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

[Justin Lecher]

commit:     bd12b7ef927260f2ce1554ff4a627b68e57938af
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 18 19:24:38 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 22 09:44:40 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd12b7ef

sci-biology/khmer: Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS

Package-Manager: portage-2.2.8-r1

---
 sci-biology/khmer/ChangeLog         |  6 ++++++
 sci-biology/khmer/khmer-0.8.ebuild  | 38 +++++++++++++++++++++++++++++++++++++
 sci-biology/khmer/khmer-9999.ebuild | 21 ++++++++++++++++++--
 3 files changed, 63 insertions(+), 2 deletions(-)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index 4f2f8a6..a2834e6 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*khmer-0.8 (18 Mar 2014)
+
+  18 Mar 2014; Justin Lecher <jlec@g.o> +khmer-0.8.ebuild,
+  khmer-9999.ebuild:
+  Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS
+
   16 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> khmer-9999.ebuild:
   sci-biology/khmer: revert to distutils to obey sandbox violation
 

diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild
new file mode 100644
index 0000000..7566b3c
--- /dev/null
+++ b/sci-biology/khmer/khmer-0.8.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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_objects/d" \
+		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
+		-e "s:'-O3',::g" \
+		-i setup.py || die
+
+	distutils-r1_python_prepare_all
+}

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index ab29463..4ac1a8b 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit distutils git-r3
+inherit distutils-r1 git-r3
 
 DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
 HOMEPAGE="https://github.com/ged-lab/khmer"
@@ -19,4 +19,21 @@ KEYWORDS=""
 IUSE=""
 
 DEPEND=""
-RDEPEND="${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_objects/d" \
+		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
+		-e "s:'-O3',::g" \
+		-i setup.py || die
+
+	distutils-r1_python_prepare_all
+}