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

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* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-16 18:27 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2014-03-16 18:27 UTC (permalink / raw
  To: gentoo-commits

commit:     f4a983de950f873267f37d7ebcd8f01b0a23a05b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 16 18:26:04 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 16 18:26:04 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f4a983de

sci-biology/khmer: revert to distutils to obey sandbox violation

Package-Manager: portage-2.2.7

---
 sci-biology/khmer/ChangeLog         | 3 +++
 sci-biology/khmer/khmer-9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index f3b89e7..4f2f8a6 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild:
+  sci-biology/khmer: revert to distutils to obey sandbox violation
+
 *khmer-9999 (16 Mar 2014)
 
   16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +khmer-9999.ebuild,

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index cbd7b2c..ab29463 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-r1 git-r3
+inherit distutils git-r3
 
 DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
 HOMEPAGE="https://github.com/ged-lab/khmer"


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2023-05-02 12:15 Andrew Ammerlaan
  0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:15 UTC (permalink / raw
  To: gentoo-commits

commit:     7f9384c065b99e3a858415a8a838438d9f70bcdf
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:08:24 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:15:10 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f9384c0

sci-biology/khmer: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/khmer/khmer-2.1.1.ebuild | 34 ----------------------------------
 sci-biology/khmer/metadata.xml       | 16 ----------------
 2 files changed, 50 deletions(-)

diff --git a/sci-biology/khmer/khmer-2.1.1.ebuild b/sci-biology/khmer/khmer-2.1.1.ebuild
deleted file mode 100644
index 11c4231e8..000000000
--- a/sci-biology/khmer/khmer-2.1.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
-HOMEPAGE="https://github.com/dib-lab/khmer"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# ToDo: Fix this:
-# ModuleNotFoundError: No module named 'khmer._khmer'
-# even happens with --install option for enable_tests
-RESTRICT="test"
-
-RDEPEND="
-	sci-biology/screed[${PYTHON_USEDEP}]
-	dev-python/bz2file[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
-	# do not depend on pytest-runner
-	sed -i "/pytest-runner/d" setup.py || die
-	distutils-r1_python_prepare_all
-}

diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml
deleted file mode 100644
index 91ed395d8..000000000
--- a/sci-biology/khmer/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">ged-lab/khmer</remote-id>
-		<remote-id type="pypi">khmer</remote-id>
-	</upstream>
-</pkgmetadata>


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2020-12-30 19:25 Aisha Tammy
  0 siblings, 0 replies; 17+ messages in thread
From: Aisha Tammy @ 2020-12-30 19:25 UTC (permalink / raw
  To: gentoo-commits

commit:     d7637214cd6c37456262bc62ff07eab1b1dae6b3
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Dec 30 18:39:36 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Wed Dec 30 19:02:35 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d7637214

sci-biology/khmer: version bump 2.1.1

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Closes: https://github.com/gentoo/sci/pull/1009
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 sci-biology/khmer/khmer-0.8.ebuild   | 39 -----------------------
 sci-biology/khmer/khmer-1.0.1.ebuild | 62 ------------------------------------
 sci-biology/khmer/khmer-2.1.1.ebuild | 34 ++++++++++++++++++++
 sci-biology/khmer/khmer-9999.ebuild  | 42 ------------------------
 4 files changed, 34 insertions(+), 143 deletions(-)

diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild
deleted file mode 100644
index e19d27e9b..000000000
--- a/sci-biology/khmer/khmer-0.8.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# 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_objects/d" \
-		-e "s:'nose >= 1.0', ::g" \
-		-e "s:'sphinx',::g" \
-		-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-1.0.1.ebuild b/sci-biology/khmer/khmer-1.0.1.ebuild
deleted file mode 100644
index 7ace41d54..000000000
--- a/sci-biology/khmer/khmer-1.0.1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# 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
-}

diff --git a/sci-biology/khmer/khmer-2.1.1.ebuild b/sci-biology/khmer/khmer-2.1.1.ebuild
new file mode 100644
index 000000000..11c4231e8
--- /dev/null
+++ b/sci-biology/khmer/khmer-2.1.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
+HOMEPAGE="https://github.com/dib-lab/khmer"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# ToDo: Fix this:
+# ModuleNotFoundError: No module named 'khmer._khmer'
+# even happens with --install option for enable_tests
+RESTRICT="test"
+
+RDEPEND="
+	sci-biology/screed[${PYTHON_USEDEP}]
+	dev-python/bz2file[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# do not depend on pytest-runner
+	sed -i "/pytest-runner/d" setup.py || die
+	distutils-r1_python_prepare_all
+}

