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

["Honza Macháček" <Hloupy.Honza@centrum.cz>]

commit:     83a6f8e906f3701f214c034c05285f7106cc5413
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Tue Jun 18 13:54:29 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Tue Jun 18 13:54:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83a6f8e9

The dependency of several packages on sci-libs/libxc modified to reflect correctly the recent change in the upgrade of sci-physics/abinit & friends.


 profiles/package.mask                              |  6 +++
 sci-chemistry/freeon/freeon-2012.05.03.ebuild      |  7 +--
 sci-chemistry/freeon/freeon-9999.ebuild            |  7 +--
 sci-chemistry/mics/ChangeLog                       | 10 ++++
 sci-chemistry/mics/Manifest                        |  1 +
 .../{mgltools-autodocktools => mics}/metadata.xml  |  0
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++++++++++++++++++
 sci-chemistry/modeller/ChangeLog                   |  6 +++
 ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} |  2 +-
 sci-chemistry/talosn/ChangeLog                     | 10 ++++
 sci-chemistry/talosn/Manifest                      |  1 +
 .../metadata.xml                                   |  0
 .../talosn/talosn-4.01.2013.148.15.55.ebuild       | 59 ++++++++++++++++++++++
 sci-libs/bigdft-abi/ChangeLog                      |  4 ++
 sci-libs/bigdft-abi/Manifest                       |  2 -
 sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild        |  5 +-
 sci-libs/libxc/Manifest                            |  2 +-
 sci-libs/libxc/libxc-9999.ebuild                   | 27 ++++++----
 sci-libs/mumps/ChangeLog                           |  5 +-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |  5 +-
 sci-physics/abinit/ChangeLog                       |  3 ++
 sci-physics/abinit/Manifest                        |  3 +-
 sci-physics/abinit/abinit-7.2.2.ebuild             |  2 +-
 sci-physics/bigdft/ChangeLog                       |  5 ++
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         |  2 +-
 sci-physics/elk/ChangeLog                          |  4 ++
 sci-physics/elk/elk-1.4.22.ebuild                  |  2 +-
 27 files changed, 196 insertions(+), 35 deletions(-)

diff --cc profiles/package.mask
index 0c270df,0c270df..f354cdf
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@@ -68,6 -68,6 +68,12 @@@
  >=sci-chemistry/coot-9999
  >=sci-chemistry/pymol-9999
  
++# Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013)
++# bigdft moved from sci-libs to sci-physics
++# sci-physics/abinit now uses sci-libs/bigdft-abi instead
++# sci-libs/bigdft should be deleted in 30 days
++sci-libs/bigdft
++
  # Justin Lecher <jlec@gentoo.org> (03 March 2013)
  # Missing deps
  sci-biology/gbrowse
diff --cc sci-chemistry/freeon/freeon-2012.05.03.ebuild
index 99805e0,99805e0..5a9cc6a
--- a/sci-chemistry/freeon/freeon-2012.05.03.ebuild
+++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild
@@@ -33,11 -33,11 +33,8 @@@ DEPEND="${DEPEND
  S="${WORKDIR}/${REAL_PN}-${REAL_PV}"
  
  src_prepare() {
--	# Get rid of the obsolete internal hdf5
--	rm -r "${S}"/hdf5-1.8.3
--	# as well as of the internal lapack
--	rm -r "${S}"/lapack
--	epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch
++	# Prevent the obsolete internal hdf5 breaking autoconf
++	epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch
  	eautoreconf
  }
  
diff --cc sci-chemistry/freeon/freeon-9999.ebuild
index 369e063,369e063..6d02d93
--- a/sci-chemistry/freeon/freeon-9999.ebuild
+++ b/sci-chemistry/freeon/freeon-9999.ebuild
@@@ -31,11 -31,11 +31,8 @@@ DEPEND="${DEPEND
  	virtual/pkgconfig"
  
  src_prepare() {
--	# Get rid of the obsolete internal hdf5
--	rm -r "${S}"/Modules/hdf5-1.8.3
--	# as well as of the internal lapack
--	rm -r "${S}"/Modules/lapack
--	epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch
++	# Prevent the obsolete internal hdf5 breaking autoconf
++	epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch
  	eautoreconf
  }
  
diff --cc sci-libs/bigdft-abi/ChangeLog
index 4c48008,4c48008..10ecead
--- a/sci-libs/bigdft-abi/ChangeLog
+++ b/sci-libs/bigdft-abi/ChangeLog
@@@ -2,6 -2,6 +2,10 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
++  bigdft-abi-1.0.4.ebuild:
++  The dependency on sci-libs/libxc modified to allow for 1.2.0-r1.
++
  *bigdft-abi-1.0.4 (17 Jun 2013)
  
