[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/, sci-biology/screed/, dev-python/ffnet/, sci-physics/bigdft/

2016-10-28 Thread Justin Lecher 
commit: 66a63f3adfe57c5e470ec0941b1db3c180b1ede6
Author: Justin Lecher  gentoo  org>
AuthorDate: Fri Oct 28 14:35:15 2016 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Fri Oct 28 14:35:15 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=66a63f3a

Follow up cleaning of obsolete python implementations

Signed-off-by: Justin Lecher  gentoo.org>

 dev-python/ffnet/ffnet-0.8.3.ebuild | 2 +-
 sci-biology/screed/screed-0.9.ebuild| 2 +-
 sci-physics/abinit/abinit-7.10.4.ebuild | 2 +-
 sci-physics/bigdft/bigdft-1.7.1.ebuild  | 2 +-
 sci-physics/bigdft/bigdft-1.7.6.ebuild  | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/dev-python/ffnet/ffnet-0.8.3.ebuild 
b/dev-python/ffnet/ffnet-0.8.3.ebuild
index 50d1a39..1cd4682 100644
--- a/dev-python/ffnet/ffnet-0.8.3.ebuild
+++ b/dev-python/ffnet/ffnet-0.8.3.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_{6,7} python3_{3,4} )
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
 
 inherit distutils-r1 fortran-2 flag-o-matic
 

diff --git a/sci-biology/screed/screed-0.9.ebuild 
b/sci-biology/screed/screed-0.9.ebuild
index 4df89f4..57e5318 100644
--- a/sci-biology/screed/screed-0.9.ebuild
+++ b/sci-biology/screed/screed-0.9.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-PYTHON_COMPAT=( python2_7 python3_1 python3_3 python3_4 python3_5 )
+PYTHON_COMPAT=( python2_7 python3_3 python3_4 python3_5 )
 
 inherit distutils-r1
 

diff --git a/sci-physics/abinit/abinit-7.10.4.ebuild 
b/sci-physics/abinit/abinit-7.10.4.ebuild
index 38ff682..ed16815 100644
--- a/sci-physics/abinit/abinit-7.10.4.ebuild
+++ b/sci-physics/abinit/abinit-7.10.4.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+PYTHON_COMPAT=( python2_7 )
 
 inherit autotools-utils eutils flag-o-matic fortran-2 multilib 
python-single-r1 toolchain-funcs
 

diff --git a/sci-physics/bigdft/bigdft-1.7.1.ebuild 
b/sci-physics/bigdft/bigdft-1.7.1.ebuild
index d964d97..274c85d 100644
--- a/sci-physics/bigdft/bigdft-1.7.1.ebuild
+++ b/sci-physics/bigdft/bigdft-1.7.1.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-PYTHON_COMPAT=( python2_5 python2_6 python2_7 )
+PYTHON_COMPAT=(  python2_7 )
 
 inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 
toolchain-funcs
 

diff --git a/sci-physics/bigdft/bigdft-1.7.6.ebuild 
b/sci-physics/bigdft/bigdft-1.7.6.ebuild
index 6d17d20..2e248cd 100644
--- a/sci-physics/bigdft/bigdft-1.7.6.ebuild
+++ b/sci-physics/bigdft/bigdft-1.7.6.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-PYTHON_COMPAT=( python2_5 python2_6 python2_7 )
+PYTHON_COMPAT=(  python2_7 )
 
 inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 
toolchain-funcs

[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/

2015-09-23 Thread Justin Lecher 
commit: b05acb97b1671493b661e2a8cdcbb7411c2d4906
Author: Justin Lecher  gentoo  org>
AuthorDate: Wed Sep 23 12:11:58 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Wed Sep 23 12:11:58 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b05acb97

sci-physics/abinit: Use default functions

Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher  gentoo.org>

 sci-physics/abinit/abinit-7.10.4.ebuild   | 2 +-
 sci-physics/abinit/abinit-7.4.2-r1.ebuild | 2 +-
 sci-physics/abinit/abinit-7.6.4-r1.ebuild | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-physics/abinit/abinit-7.10.4.ebuild 
b/sci-physics/abinit/abinit-7.10.4.ebuild
index bf228f2..38ff682 100644
--- a/sci-physics/abinit/abinit-7.10.4.ebuild
+++ b/sci-physics/abinit/abinit-7.10.4.ebuild
@@ -351,7 +351,7 @@ src_install() {
#autotools-utils_src_install() expanded
_check_build_dir
pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-   emake DESTDIR="${D}" install
+   default
 
