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

[Aisha Tammy]

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