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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit distutils-r1
DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
HOMEPAGE="https://github.com/ged-lab/khmer"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
DEPEND=""
RDEPEND="sci-biology/screed"
python_prepare_all(){
rm -rf lib/{bzip2,zlib} || die
sed \
-e 's:zlib/zlib.h:zlib.h:g' \
-e 's:bzip2/bzlib.h:bzlib.h:g' \
-i lib/read_parsers.hh lib/counting.cc || die
sed \
-e "/^EXTRA_COMPILE_ARGS/s:=.*:=[]:g" \
-i setup.py || die
cat > setup.cfg <<- EOF
[nosetests]
verbosity = 2
stop = TRUE
attr = !known_failing
[build_ext]
undef = NO_UNIQUE_RC
libraries = z,bz2
## if using system libraries
include-dirs = lib:lib/zlib:lib/bzip2
# include-dirs = lib
## if using system libraries (broken)
define = NDEBUG
# is not needed for most Linux installs
# see the OPT line in /usr/lib/python2.7/config/Makefile which gets included
# in distutils version of CFLAGS
[easy_install]
EOF
distutils-r1_python_prepare_all
}
python_test() {
esetup.py nosetests || die
}
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