use libabinit && dolib libabinit.a
 

diff --git a/sci-physics/abinit/abinit-7.4.2-r1.ebuild 
b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
index 7833909..51f7ee7 100644
--- a/sci-physics/abinit/abinit-7.4.2-r1.ebuild
+++ b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
@@ -307,7 +307,7 @@ src_install() {
#autotools-utils_src_install() expanded
_check_build_dir
pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-   emake DESTDIR="${D}" install
+   default
 
use libabinit && dolib libabinit.a
 

diff --git a/sci-physics/abinit/abinit-7.6.4-r1.ebuild 
b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
index e20fb75..61ba323 100644
--- a/sci-physics/abinit/abinit-7.6.4-r1.ebuild
+++ b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
@@ -352,7 +352,7 @@ src_install() {
#autotools-utils_src_install() expanded
_check_build_dir
pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-   emake DESTDIR="${D}" install
+   default
 
use libabinit && dolib libabinit.a

[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/, sci-physics/abinit/files/

2015-04-22 Thread Honza Macháček 
commit: 684348c37be4c96f48248c3dfff436f09850d6dc
Author: Honza Macháček  centrum  cz>
AuthorDate: Wed Apr 22 15:05:51 2015 +
Commit: Honza Macháček  centrum  cz>
CommitDate: Wed Apr 22 15:05:51 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=684348c3

Version bump to sci-physics/abinit-7.10.4, dependency for USE=bigdft changed in 
the new version from sci-libs/bigdft-abi to 
+  +abinit-7.10.4.ebuild, +files/7.10.4-libabinit_options.patch,
+  +files/7.10.4-syntax.patch:
+  Version bump to sci-physics/abinit-7.10.4, dependency for USE=bigdft changed
+  in the new version from sci-libs/bigdft-abi to http://www.abinit.org/";
+SRC_URI="http://ftp.abinit.org/${P}.tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw fftw-mpi 
+fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp 
python scalapack scripts -test +threads wannier"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+#" scalapack? ( !bigdft )"
+
+RDEPEND="virtual/blas
+   virtual/lapack
+   ${PYTHON_DEPS}
+   dev-python/numpy
+   atompaw? ( >=sci-physics/atompaw-4.0.0.10[libxc?] )
+   bigdft? ( >=sci-physics/bigdft-1.7.0.93[scalapack?]
+   =sci-libs/etsf_io-1.0.4 )
+   fftw? (
+   sci-libs/fftw:3.0
+   fftw-threads? (
+   openmp? ( sci-libs/fftw:3.0[openmp] )
+   !openmp? ( sci-libs/fftw:3.0[threads] )
+   )
+   fftw-mpi? (
+   sci-libs/fftw:3.0[mpi]
+   openmp? ( sci-libs/fftw:3.0[openmp] )
+   !openmp? ( sci-libs/fftw:3.0[threads] )
+   )
+   )
+   fox? ( >=sci-libs/fox-4.1.2-r2[sax] )
+   gsl? ( sci-libs/gsl )
+   hdf5? ( sci-libs/hdf5[fortran] )
+   levmar? ( sci-libs/levmar )
+   libxc? ( >=sci-libs/libxc-2.0.3[fortran]
+   =sci-libs/wannier90-1.2-r1 )"
+DEPEND="${RDEPEND}
+   virtual/pkgconfig
+   dev-perl/Text-Markdown"
+
+S=${WORKDIR}/${P%[a-z]}
+
+DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
+   README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+   # Doesn't compile with gcc-4.0, only >=4.1
+   if [[ $(tc-getFC) == *gfortran ]]; then
+   if [[ $(gcc-major-version) -eq 4 ]] \
+   && [[ $(gcc-minor-version) -lt 1  ]]; then
+   die "Requires gcc-4.1 or newer"
+   fi
+   fi
+
+   # fortran-2.eclass does not handle mpi wrappers
+   if use mpi; then
+   export FC="mpif90"
+   export F77="mpif77"
+   export CC="mpicc"
+   export CXX="mpic++"
+   else
+   tc-export FC F77 CC CXX
+   fi
+
+   # Preprocesor macross can make some lines really long
+   append-fflags -ffree-line-length-none
+
+   # This should be correct:
+   #   It is gcc-centric because toolchain-funcs.eclass is gcc-centric.
+   #   Should a bug be filed against toolchain-funcs.eclass?
+   # if use openmp; then
+   # tc-has-openmp || \
+   # die "Please select an openmp capable compiler like 
gcc[openmp]"
+   # fi
+   #
+   # This is completely wrong:
+   #   If other compilers than Gnu Compiler Collection can be used by 
portage,
+   #   their support of OpenMP should be properly tested. This code limits 
the test
+   #   to gcc, and blindly supposes that other compilers do support OpenMP.
+   # if use openmp && [[ $(tc-getCC)$ == *gcc* ]] &&   ! 
tc-has-openmp; then
+   #   die "Please select an openmp capable compiler like gcc[openmp]"
+   # fi
+   #
+   # Luckily Abinit is a fortran package.
+   #   fortran-2.eclass has its own test for OpenMP support,
+   #   more general than toolchain-funcs.eclass
+   #   The test itself proceeds inside fortran-2_pkg_setup
+   if use openmp; then FORTRAN_NEED_OPENMP=1; fi
+
+   fortran-2_pkg_setup
+
+   if use openmp; then
+   # based on _fortran-has-openmp() of fortran-2.eclass
+   local code=ebuild-openmp-flags
+   local ret
+   local openmp
+
+   pushd "${T}"
+   cat <<- EOF > "${code}.c"
+   # include 
+   main () {
+   int nthreads;
+   nthreads=omp_get_num_threads();
+   }
+   EOF
+
+   for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+   ${CC} ${openmp} "${code}.c" -o "${code}.o" &>> 
"${T}"/_c_compile_test.log
+   ret=$?
+   (( ${ret} )) || break
+   done
+
+   rm -f "${code}.*"
+   p

