /usr/share/doc/${PF}/html
- python_install() {
- local lib
-
- cd "${BUILD_DIR}" || die
+ local lib
- escons install
+ escons install
- find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
+ find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
- python_doscript "${FILESDIR}"/{${PN},pdb2pka}
+ python_doscript "${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
+ 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
if use doc; then
pushd doc > /dev/null
^ permalink raw reply related [flat|nested] 6+ messages in thread
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