commit: e3417554a48f19740c35e981c3a67a341e88d3c1
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 25 16:22:42 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep 25 16:22:42 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3417554
Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci
* 'master' of git+ssh://git.gentoo.org/proj/sci: (90 commits)
sci-chemistry/coot: Don't set LD_LIBRARY_PATH
www-client/casjerjs: Fix installation of casperjs executable
dev-python/metakernel_bash: Install missing kernel spec
dev-python/metakernel_python: Install missing kernel spec
dev-python/metakernel_bash: New package, ebuild written by me
dev-python/metakernel: New package, ebuild written by me
dev-python/metakernel_python: New package, ebuild written by me
sci-chemistry/votca-csgapps: sync with gx86
sci-chemistry/votca-csg: sync with gx86
sci-libs/votca-tools: sync with gx86
sys-cluster/openmpi: bump 1.10.0
Ban EAPI=4
Use default functions
sci-biology/augustus: Use default functions
sci-physics/mc-tester: Use default functions
sci-biology/Atlas2: Use default functions
sci-physics/tauola: Use default functions
media-libs/libgfx: Use default functions
dev-util/nvidia-cuda-gdk: Use default functions
dev-java/netcdf: Bump to EAPI=5
...
app-admin/eselect/eselect-1.4.5-r101.ebuild | 4 +-
app-admin/eselect/eselect-9999.ebuild | 6 +-
dev-cpp/eigen/eigen-3.2.2.ebuild | 118 ++++++-
dev-cpp/eigen/eigen-3.2.4.ebuild | 118 ++++++-
dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild | 2 +-
dev-java/netcdf/metadata.xml | 4 +-
dev-java/netcdf/netcdf-4.2.ebuild | 17 +-
dev-lang/julia/julia-9999.ebuild | 6 +-
dev-lang/julia/metadata.xml | 6 +-
dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild | 4 +-
dev-libs/libunzip/libunzip-5.52.ebuild | 18 +-
dev-ml/lacaml/lacaml-7.0.3.ebuild | 4 +-
dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild | 2 +-
dev-perl/Time-Progress/Time-Progress-1.7.ebuild | 2 +-
.../arrayfire-python-3.0.20150914.ebuild | 31 +-
dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild | 26 +-
dev-python/ipykernel/ipykernel-4.0.3.ebuild | 40 ++-
dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild | 63 +++-
.../ipython_genutils/ipython_genutils-0.1.0.ebuild | 35 ++-
dev-python/ipywidgets/ChangeLog | 4 +
dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild | 43 ++-
dev-python/ipywidgets/ipywidgets-4.0.3.ebuild | 3 +
dev-python/ipywidgets/ipywidgets-9999.ebuild | 3 +
dev-python/jupyter/jupyter-1.0.0.ebuild | 2 +-
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dev-python/line_profiler/line_profiler-9999.ebuild | 11 +-
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.../matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild | 31 +-
dev-python/metakernel/ChangeLog | 9 +
dev-python/metakernel/Manifest | 1 +
dev-python/metakernel/metadata.xml | 13 +
dev-python/metakernel/metakernel-0.11.0.ebuild | 37 +++
dev-python/metakernel_bash/ChangeLog | 15 +
dev-python/metakernel_bash/Manifest | 1 +
dev-python/metakernel_bash/files/kernel.json | 1 +
.../{ipykernel => metakernel_bash}/metadata.xml | 4 +-
.../metakernel_bash-0.11.3-r1.ebuild | 28 ++
dev-python/metakernel_python/ChangeLog | 15 +
dev-python/metakernel_python/Manifest | 1 +
dev-python/metakernel_python/files/kernel.json | 1 +
.../{ipykernel => metakernel_python}/metadata.xml | 4 +-
.../metakernel_python-0.11.3-r1.ebuild | 29 ++
dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild | 79 ++++-
dev-python/nbconvert/nbconvert-9999.ebuild | 15 +-