[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/

2015-02-08 Thread Christoph Junghans 
commit: d020a7a157212a8865c99ba428ef48fcbb7f3ff3
Author: Marius Brehler  linux  sungazer  de>
AuthorDate: Sat Feb  7 10:38:33 2015 +
Commit: Christoph Junghans  gentoo  org>
CommitDate: Sat Feb  7 10:46:35 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d020a7a1

sci-physics/abinit: Add missing, drop useless dies

---
 sci-physics/abinit/abinit-7.4.2-r1.ebuild | 14 +++---
 sci-physics/abinit/abinit-7.6.4-r1.ebuild | 14 +++---
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/sci-physics/abinit/abinit-7.4.2-r1.ebuild 
b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
index b8aa19b..3316d43 100644
--- a/sci-physics/abinit/abinit-7.4.2-r1.ebuild
+++ b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -185,7 +185,7 @@ src_prepare() {
"${FILESDIR}"/7.6.4-cuda_header.patch \
"${FILESDIR}"/7.6.4-libxc_versions.patch
eautoreconf
-   sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i 
configure
+   sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i 
configure || die
use test && python_fix_shebang "${S}"/tests
 }
 
@@ -294,7 +294,7 @@ src_compile() {
# Can Abinit use external libabinit.a?
use libabinit && autotools-utils_src_compile libabinit.a
 
-   sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc
+   sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc || die
 }
 
 src_test() {
@@ -307,7 +307,7 @@ src_install() {
#autotools-utils_src_install() expanded
_check_build_dir
pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-   emake DESTDIR="${D}" install || die "make install failed"
+   emake DESTDIR="${D}" install
 
use libabinit && dolib libabinit.a
 
@@ -321,19 +321,19 @@ src_install() {
 
# XXX: support installing them from builddir as well!!!
if [[ ${DOCS} ]]; then
-   dodoc "${DOCS[@]}" || die "dodoc failed"
+   dodoc "${DOCS[@]}"
else
local f
# same list as in PMS
for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \
THANKS BUGS FAQ CREDITS CHANGELOG; do
if [[ -s ${f} ]]; then
-   dodoc "${f}" || die "(default) dodoc ${f} 
failed"
+   dodoc "${f}"
fi
done
fi
if [[ ${HTML_DOCS} ]]; then
-   dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed"
+   dohtml -r "${HTML_DOCS[@]}"
fi
 