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
deleted file mode 100644
index 7855665e1..000000000
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
-HOMEPAGE="https://github.com/ged-lab/khmer"
-#SRC_URI=""
-EGIT_REPO_URI="https://github.com/ged-lab/khmer"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-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 "s:'nose >= 1.0', ::g" \
-#		-e "s:'sphinx',::g" \
-#		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
-#		-e "s:'-O3',::g" \
-#		-i setup.py || die
-#
-#	distutils-r1_python_prepare_all
-#}
-
-# setup.py --libraries z,bz2 || die


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2018-01-20 21:26 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2018-01-20 21:26 UTC (permalink / raw
  To: gentoo-commits

commit:     30086ecf6e63270161fcb86194fbdae746242fc2
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 20 21:24:14 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 20 21:24:14 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=30086ecf

sci-biology/khmer: switch git:// to https://

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/khmer/khmer-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index 4cd44c29e..7855665e1 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -10,7 +10,7 @@ inherit distutils-r1 git-r3
 DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
 HOMEPAGE="https://github.com/ged-lab/khmer"
 #SRC_URI=""
-EGIT_REPO_URI="git://github.com/ged-lab/khmer"
+EGIT_REPO_URI="https://github.com/ged-lab/khmer"
 
 LICENSE="BSD"
 SLOT="0"


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2017-07-28 20:05 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:05 UTC (permalink / raw
  To: gentoo-commits

commit:     adf80768d6a583d418567bb79638a549f997ce08
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 19:14:43 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=adf80768

sci-biology/khmer: added a comment how to proceed with src_compile()

Package-Manager: Portage-2.3.6, Repoman-2.3.3

 sci-biology/khmer/khmer-9999.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index cece8e617..4cd44c29e 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -38,3 +38,5 @@ RDEPEND="sci-biology/screed"
 #
 #	distutils-r1_python_prepare_all
 #}
+
+# setup.py --libraries z,bz2 || die


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2015-06-05 11:20 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-06-05 11:20 UTC (permalink / raw
  To: gentoo-commits

commit:     40f710098b525b5dacfd243677dfbe8819655b62
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun  5 11:05:44 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun  5 11:05:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=40f71009

sci-biology/khmer: Add github to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-biology/khmer/ChangeLog    | 5 ++++-
 sci-biology/khmer/metadata.xml | 1 +
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index f67fb33..dc085a6 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/khmer
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+  sci-biology/khmer: Add github to remote-id in metadata.xml
+
 *khmer-1.0.1 (15 May 2014)
 
   15 May 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,

diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml
index a1a6c99..bfbb83e 100644
--- a/sci-biology/khmer/metadata.xml
+++ b/sci-biology/khmer/metadata.xml
@@ -8,5 +8,6 @@
   </maintainer>
   <upstream>
     <remote-id type="pypi">khmer</remote-id>
+    <remote-id type="github">ged-lab/khmer</remote-id>
   </upstream>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-05-15  7:21 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-05-15  7:21 UTC (permalink / raw
  To: gentoo-commits

commit:     5b0d5724ba788d179d9a596a5e4424f601e5b794
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu May 15 07:21:06 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu May 15 07:21:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5b0d5724

sci-biology/khmer: Version BUmp

Package-Manager: portage-2.2.10

---
 sci-biology/khmer/ChangeLog                        |  6 ++++
 sci-biology/khmer/khmer-0.8.ebuild                 |  2 +-
 .../khmer/{khmer-0.8.ebuild => khmer-1.0.1.ebuild} | 35 ++++++++++++++++++----
 3 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index 47af4ab..9b61d89 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-1.0.1 (15 May 2014)
+
+  15 May 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,
+  +khmer-1.0.1.ebuild:
+  Version BUmp
+
   28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild:
   sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is
   available system-wide, upstream https://github.com/ged-lab/khmer/pull/346

diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild
index 3cbc048..a90628f 100644
--- a/sci-biology/khmer/khmer-0.8.ebuild
+++ b/sci-biology/khmer/khmer-0.8.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS=" ~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 DEPEND=""

diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-1.0.1.ebuild
similarity index 52%
copy from sci-biology/khmer/khmer-0.8.ebuild
copy to sci-biology/khmer/khmer-1.0.1.ebuild
index 3cbc048..e5f3c26 100644
--- a/sci-biology/khmer/khmer-0.8.ebuild
+++ b/sci-biology/khmer/khmer-1.0.1.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS=" ~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 DEPEND=""
@@ -29,12 +29,35 @@ python_prepare_all(){
 		-i lib/read_parsers.hh lib/counting.cc || die
 
 	sed \
-		-e "/extra_objects/d" \
-		-e "s:'nose >= 1.0', ::g" \
-		-e "s:'sphinx',::g" \
-		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
-		-e "s:'-O3',::g" \
+		-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
+}


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-31 15:28 Nicolas Bock
  0 siblings, 0 replies; 17+ messages in thread
From: Nicolas Bock @ 2014-03-31 15:28 UTC (permalink / raw
  To: gentoo-commits

commit:     abaea30881541b0d796bf2b6323d49da8ac32e5b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 20:13:47 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Mar 31 15:27:34 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=abaea308

sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is available system-wide, upstream https://github.com/ged-lab/khmer/pull/346

Package-Manager: portage-2.2.7

---
 sci-biology/khmer/ChangeLog         |  4 ++++
 sci-biology/khmer/khmer-9999.ebuild | 36 ++++++++++++++++++------------------
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index 04e1cbd..47af4ab 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild:
+  sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is
+  available system-wide, upstream https://github.com/ged-lab/khmer/pull/346
+
   24 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,
   khmer-9999.ebuild:
   Also drop sphinx as build requirement

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index 0bd7a8d..f6c6594 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -21,21 +21,21 @@ 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 "s:'nose >= 1.0', ::g" \
-		-e "s:'sphinx',::g" \
-		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
-		-e "s:'-O3',::g" \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
+#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 "s:'nose >= 1.0', ::g" \
+#		-e "s:'sphinx',::g" \
+#		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
+#		-e "s:'-O3',::g" \
+#		-i setup.py || die
+#
+#	distutils-r1_python_prepare_all
+#}


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-28 20:15 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2014-03-28 20:15 UTC (permalink / raw
  To: gentoo-commits

commit:     2ca96f9db90098568873343a1d1a547bac4eab9a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 20:13:47 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 28 20:13:47 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2ca96f9d

sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is available system-wide, upstream https://github.com/ged-lab/khmer/pull/346

Package-Manager: portage-2.2.7

---
 sci-biology/khmer/ChangeLog         |  4 ++++
 sci-biology/khmer/khmer-9999.ebuild | 36 ++++++++++++++++++------------------
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index 04e1cbd..47af4ab 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild:
+  sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is
+  available system-wide, upstream https://github.com/ged-lab/khmer/pull/346
+
   24 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,
   khmer-9999.ebuild:
   Also drop sphinx as build requirement

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index 0bd7a8d..f6c6594 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -21,21 +21,21 @@ 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 "s:'nose >= 1.0', ::g" \
-		-e "s:'sphinx',::g" \
-		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
-		-e "s:'-O3',::g" \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
+#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 "s:'nose >= 1.0', ::g" \
+#		-e "s:'sphinx',::g" \
+#		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
+#		-e "s:'-O3',::g" \
+#		-i setup.py || die
+#
+#	distutils-r1_python_prepare_all
+#}


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-24 15:28 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-03-24 15:28 UTC (permalink / raw
  To: gentoo-commits

commit:     a16c385b6548a6575fa667a84071f416a43bbd6b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 24 15:23:22 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 24 15:28:29 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a16c385b

sci-biology/khmer: Also drop sphinx as build requirement

Package-Manager: portage-2.2.9-r1

---
 sci-biology/khmer/ChangeLog         | 4 ++++
 sci-biology/khmer/khmer-0.8.ebuild  | 1 +
 sci-biology/khmer/khmer-9999.ebuild | 1 +
 3 files changed, 6 insertions(+)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index 4faddd3..04e1cbd 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  24 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,
+  khmer-9999.ebuild:
+  Also drop sphinx as build requirement
+
   20 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,
   khmer-9999.ebuild:
   Drop nose requirement during build

diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild
index 89e3e28..3cbc048 100644
--- a/sci-biology/khmer/khmer-0.8.ebuild
+++ b/sci-biology/khmer/khmer-0.8.ebuild
@@ -31,6 +31,7 @@ python_prepare_all(){
 	sed \
 		-e "/extra_objects/d" \
 		-e "s:'nose >= 1.0', ::g" \
+		-e "s:'sphinx',::g" \
 		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
 		-e "s:'-O3',::g" \
 		-i setup.py || die