    17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --cc sci-libs/bigdft-abi/Manifest
index bd17fc5,bd17fc5..e8a8b97
--- a/sci-libs/bigdft-abi/Manifest
+++ b/sci-libs/bigdft-abi/Manifest
@@@ -1,3 -1,3 +1,1 @@@
--AUX bigdft-abi-1.0.4-tests.tar.bz2 402968 SHA256 11144208456b001f63b75cadce0e9b685054ef8bbc39a76cb08af61d5c86c4fb SHA512 3594d11a8d5834916f44bf6f049630ac9d092df6a7a3171701ef65e5ab56e9d039c2bb4603698cb4935a95189c65d7bf77f44b50617ea8c971a844a2757b3202 WHIRLPOOL 492b92805a4eecb5bb204dbf76acf9a40c790b39708a914e38628a2f4dadc3377eed79f8d986231c006bc8c5be0167af60c36f72212005156e8fe3a3c619281c
  DIST bigdft-abi-1.0.4.tar.gz 8982260 SHA256 345cf49da92275710252d50b4ac8364f2f3c33e8f28d84d7b13ccf6fd0c69310 SHA512 556001d1ffd08be70b97f07a8a150d5d033a4611957180a7a25b41963754e0e3d2bb2a4e9d5b6beb8ff6fb1eb6f4ae9b51633cfe3d7f5a8ed20a85be21031c35 WHIRLPOOL b7c58732b538306f2b9b89b1310d9212cc1bb038fded782e6707e54679013ebc8376d54b5bd1bd51464dc7878fa05102fcba8f70a5d38b4571720c8d57ee3af1
--EBUILD bigdft-abi-1.0.4.ebuild 4232 SHA256 006484b64a83d7971efc05670b77d26114eed87f0d062c39e9b9bf01a4a005ce SHA512 bc34310bf3b4b3999574be8f67db51072a53b2a14fbf340edb72d046989f088b3c12b65f98a781fb5791263ce4c947786ee250dcbe4c162dcd194711321db4b5 WHIRLPOOL 28a1b685e427500acda0e210c9d2e72bbcd24bfe2be1b09112a1aab829d1efe9a896e28b45b42ec7db29c4908bc7cb3b73c83d0ad77accf9269ee9774e310537
diff --cc sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild
index c285d63,c285d63..91e3bac
--- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild
+++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild
@@@ -19,7 -19,7 +19,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux
  IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
  
  RDEPEND="
--	>=sci-libs/libxc-2.0.1[fortran]
++	>=sci-libs/libxc-1.2.0-r1[fortran]
  	virtual/blas
  	virtual/fortran
  	virtual/lapack
@@@ -75,9 -75,9 +75,6 @@@ pkg_setup() 
  }
  