if use scripts; then

diff --git a/sci-physics/abinit/abinit-7.6.4-r1.ebuild 
b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
index 708b2de..50a03fa 100644
--- a/sci-physics/abinit/abinit-7.6.4-r1.ebuild
+++ b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -201,7 +201,7 @@ src_prepare() {
"${FILESDIR}"/7.6.4-cuda_header.patch \
"${FILESDIR}"/7.6.4-libxc_versions.patch
eautoreconf
-   sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i 
configure
+   sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i 
configure || die
python_fix_shebang "${S}"
 }
 
@@ -330,7 +330,7 @@ src_compile() {
# Can Abinit use external libabinit.a?
use libabinit && autotools-utils_src_compile libabinit.a
 
-   sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc
+   sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc || die
 }
 
 src_test() {
@@ -340,7 +340,7 @@ src_test() {
pushd "${BUILD_DIR}" > /dev/null || die
 
einfo "Running the internal tests."
-   emake tests_in || die 'The internal tests failed.'
+   emake tests_in
 
einfo "Running the thorough tests. Be patient, please."
"${S}"/tests/runtests.py || ewarn "The package has not passed the 
thorough tests."
@@ -352,7 +352,7 @@ src_install() {
#autotools-utils_src_install() expanded
_check_build_dir
pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-   emake DESTDIR="${D}" install || die "make install failed"
+   emake DESTDIR="${D}" install
 
use libabinit && dolib libabinit.a
 
@@ -373,12 +373,12 @@ src_install() {
for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \
THANKS BUGS FAQ CREDITS CHANGELOG; do
if [[ -s ${f} ]]; then
-   dodoc "${f}" || die "(default) dodoc ${f} 
failed"
+   do

[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/, sci-physics/abinit/files/

2014-12-10 Thread Honza Macháček 
commit: a2bcc940353d91b0c1f8bf37ccb706db42307d4e
Author: Honza Macháček  centrum  cz>
AuthorDate: Wed Dec 10 15:28:54 2014 +
Commit: Honza Macháček  centrum  cz>
CommitDate: Wed Dec 10 15:28:54 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a2bcc940

Treated a small problem with CUDA in sci-physics/abinit, corrected its 
dependency on sci-libs/libxs versions.

Package-Manager: portage-2.2.14

---
 sci-physics/abinit/ChangeLog   |  9 +
 ...{abinit-7.4.2.ebuild => abinit-7.4.2-r1.ebuild} |  7 ++--
 ...{abinit-7.6.4.ebuild => abinit-7.6.4-r1.ebuild} |  7 ++--
 sci-physics/abinit/files/7.6.4-cuda_header.patch   | 11 ++
 .../abinit/files/7.6.4-libxc_versions.patch| 40 ++
 5 files changed, 70 insertions(+), 4 deletions(-)

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 656fde6..a2b5e94 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*abinit-7.6.4-r1 (10 Dec 2014)
+*abinit-7.4.2-r1 (10 Dec 2014)
+
+  10 Dec 2014; Honza Macháček  -abinit-7.4.2.ebuild,
+  +abinit-7.4.2-r1.ebuild, -abinit-7.6.4.ebuild, +abinit-7.6.4-r1.ebuild,
+  +files/7.6.4-cuda_header.patch, +files/7.6.4-libxc_versions.patch:
+  Treated a small problem with CUDA in sci-physics/abinit, corrected its
+  dependency on sci-libs/libxs versions.
+
   17 Sep 2014; Christoph Junghans  metadata.xml:
   updated metadata.xml
 

diff --git a/sci-physics/abinit/abinit-7.4.2.ebuild 
b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
similarity index 98%
rename from sci-physics/abinit/abinit-7.4.2.ebuild
rename to sci-physics/abinit/abinit-7.4.2-r1.ebuild
index 67f3249..b8aa19b 100644
--- a/sci-physics/abinit/abinit-7.4.2.ebuild
+++ b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
@@ -34,7 +34,8 @@ RDEPEND="virtual/blas
gsl? ( sci-libs/gsl )
hdf5? ( sci-libs/hdf5[fortran] )
levmar? ( sci-libs/levmar )
-   libxc? ( >=sci-libs/libxc-2.0.1[fortran] )
+   libxc? ( >=sci-libs/libxc-2.0[fortran]
+   
+ #include 
+ #include 
++#include 
+ #include 
+ #include 
+ #include 