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index 4bb1d2e..0bd7a8d 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -32,6 +32,7 @@ python_prepare_all(){
 	sed \
 		-e "/extra_objects/d" \
 		-e "s:'nose >= 1.0', ::g" \
+		-e "s:'sphinx',::g" \
 		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
 		-e "s:'-O3',::g" \
 		-i setup.py || die


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-22  9:45 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-03-22  9:45 UTC (permalink / raw
  To: gentoo-commits

commit:     672f6a9b37fc8014c22fe6b8e2d110d52bce7319
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 20 09:04:21 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=672f6a9b

sci-biology/khmer: Drop nose requirement during build

Package-Manager: portage-2.2.8-r1

---
 sci-biology/khmer/ChangeLog         | 4 ++++
 sci-biology/khmer/khmer-0.8.ebuild  | 1 +
 sci-biology/khmer/khmer-9999.ebuild | 1 +
 3 files changed, 6 insertions(+)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index a2834e6..4faddd3 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  20 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,
+  khmer-9999.ebuild:
+  Drop nose requirement during build
+
 *khmer-0.8 (18 Mar 2014)
 
   18 Mar 2014; Justin Lecher <jlec@gentoo.org> +khmer-0.8.ebuild,

diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild
index 7566b3c..89e3e28 100644
--- a/sci-biology/khmer/khmer-0.8.ebuild
+++ b/sci-biology/khmer/khmer-0.8.ebuild
@@ -30,6 +30,7 @@ python_prepare_all(){
 
 	sed \
 		-e "/extra_objects/d" \
+		-e "s:'nose >= 1.0', ::g" \
 		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
 		-e "s:'-O3',::g" \
 		-i setup.py || die

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index 4ac1a8b..4bb1d2e 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -31,6 +31,7 @@ python_prepare_all(){
 
 	sed \
 		-e "/extra_objects/d" \
+		-e "s:'nose >= 1.0', ::g" \
 		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
 		-e "s:'-O3',::g" \
 		-i setup.py || die


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-22  9:45 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-03-22  9:45 UTC (permalink / raw
  To: gentoo-commits

commit:     660630449671df381c0f8da1c9b95ba2b2fc6836
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 16 18:26:04 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=66063044

sci-biology/khmer: revert to distutils to obey sandbox violation

Package-Manager: portage-2.2.7

---
 sci-biology/khmer/ChangeLog         | 3 +++
 sci-biology/khmer/khmer-9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index f3b89e7..4f2f8a6 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild:
+  sci-biology/khmer: revert to distutils to obey sandbox violation
+
 *khmer-9999 (16 Mar 2014)
 
   16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +khmer-9999.ebuild,

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index cbd7b2c..ab29463 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-r1 git-r3
+inherit distutils git-r3
 
 DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
 HOMEPAGE="https://github.com/ged-lab/khmer"


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-22  9:45 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-03-22  9:45 UTC (permalink / raw
  To: gentoo-commits

commit:     48368f7f59a39b69831f08f2c9263fbe6e580695
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 16 18:02:30 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=48368f7f

sci-biology/khmer: new package

Package-Manager: portage-2.2.7

---
 sci-biology/khmer/ChangeLog         |  9 +++++++++
 sci-biology/khmer/khmer-9999.ebuild | 22 ++++++++++++++++++++++
 sci-biology/khmer/metadata.xml      |  9 +++++++++
 3 files changed, 40 insertions(+)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
new file mode 100644
index 0000000..f3b89e7
--- /dev/null
+++ b/sci-biology/khmer/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/khmer
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*khmer-9999 (16 Mar 2014)
+
+  16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +khmer-9999.ebuild,
+  +metadata.xml:
+  sci-biology/khmer: new package