  src_prepare() {
--# 	epatch \
--# 		"${FILESDIR}"/"${P}"-nolib_mods.patch
--#
  	tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/
  	eautoreconf
  }
diff --cc sci-libs/libxc/Manifest
index fa863cf,fa863cf..a85ebc8
--- a/sci-libs/libxc/Manifest
+++ b/sci-libs/libxc/Manifest
@@@ -1,2 -1,2 +1,2 @@@
--DIST libxc-1.1.0.tar.gz 543168 SHA256 b75fb2a73a9e2d75e250cc77b71d5485c8e9b11c3b25c91899c366e217283c57 SHA512 a5ed3a4a7a7abaa11321fe877d01ff00132eab976205213e578cd57fbd2073eea00ce3a3afc188e30ebbd31deb32468c4472313df9992e8d9e3148e6f619936b WHIRLPOOL 8ff70acb2ee65b3373942b71e350fe146f1c205aa4c09dbb22adc04227ba6888482ce412b3e843a9402efd51f9cf6f478f9c65b97305b2035185e59b35484d9f
  DIST libxc-1.2.0.tar.gz 895527 SHA256 ee441c3cde2e2bd87828186aa17f6e4438d17b38634c5d29bb12d3b7554461fb SHA512 3ac0fd07e40db4feb0f0a4ebe1358fdd4de0fff21f6dd369895c658a14cd3bafedbbc374b89f68320401dfcfe16a6230e05403fdaccfcbebb98349ca06593125 WHIRLPOOL 66439bf65a656567c0e52a4ee20b206658a9185bdbd3e045daca00bf01ba0199ccbedea3e5034cf90fbc36dbc04d9666cde8bde46e2577ffd160800f1718bd2a
++DIST libxc-2.0.1.tar.gz 1062846 SHA256 c332f08648ec2bc7ccce83e45a84776215aa5dfebc64fae2a23f2ac546d41ea4 SHA512 c7d87134911fdfd91d985397a3fa990a63cc05d0752f0e2522e41dae0c2f39c43f9bd87ee6eb1972ab92b1aedeefad55a33ad84b1c66032e61ca03c87db02c5b WHIRLPOOL 16a5b999bb60177fde1371421f41f35736af4fcf8df123318ea438ffd34f487dcbadc95124ab9cf6ab2edeadd7983c56e0ca9d84bf528254de1f2a003addd402
diff --cc sci-libs/libxc/libxc-9999.ebuild
index baf29d4,baf29d4..2432915
--- a/sci-libs/libxc/libxc-9999.ebuild
+++ b/sci-libs/libxc/libxc-9999.ebuild
@@@ -1,8 -1,8 +1,8 @@@
--# Copyright 1999-2012 Gentoo Foundation
++# Copyright 1999-2013 Gentoo Foundation
  # Distributed under the terms of the GNU General Public License v2
  # $Header: $
  
--EAPI=4
++EAPI=5
  
  inherit autotools-utils fortran-2 multilib subversion
  
@@@ -14,7 -14,7 +14,7 @@@ ESVN_BOOTSTRAP="eautoreconf -i
  LICENSE="LGPL-3"
  SLOT="0"
  KEYWORDS=""
--IUSE="fortran static-libs"
++IUSE="fortran static-libs -test"
  
  MAKEOPTS+=" -j1"
  
@@@ -31,14 -31,14 +31,21 @@@ src_configure() 
  	autotools-utils_src_configure
  }
  
++## Upstream recommends not running the test suite because it requires
++## human expert interpretation to determine whether output is an error or
++## expected under certain circumstances. Nevertheless, experts might want the option.
++# The autotools src_test function modified not to die. Runs emake check in build directory.
++src_test() {
++	debug-print-function ${FUNCNAME} "$@"
++
++	_check_build_dir
++	pushd "${BUILD_DIR}" > /dev/null || die
++	make check || ewarn "Make check failed. See above for details."
++	einfo "emake check done"
++	popd > /dev/null || die
++}
++
  src_install() {
  	autotools-utils_src_install
  
--	if use fortran; then
--		insinto /usr/$(get_libdir)/finclude
--		pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null
--		doins *.mod || die
--		rm -f "${D}"/usr/include/*.mod || die
--		popd >/dev/null
--	fi
  }
diff --cc sci-physics/abinit/ChangeLog
index a4f623b,a4f623b..2f76ad0
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@@ -2,6 -2,6 +2,9 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> abinit-7.2.2.ebuild:
++  The dependency on sci-libs/libxc modified to allow for 1.2.0-r1.
++
  *abinit-7.2.2 (17 Jun 2013)
  