diff --git a/sci-physics/abinit/files/7.6.4-libxc_versions.patch 
b/sci-physics/abinit/files/7.6.4-libxc_versions.patch
new file mode 100644
index 000..4f45db7
--- /dev/null
+++ b/sci-physics/abinit/files/7.6.4-libxc_versions.patch
@@ -0,0 +1,40 @@
+diff -Naurp abinit-7.6.4.orig/config/m4/conn-dft.m4 
abinit-7.6.4/config/m4/conn-dft.m4
+--- abinit-7.6.4.orig/config/m4/conn-dft.m42014-05-03 14:18:46.0 
+
 abinit-7.6.4/config/m4/conn-dft.m4 2014-12-10 14:08:19.786380878 +
+@@ -135,7 +135,7 @@ AC_DEFUN([_ABI_DFT_CHECK_BIGDFT],[
+ 
+ 
+ 
+-# _ABI_DFT_CHECK_LIBXC(API_MAJOR, API_MINOR)
++# _ABI_DFT_CHECK_LIBXC(API_MIN_MAJOR, API_MIN_MINOR, API_MAX_MAJOR, 
API_MAX_MINOR)
+ # --
+ #
+ # Check whether the LibXC library is working.
+@@ -203,7 +203,7 @@ AC_DEFUN([_ABI_DFT_CHECK_LIBXC],[
+   dnl Check that we have the correct LibXC version
+   if test "${abi_dft_libxc_has_incs}" = "yes" -a \
+   "${abi_dft_libxc_has_libs}" = "yes"; then
+-AC_MSG_CHECKING([whether this is LibXC version $1.$2])
++AC_MSG_CHECKING([whether this is LibXC version from $1.$2 to $3.$4])
+ AC_LANG_PUSH([C])
+ AC_RUN_IFELSE([AC_LANG_PROGRAM(
+   [[
+@@ -212,7 +212,8 @@ AC_DEFUN([_ABI_DFT_CHECK_LIBXC],[
+   [[
+ int major = -1, minor = -1;
+ xc_version(&major, &minor);
+-if ( (major != $1) || (minor != $2) ) {
++if ( (major < $1) || (major == $1) && (minor < $2) ||
++  (major == $3) && (minor > $4) || (major > $3) ) {
+   return 1; }
+   ]])], [abi_dft_libxc_version="yes"], [abi_dft_libxc_version="no"])
+ AC_LANG_POP([C])
+@@ -518,7 +519,7 @@ AC_DEFUN([ABI_CONNECT_DFT],[
+   ;;
+ 
+ libxc)
+-  _ABI_DFT_CHECK_LIBXC(2,0)
++  _ABI_DFT_CHECK_LIBXC(2,0,2,1)
+   if test "${abi_dft_libxc_serial}" = "yes" -o \
+   "${enable_fallbacks}" = "yes"; then
+ AC_DEFINE([HAVE_DFT_LIBXC],1,

[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/

2014-09-17 Thread Christoph Junghans 
commit: b43297bd79a945bb8961e2dae2ac7208b5cc10e6
Author: Christoph Junghans  gentoo  org>
AuthorDate: Wed Sep 17 19:58:12 2014 +
Commit: Christoph Junghans  gentoo  org>
CommitDate: Wed Sep 17 19:58:12 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b43297bd

updated metadata.xml

Package-Manager: portage-2.2.8-r1

---
 sci-physics/abinit/ChangeLog| 3 +++
 sci-physics/abinit/metadata.xml | 6 --
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 7c785b6..656fde6 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Sep 2014; Christoph Junghans  metadata.xml:
+  updated metadata.xml
+
   10 Jul 2014; Honza Macháček 
   +files/7.6.3-libabinit_options.patch:
   Added forgotten patch file 7.6.3-libabinit_options.patch for sci-

diff --git a/sci-physics/abinit/metadata.xml b/sci-physics/abinit/metadata.xml
index eb0c4e6..553687d 100644
--- a/sci-physics/abinit/metadata.xml
+++ b/sci-physics/abinit/metadata.xml
@@ -48,12 +48,6 @@ ABINIT code, different utility programs are provided.
 Enable support for FoX Fortran XML library
   