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
new file mode 100644
index 0000000..cbd7b2c
--- /dev/null
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -0,0 +1,22 @@
+# 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 git-r3
+
+DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
+HOMEPAGE="https://github.com/ged-lab/khmer"
+#SRC_URI=""
+EGIT_REPO_URI="git://github.com/ged-lab/khmer"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"

diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/khmer/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-22  9:45 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-03-22  9:45 UTC (permalink / raw
  To: gentoo-commits

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@gentoo.org> +khmer-0.8.ebuild,
+  khmer-9999.ebuild:
+  Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS
+
   16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.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
+}


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-20  9:04 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-03-20  9:04 UTC (permalink / raw
  To: gentoo-commits

commit:     391aa2b2160b456a7dbbdd34ce72378372615996
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 20 09:04:21 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 20 09:04:21 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=391aa2b2

sci-biology/khmer: Drop nose requirement during build

Package-Manager: portage-2.2.8-r1

---
 sci-biology/khmer/ChangeLog         | 4 ++++
 sci-biology/khmer/khmer-0.8.ebuild  | 1 +
 sci-biology/khmer/khmer-9999.ebuild | 1 +
 3 files changed, 6 insertions(+)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
index a2834e6..4faddd3 100644
--- a/sci-biology/khmer/ChangeLog
+++ b/sci-biology/khmer/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  20 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild,
+  khmer-9999.ebuild:
+  Drop nose requirement during build
+
 *khmer-0.8 (18 Mar 2014)
 
   18 Mar 2014; Justin Lecher <jlec@gentoo.org> +khmer-0.8.ebuild,

diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild
index 7566b3c..89e3e28 100644
--- a/sci-biology/khmer/khmer-0.8.ebuild
+++ b/sci-biology/khmer/khmer-0.8.ebuild
@@ -30,6 +30,7 @@ python_prepare_all(){
 
 	sed \
 		-e "/extra_objects/d" \
+		-e "s:'nose >= 1.0', ::g" \
 		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
 		-e "s:'-O3',::g" \
 		-i setup.py || die

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
index 4ac1a8b..4bb1d2e 100644
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -31,6 +31,7 @@ python_prepare_all(){
 
 	sed \
 		-e "/extra_objects/d" \
+		-e "s:'nose >= 1.0', ::g" \
 		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
 		-e "s:'-O3',::g" \
 		-i setup.py || die


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-18 19:28 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2014-03-18 19:28 UTC (permalink / raw
  To: gentoo-commits

commit:     2fe25927e87d9c3339465453ae165b366ff2d8f2
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: Tue Mar 18 19:24:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2fe25927

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@gentoo.org> +khmer-0.8.ebuild,
+  khmer-9999.ebuild:
+  Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS
+
   16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.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
+}


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/khmer/
@ 2014-03-16 18:03 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2014-03-16 18:03 UTC (permalink / raw
  To: gentoo-commits

commit:     80ae47968e0fdd030a0b9e5816c95d8a741b3a79
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 16 18:02:30 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 16 18:02:30 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=80ae4796

sci-biology/khmer: new package

Package-Manager: portage-2.2.7

---
 sci-biology/khmer/ChangeLog         |  9 +++++++++
 sci-biology/khmer/khmer-9999.ebuild | 22 ++++++++++++++++++++++
 sci-biology/khmer/metadata.xml      |  9 +++++++++
 3 files changed, 40 insertions(+)

diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog
new file mode 100644
index 0000000..f3b89e7
--- /dev/null
+++ b/sci-biology/khmer/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/khmer
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*khmer-9999 (16 Mar 2014)
+
+  16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +khmer-9999.ebuild,
+  +metadata.xml:
+  sci-biology/khmer: new package

diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
new file mode 100644
index 0000000..cbd7b2c
--- /dev/null
+++ b/sci-biology/khmer/khmer-9999.ebuild
@@ -0,0 +1,22 @@
+# 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 git-r3
+
+DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
+HOMEPAGE="https://github.com/ged-lab/khmer"
+#SRC_URI=""
+EGIT_REPO_URI="git://github.com/ged-lab/khmer"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"

diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/khmer/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 17+ messages in thread

end of thread, other threads:[~2023-05-02 12:15 UTC | newest]

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2014-05-15  7:21 Justin Lecher
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2014-03-28 20:15 Martin Mokrejs
2014-03-24 15:28 Justin Lecher
2014-03-22  9:45 Justin Lecher
2014-03-22  9:45 Justin Lecher
2014-03-22  9:45 Justin Lecher
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