dev-python/nbformat/nbformat-4.0.0.ebuild | 60 +++-
dev-python/nbformat/nbformat-9999.ebuild | 11 +-
dev-python/notebook/ChangeLog | 4 +
dev-python/notebook/notebook-4.0.5.ebuild | 6 +
dev-python/notebook/notebook-9999.ebuild | 6 +
dev-python/pickleshare/pickleshare-0.5.ebuild | 40 ++-
.../prettyplotlib/prettyplotlib-0.1.7.ebuild | 31 +-
dev-python/pyfftw/pyfftw-0.9.2.ebuild | 37 ++-
dev-python/pyfftw/pyfftw-9999.ebuild | 12 +-
dev-python/python-ivi/python-ivi-0.14.9.ebuild | 31 +-
dev-python/python-vxi11/python-vxi11-0.7.ebuild | 23 +-
dev-python/python-vxi11/python-vxi11-0.8.ebuild | 23 +-
dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild | 68 ++++-
dev-python/simplepam/simplepam-0.1.5.ebuild | 23 +-
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dev-python/testpath/testpath-9999.ebuild | 13 +-
dev-python/traitlets/traitlets-4.0.0.ebuild | 60 +++-
dev-util/amdapp/amdapp-2.9.1.ebuild | 2 +-
dev-util/amdapp/amdapp-2.9.ebuild | 2 +-
dev-util/amdapp/amdapp-3.0_beta.ebuild | 2 +-
dev-util/ndiff/ndiff-2.00.ebuild | 6 +-
.../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild | 2 +-
.../nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild | 2 +-
.../nvidia-cuda-gdk/nvidia-cuda-gdk-352.07.ebuild | 2 +-
.../nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild | 2 +-
media-gfx/brlcad/brlcad-7.22.0.ebuild | 2 +-
media-gfx/brlcad/brlcad-7.24.0.ebuild | 2 +-
media-gfx/brlcad/brlcad-7.24.2.ebuild | 4 +-
media-gfx/brlcad/brlcad-9999.ebuild | 2 +-
media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild | 2 +-
media-libs/libgfx/libgfx-1.1.0.ebuild | 8 +-
media-libs/libgfx/metadata.xml | 2 +-
metadata/layout.conf | 2 +-
sci-astronomy/lephare/lephare-2.2.ebuild | 14 +-
sci-astronomy/lephare/metadata.xml | 4 +-
sci-astronomy/missfits/missfits-2.8.0.ebuild | 34 ++-
sci-astronomy/psfex/psfex-3.17.0.ebuild | 71 ++++-
sci-astronomy/psfex/psfex-3.9.1.ebuild | 71 ++++-
sci-astronomy/sextractor/sextractor-2.19.5.ebuild | 74 ++++-
sci-astronomy/skymaker/skymaker-3.10.5.ebuild | 36 ++-
sci-astronomy/stiff/stiff-2.4.0.ebuild | 44 ++-
sci-astronomy/stuff/stuff-1.26.0.ebuild | 36 ++-
sci-astronomy/swarp/swarp-2.38.0.ebuild | 42 ++-
.../weightwatcher/weightwatcher-1.12.ebuild | 36 ++-
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 2 +-
.../KaKs_Calculator/KaKs_Calculator-1.2.ebuild | 2 +-
sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild | 10 +-
sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild | 13 +-
sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild | 9 +-
.../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild | 2 +-
sci-biology/abyss/abyss-1.3.3-r1.ebuild | 2 +-
sci-biology/apollo/apollo-9999.ebuild | 2 +-
sci-biology/augustus/augustus-3.1.ebuild | 2 +-
sci-biology/bambino/bambino-1.02.ebuild | 4 +-
sci-biology/bambino/bambino-1.06.ebuild | 4 +-
sci-biology/bambus/bambus-2.33.ebuild | 58 ++--
sci-biology/biopieces/biopieces-0.51.ebuild | 73 ++++-
sci-biology/blasr/blasr-9999.ebuild | 2 +-
sci-biology/cap3-bin/cap3-bin-20071221.ebuild | 4 +-
.../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild | 10 +-
sci-biology/cd-hit/cd-hit-4.6.1.ebuild | 4 +-
sci-biology/cluster/cluster-1.50-r1.ebuild | 13 +-
sci-biology/cluster/cluster-1.50.ebuild | 50 ---
sci-biology/clview/clview-0.1.ebuild | 2 +-
sci-biology/consed/consed-29.ebuild | 4 +-
sci-biology/edena/edena-3.131028.ebuild | 2 +-
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 2 +-
sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 4 +-
sci-biology/mgblast/mgblast-0.1.ebuild | 2 +-
sci-biology/minced/minced-9999.ebuild | 2 +-
sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild | 157 +++++++++-
sci-biology/nrcl/nrcl-110625.ebuild | 4 +-
sci-biology/pileup/pileup-0.6.ebuild | 4 +-
sci-biology/pvmsx/pvmsx-0.1.ebuild | 2 +-
sci-biology/samstat/samstat-20130708.ebuild | 2 +-
....ebuild => scaffold_builder-20131122-r1.ebuild} | 26 +-
sci-biology/sff_dump/sff_dump-1.04.ebuild | 4 +-
sci-biology/sga/sga-9999.ebuild | 2 +-
sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild | 4 +-
.../tablet-bin/tablet-bin-1.14.10.21.ebuild | 2 +-
sci-biology/tablet/tablet-1.14.04.10.ebuild | 50 ++-
sci-biology/tclust/tclust-110625.ebuild | 4 +-
sci-biology/trf/trf-4.07b.ebuild | 14 +-
sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild | 2 +-
sci-chemistry/concoord/concoord-2.1.ebuild | 4 +-
sci-chemistry/coot/coot-9999.ebuild | 4 +
sci-chemistry/drawxtl/drawxtl-45.ebuild | 4 +-
sci-chemistry/gamess/Manifest | 1 -
.../gamess/files/gamess-20120501.1.gentoo.patch | 271 -----------------
sci-chemistry/gamess/gamess-20120501.1.ebuild | 338 ---------------------
sci-chemistry/gamess/gamess-20130501.1.ebuild | 30 +-
sci-chemistry/jligand/jligand-1.0.40.ebuild | 2 +-
sci-chemistry/ligplot+/ligplot+-1.4.ebuild | 14 +-
sci-chemistry/simpson/simpson-3.0.1.ebuild | 11 +-
sci-chemistry/simpson/simpson-3.1.0.ebuild | 11 +-
sci-chemistry/simpson/simpson-3.1.2.ebuild | 11 +-
sci-chemistry/usf-tools/usf-tools-9999.ebuild | 8 +-
sci-chemistry/votca-csg/ChangeLog | 3 +
sci-chemistry/votca-csg/votca-csg-9999.ebuild | 39 +--
sci-chemistry/votca-csgapps/ChangeLog | 5 +-
.../votca-csgapps/votca-csgapps-9999.ebuild | 9 +-
sci-electronics/stage/stage-2.0.3.ebuild | 6 +-
sci-geosciences/pydap/pydap-3.1.1.ebuild | 2 +-
sci-geosciences/pydap/pydap-3.1.ebuild | 2 +-
.../pydap_handlers_hdf5-0.1.7.ebuild | 2 +-
.../pydap_handlers_nca-0.1.3.ebuild | 2 +-
.../pydap_handlers_netcdf-0.6.4.ebuild | 2 +-
.../pydap_handlers_proxy-0.1.1.ebuild | 2 +-
sci-libs/Cgraph/Cgraph-2.04.ebuild | 4 +-
sci-libs/Cgraph/metadata.xml | 2 +-
sci-libs/arrayfire/arrayfire-3.1.1-r2.ebuild | 2 +-
sci-libs/arrayfire/arrayfire-9999.ebuild | 2 +-
sci-libs/asl/asl-0.1.5.ebuild | 49 ++-
.../blas-reference-20131116-r1.ebuild | 119 +++++++-
.../cblas-reference-20110218-r1.ebuild | 2 +-
.../cblas-reference-20110218.ebuild | 2 +-
sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild | 2 +-
sci-libs/fdlibm/fdlibm-5.3.ebuild | 20 +-
sci-libs/fdlibm/metadata.xml | 4 +-
sci-libs/fgsl/Manifest | 1 -
sci-libs/fgsl/fgsl-0.9.3.ebuild | 63 ----
sci-libs/fgsl/fgsl-0.9.4.ebuild | 8 +-
sci-libs/fox/fox-4.1.2-r2.ebuild | 8 +-
sci-libs/framewave/framewave-1.3.1.ebuild | 7 +-
sci-libs/itk/itk-4.4.2-r1.ebuild | 2 +-
.../lapack-reference/lapack-reference-3.4.2.ebuild | 140 ++++++++-
.../lapack-reference/lapack-reference-3.5.0.ebuild | 140 ++++++++-
.../lapacke-reference-3.4.2.ebuild | 104 ++++++-
.../lapacke-reference-3.5.0.ebuild | 104 ++++++-
sci-libs/libsc/libsc-1.1.ebuild | 72 ++++-
sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild | 2 +-
sci-libs/omalloc/metadata.xml | 12 +-
sci-libs/omalloc/omalloc-0.9.6.ebuild | 13 +-
sci-libs/openblas/openblas-0.2.12.ebuild | 228 +++++++++++++-
sci-libs/openblas/openblas-0.2.14.ebuild | 228 +++++++++++++-
sci-libs/openlibm/openlibm-9999.ebuild | 2 +-
sci-libs/p4est/p4est-1.1.ebuild | 100 +++++-
sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild | 13 +-
sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild | 8 +-
sci-libs/spglib/spglib-1.6.0.ebuild | 2 +-
sci-libs/tmglib/tmglib-3.4.2.ebuild | 4 +-
sci-libs/votca-tools/ChangeLog | 5 +-
sci-libs/votca-tools/votca-tools-9999.ebuild | 8 +-
sci-libs/wannier90/metadata.xml | 2 +-
sci-libs/wannier90/wannier90-1.2-r3.ebuild | 11 +-
sci-libs/wannier90/wannier90-2.0.0.ebuild | 11 +-
sci-libs/wannier90/wannier90-2.0.1.ebuild | 9 +-
sci-mathematics/aribas/aribas-1.63.ebuild | 22 +-
sci-mathematics/cadabra/cadabra-1.39.ebuild | 2 +-
sci-mathematics/htk/htk-3.4.1.ebuild | 43 ++-
sci-mathematics/htk/metadata.xml | 2 +-
sci-mathematics/kash-bin/kash-bin-3.ebuild | 31 +-
sci-mathematics/kash-bin/metadata.xml | 10 +-
sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild | 2 +-
sci-mathematics/pff/pff-8.4.ebuild | 2 +-
sci-mathematics/scilab/scilab-5.5.2-r1.ebuild | 2 +-
sci-mathematics/why3/why3-0.83.ebuild | 2 +-
sci-mathematics/yorick/yorick-2.1.06.ebuild | 2 +-
sci-misc/foma/foma-0.9.14_alpha.ebuild | 8 +-
sci-misc/foma/foma-0.9.16_alpha.ebuild | 11 +-
sci-misc/hfst/hfst-2.2.ebuild | 4 +-
sci-misc/hfst/hfst-3.0.2.ebuild | 4 +-
sci-misc/hfst/hfst-3.3.12.ebuild | 6 +-
sci-misc/kaldi/kaldi-0_p20150709.ebuild | 2 +-
sci-misc/openfst/openfst-1.3.4.ebuild | 2 +-
sci-misc/openfst/openfst-1.4.1.ebuild | 2 +-
.../opennlp-maxent/opennlp-maxent-2.4.0.ebuild | 2 +-
sci-misc/sfst/sfst-1.4.2.ebuild | 26 +-
sci-misc/sfst/sfst-1.4.6g.ebuild | 28 +-
sci-physics/abinit/abinit-7.10.4.ebuild | 4 +-
sci-physics/abinit/abinit-7.4.2-r1.ebuild | 2 +-
sci-physics/abinit/abinit-7.6.4-r1.ebuild | 4 +-
.../fullprof-bin/fullprof-bin-20313.04.ebuild | 2 +-
sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild | 4 +-
sci-physics/genfit/genfit-02.00.00.ebuild | 60 +++-
sci-physics/mc-tester/mc-tester-1.25.0.ebuild | 6 +-
sci-physics/mc-tester/metadata.xml | 18 +-
sci-physics/root/metadata.xml | 30 +-
sci-physics/root/root-9999.ebuild | 2 +-
sci-physics/tauola/tauola-1.1.3.ebuild | 8 +-
sci-physics/tauola/tauola-1.1.4.ebuild | 6 +-
sci-physics/tauola/tauola-1.1.5.ebuild | 6 +-
sci-physics/tauola/tauola-9999.ebuild | 6 +-
sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild | 2 +-
sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild | 2 +-
sci-visualization/gnuplot/metadata.xml | 6 +-
sci-visualization/nodemon/metadata.xml | 18 +-
sci-visualization/nodemon/nodemon-0.3.5.ebuild | 11 +-
sci-visualization/v_sim/v_sim-3.6.0.ebuild | 13 +-
sys-cluster/blcr/blcr-0.8.4.ebuild | 10 +-
sys-cluster/hpl/hpl-2.0-r1.ebuild | 4 +-
sys-cluster/hpx/hpx-9999.ebuild | 4 +-
sys-cluster/hpx/metadata.xml | 24 +-
sys-cluster/modules/modules-3.2.10.ebuild | 2 +-
sys-cluster/modules/modules-3.2.9c-r1.ebuild | 2 +-
sys-cluster/modules/modules-3.2.9c.ebuild | 2 +-
sys-cluster/nullmpi/nullmpi-0.7.ebuild | 4 +-
sys-cluster/openmpi/ChangeLog | 5 +
sys-cluster/openmpi/Manifest | 1 +
...{openmpi-1.8.8.ebuild => openmpi-1.10.0.ebuild} | 16 +-
sys-cluster/openmpi/openmpi-1.6.5.ebuild | 6 +-
sys-cluster/openmpi/openmpi-1.7.3.ebuild | 4 +-
sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild | 4 +-
sys-cluster/openmpi/openmpi-1.8.8.ebuild | 4 +-
sys-cluster/ovis/ovis-3.0.1.ebuild | 10 +-
sys-devel/gdebugger/gdebugger-6.2.438.ebuild | 7 +-
www-client/casperjs/ChangeLog | 12 +
www-client/casperjs/Manifest | 1 +
www-client/casperjs/casperjs-1.1_beta3.ebuild | 42 +++
.../omniorbpy => www-client/casperjs}/metadata.xml | 2 +-
254 files changed, 3956 insertions(+), 1415 deletions(-)