   
-
-  Build the abinit GUI (requires java);
-  since 7.4.0 a separate package
-
-  
-  
 
   Enable support for sci-libs/levmar,
   the Levenberg-Marquardt least-squares optimisation

[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/files/, sci-physics/abinit/

2014-07-10 Thread Honza Macháček 
commit: 1d3d7a5552332945d6153c3073e42500b59a36b1
Author: Honza Macháček  centrum  cz>
AuthorDate: Thu Jul 10 07:07:09 2014 +
Commit: Honza Macháček  centrum  cz>
CommitDate: Thu Jul 10 07:07:09 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1d3d7a55

Added forgotten patch file 7.6.3-libabinit_options.patch for sci-physics/abinit

Package-Manager: portage-2.2.10

---
 sci-physics/abinit/ChangeLog   |  5 ++
 .../abinit/files/7.6.3-libabinit_options.patch | 80 ++
 2 files changed, 85 insertions(+)

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 11dd22a..7c785b6 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jul 2014; Honza Macháček 
+  +files/7.6.3-libabinit_options.patch:
+  Added forgotten patch file 7.6.3-libabinit_options.patch for sci-
+  physics/abinit
+
 *abinit-7.6.4 (27 Jun 2014)
 
   27 Jun 2014; Honza Macháček  +abinit-7.6.4.ebuild,

diff --git a/sci-physics/abinit/files/7.6.3-libabinit_options.patch 
b/sci-physics/abinit/files/7.6.3-libabinit_options.patch
new file mode 100644
index 000..d97d2dae
--- /dev/null
+++ b/sci-physics/abinit/files/7.6.3-libabinit_options.patch
@@ -0,0 +1,80 @@
+diff -Naurp abinit-7.6.3.orig/Makefile.am abinit-7.6.3/Makefile.am
+--- abinit-7.6.3.orig/Makefile.am  2014-04-06 20:33:21.0 +
 abinit-7.6.3/Makefile.am   2014-05-02 10:33:49.836301391 +
+@@ -1622,7 +1622,9 @@ libabinit.a:
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a
++if DO_BUILD_15_GPU_TOOLBOX
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
++endif
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/18_timing/lib18_timing.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a
+@@ -1642,7 +1644,9 @@ libabinit.a:
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a
++if DO_BUILD_52_MANAGE_CUDA
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
++endif
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/53_ffts/lib53_ffts.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a
+@@ -1661,14 +1665,18 @@ libabinit.a:
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/63_bader/lib63_bader.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a
++if DO_BUILD_65_LOTF_BASE
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a
++endif
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/65_psp/lib65_psp.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/66_paw/lib66_paw.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/66_wfs/lib66_wfs.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/67_common/lib67_common.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/68_dmft/lib68_dmft.a
++if DO_BUILD_68_LOTF
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/68_lotf/lib68_lotf.a
++endif
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/68_recursion/lib68_recursion.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a
+diff -Naurp abinit-7.6.3.orig/Makefile.in abinit-7.6.3/Makefile.in
+--- abinit-7.6.3.orig/Makefile.in  2014-04-06 20:33:32.0 +
 abinit-7.6.3/Makefile.in   2014-05-02 11:25:34.961648440 +
+@@ -2746,7 +2746,7 @@ libabinit.a:
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a
+   cd $(libabinit_tmpdir) && $(AR) xv 
$(abs_top_builddir)/src/12_hide_mp

[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/

2014-06-27 Thread Honza Macháček 
commit: 4f1c3ab6bcdefdade71186214b625663eada8a77
Author: Honza Macháček  centrum  cz>
AuthorDate: Fri Jun 27 13:53:49 2014 +
Commit: Honza Macháček  centrum  cz>
CommitDate: Fri Jun 27 13:53:49 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4f1c3ab6

Version bumped to 7.6.4. ScaLAPACK support, and use of the MPI implementation 
of sci-libs/fftw added. Minor attempts on enhancements and cleanup.

