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
