[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/

2020-02-09 Thread Michał Górny 
commit: 0c2a5cb0f6a062b7da6f9a90cbb06e3784df29a6
Author: Michał Górny  gentoo  org>
AuthorDate: Sat Feb  8 12:36:34 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Sun Feb  9 15:54:21 2020 +
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  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:///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

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/

2020-01-22 Thread Michał Górny 
commit: a28df1dc4dc33e567509aee29ae78a923e3c2596
Author: Michał Górny  gentoo  org>
AuthorDate: Wed Jan 22 21:44:12 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Wed Jan 22 21:49:54 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a28df1dc

sci-chemistry/pdb2pqr: Revbump post dep change

Signed-off-by: Michał Górny  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

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/

2020-01-15 Thread Michał Górny 
commit: 1c501ce62778e8e8dda63bb285de2ae421551826
Author: Michał Górny  gentoo  org>
AuthorDate: Thu Jan 16 06:27:06 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Thu Jan 16 06:38:03 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1c501ce6

sci-chemistry/pdb2pqr: Permit numpy-python2

Signed-off-by: Michał Górny  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] )"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/

2020-01-15 Thread Michał Górny 
commit: 86dd55fe750ec8bfed6c980e0ae4abc8c4f08b3c
Author: Michał Górny  gentoo  org>
AuthorDate: Thu Jan 16 06:35:49 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Thu Jan 16 06:38:22 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=86dd55fe

sci-chemistry/pdb2pqr: Use HTTPS

Signed-off-by: Michał Górny  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"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/

2017-12-01 Thread David Seifert 
commit: f614fac2421fe5f99aa062cadb21c4a267ce40cc
Author: David Seifert  gentoo  org>
AuthorDate: Fri Dec  1 22:42:28 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Dec  1 23:00:35 2017 +
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;

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pdb2pqr/

2017-09-12 Thread Matt Turner 
commit: bea5d2739b62eea6cfb4df528f8bed8113d8b911
Author: Matt Turner  gentoo  org>
AuthorDate: Tue Sep 12 22:56:56 2017 +
Commit: Matt Turner  gentoo  org>
CommitDate: Tue Sep 12 22:58:17 2017 +
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}"