Package-Manager: portage-2.2.10

---
 sci-physics/abinit/ChangeLog   |   9 +-
 sci-physics/abinit/abinit-7.6.4.ebuild | 388 +
 sci-physics/abinit/metadata.xml|  23 +-
 3 files changed, 415 insertions(+), 5 deletions(-)

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 6baa378..11dd22a 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-physics/abinit
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*abinit-7.6.4 (27 Jun 2014)
+
+  27 Jun 2014; Honza Macháček  +abinit-7.6.4.ebuild,
+  metadata.xml:
+  Version bumped to 7.6.4. ScaLAPACK support, and use of the MPI implementation
+  of sci-libs/fftw added. Minor attempts on enhancements and cleanup.
+
   10 Oct 2013; Honza Macháček  abinit-7.4.2.ebuild,
   +files/7.4.2-cuda_link_stdc++.patch:
   Added a patch to link libstdc++ with the C++ CUDA objects.

diff --git a/sci-physics/abinit/abinit-7.6.4.ebuild 
b/sci-physics/abinit/abinit-7.6.4.ebuild
new file mode 100644
index 000..6947f11
--- /dev/null
+++ b/sci-physics/abinit/abinit-7.6.4.ebuild
@@ -0,0 +1,388 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+
+inherit autotools-utils eutils flag-o-matic fortran-2 multilib 
python-single-r1 toolchain-funcs
+
+DESCRIPTION="Find total energy, charge density and electronic structure using 
density functional theory"
+HOMEPAGE="http://www.abinit.org/";
+SRC_URI="http://ftp.abinit.org/${P}.tar.gz";
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw fftw-mpi 
+fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp 
python scalapack scripts -test +threads wannier"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+#" scalapack? ( !bigdft )"
+
+RDEPEND="virtual/blas
+   virtual/lapack
+   ${PYTHON_DEPS}
+   dev-python/numpy
+   atompaw? ( >=sci-physics/atompaw-3.0.1.9-r1[libxc?] )
+   bigdft? ( ~sci-libs/bigdft-abi-1.0.4[scalapack?] )
+   cuda? ( dev-util/nvidia-cuda-sdk )
+   etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 )
+   fftw? (
+   sci-libs/fftw:3.0
+   fftw-threads? (
+   openmp? ( sci-libs/fftw:3.0[openmp] )
+   !openmp? ( sci-libs/fftw:3.0[threads] )
+   )
+   fftw-mpi? (
+   sci-libs/fftw:3.0[mpi]
+   openmp? ( sci-libs/fftw:3.0[openmp] )
+   !openmp? ( sci-libs/fftw:3.0[threads] )
+   )
+   )
+   fox? ( >=sci-libs/fox-4.1.2-r2[sax] )
+   gsl? ( sci-libs/gsl )
+   hdf5? ( sci-libs/hdf5[fortran] )
+   levmar? ( sci-libs/levmar )
+   libxc? ( =sci-libs/libxc-2.0*[fortran] )
+   netcdf? (
+   sci-libs/netcdf[hdf5?]
+   || (
+   sci-libs/netcdf[fortran]
+   sci-libs/netcdf-fortran
+   )
+   )
+   mpi? ( virtual/mpi )
+   scalapack? ( virtual/scalapack )
+   scripts? ( dev-python/PyQt4 )
+   wannier? ( >=sci-libs/wannier90-1.2-r1 )"
+DEPEND="${RDEPEND}
+   virtual/pkgconfig
+   dev-perl/Text-Markdown"
+
+S=${WORKDIR}/${P%[a-z]}
+
+DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
+   README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+   # Doesn't compile with gcc-4.0, only >=4.1
+   if [[ $(tc-getFC) == *gfortran ]]; then
+   if [[ $(gcc-major-version) -eq 4 ]] \
+   && [[ $(gcc-minor-version) -lt 1  ]]; then
+   die "Requires gcc-4.1 or newer"
+   fi
+   fi
+
+   # fortran-2.eclass does not handle mpi wrappers
+   if use mpi; then
+   export FC="mpif90"
+   export F77="mpif77"
+   export CC="mpicc"
+   export CXX="mpic++"
+   else
+   tc-export FC F77 CC CXX
+   fi
+
+   # Preprocesor macross can make some lines really long
+   append-fflags -ffree-line-length-none
+
+   # This should be correct:
+   #   It is gcc-centric because toolchain-fun