    17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> -abinit-7.0.4.ebuild,
diff --cc sci-physics/abinit/Manifest
index dee0365,dee0365..f000cdc
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@@ -1,2 -1,2 +1,1 @@@
--DIST abinit-7.0.4.tar.gz 61715030 SHA256 b3ad895b75b92b3ff05e873d42d0b26f6e6113b9de4579966f7b6d1b49d6004e SHA512 8edfe4019c968e6f912d0678fe331fc8a6ce2848f1b16973336d4181d010a776ed1ea2c5500499dac895d9d773d72165e20524705cf8928f91ede873272b0417 WHIRLPOOL 35da8681a68e435b460a11112e6cf6990fdf141d53d5849be45225d50e803e2bfc65cb05e5e576c704411be5734e47ed2e4ccca1fd1689311bd4febea937f0f8
--DIST abinit-7.0.5.tar.gz 61711550 SHA256 b16556aa05448781d872ab18f76ca6446a52be9eeed8d22015a0b63f4adf0f54 SHA512 007292cc7cdf459a5d62e907b29009d9496955952b5f491fa9183a5abb86dbf48020eb435b784d74037e381d65d2255a2b9a130322ee9bfecbff8ca075488ecd WHIRLPOOL 74d83a3a05817eaca402ace1b7ec3c3a6db3697a7ca0166549aee8155edfa2a7c8d516e2ae210a6f0e855f72617d704785bbb10e3a3ee262140964913608a307
++DIST abinit-7.2.2.tar.gz 63683267 SHA256 96f83e3af63e993cb886d9d6cd1c4fac04d50b5e460d5620330441050a909533 SHA512 fbc4898ae4625e12ea22d8f2da63e037eb947320fedf800bd40bd7e0015633ce54b7cb224cee3fc931d015774c51df5f8594ebe26a409cb0325e7a3ab0bf5e4a WHIRLPOOL a149d7ecea9b2b19b94b4e873f1924ce5fe221e037c642d6428727b552dc0c428b288551dda708286995da26080171c385a3ef3ad3766e065073139d4ef0f2e8
diff --cc sci-physics/abinit/abinit-7.2.2.ebuild
index 0a2b49b,0a2b49b..a420f51
--- a/sci-physics/abinit/abinit-7.2.2.ebuild
+++ b/sci-physics/abinit/abinit-7.2.2.ebuild
@@@ -16,7 -16,7 +16,7 @@@ KEYWORDS="~amd64 ~x86
  IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc"
  
  RDEPEND="~sci-libs/bigdft-abi-1.0.4
--	>=sci-libs/libxc-2.0.1[fortran]
++	>=sci-libs/libxc-1.2.0-r1[fortran]
  	>=sci-physics/atompaw-3.0.1.9-r1[libxc]
  	etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 )
  	fox? ( >=sci-libs/fox-4.1.2-r2[sax] )
diff --cc sci-physics/bigdft/ChangeLog
index 0c32817,0c32817..3e78db9
--- a/sci-physics/bigdft/ChangeLog
+++ b/sci-physics/bigdft/ChangeLog
@@@ -2,6 -2,6 +2,11 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
++  bigdft-1.7_pre24.ebuild:
++  The dependency on sci-libs/libxc corrected to reflect the recent change in
++  the upgrade of sci-physics/abinit & friends.
++
  *bigdft-1.7_pre24 (17 Jun 2013)
  
    17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --cc sci-physics/bigdft/bigdft-1.7_pre24.ebuild
index d74906a,d74906a..4a354aa
--- a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
+++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
@@@ -20,7 -20,7 +20,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux
  IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
  
  RDEPEND="
--	>=sci-libs/libxc-1.0[fortran]
++	>=sci-libs/libxc-1.2.0-r1[fortran]
  	virtual/blas
  	virtual/fortran
  	virtual/lapack
diff --cc sci-physics/elk/ChangeLog
index 28ac97d,28ac97d..2a837bc
--- a/sci-physics/elk/ChangeLog
+++ b/sci-physics/elk/ChangeLog
@@@ -2,6 -2,6 +2,10 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> elk-1.4.22.ebuild:
++  The dependency on sci-libs/libxc adapted to its recent change in the upgrade
++  of sci-physics/abinit & friends.
++
    21 Feb 2013; Justin Lecher <jlec@gentoo.org> elk-1.4.22.ebuild:
    Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config;
    add missing dep on virtual/pkgconfig; cleaning of ebuild
diff --cc sci-physics/elk/elk-1.4.22.ebuild
index ab7cd8d,ab7cd8d..5e99d05
--- a/sci-physics/elk/elk-1.4.22.ebuild
+++ b/sci-physics/elk/elk-1.4.22.ebuild
@@@ -19,7 -19,7 +19,7 @@@ RDEPEND=
  	lapack? (
  		virtual/blas
  		virtual/lapack )
--	libxc? ( =sci-libs/libxc-1*[fortran] )
++	libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] )
  	mpi? ( virtual/mpi )"
  DEPEND="${RDEPEND}
  	perl? ( dev-lang/perl )